From 0b0b07f24bea443acdc83dbae36872f3007eeafb Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Sun, 22 Jun 2014 15:04:09 +0200
Subject: [PATCH 0001/1356] add script to clean up gists

The script cleans up gists from closed/merged PR's.
---
 easybuild/scripts/clean_gists.py | 99 ++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100755 easybuild/scripts/clean_gists.py

diff --git a/easybuild/scripts/clean_gists.py b/easybuild/scripts/clean_gists.py
new file mode 100755
index 0000000000..066d4a53f2
--- /dev/null
+++ b/easybuild/scripts/clean_gists.py
@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+##
+# Copyright 2014 Ward Poelmans
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+This script cleans up old gists created by easybuild. It checks if the gists was
+created from a pull-request and if that PR is closed/merged, it will delete the gist.
+You need a github token for this. The script uses the same username and token
+as easybuild. Optionally, you can specify a different github username.
+
+Usage: ./clean_gists.py [<git username>]
+
+
+@author: Ward Poelmans
+"""
+
+
+import re
+import sys
+
+from vsc.utils import fancylogger
+from vsc.utils.rest import RestClient
+from easybuild.tools.github import GITHUB_API_URL, HTTP_STATUS_OK, GITHUB_EASYCONFIGS_REPO, GITHUB_EB_MAIN, fetch_github_token
+from easybuild.tools.options import EasyBuildOptions
+
+HTTP_DELETE_OK = 204
+
+
+def main(username=None):
+    """the main function"""
+    fancylogger.setLogLevelInfo()
+    fancylogger.logToScreen(enable=True, stdout=True)
+    log = fancylogger.getLogger()
+
+    if username is None:
+        eb_go = EasyBuildOptions(envvar_prefix='EASYBUILD', go_args=[])
+        username = eb_go.options.github_user
+
+    if username is None:
+        log.error("Could not find a github username")
+    else:
+        log.info("Using username = %s" % username)
+
+    token = fetch_github_token(username)
+
+    gh = RestClient(GITHUB_API_URL, username=username, token=token)
+    # ToDo: add support for pagination
+    status, gists = gh.gists.get(per_page=100)
+
+    if status != HTTP_STATUS_OK:
+        log.error("Failed to get a lists of gists for user %s: error code %s, message = %s" %
+                  (username, status, gists))
+    else:
+        log.info("Found %s gists" % len(gists))
+
+    regex = re.compile("(EasyBuild test report for easyconfigs|EasyBuild log for failed build of).*PR #([0-9]+)")
+
+    for gist in gists:
+        re_pr_num = regex.search(gist["description"])
+        if re_pr_num:
+            pr_num = re_pr_num.group(2)
+            log.info("Found Easybuild test report for PR #%s" % pr_num)
+            status, pr = gh.repos[GITHUB_EB_MAIN][GITHUB_EASYCONFIGS_REPO].pulls[pr_num].get()
+
+            if status != HTTP_STATUS_OK:
+                log.error("Failed to get pull-request #%s: error code %s, message = %s" %
+                          (pr_num, status, pr))
+
+            if pr["state"] == "closed":
+                log.debug("Found gist of closed PR #%s" % pr_num)
+
+                status, del_gist = gh.gists[gist["id"]].delete()
+
+                if status != HTTP_DELETE_OK:
+                    log.error("Unable to remove gist (id=%s): error code %s, message = %s" %
+                              (gist["id"], status, del_gist))
+                else:
+                    log.info("Delete gist from closed PR #%s" % pr_num)
+
+
+if __name__ == '__main__':
+    if len(sys.argv) == 2:
+        main(username=sys.argv[1])
+    else:
+        main()

From c428da3a34461a6b8d41a4a2943cbb444974f87e Mon Sep 17 00:00:00 2001
From: pescobar <pescobar001@gmail.com>
Date: Fri, 27 Jun 2014 16:05:39 +0200
Subject: [PATCH 0002/1356] replaced sse3 option in amd by mavx option

---
 easybuild/toolchains/compiler/inteliccifort.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index c224278eeb..ac8b75e65e 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -70,7 +70,7 @@ class IntelIccIfort(Compiler):
 
     COMPILER_OPTIMAL_ARCHITECTURE_OPTION = {
         systemtools.INTEL : 'xHOST',
-        systemtools.AMD : 'msse3',
+        systemtools.AMD : 'mavx',
     }
 
     COMPILER_CC = 'icc'

From 9a19551ec1f461bcaf51aa2ca678a47fe30e03f8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Jul 2014 17:36:21 +0200
Subject: [PATCH 0003/1356] bump version to v1.14.1dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 9df8020d5f..d9336e7795 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.14.0")
+VERSION = LooseVersion("1.14.1dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 85b16890a63f93cce063aa78627b7f87517fa589 Mon Sep 17 00:00:00 2001
From: Mesocentrefc <meso-admins@univ-fcomte.fr>
Date: Sat, 12 Jul 2014 09:51:57 +0200
Subject: [PATCH 0004/1356] Add download-only basic option to only download
 sources and extensions without build software.

---
 easybuild/framework/easyconfig/tools.py | 43 +++++++++++++++++++++++++
 easybuild/main.py                       |  9 ++++--
 easybuild/tools/config.py               |  1 +
 easybuild/tools/options.py              |  1 +
 4 files changed, 52 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index d834141ab8..5db7b7bbd7 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -66,6 +66,7 @@
     graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz")
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
+from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file, get_easyblock_class
 from easybuild.framework.easyconfig.easyconfig import process_easyconfig, robot_find_easyconfig
 from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.config import build_option
@@ -238,6 +239,48 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
     return ordered_ecs
 
 
+def download_source_only(easyconfigs, build_specs=None):
+    """
+    Download sources and extensions only
+    @param easyconfigs: list of easyconfig files
+    @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
+    """
+    silent = build_option('silent')
+
+    if build_option('robot_path') is None:
+        print_msg("Download sources and extensions", log=_log, silent=silent)
+        ecs = easyconfigs
+    else:
+        print_msg("Download sources and extensions with dependencies", log=_log, silent=silent)
+        ecs = resolve_dependencies(easyconfigs, build_specs=build_specs, retain_all_deps=True)
+
+    for ec in ecs:
+        spec = ec['spec']
+
+        print_msg("[*] processing %s" % spec, log=_log, silent=silent, prefix=False)
+
+        easyblock = build_option('easyblock')
+        if not easyblock:
+            easyblock = fetch_parameter_from_easyconfig_file(spec, 'easyblock')
+
+        name = ec['ec']['name']
+        try: 
+            app_class = get_easyblock_class(easyblock, name=name)
+            app = app_class(ec['ec'])
+            _log.info("Obtained application instance of for %s (easyblock: %s)" % (name, easyblock))
+        except EasyBuildError, err: 
+            tup = (name, easyblock, err.msg)
+            print_error("Failed to get application instance for %s (easyblock: %s): %s" % tup, silent=silent)
+
+        sources = app.cfg['sources']
+        if sources:
+            app.fetch_sources(sources, checksums=app.cfg['checksums'])
+        else:
+            app.log.info('no sources provided')
+
+        app.fetch_extension_sources()
+
+
 def print_dry_run(easyconfigs, short=False, build_specs=None):
     """
     Print dry run information
diff --git a/easybuild/main.py b/easybuild/main.py
index 89d001e809..40f7680d2d 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -52,7 +52,7 @@
 import easybuild.tools.options as eboptions
 from easybuild.framework.easyblock import EasyBlock, build_and_install_one
 from easybuild.framework.easyconfig.easyconfig import process_easyconfig
-from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, print_dry_run
+from easybuild.framework.easyconfig.tools import dep_graph, download_source_only, get_paths_for, print_dry_run
 from easybuild.framework.easyconfig.tools import resolve_dependencies, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_path, tweak
 from easybuild.tools.config import get_repository, module_classes, get_repositorypath, set_tmpdir
@@ -234,6 +234,7 @@ def main(testing_data=(None, None, None)):
         'cleanup_builddir': options.cleanup_builddir,
         'command_line': eb_command_line,
         'debug': options.debug,
+        'download_only': options.download_only,
         'dry_run': options.dry_run or options.dry_run_short,
         'easyblock': options.easyblock,
         'experimental': options.experimental,
@@ -374,11 +375,15 @@ def main(testing_data=(None, None, None)):
     # before building starts, take snapshot of environment (watch out -t option!)
     os.chdir(os.environ['PWD'])
 
+    # Download only
+    if options.download_only:
+        download_source_only(easyconfigs, build_specs=build_specs)
+
     # dry_run: print all easyconfigs and dependencies, and whether they are already built
     if options.dry_run or options.dry_run_short:
         print_dry_run(easyconfigs, short=not options.dry_run, build_specs=build_specs)
 
-    if any([options.dry_run, options.dry_run_short, options.regtest, options.search, options.search_short]):
+    if any([options.dry_run, options.dry_run_short, options.regtest, options.search, options.search_short, options.download_only]):
         cleanup(logfile, eb_tmpdir, testing)
         sys.exit(0)
 
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 50e0f5ac14..ee169c5968 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -76,6 +76,7 @@
     'cleanup_builddir': True,
     'command_line': None,
     'debug': False,
+    'download_only': False,
     'dry_run': False,
     'easyblock': None,
     'experimental': False,
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index d1f2173033..2600763ac3 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -88,6 +88,7 @@ def basic_options(self):
         descr = ("Basic options", "Basic runtime options for EasyBuild.")
 
         opts = OrderedDict({
+            'download-only': ("Only download sources and extensions, don't build", None, 'store_true', False),
             'dry-run': ("Print build overview incl. dependencies (full paths)", None, 'store_true', False),
             'dry-run-short': ("Print build overview incl. dependencies (short paths)", None, 'store_true', False, 'D'),
             'force': ("Force to rebuild software even if it's already installed (i.e. if it can be found as module)",

From 3e7decbc8a7a4f41119d787c063fd294a29bdd11 Mon Sep 17 00:00:00 2001
From: Mesocentrefc <meso-admins@univ-fcomte.fr>
Date: Tue, 15 Jul 2014 12:43:16 +0200
Subject: [PATCH 0005/1356] Move fetch_extension_source in fetch_step, to allow
 use of --stop=fetch to only download sources and extensions archives.

---
 easybuild/framework/easyblock.py        |  5 ++-
 easybuild/framework/easyconfig/tools.py | 43 -------------------------
 easybuild/main.py                       |  9 ++----
 easybuild/tools/config.py               |  1 -
 easybuild/tools/options.py              |  1 -
 5 files changed, 6 insertions(+), 53 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 7e5ee5c023..08fc982f8e 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1158,6 +1158,10 @@ def fetch_step(self, skip_checksums=False):
         else:
             self.log.info('no sources provided')
 
+        # fetch extensions
+        if len(self.cfg['exts_list']) > 0:
+            self.exts = self.fetch_extension_sources()
+ 
         # fetch patches
         if self.cfg['patches']:
             if isinstance(self.cfg['checksums'], (list, tuple)):
@@ -1300,7 +1304,6 @@ def extensions_step(self):
 
         self.prepare_for_extensions()
 
-        self.exts = self.fetch_extension_sources()
         self.exts_all = self.exts[:]  # retain a copy of all extensions, regardless of filtering/skipping
 
         if self.skip:
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 5db7b7bbd7..d834141ab8 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -66,7 +66,6 @@
     graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz")
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
-from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file, get_easyblock_class
 from easybuild.framework.easyconfig.easyconfig import process_easyconfig, robot_find_easyconfig
 from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.config import build_option
@@ -239,48 +238,6 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
     return ordered_ecs
 
 
-def download_source_only(easyconfigs, build_specs=None):
-    """
-    Download sources and extensions only
-    @param easyconfigs: list of easyconfig files
-    @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
-    """
-    silent = build_option('silent')
-
-    if build_option('robot_path') is None:
-        print_msg("Download sources and extensions", log=_log, silent=silent)
-        ecs = easyconfigs
-    else:
-        print_msg("Download sources and extensions with dependencies", log=_log, silent=silent)
-        ecs = resolve_dependencies(easyconfigs, build_specs=build_specs, retain_all_deps=True)
-
-    for ec in ecs:
-        spec = ec['spec']
-
-        print_msg("[*] processing %s" % spec, log=_log, silent=silent, prefix=False)
-
-        easyblock = build_option('easyblock')
-        if not easyblock:
-            easyblock = fetch_parameter_from_easyconfig_file(spec, 'easyblock')
-
-        name = ec['ec']['name']
-        try: 
-            app_class = get_easyblock_class(easyblock, name=name)
-            app = app_class(ec['ec'])
-            _log.info("Obtained application instance of for %s (easyblock: %s)" % (name, easyblock))
-        except EasyBuildError, err: 
-            tup = (name, easyblock, err.msg)
-            print_error("Failed to get application instance for %s (easyblock: %s): %s" % tup, silent=silent)
-
-        sources = app.cfg['sources']
-        if sources:
-            app.fetch_sources(sources, checksums=app.cfg['checksums'])
-        else:
-            app.log.info('no sources provided')
-
-        app.fetch_extension_sources()
-
-
 def print_dry_run(easyconfigs, short=False, build_specs=None):
     """
     Print dry run information
diff --git a/easybuild/main.py b/easybuild/main.py
index 40f7680d2d..89d001e809 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -52,7 +52,7 @@
 import easybuild.tools.options as eboptions
 from easybuild.framework.easyblock import EasyBlock, build_and_install_one
 from easybuild.framework.easyconfig.easyconfig import process_easyconfig
-from easybuild.framework.easyconfig.tools import dep_graph, download_source_only, get_paths_for, print_dry_run
+from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, print_dry_run
 from easybuild.framework.easyconfig.tools import resolve_dependencies, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_path, tweak
 from easybuild.tools.config import get_repository, module_classes, get_repositorypath, set_tmpdir
@@ -234,7 +234,6 @@ def main(testing_data=(None, None, None)):
         'cleanup_builddir': options.cleanup_builddir,
         'command_line': eb_command_line,
         'debug': options.debug,
-        'download_only': options.download_only,
         'dry_run': options.dry_run or options.dry_run_short,
         'easyblock': options.easyblock,
         'experimental': options.experimental,
@@ -375,15 +374,11 @@ def main(testing_data=(None, None, None)):
     # before building starts, take snapshot of environment (watch out -t option!)
     os.chdir(os.environ['PWD'])
 
-    # Download only
-    if options.download_only:
-        download_source_only(easyconfigs, build_specs=build_specs)
-
     # dry_run: print all easyconfigs and dependencies, and whether they are already built
     if options.dry_run or options.dry_run_short:
         print_dry_run(easyconfigs, short=not options.dry_run, build_specs=build_specs)
 
-    if any([options.dry_run, options.dry_run_short, options.regtest, options.search, options.search_short, options.download_only]):
+    if any([options.dry_run, options.dry_run_short, options.regtest, options.search, options.search_short]):
         cleanup(logfile, eb_tmpdir, testing)
         sys.exit(0)
 
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index ee169c5968..50e0f5ac14 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -76,7 +76,6 @@
     'cleanup_builddir': True,
     'command_line': None,
     'debug': False,
-    'download_only': False,
     'dry_run': False,
     'easyblock': None,
     'experimental': False,
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 2600763ac3..d1f2173033 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -88,7 +88,6 @@ def basic_options(self):
         descr = ("Basic options", "Basic runtime options for EasyBuild.")
 
         opts = OrderedDict({
-            'download-only': ("Only download sources and extensions, don't build", None, 'store_true', False),
             'dry-run': ("Print build overview incl. dependencies (full paths)", None, 'store_true', False),
             'dry-run-short': ("Print build overview incl. dependencies (short paths)", None, 'store_true', False, 'D'),
             'force': ("Force to rebuild software even if it's already installed (i.e. if it can be found as module)",

From 3dddd168b113d053fa1b1f2d89314c9322c69052 Mon Sep 17 00:00:00 2001
From: Mesocentrefc <meso-admins@univ-fcomte.fr>
Date: Tue, 15 Jul 2014 13:19:37 +0200
Subject: [PATCH 0006/1356] Add missing check for exts before copying in
 exts_all.

---
 easybuild/framework/easyblock.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 08fc982f8e..01e808b2e0 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1304,7 +1304,10 @@ def extensions_step(self):
 
         self.prepare_for_extensions()
 
-        self.exts_all = self.exts[:]  # retain a copy of all extensions, regardless of filtering/skipping
+        if self.exts:
+            self.exts_all = self.exts[:]  # retain a copy of all extensions, regardless of filtering/skipping
+        else:
+            self.exts = []
 
         if self.skip:
             self.skip_extensions()

From 4b1b1749481ac4f5ef7b1038f3a6f8409a5bdd4d Mon Sep 17 00:00:00 2001
From: Mesocentrefc <meso-admins@univ-fcomte.fr>
Date: Tue, 15 Jul 2014 14:07:26 +0200
Subject: [PATCH 0007/1356] Add fetch argument to extensions_step for testing
 purpose.

---
 easybuild/framework/easyblock.py | 10 +++++-----
 test/framework/easyblock.py      |  8 ++++----
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 01e808b2e0..16ce8e846d 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1287,7 +1287,7 @@ def install_step(self):
         """Install built software (abstract method)."""
         raise NotImplementedError
 
-    def extensions_step(self):
+    def extensions_step(self, fetch=False):
         """
         After make install, run this.
         - only if variable len(exts_list) > 0
@@ -1304,10 +1304,10 @@ def extensions_step(self):
 
         self.prepare_for_extensions()
 
-        if self.exts:
-            self.exts_all = self.exts[:]  # retain a copy of all extensions, regardless of filtering/skipping
-        else:
-            self.exts = []
+        if fetch:
+            self.exts = self.fetch_extension_sources()
+            
+        self.exts_all = self.exts[:]  # retain a copy of all extensions, regardless of filtering/skipping
 
         if self.skip:
             self.skip_extensions()
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 2e528af76e..3b52405a5c 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -212,8 +212,8 @@ def test_extensions_step(self):
         # test for proper error message without the exts_defaultclass set
         eb = EasyBlock(EasyConfig(self.eb_file))
         eb.installdir = config.install_path()
-        self.assertRaises(EasyBuildError, eb.extensions_step)
-        self.assertErrorRegex(EasyBuildError, "No default extension class set", eb.extensions_step)
+        self.assertRaises(EasyBuildError, eb.extensions_step, fetch=True)
+        self.assertErrorRegex(EasyBuildError, "No default extension class set", eb.extensions_step, fetch=True)
 
         # test if everything works fine if set
         self.contents += "\nexts_defaultclass = ['easybuild.framework.extension', 'Extension']"
@@ -221,7 +221,7 @@ def test_extensions_step(self):
         eb = EasyBlock(EasyConfig(self.eb_file))
         eb.builddir = config.build_path()
         eb.installdir = config.install_path()
-        eb.extensions_step()
+        eb.extensions_step(fetch=True)
 
         # test for proper error message when skip is set, but no exts_filter is set
         self.assertRaises(EasyBuildError, eb.skip_extensions)
@@ -250,7 +250,7 @@ def test_skip_extensions_step(self):
         eb.builddir = config.build_path()
         eb.installdir = config.install_path()
         eb.skip = True
-        eb.extensions_step()
+        eb.extensions_step(fetch=True)
         # 'ext1' should be in eb.exts
         self.assertTrue('ext1' in [y for x in eb.exts for y in x.values()])
         # 'ext2' should not

From 1c64f9b1ffe43b54655f513de18a2d4517c89eea Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 16 Jul 2014 12:03:23 +0200
Subject: [PATCH 0008/1356] Small fix for forgotten deprecated warning

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 7e5ee5c023..9fdf118ad3 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1320,7 +1320,7 @@ def extensions_step(self):
         legacy = False
         if hasattr(exts_defaultclass, '__iter__'):
             # LEGACY: module path is explicitely specified
-            self.log.warning("LEGACY: using specified module path for default class (will be deprecated soon)")
+            self.log.deprecated("Using specified module path for default class", "2.0")
             default_class_modpath = exts_defaultclass[0]
             default_class = exts_defaultclass[1]
             derived_mod_path = get_module_path(default_class, generic=True)

From 10998b2b0debdc8ba4ecfaf5656951d6c7cf75f7 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 16 Jul 2014 12:21:42 +0200
Subject: [PATCH 0009/1356] clean_gists.py: added options

---
 easybuild/scripts/clean_gists.py | 39 +++++++++++++++++++-------------
 1 file changed, 23 insertions(+), 16 deletions(-)

diff --git a/easybuild/scripts/clean_gists.py b/easybuild/scripts/clean_gists.py
index 066d4a53f2..df5f2d0452 100755
--- a/easybuild/scripts/clean_gists.py
+++ b/easybuild/scripts/clean_gists.py
@@ -22,33 +22,43 @@
 You need a github token for this. The script uses the same username and token
 as easybuild. Optionally, you can specify a different github username.
 
-Usage: ./clean_gists.py [<git username>]
-
-
 @author: Ward Poelmans
 """
 
 
 import re
-import sys
 
 from vsc.utils import fancylogger
+from vsc.utils.generaloption import simple_option
 from vsc.utils.rest import RestClient
-from easybuild.tools.github import GITHUB_API_URL, HTTP_STATUS_OK, GITHUB_EASYCONFIGS_REPO, GITHUB_EB_MAIN, fetch_github_token
+from easybuild.tools.github import GITHUB_API_URL, HTTP_STATUS_OK, GITHUB_EASYCONFIGS_REPO
+from easybuild.tools.github import GITHUB_EB_MAIN, fetch_github_token
 from easybuild.tools.options import EasyBuildOptions
 
 HTTP_DELETE_OK = 204
 
 
-def main(username=None):
+def main():
     """the main function"""
     fancylogger.setLogLevelInfo()
     fancylogger.logToScreen(enable=True, stdout=True)
     log = fancylogger.getLogger()
 
-    if username is None:
+    options = {
+        'github-user': ('Your github username to use', None, 'store', None, 'g'),
+        'closed-pr': ('Delete all gists from closed pull-requests', None, 'store_true', True, 'p'),
+        'all': ('Delete all gists from Easybuild ', None, 'store_true', False, 'a'),
+        'orphans': ('Delete all gists without a pull-request', None, 'store_true', False, 'o'),
+    }
+
+    go = simple_option(options)
+
+    if go.options.github_user is None:
         eb_go = EasyBuildOptions(envvar_prefix='EASYBUILD', go_args=[])
         username = eb_go.options.github_user
+        log.debug("Fetch github username from easybuild, found: %s" % username)
+    else:
+        username = go.options.github_user
 
     if username is None:
         log.error("Could not find a github username")
@@ -67,12 +77,12 @@ def main(username=None):
     else:
         log.info("Found %s gists" % len(gists))
 
-    regex = re.compile("(EasyBuild test report for easyconfigs|EasyBuild log for failed build of).*PR #([0-9]+)")
+    regex = re.compile(r"(EasyBuild test report|EasyBuild log for failed build).+?(?:PR #(?P<PR>[0-9]+))?\)?$")
 
     for gist in gists:
         re_pr_num = regex.search(gist["description"])
-        if re_pr_num:
-            pr_num = re_pr_num.group(2)
+        if re_pr_num and re_pr_num.group("PR"):
+            pr_num = re_pr_num.group("PR")
             log.info("Found Easybuild test report for PR #%s" % pr_num)
             status, pr = gh.repos[GITHUB_EB_MAIN][GITHUB_EASYCONFIGS_REPO].pulls[pr_num].get()
 
@@ -80,8 +90,8 @@ def main(username=None):
                 log.error("Failed to get pull-request #%s: error code %s, message = %s" %
                           (pr_num, status, pr))
 
-            if pr["state"] == "closed":
-                log.debug("Found gist of closed PR #%s" % pr_num)
+            if pr["state"] == "closed" and (go.options.closed_pr or go.options.all):
+                log.debug("Found report from closed PR #%s" % pr_num)
 
                 status, del_gist = gh.gists[gist["id"]].delete()
 
@@ -93,7 +103,4 @@ def main(username=None):
 
 
 if __name__ == '__main__':
-    if len(sys.argv) == 2:
-        main(username=sys.argv[1])
-    else:
-        main()
+    main()

From 5b278cd9feffe2cbeab91953475fe7c79b555f70 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 16 Jul 2014 22:55:57 +0200
Subject: [PATCH 0010/1356] clean_gists: implement all options

Everything should work now
---
 easybuild/scripts/clean_gists.py | 75 +++++++++++++++++++++-----------
 1 file changed, 49 insertions(+), 26 deletions(-)

diff --git a/easybuild/scripts/clean_gists.py b/easybuild/scripts/clean_gists.py
index df5f2d0452..4c9adc44d4 100755
--- a/easybuild/scripts/clean_gists.py
+++ b/easybuild/scripts/clean_gists.py
@@ -40,30 +40,33 @@
 
 def main():
     """the main function"""
-    fancylogger.setLogLevelInfo()
     fancylogger.logToScreen(enable=True, stdout=True)
+    fancylogger.setLogLevelInfo()
     log = fancylogger.getLogger()
 
     options = {
         'github-user': ('Your github username to use', None, 'store', None, 'g'),
-        'closed-pr': ('Delete all gists from closed pull-requests', None, 'store_true', True, 'p'),
+        'closed-pr': ('Delete all gists from closed pull-requests', None, 'store_true', False, 'p'),
         'all': ('Delete all gists from Easybuild ', None, 'store_true', False, 'a'),
         'orphans': ('Delete all gists without a pull-request', None, 'store_true', False, 'o'),
     }
 
     go = simple_option(options)
 
+    if not (go.options.all or go.options.closed_pr or go.options.orphans):
+        log.error("Please tell me what to do?")
+
     if go.options.github_user is None:
         eb_go = EasyBuildOptions(envvar_prefix='EASYBUILD', go_args=[])
         username = eb_go.options.github_user
-        log.debug("Fetch github username from easybuild, found: %s" % username)
+        log.debug("Fetch github username from easybuild, found: %s", username)
     else:
         username = go.options.github_user
 
     if username is None:
         log.error("Could not find a github username")
     else:
-        log.info("Using username = %s" % username)
+        log.info("Using username = %s", username)
 
     token = fetch_github_token(username)
 
@@ -72,34 +75,54 @@ def main():
     status, gists = gh.gists.get(per_page=100)
 
     if status != HTTP_STATUS_OK:
-        log.error("Failed to get a lists of gists for user %s: error code %s, message = %s" %
-                  (username, status, gists))
+        log.error("Failed to get a lists of gists for user %s: error code %s, message = %s",
+                  username, status, gists)
     else:
-        log.info("Found %s gists" % len(gists))
+        log.info("Found %s gists", len(gists))
 
-    regex = re.compile(r"(EasyBuild test report|EasyBuild log for failed build).+?(?:PR #(?P<PR>[0-9]+))?\)?$")
+    regex = re.compile(r"(EasyBuild test report|EasyBuild log for failed build).*?(?:PR #(?P<PR>[0-9]+))?\)?$")
+
+    pr_cache = {}
+    num_deleted = 0
 
     for gist in gists:
         re_pr_num = regex.search(gist["description"])
-        if re_pr_num and re_pr_num.group("PR"):
-            pr_num = re_pr_num.group("PR")
-            log.info("Found Easybuild test report for PR #%s" % pr_num)
-            status, pr = gh.repos[GITHUB_EB_MAIN][GITHUB_EASYCONFIGS_REPO].pulls[pr_num].get()
+        delete_gist = False
 
-            if status != HTTP_STATUS_OK:
-                log.error("Failed to get pull-request #%s: error code %s, message = %s" %
-                          (pr_num, status, pr))
-
-            if pr["state"] == "closed" and (go.options.closed_pr or go.options.all):
-                log.debug("Found report from closed PR #%s" % pr_num)
-
-                status, del_gist = gh.gists[gist["id"]].delete()
-
-                if status != HTTP_DELETE_OK:
-                    log.error("Unable to remove gist (id=%s): error code %s, message = %s" %
-                              (gist["id"], status, del_gist))
-                else:
-                    log.info("Delete gist from closed PR #%s" % pr_num)
+        if re_pr_num:
+            log.debug("Found a Easybuild gist (id=%s)", gist["id"])
+            pr_num = re_pr_num.group("PR")
+            if go.options.all:
+                delete_gist = True
+            elif pr_num and go.options.closed_pr:
+                log.debug("Found Easybuild test report for PR #%s", pr_num)
+
+                if pr_num not in pr_cache:
+                    status, pr = gh.repos[GITHUB_EB_MAIN][GITHUB_EASYCONFIGS_REPO].pulls[pr_num].get()
+                    if status != HTTP_STATUS_OK:
+                        log.error("Failed to get pull-request #%s: error code %s, message = %s",
+                                  pr_num, status, pr)
+                    pr_cache[pr_num] = pr["state"]
+
+                if pr_cache[pr_num] == "closed":
+                    log.debug("Found report from closed PR #%s (id=%s)", pr_num, gist["id"])
+                    delete_gist = True
+
+            elif not pr_num and go.options.orphans:
+                log.debug("Found Easybuild test report without PR (id=%s)", gist["id"])
+                delete_gist = True
+
+        if delete_gist:
+            status, del_gist = gh.gists[gist["id"]].delete()
+
+            if status != HTTP_DELETE_OK:
+                log.error("Unable to remove gist (id=%s): error code %s, message = %s",
+                          gist["id"], status, del_gist)
+            else:
+                log.info("Delete gist with id=%s", gist["id"])
+                num_deleted += 1
+
+    log.info("Deleted %s gists", num_deleted)
 
 
 if __name__ == '__main__':

From 157ea172e97ae7510d2a7414b11406958366377c Mon Sep 17 00:00:00 2001
From: Kilian Cavalotti <kilian@stanford.edu>
Date: Wed, 16 Jul 2014 15:40:52 -0700
Subject: [PATCH 0011/1356] fix for #980

---
 .../module_naming_scheme/hierarchical_mns.py  | 28 +++++++++++--------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 48a4bc9e05..20df4388d3 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -74,20 +74,24 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         """
         Determine toolchain compiler tag, for given list of compilers.
         """
-        if len(tc_comps) == 1:
-            tc_comp_name = tc_comps[0]['name']
-            tc_comp_ver = tc_comps[0]['version']
+        # no compiler in toolchain, dummy toolchain
+        if tc_comps is None:
+            tc_comp_name = tc_comp_ver = 'dummy'
         else:
-            tc_comp_names = [comp['name'] for comp in tc_comps]
-            if set(tc_comp_names) == set(['icc', 'ifort']):
-                tc_comp_name = 'intel'
-                if tc_comps[0]['version'] == tc_comps[1]['version']:
-                    tc_comp_ver = tc_comps[0]['version']
-                else:
-                    _log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
+            if len(tc_comps) == 1:
+                tc_comp_name = tc_comps[0]['name']
+                tc_comp_ver = tc_comps[0]['version']
             else:
-                mns = self.__class__.__name__
-                _log.error("Unknown set of toolchain compilers, %s needs to be enhanced first." % mns)
+                tc_comp_names = [comp['name'] for comp in tc_comps]
+                if set(tc_comp_names) == set(['icc', 'ifort']):
+                    tc_comp_name = 'intel'
+                    if tc_comps[0]['version'] == tc_comps[1]['version']:
+                        tc_comp_ver = tc_comps[0]['version']
+                    else:
+                        _log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
+                else:
+                    mns = self.__class__.__name__
+                    _log.error("Unknown set of toolchain compilers, %s needs to be enhanced first." % mns)
         return tc_comp_name, tc_comp_ver
 
     def det_module_subdir(self, ec):

From 0806a1dda69dd5772489ef134e131f959ec6ebfe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 30 Jul 2014 18:33:37 +0200
Subject: [PATCH 0012/1356] short-circuit to returning None in
 det_toolchain_compilers_name_version for dummy toolchain, add FIXME
 placeholder

---
 .../module_naming_scheme/hierarchical_mns.py  | 44 +++++++++++--------
 1 file changed, 25 insertions(+), 19 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 20df4388d3..a1c3aa96cb 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -74,25 +74,25 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         """
         Determine toolchain compiler tag, for given list of compilers.
         """
-        # no compiler in toolchain, dummy toolchain
         if tc_comps is None:
-            tc_comp_name = tc_comp_ver = 'dummy'
+            # no compiler in toolchain, dummy toolchain
+            res = None
+        elif len(tc_comps) == 1:
+            res = (tc_comps[0]['name'], tc_comps[0]['version'])
         else:
-            if len(tc_comps) == 1:
-                tc_comp_name = tc_comps[0]['name']
-                tc_comp_ver = tc_comps[0]['version']
-            else:
-                tc_comp_names = [comp['name'] for comp in tc_comps]
-                if set(tc_comp_names) == set(['icc', 'ifort']):
-                    tc_comp_name = 'intel'
-                    if tc_comps[0]['version'] == tc_comps[1]['version']:
-                        tc_comp_ver = tc_comps[0]['version']
-                    else:
-                        _log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
+            tc_comp_names = [comp['name'] for comp in tc_comps]
+            if set(tc_comp_names) == set(['icc', 'ifort']):
+                tc_comp_name = 'intel'
+                if tc_comps[0]['version'] == tc_comps[1]['version']:
+                    tc_comp_ver = tc_comps[0]['version']
                 else:
-                    mns = self.__class__.__name__
-                    _log.error("Unknown set of toolchain compilers, %s needs to be enhanced first." % mns)
-        return tc_comp_name, tc_comp_ver
+                    _log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
+            else:
+                mns = self.__class__.__name__
+                _log.error("Unknown set of toolchain compilers, %s needs to be enhanced first." % mns)
+            res = (tc_comp_name, tc_comp_ver)
+
+        return res
 
     def det_module_subdir(self, ec):
         """
@@ -130,9 +130,15 @@ def det_modpath_extensions(self, ec):
             paths.append(os.path.join(COMPILER, ec['name'], ec['version']))
         elif modclass == 'mpi':
             tc_comps = det_toolchain_compilers(ec)
-            tc_comp_name, tc_comp_ver = self.det_toolchain_compilers_name_version(tc_comps)
-            fullver = ec['version'] + ec['versionsuffix']
-            paths.append(os.path.join(MPI, tc_comp_name, tc_comp_ver, ec['name'], fullver))
+            tc_comp_info = self.det_toolchain_compilers_name_version(tc_comps)
+            if tc_comp_info is None:
+                # MPI installed with a dummy toolchain
+                # FIXME: how do we determine the correct module path extension?
+                raise NotImplementedError
+            else:
+                tc_comp_name, tc_comp_ver = tc_comp_info
+                fullver = ec['version'] + ec['versionsuffix']
+                paths.append(os.path.join(MPI, tc_comp_name, tc_comp_ver, ec['name'], fullver))
 
         return paths
 

From 30c1ef6746e41cf262cf5dc55e4a9eead7cd0e35 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Wed, 30 Jul 2014 19:51:44 +0200
Subject: [PATCH 0013/1356] Intel fftw mpi update for MKL >= 11.1

---
 easybuild/toolchains/fft/intelfftw.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index 4dc4c12ca6..1efaa8f3b3 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -52,6 +52,19 @@ def _set_fftw_variables(self):
         fftwsuff = ""
         if self.options.get('pic', None):
             fftwsuff = "_pic"
+        fftw_bitness = "_lp64_intel"
+        if self.options.get('i8', None):
+            # ilp64/i8
+            fftw_bitness = "_ilp64_intel"
+        # can't use toolchain.mpi_family, because of dummy toolchain
+        mpi_name_in_lib = ''
+        if get_software_root('MPICH2'):
+            mpi_name_in_lib = '_MPICH2'
+        if get_software_root('MVAPICH2'):
+            mpi_name_in_lib = '_MVAPICH2'
+        if get_software_root('OpenMPI'):
+            mpi_name_in_lib = '_OpenMPI'
+   
         fftw_libs = ["fftw3xc_intel%s" % fftwsuff]
         if self.options['usempi']:
             # add cluster interface
@@ -60,8 +73,10 @@ def _set_fftw_variables(self):
                     fftw_libs.append("fftw3x_cdft_lp64%s" % fftwsuff)
                 elif LooseVersion(imklver) >= LooseVersion("10.3"):
                     fftw_libs.append("fftw3x_cdft%s" % fftwsuff)
-                fftw_libs.append("mkl_cdft_core")  # add cluster dft
-                fftw_libs.extend(self.variables['LIBBLACS'].flatten()) ## add BLACS; use flatten because ListOfList
+            else:
+                fftw_libs.append("fftw3x_cdft%s%s%s" % (fftw_bitness, fftwsuff, mpi_name_in_lib))
+            fftw_libs.append("mkl_cdft_core")  # add cluster dft
+            fftw_libs.extend(self.variables['LIBBLACS'].flatten()) ## add BLACS; use flatten because ListOfList
 
         self.log.debug('fftw_libs %s' % fftw_libs.__repr__())
         fftw_libs.extend(self.variables['LIBBLAS'].flatten()) ## add core (contains dft) ; use flatten because ListOfList

From c07cd69e857763798fd0bbed17a4b4a870390ddf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 10:54:10 +0200
Subject: [PATCH 0014/1356] enhance write_file with append mode, extend
 filetools unit tests

---
 easybuild/tools/filetools.py |  7 +++++--
 test/framework/filetools.py  | 15 +++++++++++++++
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index bd390a646b..f15d93c060 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -153,13 +153,16 @@ def read_file(path, log_error=True):
             return None
 
 
-def write_file(path, txt):
+def write_file(path, txt, append=False):
     """Write given contents to file at given path (overwrites current file contents!)."""
     f = None
     # note: we can't use try-except-finally, because Python 2.4 doesn't support it as a single block
     try:
         mkdir(os.path.dirname(path), parents=True)
-        f = open(path, 'w')
+        if append:
+            f = open(path, 'a')
+        else:
+            f = open(path, 'w')
         f.write(txt)
         f.close()
     except IOError, err:
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 367c91e5a0..651ea77c30 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -243,6 +243,21 @@ def check_mkdir(path, error=None, **kwargs):
 
         shutil.rmtree(tmpdir)
 
+    def test_read_write_file(self):
+        """Test reading/writing files."""
+        tmpdir = tempfile.mkdtemp()
+
+        fp = os.path.join(tmpdir, 'test.txt')
+        txt = "test123"
+        ft.write_file(fp, txt)
+        self.assertEqual(ft.read_file(fp), txt)
+
+        txt2 = '\n'.join(['test', '123'])
+        ft.write_file(fp, txt2, append=True)
+        self.assertEqual(ft.read_file(fp), txt+txt2)
+
+        shutil.rmtree(tmpdir)
+
     def test_det_patched_files(self):
         """Test det_patched_files function."""
         pf = os.path.join(os.path.dirname(__file__), 'sandbox', 'sources', 'toy', 'toy-0.0_typo.patch')

From 78bcc1e5699054f140c2d1bb660f1a51d39fa501 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 10:54:48 +0200
Subject: [PATCH 0015/1356] use read_file/write_file in toy_build unit tests to
 avoid occasionally failing tests due to garbage collection

---
 test/framework/toy_build.py | 45 ++++++++++++++++---------------------
 1 file changed, 19 insertions(+), 26 deletions(-)

diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 6c0a5d4cfd..2634ecf6d3 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -43,7 +43,7 @@
 
 import easybuild.tools.module_naming_scheme  # required to dynamically load test module naming scheme(s)
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import mkdir, write_file
+from easybuild.tools.filetools import mkdir, read_file, write_file
 
 
 class ToyBuildTest(EnhancedTestCase):
@@ -153,7 +153,7 @@ def test_toy_build(self, extra_args=None, ec_file=None, tmpdir=None, verify=True
         if test_readme:
             # make sure postinstallcmds were used
             toy_install_path = os.path.join(self.test_installpath, 'software', 'toy', full_ver)
-            self.assertEqual(open(os.path.join(toy_install_path, 'README'), 'r').read(), "TOY\n")
+            self.assertEqual(read_file(os.path.join(toy_install_path, 'README')), "TOY\n")
 
         # make sure full test report was dumped, and contains sensible information
         if test_report is not None:
@@ -171,7 +171,7 @@ def test_toy_build(self, extra_args=None, ec_file=None, tmpdir=None, verify=True
                 r"List of loaded modules",
                 r"Environment",
             ]
-            test_report_txt = open(test_report).read()
+            test_report_txt = read_file(test_report)
             for regex_pattern in regex_patterns:
                 regex = re.compile(regex_pattern, re.M)
                 msg = "Pattern %s found in full test report: %s" % (regex.pattern, test_report_txt)
@@ -185,11 +185,9 @@ def test_toy_broken(self):
         tmpdir = tempfile.mkdtemp()
         broken_toy_ec = os.path.join(tmpdir, "toy-broken.eb")
         toy_ec_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
-        broken_toy_ec_txt = open(toy_ec_file, 'r').read()
+        broken_toy_ec_txt = read_file(toy_ec_file)
         broken_toy_ec_txt += "checksums = ['clearywrongchecksum']"
-        f = open(broken_toy_ec, 'w')
-        f.write(broken_toy_ec_txt)
-        f.close()
+        write_file(broken_toy_ec, broken_toy_ec_txt)
         error_regex = "Checksum verification .* failed"
         self.assertErrorRegex(EasyBuildError, error_regex, self.test_toy_build, ec_file=broken_toy_ec, tmpdir=tmpdir,
                               verify=False, fails=True, verbose=False, raise_error=True)
@@ -224,7 +222,7 @@ def test_toy_tweaked(self):
             "modloadmsg =  'THANKS FOR LOADING ME, I AM %(name)s v%(version)s'",
             "modtclfooter = 'puts stderr \"oh hai!\"'",
         ])
-        open(ec_file, 'a').write(ec_extra)
+        write_file(ec_file, ec_extra, append=True)
 
         args = [
             ec_file,
@@ -237,7 +235,7 @@ def test_toy_tweaked(self):
         outtxt = self.eb_main(args, do_build=True, verbose=True, raise_error=True)
         self.check_toy(self.test_installpath, outtxt, versionsuffix='-tweaked')
         toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0-tweaked')
-        toy_module_txt = open(toy_module, 'r').read()
+        toy_module_txt = read_file(toy_module)
 
         self.assertTrue(re.search('setenv\s*FOO\s*"bar"', toy_module_txt))
         self.assertTrue(re.search('prepend-path\s*SOMEPATH\s*\$root/foo/bar', toy_module_txt))
@@ -357,11 +355,9 @@ def test_toy_download_sources(self):
         tmpdir = tempfile.mkdtemp()
         # copy toy easyconfig file, and append source_urls to it
         shutil.copy2(os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb'), tmpdir)
-        ec_file = os.path.join(tmpdir, 'toy-0.0.eb')
-        f = open(ec_file, 'a')
         source_url = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'sandbox', 'sources', 'toy')
-        f.write('\nsource_urls = ["file://%s"]\n' % source_url)
-        f.close()
+        ec_file = os.path.join(tmpdir, 'toy-0.0.eb')
+        write_file(ec_file, '\nsource_urls = ["file://%s"]\n' % source_url, append=True)
 
         # unset $EASYBUILD_XPATH env vars, to make sure --prefix is picked up
         for cfg_opt in ['build', 'install', 'source']:
@@ -423,9 +419,7 @@ def test_toy_permissions(self):
             elif ec_group is not None:
                 shutil.copy2(toy_ec_file, self.test_buildpath)
                 tmp_ec_file = os.path.join(self.test_buildpath, os.path.basename(toy_ec_file))
-                f = open(tmp_ec_file, 'a')
-                f.write("\ngroup = '%s'" % ec_group)
-                f.close()
+                write_file(tmp_ec_file, "\ngroup = '%s'" % ec_group, append=True)
                 allargs = [tmp_ec_file]
             allargs.extend(args)
             if umask is not None:
@@ -520,9 +514,7 @@ def test_allow_system_deps(self):
         # copy toy easyconfig file, and append source_urls to it
         shutil.copy2(os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb'), tmpdir)
         ec_file = os.path.join(tmpdir, 'toy-0.0.eb')
-        f = open(ec_file, 'a')
-        f.write("\nallow_system_deps = [('Python', SYS_PYTHON_VERSION)]\n")
-        f.close()
+        write_file(ec_file, "\nallow_system_deps = [('Python', SYS_PYTHON_VERSION)]\n", append=True)
         self.test_toy_build(ec_file=ec_file)
 
     def test_toy_hierarchical(self):
@@ -572,12 +564,12 @@ def test_toy_hierarchical(self):
         self.assertTrue(os.path.exists(toy_module_path))
 
         # check that toolchain load is expanded to loads for toolchain dependencies
-        modtxt = open(toy_module_path, 'r').read()
+        modtxt = read_file(toy_module_path)
         self.assertFalse(re.search("load gompi", modtxt))
         self.assertTrue(re.search("load GCC", modtxt))
         self.assertTrue(re.search("load OpenMPI", modtxt))
 
-        # test module path with GCC/4.8.2 build
+        # test module path with GCC/4.7.2 build
         extra_args = [
             '--try-toolchain=GCC,4.7.2',
         ]
@@ -588,10 +580,11 @@ def test_toy_hierarchical(self):
         self.assertTrue(os.path.exists(toy_module_path))
 
         # no dependencies or toolchain => no module load statements in module file
-        modtxt = open(toy_module_path, 'r').read()
+        modtxt = read_file(toy_module_path)
         self.assertFalse(re.search("module load", modtxt))
+        os.remove(toy_module_path)
 
-        # test module path with GCC/4.8.2 build, pretend to be an MPI lib by setting moduleclass
+        # test module path with GCC/4.7.2 build, pretend to be an MPI lib by setting moduleclass
         extra_args = [
             '--try-toolchain=GCC,4.7.2',
             '--try-amend=moduleclass=mpi',
@@ -603,7 +596,7 @@ def test_toy_hierarchical(self):
         self.assertTrue(os.path.exists(toy_module_path))
 
         # no dependencies or toolchain => no module load statements in module file
-        modtxt = open(toy_module_path, 'r').read()
+        modtxt = read_file(toy_module_path)
         modpath_extension = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'toy', '0.0')
         self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
 
@@ -618,7 +611,7 @@ def test_toy_hierarchical(self):
         self.assertTrue(os.path.exists(toy_module_path))
 
         # no dependencies or toolchain => no module load statements in module file
-        modtxt = open(toy_module_path, 'r').read()
+        modtxt = read_file(toy_module_path)
         self.assertFalse(re.search("module load", modtxt))
 
         # test module path with dummy/dummy build, pretend to be a compiler by setting moduleclass
@@ -633,7 +626,7 @@ def test_toy_hierarchical(self):
         self.assertTrue(os.path.exists(toy_module_path))
 
         # no dependencies or toolchain => no module load statements in module file
-        modtxt = open(toy_module_path, 'r').read()
+        modtxt = read_file(toy_module_path)
         modpath_extension = os.path.join(mod_prefix, 'Compiler', 'toy', '0.0')
         self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
 

From 4d96bc94b00b5392d245508af776c5ece9326235 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 11:48:20 +0200
Subject: [PATCH 0016/1356] use a local test install path rather than
 self.test_installpath purposely, to avoid garbage collection in Python 2.6
 cleaning up the install path prematurely

---
 test/framework/toy_build.py | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 2634ecf6d3..33ca896d03 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -520,24 +520,26 @@ def test_allow_system_deps(self):
     def test_toy_hierarchical(self):
         """Test toy build under example hierarchical module naming scheme."""
 
-        mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
+        # use a local test install path rather than self.test_installpath purposely,
+        # to avoid garbage collection in Python 2.6 cleaning up the install path prematurely
+        local_test_installpath = tempfile.mkdtemp()
+        mod_prefix = os.path.join(local_test_installpath, 'modules', 'all')
 
         # simply copy module files under 'Core' and 'Compiler' to test install path
         # EasyBuild is responsible for making sure that the toolchain can be loaded using the short module name
-        install_mod_path = os.path.join(self.test_installpath, 'modules', 'all')
-        mkdir(install_mod_path, parents=True)
+        mkdir(mod_prefix, parents=True)
         for mod_subdir in ['Core', 'Compiler']:
             src_mod_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'modules', mod_subdir)
-            shutil.copytree(src_mod_path, os.path.join(install_mod_path, mod_subdir))
+            shutil.copytree(src_mod_path, os.path.join(mod_prefix, mod_subdir))
 
         # tweak prepend-path statements in GCC/OpenMPI modules to ensure correct paths
         for modfile in [
-            os.path.join(install_mod_path, 'Core', 'GCC', '4.7.2'),
-            os.path.join(install_mod_path, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'),
+            os.path.join(mod_prefix, 'Core', 'GCC', '4.7.2'),
+            os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'),
         ]:
             for line in fileinput.input(modfile, inplace=1):
                 line = re.sub(r"(module\s*use\s*)/tmp/modules/all",
-                              r"\1%s/modules/all" % self.test_installpath,
+                              r"\1%s/modules/all" % local_test_installpath,
                               line)
                 sys.stdout.write(line)
 
@@ -545,7 +547,7 @@ def test_toy_hierarchical(self):
             os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb'),
             '--sourcepath=%s' % self.test_sourcepath,
             '--buildpath=%s' % self.test_buildpath,
-            '--installpath=%s' % self.test_installpath,
+            '--installpath=%s' % local_test_installpath,
             '--debug',
             '--unittest-file=%s' % self.logfile,
             '--force',

From afbd50448828778fa988dcdca3f6bf71f9ca7942 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 12:21:32 +0200
Subject: [PATCH 0017/1356] no need for a local test installpath, remove
 generated modules after subtests

---
 test/framework/toy_build.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 33ca896d03..eeb72aa89e 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -520,10 +520,7 @@ def test_allow_system_deps(self):
     def test_toy_hierarchical(self):
         """Test toy build under example hierarchical module naming scheme."""
 
-        # use a local test install path rather than self.test_installpath purposely,
-        # to avoid garbage collection in Python 2.6 cleaning up the install path prematurely
-        local_test_installpath = tempfile.mkdtemp()
-        mod_prefix = os.path.join(local_test_installpath, 'modules', 'all')
+        mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
 
         # simply copy module files under 'Core' and 'Compiler' to test install path
         # EasyBuild is responsible for making sure that the toolchain can be loaded using the short module name
@@ -539,7 +536,7 @@ def test_toy_hierarchical(self):
         ]:
             for line in fileinput.input(modfile, inplace=1):
                 line = re.sub(r"(module\s*use\s*)/tmp/modules/all",
-                              r"\1%s/modules/all" % local_test_installpath,
+                              r"\1%s/modules/all" % self.test_installpath,
                               line)
                 sys.stdout.write(line)
 
@@ -547,7 +544,7 @@ def test_toy_hierarchical(self):
             os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb'),
             '--sourcepath=%s' % self.test_sourcepath,
             '--buildpath=%s' % self.test_buildpath,
-            '--installpath=%s' % local_test_installpath,
+            '--installpath=%s' % self.test_installpath,
             '--debug',
             '--unittest-file=%s' % self.logfile,
             '--force',
@@ -570,6 +567,7 @@ def test_toy_hierarchical(self):
         self.assertFalse(re.search("load gompi", modtxt))
         self.assertTrue(re.search("load GCC", modtxt))
         self.assertTrue(re.search("load OpenMPI", modtxt))
+        os.remove(toy_module_path)
 
         # test module path with GCC/4.7.2 build
         extra_args = [
@@ -601,6 +599,7 @@ def test_toy_hierarchical(self):
         modtxt = read_file(toy_module_path)
         modpath_extension = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'toy', '0.0')
         self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        os.remove(toy_module_path)
 
         # test module path with dummy/dummy build
         extra_args = [
@@ -615,6 +614,7 @@ def test_toy_hierarchical(self):
         # no dependencies or toolchain => no module load statements in module file
         modtxt = read_file(toy_module_path)
         self.assertFalse(re.search("module load", modtxt))
+        os.remove(toy_module_path)
 
         # test module path with dummy/dummy build, pretend to be a compiler by setting moduleclass
         extra_args = [
@@ -631,6 +631,7 @@ def test_toy_hierarchical(self):
         modtxt = read_file(toy_module_path)
         modpath_extension = os.path.join(mod_prefix, 'Compiler', 'toy', '0.0')
         self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        os.remove(toy_module_path)
 
     def test_toy_advanced(self):
         """Test toy build with extensions and non-dummy toolchain."""

From 3df723b3271327ccaadea383f281149822404005 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Thu, 31 Jul 2014 12:27:03 +0200
Subject: [PATCH 0018/1356] removed MPI name form lib

---
 easybuild/toolchains/fft/intelfftw.py | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index 1efaa8f3b3..15f1da3f70 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -56,15 +56,8 @@ def _set_fftw_variables(self):
         if self.options.get('i8', None):
             # ilp64/i8
             fftw_bitness = "_ilp64_intel"
-        # can't use toolchain.mpi_family, because of dummy toolchain
-        mpi_name_in_lib = ''
-        if get_software_root('MPICH2'):
-            mpi_name_in_lib = '_MPICH2'
-        if get_software_root('MVAPICH2'):
-            mpi_name_in_lib = '_MVAPICH2'
-        if get_software_root('OpenMPI'):
-            mpi_name_in_lib = '_OpenMPI'
-   
+        if self.options['usempi']:
+
         fftw_libs = ["fftw3xc_intel%s" % fftwsuff]
         if self.options['usempi']:
             # add cluster interface
@@ -74,7 +67,7 @@ def _set_fftw_variables(self):
                 elif LooseVersion(imklver) >= LooseVersion("10.3"):
                     fftw_libs.append("fftw3x_cdft%s" % fftwsuff)
             else:
-                fftw_libs.append("fftw3x_cdft%s%s%s" % (fftw_bitness, fftwsuff, mpi_name_in_lib))
+                fftw_libs.append("fftw3x_cdft%s%s" % (fftw_bitness, fftwsuff))
             fftw_libs.append("mkl_cdft_core")  # add cluster dft
             fftw_libs.extend(self.variables['LIBBLACS'].flatten()) ## add BLACS; use flatten because ListOfList
 

From 4224950e9ad1a227cc64a3060d470727fea6a817 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <hajgato@vub.ac.be>
Date: Thu, 31 Jul 2014 12:33:50 +0200
Subject: [PATCH 0019/1356] Oops forget to delete one extra line...

---
 easybuild/toolchains/fft/intelfftw.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index 15f1da3f70..ce05771872 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -56,7 +56,6 @@ def _set_fftw_variables(self):
         if self.options.get('i8', None):
             # ilp64/i8
             fftw_bitness = "_ilp64_intel"
-        if self.options['usempi']:
 
         fftw_libs = ["fftw3xc_intel%s" % fftwsuff]
         if self.options['usempi']:

From ad784fbaa0c87efc458175a17fe262151fb211db Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 12:54:12 +0200
Subject: [PATCH 0020/1356] don't redefine self.test_buildpath and co in
 toy_build tests, use self.test_*path where it wasn't used yet

---
 test/framework/easyblock.py |  1 +
 test/framework/options.py   | 77 ++++++++++---------------------------
 test/framework/toy_build.py |  5 +--
 3 files changed, 22 insertions(+), 61 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 2e528af76e..01e3cef91e 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -455,6 +455,7 @@ def tearDown(self):
         os.remove(self.eb_file)
         if self.orig_tmp_logdir is not None:
             os.environ['EASYBUILD_TMP_LOGDIR'] = self.orig_tmp_logdir
+            shutil.rmtree(self.test_tmp_logdir, True)
 
 
 def suite():
diff --git a/test/framework/options.py b/test/framework/options.py
index 67d580a476..30eff4fbaa 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -196,20 +196,15 @@ def test_force(self):
     def test_skip(self):
         """Test skipping installation of module (--skip, -k)."""
 
-        # use temporary paths for build/install paths, make sure sources can be found
-        buildpath = tempfile.mkdtemp()
-        installpath = tempfile.mkdtemp()
-        sourcepath = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'sources')
-
         # use toy-0.0.eb easyconfig file that comes with the tests
         eb_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
 
         # check log message with --skip for existing module
         args = [
             eb_file,
-            '--sourcepath=%s' % sourcepath,
-            '--buildpath=%s' % buildpath,
-            '--installpath=%s' % installpath,
+            '--sourcepath=%s' % self.test_sourcepath,
+            '--buildpath=%s' % self.test_buildpath,
+            '--installpath=%s' % self.test_installpath,
             '--force',
             '--debug',
         ]
@@ -236,9 +231,9 @@ def test_skip(self):
         # check log message with --skip for non-existing module
         args = [
             eb_file,
-            '--sourcepath=%s' % sourcepath,
-            '--buildpath=%s' % buildpath,
-            '--installpath=%s' % installpath,
+            '--sourcepath=%s' % self.test_sourcepath,
+            '--buildpath=%s' % self.test_buildpath,
+            '--installpath=%s' % self.test_installpath,
             '--try-software-version=1.2.3.4.5.6.7.8.9',
             '--try-amend=sources=toy-0.0.tar.gz,toy-0.0.tar.gz',  # hackish, but fine
             '--force',
@@ -260,10 +255,6 @@ def test_skip(self):
         modify_env(os.environ, self.orig_environ)
         modules_tool()
 
-        # cleanup
-        shutil.rmtree(buildpath)
-        shutil.rmtree(installpath)
-
     def test_job(self):
         """Test submitting build as a job."""
 
@@ -684,11 +675,6 @@ def test_no_such_software(self):
 
     def test_footer(self):
         """Test specifying a module footer."""
-        # use temporary paths for build/install paths, make sure sources can be found
-        buildpath = tempfile.mkdtemp()
-        installpath = tempfile.mkdtemp()
-        tmpdir = tempfile.mkdtemp()
-        sourcepath = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'sources')
 
         # create file containing modules footer
         module_footer_txt = '\n'.join([
@@ -707,45 +693,36 @@ def test_footer(self):
         # check log message with --skip for existing module
         args = [
             eb_file,
-            '--sourcepath=%s' % sourcepath,
-            '--buildpath=%s' % buildpath,
-            '--installpath=%s' % installpath,
+            '--sourcepath=%s' % self.test_sourcepath,
+            '--buildpath=%s' % self.test_buildpath,
+            '--installpath=%s' % self.test_installpath,
             '--debug',
             '--force',
             '--modules-footer=%s' % modules_footer,
         ]
         self.eb_main(args, do_build=True)
 
-        toy_module = os.path.join(installpath, 'modules', 'all', 'toy', '0.0')
+        toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0')
         toy_module_txt = read_file(toy_module)
         footer_regex = re.compile(r'%s$' % module_footer_txt, re.M)
         msg = "modules footer '%s' is present in '%s'" % (module_footer_txt, toy_module_txt)
         self.assertTrue(footer_regex.search(toy_module_txt), msg)
 
         # cleanup
-        shutil.rmtree(buildpath)
-        shutil.rmtree(installpath)
-        shutil.rmtree(tmpdir)
         os.remove(modules_footer)
 
     def test_recursive_module_unload(self):
         """Test generating recursively unloading modules."""
 
-        # use temporary paths for build/install paths, make sure sources can be found
-        buildpath = tempfile.mkdtemp()
-        installpath = tempfile.mkdtemp()
-        tmpdir = tempfile.mkdtemp()
-        sourcepath = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'sources')
-
         # use toy-0.0.eb easyconfig file that comes with the tests
         eb_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0-deps.eb')
 
         # check log message with --skip for existing module
         args = [
             eb_file,
-            '--sourcepath=%s' % sourcepath,
-            '--buildpath=%s' % buildpath,
-            '--installpath=%s' % installpath,
+            '--sourcepath=%s' % self.test_sourcepath,
+            '--buildpath=%s' % self.test_buildpath,
+            '--installpath=%s' % self.test_installpath,
             '--debug',
             '--force',
             '--recursive-module-unload',
@@ -757,19 +734,11 @@ def test_recursive_module_unload(self):
         is_loaded_regex = re.compile(r"if { !\[is-loaded gompi/1.3.12\] }", re.M)
         self.assertFalse(is_loaded_regex.search(toy_module_txt), "Recursive unloading is used: %s" % toy_module_txt)
 
-        # cleanup
-        shutil.rmtree(buildpath)
-        shutil.rmtree(installpath)
-        shutil.rmtree(tmpdir)
-
     def test_tmpdir(self):
         """Test setting temporary directory to use by EasyBuild."""
 
         # use temporary paths for build/install paths, make sure sources can be found
-        buildpath = tempfile.mkdtemp()
-        installpath = tempfile.mkdtemp()
         tmpdir = tempfile.mkdtemp()
-        sourcepath = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'sources')
 
         # use toy-0.0.eb easyconfig file that comes with the tests
         eb_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
@@ -777,9 +746,9 @@ def test_tmpdir(self):
         # check log message with --skip for existing module
         args = [
             eb_file,
-            '--sourcepath=%s' % sourcepath,
-            '--buildpath=%s' % buildpath,
-            '--installpath=%s' % installpath,
+            '--sourcepath=%s' % self.test_sourcepath,
+            '--buildpath=%s' % self.test_buildpath,
+            '--installpath=%s' % self.test_installpath,
             '--debug',
             '--tmpdir=%s' % tmpdir,
         ]
@@ -798,8 +767,6 @@ def test_tmpdir(self):
         self.assertTrue(tempfile_tmpfile.startswith(os.path.join(tmpdir, 'easybuild-')))
 
         # cleanup
-        shutil.rmtree(buildpath)
-        shutil.rmtree(installpath)
         os.close(fd)
         shutil.rmtree(tmpdir)
 
@@ -1069,18 +1036,14 @@ def test_filter_deps(self):
     def test_test_report_env_filter(self):
         """Test use of --test-report-env-filter."""
 
-        sourcepath = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'sources')
-
         def toy(extra_args=None):
             """Build & install toy, return contents of test report."""
-            buildpath = tempfile.mkdtemp()
-            installpath = tempfile.mkdtemp()
             eb_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
             args = [
                 eb_file,
-                '--sourcepath=%s' % sourcepath,
-                '--buildpath=%s' % buildpath,
-                '--installpath=%s' % installpath,
+                '--sourcepath=%s' % self.test_sourcepath,
+                '--buildpath=%s' % self.test_buildpath,
+                '--installpath=%s' % self.test_installpath,
                 '--force',
                 '--debug',
             ]
@@ -1088,7 +1051,7 @@ def toy(extra_args=None):
                 args.extend(extra_args)
             self.eb_main(args, do_build=True, raise_error=True, verbose=True)
 
-            software_path = os.path.join(installpath, 'software', 'toy', '0.0')
+            software_path = os.path.join(self.test_installpath, 'software', 'toy', '0.0')
             test_report_path_pattern = os.path.join(software_path, 'easybuild', 'easybuild-toy-0.0*test_report.md')
             f = open(glob.glob(test_report_path_pattern)[0], 'r')
             test_report_txt = f.read()
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index eeb72aa89e..50b586f740 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -70,10 +70,6 @@ def setUp(self):
         # clear log
         write_file(self.logfile, '')
 
-        self.test_buildpath = tempfile.mkdtemp()
-        self.test_installpath = tempfile.mkdtemp()
-        self.test_sourcepath = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'sources')
-
     def tearDown(self):
         """Cleanup."""
         super(ToyBuildTest, self).tearDown()
@@ -516,6 +512,7 @@ def test_allow_system_deps(self):
         ec_file = os.path.join(tmpdir, 'toy-0.0.eb')
         write_file(ec_file, "\nallow_system_deps = [('Python', SYS_PYTHON_VERSION)]\n", append=True)
         self.test_toy_build(ec_file=ec_file)
+        shutil.rmtree(tmpdir)
 
     def test_toy_hierarchical(self):
         """Test toy build under example hierarchical module naming scheme."""

From f7faa9ccc300f9a00823c845ba1f31fdd89f16ea Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 13:37:36 +0200
Subject: [PATCH 0021/1356] fix typo

---
 test/framework/options.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 30eff4fbaa..6ffebedc8f 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -729,7 +729,7 @@ def test_recursive_module_unload(self):
         ]
         self.eb_main(args, do_build=True, verbose=True)
 
-        toy_module = os.path.join(installpath, 'modules', 'all', 'toy', '0.0-deps')
+        toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0-deps')
         toy_module_txt = read_file(toy_module)
         is_loaded_regex = re.compile(r"if { !\[is-loaded gompi/1.3.12\] }", re.M)
         self.assertFalse(is_loaded_regex.search(toy_module_txt), "Recursive unloading is used: %s" % toy_module_txt)

From 8182e2a095c2fea534049286f7a4aec778062de9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 14:15:06 +0200
Subject: [PATCH 0022/1356] include debug info for failing scripts test

---
 test/framework/scripts.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 27b75128b5..527b7e274a 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -66,7 +66,8 @@ def test_generate_software_list(self):
         out, ec = run_cmd(cmd, simple=False)
 
         # make sure output is kind of what we expect it to be
-        self.assertTrue(re.search(r"Supported Packages \(11", out))
+        regex = r"Supported Packages \(11 "
+        self.assertTrue(re.search(regex, out), "Pattern '%s' found in output: %s" % (regex, out))
         per_letter = {
             'F': '1',  # FFTW
             'G': '4',  # GCC, gompi, goolf, gzip

From d7b0085dae41731da6f17107bc547e1c36d9fa1d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 15:50:01 +0200
Subject: [PATCH 0023/1356] reorganize changes in intelfftw.py, also
 parametrize compiler suffix for fftw wrapper libs

---
 easybuild/toolchains/fft/intelfftw.py | 33 +++++++++++++++------------
 1 file changed, 19 insertions(+), 14 deletions(-)

diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index ce05771872..65be2025e3 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -49,29 +49,34 @@ def _set_fftw_variables(self):
 
         imklver = get_software_version(self.FFT_MODULE_NAME[0])
 
-        fftwsuff = ""
+        picsuff = ''
         if self.options.get('pic', None):
-            fftwsuff = "_pic"
-        fftw_bitness = "_lp64_intel"
+            picsuff = '_pic'
+        bitsuff = '_lp64'
         if self.options.get('i8', None):
-            # ilp64/i8
-            fftw_bitness = "_ilp64_intel"
+            bitsuff = '_ilp64'
+        compsuff = '_intel'
+        if get_software_root('icc') is None:
+            if get_software_root('GCC'):
+                compsuff = '_gnu'
+            else:
+                self.log.error("Not using Intel compilers or GCC, don't know compiler suffix for FFTW libraries.")
 
-        fftw_libs = ["fftw3xc_intel%s" % fftwsuff]
+        fftw_libs = ["fftw3xc%s%s" % (compsuff, picsuff)]
         if self.options['usempi']:
             # add cluster interface
-            if LooseVersion(imklver) < LooseVersion("11.1"):
-                if LooseVersion(imklver) >= LooseVersion("11.0"):
-                    fftw_libs.append("fftw3x_cdft_lp64%s" % fftwsuff)
-                elif LooseVersion(imklver) >= LooseVersion("10.3"):
-                    fftw_libs.append("fftw3x_cdft%s" % fftwsuff)
+            if LooseVersion(imklver) >= LooseVersion("11.1"):
+                fftw_libs.append("fftw3x_cdft%s%s" % (bitsuff, compsuff, picsuff))
             else:
-                fftw_libs.append("fftw3x_cdft%s%s" % (fftw_bitness, fftwsuff))
+                if LooseVersion(imklver) >= LooseVersion("11.0.2"):
+                    fftw_libs.append("fftw3x_cdft%s%s" % (bitsuff, picsuff))
+                elif LooseVersion(imklver) >= LooseVersion("10.3"):
+                    fftw_libs.append("fftw3x_cdft%s" % picsuff)
             fftw_libs.append("mkl_cdft_core")  # add cluster dft
-            fftw_libs.extend(self.variables['LIBBLACS'].flatten()) ## add BLACS; use flatten because ListOfList
+            fftw_libs.extend(self.variables['LIBBLACS'].flatten()) # add BLACS; use flatten because ListOfList
 
         self.log.debug('fftw_libs %s' % fftw_libs.__repr__())
-        fftw_libs.extend(self.variables['LIBBLAS'].flatten()) ## add core (contains dft) ; use flatten because ListOfList
+        fftw_libs.extend(self.variables['LIBBLAS'].flatten())  # add BLAS libs (contains dft)
         self.log.debug('fftw_libs %s' % fftw_libs.__repr__())
 
         self.FFT_LIB_DIR = self.BLAS_LIB_DIR

From ab185b7f7f03e94e9ece491e7df89d78e3d28ebd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 16:13:27 +0200
Subject: [PATCH 0024/1356] fix typo

---
 easybuild/toolchains/fft/intelfftw.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index 65be2025e3..d636a9f4d8 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -66,7 +66,7 @@ def _set_fftw_variables(self):
         if self.options['usempi']:
             # add cluster interface
             if LooseVersion(imklver) >= LooseVersion("11.1"):
-                fftw_libs.append("fftw3x_cdft%s%s" % (bitsuff, compsuff, picsuff))
+                fftw_libs.append("fftw3x_cdft%s%s%s" % (bitsuff, compsuff, picsuff))
             else:
                 if LooseVersion(imklver) >= LooseVersion("11.0.2"):
                     fftw_libs.append("fftw3x_cdft%s%s" % (bitsuff, picsuff))

From fec41ebe0465ef5dc5f872b62b1575e56ec58e15 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 22:17:04 +0200
Subject: [PATCH 0025/1356] no compiler suffix in cdft libfftw libs

---
 easybuild/toolchains/fft/intelfftw.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index d636a9f4d8..4673831db3 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -66,7 +66,7 @@ def _set_fftw_variables(self):
         if self.options['usempi']:
             # add cluster interface
             if LooseVersion(imklver) >= LooseVersion("11.1"):
-                fftw_libs.append("fftw3x_cdft%s%s%s" % (bitsuff, compsuff, picsuff))
+                fftw_libs.append("fftw3x_cdft%s%s" % (bitsuff, picsuff))
             else:
                 if LooseVersion(imklver) >= LooseVersion("11.0.2"):
                     fftw_libs.append("fftw3x_cdft%s%s" % (bitsuff, picsuff))

From 606322a7cd040016415b9b2d5e25ad1cf9ab0e79 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 31 Jul 2014 22:50:33 +0200
Subject: [PATCH 0026/1356] filter out gfortran from list of FFTW libraries to
 check for with imkl

---
 easybuild/toolchains/fft/intelfftw.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index 4673831db3..03f2d2d43a 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -86,7 +86,10 @@ def _set_fftw_variables(self):
         # so make sure libraries are there before FFT_LIB is set
         imklroot = get_software_root(self.FFT_MODULE_NAME[0])
         fft_lib_dirs = [os.path.join(imklroot, d) for d in self.FFT_LIB_DIR]
-        if all([any([os.path.exists(os.path.join(d, "lib%s.a" % lib)) for d in fft_lib_dirs]) for lib in fftw_libs]):
+        # filter out gfortran from list of FFTW libraries to check for, since it's not provided by imkl
+        check_fftw_libs = [lib for lib in fftw_libs if lib != 'gfortran']
+        fftw_lib_exists = lambda x: any([os.path.exists(os.path.join(d, "lib%s.a" % x)) for d in fft_lib_dirs])
+        if all([fftw_lib_exists(lib) for lib in check_fftw_libs]):
             self.FFT_LIB = fftw_libs
         else:
             msg = "Not all FFTW interface libraries %s are found in %s, can't set FFT_LIB." % (fftw_libs, fft_lib_dirs)

From 92a564d0dce917d72b62a7a8f9a99b2d296ec582 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 1 Aug 2014 07:50:41 +0200
Subject: [PATCH 0027/1356] also include libgomp.a in list of libraries for
 multithreading for GCC

---
 easybuild/toolchains/compiler/gcc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py
index e47a9c4778..4889746920 100644
--- a/easybuild/toolchains/compiler/gcc.py
+++ b/easybuild/toolchains/compiler/gcc.py
@@ -77,7 +77,7 @@ class Gcc(Compiler):
     COMPILER_F90 = 'gfortran'
     COMPILER_F_UNIQUE_FLAGS = ['f2c']
 
-    LIB_MULTITHREAD = ['pthread']
+    LIB_MULTITHREAD = ['gomp', 'pthread']
     LIB_MATH = ['m']
 
     def _set_compiler_vars(self):

From 479f5d46f0b8ffb7632ca4f410c1140081c6e0c6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 1 Aug 2014 08:37:20 +0200
Subject: [PATCH 0028/1356] fix toolchain unit test w.r.t. including -lgomp

---
 test/framework/toolchain.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 45eefd7ad8..8056c71d12 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -381,7 +381,7 @@ def test_goolfc(self):
         nvcc_flags = r' '.join([
             r'-Xcompiler="-O2 -march=native"',
             # the use of -lcudart in -Xlinker is a bit silly but hard to avoid
-            r'-Xlinker=".* -lm -lrt -lcudart -lpthread"',
+            r'-Xlinker=".* -lm -lrt -lcudart -lgomp -lpthread"',
             r' '.join(["-gencode %s" % x for x in opts['cuda_gencode']]),
         ])
 

From 2e419bb366584ca699f5ef0147cb6897f089a5df Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 1 Aug 2014 09:50:32 +0200
Subject: [PATCH 0029/1356] remove duplicate code in handling of FFTW cdft libs

---
 easybuild/toolchains/fft/intelfftw.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index 03f2d2d43a..b13388382f 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -64,14 +64,11 @@ def _set_fftw_variables(self):
 
         fftw_libs = ["fftw3xc%s%s" % (compsuff, picsuff)]
         if self.options['usempi']:
-            # add cluster interface
-            if LooseVersion(imklver) >= LooseVersion("11.1"):
+            # add cluster interface for recent imkl versions
+            if LooseVersion(imklver) >= LooseVersion("11.0.2"):
                 fftw_libs.append("fftw3x_cdft%s%s" % (bitsuff, picsuff))
-            else:
-                if LooseVersion(imklver) >= LooseVersion("11.0.2"):
-                    fftw_libs.append("fftw3x_cdft%s%s" % (bitsuff, picsuff))
-                elif LooseVersion(imklver) >= LooseVersion("10.3"):
-                    fftw_libs.append("fftw3x_cdft%s" % picsuff)
+            elif LooseVersion(imklver) >= LooseVersion("10.3"):
+                fftw_libs.append("fftw3x_cdft%s" % picsuff)
             fftw_libs.append("mkl_cdft_core")  # add cluster dft
             fftw_libs.extend(self.variables['LIBBLACS'].flatten()) # add BLACS; use flatten because ListOfList
 

From b428bbe0e1b82ee55d0df57e81f194e2d746020c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 1 Aug 2014 14:01:54 +0200
Subject: [PATCH 0030/1356] make sure $SCALAPACK_INC_DIR (and
 $SCALAPACK_LIB_DIR) are defined when using imkl

---
 easybuild/toolchains/linalg/intelmkl.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index 415921f2e5..2f1186f6ee 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -153,5 +153,8 @@ def _set_scalapack_variables(self):
             # ilp64/i8
             self.SCALAPACK_LIB_MAP.update({"lp64_sc":'_ilp64'})
 
+        self.SCALAPACK_LIB_DIR = self.BLAS_LIB_DIR
+        self.SCALAPACK_INCLUDE_DIR = self.BLAS_INCLUDE_DIR
+
         super(IntelMKL, self)._set_scalapack_variables()
 

From 9b4e9d6a69bf0af750fe09a0db590bc9b33261e8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 1 Aug 2014 17:40:21 +0200
Subject: [PATCH 0031/1356] fix error message on missing FFTW wrapper libs

---
 easybuild/toolchains/fft/intelfftw.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index b13388382f..12f35035b9 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -89,5 +89,6 @@ def _set_fftw_variables(self):
         if all([fftw_lib_exists(lib) for lib in check_fftw_libs]):
             self.FFT_LIB = fftw_libs
         else:
-            msg = "Not all FFTW interface libraries %s are found in %s, can't set FFT_LIB." % (fftw_libs, fft_lib_dirs)
+            tup = (check_fftw_libs, fft_lib_dirs)
+            msg = "Not all FFTW interface libraries %s are found in %s, can't set FFT_LIB." % tup
             self.log.error(msg)

From f6d2d081cfdbd100e1ffb0e124c5bb528f7baa1a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 1 Aug 2014 18:36:55 +0200
Subject: [PATCH 0032/1356] include clear error message when an MPI library is
 being installed without a proper toolchain

---
 .../module_naming_scheme/hierarchical_mns.py   | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index a1c3aa96cb..e2243308e5 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -41,9 +41,6 @@
 MPI = 'MPI'
 
 
-_log = fancylogger.getLogger('HierarchicalMNS')
-
-
 class HierarchicalMNS(ModuleNamingScheme):
     """Class implementing an example hierarchical module naming scheme."""
 
@@ -86,10 +83,10 @@ def det_toolchain_compilers_name_version(self, tc_comps):
                 if tc_comps[0]['version'] == tc_comps[1]['version']:
                     tc_comp_ver = tc_comps[0]['version']
                 else:
-                    _log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
+                    self.log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
             else:
                 mns = self.__class__.__name__
-                _log.error("Unknown set of toolchain compilers, %s needs to be enhanced first." % mns)
+                self.log.error("Unknown set of toolchain compilers, %s needs to be enhanced first." % mns)
             res = (tc_comp_name, tc_comp_ver)
 
         return res
@@ -131,14 +128,15 @@ def det_modpath_extensions(self, ec):
         elif modclass == 'mpi':
             tc_comps = det_toolchain_compilers(ec)
             tc_comp_info = self.det_toolchain_compilers_name_version(tc_comps)
-            if tc_comp_info is None:
-                # MPI installed with a dummy toolchain
-                # FIXME: how do we determine the correct module path extension?
-                raise NotImplementedError
-            else:
+            if not tc_comp_info is None:
                 tc_comp_name, tc_comp_ver = tc_comp_info
                 fullver = ec['version'] + ec['versionsuffix']
                 paths.append(os.path.join(MPI, tc_comp_name, tc_comp_ver, ec['name'], fullver))
+            else:
+                tup = (ec['toolchain'], ec['name'], ec['version'])
+                error_msg = "No compiler available in toolchain %s used to install MPI library %s v%s, " % tup
+                error_msg += "which is required by the active module naming scheme %s." % self.__class__.__name__
+                self.log.error(error_msg)
 
         return paths
 

From 3b0e62dac0198b669d6dbe07d2b66c0de2817634 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 4 Aug 2014 09:57:46 +0200
Subject: [PATCH 0033/1356] add iimpi toolchain definition

---
 easybuild/toolchains/iimpi.py | 42 +++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100755 easybuild/toolchains/iimpi.py

diff --git a/easybuild/toolchains/iimpi.py b/easybuild/toolchains/iimpi.py
new file mode 100755
index 0000000000..7a7c1382b1
--- /dev/null
+++ b/easybuild/toolchains/iimpi.py
@@ -0,0 +1,42 @@
+##
+# Copyright 2012-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for intel compiler toolchain (includes Intel compilers (icc, ifort), Intel MPI).
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+"""
+
+from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.toolchains.fft.intelfftw import IntelFFTW
+from easybuild.toolchains.mpi.intelmpi import IntelMPI
+from easybuild.toolchains.linalg.intelmkl import IntelMKL
+
+
+class Intel(IntelIccIfort, IntelMPI):
+    """
+    Compiler toolchain with Intel compilers (icc/ifort), Intel MPI.
+    """
+    NAME = 'iimpi'

From 7291c99437281dd03794a4dae1eed0cdbfc7bff3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 4 Aug 2014 11:26:30 +0200
Subject: [PATCH 0034/1356] enhance unit test for --list-toolchains

---
 test/framework/options.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 6ffebedc8f..121f52351b 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -396,12 +396,19 @@ def test__list_toolchains(self):
 
         info_msg = r"INFO List of known toolchains \(toolchainname: module\[,module\.\.\.\]\):"
         self.assertTrue(re.search(info_msg, outtxt), "Info message with list of known compiler toolchains")
-        for tc in ["dummy", "goalf", "ictce"]:
-            res = re.findall("^\s*%s: " % tc, outtxt, re.M)
+        tcs = {
+            'dummy': [],
+            'goalf': ['ATLAS', 'BLACS', 'FFTW', 'GCC', 'OpenMPI', 'ScaLAPACK'],
+            'ictce': ['icc', 'ifort', 'imkl', 'impi'],
+        }
+        for tc, tcelems in tcs.items():
+            res = re.findall("^\s*%s: .*" % tc, outtxt, re.M)
             self.assertTrue(res, "Toolchain %s is included in list of known compiler toolchains" % tc)
             # every toolchain should only be mentioned once
             n = len(res)
             self.assertEqual(n, 1, "Toolchain %s is only mentioned once (count: %d)" % (tc, n))
+            # make sure definition is correct
+            self.assertEqual("\t%s: %s" % (tc, ', '.join(tcelems)), res[0])
 
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)

From 6d413d8f63022cb809b9f1f9d352fcbe0508abf4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 4 Aug 2014 11:27:09 +0200
Subject: [PATCH 0035/1356] only list toolchain elements once in output of
 --list-toolchains (fixes #984)

---
 easybuild/tools/options.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index d1f2173033..a5c0dc597a 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -37,6 +37,7 @@
 import re
 import sys
 from distutils.version import LooseVersion
+from vsc.utils.missing import nub
 
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig.constants import constant_documentation
@@ -572,8 +573,8 @@ def avail_toolchains(self):
 
         for (tcname, tcc) in tclist:
             tc = tcc(version='1.2.3')  # version doesn't matter here, but something needs to be there
-            tc_elems = [e for es in tc.definition().values() for e in es]
-            txt.append("\t%s: %s" % (tcname, ', '.join(sorted(tc_elems))))
+            tc_elems = nub(sorted([e for es in tc.definition().values() for e in es]))
+            txt.append("\t%s: %s" % (tcname, ', '.join(tc_elems)))
 
         return '\n'.join(txt)
 

From d2778eec00e2b403019e9ec501ebcfc9871649ad Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 4 Aug 2014 11:53:51 +0200
Subject: [PATCH 0036/1356] fix remarks

---
 easybuild/toolchains/iimpi.py | 2 +-
 test/framework/options.py     | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/toolchains/iimpi.py b/easybuild/toolchains/iimpi.py
index 7a7c1382b1..781223ca34 100755
--- a/easybuild/toolchains/iimpi.py
+++ b/easybuild/toolchains/iimpi.py
@@ -35,7 +35,7 @@
 from easybuild.toolchains.linalg.intelmkl import IntelMKL
 
 
-class Intel(IntelIccIfort, IntelMPI):
+class Iimpi(IntelIccIfort, IntelMPI):
     """
     Compiler toolchain with Intel compilers (icc/ifort), Intel MPI.
     """
diff --git a/test/framework/options.py b/test/framework/options.py
index 121f52351b..2777af5bb7 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -396,6 +396,7 @@ def test__list_toolchains(self):
 
         info_msg = r"INFO List of known toolchains \(toolchainname: module\[,module\.\.\.\]\):"
         self.assertTrue(re.search(info_msg, outtxt), "Info message with list of known compiler toolchains")
+        # toolchain elements should be in alphabetical order
         tcs = {
             'dummy': [],
             'goalf': ['ATLAS', 'BLACS', 'FFTW', 'GCC', 'OpenMPI', 'ScaLAPACK'],
@@ -407,7 +408,7 @@ def test__list_toolchains(self):
             # every toolchain should only be mentioned once
             n = len(res)
             self.assertEqual(n, 1, "Toolchain %s is only mentioned once (count: %d)" % (tc, n))
-            # make sure definition is correct
+            # make sure definition is correct (each element only named once, in alphabetical order)
             self.assertEqual("\t%s: %s" % (tc, ', '.join(tcelems)), res[0])
 
         if os.path.exists(dummylogfn):

From 751e401403cbf22da1711f63e309a503548b8883 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Mon, 4 Aug 2014 21:27:47 +0200
Subject: [PATCH 0037/1356] clean_gists: delete closed pr gists by default

---
 easybuild/scripts/clean_gists.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/clean_gists.py b/easybuild/scripts/clean_gists.py
index 4c9adc44d4..ba847e6198 100755
--- a/easybuild/scripts/clean_gists.py
+++ b/easybuild/scripts/clean_gists.py
@@ -46,7 +46,7 @@ def main():
 
     options = {
         'github-user': ('Your github username to use', None, 'store', None, 'g'),
-        'closed-pr': ('Delete all gists from closed pull-requests', None, 'store_true', False, 'p'),
+        'closed-pr': ('Delete all gists from closed pull-requests', None, 'store_true', True, 'p'),
         'all': ('Delete all gists from Easybuild ', None, 'store_true', False, 'a'),
         'orphans': ('Delete all gists without a pull-request', None, 'store_true', False, 'o'),
     }

From 9f73f20f97e6615c2795c4a61aadfde1024ac7d8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 7 Aug 2014 16:14:32 +0200
Subject: [PATCH 0038/1356] prepend robot path with download location of files
 when --from-pr is used

---
 easybuild/main.py         |  8 +++++++-
 test/framework/options.py | 10 +++++++++-
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 89d001e809..95fb69d0fc 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -226,6 +226,13 @@ def main(testing_data=(None, None, None)):
     if options.dep_graph or options.dry_run or options.dry_run_short:
         options.ignore_osdeps = True
 
+    pr_path = None
+    if options.from_pr:
+        # extend robot search path with location where files touch in PR will be downloaded to
+        pr_path = os.path.join(eb_tmpdir, "files_pr%s" % options.from_pr)
+        robot_path.insert(0, pr_path)
+        _log.info("Prepended list of robot search paths with %s: %s" % (pr_path, robot_path))
+
     config.init_build_options({
         'aggregate_regtest': options.aggregate_regtest,
         'allow_modules_tool_mismatch': options.allow_modules_tool_mismatch,
@@ -281,7 +288,6 @@ def main(testing_data=(None, None, None)):
     paths = []
     if len(orig_paths) == 0:
         if options.from_pr:
-            pr_path = os.path.join(eb_tmpdir, "files_pr%s" % options.from_pr)
             pr_files = fetch_easyconfigs_from_pr(options.from_pr, path=pr_path, github_user=options.github_user)
             paths = [(path, False) for path in pr_files if path.endswith('.eb')]
         elif 'name' in build_specs:
diff --git a/test/framework/options.py b/test/framework/options.py
index 2777af5bb7..2d24f43321 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -641,13 +641,15 @@ def test_from_pr(self):
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
+        tmpdir = tempfile.mkdtemp()
         args = [
             # PR for ictce/6.2.5, see https://github.com/hpcugent/easybuild-easyconfigs/pull/726/files
             '--from-pr=726',
             '--dry-run',
-            '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+            '--robot',
             '--unittest-file=%s' % self.logfile,
             '--github-user=easybuild_test',  # a GitHub token should be available for this user
+            '--tmpdir=%s' % tmpdir,
         ]
         outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
 
@@ -664,6 +666,12 @@ def test_from_pr(self):
             regex = re.compile(r"^ \* \[.\] .*/%s \(module: %s\)$" % (ec_fn, module), re.M)
             self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
 
+        pr_tmpdir = os.path.join(tmpdir, 'easybuild-\S{6}', 'files_pr726')
+        regex = re.compile("Prepended list of robot search paths with %s:" % pr_tmpdir, re.M)
+        self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
+
+        shutil.rmtree(tmpdir)
+
     def test_no_such_software(self):
         """Test using no arguments."""
 

From f22c5305265a89a50daddc002a6d0ed4916407cc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 7 Aug 2014 16:30:08 +0200
Subject: [PATCH 0039/1356] fix broken unit test

---
 test/framework/options.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 2d24f43321..6ec2cc012f 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -646,7 +646,8 @@ def test_from_pr(self):
             # PR for ictce/6.2.5, see https://github.com/hpcugent/easybuild-easyconfigs/pull/726/files
             '--from-pr=726',
             '--dry-run',
-            '--robot',
+            # an argument must be specified to --robot, since easybuild-easyconfigs may not be installed
+            '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
             '--unittest-file=%s' % self.logfile,
             '--github-user=easybuild_test',  # a GitHub token should be available for this user
             '--tmpdir=%s' % tmpdir,

From c0a49758ccf911ff4c02296e6456e051353929c4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 8 Aug 2014 11:41:04 +0200
Subject: [PATCH 0040/1356] fix det_modpath_extensions for Intel compilers

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index e2243308e5..ca2adb21b7 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -124,7 +124,11 @@ def det_modpath_extensions(self, ec):
 
         paths = []
         if modclass == 'compiler':
-            paths.append(os.path.join(COMPILER, ec['name'], ec['version']))
+            if ec['name'] in ['icc', 'ifort']:
+                compdir = 'intel'
+            else:
+                compdir = ec['name']
+            paths.append(os.path.join(COMPILER, compdir, ec['version']))
         elif modclass == 'mpi':
             tc_comps = det_toolchain_compilers(ec)
             tc_comp_info = self.det_toolchain_compilers_name_version(tc_comps)

From dbed38cad6e47952c0720dba107a8d3c27dfb11d Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Wed, 13 Aug 2014 10:37:22 +0200
Subject: [PATCH 0041/1356] add download_repo() method

---
 easybuild/tools/github.py | 67 ++++++++++++++++++++++++++++-----------
 1 file changed, 48 insertions(+), 19 deletions(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 5e0f1f0729..6d1389dce5 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -27,6 +27,7 @@
 
 @author: Jens Timmerman (Ghent University)
 @author: Kenneth Hoste (Ghent University)
+@author: Toon Willems (Ghent University)
 """
 import base64
 import os
@@ -56,7 +57,7 @@
     _log.warning("Failed to import from 'vsc.utils.rest' Python module: %s" % err)
     HAVE_GITHUB_API = False
 
-from easybuild.tools.filetools import det_patched_files, mkdir
+from easybuild.tools.filetools import det_patched_files, mkdir, extract_file
 
 
 GITHUB_API_URL = 'https://api.github.com'
@@ -188,26 +189,54 @@ class GithubError(Exception):
     """Error raised by the Githubfs"""
     pass
 
+def download_repo(branch='master', path=None):
+    """Download entire easyconfigs repo"""
+    if path is None:
+        path = tempfile.mkdtemp()
+    else:
+        # make sure path exists, create it if necessary
+        mkdir(path, parents=True)
+
+    extracted_dir_name = "%s-%s" % (GITHUB_EASYCONFIGS_REPO, branch)
+    base_name = ("%s.tar.gz" % branch)
+
+    url = URL_SEPARATOR.join(["https://github.com",GITHUB_EB_MAIN, GITHUB_EASYCONFIGS_REPO, 'archive', base_name])
+    _log.debug("download from %s" % url)
+    _download(url, os.path.join(path,base_name))
+    _log.debug("archive downloaded to %s, extracting now" % path)
+
+    extracted_path = extract_file(os.path.join(path, base_name), path)
+    extracted_path = os.path.join(extracted_path, extracted_dir_name)
+    # check if extracted_path exists
+    if not os.path.isdir(extracted_path):
+        _log.error("We expected %s to exists and contain the repo" % extracted_path)
+
+    _log.debug("Repo extracted into %s" % extracted_path)
+    return extracted_path
+
+def _download(url, path=None):
+    """Download file from specified URL to specified path."""
+    if path is not None:
+        try:
+            _, httpmsg = urllib.urlretrieve(url, path)
+            _log.debug("Downloaded %s to %s" % (url, path))
+        except IOError, err:
+            _log.error("Failed to download %s to %s: %s" % (url, path, err))
+
+        '''
+        if httpmsg.type != 'text/plain' or httpmsg.type != 'application/x-gzip' :
+            _log.error("Unexpected file type for %s: %s" % (path, httpmsg.type))
+        '''
+    else:
+        try:
+            return urllib2.urlopen(url).read()
+        except urllib2.URLError, err:
+            _log.error("Failed to open %s for reading: %s" % (url, err))
+
 
 def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
     """Fetch patched easyconfig files for a particular PR."""
 
-    def download(url, path=None):
-        """Download file from specified URL to specified path."""
-        if path is not None:
-            try:
-                _, httpmsg = urllib.urlretrieve(url, path)
-                _log.debug("Downloaded %s to %s" % (url, path))
-            except IOError, err:
-                _log.error("Failed to download %s to %s: %s" % (url, path, err))
-
-            if not httpmsg.type == 'text/plain':
-                _log.error("Unexpected file type for %s: %s" % (path, httpmsg.type))
-        else:
-            try:
-                return urllib2.urlopen(url).read()
-            except urllib2.URLError, err:
-                _log.error("Failed to open %s for reading: %s" % (url, err))
 
     # a GitHub token is optional here, but can be used if available in order to be less susceptible to rate limiting
     github_token = fetch_github_token(github_user)
@@ -242,7 +271,7 @@ def download(url, path=None):
         _log.debug("\n%s:\n\n%s\n" % (key, val))
 
     # determine list of changed files via diff
-    diff_txt = download(pr_data['diff_url'])
+    diff_txt = _download(pr_data['diff_url'])
 
     patched_files = det_patched_files(txt=diff_txt, omit_ab_prefix=True)
     _log.debug("List of patches files: %s" % patched_files)
@@ -258,7 +287,7 @@ def download(url, path=None):
         sha = last_commit['sha']
         full_url = URL_SEPARATOR.join([GITHUB_RAW, GITHUB_EB_MAIN, GITHUB_EASYCONFIGS_REPO, sha, patched_file])
         _log.info("Downloading %s from %s" % (fn, full_url))
-        download(full_url, path=os.path.join(path, fn))
+        _download(full_url, path=os.path.join(path, fn))
 
     all_files = [os.path.basename(x) for x in patched_files]
     tmp_files = os.listdir(path)

From 034f7551de40151117e6d1079a79f1855fe9c684 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 Aug 2014 12:11:31 +0200
Subject: [PATCH 0042/1356] add support for excluding module path extensions
 from generated modules

---
 easybuild/framework/easyblock.py          |  9 ++++++---
 easybuild/framework/easyconfig/default.py |  1 +
 test/framework/toy_build.py               | 10 +++++++++-
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 9fdf118ad3..998d08e067 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -864,16 +864,19 @@ def make_module_extend_modpath(self):
         """
         Include prepend-path statements for extending $MODULEPATH.
         """
-        top_modpath = install_path('mod')
-        modpath_exts = ActiveMNS().det_modpath_extensions(self.cfg)
         txt = ''
-        if modpath_exts:
+        if self.cfg['include_modpath_extensions']:
+            top_modpath = install_path('mod')
             mod_path_suffix = build_option('suffix_modules_path')
+            modpath_exts = ActiveMNS().det_modpath_extensions(self.cfg)
+            self.log.debug("Including module path extensions returned by module naming scheme: %s" % modpath_exts)
             full_path_modpath_extensions = [os.path.join(top_modpath, mod_path_suffix, ext) for ext in modpath_exts]
             # module path extensions must exist, otherwise loading this module file will fail
             for modpath_extension in full_path_modpath_extensions:
                 mkdir(modpath_extension, parents=True)
             txt = self.moduleGenerator.use(full_path_modpath_extensions)
+        else:
+            self.log.debug("Not including module path extensions, as specified.")
         return txt
 
     def make_module_req(self):
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 20640e0af7..aea517b484 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -168,6 +168,7 @@
     'moduleclass': ['base', 'Module class to be used for this software', MODULES],
     'moduleforceunload': [False, 'Force unload of all modules when loading the extension', MODULES],
     'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", MODULES],
+    'include_modpath_extensions': [True, "Include $MODULEPATH extensions specified by module naming scheme.", MODULES],
 
     # OTHER easyconfig parameters
     'buildstats': [None, "A list of dicts with build statistics", OTHER],
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 50b586f740..a8c3b2b19e 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -592,12 +592,20 @@ def test_toy_hierarchical(self):
         toy_module_path = os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'toy', '0.0')
         self.assertTrue(os.path.exists(toy_module_path))
 
-        # no dependencies or toolchain => no module load statements in module file
+        # 'module use' statements to extend $MODULEPATH are present
         modtxt = read_file(toy_module_path)
         modpath_extension = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'toy', '0.0')
         self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
         os.remove(toy_module_path)
 
+        # ... unless they shouldn't be
+        extra_args.append('--try-amend=include_modpath_extensions=')  # pass empty string as equivalent to False
+        self.eb_main(args + extra_args, logfile=self.dummylogfn, do_build=True, verbose=True, raise_error=True)
+        modtxt = read_file(toy_module_path)
+        modpath_extension = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'toy', '0.0')
+        self.assertFalse(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        os.remove(toy_module_path)
+
         # test module path with dummy/dummy build
         extra_args = [
             '--try-toolchain=dummy,dummy',

From b3eef1fb7f3ce2908bf4faad6de2f9e3c059908b Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Wed, 13 Aug 2014 14:26:33 +0200
Subject: [PATCH 0043/1356] compare push

---
 easybuild/framework/easyconfig/easyconfig.py |  29 +++
 easybuild/main.py                            |  27 +-
 easybuild/tools/github.py                    |   2 +-
 easybuild/tools/multi_diff.py                | 252 +++++++++++++++++++
 easybuild/tools/options.py                   |   1 +
 5 files changed, 308 insertions(+), 3 deletions(-)
 create mode 100644 easybuild/tools/multi_diff.py

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 45caac97cc..28096f2730 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -37,6 +37,7 @@
 
 import copy
 import difflib
+import glob
 import os
 import re
 from vsc.utils import fancylogger
@@ -858,6 +859,34 @@ def resolve_template(value, tmpl_dict):
 
     return value
 
+def find_relevant_easyconfigs(path, ec):
+    """
+    Find relevant easyconfigs for ec in path based on a simple heuristic
+    """
+    # make sure we are working with an EasyConfig object
+    if not isinstance(ec, EasyConfig):
+        # we can safely only take the first one
+        ec = process_easyconfig(ec, parse_only=True)[0]['ec']
+
+    name = ec.name
+    version = ec.version
+    toolchain_name = ec['toolchain']['name']
+    toolchain = "%s-%s" % (toolchain_name, ec['toolchain']['version'])
+
+    cand_paths = [
+        # Same version, any toolchain
+        (name.lower()[0], name, "%s-%s-*" % (name, version)),
+        # any version, same toolchain
+        (name.lower()[0], name, "%s-*-%s-*" % (name, toolchain)),
+        # any version, same toolchain name
+        (name.lower()[0], name, "%s-*-%s-*" % (name, toolchain_name)),
+        # any version, any toolchain
+        (name.lower()[0], name, "%s-*" % (name)),
+    ]
+    relevant_files = [glob.glob("%s.eb" % os.path.join(path, *cand_path)) for cand_path in cand_paths]
+
+    return relevant_files
+
 
 def process_easyconfig(path, build_specs=None, validate=True, parse_only=False):
     """
diff --git a/easybuild/main.py b/easybuild/main.py
index 95fb69d0fc..8351eb3125 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -51,13 +51,14 @@
 import easybuild.tools.config as config
 import easybuild.tools.options as eboptions
 from easybuild.framework.easyblock import EasyBlock, build_and_install_one
-from easybuild.framework.easyconfig.easyconfig import process_easyconfig
+from easybuild.framework.easyconfig.easyconfig import process_easyconfig, find_relevant_easyconfigs
 from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, print_dry_run
 from easybuild.framework.easyconfig.tools import resolve_dependencies, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_path, tweak
 from easybuild.tools.config import get_repository, module_classes, get_repositorypath, set_tmpdir
 from easybuild.tools.filetools import cleanup, find_easyconfigs, search_file, write_file
-from easybuild.tools.github import fetch_easyconfigs_from_pr
+from easybuild.tools.github import fetch_easyconfigs_from_pr, download_easyconfig_repo
+from easybuild.tools.multi_diff import multi_diff
 from easybuild.tools.options import process_software_build_specs
 from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
 from easybuild.tools.repository.repository import init_repository
@@ -226,6 +227,7 @@ def main(testing_data=(None, None, None)):
     if options.dep_graph or options.dry_run or options.dry_run_short:
         options.ignore_osdeps = True
 
+
     pr_path = None
     if options.from_pr:
         # extend robot search path with location where files touch in PR will be downloaded to
@@ -285,6 +287,26 @@ def main(testing_data=(None, None, None)):
         silent = config.build_option('silent')
         search_file(search_path, query, short=not options.search, ignore_dirs=ignore_dirs, silent=silent)
 
+    if options.review_pr:
+        repo_path = os.path.join(download_easyconfig_repo('develop'),'easybuild','easyconfigs')
+        pr_files = [path for path in fetch_easyconfigs_from_pr(options.review_pr)
+                        if path.endswith('.eb')]
+        _log.info(pr_files)
+
+        for easyconfig in pr_files:
+            most, second, third, last = find_relevant_easyconfigs(repo_path, easyconfig)
+            if most:
+                diff = multi_diff(easyconfig, most)
+            elif second:
+                diff = multi_diff(easyconfig, second)
+            elif third:
+                diff = multi_diff(easyconfig, third)
+            elif last:
+                diff = multi_diff(easyconfig, last)
+            diff.write_out()
+
+        os.sys.exit()
+
     paths = []
     if len(orig_paths) == 0:
         if options.from_pr:
@@ -349,6 +371,7 @@ def main(testing_data=(None, None, None)):
             _log.info("Regression test failed (partially)!")
             sys.exit(31)  # exit -> 3x1t -> 31
 
+
     # read easyconfig files
     easyconfigs = []
     generated_ecs = False
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 6d1389dce5..8551f4afb0 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -189,7 +189,7 @@ class GithubError(Exception):
     """Error raised by the Githubfs"""
     pass
 
-def download_repo(branch='master', path=None):
+def download_easyconfig_repo(branch='master', path=None):
     """Download entire easyconfigs repo"""
     if path is None:
         path = tempfile.mkdtemp()
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
new file mode 100644
index 0000000000..ea7503f7f4
--- /dev/null
+++ b/easybuild/tools/multi_diff.py
@@ -0,0 +1,252 @@
+import difflib
+import os
+import sys
+from collections import defaultdict
+from pprint import pprint
+
+import collections
+
+class bcolors:
+        HEADER = '\033[95m'
+        OKBLUE = '\033[94m'
+        OKGREEN = '\033[92m'
+        WARNING = '\033[93m'
+        FAIL = '\033[91m'
+        ENDC = '\033[0m'
+
+class OrderedSet(collections.MutableSet):
+    '''Set that remembers original insertion order.'''
+
+    KEY, PREV, NEXT = range(3)
+
+    def __init__(self, iterable=None):
+        self.end = end = []
+        end += [None, end, end]         # sentinel node for doubly linked list
+        self.map = {}                   # key --> [key, prev, next]
+        if iterable is not None:
+            self |= iterable
+
+    ### Collection Methods
+    def __contains__(self, key):
+        return key in self.map
+
+    def __eq__(self, other):
+        if isinstance(other, OrderedSet):
+            return len(self) == len(other) and list(self) == list(other)
+        return set(self) == set(other)
+
+    def __iter__(self):
+        end = self.end
+        curr = end[self.NEXT]
+        while curr is not end:
+            yield curr[self.KEY]
+            curr = curr[self.NEXT]
+
+    def __len__(self):
+        return len(self.map)
+
+    def __reversed__(self):
+        end = self.end
+        curr = end[self.PREV]
+        while curr is not end:
+            yield curr[self.KEY]
+            curr = curr[self.PREV]
+
+    def add(self, key):
+        if key not in self.map:
+            end = self.end
+            curr = end[self.PREV]
+            curr[self.NEXT] = end[self.PREV] = self.map[key] = [key, curr, end]
+
+    def discard(self, key):
+        if key in self.map:
+            key, prev, next = self.map.pop(key)
+            prev[self.NEXT] = next
+            next[self.PREV] = prev
+
+    def pop(self, last=True):
+        if not self:
+            raise KeyError('set is empty')
+        key = next(reversed(self)) if last else next(iter(self))
+        self.discard(key)
+        return key
+
+    ### General Methods
+    def __del__(self):
+        self.clear()                    # remove circular references
+
+    def __repr__(self):
+        class_name = self.__class__.__name__
+        if not self:
+            return '{0!s}()'.format(class_name)
+        return '{0!s}({1!r})'.format(class_name, list(self))
+
+class Diff:
+    def __init__(self, base, files):
+        self.base = base
+        self.base_lines = open(base).readlines()
+        self.diff_info = defaultdict(dict)
+        self.files = files
+        self.num_files = len(files)
+
+    def add_line(self,line_no, diff_line, meta, squigly_line=None):
+        if diff_line.startswith('+'):
+            self._add_diff(line_no, diff_line.rstrip(), meta, squigly_line)
+        elif diff_line.startswith('-'):
+            self._remove_diff(line_no, diff_line.rstrip(), meta, squigly_line)
+
+    def write_out(self):
+        print "Comparing %s with %s" % (os.path.basename(self.base), ", ".join(map(os.path.basename,self.files)))
+        for i in range(len(self.base_lines)):
+            self.get_line(i)
+
+    def get_line(self, line_no):
+        removal_dict = dict()
+        addition_dict = dict()
+        squigly_dict = dict()
+        order = OrderedSet([])
+        if 'removal' in self.diff_info[line_no]:
+            for (diff_line, meta, squigly_line) in self.diff_info[line_no]['removal']:
+                if squigly_line:
+                    squigly_dict[diff_line] = squigly_line
+                order.add(diff_line)
+                if diff_line not in removal_dict:
+                    removal_dict[diff_line] = set([meta])
+                else:
+                    removal_dict[diff_line].add(meta)
+
+        for diff_line in order:
+            print line_no, self._colorize(diff_line, squigly_dict.get(diff_line)),
+            if len(removal_dict[diff_line]) != self.num_files:
+                print bcolors.OKBLUE, ', '.join(removal_dict[diff_line]), bcolors.ENDC
+            else:
+                print
+
+        squigly_dict = dict()
+        order = OrderedSet([])
+
+        if 'addition' in self.diff_info[line_no]:
+            for (diff_line, meta, squigly_line) in self.diff_info[line_no]['addition']:
+                if squigly_line:
+                    squigly_dict[diff_line] = self._merge_squigly(squigly_dict.get(diff_line, squigly_line), squigly_line)
+                order.add(diff_line)
+                if diff_line not in addition_dict:
+                    addition_dict[diff_line] = set([meta])
+                else:
+                    addition_dict[diff_line].add(meta)
+        for diff_line in order:
+            print line_no, self._colorize(diff_line, squigly_dict.get(diff_line)),
+            if len(addition_dict[diff_line]) != self.num_files:
+                print bcolors.OKBLUE, ', '.join(addition_dict[diff_line]), bcolors.ENDC
+            else:
+                print
+
+        # print seperator
+        if self.diff_info[line_no] and 'addition' not in self.diff_info[line_no+1] and 'removal' not in self.diff_info[line_no + 1]:
+            print '-----'
+
+
+    def _remove_diff(self,line_no, diff_line, meta, squigly_line=None):
+        if 'removal' not in self.diff_info[line_no]:
+            self.diff_info[line_no]['removal'] = []
+
+        self.diff_info[line_no]['removal'].append((diff_line, meta, squigly_line))
+
+    def _add_diff(self,line_no, diff_line, meta, squigly_line=None):
+        if 'addition' not in self.diff_info[line_no]:
+            self.diff_info[line_no]['addition'] = []
+
+        self.diff_info[line_no]['addition'].append((diff_line, meta, squigly_line))
+
+    def _colorize(self, line, squigly):
+        chars = list(line)
+        flag = ' '
+        compensator = 0
+        if not squigly:
+            if line.startswith('+'):
+                chars.insert(0, bcolors.OKGREEN)
+            elif line.startswith('-'):
+                chars.insert(0, bcolors.FAIL)
+        else:
+            for i in range(len(squigly)):
+                if squigly[i] == '+' and flag != '+':
+                    chars.insert(i+compensator, bcolors.OKGREEN)
+                    compensator += 1
+                    flag = '+'
+                if squigly[i] == '^' and flag != '^':
+                    chars.insert(i+compensator, bcolors.WARNING)
+                    compensator += 1
+                    flag = '^'
+                if squigly[i] == '-' and flag != '-':
+                    chars.insert(i+compensator, bcolors.FAIL)
+                    compensator += 1
+                    flag = '-'
+                if squigly[i] != flag:
+                    chars.insert(i+compensator, bcolors.ENDC)
+                    compensator += 1
+                    flag = squigly[i]
+
+        chars.append(bcolors.ENDC)
+        return ''.join(chars)
+
+    def _merge_squigly(self, squigly1, squigly2):
+        """Combine 2 diff lines into 1 """
+        sq1 = list(squigly1)
+        sq2 = list(squigly2)
+        base,other = (sq1, sq2) if len(sq1) > len(sq2) else (sq2,sq1)
+
+        for i in range(len(other)):
+            if base[i] != other[i] and base[i] == ' ':
+                base[i] = other[i]
+            if base[i] != other[i] and base[i] == '^':
+                base[i] = other[i]
+
+
+        return ''.join(base)
+
+def merge_diff_info(diffs):
+    ### Combine multiple diff squigly lines into a single one.
+    base = list(max(diffs,key=len))
+    for line in diffs:
+        for i in range(len(line)):
+            if base[i] != line[i]:
+                if base[i] == ' ' and line[i] != "\n":
+                    base[i] = line[i]
+    return ''.join(base).rstrip()
+
+def multi_diff(base,files):
+    d = difflib.Differ()
+    base_lines = open(base).readlines()
+
+    diff_information = dict()
+    enters = []
+
+    differ = Diff(base, files)
+
+    # store diff information in dict
+    for file_name in files:
+        diff = list(d.compare(open(file_name).readlines(), base_lines))
+        file_name = os.path.basename(file_name)
+
+        local_diff = defaultdict(list)
+        squigly_dict = dict()
+        last_added = None
+        compensator = 1
+        for (i, line) in enumerate(diff):
+            if line.startswith('?'):
+                squigly_dict[last_added] = (line)
+                compensator -= 1
+            elif line.startswith('+'):
+                local_diff[i+compensator].append((line, file_name))
+                last_added = line
+            elif line.startswith('-'):
+                local_diff[i+compensator].append((line, file_name))
+                last_added = line
+                compensator -= 1
+
+
+        for line_no in local_diff:
+            for (line, file_name) in local_diff[line_no]:
+                differ.add_line(line_no, line, file_name, squigly_dict.get(line, None))
+
+    return differ
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index a5c0dc597a..a1a11ff8cc 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -142,6 +142,7 @@ def software_options(self):
         # additional options that don't need a --try equivalent
         opts.update({
             'from-pr': ("Obtain easyconfigs from specified PR", int, 'store', None, {'metavar': 'PR#'}),
+            'review-pr': ("Review specified pull request", int, 'store', None, {'metavar': 'PR#'}),
         })
 
         self.log.debug("software_options: descr %s opts %s" % (descr, opts))

From 5da7c8d407648b43b496e5428810dd78e9aa9958 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 Aug 2014 15:30:59 +0200
Subject: [PATCH 0044/1356] add support for installing hidden module files

---
 easybuild/framework/easyblock.py    | 2 +-
 easybuild/main.py                   | 1 +
 easybuild/tools/config.py           | 1 +
 easybuild/tools/module_generator.py | 9 +++++++--
 easybuild/tools/options.py          | 1 +
 test/framework/toy_build.py         | 6 ++++++
 6 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 9fdf118ad3..05144f8491 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1626,7 +1626,7 @@ def make_module_step(self, fake=False):
 
         write_file(self.moduleGenerator.filename, txt)
 
-        self.log.info("Added modulefile: %s" % (self.moduleGenerator.filename))
+        self.log.info("Module file %s written" % self.moduleGenerator.filename)
 
         self.modules_tool.update()
         self.moduleGenerator.create_symlinks()
diff --git a/easybuild/main.py b/easybuild/main.py
index 95fb69d0fc..acb69b15d4 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -247,6 +247,7 @@ def main(testing_data=(None, None, None)):
         'force': options.force,
         'github_user': options.github_user,
         'group': options.group,
+        'hidden': options.hidden,
         'ignore_dirs': options.ignore_dirs,
         'modules_footer': options.modules_footer,
         'only_blocks': options.only_blocks,
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 50e0f5ac14..d595b79803 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -82,6 +82,7 @@
     'force': False,
     'github_user': None,
     'group': None,
+    'hidden': False,
     'ignore_dirs': None,
     'modules_footer': None,
     'only_blocks': None,
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 525a43d508..58a2977b2e 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -63,11 +63,16 @@ def prepare(self):
         Creates the absolute filename for the module.
         """
         mod_path_suffix = build_option('suffix_modules_path')
+        hidden = build_option('hidden')
+        full_mod_name = self.app.full_mod_name
+        if build_option('hidden'):
+            full_mod_name = os.path.join(os.path.dirname(full_mod_name), '.%s' % os.path.basename(full_mod_name))
+            _log.debug("Prefixed module filename with '.' to make it hidden: %s" % full_mod_name)
         # module file goes in general moduleclass category
-        self.filename = os.path.join(self.module_path, mod_path_suffix, self.app.full_mod_name)
+        self.filename = os.path.join(self.module_path, mod_path_suffix, full_mod_name)
         # make symlink in moduleclass category
         mod_symlink_paths = ActiveMNS().det_module_symlink_paths(self.app.cfg)
-        self.class_mod_files = [os.path.join(self.module_path, p, self.app.full_mod_name) for p in mod_symlink_paths]
+        self.class_mod_files = [os.path.join(self.module_path, p, full_mod_name) for p in mod_symlink_paths]
 
         # create directories and links
         for path in [os.path.dirname(x) for x in [self.filename] + self.class_mod_files]:
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index a5c0dc597a..ee44159a30 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -162,6 +162,7 @@ def override_options(self):
             'experimental': ("Allow experimental code (with behaviour that can be changed or removed at any given time).",
                              None, 'store_true', False),
             'group': ("Group to be used for software installations (only verified, not set)", None, 'store', None),
+            'hidden': ("Install 'hidden' module file(s) by prefixing their name with '.'", None, 'store_true', False),
             'ignore-osdeps': ("Ignore any listed OS dependencies", None, 'store_true', False),
             'filter-deps': ("Comma separated list of dependencies that you DON'T want to install with EasyBuild, "
                             "because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses)",
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 50b586f740..62321d6e22 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -637,6 +637,12 @@ def test_toy_advanced(self):
         test_ec = os.path.join(test_dir, 'easyconfigs', 'toy-0.0-gompi-1.3.12.eb')
         self.test_toy_build(ec_file=test_ec, versionsuffix='-gompi-1.3.12')
 
+    def test_toy_hidden(self):
+        """Test installing a hidden module."""
+        self.test_toy_build(extra_args=['--hidden'], verify=False)
+        toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '.0.0')
+        self.assertTrue(os.path.exists(toy_module), 'Found hidden module %s' % toy_module)
+
     def test_module_filepath_tweaking(self):
         """Test using --suffix-modules-path."""
         # install test module naming scheme dynamically

From 7dbbffb3efc03337d30157dea24365bde9136776 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Wed, 13 Aug 2014 15:39:16 +0200
Subject: [PATCH 0045/1356] change outputter

---
 easybuild/framework/easyconfig/easyconfig.py |  2 +-
 easybuild/main.py                            |  1 -
 easybuild/tools/multi_diff.py                | 69 +++++++++++++-------
 3 files changed, 45 insertions(+), 27 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 28096f2730..04105588ef 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -877,7 +877,7 @@ def find_relevant_easyconfigs(path, ec):
         # Same version, any toolchain
         (name.lower()[0], name, "%s-%s-*" % (name, version)),
         # any version, same toolchain
-        (name.lower()[0], name, "%s-*-%s-*" % (name, toolchain)),
+        (name.lower()[0], name, "%s*%s-*" % (name, toolchain)),
         # any version, same toolchain name
         (name.lower()[0], name, "%s-*-%s-*" % (name, toolchain_name)),
         # any version, any toolchain
diff --git a/easybuild/main.py b/easybuild/main.py
index 8351eb3125..e2c2a0d410 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -291,7 +291,6 @@ def main(testing_data=(None, None, None)):
         repo_path = os.path.join(download_easyconfig_repo('develop'),'easybuild','easyconfigs')
         pr_files = [path for path in fetch_easyconfigs_from_pr(options.review_pr)
                         if path.endswith('.eb')]
-        _log.info(pr_files)
 
         for easyconfig in pr_files:
             most, second, third, last = find_relevant_easyconfigs(repo_path, easyconfig)
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index ea7503f7f4..ed6ad93963 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -3,16 +3,18 @@
 import sys
 from collections import defaultdict
 from pprint import pprint
-
 import collections
 
+import easybuild.tools.terminal as terminal
+
 class bcolors:
-        HEADER = '\033[95m'
-        OKBLUE = '\033[94m'
-        OKGREEN = '\033[92m'
-        WARNING = '\033[93m'
-        FAIL = '\033[91m'
-        ENDC = '\033[0m'
+        HEADER = "\033[95m"
+        OKBLUE = "\033[94m"
+        GREEN = "\033[92m"
+        PURPLE = "\033[0;35m"
+        GRAY = "\033[1;37m"
+        RED = "\033[91m"
+        ENDC = "\033[0m"
 
 class OrderedSet(collections.MutableSet):
     '''Set that remembers original insertion order.'''
@@ -96,15 +98,26 @@ def add_line(self,line_no, diff_line, meta, squigly_line=None):
             self._remove_diff(line_no, diff_line.rstrip(), meta, squigly_line)
 
     def write_out(self):
-        print "Comparing %s with %s" % (os.path.basename(self.base), ", ".join(map(os.path.basename,self.files)))
+        def limit(text, length):
+            if len(text) > length:
+                return text[0:length-3] + '...'
+            else:
+                return text
+
+        w,h = terminal.get_terminal_size()
+        print " ".join(["Comparing", bcolors.PURPLE, os.path.basename(self.base), bcolors.ENDC, "with", bcolors.GRAY, ", ".join(map(os.path.basename,self.files)), bcolors.ENDC])
+
         for i in range(len(self.base_lines)):
-            self.get_line(i)
+            lines = self.get_line(i)
+            if filter(None,lines):
+                print "\n".join(map(lambda line: limit(line,w),lines))
 
     def get_line(self, line_no):
         removal_dict = dict()
         addition_dict = dict()
         squigly_dict = dict()
         order = OrderedSet([])
+        output = []
         if 'removal' in self.diff_info[line_no]:
             for (diff_line, meta, squigly_line) in self.diff_info[line_no]['removal']:
                 if squigly_line:
@@ -116,11 +129,11 @@ def get_line(self, line_no):
                     removal_dict[diff_line].add(meta)
 
         for diff_line in order:
-            print line_no, self._colorize(diff_line, squigly_dict.get(diff_line)),
-            if len(removal_dict[diff_line]) != self.num_files:
-                print bcolors.OKBLUE, ', '.join(removal_dict[diff_line]), bcolors.ENDC
-            else:
-                print
+            line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
+            files = removal_dict[diff_line]
+            if files != self.num_files:
+                line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), ', '.join(files), bcolors.ENDC])
+            output.append(" ".join(line))
 
         squigly_dict = dict()
         order = OrderedSet([])
@@ -134,16 +147,21 @@ def get_line(self, line_no):
                     addition_dict[diff_line] = set([meta])
                 else:
                     addition_dict[diff_line].add(meta)
+
         for diff_line in order:
-            print line_no, self._colorize(diff_line, squigly_dict.get(diff_line)),
-            if len(addition_dict[diff_line]) != self.num_files:
-                print bcolors.OKBLUE, ', '.join(addition_dict[diff_line]), bcolors.ENDC
-            else:
-                print
+            line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
+            files = addition_dict[diff_line]
+            if files != self.num_files:
+                line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), ', '.join(files), bcolors.ENDC])
+            output.append(" ".join(line))
 
         # print seperator
         if self.diff_info[line_no] and 'addition' not in self.diff_info[line_no+1] and 'removal' not in self.diff_info[line_no + 1]:
-            print '-----'
+            output.append('')
+            output.append('-----')
+            output.append('')
+
+        return output
 
 
     def _remove_diff(self,line_no, diff_line, meta, squigly_line=None):
@@ -164,21 +182,22 @@ def _colorize(self, line, squigly):
         compensator = 0
         if not squigly:
             if line.startswith('+'):
-                chars.insert(0, bcolors.OKGREEN)
+                chars.insert(0, bcolors.GREEN)
             elif line.startswith('-'):
-                chars.insert(0, bcolors.FAIL)
+                chars.insert(0, bcolors.RED)
         else:
             for i in range(len(squigly)):
                 if squigly[i] == '+' and flag != '+':
-                    chars.insert(i+compensator, bcolors.OKGREEN)
+                    chars.insert(i+compensator, bcolors.GREEN)
                     compensator += 1
                     flag = '+'
                 if squigly[i] == '^' and flag != '^':
-                    chars.insert(i+compensator, bcolors.WARNING)
+                    color = bcolors.GREEN if line.startswith('+') else bcolors.RED
+                    chars.insert(i+compensator, color)
                     compensator += 1
                     flag = '^'
                 if squigly[i] == '-' and flag != '-':
-                    chars.insert(i+compensator, bcolors.FAIL)
+                    chars.insert(i+compensator, bcolors.RED)
                     compensator += 1
                     flag = '-'
                 if squigly[i] != flag:

From 839e7161001c044f9316885aa7824849252e9938 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Wed, 13 Aug 2014 15:39:36 +0200
Subject: [PATCH 0046/1356] add tool to determine terminal size

---
 easybuild/tools/terminal.py | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/tools/terminal.py

diff --git a/easybuild/tools/terminal.py b/easybuild/tools/terminal.py
new file mode 100644
index 0000000000..3be961d50f
--- /dev/null
+++ b/easybuild/tools/terminal.py
@@ -0,0 +1,29 @@
+import os
+
+def get_terminal_size():
+    env = os.environ
+    def ioctl_GWINSZ(fd):
+        try:
+            import fcntl, termios, struct, os
+            cr = struct.unpack('hh', fcntl.ioctl(fd, termios.TIOCGWINSZ,
+        '1234'))
+        except:
+            return
+        return cr
+    cr = ioctl_GWINSZ(0) or ioctl_GWINSZ(1) or ioctl_GWINSZ(2)
+    if not cr:
+        try:
+            fd = os.open(os.ctermid(), os.O_RDONLY)
+            cr = ioctl_GWINSZ(fd)
+            os.close(fd)
+        except:
+            pass
+    if not cr:
+        cr = (env.get('LINES', 25), env.get('COLUMNS', 80))
+
+        ### Use get(key[, default]) instead of a try/catch
+        #try:
+        #    cr = (env['LINES'], env['COLUMNS'])
+        #except:
+        #    cr = (25, 80)
+    return int(cr[1]), int(cr[0])

From 422f5d168bffb25eb75acadb28a64d53621c8067 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Wed, 13 Aug 2014 15:54:12 +0200
Subject: [PATCH 0047/1356] don't need no ordering

---
 easybuild/tools/multi_diff.py | 81 ++++-------------------------------
 1 file changed, 8 insertions(+), 73 deletions(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index ed6ad93963..ad0370fea0 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -8,81 +8,12 @@
 import easybuild.tools.terminal as terminal
 
 class bcolors:
-        HEADER = "\033[95m"
-        OKBLUE = "\033[94m"
         GREEN = "\033[92m"
         PURPLE = "\033[0;35m"
         GRAY = "\033[1;37m"
         RED = "\033[91m"
         ENDC = "\033[0m"
 
-class OrderedSet(collections.MutableSet):
-    '''Set that remembers original insertion order.'''
-
-    KEY, PREV, NEXT = range(3)
-
-    def __init__(self, iterable=None):
-        self.end = end = []
-        end += [None, end, end]         # sentinel node for doubly linked list
-        self.map = {}                   # key --> [key, prev, next]
-        if iterable is not None:
-            self |= iterable
-
-    ### Collection Methods
-    def __contains__(self, key):
-        return key in self.map
-
-    def __eq__(self, other):
-        if isinstance(other, OrderedSet):
-            return len(self) == len(other) and list(self) == list(other)
-        return set(self) == set(other)
-
-    def __iter__(self):
-        end = self.end
-        curr = end[self.NEXT]
-        while curr is not end:
-            yield curr[self.KEY]
-            curr = curr[self.NEXT]
-
-    def __len__(self):
-        return len(self.map)
-
-    def __reversed__(self):
-        end = self.end
-        curr = end[self.PREV]
-        while curr is not end:
-            yield curr[self.KEY]
-            curr = curr[self.PREV]
-
-    def add(self, key):
-        if key not in self.map:
-            end = self.end
-            curr = end[self.PREV]
-            curr[self.NEXT] = end[self.PREV] = self.map[key] = [key, curr, end]
-
-    def discard(self, key):
-        if key in self.map:
-            key, prev, next = self.map.pop(key)
-            prev[self.NEXT] = next
-            next[self.PREV] = prev
-
-    def pop(self, last=True):
-        if not self:
-            raise KeyError('set is empty')
-        key = next(reversed(self)) if last else next(iter(self))
-        self.discard(key)
-        return key
-
-    ### General Methods
-    def __del__(self):
-        self.clear()                    # remove circular references
-
-    def __repr__(self):
-        class_name = self.__class__.__name__
-        if not self:
-            return '{0!s}()'.format(class_name)
-        return '{0!s}({1!r})'.format(class_name, list(self))
-
 class Diff:
     def __init__(self, base, files):
         self.base = base
@@ -116,7 +47,7 @@ def get_line(self, line_no):
         removal_dict = dict()
         addition_dict = dict()
         squigly_dict = dict()
-        order = OrderedSet([])
+        order = set()
         output = []
         if 'removal' in self.diff_info[line_no]:
             for (diff_line, meta, squigly_line) in self.diff_info[line_no]['removal']:
@@ -131,12 +62,14 @@ def get_line(self, line_no):
         for diff_line in order:
             line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
             files = removal_dict[diff_line]
-            if files != self.num_files:
+            if len(files) != self.num_files:
                 line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), ', '.join(files), bcolors.ENDC])
+            else:
+                line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), bcolors.ENDC])
             output.append(" ".join(line))
 
         squigly_dict = dict()
-        order = OrderedSet([])
+        order = set()
 
         if 'addition' in self.diff_info[line_no]:
             for (diff_line, meta, squigly_line) in self.diff_info[line_no]['addition']:
@@ -151,8 +84,10 @@ def get_line(self, line_no):
         for diff_line in order:
             line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
             files = addition_dict[diff_line]
-            if files != self.num_files:
+            if len(files) != self.num_files:
                 line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), ', '.join(files), bcolors.ENDC])
+            else:
+                line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), bcolors.ENDC])
             output.append(" ".join(line))
 
         # print seperator

From 01325ee735410cb7820f9925c935bf16ef0b6823 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Wed, 13 Aug 2014 16:57:16 +0200
Subject: [PATCH 0048/1356] some minor fixes

---
 easybuild/framework/easyconfig/easyconfig.py |  7 +-
 easybuild/main.py                            | 17 ++---
 easybuild/tools/multi_diff.py                | 71 ++++++++------------
 3 files changed, 41 insertions(+), 54 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 04105588ef..d497209ce0 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -872,12 +872,17 @@ def find_relevant_easyconfigs(path, ec):
     version = ec.version
     toolchain_name = ec['toolchain']['name']
     toolchain = "%s-%s" % (toolchain_name, ec['toolchain']['version'])
+    exact_name = det_full_ec_version(ec)
 
     cand_paths = [
+        # exact match
+        (name.lower()[0], name, exact_name),
+        # same version, same toolchain name
+        (name.lower()[0], name, "%s-%s-%s-*" % (name, version, toolchain_name)),
         # Same version, any toolchain
         (name.lower()[0], name, "%s-%s-*" % (name, version)),
         # any version, same toolchain
-        (name.lower()[0], name, "%s*%s-*" % (name, toolchain)),
+        (name.lower()[0], name, "%s-*-%s-*" % (name, toolchain)),
         # any version, same toolchain name
         (name.lower()[0], name, "%s-*-%s-*" % (name, toolchain_name)),
         # any version, any toolchain
diff --git a/easybuild/main.py b/easybuild/main.py
index e2c2a0d410..c6d5ff1ef0 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -293,16 +293,13 @@ def main(testing_data=(None, None, None)):
                         if path.endswith('.eb')]
 
         for easyconfig in pr_files:
-            most, second, third, last = find_relevant_easyconfigs(repo_path, easyconfig)
-            if most:
-                diff = multi_diff(easyconfig, most)
-            elif second:
-                diff = multi_diff(easyconfig, second)
-            elif third:
-                diff = multi_diff(easyconfig, third)
-            elif last:
-                diff = multi_diff(easyconfig, last)
-            diff.write_out()
+            files = find_relevant_easyconfigs(repo_path, easyconfig)
+            for listing in files:
+                if listing:
+                    diff = multi_diff(easyconfig, listing)
+                    diff.write_out()
+                    break
+
 
         os.sys.exit()
 
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index ad0370fea0..ff2fed3e83 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -44,51 +44,36 @@ def limit(text, length):
                 print "\n".join(map(lambda line: limit(line,w),lines))
 
     def get_line(self, line_no):
-        removal_dict = dict()
-        addition_dict = dict()
-        squigly_dict = dict()
-        order = set()
         output = []
-        if 'removal' in self.diff_info[line_no]:
-            for (diff_line, meta, squigly_line) in self.diff_info[line_no]['removal']:
-                if squigly_line:
-                    squigly_dict[diff_line] = squigly_line
-                order.add(diff_line)
-                if diff_line not in removal_dict:
-                    removal_dict[diff_line] = set([meta])
-                else:
-                    removal_dict[diff_line].add(meta)
-
-        for diff_line in order:
-            line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
-            files = removal_dict[diff_line]
-            if len(files) != self.num_files:
-                line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), ', '.join(files), bcolors.ENDC])
-            else:
-                line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), bcolors.ENDC])
-            output.append(" ".join(line))
-
-        squigly_dict = dict()
-        order = set()
-
-        if 'addition' in self.diff_info[line_no]:
-            for (diff_line, meta, squigly_line) in self.diff_info[line_no]['addition']:
-                if squigly_line:
-                    squigly_dict[diff_line] = self._merge_squigly(squigly_dict.get(diff_line, squigly_line), squigly_line)
-                order.add(diff_line)
-                if diff_line not in addition_dict:
-                    addition_dict[diff_line] = set([meta])
+        for key in ['removal','addition']:
+            lines = set()
+            changes_dict = dict()
+            squigly_dict = dict()
+            if key in self.diff_info[line_no]:
+                for (diff_line, meta, squigly_line) in self.diff_info[line_no][key]:
+                    if squigly_line:
+                        squigly_dict[diff_line] = squigly_line
+                    lines.add(diff_line)
+                    if diff_line not in changes_dict:
+                        changes_dict[diff_line] = set([meta])
+                    else:
+                        changes_dict[diff_line].add(meta)
+
+            # restrict displaying of removals to 3 groups
+            if len(lines) > 2:
+                lines = (sorted([(len(changes_dict[line]), line) for line in lines],
+                                key=lambda (l, line): l))
+                lines.reverse()
+                lines = map(lambda (l,x): x,lines[0:1])
+
+            for diff_line in lines:
+                line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
+                files = changes_dict[diff_line]
+                if len(files) != self.num_files:
+                    line.extend([bcolors.GRAY, "\t(%d/%d)" % (len(files), self.num_files), ', '.join(files), bcolors.ENDC])
                 else:
-                    addition_dict[diff_line].add(meta)
-
-        for diff_line in order:
-            line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
-            files = addition_dict[diff_line]
-            if len(files) != self.num_files:
-                line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), ', '.join(files), bcolors.ENDC])
-            else:
-                line.extend([bcolors.GRAY, "(%d/%d)" % (len(files), self.num_files), bcolors.ENDC])
-            output.append(" ".join(line))
+                    line.extend([bcolors.GRAY, "\t(%d/%d)" % (len(files), self.num_files), bcolors.ENDC])
+                output.append(" ".join(line))
 
         # print seperator
         if self.diff_info[line_no] and 'addition' not in self.diff_info[line_no+1] and 'removal' not in self.diff_info[line_no + 1]:

From e7f038604db9e727136788e4da2cd89979e0cc68 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Wed, 13 Aug 2014 17:14:11 +0200
Subject: [PATCH 0049/1356] fix exact matching

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 easybuild/main.py                            | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index d497209ce0..0cb5d73d38 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -876,7 +876,7 @@ def find_relevant_easyconfigs(path, ec):
 
     cand_paths = [
         # exact match
-        (name.lower()[0], name, exact_name),
+        (name.lower()[0], name, "%s-%s" % (name, exact_name)),
         # same version, same toolchain name
         (name.lower()[0], name, "%s-%s-%s-*" % (name, version, toolchain_name)),
         # Same version, any toolchain
diff --git a/easybuild/main.py b/easybuild/main.py
index c6d5ff1ef0..5e8acac896 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -300,7 +300,6 @@ def main(testing_data=(None, None, None)):
                     diff.write_out()
                     break
 
-
         os.sys.exit()
 
     paths = []

From cff818ff97b76fec6c37254b976e440316b78435 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 Aug 2014 20:21:21 +0200
Subject: [PATCH 0050/1356] fix link to code style wiki page in CONTRIBUTING.md

---
 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index a85d1b5eba..26b8b331fb 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -138,7 +138,7 @@ You might also want to look into [hub](https://github.com/defunkt/hub) for more
 
 ### Review process
 
-A member of the EasyBuild team will then review your pull request, paying attention to what you're contributing, how you implemented it and [code style](Code style).
+A member of the EasyBuild team will then review your pull request, paying attention to what you're contributing, how you implemented it and [code style](https://github.com/hpcugent/easybuild/wiki/Code-style).
 
 Most likely, some remarks will be made on your pull request. Note that this is nothing personal, we're just trying to keep the EasyBuild codebase as high quality as possible. Even when an EasyBuild team member makes changes, the same public review process is followed.
 

From d0b0952221b54b66d7f1aa897361013345caecdd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 Aug 2014 22:31:38 +0200
Subject: [PATCH 0051/1356] implement and use get_hidden_modname

---
 easybuild/tools/module_generator.py               | 3 ++-
 easybuild/tools/module_naming_scheme/utilities.py | 7 +++++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 58a2977b2e..a79603d3d3 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -40,6 +40,7 @@
 from easybuild.tools import config
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import mkdir
+from easybuild.tools.module_naming_scheme.utilities import det_hidden_modname
 from easybuild.tools.utilities import quote_str
 
 
@@ -66,7 +67,7 @@ def prepare(self):
         hidden = build_option('hidden')
         full_mod_name = self.app.full_mod_name
         if build_option('hidden'):
-            full_mod_name = os.path.join(os.path.dirname(full_mod_name), '.%s' % os.path.basename(full_mod_name))
+            full_mod_name = det_hidden_modname(full_mod_name)
             _log.debug("Prefixed module filename with '.' to make it hidden: %s" % full_mod_name)
         # module file goes in general moduleclass category
         self.filename = os.path.join(self.module_path, mod_path_suffix, full_mod_name)
diff --git a/easybuild/tools/module_naming_scheme/utilities.py b/easybuild/tools/module_naming_scheme/utilities.py
index db121c4744..951d8015b3 100644
--- a/easybuild/tools/module_naming_scheme/utilities.py
+++ b/easybuild/tools/module_naming_scheme/utilities.py
@@ -101,3 +101,10 @@ def is_valid_module_name(mod_name):
             return False
     _log.debug("Module name %s validated" % mod_name)
     return True
+
+
+def det_hidden_modname(modname):
+    """Determine the hidden equivalent of the specified module name."""
+    moddir = os.path.dirname(modname)
+    modfile = os.path.basename(modname)
+    return os.path.join(moddir, '.%s' % modfile).lstrip(os.path.sep)

From 2dc50821eb6d24597e2ed622d5c02458ad4637db Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 Aug 2014 22:34:59 +0200
Subject: [PATCH 0052/1356] implement 'exists' method for module tools using
 'show' subcommand, use 'exists' in 'skip_available'

---
 easybuild/framework/easyconfig/tools.py |  6 +++---
 easybuild/tools/modules.py              | 10 ++++++++--
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index d834141ab8..d80a20f977 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -79,12 +79,12 @@
 
 
 def skip_available(easyconfigs, testing=False):
-    """Skip building easyconfigs for which a module is already available."""
-    avail_modules = modules_tool().available()
+    """Skip building easyconfigs for existing modules."""
+    modtool = modules_tool()
     easyconfigs, check_easyconfigs = [], easyconfigs
     for ec in check_easyconfigs:
         module = ec['full_mod_name']
-        if module in avail_modules:
+        if modtool.exists(module):
             msg = "%s is already installed (module found), skipping" % module
             print_msg(msg, log=_log, silent=testing)
             _log.info(msg)
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 9139e5f1d6..6c0b36bc5f 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -333,7 +333,13 @@ def exists(self, mod_name):
         """
         Check if module with specified name exists.
         """
-        return mod_name in self.available(mod_name)
+        # implemented via 'show' subcommand, since obtaining list of available modules can be very slow
+        # also, it doesn't include hidden modules
+        txt = self.show(mod_name)
+        # 'show' output always contains full path to existing module file
+        # enforce that only True is returned via ':' at the end of the regex
+        exists_re = re.compile('^\s*\S*/%s:\s*$' % mod_name, re.M)
+        return bool(exists_re.search(txt))
 
     def load(self, modules, mod_paths=None, purge=False, orig_env=None):
         """
@@ -404,7 +410,7 @@ def get_value_from_modulefile(self, mod_name, regex):
             else:
                 self.log.error("Failed to determine value from 'show' (pattern: '%s') in %s" % (regex.pattern, modinfo))
         else:
-            raise EasyBuildError("Can't get module file path for non-existing module %s" % mod_name)
+            raise EasyBuildError("Can't get value from a non-existing module %s" % mod_name)
 
     def modulefile_path(self, mod_name):
         """Get the path of the module file for the specified module."""

From d535a33df969f1a6cc78280ee8650a0c5fae28a0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 Aug 2014 00:44:01 +0200
Subject: [PATCH 0053/1356] add support for dependencies installed as hidden
 modules

---
 easybuild/framework/easyconfig/default.py    |  1 +
 easybuild/framework/easyconfig/easyconfig.py | 67 ++++++++++++++------
 easybuild/framework/easyconfig/tools.py      |  5 +-
 3 files changed, 52 insertions(+), 21 deletions(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 20640e0af7..0109709b2a 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -143,6 +143,7 @@
     'allow_system_deps': [[], "Allow listed system dependencies (format: (<name>, <version>))", DEPENDENCIES],
     'builddependencies': [[], "List of build dependencies", DEPENDENCIES],
     'dependencies': [[], "List of dependencies", DEPENDENCIES],
+    'hiddendependencies': [[], "List of dependencies available as hidden modules", DEPENDENCIES],
     'osdependencies': [[], "OS dependencies that should be present on the system", DEPENDENCIES],
 
     # LICENSE easyconfig parameters
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 45caac97cc..6229e703dd 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -49,7 +49,7 @@
 from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
-from easybuild.tools.module_naming_scheme.utilities import is_valid_module_name
+from easybuild.tools.module_naming_scheme.utilities import det_hidden_modname, is_valid_module_name
 from easybuild.tools.modules import get_software_root_env_var_name, get_software_version_env_var_name
 from easybuild.tools.systemtools import check_os_dependency
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
@@ -127,7 +127,7 @@ class EasyConfig(object):
     Class which handles loading, reading, validation of easyconfigs
     """
 
-    def __init__(self, path, extra_options=None, build_specs=None, validate=True):
+    def __init__(self, path, extra_options=None, build_specs=None, validate=True, hidden=None):
         """
         initialize an easyconfig.
         @param path: path to easyconfig file to be parsed
@@ -215,6 +215,9 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True):
             self.validate(check_osdeps=build_option('check_osdeps'))
 
         # set module info
+        if hidden is None:
+            hidden = build_option('hidden')
+        self.hidden = hidden
         mns = ActiveMNS()
         self.full_mod_name = mns.det_full_module_name(self)
         self.short_mod_name = mns.det_short_module_name(self)
@@ -225,7 +228,7 @@ def copy(self):
         Return a copy of this EasyConfig instance.
         """
         # create a new EasyConfig instance
-        ec = EasyConfig(self.path, validate=self.validation)
+        ec = EasyConfig(self.path, validate=self.validation, hidden=self.hidden)
         # take a copy of the actual config dictionary (which already contains the extra options)
         ec._config = copy.deepcopy(self._config)
 
@@ -284,6 +287,8 @@ def parse(self):
             if key in self._config.keys() + DEPRECATED_OPTIONS.keys():
                 if key in ['builddependencies', 'dependencies']:
                     self[key] = [self._parse_dependency(dep) for dep in local_vars[key]]
+                elif key in ['hiddendependencies']:
+                    self[key] = [self._parse_dependency(dep, hidden=True) for dep in local_vars[key]]
                 else:
                     self[key] = local_vars[key]
                 tup = (key, self[key], type(self[key]))
@@ -404,7 +409,7 @@ def dependencies(self):
         Returns an array of parsed dependencies (after filtering, if requested)
         dependency = {'name': '', 'version': '', 'dummy': (False|True), 'versionsuffix': '', 'toolchain': ''}
         """
-        deps = self['dependencies'] + self.builddependencies()
+        deps = self['dependencies'] + self['builddependencies'] + self['hiddendependencies']
 
         # if filter-deps option is provided we "clean" the list of dependencies for
         # each processed easyconfig to remove the unwanted dependencies
@@ -473,15 +478,15 @@ def to_str(x):
 
         # ordered groups of keys to obtain a nice looking easyconfig file
         grouped_keys = [
-                        ["name", "version", "versionprefix", "versionsuffix"],
-                        ["homepage", "description"],
-                        ["toolchain", "toolchainopts"],
-                        ["source_urls", "sources"],
-                        ["patches"],
-                        ["dependencies"],
-                        ["parallel", "maxparallel"],
-                        ["osdependencies"]
-                        ]
+            ['name', 'version', 'versionprefix', 'versionsuffix'],
+            ['homepage', 'description'],
+            ['toolchain', 'toolchainopts'],
+            ['source_urls', 'sources'],
+            ['patches'],
+            ['builddependencies', 'dependencies', 'hiddendependencies'],
+            ['parallel', 'maxparallel'],
+            ['osdependencies']
+        ]
 
         # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
@@ -515,7 +520,7 @@ def _validate(self, attr, values):  # private method
             self.log.error("%s provided '%s' is not valid: %s" % (attr, self[attr], values))
 
     # private method
-    def _parse_dependency(self, dep):
+    def _parse_dependency(self, dep, hidden=False):
         """
         parses the dependency into a usable dict with a common format
         dep can be a dict, a tuple or a list.
@@ -538,6 +543,7 @@ def _parse_dependency(self, dep):
             'toolchain': None,
             'version': '',
             'versionsuffix': '',
+            'hidden': hidden,
         }
         if isinstance(dep, dict):
             dependency.update(dep)
@@ -859,7 +865,7 @@ def resolve_template(value, tmpl_dict):
     return value
 
 
-def process_easyconfig(path, build_specs=None, validate=True, parse_only=False):
+def process_easyconfig(path, build_specs=None, validate=True, parse_only=False, hidden=None):
     """
     Process easyconfig, returning some information for each block
     @param path: path to easyconfig file
@@ -868,6 +874,9 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False):
     """
     blocks = retrieve_blocks_in_spec(path, build_option('only_blocks'))
 
+    if hidden is None:
+        hidden = build_option('hidden')
+
     # only cache when no build specifications are involved (since those can't be part of a dict key)
     cache_key = None
     if build_specs is None:
@@ -882,7 +891,7 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False):
 
         # create easyconfig
         try:
-            ec = EasyConfig(spec, build_specs=build_specs, validate=validate)
+            ec = EasyConfig(spec, build_specs=build_specs, validate=validate, hidden=hidden)
         except EasyBuildError, err:
             msg = "Failed to process easyconfig %s:\n%s" % (spec, err.msg)
             _log.exception(msg)
@@ -902,16 +911,28 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False):
                 'full_mod_name': ec.full_mod_name,
                 'dependencies': [],
                 'builddependencies': [],
+                'hiddendependencies': [],
+                'hidden': hidden,
             })
+            if hidden:
+                easyconfig.update({
+                    'short_mod_name': ec.short_mod_name,
+                    'full_mod_name': ec.full_mod_name,
+                })
             if len(blocks) > 1:
                 easyconfig['original_spec'] = path
 
-            # add build dependencies
-            for dep in ec.builddependencies():
+            # add build/hidden dependencies
+            for dep in ec['builddependencies']:
                 _log.debug("Adding build dependency %s for app %s." % (dep, name))
                 easyconfig['builddependencies'].append(dep)
 
-            # add dependencies (including build dependencies)
+            # add build/hidden dependencies
+            for dep in ec['hiddendependencies']:
+                _log.debug("Adding hidden dependency %s for app %s." % (dep, name))
+                easyconfig['hiddendependencies'].append(dep)
+
+            # add dependencies (including build & hidden dependencies)
             for dep in ec.dependencies():
                 _log.debug("Adding dependency %s for app %s." % (dep, name))
                 easyconfig['dependencies'].append(dep)
@@ -1032,6 +1053,9 @@ def det_full_module_name(self, ec):
         else:
             self.log.debug("Obtained valid full module name %s" % mod_name)
 
+        if getattr(ec, 'hidden', False) or ec.get('hidden', False):
+            mod_name = det_hidden_modname(mod_name)
+
         return mod_name
 
     def det_devel_module_filename(self, ec):
@@ -1042,10 +1066,15 @@ def det_short_module_name(self, ec):
         """Determine module name according to module naming scheme."""
         self.log.debug("Determining module name for %s" % ec)
         mod_name = self.mns.det_short_module_name(self.check_ec_type(ec))
+
         if not is_valid_module_name(mod_name):
             self.log.error("%s is not a valid module name" % str(mod_name))
         else:
             self.log.debug("Obtained valid module name %s" % mod_name)
+
+        if getattr(ec, 'hidden', False) or ec.get('hidden', False):
+            mod_name = det_hidden_modname(mod_name)
+
         return mod_name
 
     def det_module_subdir(self, ec):
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index d80a20f977..37924efa00 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -71,7 +71,7 @@
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import det_common_path_prefix, run_cmd, write_file
 from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS
-from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
+from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version, det_hidden_modname
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.ordereddict import OrderedDict
 
@@ -202,7 +202,8 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
                         _log.info("Robot: resolving dependency %s with %s" % (cand_dep, path))
                         # build specs should not be passed down to resolved dependencies,
                         # to avoid that e.g. --try-toolchain trickles down into the used toolchain itself
-                        processed_ecs = process_easyconfig(path, validate=not retain_all_deps)
+                        hidden = cand_dep.get('hidden', False)
+                        processed_ecs = process_easyconfig(path, validate=not retain_all_deps, hidden=hidden)
 
                         # ensure that selected easyconfig provides required dependency
                         mods = [spec['ec'].full_mod_name for spec in processed_ecs]

From 1a0d132af385930d0ed25e7e1fa0351a8a98868b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 Aug 2014 00:44:17 +0200
Subject: [PATCH 0054/1356] enhance unit tests

---
 test/framework/easyblock.py                   | 27 +++++++++++++----
 .../easyconfigs/gzip-1.4-GCC-4.6.3.eb         |  2 ++
 test/framework/modules.py                     |  2 ++
 test/framework/robot.py                       | 30 +++++++++++++++++--
 4 files changed, 54 insertions(+), 7 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 01e3cef91e..c70d0ea6a9 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -264,6 +264,8 @@ def test_make_module_step(self):
         """Test the make_module_step"""
         name = "pi"
         version = "3.14"
+        deps = [('GCC', '4.6.4')]
+        hiddendeps = [('toy', '0.0-deps')]
         modextravars = {'PI': '3.1415', 'FOO': 'bar'}
         modextrapaths = {'PATH': 'pibin', 'CPATH': 'pi/include'}
         self.contents = '\n'.join([
@@ -272,16 +274,23 @@ def test_make_module_step(self):
             'homepage = "http://example.com"',
             'description = "test easyconfig"',
             "toolchain = {'name': 'dummy', 'version': 'dummy'}",
-            "dependencies = [('foo', '1.2.3')]",
-            "builddependencies = [('bar', '9.8.7')]",
+            "dependencies = %s" % str(deps),
+            "hiddendependencies = %s" % str(hiddendeps),
+            "builddependencies = [('OpenMPI', '1.6.4-GCC-4.6.4')]",
             "modextravars = %s" % str(modextravars),
             "modextrapaths = %s" % str(modextrapaths),
         ])
 
+        test_dir = os.path.dirname(os.path.abspath(__file__))
+        os.environ['MODULEPATH'] = os.path.join(test_dir, 'modules')
+
         # test if module is generated correctly
         self.writeEC()
-        eb = EasyBlock(EasyConfig(self.eb_file))
+        ec = EasyConfig(self.eb_file)
+        eb = EasyBlock(ec)
+        #eb.builddir = self.test_buildpath
         eb.installdir = os.path.join(config.install_path(), 'pi', '3.14')
+        eb.check_readiness_step()
 
         modpath = os.path.join(eb.make_module_step(), name, version)
         self.assertTrue(os.path.exists(modpath), "%s exists" % modpath)
@@ -296,9 +305,17 @@ def test_make_module_step(self):
         self.assertTrue(re.search('^setenv\s+EBROOT%s\s+".root"\s*$' % name.upper(), txt, re.M))
         self.assertTrue(re.search('^setenv\s+EBVERSION%s\s+"%s"$' % (name.upper(), version), txt, re.M))
         for (key, val) in modextravars.items():
-            self.assertTrue(re.search('^setenv\s+%s\s+"%s"$' % (key, val), txt, re.M))
+            regex = re.compile('^setenv\s+%s\s+"%s"$' % (key, val), re.M)
+            self.assertTrue(regex.search(txt), "Pattern %s found in %s" % (regex.pattern, txt))
         for (key, val) in modextrapaths.items():
-            self.assertTrue(re.search('^prepend-path\s+%s\s+\$root/%s$' % (key, val), txt, re.M))
+            regex = re.compile('^prepend-path\s+%s\s+\$root/%s$' % (key, val), re.M)
+            self.assertTrue(regex.search(txt), "Pattern %s found in %s" % (regex.pattern, txt))
+        for (name, ver) in deps:
+            regex = re.compile('^\s*module load %s\s*$' % os.path.join(name, ver), re.M)
+            self.assertTrue(regex.search(txt), "Pattern %s found in %s" % (regex.pattern, txt))
+        for (name, ver) in hiddendeps:
+            regex = re.compile('^\s*module load %s/.%s\s*$' % (name, ver), re.M)
+            self.assertTrue(regex.search(txt), "Pattern %s found in %s" % (regex.pattern, txt))
 
     def test_gen_dirs(self):
         """Test methods that generate/set build/install directory names."""
diff --git a/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb b/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
index 9f1c615c51..b59e6160d2 100644
--- a/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
@@ -25,6 +25,8 @@ sources = ['%s-%s.tar.gz'%(name,version)]
 # download location for source files
 source_urls = [GNU_SOURCE]
 
+hiddendependencies = [('toy', '0.0', '-deps', True)]
+
 # make sure the gzip and gunzip binaries are available after installation
 sanity_check_paths = {
     'files': ["bin/gunzip", "bin/gzip"],
diff --git a/test/framework/modules.py b/test/framework/modules.py
index f8b96e27b2..bc74426282 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -112,6 +112,8 @@ def test_exists(self):
         self.init_testmods()
         self.assertTrue(self.testmods.exists('OpenMPI/1.6.4-GCC-4.6.4'))
         self.assertTrue(not self.testmods.exists(mod_name='foo/1.2.3'))
+        # exists should not return True for incomplete module names
+        self.assertFalse(self.testmods.exists('GCC'))
 
     def test_load(self):
         """ test if we load one module it is in the loaded_modules """
diff --git a/test/framework/robot.py b/test/framework/robot.py
index 532d39450b..9ab23ea4ee 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -56,9 +56,17 @@ class MockModule(modules.ModulesTool):
     avail_modules = []
 
     def available(self, *args):
-        """ no module should be available """
+        """Dummy implementation of available."""
         return self.avail_modules
 
+    def show(self, modname):
+        """Dummy implementation of show, which includes full path to (existing) module files."""
+        if modname in self.avail_modules:
+            txt =  '  %s:' % os.path.join('/tmp', modname)
+        else:
+            txt = 'Module %s not found' % modname
+        return txt
+
 def mock_module(mod_paths=None):
     """Get mock module instance."""
     return MockModule(mod_paths=mod_paths)
@@ -123,7 +131,25 @@ def test_resolve_dependencies(self):
         self.assertEqual('gzip/1.4', res[0]['full_mod_name'])
         self.assertEqual('foo/1.2.3', res[-1]['full_mod_name'])
 
-        # here we have include a Dependency in the easyconfig list
+        # hidden dependencies are found too
+        hidden_dep = {
+            'name': 'toy',
+            'version': '0.0',
+            'versionsuffix': '-deps',
+            'toolchain': {'name': 'dummy', 'version': 'dummy'},
+            'dummy': True,
+            'hidden': True,
+        }
+        easyconfig_moredeps = deepcopy(easyconfig_dep)
+        easyconfig_moredeps['dependencies'].append(hidden_dep)
+        easyconfig_moredeps['hiddendependencies'] = [hidden_dep]
+        res = resolve_dependencies([deepcopy(easyconfig_moredeps)])
+        self.assertEqual(len(res), 7)  # hidden dep toy/.0.0-deps (+1) depends on gompi (+4)
+        self.assertEqual('gzip/1.4', res[0]['full_mod_name'])
+        self.assertEqual('foo/1.2.3', res[-1]['full_mod_name'])
+        self.assertTrue('toy/.0.0-deps' in [ec['full_mod_name'] for ec in res])
+
+        # here we have included a dependency in the easyconfig list
         easyconfig['full_mod_name'] = 'gzip/1.4'
 
         ecs = [deepcopy(easyconfig_dep), deepcopy(easyconfig)]

From 429bc460999f006417513f5eb92761fe50ad71f4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 Aug 2014 00:55:14 +0200
Subject: [PATCH 0055/1356] fix and enhance broken test

---
 test/framework/easyconfig.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index ec7c411f94..4c89afe53a 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -567,6 +567,7 @@ def test_obtain_easyconfig(self):
         specs.update({
             'patches': new_patches[:],
             'dependencies': [('foo', '1.2.3'), ('bar', '666', '-bleh', ('gompi', '1.4.10'))],
+            'hiddendependencies': [('test', '3.2.1')],
         })
         parsed_deps = [
             {
@@ -577,6 +578,7 @@ def test_obtain_easyconfig(self):
                 'dummy': False,
                 'short_mod_name': 'foo/1.2.3-GCC-4.4.5',
                 'full_mod_name': 'foo/1.2.3-GCC-4.4.5',
+                'hidden': False,
             },
             {
                 'name': 'bar',
@@ -586,13 +588,24 @@ def test_obtain_easyconfig(self):
                 'dummy': False,
                 'short_mod_name': 'bar/666-gompi-1.4.10-bleh',
                 'full_mod_name': 'bar/666-gompi-1.4.10-bleh',
+                'hidden': False,
+            },
+            {
+                'name': 'test',
+                'version': '3.2.1',
+                'versionsuffix': '',
+                'toolchain': ec['toolchain'],
+                'dummy': False,
+                'short_mod_name': 'test/.3.2.1-GCC-4.4.5',
+                'full_mod_name': 'test/.3.2.1-GCC-4.4.5',
+                'hidden': True,
             },
         ]
         res = obtain_ec_for(specs, [self.ec_dir], None)
         self.assertEqual(res[0], True)
         ec = EasyConfig(res[1])
         self.assertEqual(ec['patches'], specs['patches'])
-        self.assertEqual(ec['dependencies'], parsed_deps)
+        self.assertEqual(ec.dependencies(), parsed_deps)
         os.remove(res[1])
 
         # verify append functionality for lists

From e6ea24f4cabb2aa8649e3a68c642c80068735289 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 Aug 2014 07:44:25 +0200
Subject: [PATCH 0056/1356] add test hidden module

---
 test/framework/modules/toy/.0.0-deps | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 test/framework/modules/toy/.0.0-deps

diff --git a/test/framework/modules/toy/.0.0-deps b/test/framework/modules/toy/.0.0-deps
new file mode 100644
index 0000000000..d2bedec555
--- /dev/null
+++ b/test/framework/modules/toy/.0.0-deps
@@ -0,0 +1,25 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   Toy C program. - Homepage: http://hpcugent.github.com/easybuild
+    }
+}
+
+module-whatis {Toy C program. - Homepage: http://hpcugent.github.com/easybuild}
+
+set root    /var/folders/6y/x4gmwgjn5qz63b7ftg4j_40m0000gn/T/tmpviG1OT/software/toy/0.0-deps
+
+conflict    toy
+
+if { ![is-loaded gompi/1.3.12] } {
+    module load gompi/1.3.12
+}
+
+prepend-path	PATH		$root/bin
+
+setenv	EBROOTTOY		"$root"
+setenv	EBVERSIONTOY		"0.0-deps"
+setenv	EBDEVELTOY		"$root/easybuild/toy-0.0-deps-easybuild-devel"
+
+
+# built with EasyBuild version 1.8.0dev

From f92fffbd34ae82f16c487f4b0536c964806c38fe Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:00:24 +0200
Subject: [PATCH 0057/1356] move review code to dedicated module

---
 easybuild/framework/easyconfig/review.py | 52 ++++++++++++++++++++++++
 easybuild/main.py                        | 19 ++-------
 2 files changed, 56 insertions(+), 15 deletions(-)
 create mode 100644 easybuild/framework/easyconfig/review.py

diff --git a/easybuild/framework/easyconfig/review.py b/easybuild/framework/easyconfig/review.py
new file mode 100644
index 0000000000..9b1253fb8c
--- /dev/null
+++ b/easybuild/framework/easyconfig/review.py
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+# #
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Review module for pull requests on the easyconfigs repo"
+
+@author: Toon Willems (Ghent University)
+"""
+import os
+from vsc.utils import fancylogger
+
+from easybuild.framework.easyconfig.easyconfig import find_related_easyconfigs
+from easybuild.tools.github import fetch_easyconfigs_from_pr, download_repo
+from easybuild.tools.multi_diff import multi_diff
+
+
+_log = fancylogger.getLogger('easyconfig.review', fname=False)
+
+def review_pr(pull_request):
+    repo_path = os.path.join(download_repo(branch='develop'),'easybuild','easyconfigs')
+    pr_files = [path for path in fetch_easyconfigs_from_pr(pull_request) if path.endswith('.eb')]
+
+    for easyconfig in pr_files:
+        files = find_related_easyconfigs(repo_path, easyconfig)
+        _log.debug("File in pull request %s has these related easyconfigs: %s" % (easyconfig, files))
+        for listing in files:
+            if listing:
+                diff = multi_diff(easyconfig, listing)
+                diff.write_out()
+                break
diff --git a/easybuild/main.py b/easybuild/main.py
index 5e8acac896..5ed0bc9b7d 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -51,14 +51,14 @@
 import easybuild.tools.config as config
 import easybuild.tools.options as eboptions
 from easybuild.framework.easyblock import EasyBlock, build_and_install_one
-from easybuild.framework.easyconfig.easyconfig import process_easyconfig, find_relevant_easyconfigs
+from easybuild.framework.easyconfig.easyconfig import process_easyconfig
+from easybuild.framework.easyconfig.review import review_pr
 from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, print_dry_run
 from easybuild.framework.easyconfig.tools import resolve_dependencies, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_path, tweak
 from easybuild.tools.config import get_repository, module_classes, get_repositorypath, set_tmpdir
 from easybuild.tools.filetools import cleanup, find_easyconfigs, search_file, write_file
-from easybuild.tools.github import fetch_easyconfigs_from_pr, download_easyconfig_repo
-from easybuild.tools.multi_diff import multi_diff
+from easybuild.tools.github import fetch_easyconfigs_from_pr
 from easybuild.tools.options import process_software_build_specs
 from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
 from easybuild.tools.repository.repository import init_repository
@@ -288,18 +288,7 @@ def main(testing_data=(None, None, None)):
         search_file(search_path, query, short=not options.search, ignore_dirs=ignore_dirs, silent=silent)
 
     if options.review_pr:
-        repo_path = os.path.join(download_easyconfig_repo('develop'),'easybuild','easyconfigs')
-        pr_files = [path for path in fetch_easyconfigs_from_pr(options.review_pr)
-                        if path.endswith('.eb')]
-
-        for easyconfig in pr_files:
-            files = find_relevant_easyconfigs(repo_path, easyconfig)
-            for listing in files:
-                if listing:
-                    diff = multi_diff(easyconfig, listing)
-                    diff.write_out()
-                    break
-
+        review_pr(options.review_pr)
         os.sys.exit()
 
     paths = []

From fc672b60b5f08acd131ad74b2cc9ba592c49c88f Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:00:57 +0200
Subject: [PATCH 0058/1356] add SO reference to terminal.py

---
 easybuild/tools/terminal.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/terminal.py b/easybuild/tools/terminal.py
index 3be961d50f..7fd9502166 100644
--- a/easybuild/tools/terminal.py
+++ b/easybuild/tools/terminal.py
@@ -1,3 +1,4 @@
+# http://stackoverflow.com/questions/566746/how-to-get-console-window-width-in-python
 import os
 
 def get_terminal_size():

From e3c3255ae3decbad7753b6585a124d48dffdbff6 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:01:41 +0200
Subject: [PATCH 0059/1356] improve logging, make download_repo generic

---
 easybuild/tools/github.py | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 8551f4afb0..d602c94816 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -189,8 +189,8 @@ class GithubError(Exception):
     """Error raised by the Githubfs"""
     pass
 
-def download_easyconfig_repo(branch='master', path=None):
-    """Download entire easyconfigs repo"""
+def download_repo(repo=GITHUB_EASYCONFIGS_REPO, branch='master', account=GITHUB_EB_MAIN, path=None):
+    """Download entire repo as a tar.gz archive and extract it into path"""
     if path is None:
         path = tempfile.mkdtemp()
     else:
@@ -198,20 +198,26 @@ def download_easyconfig_repo(branch='master', path=None):
         mkdir(path, parents=True)
 
     extracted_dir_name = "%s-%s" % (GITHUB_EASYCONFIGS_REPO, branch)
-    base_name = ("%s.tar.gz" % branch)
+    base_name = "%s.tar.gz" % branch
 
-    url = URL_SEPARATOR.join(["https://github.com",GITHUB_EB_MAIN, GITHUB_EASYCONFIGS_REPO, 'archive', base_name])
-    _log.debug("download from %s" % url)
+    # check if directory already exists, and don't download if it does
+    expected_path = os.path.join(path, extracted_dir_name)
+    if os.path.isdir(expected_path):
+        return expected_path
+
+    url = URL_SEPARATOR.join(["https://github.com",account, repo, 'archive', base_name])
+
+    _log.debug("download repo %s/%s as archive from %s" % (account,repo, url))
     _download(url, os.path.join(path,base_name))
-    _log.debug("archive downloaded to %s, extracting now" % path)
+    _log.debug("%s downloaded to %s, extracting now" % (base_name, path))
 
     extracted_path = extract_file(os.path.join(path, base_name), path)
     extracted_path = os.path.join(extracted_path, extracted_dir_name)
     # check if extracted_path exists
     if not os.path.isdir(extracted_path):
-        _log.error("We expected %s to exists and contain the repo" % extracted_path)
+        _log.error("We expected %s to exists and contain the repo %s at branch %s" % (extracted_path, repo, branch))
 
-    _log.debug("Repo extracted into %s" % extracted_path)
+    _log.debug("Repo %s at branch %s extracted into %s" % (repo, branch, extracted_path))
     return extracted_path
 
 def _download(url, path=None):
@@ -223,10 +229,8 @@ def _download(url, path=None):
         except IOError, err:
             _log.error("Failed to download %s to %s: %s" % (url, path, err))
 
-        '''
-        if httpmsg.type != 'text/plain' or httpmsg.type != 'application/x-gzip' :
+        if httpmsg.type != 'text/plain' and httpmsg.type != 'application/x-gzip' :
             _log.error("Unexpected file type for %s: %s" % (path, httpmsg.type))
-        '''
     else:
         try:
             return urllib2.urlopen(url).read()

From e4be300c806607dbb7e130b0a1a640737b4035e9 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:02:05 +0200
Subject: [PATCH 0060/1356] cleanup find_related_easyconfigs

---
 easybuild/framework/easyconfig/easyconfig.py | 34 ++++++++++++--------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 0cb5d73d38..bea949d69d 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -859,38 +859,46 @@ def resolve_template(value, tmpl_dict):
 
     return value
 
-def find_relevant_easyconfigs(path, ec):
+def find_related_easyconfigs(path, ec):
     """
-    Find relevant easyconfigs for ec in path based on a simple heuristic
+    Find related easyconfigs for ec in path based on a simple heuristic
+    - It first tries to match easyconfigs the exact same name.
+    - Then it matches those with the same version and same toolchain name
+    - Then it takes those with the same version and any toolchain name
+    - Then it takes the ones with any version and same toolchain (including version)
+    - Then it takes the ones with any version and same toolchain name
+    - Then it takes those with any version and any toolchain
     """
     # make sure we are working with an EasyConfig object
     if not isinstance(ec, EasyConfig):
         # we can safely only take the first one
-        ec = process_easyconfig(ec, parse_only=True)[0]['ec']
+        easyconfigs = process_easyconfig(ec, parse_only=True)
+        if len(easyconfigs) > 1:
+            _log.error("Expected only one easyconfig to be found, exiting!")
+        ec = easyconfigs[0]['ec']
 
     name = ec.name
     version = ec.version
     toolchain_name = ec['toolchain']['name']
     toolchain = "%s-%s" % (toolchain_name, ec['toolchain']['version'])
-    exact_name = det_full_ec_version(ec)
+    full_version = det_full_ec_version(ec)
 
-    cand_paths = [
+    patterns = [
         # exact match
-        (name.lower()[0], name, "%s-%s" % (name, exact_name)),
+        ("%s-%s" % (name, full_version)),
         # same version, same toolchain name
-        (name.lower()[0], name, "%s-%s-%s-*" % (name, version, toolchain_name)),
+        ("%s-%s-%s-*" % (name, version, toolchain_name)),
         # Same version, any toolchain
-        (name.lower()[0], name, "%s-%s-*" % (name, version)),
+        ("%s-%s-*" % (name, version)),
         # any version, same toolchain
-        (name.lower()[0], name, "%s-*-%s-*" % (name, toolchain)),
+        ("%s-*-%s-*" % (name, toolchain)),
         # any version, same toolchain name
-        (name.lower()[0], name, "%s-*-%s-*" % (name, toolchain_name)),
+        ("%s-*-%s-*" % (name, toolchain_name)),
         # any version, any toolchain
-        (name.lower()[0], name, "%s-*" % (name)),
+        ("*"),
     ]
-    relevant_files = [glob.glob("%s.eb" % os.path.join(path, *cand_path)) for cand_path in cand_paths]
 
-    return relevant_files
+    return [glob.glob("%s.eb" % os.path.join(path, name.lower()[0], name, *cand_path)) for cand_path in patterns]
 
 
 def process_easyconfig(path, build_specs=None, validate=True, parse_only=False):

From 31b43d36522dd301af269f8045bf61dd77a1eecb Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:02:22 +0200
Subject: [PATCH 0061/1356] add header, general cleanup of multi_diff

---
 easybuild/tools/multi_diff.py | 144 +++++++++++++++++++++-------------
 1 file changed, 89 insertions(+), 55 deletions(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index ff2fed3e83..42f7201e3f 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -1,34 +1,71 @@
+#!/usr/bin/env python
+# #
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Module which allows the diffing of multiple files
+
+@author: Toon Willems (Ghent University)
+"""
+
 import difflib
 import os
 import sys
-from collections import defaultdict
-from pprint import pprint
-import collections
 
 import easybuild.tools.terminal as terminal
 
-class bcolors:
-        GREEN = "\033[92m"
-        PURPLE = "\033[0;35m"
-        GRAY = "\033[1;37m"
-        RED = "\033[91m"
-        ENDC = "\033[0m"
+GREEN = "\033[92m"
+PURPLE = "\033[0;35m"
+GRAY = "\033[1;37m"
+RED = "\033[91m"
+ENDC = "\033[0m"
+
+class MultiDiff(object):
+    """
+    This class holds the diff information
+    """
 
-class Diff:
     def __init__(self, base, files):
         self.base = base
         self.base_lines = open(base).readlines()
-        self.diff_info = defaultdict(dict)
+        self.diff_info = dict()
         self.files = files
-        self.num_files = len(files)
 
-    def add_line(self,line_no, diff_line, meta, squigly_line=None):
+    def parse_line(self,line_no, diff_line, meta, squigly_line=None):
+        """
+        Parse a line as generated by difflib
+        """
         if diff_line.startswith('+'):
-            self._add_diff(line_no, diff_line.rstrip(), meta, squigly_line)
+            action = self._add_diff
         elif diff_line.startswith('-'):
-            self._remove_diff(line_no, diff_line.rstrip(), meta, squigly_line)
+            action = self._remove_diff
+        action(line_no, diff_line.rstrip(), meta, squigly_line)
 
     def write_out(self):
+        """
+        Write the entire diff to the terminal
+        """
         def limit(text, length):
             if len(text) > length:
                 return text[0:length-3] + '...'
@@ -36,7 +73,7 @@ def limit(text, length):
                 return text
 
         w,h = terminal.get_terminal_size()
-        print " ".join(["Comparing", bcolors.PURPLE, os.path.basename(self.base), bcolors.ENDC, "with", bcolors.GRAY, ", ".join(map(os.path.basename,self.files)), bcolors.ENDC])
+        print " ".join(["Comparing", PURPLE, os.path.basename(self.base), ENDC, "with", GRAY, ", ".join(map(os.path.basename,self.files)), ENDC])
 
         for i in range(len(self.base_lines)):
             lines = self.get_line(i)
@@ -44,12 +81,15 @@ def limit(text, length):
                 print "\n".join(map(lambda line: limit(line,w),lines))
 
     def get_line(self, line_no):
+        """
+        Return the line information for a specific line
+        """
         output = []
         for key in ['removal','addition']:
             lines = set()
             changes_dict = dict()
             squigly_dict = dict()
-            if key in self.diff_info[line_no]:
+            if key in self.diff_info.get(line_no, []):
                 for (diff_line, meta, squigly_line) in self.diff_info[line_no][key]:
                     if squigly_line:
                         squigly_dict[diff_line] = squigly_line
@@ -60,23 +100,28 @@ def get_line(self, line_no):
                         changes_dict[diff_line].add(meta)
 
             # restrict displaying of removals to 3 groups
-            if len(lines) > 2:
-                lines = (sorted([(len(changes_dict[line]), line) for line in lines],
-                                key=lambda (l, line): l))
+            max_groups = 2
+            if len(lines) > max_groups:
+                # find number of occurences
+                count = [(len(changes_dict[line]), line) for line in lines]
+                # sort highest first
+                lines = sorted(count, key=lambda (length, line): length)
                 lines.reverse()
-                lines = map(lambda (l,x): x,lines[0:1])
+                # limit to max_groups
+                lines = [ x for (l,x) in lines][0:max_groups-1]
 
             for diff_line in lines:
                 line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
                 files = changes_dict[diff_line]
-                if len(files) != self.num_files:
-                    line.extend([bcolors.GRAY, "\t(%d/%d)" % (len(files), self.num_files), ', '.join(files), bcolors.ENDC])
+                num_files = len(self.files)
+                if len(files) != num_files:
+                    line.extend([GRAY, "\t(%d/%d)" % (len(files), num_files), ', '.join(files), ENDC])
                 else:
-                    line.extend([bcolors.GRAY, "\t(%d/%d)" % (len(files), self.num_files), bcolors.ENDC])
+                    line.extend([GRAY, "\t(%d/%d)" % (len(files), num_files), ENDC])
                 output.append(" ".join(line))
 
         # print seperator
-        if self.diff_info[line_no] and 'addition' not in self.diff_info[line_no+1] and 'removal' not in self.diff_info[line_no + 1]:
+        if self.diff_info.get(line_no, None) and 'addition' not in self.diff_info.get(line_no+1, {}) and 'removal' not in self.diff_info.get(line_no + 1, {}):
             output.append('')
             output.append('-----')
             output.append('')
@@ -85,13 +130,13 @@ def get_line(self, line_no):
 
 
     def _remove_diff(self,line_no, diff_line, meta, squigly_line=None):
-        if 'removal' not in self.diff_info[line_no]:
+        if 'removal' not in self.diff_info.setdefault(line_no, {}):
             self.diff_info[line_no]['removal'] = []
 
         self.diff_info[line_no]['removal'].append((diff_line, meta, squigly_line))
 
     def _add_diff(self,line_no, diff_line, meta, squigly_line=None):
-        if 'addition' not in self.diff_info[line_no]:
+        if 'addition' not in self.diff_info.setdefault(line_no, {}):
             self.diff_info[line_no]['addition'] = []
 
         self.diff_info[line_no]['addition'].append((diff_line, meta, squigly_line))
@@ -102,30 +147,30 @@ def _colorize(self, line, squigly):
         compensator = 0
         if not squigly:
             if line.startswith('+'):
-                chars.insert(0, bcolors.GREEN)
+                chars.insert(0, GREEN)
             elif line.startswith('-'):
-                chars.insert(0, bcolors.RED)
+                chars.insert(0, RED)
         else:
             for i in range(len(squigly)):
                 if squigly[i] == '+' and flag != '+':
-                    chars.insert(i+compensator, bcolors.GREEN)
+                    chars.insert(i+compensator, GREEN)
                     compensator += 1
                     flag = '+'
                 if squigly[i] == '^' and flag != '^':
-                    color = bcolors.GREEN if line.startswith('+') else bcolors.RED
+                    color = GREEN if line.startswith('+') else RED
                     chars.insert(i+compensator, color)
                     compensator += 1
                     flag = '^'
                 if squigly[i] == '-' and flag != '-':
-                    chars.insert(i+compensator, bcolors.RED)
+                    chars.insert(i+compensator, RED)
                     compensator += 1
                     flag = '-'
                 if squigly[i] != flag:
-                    chars.insert(i+compensator, bcolors.ENDC)
+                    chars.insert(i+compensator, ENDC)
                     compensator += 1
                     flag = squigly[i]
 
-        chars.append(bcolors.ENDC)
+        chars.append(ENDC)
         return ''.join(chars)
 
     def _merge_squigly(self, squigly1, squigly2):
@@ -140,34 +185,23 @@ def _merge_squigly(self, squigly1, squigly2):
             if base[i] != other[i] and base[i] == '^':
                 base[i] = other[i]
 
-
         return ''.join(base)
 
-def merge_diff_info(diffs):
-    ### Combine multiple diff squigly lines into a single one.
-    base = list(max(diffs,key=len))
-    for line in diffs:
-        for i in range(len(line)):
-            if base[i] != line[i]:
-                if base[i] == ' ' and line[i] != "\n":
-                    base[i] = line[i]
-    return ''.join(base).rstrip()
-
 def multi_diff(base,files):
+    """
+    generate a Diff for multiple files, all compared to base
+    """
     d = difflib.Differ()
     base_lines = open(base).readlines()
 
-    diff_information = dict()
-    enters = []
-
-    differ = Diff(base, files)
+    differ = MultiDiff(base, files)
 
-    # store diff information in dict
+    # use the Diff class to store the information
     for file_name in files:
         diff = list(d.compare(open(file_name).readlines(), base_lines))
         file_name = os.path.basename(file_name)
 
-        local_diff = defaultdict(list)
+        local_diff = dict()
         squigly_dict = dict()
         last_added = None
         compensator = 1
@@ -176,16 +210,16 @@ def multi_diff(base,files):
                 squigly_dict[last_added] = (line)
                 compensator -= 1
             elif line.startswith('+'):
-                local_diff[i+compensator].append((line, file_name))
+                local_diff.setdefault(i+compensator, []).append((line, file_name))
                 last_added = line
             elif line.startswith('-'):
-                local_diff[i+compensator].append((line, file_name))
+                local_diff.setdefault(i+compensator, []).append((line, file_name))
                 last_added = line
                 compensator -= 1
 
-
+        # construct the Diff based on the above dict
         for line_no in local_diff:
             for (line, file_name) in local_diff[line_no]:
-                differ.add_line(line_no, line, file_name, squigly_dict.get(line, None))
+                differ.parse_line(line_no, line, file_name, squigly_dict.get(line, None))
 
     return differ

From 587976bb48b75129c8652e4605a59556bba24bc0 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:03:18 +0200
Subject: [PATCH 0062/1356] remove unneeded whitespace in main.py

---
 easybuild/main.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 5ed0bc9b7d..9b5f9faf80 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -355,7 +355,6 @@ def main(testing_data=(None, None, None)):
             _log.info("Regression test failed (partially)!")
             sys.exit(31)  # exit -> 3x1t -> 31
 
-
     # read easyconfig files
     easyconfigs = []
     generated_ecs = False

From 5fb9d5d35f67cf2827cc58a9a0ba929e129a7402 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:17:49 +0200
Subject: [PATCH 0063/1356] use setdefault, __str__

---
 easybuild/framework/easyconfig/review.py |  2 +-
 easybuild/tools/multi_diff.py            | 16 +++++++++-------
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/easybuild/framework/easyconfig/review.py b/easybuild/framework/easyconfig/review.py
index 9b1253fb8c..aac950605d 100644
--- a/easybuild/framework/easyconfig/review.py
+++ b/easybuild/framework/easyconfig/review.py
@@ -48,5 +48,5 @@ def review_pr(pull_request):
         for listing in files:
             if listing:
                 diff = multi_diff(easyconfig, listing)
-                diff.write_out()
+                print diff
                 break
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 42f7201e3f..d6d9cc35bb 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -62,23 +62,28 @@ def parse_line(self,line_no, diff_line, meta, squigly_line=None):
             action = self._remove_diff
         action(line_no, diff_line.rstrip(), meta, squigly_line)
 
-    def write_out(self):
+    def __str__(self):
         """
         Write the entire diff to the terminal
         """
         def limit(text, length):
+            """ limit text to certain length """
             if len(text) > length:
                 return text[0:length-3] + '...'
             else:
                 return text
 
+        output = []
+
         w,h = terminal.get_terminal_size()
-        print " ".join(["Comparing", PURPLE, os.path.basename(self.base), ENDC, "with", GRAY, ", ".join(map(os.path.basename,self.files)), ENDC])
+        output.append(" ".join(["Comparing", PURPLE, os.path.basename(self.base), ENDC, "with", GRAY, ", ".join(map(os.path.basename,self.files)), ENDC]))
 
         for i in range(len(self.base_lines)):
             lines = self.get_line(i)
             if filter(None,lines):
-                print "\n".join(map(lambda line: limit(line,w),lines))
+                output.append("\n".join([limit(line,w) for line in lines]))
+
+        return "\n".join(output)
 
     def get_line(self, line_no):
         """
@@ -94,10 +99,7 @@ def get_line(self, line_no):
                     if squigly_line:
                         squigly_dict[diff_line] = squigly_line
                     lines.add(diff_line)
-                    if diff_line not in changes_dict:
-                        changes_dict[diff_line] = set([meta])
-                    else:
-                        changes_dict[diff_line].add(meta)
+                    changes_dict.setdefault(diff_line,set()).add(meta)
 
             # restrict displaying of removals to 3 groups
             max_groups = 2

From 88f118b2015cb5486826ba8e5402187ffca5b40c Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:35:44 +0200
Subject: [PATCH 0064/1356] change to positive logic

---
 easybuild/tools/github.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index d602c94816..17313acf75 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -222,7 +222,12 @@ def download_repo(repo=GITHUB_EASYCONFIGS_REPO, branch='master', account=GITHUB_
 
 def _download(url, path=None):
     """Download file from specified URL to specified path."""
-    if path is not None:
+    if path is None:
+        try:
+            return urllib2.urlopen(url).read()
+        except urllib2.URLError, err:
+            _log.error("Failed to open %s for reading: %s" % (url, err))
+    else:
         try:
             _, httpmsg = urllib.urlretrieve(url, path)
             _log.debug("Downloaded %s to %s" % (url, path))
@@ -231,11 +236,6 @@ def _download(url, path=None):
 
         if httpmsg.type != 'text/plain' and httpmsg.type != 'application/x-gzip' :
             _log.error("Unexpected file type for %s: %s" % (path, httpmsg.type))
-    else:
-        try:
-            return urllib2.urlopen(url).read()
-        except urllib2.URLError, err:
-            _log.error("Failed to open %s for reading: %s" % (url, err))
 
 
 def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):

From 10d5256b4711e9e5d17af7c12f8529f47ef85c7a Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:36:05 +0200
Subject: [PATCH 0065/1356] use constant instead of random strings

---
 easybuild/tools/multi_diff.py | 38 +++++++++++++++--------------------
 1 file changed, 16 insertions(+), 22 deletions(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index d6d9cc35bb..cc2f88a18b 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -46,6 +46,9 @@ class MultiDiff(object):
     This class holds the diff information
     """
 
+    REMOVED_KEY = 'removed'
+    ADDED_KEY = 'added'
+
     def __init__(self, base, files):
         self.base = base
         self.base_lines = open(base).readlines()
@@ -57,10 +60,14 @@ def parse_line(self,line_no, diff_line, meta, squigly_line=None):
         Parse a line as generated by difflib
         """
         if diff_line.startswith('+'):
-            action = self._add_diff
+            key = self.ADDED_KEY
         elif diff_line.startswith('-'):
-            action = self._remove_diff
-        action(line_no, diff_line.rstrip(), meta, squigly_line)
+            key = self.REMOVED_KEY
+
+        if key not in self.diff_info.setdefault(line_no, {}):
+            self.diff_info[line_no][key] = []
+
+        self.diff_info[line_no][key].append((diff_line.rstrip(), meta, squigly_line))
 
     def __str__(self):
         """
@@ -90,7 +97,7 @@ def get_line(self, line_no):
         Return the line information for a specific line
         """
         output = []
-        for key in ['removal','addition']:
+        for key in [self.REMOVED_KEY, self.ADDED_KEY]:
             lines = set()
             changes_dict = dict()
             squigly_dict = dict()
@@ -122,27 +129,14 @@ def get_line(self, line_no):
                     line.extend([GRAY, "\t(%d/%d)" % (len(files), num_files), ENDC])
                 output.append(" ".join(line))
 
-        # print seperator
-        if self.diff_info.get(line_no, None) and 'addition' not in self.diff_info.get(line_no+1, {}) and 'removal' not in self.diff_info.get(line_no + 1, {}):
-            output.append('')
-            output.append('-----')
-            output.append('')
+        # print seperator only if needed
+        if self.diff_info.get(line_no, None) \
+           and self.ADDED_KEY not in self.diff_info.get(line_no+1, {}) \
+           and self.REMOVED_KEY not in self.diff_info.get(line_no + 1, {}):
+            output.extend(['', '-----', ''])
 
         return output
 
-
-    def _remove_diff(self,line_no, diff_line, meta, squigly_line=None):
-        if 'removal' not in self.diff_info.setdefault(line_no, {}):
-            self.diff_info[line_no]['removal'] = []
-
-        self.diff_info[line_no]['removal'].append((diff_line, meta, squigly_line))
-
-    def _add_diff(self,line_no, diff_line, meta, squigly_line=None):
-        if 'addition' not in self.diff_info.setdefault(line_no, {}):
-            self.diff_info[line_no]['addition'] = []
-
-        self.diff_info[line_no]['addition'].append((diff_line, meta, squigly_line))
-
     def _colorize(self, line, squigly):
         chars = list(line)
         flag = ' '

From bdc096c43d7cf8a946f70dc27e1b2d668dab9cce Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:40:54 +0200
Subject: [PATCH 0066/1356] add header, note about failing imports

---
 easybuild/tools/terminal.py | 37 +++++++++++++++++++++++++++++++------
 1 file changed, 31 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/terminal.py b/easybuild/tools/terminal.py
index 7fd9502166..b874fd747b 100644
--- a/easybuild/tools/terminal.py
+++ b/easybuild/tools/terminal.py
@@ -1,10 +1,40 @@
-# http://stackoverflow.com/questions/566746/how-to-get-console-window-width-in-python
+#!/usr/bin/env python
+# #
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Module for checking the terminal dimensions
+copied from http://stackoverflow.com/questions/566746/how-to-get-console-window-width-in-python
+"""
+
 import os
 
 def get_terminal_size():
     env = os.environ
     def ioctl_GWINSZ(fd):
         try:
+            # these might fail because they are only available on Unix
             import fcntl, termios, struct, os
             cr = struct.unpack('hh', fcntl.ioctl(fd, termios.TIOCGWINSZ,
         '1234'))
@@ -22,9 +52,4 @@ def ioctl_GWINSZ(fd):
     if not cr:
         cr = (env.get('LINES', 25), env.get('COLUMNS', 80))
 
-        ### Use get(key[, default]) instead of a try/catch
-        #try:
-        #    cr = (env['LINES'], env['COLUMNS'])
-        #except:
-        #    cr = (25, 80)
     return int(cr[1]), int(cr[0])

From 7daded02b5152ee8d99025a1275825a8ad7d5f1d Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 10:59:55 +0200
Subject: [PATCH 0067/1356] creative use of setdefault

---
 easybuild/tools/multi_diff.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index cc2f88a18b..75ecbf3f59 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -64,14 +64,11 @@ def parse_line(self,line_no, diff_line, meta, squigly_line=None):
         elif diff_line.startswith('-'):
             key = self.REMOVED_KEY
 
-        if key not in self.diff_info.setdefault(line_no, {}):
-            self.diff_info[line_no][key] = []
-
-        self.diff_info[line_no][key].append((diff_line.rstrip(), meta, squigly_line))
+        self.diff_info.setdefault(line_no, {}).setdefault(key,[]).append((diff_line.rstrip(), meta, squigly_line))
 
     def __str__(self):
         """
-        Write the entire diff to the terminal
+        Create a string representation of this multi diff
         """
         def limit(text, length):
             """ limit text to certain length """

From 994f3eb9241dfe1cc9cefac87fbdf5712719a1e3 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 11:03:51 +0200
Subject: [PATCH 0068/1356] wrap long line

---
 easybuild/tools/multi_diff.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 75ecbf3f59..767ef1493b 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -80,7 +80,8 @@ def limit(text, length):
         output = []
 
         w,h = terminal.get_terminal_size()
-        output.append(" ".join(["Comparing", PURPLE, os.path.basename(self.base), ENDC, "with", GRAY, ", ".join(map(os.path.basename,self.files)), ENDC]))
+        output.append(" ".join(["Comparing", PURPLE, os.path.basename(self.base), ENDC, "with",
+                                GRAY, ", ".join(map(os.path.basename,self.files)), ENDC]))
 
         for i in range(len(self.base_lines)):
             lines = self.get_line(i)

From fe05cf1311edb0db40338f18ff07fbf813debb8d Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 11:39:34 +0200
Subject: [PATCH 0069/1356] remove 2/3 _download references

---
 easybuild/main.py             |  2 +-
 easybuild/tools/github.py     |  6 ++++--
 easybuild/tools/multi_diff.py | 10 ++++++----
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 9b5f9faf80..18ec9c30eb 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -289,7 +289,7 @@ def main(testing_data=(None, None, None)):
 
     if options.review_pr:
         review_pr(options.review_pr)
-        os.sys.exit()
+        sys.exit()
 
     paths = []
     if len(orig_paths) == 0:
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 17313acf75..1f4fac6c2e 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -39,6 +39,8 @@
 from vsc.utils import fancylogger
 from vsc.utils.patterns import Singleton
 
+from easybuild.tools.filetools import download_file
+
 
 _log = fancylogger.getLogger('github', fname=False)
 
@@ -208,7 +210,7 @@ def download_repo(repo=GITHUB_EASYCONFIGS_REPO, branch='master', account=GITHUB_
     url = URL_SEPARATOR.join(["https://github.com",account, repo, 'archive', base_name])
 
     _log.debug("download repo %s/%s as archive from %s" % (account,repo, url))
-    _download(url, os.path.join(path,base_name))
+    download_file(base_name, url, os.path.join(path,base_name))
     _log.debug("%s downloaded to %s, extracting now" % (base_name, path))
 
     extracted_path = extract_file(os.path.join(path, base_name), path)
@@ -291,7 +293,7 @@ def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
         sha = last_commit['sha']
         full_url = URL_SEPARATOR.join([GITHUB_RAW, GITHUB_EB_MAIN, GITHUB_EASYCONFIGS_REPO, sha, patched_file])
         _log.info("Downloading %s from %s" % (fn, full_url))
-        _download(full_url, path=os.path.join(path, fn))
+        download_file(fn, full_url, path=os.path.join(path, fn))
 
     all_files = [os.path.basename(x) for x in patched_files]
     tmp_files = os.listdir(path)
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 767ef1493b..931dc259ad 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -85,7 +85,7 @@ def limit(text, length):
 
         for i in range(len(self.base_lines)):
             lines = self.get_line(i)
-            if filter(None,lines):
+            if lines:
                 output.append("\n".join([limit(line,w) for line in lines]))
 
         return "\n".join(output)
@@ -99,14 +99,16 @@ def get_line(self, line_no):
             lines = set()
             changes_dict = dict()
             squigly_dict = dict()
-            if key in self.diff_info.get(line_no, []):
+
+            if key in self.diff_info.get(line_no, {}):
                 for (diff_line, meta, squigly_line) in self.diff_info[line_no][key]:
                     if squigly_line:
-                        squigly_dict[diff_line] = squigly_line
+                        squigly_line2 = squigly_dict.get(diff_line, squigly_line)
+                        squigly_dict[diff_line] = self._merge_squigly(squigly_line, squigly_line2)
                     lines.add(diff_line)
                     changes_dict.setdefault(diff_line,set()).add(meta)
 
-            # restrict displaying of removals to 3 groups
+            # restrict displaying of removals to max_groups
             max_groups = 2
             if len(lines) > max_groups:
                 # find number of occurences

From ce87340dc27fa41674e6c86eba0c80402addd3ba Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 12:05:52 +0200
Subject: [PATCH 0070/1356] cleanup sorting / filtering

---
 easybuild/tools/multi_diff.py | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 931dc259ad..7851314cfe 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -110,14 +110,10 @@ def get_line(self, line_no):
 
             # restrict displaying of removals to max_groups
             max_groups = 2
-            if len(lines) > max_groups:
-                # find number of occurences
-                count = [(len(changes_dict[line]), line) for line in lines]
-                # sort highest first
-                lines = sorted(count, key=lambda (length, line): length)
-                lines.reverse()
-                # limit to max_groups
-                lines = [ x for (l,x) in lines][0:max_groups-1]
+            # sort highest first
+            lines = sorted(lines, key=lambda line: len(changes_dict[line]))
+            # limit to max_groups
+            lines = lines[::-1][:max_groups]
 
             for diff_line in lines:
                 line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]

From f80be4e7ad7d91a9dd4628f76e4fe04a27635a18 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 12:08:37 +0200
Subject: [PATCH 0071/1356] cleanup ifs

---
 easybuild/tools/multi_diff.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 7851314cfe..b0734fefeb 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -126,9 +126,7 @@ def get_line(self, line_no):
                 output.append(" ".join(line))
 
         # print seperator only if needed
-        if self.diff_info.get(line_no, None) \
-           and self.ADDED_KEY not in self.diff_info.get(line_no+1, {}) \
-           and self.REMOVED_KEY not in self.diff_info.get(line_no + 1, {}):
+        if self.diff_info.get(line_no, None) and self.diff_info.get(line_no + 1, {}):
             output.extend(['', '-----', ''])
 
         return output

From 702c81189bce308256967fa3ae5fe6dfc0e1398f Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 13:28:42 +0200
Subject: [PATCH 0072/1356] fix colorize

---
 easybuild/tools/multi_diff.py | 45 +++++++++++++----------------------
 1 file changed, 16 insertions(+), 29 deletions(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index b0734fefeb..1a09b7fc53 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -95,13 +95,14 @@ def get_line(self, line_no):
         Return the line information for a specific line
         """
         output = []
+        diff_dict = self.diff_info.get(line_no, {})
         for key in [self.REMOVED_KEY, self.ADDED_KEY]:
             lines = set()
             changes_dict = dict()
             squigly_dict = dict()
 
-            if key in self.diff_info.get(line_no, {}):
-                for (diff_line, meta, squigly_line) in self.diff_info[line_no][key]:
+            if key in diff_dict:
+                for (diff_line, meta, squigly_line) in diff_dict[key]:
                     if squigly_line:
                         squigly_line2 = squigly_dict.get(diff_line, squigly_line)
                         squigly_dict[diff_line] = self._merge_squigly(squigly_line, squigly_line2)
@@ -119,14 +120,14 @@ def get_line(self, line_no):
                 line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
                 files = changes_dict[diff_line]
                 num_files = len(self.files)
+                line.extend([GRAY, "\t(%d/%d)" % (len(files), num_files)])
                 if len(files) != num_files:
-                    line.extend([GRAY, "\t(%d/%d)" % (len(files), num_files), ', '.join(files), ENDC])
-                else:
-                    line.extend([GRAY, "\t(%d/%d)" % (len(files), num_files), ENDC])
+                        line.append(', '.join(files))
+                line.append(ENDC)
                 output.append(" ".join(line))
 
         # print seperator only if needed
-        if self.diff_info.get(line_no, None) and self.diff_info.get(line_no + 1, {}):
+        if diff_dict and not self.diff_info.get(line_no + 1, {}):
             output.extend(['', '-----', ''])
 
         return output
@@ -135,30 +136,16 @@ def _colorize(self, line, squigly):
         chars = list(line)
         flag = ' '
         compensator = 0
-        if not squigly:
-            if line.startswith('+'):
-                chars.insert(0, GREEN)
-            elif line.startswith('-'):
-                chars.insert(0, RED)
+        cmap = {'-': RED, '+' : GREEN, '^': GREEN if line.startswith('+') else RED}
+        if squigly:
+            for i,s in enumerate(squigly):
+                if s == flag: continue
+                chars.insert(i + compensator, ENDC)
+                compensator += 1
+                flag = s
+                chars.insert(i + compensator, cmap.get(s, ''))
         else:
-            for i in range(len(squigly)):
-                if squigly[i] == '+' and flag != '+':
-                    chars.insert(i+compensator, GREEN)
-                    compensator += 1
-                    flag = '+'
-                if squigly[i] == '^' and flag != '^':
-                    color = GREEN if line.startswith('+') else RED
-                    chars.insert(i+compensator, color)
-                    compensator += 1
-                    flag = '^'
-                if squigly[i] == '-' and flag != '-':
-                    chars.insert(i+compensator, RED)
-                    compensator += 1
-                    flag = '-'
-                if squigly[i] != flag:
-                    chars.insert(i+compensator, ENDC)
-                    compensator += 1
-                    flag = squigly[i]
+            chars.insert(0, cmap.get(line[0],''))
 
         chars.append(ENDC)
         return ''.join(chars)

From 9b69d78bdeec49b2bcdeca891ed2a2e05458caf1 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 15:16:58 +0200
Subject: [PATCH 0073/1356] add support to disable colors

---
 easybuild/framework/easyconfig/review.py |  4 +-
 easybuild/main.py                        |  2 +-
 easybuild/tools/multi_diff.py            | 85 +++++++++++++++---------
 easybuild/tools/options.py               |  1 +
 4 files changed, 59 insertions(+), 33 deletions(-)

diff --git a/easybuild/framework/easyconfig/review.py b/easybuild/framework/easyconfig/review.py
index aac950605d..85b82b5be5 100644
--- a/easybuild/framework/easyconfig/review.py
+++ b/easybuild/framework/easyconfig/review.py
@@ -38,7 +38,7 @@
 
 _log = fancylogger.getLogger('easyconfig.review', fname=False)
 
-def review_pr(pull_request):
+def review_pr(pull_request, colored):
     repo_path = os.path.join(download_repo(branch='develop'),'easybuild','easyconfigs')
     pr_files = [path for path in fetch_easyconfigs_from_pr(pull_request) if path.endswith('.eb')]
 
@@ -47,6 +47,6 @@ def review_pr(pull_request):
         _log.debug("File in pull request %s has these related easyconfigs: %s" % (easyconfig, files))
         for listing in files:
             if listing:
-                diff = multi_diff(easyconfig, listing)
+                diff = multi_diff(easyconfig, listing, colored)
                 print diff
                 break
diff --git a/easybuild/main.py b/easybuild/main.py
index 18ec9c30eb..9ab8a8a006 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -288,7 +288,7 @@ def main(testing_data=(None, None, None)):
         search_file(search_path, query, short=not options.search, ignore_dirs=ignore_dirs, silent=silent)
 
     if options.review_pr:
-        review_pr(options.review_pr)
+        review_pr(options.review_pr, options.color)
         sys.exit()
 
     paths = []
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 1a09b7fc53..f7831cdab3 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -30,16 +30,18 @@
 """
 
 import difflib
+import math
 import os
 import sys
 
 import easybuild.tools.terminal as terminal
 
-GREEN = "\033[92m"
+GREEN = "\033[0;32m"
 PURPLE = "\033[0;35m"
-GRAY = "\033[1;37m"
-RED = "\033[91m"
+RED = "\033[0;21m"
 ENDC = "\033[0m"
+B_GREEN = "\033[0;42m"
+B_RED = "\033[0;41m"
 
 class MultiDiff(object):
     """
@@ -49,11 +51,12 @@ class MultiDiff(object):
     REMOVED_KEY = 'removed'
     ADDED_KEY = 'added'
 
-    def __init__(self, base, files):
+    def __init__(self, base, files, colored=True):
         self.base = base
         self.base_lines = open(base).readlines()
         self.diff_info = dict()
         self.files = files
+        self.colored = colored
 
     def parse_line(self,line_no, diff_line, meta, squigly_line=None):
         """
@@ -71,20 +74,21 @@ def __str__(self):
         Create a string representation of this multi diff
         """
         def limit(text, length):
-            """ limit text to certain length """
+            """ limit text to certain length, add ENDC if needd """
             if len(text) > length:
-                return text[0:length-3] + '...'
+                return text[0:length-3] + ENDC + '...'
             else:
                 return text
 
         output = []
 
         w,h = terminal.get_terminal_size()
-        output.append(" ".join(["Comparing", PURPLE, os.path.basename(self.base), ENDC, "with",
-                                GRAY, ", ".join(map(os.path.basename,self.files)), ENDC]))
+        output.append(" ".join(["Comparing", self._color(os.path.basename(self.base), PURPLE), "with",
+                                ", ".join(map(os.path.basename,self.files))]))
 
         for i in range(len(self.base_lines)):
-            lines = self.get_line(i)
+            lines = filter(None,self.get_line(i))
+
             if lines:
                 output.append("\n".join([limit(line,w) for line in lines]))
 
@@ -117,61 +121,82 @@ def get_line(self, line_no):
             lines = lines[::-1][:max_groups]
 
             for diff_line in lines:
-                line = [str(line_no), self._colorize(diff_line, squigly_dict.get(diff_line))]
+                line = [str(line_no)]
+                squigly_line = squigly_dict.get(diff_line,'')
+                line.append(self._colorize(diff_line, squigly_line))
+
                 files = changes_dict[diff_line]
                 num_files = len(self.files)
-                line.extend([GRAY, "\t(%d/%d)" % (len(files), num_files)])
+
+                line.append("(%d/%d)" % (len(files), num_files))
                 if len(files) != num_files:
                         line.append(', '.join(files))
-                line.append(ENDC)
+
                 output.append(" ".join(line))
+                # prepend spaces to match line number length
+                if not self.colored and squigly_line:
+                    prepend = ' ' * (2 + int(math.log10(line_no)))
+                    output.append(''.join([prepend,squigly_line]))
 
         # print seperator only if needed
         if diff_dict and not self.diff_info.get(line_no + 1, {}):
-            output.extend(['', '-----', ''])
+            output.extend([' ', '-----', ' '])
 
         return output
 
     def _colorize(self, line, squigly):
+        """Add colors to the diff line based on the squiqly line"""
+        if not self.colored:
+            return line
+
         chars = list(line)
         flag = ' '
         compensator = 0
-        cmap = {'-': RED, '+' : GREEN, '^': GREEN if line.startswith('+') else RED}
+        color_map = {'-': B_RED, '+': B_GREEN, '^': B_GREEN if line.startswith('+') else B_RED}
         if squigly:
             for i,s in enumerate(squigly):
-                if s == flag: continue
-                chars.insert(i + compensator, ENDC)
-                compensator += 1
-                flag = s
-                chars.insert(i + compensator, cmap.get(s, ''))
+                if s != flag:
+                    chars.insert(i + compensator, ENDC)
+                    compensator += 1
+                    if s in ('+','-','^'):
+                        chars.insert(i + compensator, color_map.get(s, ''))
+                        compensator += 1
+                    flag = s
+            chars.insert(len(squigly)+compensator, ENDC)
         else:
-            chars.insert(0, cmap.get(line[0],''))
+            chars.insert(0, color_map.get(line[0],''))
+            chars.append(ENDC)
+
+
 
-        chars.append(ENDC)
         return ''.join(chars)
 
+    def _color(self, line, color):
+        if self.colored:
+            return ''.join([color, line, ENDC])
+        else:
+            return line
+
     def _merge_squigly(self, squigly1, squigly2):
         """Combine 2 diff lines into 1 """
         sq1 = list(squigly1)
         sq2 = list(squigly2)
         base,other = (sq1, sq2) if len(sq1) > len(sq2) else (sq2,sq1)
 
-        for i in range(len(other)):
-            if base[i] != other[i] and base[i] == ' ':
-                base[i] = other[i]
-            if base[i] != other[i] and base[i] == '^':
-                base[i] = other[i]
+        for i,o in enumerate(other):
+            if base[i] in (' ', '^') and base[i] != o:
+                base[i]=o
 
         return ''.join(base)
 
-def multi_diff(base,files):
+def multi_diff(base,files, colored=True):
     """
     generate a Diff for multiple files, all compared to base
     """
     d = difflib.Differ()
-    base_lines = open(base).readlines()
+    differ = MultiDiff(base, files, colored)
 
-    differ = MultiDiff(base, files)
+    base_lines = differ.base_lines
 
     # use the Diff class to store the information
     for file_name in files:
@@ -197,6 +222,6 @@ def multi_diff(base,files):
         # construct the Diff based on the above dict
         for line_no in local_diff:
             for (line, file_name) in local_diff[line_no]:
-                differ.parse_line(line_no, line, file_name, squigly_dict.get(line, None))
+                differ.parse_line(line_no, line, file_name, squigly_dict.get(line, '').rstrip())
 
     return differ
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index a1a11ff8cc..ec59d3fd6c 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -143,6 +143,7 @@ def software_options(self):
         opts.update({
             'from-pr': ("Obtain easyconfigs from specified PR", int, 'store', None, {'metavar': 'PR#'}),
             'review-pr': ("Review specified pull request", int, 'store', None, {'metavar': 'PR#'}),
+            'color': ("Allow color output", None, 'store_true', True),
         })
 
         self.log.debug("software_options: descr %s opts %s" % (descr, opts))

From 7aecf05803985b3f66ceefd3f7d25a410e8bbd7e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 Aug 2014 15:49:04 +0200
Subject: [PATCH 0074/1356] make sure install dir is not hidden, factor
 duplicate code in ActiveMNS, fix unit tests

---
 easybuild/framework/easyblock.py             |  7 ++-
 easybuild/framework/easyconfig/easyconfig.py | 64 +++++++++++---------
 easybuild/tools/module_generator.py          |  4 --
 easybuild/tools/toolchain/toolchain.py       |  1 +
 test/framework/module_generator.py           |  7 ++-
 test/framework/toy_build.py                  |  9 ++-
 6 files changed, 56 insertions(+), 36 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 05144f8491..dc1da9f1b7 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -148,6 +148,9 @@ def __init__(self, ec):
         else:
             _log.error("Value of incorrect type passed to EasyBlock constructor: %s ('%s')" % (type(ec), ec))
 
+        # determine install subdirectory, based on module name
+        self.install_subdir = ActiveMNS().det_full_module_name(self.cfg, hidden=False)
+
         # indicates whether build should be performed in installation dir
         self.build_in_installdir = self.cfg['buildininstalldir']
 
@@ -648,7 +651,7 @@ def gen_installdir(self):
         basepath = install_path()
 
         if basepath:
-            installdir = os.path.join(basepath, self.full_mod_name)
+            installdir = os.path.join(basepath, self.install_subdir)
             self.installdir = os.path.abspath(installdir)
         else:
             self.log.error("Can't set installation directory")
@@ -1184,7 +1187,7 @@ def fetch_step(self, skip_checksums=False):
         # this is required when building in parallel
         mod_path_suffix = build_option('suffix_modules_path')
         mod_symlink_paths = ActiveMNS().det_module_symlink_paths(self.cfg)
-        parent_subdir = os.path.dirname(self.full_mod_name)
+        parent_subdir = os.path.dirname(self.install_subdir)
         pardirs = [
             os.path.join(install_path(), parent_subdir),
             os.path.join(install_path('mod'), mod_path_suffix, parent_subdir),
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 6229e703dd..afaf5087a3 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -214,11 +214,14 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         if self.validation:
             self.validate(check_osdeps=build_option('check_osdeps'))
 
-        # set module info
+        # keep track of whether the generated module file should be hidden
         if hidden is None:
             hidden = build_option('hidden')
         self.hidden = hidden
+
+        # set installdir/module info
         mns = ActiveMNS()
+        self.install_subdir = mns.det_full_module_name(self, hidden=False)
         self.full_mod_name = mns.det_full_module_name(self)
         self.short_mod_name = mns.det_short_module_name(self)
         self.mod_subdir = mns.det_module_subdir(self)
@@ -1018,15 +1021,14 @@ def requires_full_easyconfig(self, keys):
 
     def check_ec_type(self, ec):
         """
-        Query module naming scheme using specified method and argument.
-        Obtain and pass a full parsed easyconfig file if provided keys are insufficient.
+        Obtain a full parsed easyconfig file to pass to naming scheme methods if provided keys are insufficient.
         """
         if not isinstance(ec, EasyConfig) and self.requires_full_easyconfig(ec.keys()):
             self.log.debug("A parsed easyconfig is required by the module naming scheme, so finding one for %s" % ec)
             # fetch/parse easyconfig file if deemed necessary
             eb_file = robot_find_easyconfig(ec['name'], det_full_ec_version(ec))
             if eb_file is not None:
-                parsed_ec = process_easyconfig(eb_file, parse_only=True)
+                parsed_ec = process_easyconfig(eb_file, parse_only=True, hidden=ec['hidden'])
                 if len(parsed_ec) > 1:
                     self.log.warning("More than one parsed easyconfig obtained from %s, only retaining first" % eb_file)
                     self.log.debug("Full list of parsed easyconfigs: %s" % parsed_ec)
@@ -1036,45 +1038,51 @@ def check_ec_type(self, ec):
 
         return ec
 
-    def det_full_module_name(self, ec):
+    def det_module_name_with(self, mns_method, ec, hidden=None):
+        """
+        Determine module name using specified module naming scheme method, based on supplied easyconfig.
+        Returns a string representing the module name, e.g. 'GCC/4.6.3', 'Python/2.7.5-ictce-4.1.13',
+        with the following requirements:
+            - module name is specified as a relative path
+            - string representing module name has length > 0
+            - module name only contains printable characters (string.printable, except carriage-control chars)
+        """
         """
-        Determine full module name by selected module naming scheme, based on supplied easyconfig.
         Returns a string representing the module name, e.g. 'GCC/4.6.3', 'Python/2.7.5-ictce-4.1.13',
         with the following requirements:
             - module name is specified as a relative path
             - string representing module name has length > 0
             - module name only contains printable characters (string.printable, except carriage-control chars)
         """
-        self.log.debug("Determining full module name for %s" % ec)
-        mod_name = self.mns.det_full_module_name(self.check_ec_type(ec))
+        mod_name = mns_method(self.check_ec_type(ec))
 
         if not is_valid_module_name(mod_name):
-            self.log.error("%s is not a valid full module name" % str(mod_name))
-        else:
-            self.log.debug("Obtained valid full module name %s" % mod_name)
+            self.log.error("%s is not a valid module name" % str(mod_name))
 
-        if getattr(ec, 'hidden', False) or ec.get('hidden', False):
+        # check whether module name should be hidden or not
+        # ec may be either a dict or an EasyConfig instance, 'hidden' argument overrules if set
+        if (ec.get('hidden', False) or getattr(ec, 'hidden', False)) and (hidden is None or hidden):
             mod_name = det_hidden_modname(mod_name)
 
         return mod_name
 
-    def det_devel_module_filename(self, ec):
-        """Determine devel module filename."""
-        return self.mns.det_full_module_name(self.check_ec_type(ec)).replace(os.path.sep, '-') + DEVEL_MODULE_SUFFIX
-
-    def det_short_module_name(self, ec):
-        """Determine module name according to module naming scheme."""
-        self.log.debug("Determining module name for %s" % ec)
-        mod_name = self.mns.det_short_module_name(self.check_ec_type(ec))
-
-        if not is_valid_module_name(mod_name):
-            self.log.error("%s is not a valid module name" % str(mod_name))
-        else:
-            self.log.debug("Obtained valid module name %s" % mod_name)
-
-        if getattr(ec, 'hidden', False) or ec.get('hidden', False):
-            mod_name = det_hidden_modname(mod_name)
+    def det_full_module_name(self, ec, hidden=None):
+        """Determine full module name by selected module naming scheme, based on supplied easyconfig."""
+        self.log.debug("Determining full module name for %s (hidden: %s)" % (ec, hidden))
+        mod_name = self.det_module_name_with(self.mns.det_full_module_name, ec, hidden=hidden)
+        self.log.debug("Obtained valid full module name %s" % mod_name)
+        return mod_name
 
+    def det_devel_module_filename(self, ec, hidden=None):
+        """Determine devel module filename."""
+        modname = self.det_full_module_name(ec, hidden=hidden)
+        return modname.replace(os.path.sep, '-') + DEVEL_MODULE_SUFFIX
+
+    def det_short_module_name(self, ec, hidden=None):
+        """Determine short module name according to module naming scheme."""
+        self.log.debug("Determining short module name for %s (hidden: %s)" % (ec, hidden))
+        mod_name = self.det_module_name_with(self.mns.det_short_module_name, ec, hidden=hidden)
+        self.log.debug("Obtained valid short module name %s" % mod_name)
         return mod_name
 
     def det_module_subdir(self, ec):
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index a79603d3d3..40553d1915 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -64,11 +64,7 @@ def prepare(self):
         Creates the absolute filename for the module.
         """
         mod_path_suffix = build_option('suffix_modules_path')
-        hidden = build_option('hidden')
         full_mod_name = self.app.full_mod_name
-        if build_option('hidden'):
-            full_mod_name = det_hidden_modname(full_mod_name)
-            _log.debug("Prefixed module filename with '.' to make it hidden: %s" % full_mod_name)
         # module file goes in general moduleclass category
         self.filename = os.path.join(self.module_path, mod_path_suffix, full_mod_name)
         # make symlink in moduleclass category
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 939bec0c2a..e804181283 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -215,6 +215,7 @@ def as_dict(self, name=None, version=None):
             'versionsuffix': '',
             'dummy': True,
             'parsed': True,  # pretend this is a parsed easyconfig file, as may be required by det_short_module_name
+            'hidden': False,
         }
 
     def det_short_module_name(self):
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 8c5f9167c9..c101271674 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -287,30 +287,35 @@ def test_mns():
 
         # test determining module name for dependencies (i.e. non-parsed easyconfigs)
         # using a module naming scheme that requires all easyconfig parameters
+        ec2mod_map['gzip-1.5-goolf-1.4.10.eb'] = 'gzip/.b63c2b8cc518905473ccda023100b2d3cff52d55'
         for dep_ec, dep_spec in [
             ('GCC-4.6.3.eb', {
                 'name': 'GCC',
                 'version': '4.6.3',
                 'versionsuffix': '',
                 'toolchain': {'name': 'dummy', 'version': 'dummy'},
+                'hidden': False,
             }),
             ('gzip-1.5-goolf-1.4.10.eb', {
                 'name': 'gzip',
                 'version': '1.5',
                 'versionsuffix': '',
                 'toolchain': {'name': 'goolf', 'version': '1.4.10'},
+                'hidden': True,
             }),
             ('toy-0.0-multiple.eb', {
                 'name': 'toy',
                 'version': '0.0',
                 'versionsuffix': '-multiple',
                 'toolchain': {'name': 'dummy', 'version': 'dummy'},
+                'hidden': False,
             }),
         ]:
             # determine full module name
             self.assertEqual(ActiveMNS().det_full_module_name(dep_spec), ec2mod_map[dep_ec])
 
-        ec = EasyConfig(os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
+        ec = EasyConfig(os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'), hidden=True)
+        self.assertEqual(ec.full_mod_name, ec2mod_map['gzip-1.5-goolf-1.4.10.eb'])
         self.assertEqual(ec.toolchain.det_short_module_name(), 'goolf/b7515d0efd346970f55e7aa8522e239a70007021')
 
         # restore default module naming scheme, and retest
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 62321d6e22..dd785b029d 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -176,6 +176,8 @@ def test_toy_build(self, extra_args=None, ec_file=None, tmpdir=None, verify=True
         if raise_error and (myerr is not None):
             raise myerr
 
+        return outtxt
+
     def test_toy_broken(self):
         """Test deliberately broken toy build."""
         tmpdir = tempfile.mkdtemp()
@@ -639,9 +641,14 @@ def test_toy_advanced(self):
 
     def test_toy_hidden(self):
         """Test installing a hidden module."""
-        self.test_toy_build(extra_args=['--hidden'], verify=False)
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0.eb')
+        self.test_toy_build(ec_file=ec_file, extra_args=['--hidden'], verify=False)
+        # module file is hidden
         toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '.0.0')
         self.assertTrue(os.path.exists(toy_module), 'Found hidden module %s' % toy_module)
+        # installed software is not hidden
+        toybin = os.path.join(self.test_installpath, 'software', 'toy', '0.0', 'bin', 'toy')
+        self.assertTrue(os.path.exists(toybin))
 
     def test_module_filepath_tweaking(self):
         """Test using --suffix-modules-path."""

From 841cc4405a619025d4536e83f53a4c2e535b08ab Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 16:15:06 +0200
Subject: [PATCH 0075/1356] add check for not redownloading github archive

---
 easybuild/framework/easyconfig/review.py |  4 +-
 easybuild/tools/github.py                | 70 +++++++++++++++++-------
 2 files changed, 54 insertions(+), 20 deletions(-)

diff --git a/easybuild/framework/easyconfig/review.py b/easybuild/framework/easyconfig/review.py
index 85b82b5be5..74e12ec86f 100644
--- a/easybuild/framework/easyconfig/review.py
+++ b/easybuild/framework/easyconfig/review.py
@@ -34,12 +34,14 @@
 from easybuild.framework.easyconfig.easyconfig import find_related_easyconfigs
 from easybuild.tools.github import fetch_easyconfigs_from_pr, download_repo
 from easybuild.tools.multi_diff import multi_diff
+from easybuild.tools.config import build_path
 
 
 _log = fancylogger.getLogger('easyconfig.review', fname=False)
 
 def review_pr(pull_request, colored):
-    repo_path = os.path.join(download_repo(branch='develop'),'easybuild','easyconfigs')
+    download_repo_path = download_repo(branch='develop', path=build_path())
+    repo_path = os.path.join(download_repo_path, 'easybuild', 'easyconfigs')
     pr_files = [path for path in fetch_easyconfigs_from_pr(pull_request) if path.endswith('.eb')]
 
     for easyconfig in pr_files:
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 1f4fac6c2e..673dcbd15a 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -191,23 +191,62 @@ class GithubError(Exception):
     """Error raised by the Githubfs"""
     pass
 
+
+def _do_request(lmb, github_user=None):
+    token = fetch_github_token(github_user)
+    g = RestClient(GITHUB_API_URL, username=github_user, token=token)
+
+    # call our lambda
+    url = lmb(g)
+
+    try:
+        status, data = url.get()
+    except socket.gaierror, err:
+        status, data = 0, None
+    _log.debug("status: %d, data: %s" % (status, data))
+
+    return (status, data)
+
+def fetch_latest_commit_sha(repo, account, branch='master'):
+    """fetches the latest sha for a specified branch"""
+
+    status, data = _do_request(lambda x: x.repos[account][repo].branches)
+    if not status == HTTP_STATUS_OK:
+        tup = (branch, account, repo, status, data)
+        _log.error("Failed to get latest commit sha for branch %s from %s/%s (status: %d %s)" % tup)
+
+    branch = [br for br in data if br[u'name'] == branch]
+    if len(branch) != 1:
+        _log.error('no branch with name %s found in repo %s/%s' % (branch, account, repo))
+
+    branch = branch[0]
+
+    return branch['commit']['sha']
+
 def download_repo(repo=GITHUB_EASYCONFIGS_REPO, branch='master', account=GITHUB_EB_MAIN, path=None):
     """Download entire repo as a tar.gz archive and extract it into path"""
-    if path is None:
+    # make sure path exists, create it if necessary
+    if path = None:
         path = tempfile.mkdtemp()
-    else:
-        # make sure path exists, create it if necessary
-        mkdir(path, parents=True)
+
+    # add account subdir
+    path = os.path.join(path, account)
+    mkdir(path, parents=True)
 
     extracted_dir_name = "%s-%s" % (GITHUB_EASYCONFIGS_REPO, branch)
     base_name = "%s.tar.gz" % branch
 
+    latest_commit_sha = fetch_latest_commit_sha(repo, account, branch)
+
     # check if directory already exists, and don't download if it does
     expected_path = os.path.join(path, extracted_dir_name)
     if os.path.isdir(expected_path):
-        return expected_path
+        sha = open(os.path.join(expected_path, "latest-sha")).readlines()[0]
+        if latest_commit_sha == sha.rstrip():
+            _log.debug("Not redownloading %s/%s as it already exists" % (account, repo))
+            return expected_path
 
-    url = URL_SEPARATOR.join(["https://github.com",account, repo, 'archive', base_name])
+    url = URL_SEPARATOR.join(["https://github.com", account, repo, 'archive', base_name])
 
     _log.debug("download repo %s/%s as archive from %s" % (account,repo, url))
     download_file(base_name, url, os.path.join(path,base_name))
@@ -219,6 +258,9 @@ def download_repo(repo=GITHUB_EASYCONFIGS_REPO, branch='master', account=GITHUB_
     if not os.path.isdir(extracted_path):
         _log.error("We expected %s to exists and contain the repo %s at branch %s" % (extracted_path, repo, branch))
 
+    f = open(os.path.join(extracted_path, 'latest-sha'), 'w')
+    f.write(latest_commit_sha)
+
     _log.debug("Repo %s at branch %s extracted into %s" % (repo, branch, extracted_path))
     return extracted_path
 
@@ -243,10 +285,6 @@ def _download(url, path=None):
 def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
     """Fetch patched easyconfig files for a particular PR."""
 
-
-    # a GitHub token is optional here, but can be used if available in order to be less susceptible to rate limiting
-    github_token = fetch_github_token(github_user)
-
     if path is None:
         path = tempfile.mkdtemp()
     else:
@@ -254,15 +292,9 @@ def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
         mkdir(path, parents=True)
 
     _log.debug("Fetching easyconfigs from PR #%s into %s" % (pr, path))
+    pr_url = lambda g: g.repos[GITHUB_EB_MAIN][GITHUB_EASYCONFIGS_REPO].pulls[pr]
 
-    # fetch data for specified PR
-    g = RestClient(GITHUB_API_URL, username=github_user, token=github_token)
-    pr_url = g.repos[GITHUB_EB_MAIN][GITHUB_EASYCONFIGS_REPO].pulls[pr]
-    try:
-        status, pr_data = pr_url.get()
-    except socket.gaierror, err:
-        status, pr_data = 0, None
-    _log.debug("status: %d, data: %s" % (status, pr_data))
+    status, pr_data = _do_request(pr_url, github_user)
     if not status == HTTP_STATUS_OK:
         tup = (pr, GITHUB_EB_MAIN, GITHUB_EASYCONFIGS_REPO, status, pr_data)
         _log.error("Failed to get data for PR #%d from %s/%s (status: %d %s)" % tup)
@@ -283,7 +315,7 @@ def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
     _log.debug("List of patches files: %s" % patched_files)
 
     # obtain last commit
-    status, commits_data = pr_url.commits.get()
+    status, commits_data = _do_request(lambda g: pr_url(g).commits, github_user)
     last_commit = commits_data[-1]
     _log.debug("Commits: %s" % commits_data)
 

From 78bd67e1d796fc14b03a4d9fe33863ec0239acc0 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 16:23:22 +0200
Subject: [PATCH 0076/1356] add some docstrings

---
 easybuild/framework/easyconfig/review.py | 4 ++--
 easybuild/tools/github.py                | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/review.py b/easybuild/framework/easyconfig/review.py
index 74e12ec86f..1f3d9ab381 100644
--- a/easybuild/framework/easyconfig/review.py
+++ b/easybuild/framework/easyconfig/review.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2014 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -24,7 +24,7 @@
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 # #
 """
-Review module for pull requests on the easyconfigs repo"
+Review module for pull requests on the easyconfigs repo
 
 @author: Toon Willems (Ghent University)
 """
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 673dcbd15a..e100af07d8 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -193,6 +193,7 @@ class GithubError(Exception):
 
 
 def _do_request(lmb, github_user=None):
+    """Helper method, for performing get requests"""
     token = fetch_github_token(github_user)
     g = RestClient(GITHUB_API_URL, username=github_user, token=token)
 

From 27d2709ae9e0d1356eb352bd40dd28daaf810104 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 16:24:48 +0200
Subject: [PATCH 0077/1356] change some docstrings around

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index bea949d69d..c15f7c9250 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -862,7 +862,7 @@ def resolve_template(value, tmpl_dict):
 def find_related_easyconfigs(path, ec):
     """
     Find related easyconfigs for ec in path based on a simple heuristic
-    - It first tries to match easyconfigs the exact same name.
+    - It first returns those that matches easyconfigs with the exact same name.
     - Then it matches those with the same version and same toolchain name
     - Then it takes those with the same version and any toolchain name
     - Then it takes the ones with any version and same toolchain (including version)

From 30a27746f35911e65953889a1d412a2303f077da Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 16:26:20 +0200
Subject: [PATCH 0078/1356] syntax error

---
 easybuild/tools/github.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index e100af07d8..9fed87ad16 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -227,7 +227,7 @@ def fetch_latest_commit_sha(repo, account, branch='master'):
 def download_repo(repo=GITHUB_EASYCONFIGS_REPO, branch='master', account=GITHUB_EB_MAIN, path=None):
     """Download entire repo as a tar.gz archive and extract it into path"""
     # make sure path exists, create it if necessary
-    if path = None:
+    if path == None:
         path = tempfile.mkdtemp()
 
     # add account subdir

From 2ef71c0a94c30bb878c4b3af32be885c8ba560f7 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 16:28:06 +0200
Subject: [PATCH 0079/1356] copyright year

---
 easybuild/tools/multi_diff.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index f7831cdab3..8ae78065bb 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2014 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

From 46ca7e397780332b51111305468efa78e0ec0617 Mon Sep 17 00:00:00 2001
From: Toon Willems <willemstoon@gmail.com>
Date: Thu, 14 Aug 2014 17:18:28 +0200
Subject: [PATCH 0080/1356] fix all the things

---
 easybuild/framework/easyconfig/easyconfig.py | 31 ++++++++++++++------
 easybuild/framework/easyconfig/review.py     |  1 -
 easybuild/tools/multi_diff.py                |  3 --
 easybuild/tools/terminal.py                  |  1 -
 4 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index c15f7c9250..e266dc30c6 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -883,22 +883,35 @@ def find_related_easyconfigs(path, ec):
     toolchain = "%s-%s" % (toolchain_name, ec['toolchain']['version'])
     full_version = det_full_ec_version(ec)
 
-    patterns = [
+    potential_paths = [os.path.dirname(path) for path in create_paths(path, name, version)]
+    result_potential_paths = []
+
+    for pot in potential_paths:
+        try:
+            result_potential_paths.append([os.path.join(pot,base) for base in os.listdir(pot) if os.path.isfile(os.path.join(pot,base))])
+        except:
+            None
+
+    # flatten
+    result_potential_paths = sum(result_potential_paths, [])
+
+    regexes = [
         # exact match
-        ("%s-%s" % (name, full_version)),
+        re.compile(("^\S*/%s-%s.eb$" % (name, full_version))),
         # same version, same toolchain name
-        ("%s-%s-%s-*" % (name, version, toolchain_name)),
+        re.compile(("^\S*/%s-%s-%s-\S*.eb$" % (name, version, toolchain_name))),
         # Same version, any toolchain
-        ("%s-%s-*" % (name, version)),
+        re.compile(("^\S*/%s-%s-\S*.eb$" % (name, version))),
         # any version, same toolchain
-        ("%s-*-%s-*" % (name, toolchain)),
+        re.compile(("^\S*/%s-\S*-%s-\S*.eb$" % (name, toolchain))),
         # any version, same toolchain name
-        ("%s-*-%s-*" % (name, toolchain_name)),
-        # any version, any toolchain
-        ("*"),
+        re.compile(("^\S*/%s-\S*-%s-\S*.eb$" % (name, toolchain_name))),
     ]
+    _log.debug("found these potential paths: %s" % result_potential_paths)
 
-    return [glob.glob("%s.eb" % os.path.join(path, name.lower()[0], name, *cand_path)) for cand_path in patterns]
+    result = [filter(lambda path: regex.match(path),result_potential_paths) for regex in regexes]
+    result.append(result_potential_paths)
+    return result
 
 
 def process_easyconfig(path, build_specs=None, validate=True, parse_only=False):
diff --git a/easybuild/framework/easyconfig/review.py b/easybuild/framework/easyconfig/review.py
index 1f3d9ab381..5fdb5927c1 100644
--- a/easybuild/framework/easyconfig/review.py
+++ b/easybuild/framework/easyconfig/review.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # #
 # Copyright 2014 Ghent University
 #
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 8ae78065bb..37aed2747f 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # #
 # Copyright 2014 Ghent University
 #
@@ -167,8 +166,6 @@ def _colorize(self, line, squigly):
             chars.insert(0, color_map.get(line[0],''))
             chars.append(ENDC)
 
-
-
         return ''.join(chars)
 
     def _color(self, line, color):
diff --git a/easybuild/tools/terminal.py b/easybuild/tools/terminal.py
index b874fd747b..80e8d67ea7 100644
--- a/easybuild/tools/terminal.py
+++ b/easybuild/tools/terminal.py
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # #
 # Copyright 2009-2014 Ghent University
 #

From 26161c9014425a65e2fbfa4f73479287b9a2b912 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@ugent.be>
Date: Mon, 18 Aug 2014 10:40:57 +0200
Subject: [PATCH 0081/1356] fixed link to style guide

---
 CONTRIBUTING.md | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index a85d1b5eba..806847ada9 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,21 +1,21 @@
 We'd love you to contribute back to EasyBuild, and here's how you can do it: the branch - hack - pull request cycle.
 
 # License
-Contributions can be made under the MIT or 
+Contributions can be made under the MIT or
 BSD licenses (in the three-clause and two-clause forms, though not the original four-clause form).
 
 Or alteratively the contributor must agree with following contributor agreement:
 
 ## Contributor Agreement.
-In this case the contributor must agree that Ghent University shall have the irrevocable and perpetual right to make and 
+In this case the contributor must agree that Ghent University shall have the irrevocable and perpetual right to make and
 distribute copies of any Contribution, as well as to create and distribute collective works and derivative works of
-any Contribution, under the Initial License or under any other open source license. 
+any Contribution, under the Initial License or under any other open source license.
 (as defined by The Open Source Initiative (OSI) http://opensource.org/).
-Contributor shall identify each Contribution by placing the following notice in its source code adjacent to 
-Contributor's valid copyright notice: "Licensed to Ghent University under a Contributor Agreement." 
+Contributor shall identify each Contribution by placing the following notice in its source code adjacent to
+Contributor's valid copyright notice: "Licensed to Ghent University under a Contributor Agreement."
 The currently acceptable license is GPLv2 or any other GPLv2 compatible license.
 
-Ghent University understands and agrees that Contributor retains copyright in its Contributions. 
+Ghent University understands and agrees that Contributor retains copyright in its Contributions.
 Nothing in this Contributor Agreement shall be interpreted to prohibit Contributor from licensing its Contributions
 under different terms from the Initial License or this Contributor Agreement.
 
@@ -31,7 +31,7 @@ You should also register an SSH public key, so you can easily clone, push to and
 
 ### Clone the easybuild-framework repository
 
-Clone your fork of the easybuild-framework repository to your favorite workstation. 
+Clone your fork of the easybuild-framework repository to your favorite workstation.
 
 ```bash
 git clone git@github.com:YOUR\_GITHUB\_LOGIN/easybuild-framework.git
@@ -51,7 +51,7 @@ git pull github_hpcugent develop
 
 ### Keep develop up-to-date
 
-The _develop_ branch hosts the latest bleeding-edge version of easybuild-framework, and is merged into _master_ regularly (after thorough testing). 
+The _develop_ branch hosts the latest bleeding-edge version of easybuild-framework, and is merged into _master_ regularly (after thorough testing).
 
 Make sure you update it every time you create a feature branch (see below):
 
@@ -82,7 +82,7 @@ git checkout <BRANCH_NAME>
 
 Make sure to always base your features branches on _develop_, not on _master_!
 
- 
+
 
 ## Hack
 
@@ -108,7 +108,7 @@ When you've finished the implementation of a particular contribution, here's how
 ### Push your branch
 
 Push your branch to your easybuild-framework repository on GitHub:
- 
+
 ```bash
 git push origin <BRANCH_NAME>
 ```
@@ -127,7 +127,7 @@ Issue a pull request for your branch into the mair easybuild-framework repositor
 ### Issue pull request for existing ticket (from command line)
 
 If you're contributing code to an existing issue you can also convert the issue to a pull request by running
-``` 
+```
 GITHUBUSER=your_username && PASSWD=your_password && BRANCH=branch_name && ISSUE=issue_number && \
 curl --user "$GITHUBUSER:$PASSWD" --request POST \
 --data "{\"issue\": \"$ISSUE\", \"head\": \"$GITHUBUSER:$BRANCH\", \"base\": \"develop\"}" \
@@ -138,7 +138,7 @@ You might also want to look into [hub](https://github.com/defunkt/hub) for more
 
 ### Review process
 
-A member of the EasyBuild team will then review your pull request, paying attention to what you're contributing, how you implemented it and [code style](Code style).
+A member of the EasyBuild team will then review your pull request, paying attention to what you're contributing, how you implemented it and [https://github.com/hpcugent/easybuild/wiki/Code-style](Code style).
 
 Most likely, some remarks will be made on your pull request. Note that this is nothing personal, we're just trying to keep the EasyBuild codebase as high quality as possible. Even when an EasyBuild team member makes changes, the same public review process is followed.
 

From ada16b6f5bc78f27b5190c1a3fb30973c8345e00 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@ugent.be>
Date: Mon, 18 Aug 2014 10:42:15 +0200
Subject: [PATCH 0082/1356] fixed link to style guide

---
 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 806847ada9..10649cddab 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -138,7 +138,7 @@ You might also want to look into [hub](https://github.com/defunkt/hub) for more
 
 ### Review process
 
-A member of the EasyBuild team will then review your pull request, paying attention to what you're contributing, how you implemented it and [https://github.com/hpcugent/easybuild/wiki/Code-style](Code style).
+A member of the EasyBuild team will then review your pull request, paying attention to what you're contributing, how you implemented it and [Code style](https://github.com/hpcugent/easybuild/wiki/Code-style).
 
 Most likely, some remarks will be made on your pull request. Note that this is nothing personal, we're just trying to keep the EasyBuild codebase as high quality as possible. Even when an EasyBuild team member makes changes, the same public review process is followed.
 

From 34e5c30cd05cd70e419baa2443d9d72417ff8916 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 19 Aug 2014 15:25:23 +0200
Subject: [PATCH 0083/1356] escape module name before including it into regex

---
 easybuild/tools/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 6c0b36bc5f..ca4435d60e 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -338,7 +338,7 @@ def exists(self, mod_name):
         txt = self.show(mod_name)
         # 'show' output always contains full path to existing module file
         # enforce that only True is returned via ':' at the end of the regex
-        exists_re = re.compile('^\s*\S*/%s:\s*$' % mod_name, re.M)
+        exists_re = re.compile('^\s*\S*/%s:\s*$' % re.escape(mod_name), re.M)
         return bool(exists_re.search(txt))
 
     def load(self, modules, mod_paths=None, purge=False, orig_env=None):

From 7c13f3b336453871f8f6be8a20186090bbf1ee4c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 20 Aug 2014 16:02:19 +0200
Subject: [PATCH 0084/1356] redefine ModulesTool.exist method to check whether
 (hidden) modules exist

---
 easybuild/framework/easyblock.py        | 13 ++++---
 easybuild/framework/easyconfig/tools.py | 17 +++++----
 easybuild/tools/modules.py              | 50 +++++++++++++++++++------
 easybuild/tools/toolchain/toolchain.py  | 10 +++--
 test/framework/modules.py               | 19 +++++++++-
 5 files changed, 79 insertions(+), 30 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index dc1da9f1b7..4aa3fe0c21 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -149,7 +149,7 @@ def __init__(self, ec):
             _log.error("Value of incorrect type passed to EasyBlock constructor: %s ('%s')" % (type(ec), ec))
 
         # determine install subdirectory, based on module name
-        self.install_subdir = ActiveMNS().det_full_module_name(self.cfg, hidden=False)
+        self.install_subdir = None
 
         # indicates whether build should be performed in installation dir
         self.build_in_installdir = self.cfg['buildininstalldir']
@@ -197,6 +197,10 @@ def __init__(self, ec):
         if group_name is not None:
             self.group = use_group(group_name)
 
+        # generate build/install directories
+        self.gen_builddir()
+        self.gen_installdir()
+
         self.log.info("Init completed for application name %s version %s" % (self.name, self.version))
 
     # INIT/CLOSE LOG
@@ -649,10 +653,11 @@ def gen_installdir(self):
         Generate the name of the installation directory.
         """
         basepath = install_path()
-
         if basepath:
+            self.install_subdir = ActiveMNS().det_full_module_name(self.cfg, hidden=False)
             installdir = os.path.join(basepath, self.install_subdir)
             self.installdir = os.path.abspath(installdir)
+            self.log.info("Install dir set to %s" % self.installdir)
         else:
             self.log.error("Can't set installation directory")
 
@@ -1134,7 +1139,7 @@ def check_readiness_step(self):
         # - if a current module can be found, skip is ok
         # -- this is potentially very dangerous
         if self.cfg['skip']:
-            if self.modules_tool.exists(self.full_mod_name):
+            if self.modules_tool.exist([self.full_mod_name])[0]:
                 self.skip = True
                 self.log.info("Module %s found." % self.full_mod_name)
                 self.log.info("Going to skip actual main build and potential existing extensions. Expert only.")
@@ -1700,8 +1705,6 @@ def get_step(tag, descr, substeps, skippable, initial=True):
         # list of substeps for steps that are slightly different from 2nd iteration onwards
         ready_substeps = [
             (False, lambda x: x.check_readiness_step()),
-            (False, lambda x: x.gen_builddir()),
-            (False, lambda x: x.gen_installdir()),
             (True, lambda x: x.make_builddir()),
             (True, lambda x: env.reset_changes()),
             (True, lambda x: x.handle_iterate_opts()),
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 37924efa00..b491fa9501 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -81,17 +81,18 @@
 def skip_available(easyconfigs, testing=False):
     """Skip building easyconfigs for existing modules."""
     modtool = modules_tool()
-    easyconfigs, check_easyconfigs = [], easyconfigs
-    for ec in check_easyconfigs:
-        module = ec['full_mod_name']
-        if modtool.exists(module):
-            msg = "%s is already installed (module found), skipping" % module
+    module_names = [ec['full_mod_name'] for ec in easyconfigs]
+    modules_exist = modtool.exist(module_names)
+    retained_easyconfigs = []
+    for ec, mod_name, mod_exists in zip(easyconfigs, module_names, modules_exist):
+        if mod_exists:
+            msg = "%s is already installed (module found), skipping" % mod_name
             print_msg(msg, log=_log, silent=testing)
             _log.info(msg)
         else:
-            _log.debug("%s is not installed yet, so retaining it" % module)
-            easyconfigs.append(ec)
-    return easyconfigs
+            _log.debug("%s is not installed yet, so retaining it" % mod_name)
+            retained_easyconfigs.append(ec)
+    return retained_easyconfigs
 
 
 def find_resolved_modules(unprocessed, avail_modules):
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index ca4435d60e..e5956b10cd 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -206,8 +206,12 @@ def set_and_check_version(self):
         if self.REQ_VERSION is None:
             self.log.debug('No version requirement defined.')
         else:
-            # replace 'rc' by 'b', to make StrictVersion treat it as a beta-release
-            if StrictVersion(self.version.replace('rc', 'b')) < StrictVersion(self.REQ_VERSION):
+            # make sure version is a valid StrictVersion (e.g., 5.7.3.1 is invalid),
+            # and replace 'rc' by 'b', to make StrictVersion treat it as a beta-release
+            check_ver = self.version.replace('rc', 'b')
+            if len(check_ver.split('.')) > 3:
+                check_ver = '.'.join(check_ver.split('.')[:3])
+            if StrictVersion(check_ver) < StrictVersion(self.REQ_VERSION):
                 msg = "EasyBuild requires v%s >= v%s (no rc), found v%s"
                 self.log.error(msg % (self.__class__.__name__, self.REQ_VERSION, self.version))
             else:
@@ -329,17 +333,39 @@ def available(self, mod_name=None):
         self.log.debug("'module available %s' gave %d answers: %s" % (mod_name, len(ans), ans))
         return ans
 
-    def exists(self, mod_name):
+    def exist(self, mod_names):
         """
-        Check if module with specified name exists.
+        Check if modules with specified names exists.
         """
-        # implemented via 'show' subcommand, since obtaining list of available modules can be very slow
-        # also, it doesn't include hidden modules
-        txt = self.show(mod_name)
-        # 'show' output always contains full path to existing module file
-        # enforce that only True is returned via ':' at the end of the regex
-        exists_re = re.compile('^\s*\S*/%s:\s*$' % re.escape(mod_name), re.M)
-        return bool(exists_re.search(txt))
+        # resort to use 'show' for short lists of module names (3 or less)
+        use_show = False
+        avail_mod_names = None
+        if len(mod_names) <= 3:
+            use_show = True
+        else:
+            avail_mod_names = self.available()
+
+        # differentiate between hidden and visible modules
+        mod_names = [(mod_name, not os.path.basename(mod_name).startswith('.')) for mod_name in mod_names]
+
+        mods_exist = []
+        for (mod_name, visible) in mod_names:
+            if visible and not use_show:
+                mods_exist.append(mod_name in avail_mod_names)
+            else:
+                # hidden modules are not visible in 'avail', need to use 'show' instead
+                modtype = ('hidden', 'visible (not hidden)')[visible]
+                self.log.debug("checking whether %s module %s exists via 'show'..." % (modtype, mod_name))
+                txt = self.show(mod_name)
+                mods_exist_re = re.compile('^\s*\S*/%s:\s*$' % re.escape(mod_name), re.M)
+                mods_exist.append(bool(mods_exist_re.search(txt)))
+
+        return mods_exist
+
+    def exists(self, mod_name):
+        """Check if a module with the specified name exists."""
+        self.log.deprecated("exists(<mod_name>) is deprecated, use exist([<mod_name>]) instead", '2.0')
+        return self.exist([mod_name])[0]
 
     def load(self, modules, mod_paths=None, purge=False, orig_env=None):
         """
@@ -401,7 +427,7 @@ def get_value_from_modulefile(self, mod_name, regex):
         @param mod_name: module name
         @param regex: (compiled) regular expression, with one group
         """
-        if self.exists(mod_name):
+        if self.exist([mod_name])[0]:
             modinfo = self.show(mod_name)
             self.log.debug("modinfo: %s" % modinfo)
             res = regex.search(modinfo)
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index e804181283..09920f6c94 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -236,7 +236,7 @@ def _toolchain_exists(self):
             if self.mod_short_name is None:
                 self.log.error("Toolchain module name was not set yet (using set_module_info).")
             # check whether a matching module exists if self.mod_short_name contains a module name
-            return self.modules_tool.exists(self.mod_full_name)
+            return self.modules_tool.exist([self.mod_full_name])[0]
 
     def set_options(self, options):
         """ Process toolchain options """
@@ -284,10 +284,12 @@ def get_dependency_version(self, dependency):
     def add_dependencies(self, dependencies):
         """ Verify if the given dependencies exist and add them """
         self.log.debug("add_dependencies: adding toolchain dependencies %s" % dependencies)
-        for dep in dependencies:
+        dep_mod_names = [dep['full_mod_name'] for dep in dependencies]
+        deps_exist = self.modules_tool.exist(dep_mod_names)
+        for dep, dep_mod_name, dep_exists in zip(dependencies, dep_mod_names, deps_exist):
             self.log.debug("add_dependencies: MODULEPATH: %s" % os.environ['MODULEPATH'])
-            if not self.modules_tool.exists(dep['full_mod_name']):
-                tup = (dep['full_mod_name'], dep)
+            if not dep_exists:
+                tup = (dep_mod_name, dep)
                 self.log.error("add_dependencies: no module '%s' found for dependency %s" % tup)
             else:
                 self.dependencies.append(dep)
diff --git a/test/framework/modules.py b/test/framework/modules.py
index bc74426282..5b3bd1a9aa 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -110,8 +110,25 @@ def test_avail(self):
     def test_exists(self):
         """Test if testing for module existence works."""
         self.init_testmods()
+        self.assertEqual(self.testmods.exist(['OpenMPI/1.6.4-GCC-4.6.4']), [True])
+        self.assertEqual(self.testmods.exist(['foo/1.2.3']), [False])
+        # exists should not return True for incomplete module names
+        self.assertEqual(self.testmods.exist(['GCC']), [False])
+
+        # exists works on hidden modules
+        self.assertEqual(self.testmods.exist(['toy/.0.0-deps']), [True])
+
+        # exists also works on lists of module names
+        # list should be sufficiently long, since for short lists 'show' is always used
+        mod_names = ['OpenMPI/1.6.4-GCC-4.6.4', 'foo/1.2.3', 'GCC',
+                     'ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED',
+                     'ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1',
+                     'Compiler/GCC/4.7.2/OpenMPI/1.6.4', 'toy/.0.0-deps']
+        self.assertEqual(self.testmods.exist(mod_names), [True, False, False, False, True, True, True])
+
+        # test deprecated functionality
         self.assertTrue(self.testmods.exists('OpenMPI/1.6.4-GCC-4.6.4'))
-        self.assertTrue(not self.testmods.exists(mod_name='foo/1.2.3'))
+        self.assertFalse(self.testmods.exists('foo/1.2.3'))
         # exists should not return True for incomplete module names
         self.assertFalse(self.testmods.exists('GCC'))
 

From 9b93346ff3b13c193c186e07222cde6054cc385e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 20 Aug 2014 16:37:19 +0200
Subject: [PATCH 0085/1356] fix remarks

---
 easybuild/framework/easyconfig/easyconfig.py | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index afaf5087a3..00ff6988e9 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -134,6 +134,7 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         @param extra_options: dictionary with extra variables that can be set for this specific instance
         @param build_specs: dictionary of build specifications (see EasyConfig class, default: {})
         @param validate: indicates whether validation should be performed (note: combined with 'validate' build option)
+        @param hidden: indicate whether corresponding module file should be installed hidden ('.'-prefixed)
         """
         self.template_values = None
         self.enable_templating = True  # a boolean to control templating
@@ -532,7 +533,9 @@ def _parse_dependency(self, dep, hidden=False):
         of these attributes, 'name' and 'version' are mandatory
 
         output dict contains these attributes:
-        ['name', 'version', 'versionsuffix', 'dummy', 'toolchain', 'short_mod_name', 'full_mod_name']
+        ['name', 'version', 'versionsuffix', 'dummy', 'toolchain', 'short_mod_name', 'full_mod_name', 'hidden']
+
+        @param hidden: indicate whether corresponding module file should be installed hidden ('.'-prefixed)
         """
         # convert tuple to string otherwise python might complain about the formatting
         self.log.debug("Parsing %s as a dependency" % str(dep))
@@ -874,6 +877,7 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False,
     @param path: path to easyconfig file
     @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
     @param validate: whether or not to perform validation
+    @param hidden: indicate whether corresponding module file should be installed hidden ('.'-prefixed)
     """
     blocks = retrieve_blocks_in_spec(path, build_option('only_blocks'))
 
@@ -917,20 +921,15 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False,
                 'hiddendependencies': [],
                 'hidden': hidden,
             })
-            if hidden:
-                easyconfig.update({
-                    'short_mod_name': ec.short_mod_name,
-                    'full_mod_name': ec.full_mod_name,
-                })
             if len(blocks) > 1:
                 easyconfig['original_spec'] = path
 
-            # add build/hidden dependencies
+            # add build dependencies
             for dep in ec['builddependencies']:
                 _log.debug("Adding build dependency %s for app %s." % (dep, name))
                 easyconfig['builddependencies'].append(dep)
 
-            # add build/hidden dependencies
+            # add hidden dependencies
             for dep in ec['hiddendependencies']:
                 _log.debug("Adding hidden dependency %s for app %s." % (dep, name))
                 easyconfig['hiddendependencies'].append(dep)

From 00d523b26300859cfa8c5847d7f36c6c8d54449e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 20 Aug 2014 17:36:56 +0200
Subject: [PATCH 0086/1356] rename 'hidden' method argument in ActiveMNS to
 'force_visible' to make it easier to grok

---
 easybuild/framework/easyblock.py             |  2 +-
 easybuild/framework/easyconfig/easyconfig.py | 23 ++++++++++----------
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 4aa3fe0c21..af24e79119 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -654,7 +654,7 @@ def gen_installdir(self):
         """
         basepath = install_path()
         if basepath:
-            self.install_subdir = ActiveMNS().det_full_module_name(self.cfg, hidden=False)
+            self.install_subdir = ActiveMNS().det_full_module_name(self.cfg, force_visible=True)
             installdir = os.path.join(basepath, self.install_subdir)
             self.installdir = os.path.abspath(installdir)
             self.log.info("Install dir set to %s" % self.installdir)
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 00ff6988e9..094770d207 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -222,7 +222,6 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
 
         # set installdir/module info
         mns = ActiveMNS()
-        self.install_subdir = mns.det_full_module_name(self, hidden=False)
         self.full_mod_name = mns.det_full_module_name(self)
         self.short_mod_name = mns.det_short_module_name(self)
         self.mod_subdir = mns.det_module_subdir(self)
@@ -1037,7 +1036,7 @@ def check_ec_type(self, ec):
 
         return ec
 
-    def det_module_name_with(self, mns_method, ec, hidden=None):
+    def _det_module_name_with(self, mns_method, ec, force_visible=False):
         """
         Determine module name using specified module naming scheme method, based on supplied easyconfig.
         Returns a string representing the module name, e.g. 'GCC/4.6.3', 'Python/2.7.5-ictce-4.1.13',
@@ -1059,28 +1058,28 @@ def det_module_name_with(self, mns_method, ec, hidden=None):
             self.log.error("%s is not a valid module name" % str(mod_name))
 
         # check whether module name should be hidden or not
-        # ec may be either a dict or an EasyConfig instance, 'hidden' argument overrules if set
-        if (ec.get('hidden', False) or getattr(ec, 'hidden', False)) and (hidden is None or hidden):
+        # ec may be either a dict or an EasyConfig instance, 'force_visible' argument overrules
+        if (ec.get('hidden', False) or getattr(ec, 'hidden', False)) and not force_visible:
             mod_name = det_hidden_modname(mod_name)
 
         return mod_name
 
-    def det_full_module_name(self, ec, hidden=None):
+    def det_full_module_name(self, ec, force_visible=False):
         """Determine full module name by selected module naming scheme, based on supplied easyconfig."""
-        self.log.debug("Determining full module name for %s (hidden: %s)" % (ec, hidden))
-        mod_name = self.det_module_name_with(self.mns.det_full_module_name, ec, hidden=hidden)
+        self.log.debug("Determining full module name for %s (force_visible: %s)" % (ec, force_visible))
+        mod_name = self._det_module_name_with(self.mns.det_full_module_name, ec, force_visible=force_visible)
         self.log.debug("Obtained valid full module name %s" % mod_name)
         return mod_name
 
-    def det_devel_module_filename(self, ec, hidden=None):
+    def det_devel_module_filename(self, ec, force_visible=False):
         """Determine devel module filename."""
-        modname = self.det_full_module_name(ec, hidden=hidden)
+        modname = self.det_full_module_name(ec, force_visible=force_visible)
         return modname.replace(os.path.sep, '-') + DEVEL_MODULE_SUFFIX
 
-    def det_short_module_name(self, ec, hidden=None):
+    def det_short_module_name(self, ec, force_visible=False):
         """Determine short module name according to module naming scheme."""
-        self.log.debug("Determining short module name for %s (hidden: %s)" % (ec, hidden))
-        mod_name = self.det_module_name_with(self.mns.det_short_module_name, ec, hidden=hidden)
+        self.log.debug("Determining short module name for %s (force_visible: %s)" % (ec, force_visible))
+        mod_name = self._det_module_name_with(self.mns.det_short_module_name, ec, force_visible=force_visible)
         self.log.debug("Obtained valid short module name %s" % mod_name)
         return mod_name
 

From 843879a7a3effa98e1313e5c9e59aa858ac9b51d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 21 Aug 2014 14:18:06 +0200
Subject: [PATCH 0087/1356] filter out load statements that extend the
 $MODULEPATH to make the module being installed available

---
 easybuild/framework/easyblock.py | 76 +++++++++++++++++++++++++-------
 easybuild/tools/modules.py       | 23 ++++++++--
 2 files changed, 78 insertions(+), 21 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 42cf3e6af5..358a844f03 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -56,7 +56,7 @@
 from easybuild.tools.build_details import get_build_stats
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_path, get_log_filename, get_repository, get_repositorypath, install_path
-from easybuild.tools.config import log_path, read_only_installdir, source_paths, build_option
+from easybuild.tools.config import log_path, read_only_installdir, source_paths, build_option, install_path
 from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import DEFAULT_CHECKSUM
 from easybuild.tools.filetools import adjust_permissions, apply_patch, convert_name, download_file, encode_class_name
@@ -766,7 +766,20 @@ def make_module_dep(self):
         """
         Make the dependencies for the module file.
         """
-        load = unload = ''
+        deps = []
+
+        # include load statements for toolchain, either directly or for toolchain dependencies
+        # purposely after dependencies which may be critical,
+        # e.g. when unloading a module in a hierarchical naming scheme
+        if self.toolchain.name != DUMMY_TOOLCHAIN_NAME:
+            mns = ActiveMNS()
+            if mns.expand_toolchain_load():
+                mod_names = self.toolchain.toolchain_dependencies
+                deps.extend(mod_names)
+                self.log.debug("Adding toolchain components as module dependencies: %s" % mod_names)
+            else:
+                deps.append(self.toolchain.det_short_module_name())
+                self.log.debug("Adding toolchain %s as a module dependency" % deps[-1])
 
         # include load/unload statements for dependencies
         builddeps = self.cfg.builddependencies()
@@ -775,28 +788,57 @@ def make_module_dep(self):
             if not dep in builddeps:
                 modname = dep['short_mod_name']
                 self.log.debug("Adding %s as a module dependency" % modname)
-                load += self.moduleGenerator.load_module(modname, recursive_unload=self.recursive_mod_unload)
-                unload += self.moduleGenerator.unload_module(modname)
+                deps.append(modname)
             else:
                 self.log.debug("Skipping build dependency %s" % str(dep))
 
-        # include load statements for toolchain, either directly or for toolchain dependencies
-        # purposely after dependencies which may be critical,
-        # e.g. when unloading a module in a hierarchical naming scheme
-        if self.toolchain.name != DUMMY_TOOLCHAIN_NAME:
-            if ActiveMNS().expand_toolchain_load():
-                mod_names = self.toolchain.toolchain_dependencies
-            else:
-                mod_names = [self.toolchain.det_short_module_name()]
-            for mod_name in mod_names:
-                load += self.moduleGenerator.load_module(mod_name, recursive_unload=self.recursive_mod_unload)
-                unload += self.moduleGenerator.unload_module(mod_name)
+        self.log.debug("Full list of dependencies: %s" % deps)
+
+        # determine full module path extensions for each of the modules
+        modpaths = os.environ['MODULEPATH'].split(os.pathsep)
+        mod_install_path = os.path.join(install_path('mod'), build_option('suffix_modules_path')).rstrip(os.path.sep)
+        full_mod_subdir = os.path.join(mod_install_path, self.cfg.mod_subdir).rstrip(os.path.sep)
+        all_modpath_exts = {}
+        if full_mod_subdir != mod_install_path:
+            for dep in deps:
+                all_modpath_exts.update({dep: []})
+                for full_modpath_ext in self.modules_tool.modpath_extensions_for(dep):
+                    for modpath in modpaths:
+                        if full_modpath_ext.startswith(modpath):
+                            modpath_ext = full_modpath_ext[len(modpath)+1:]
+                            if modpath_ext:
+                                all_modpath_exts[dep].append(modpath_ext)
+            self.log.debug("Module path extensions for dependencies: %s" % all_modpath_exts)
+
+        # determine dependencies to exclude based on their $MODULEPATH extensions, recursively
+        excluded_deps = []
+        extended = True
+        while full_mod_subdir != mod_install_path and extended:
+            extended = False
+            self.log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
+            for dep, modpath_exts in all_modpath_exts.items():
+                # if $MODULEPATH extension is identical to where this module will be installed, we have a hit
+                full_modpath_exts = [os.path.join(mod_install_path, e).rstrip(os.path.sep) for e in modpath_exts]
+                if full_mod_subdir in full_modpath_exts:
+                    # figure out module subdir for this dep, so we can recurse
+                    modfile_path = self.modules_tool.modulefile_path(dep)
+                    full_mod_subdir = modfile_path[:-len(dep)].rstrip(os.path.sep)
+                    excluded_deps.append(dep)
+                    extended = True
+                    tup = (dep, full_mod_subdir, all_modpath_exts.pop(dep))
+                    self.log.debug("Excluded dependency %s (subdir: %s) with module path extensions %s" % tup)
+                    break
+
+        deps = [d for d in deps if d not in excluded_deps]
+        self.log.debug("List of retained dependencies: %s" % deps)
+        loads = [self.moduleGenerator.load_module(d, recursive_unload=self.recursive_mod_unload) for d in deps]
+        unloads = [self.moduleGenerator.unload_module(d) for d in deps]
 
         # Force unloading any other modules
         if self.cfg['moduleforceunload']:
-            return unload + load
+            return ''.join(unloads) + ''.join(loads)
         else:
-            return load
+            return ''.join(loads)
 
     def make_module_description(self):
         """
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index e5956b10cd..4b4ce32db6 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -563,16 +563,21 @@ def loaded_modules(self):
 
         return loaded_modules
 
-    # depth=sys.maxint should be equivalent to infinite recursion depth
-    def dependencies_for(self, mod_name, depth=sys.maxint):
+    def read_module_file(self, mod_name):
         """
-        Obtain a list of dependencies for the given module, determined recursively, up to a specified depth (optionally)
+        Read module file with specified name.
         """
         modfilepath = self.modulefile_path(mod_name)
         self.log.debug("modulefile path %s: %s" % (mod_name, modfilepath))
 
-        modtxt = read_file(modfilepath)
+        return read_file(modfilepath)
 
+    # depth=sys.maxint should be equivalent to infinite recursion depth
+    def dependencies_for(self, mod_name, depth=sys.maxint):
+        """
+        Obtain a list of dependencies for the given module, determined recursively, up to a specified depth (optionally)
+        """
+        modtxt = self.read_module_file(mod_name)
         loadregex = re.compile(r"^\s+module load\s+(.*)$", re.M)
         mods = loadregex.findall(modtxt)
 
@@ -591,6 +596,16 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
 
         return mods
 
+    def modpath_extensions_for(self, mod_name):
+        """
+        Determine list of $MODULEPATH extensions for specified module.
+        """
+        modtxt = self.read_module_file(mod_name)
+        useregex = re.compile(r"^\s*module use\s+(.*)$", re.M)
+        exts = useregex.findall(modtxt)
+
+        return exts
+
     def update(self):
         """Update after new modules were added."""
         raise NotImplementedError

From 37e704d80982a3a6843fc61f160237899f9805c1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 21 Aug 2014 14:18:16 +0200
Subject: [PATCH 0088/1356] enhance tests to check correctness of load
 statements in modules generated with HierarchicalMNS

---
 test/framework/easyconfigs/toy-0.0-deps.eb    |  2 +-
 test/framework/modules.py                     | 14 ++++++-
 test/framework/modules/Core/goolf/1.4.10      | 39 +++++++++++++++++++
 .../MPI/GCC/4.7.2/OpenMPI/1.6.4/FFTW/3.3.3    | 27 +++++++++++++
 .../OpenMPI/1.6.4/OpenBLAS/0.2.6-LAPACK-3.4.2 | 22 +++++++++++
 .../2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2         | 28 +++++++++++++
 test/framework/robot.py                       |  2 +-
 test/framework/toy_build.py                   | 23 +++++++----
 8 files changed, 146 insertions(+), 11 deletions(-)
 create mode 100644 test/framework/modules/Core/goolf/1.4.10
 create mode 100644 test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/FFTW/3.3.3
 create mode 100644 test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/OpenBLAS/0.2.6-LAPACK-3.4.2
 create mode 100644 test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2

diff --git a/test/framework/easyconfigs/toy-0.0-deps.eb b/test/framework/easyconfigs/toy-0.0-deps.eb
index 6ab5bce42f..646f9db067 100644
--- a/test/framework/easyconfigs/toy-0.0-deps.eb
+++ b/test/framework/easyconfigs/toy-0.0-deps.eb
@@ -18,7 +18,7 @@ checksums = [[
 ]]
 patches = ['toy-0.0_typo.patch']
 
-dependencies = [('gompi', '1.3.12')]
+dependencies = [('ictce', '4.1.13', '', True)]
 
 sanity_check_paths = {
     'files': [('bin/yot', 'bin/toy')],
diff --git a/test/framework/modules.py b/test/framework/modules.py
index 5b3bd1a9aa..eda5e5750b 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -42,7 +42,7 @@
 
 
 # number of modules included for testing purposes
-TEST_MODULES_COUNT = 38
+TEST_MODULES_COUNT = 42
 
 
 class ModulesTest(EnhancedTestCase):
@@ -136,13 +136,23 @@ def test_load(self):
         """ test if we load one module it is in the loaded_modules """
         self.init_testmods()
         ms = self.testmods.available()
-        ms = [m for m in ms if not m.startswith('Core/') and not m.startswith('Compiler/')]
+        # exclude modules not on the top level of a hierarchy
+        ms = [m for m in ms if not (m.startswith('Core') or m.startswith('Compiler/') or m.startswith('MPI/'))]
 
         for m in ms:
             self.testmods.load([m])
             self.assertTrue(m in self.testmods.loaded_modules())
             self.testmods.purge()
 
+        # trying to load a module not on the top level of a hierarchy should fail
+        mods = [
+            'Compiler/GCC/4.7.2/OpenMPI/1.6.4',  # module use on non-existent directory
+            'Core/GCC/4.7.2',  # module use on non-existent directory
+            'MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2',  # missing deps
+        ]
+        for mod in mods:
+            self.assertErrorRegex(EasyBuildError, '.*', self.testmods.load, [mod])
+
     def test_ld_library_path(self):
         """Make sure LD_LIBRARY_PATH is what it should be when loaded multiple modules."""
         self.init_testmods()
diff --git a/test/framework/modules/Core/goolf/1.4.10 b/test/framework/modules/Core/goolf/1.4.10
new file mode 100644
index 0000000000..b199b678fc
--- /dev/null
+++ b/test/framework/modules/Core/goolf/1.4.10
@@ -0,0 +1,39 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   GNU Compiler Collection (GCC) based compiler toolchain,
+ including OpenMPI for MPI support. - Homepage: (none)
+    }
+}
+
+module-whatis {Description: GNU Compiler Collection (GCC) based compiler toolchain,
+ including OpenMPI for MPI support. - Homepage: (none)}
+
+set root    /tmp/software/Core/gompi/1.4.10
+
+conflict    gompi
+
+if { ![is-loaded GCC/4.7.2] } {
+    module load GCC/4.7.2
+}
+
+if { ![is-loaded OpenMPI/1.6.4] } {
+    module load OpenMPI/1.6.4
+}
+
+if { ![is-loaded FFTW/3.3.3] } {
+    module load FFTW/3.3.3
+}
+
+if { ![is-loaded OpenBLAS/0.2.6-LAPACK-3.4.2] } {
+    module load OpenBLAS/0.2.6-LAPACK-3.4.2
+}
+
+if { ![is-loaded ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2] } {
+    module load ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
+}
+
+setenv	EBROOTGOMPI		"$root"
+setenv	EBVERSIONGOMPI		"1.4.10"
+setenv	EBDEVELGOMPI		"$root/easybuild/Core-gompi-1.4.10-easybuild-devel"
+
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/FFTW/3.3.3 b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/FFTW/3.3.3
new file mode 100644
index 0000000000..f5558adc35
--- /dev/null
+++ b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/FFTW/3.3.3
@@ -0,0 +1,27 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+in one or more dimensions, of arbitrary input size, and of both real and complex data. - Homepage: http://www.fftw.org
+}
+}
+
+module-whatis {FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+in one or more dimensions, of arbitrary input size, and of both real and complex data. - Homepage: http://www.fftw.org}
+
+set root    /home-2/khoste/.local/easybuild/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/FFTW/3.3.3
+
+conflict    FFTW
+
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+prepend-path	MANPATH		$root/share/man
+prepend-path	PATH		$root/bin
+prepend-path	PKG_CONFIG_PATH		$root/lib/pkgconfig
+
+setenv	EBROOTFFTW		"$root"
+setenv	EBVERSIONFFTW		"3.3.3"
+setenv	EBDEVELFFTW		"$root/easybuild/FFTW-3.3.3-gompi-1.4.10-easybuild-devel"
+
+
+# built with EasyBuild version 1.4.0dev
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/OpenBLAS/0.2.6-LAPACK-3.4.2 b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/OpenBLAS/0.2.6-LAPACK-3.4.2
new file mode 100644
index 0000000000..f81a3b5d44
--- /dev/null
+++ b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/OpenBLAS/0.2.6-LAPACK-3.4.2
@@ -0,0 +1,22 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. - Homepage: http://xianyi.github.com/OpenBLAS/
+}
+}
+
+module-whatis {OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. - Homepage: http://xianyi.github.com/OpenBLAS/}
+
+set root    /home-2/khoste/.local/easybuild/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/OpenBLAS/0.2.6-LAPACK-3.4.2
+
+conflict    OpenBLAS
+
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+
+setenv	EBROOTOPENBLAS		"$root"
+setenv	EBVERSIONOPENBLAS		"0.2.6"
+setenv	EBDEVELOPENBLAS		"$root/easybuild/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2-easybuild-devel"
+
+
+# built with EasyBuild version 1.4.0dev
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2 b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
new file mode 100644
index 0000000000..31166dc2f3
--- /dev/null
+++ b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
@@ -0,0 +1,28 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
+redesigned for distributed memory MIMD parallel computers. - Homepage: http://www.netlib.org/scalapack/
+}
+}
+
+module-whatis {The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
+redesigned for distributed memory MIMD parallel computers. - Homepage: http://www.netlib.org/scalapack/}
+
+set root    /home-2/khoste/.local/easybuild/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
+
+conflict    ScaLAPACK
+
+if { ![is-loaded OpenBLAS/0.2.6-LAPACK-3.4.2] } {
+    module load OpenBLAS/0.2.6-LAPACK-3.4.2
+}
+
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+
+setenv	EBROOTSCALAPACK		"$root"
+setenv	EBVERSIONSCALAPACK		"2.0.2"
+setenv	EBDEVELSCALAPACK		"$root/easybuild/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2-easybuild-devel"
+
+
+# built with EasyBuild version 1.4.0dev
diff --git a/test/framework/robot.py b/test/framework/robot.py
index 9ab23ea4ee..6b83103e42 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -144,7 +144,7 @@ def test_resolve_dependencies(self):
         easyconfig_moredeps['dependencies'].append(hidden_dep)
         easyconfig_moredeps['hiddendependencies'] = [hidden_dep]
         res = resolve_dependencies([deepcopy(easyconfig_moredeps)])
-        self.assertEqual(len(res), 7)  # hidden dep toy/.0.0-deps (+1) depends on gompi (+4)
+        self.assertEqual(len(res), 4)  # hidden dep toy/.0.0-deps (+1) depends on (fake) ictce/4.1.13 (+1)
         self.assertEqual('gzip/1.4', res[0]['full_mod_name'])
         self.assertEqual('foo/1.2.3', res[-1]['full_mod_name'])
         self.assertTrue('toy/.0.0-deps' in [ec['full_mod_name'] for ec in res])
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 1f4a75d075..4fa3a16ae6 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -524,14 +524,18 @@ def test_toy_hierarchical(self):
         # simply copy module files under 'Core' and 'Compiler' to test install path
         # EasyBuild is responsible for making sure that the toolchain can be loaded using the short module name
         mkdir(mod_prefix, parents=True)
-        for mod_subdir in ['Core', 'Compiler']:
+        for mod_subdir in ['Core', 'Compiler', 'MPI']:
             src_mod_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'modules', mod_subdir)
             shutil.copytree(src_mod_path, os.path.join(mod_prefix, mod_subdir))
 
-        # tweak prepend-path statements in GCC/OpenMPI modules to ensure correct paths
+        # tweak use statements in GCC/OpenMPI modules to ensure correct paths
+        mpi_pref = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
         for modfile in [
             os.path.join(mod_prefix, 'Core', 'GCC', '4.7.2'),
             os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'),
+            os.path.join(mpi_pref, 'FFTW', '3.3.3'),
+            os.path.join(mpi_pref, 'OpenBLAS', '0.2.6-LAPACK-3.4.2'),
+            os.path.join(mpi_pref, 'ScaLAPACK', '2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2'),
         ]:
             for line in fileinput.input(modfile, inplace=1):
                 line = re.sub(r"(module\s*use\s*)/tmp/modules/all",
@@ -553,7 +557,7 @@ def test_toy_hierarchical(self):
 
         # test module paths/contents with gompi build
         extra_args = [
-            '--try-toolchain=gompi,1.4.10',
+            '--try-toolchain=goolf,1.4.10',
         ]
         self.eb_main(args + extra_args, logfile=self.dummylogfn, do_build=True, verbose=True, raise_error=True)
 
@@ -561,11 +565,16 @@ def test_toy_hierarchical(self):
         toy_module_path = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4', 'toy', '0.0')
         self.assertTrue(os.path.exists(toy_module_path))
 
-        # check that toolchain load is expanded to loads for toolchain dependencies
+        # check that toolchain load is expanded to loads for toolchain dependencies,
+        # except for the ones that extend $MODULEPATH to make the toy module available
         modtxt = read_file(toy_module_path)
-        self.assertFalse(re.search("load gompi", modtxt))
-        self.assertTrue(re.search("load GCC", modtxt))
-        self.assertTrue(re.search("load OpenMPI", modtxt))
+        for dep in ['goolf', 'GCC', 'OpenMPI']:
+            load_regex = re.compile("load %s" % dep)
+            self.assertFalse(load_regex.search(modtxt), "Pattern '%s' not found in %s" % (load_regex.pattern, modtxt))
+        for dep in ['OpenBLAS', 'FFTW', 'ScaLAPACK']:
+            load_regex = re.compile("load %s" % dep)
+            self.assertTrue(load_regex.search(modtxt), "Pattern '%s' found in %s" % (load_regex.pattern, modtxt))
+
         os.remove(toy_module_path)
 
         # test module path with GCC/4.7.2 build

From 32dbec3db9d476f2470c7d34e4e777b28f8f38ca Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 21 Aug 2014 14:48:30 +0200
Subject: [PATCH 0089/1356] minor cleanup in HierarchicalMNS.det_module_subdir

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index ca2adb21b7..bbf1e6d7e8 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -97,13 +97,14 @@ def det_module_subdir(self, ec):
         This determines the separation between module names exposed to users, and what's part of the $MODULEPATH.
         Examples: Core, Compiler/GCC/4.8.3, MPI/GCC/4.8.3/OpenMPI/1.6.5
         """
-        # determine prefix based on type of toolchain used
         tc_comps = det_toolchain_compilers(ec)
-        if tc_comps is None:
+        tc_comp_info = self.det_toolchain_compilers_name_version(tc_comps)
+        # determine prefix based on type of toolchain used
+        if tc_comp_info is None:
             # no compiler in toolchain, dummy toolchain => Core module
             subdir = CORE
         else:
-            tc_comp_name, tc_comp_ver = self.det_toolchain_compilers_name_version(tc_comps)
+            tc_comp_name, tc_comp_ver = tc_comp_info
             tc_mpi = det_toolchain_mpi(ec)
             if tc_mpi is None:
                 # compiler-only toolchain => Compiler/<compiler_name>/<compiler_version> namespace

From 07d5208ec3307567b2654faf7fde93b346fd7a24 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 21 Aug 2014 20:36:44 +0200
Subject: [PATCH 0090/1356] fix unit test case that works with Lmod but is
 broken with Tcl-based env mods

---
 test/framework/modules.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index eda5e5750b..ee97938ab8 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -146,9 +146,8 @@ def test_load(self):
 
         # trying to load a module not on the top level of a hierarchy should fail
         mods = [
-            'Compiler/GCC/4.7.2/OpenMPI/1.6.4',  # module use on non-existent directory
-            'Core/GCC/4.7.2',  # module use on non-existent directory
-            'MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2',  # missing deps
+            'Compiler/GCC/4.7.2/OpenMPI/1.6.4',  # module use on non-existent dir (Tcl-based env mods), or missing dep (Lmod)
+            'MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2',  # missing dep
         ]
         for mod in mods:
             self.assertErrorRegex(EasyBuildError, '.*', self.testmods.load, [mod])

From b56f7c00981af33dad124dca70050957a5f52b98 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 22 Aug 2014 11:05:13 +0200
Subject: [PATCH 0091/1356] fix conflict specification included in module
 files, should use short module name obtain from active module naming scheme

---
 easybuild/framework/easyblock.py    | 9 ++++++++-
 easybuild/tools/module_generator.py | 7 ++++++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 42cf3e6af5..798267fe52 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -595,10 +595,17 @@ def toolchain(self):
     @property
     def full_mod_name(self):
         """
-        Toolchain used to build this easyblock
+        Full module name (including subdirectory in module install path)
         """
         return self.cfg.full_mod_name
 
+    @property
+    def short_mod_name(self):
+        """
+        Short module name (not including subdirectory in module install path)
+        """
+        return self.cfg.short_mod_name
+
     #
     # DIRECTORY UTILITY FUNCTIONS
     #
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 40553d1915..3c1533b2af 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -123,7 +123,12 @@ def get_description(self, conflict=True):
             ])
 
         elif conflict:
-            lines.append("conflict    %s\n" % self.app.name)
+            # conflict on 'name' part of module name (excluding version part at the end)
+            # examples:
+            # - 'conflict GCC' for 'GCC/4.8.3'
+            # - 'conflict Core/GCC' for 'Core/GCC/4.8.2'
+            # - 'conflict Compiler/GCC/4.8.2/OpenMPI' for 'Compiler/GCC/4.8.2/OpenMPI/1.6.4'
+            lines.append("conflict %s\n" % os.path.dirname(self.app.short_mod_name))
 
         txt = '\n'.join(lines) % {
             'name': self.app.name,

From a567ada38086aed9bf61d6e72cc6f6bf367d7c08 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 22 Aug 2014 12:30:10 +0200
Subject: [PATCH 0092/1356] add unit test for toolchain definition verification

---
 test/framework/modules.py                     |  2 +-
 .../modules/goalf/1.1.0-no-OFED-brokenBLACS   | 48 +++++++++++++++++++
 .../modules/goalf/1.1.0-no-OFED-brokenFFTW    | 47 ++++++++++++++++++
 test/framework/toolchain.py                   | 33 +++++++++++++
 4 files changed, 129 insertions(+), 1 deletion(-)
 create mode 100644 test/framework/modules/goalf/1.1.0-no-OFED-brokenBLACS
 create mode 100644 test/framework/modules/goalf/1.1.0-no-OFED-brokenFFTW

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 5b3bd1a9aa..b80b6b3bbd 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -42,7 +42,7 @@
 
 
 # number of modules included for testing purposes
-TEST_MODULES_COUNT = 38
+TEST_MODULES_COUNT = 40
 
 
 class ModulesTest(EnhancedTestCase):
diff --git a/test/framework/modules/goalf/1.1.0-no-OFED-brokenBLACS b/test/framework/modules/goalf/1.1.0-no-OFED-brokenBLACS
new file mode 100644
index 0000000000..daaa81cb83
--- /dev/null
+++ b/test/framework/modules/goalf/1.1.0-no-OFED-brokenBLACS
@@ -0,0 +1,48 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   GNU Compiler Collection (GCC) based compiler toolchain, including
+OpenMPI for MPI support, ATLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. - Homepage: (none)
+}
+}
+
+module-whatis {GNU Compiler Collection (GCC) based compiler toolchain, including
+OpenMPI for MPI support, ATLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. - Homepage: (none)}
+
+set root    /home/kehoste/.local/easybuild/software/goalf/1.1.0-no-OFED-noblacs
+
+conflict    goalf
+
+if { ![is-loaded GCC/4.6.3] } {
+    module load GCC/4.6.3
+}
+
+if { ![is-loaded OpenMPI/1.4.5-GCC-4.6.3-no-OFED] } {
+    module load OpenMPI/1.4.5-GCC-4.6.3-no-OFED
+}
+
+if { ![is-loaded ATLAS/3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0] } {
+    module load ATLAS/3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0
+}
+
+if { ![is-loaded FFTW/3.3.1-gompi-1.1.0-no-OFED] } {
+    module load FFTW/3.3.1-gompi-1.1.0-no-OFED
+}
+
+# load statement for BLACS purposely omitted, which doesn't match the toolchain definition
+# BLACS is optional, but still required here since ScaLAPACK version is < 2.0
+#if { ![is-loaded BLACS/1.1-gompi-1.1.0-no-OFED] } {
+#    module load BLACS/1.1-gompi-1.1.0-no-OFED
+#}
+
+if { ![is-loaded ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1] } {
+    module load ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1
+}
+
+
+setenv	EBROOTGOALF		$root
+setenv	EBVERSIONGOALF		1.1.0
+setenv	EBDEVELGOALF		$root/easybuild/goalf-1.1.0-no-OFED-noblacs-easybuild-devel
+
+
+# built with EasyBuild version 0.9dev
diff --git a/test/framework/modules/goalf/1.1.0-no-OFED-brokenFFTW b/test/framework/modules/goalf/1.1.0-no-OFED-brokenFFTW
new file mode 100644
index 0000000000..07d9cac1b6
--- /dev/null
+++ b/test/framework/modules/goalf/1.1.0-no-OFED-brokenFFTW
@@ -0,0 +1,47 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   GNU Compiler Collection (GCC) based compiler toolchain, including
+OpenMPI for MPI support, ATLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. - Homepage: (none)
+}
+}
+
+module-whatis {GNU Compiler Collection (GCC) based compiler toolchain, including
+OpenMPI for MPI support, ATLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. - Homepage: (none)}
+
+set root    /home/kehoste/.local/easybuild/software/goalf/1.1.0-no-OFED-broken
+
+conflict    goalf
+
+if { ![is-loaded GCC/4.6.3] } {
+    module load GCC/4.6.3
+}
+
+if { ![is-loaded OpenMPI/1.4.5-GCC-4.6.3-no-OFED] } {
+    module load OpenMPI/1.4.5-GCC-4.6.3-no-OFED
+}
+
+if { ![is-loaded ATLAS/3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0] } {
+    module load ATLAS/3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0
+}
+
+# load statement for FFTW purposely omitted, which doesn't match the toolchain definition
+#if { ![is-loaded FFTW/3.3.1-gompi-1.1.0-no-OFED] } {
+#    module load FFTW/3.3.1-gompi-1.1.0-no-OFED
+#}
+
+if { ![is-loaded BLACS/1.1-gompi-1.1.0-no-OFED] } {
+    module load BLACS/1.1-gompi-1.1.0-no-OFED
+}
+
+if { ![is-loaded ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1] } {
+    module load ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1
+}
+
+
+setenv	EBROOTGOALF		$root
+setenv	EBVERSIONGOALF		1.1.0
+setenv	EBDEVELGOALF		$root/easybuild/goalf-1.1.0-no-OFED-broken-easybuild-devel
+
+
+# built with EasyBuild version 0.9dev
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 8056c71d12..f129156cbf 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -37,6 +37,7 @@
 
 import easybuild.tools.modules as modules
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.utilities import search_toolchain
 from test.framework.utilities import find_full_path
 
@@ -215,6 +216,7 @@ def test_optimization_flags(self):
                         self.assertTrue(tc.COMPILER_SHARED_OPTION_MAP[opt] in flags)
                     else:
                         self.assertTrue(tc.COMPILER_SHARED_OPTION_MAP[opt] in flags)
+                modules.modules_tool().purge()
 
     def test_optimization_flags_combos(self):
         """Test whether combining optimization levels works as expected."""
@@ -230,6 +232,7 @@ def test_optimization_flags_combos(self):
             flags = tc.get_variable(var)
             flag = '-%s' % tc.COMPILER_SHARED_OPTION_MAP['lowopt']
             self.assertTrue(flag in flags)
+        modules.modules_tool().purge()
 
         tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
         tc.set_options({'noopt': True, 'lowopt':True})
@@ -238,6 +241,7 @@ def test_optimization_flags_combos(self):
             flags = tc.get_variable(var)
             flag = '-%s' % tc.COMPILER_SHARED_OPTION_MAP['noopt']
             self.assertTrue(flag in flags)
+        modules.modules_tool().purge()
 
         tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
         tc.set_options({'noopt':True, 'lowopt': True, 'opt':True})
@@ -266,6 +270,7 @@ def test_misc_flags_shared(self):
                         self.assertTrue(flag in flags, "%s: True means %s in %s" % (opt, flag, flags))
                     else:
                         self.assertTrue(flag not in flags, "%s: False means no %s in %s" % (opt, flag, flags))
+                modules.modules_tool().purge()
 
     def test_misc_flags_unique(self):
         """Test whether unique compiler flags are set correctly."""
@@ -285,6 +290,7 @@ def test_misc_flags_unique(self):
                         self.assertTrue(flag in flags, "%s: True means %s in %s" % (opt, flag, flags))
                     else:
                         self.assertTrue(flag not in flags, "%s: False means no %s in %s" % (opt, flag, flags))
+                modules.modules_tool().purge()
 
     def test_override_optarch(self):
         """Test whether overriding the optarch flag works."""
@@ -308,6 +314,7 @@ def test_override_optarch(self):
                         self.assertTrue(flag in flags, "optarch: True means %s in %s" % (flag, flags))
                     else:
                         self.assertFalse(flag in flags, "optarch: False means no %s in %s" % (flag, flags))
+                modules.modules_tool().purge()
 
     def test_misc_flags_unique_fortran(self):
         """Test whether unique Fortran compiler flags are set correctly."""
@@ -327,6 +334,7 @@ def test_misc_flags_unique_fortran(self):
                         self.assertTrue(flag in flags, "%s: True means %s in %s" % (opt, flag, flags))
                     else:
                         self.assertTrue(flag not in flags, "%s: False means no %s in %s" % (opt, flag, flags))
+                modules.modules_tool().purge()
 
     def test_precision_flags(self):
         """Test whether precision flags are being set correctly."""
@@ -354,6 +362,7 @@ def test_precision_flags(self):
                         self.assertTrue(val in flags)
                     else:
                         self.assertTrue(val not in flags)
+                modules.modules_tool().purge()
 
     def test_cgoolf_toolchain(self):
         """Test for cgoolf toolchain."""
@@ -426,6 +435,7 @@ def test_ictce_toolchain(self):
         self.assertEqual(tc.get_variable('CXX'), 'icpc')
         self.assertEqual(tc.get_variable('F77'), 'ifort')
         self.assertEqual(tc.get_variable('F90'), 'ifort')
+        modules.modules_tool().purge()
 
         tc = self.get_toolchain("ictce", version="4.1.13")
         opts = {'usempi': True}
@@ -440,6 +450,7 @@ def test_ictce_toolchain(self):
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
         self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
+        modules.modules_tool().purge()
 
         tc = self.get_toolchain("ictce", version="4.1.13")
         opts = {'usempi': True, 'openmp': True}
@@ -463,6 +474,28 @@ def test_ictce_toolchain(self):
         shutil.rmtree(tmpdir)
         open(imkl_module_path, 'w').write(imkl_module_txt)
 
+    def test_toolchain_verification(self):
+        """Test verification of toolchain definition."""
+        tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
+        tc.prepare()
+        modules.modules_tool().purge()
+
+        # toolchain modules missing a toolchain element should fail verification
+        error_msg = "List of toolchain dependency modules and toolchain definition do not match"
+        tc = self.get_toolchain("goalf", version="1.1.0-no-OFED-brokenFFTW")
+        self.assertErrorRegex(EasyBuildError, error_msg, tc.prepare)
+        modules.modules_tool().purge()
+
+        tc = self.get_toolchain("goalf", version="1.1.0-no-OFED-brokenBLACS")
+        self.assertErrorRegex(EasyBuildError, error_msg, tc.prepare)
+        modules.modules_tool().purge()
+
+        # missing optional toolchain elements are fine
+        tc = self.get_toolchain('goolfc', version='1.3.12')
+        opts = {'cuda_gencode': ['arch=compute_35,code=sm_35', 'arch=compute_10,code=compute_10']}
+        tc.set_options(opts)
+        tc.prepare()
+
     def tearDown(self):
         """Cleanup."""
         # purge any loaded modules before restoring $MODULEPATH

From 839bed269503cbbe8268856528dba0e1c351bcf4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 22 Aug 2014 13:40:17 +0200
Subject: [PATCH 0093/1356] fix test_descr unit test w.r.t. spacing in
 'conflict' line

---
 test/framework/module_generator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index c101271674..cefed5274c 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -89,7 +89,7 @@ def test_descr(self):
             "",
             "set root    %s" % self.modgen.app.installdir,
             "",
-            "conflict    gzip",
+            "conflict gzip",
             "",
         ]) 
 

From 4a4fee05e80ef7f7eb3245e948253298cc57288c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 22 Aug 2014 13:47:19 +0200
Subject: [PATCH 0094/1356] get rid of module_software_name method in
 ModulesTool, verify toolchain definition vs loaded toolchain module
 differently

---
 easybuild/framework/easyblock.py       |  2 +-
 easybuild/tools/modules.py             | 16 -----------
 easybuild/tools/toolchain/toolchain.py | 40 +++++++++++++++++---------
 3 files changed, 28 insertions(+), 30 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 798267fe52..340427cb8a 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -792,7 +792,7 @@ def make_module_dep(self):
         # e.g. when unloading a module in a hierarchical naming scheme
         if self.toolchain.name != DUMMY_TOOLCHAIN_NAME:
             if ActiveMNS().expand_toolchain_load():
-                mod_names = self.toolchain.toolchain_dependencies
+                mod_names = self.toolchain.toolchain_dep_mods
             else:
                 mod_names = [self.toolchain.det_short_module_name()]
             for mod_name in mod_names:
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index e5956b10cd..33d4a5c060 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -445,10 +445,6 @@ def modulefile_path(self, mod_name):
         modpath_re = re.compile('^\s*(?P<modpath>[^/\n]*/[^ ]+):$', re.M)
         return self.get_value_from_modulefile(mod_name, modpath_re)
 
-    def module_software_name(self, mod_name):
-        """Get the software name for a given module name."""
-        raise NotImplementedError
-
     def set_ld_library_path(self, ld_library_paths):
         """Set $LD_LIBRARY_PATH to the given list of paths."""
         os.environ['LD_LIBRARY_PATH'] = ':'.join(ld_library_paths)
@@ -602,12 +598,6 @@ class EnvironmentModulesC(ModulesTool):
     REQ_VERSION = '3.2.10'
     VERSION_REGEXP = r'^\s*(VERSION\s*=\s*)?(?P<version>\d\S*)\s*'
 
-    def module_software_name(self, mod_name):
-        """Get the software name for a given module name."""
-        # line that specified conflict contains software name
-        name_re = re.compile('^conflict\s*(?P<name>\S+).*$', re.M)
-        return self.get_value_from_modulefile(mod_name, name_re)
-
     def update(self):
         """Update after new modules were added."""
         pass
@@ -748,12 +738,6 @@ def update(self):
             except (IOError, OSError), err:
                 self.log.error("Failed to update Lmod spider cache %s: %s" % (cache_filefn, err))
 
-    def module_software_name(self, mod_name):
-        """Get the software name for a given module name."""
-        # line that specified conflict contains software name
-        name_re = re.compile('^conflict\("*(?P<name>[^ "]+)"\).*$', re.M)
-        return self.get_value_from_modulefile(mod_name, name_re)
-
     def prepend_module_path(self, path):
         # Lmod pushes a path to the front on 'module use'
         self.use(path)
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 09920f6c94..ea48abae1b 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -32,7 +32,9 @@
 """
 
 import os
+import re
 from vsc.utils import fancylogger
+from vsc.utils.missing import all, any
 
 from easybuild.tools.config import build_option, install_path
 from easybuild.tools.environment import setvar
@@ -75,7 +77,7 @@ def __init__(self, name=None, version=None, mns=None):
         self.base_init()
 
         self.dependencies = []
-        self.toolchain_dependencies = []
+        self.toolchain_dep_mods = []
 
         if name is None:
             name = self.NAME
@@ -349,29 +351,41 @@ def prepare(self, onlymod=None):
 
         # determine direct toolchain dependencies
         mod_name = self.det_short_module_name()
-        self.toolchain_dependencies = self.modules_tool.dependencies_for(mod_name, depth=0)
-        self.log.debug('prepare: list of direct toolchain dependencies: %s' % self.toolchain_dependencies)
+        self.toolchain_dep_mods = self.modules_tool.dependencies_for(mod_name, depth=0)
+        self.log.debug('prepare: list of direct toolchain dependencies: %s' % self.toolchain_dep_mods)
 
-        # verify whether elements in toolchain definition match toolchain deps specified by loaded toolchain module
-        toolchain_module_deps = set([self.modules_tool.module_software_name(d) for d in self.toolchain_dependencies])
         # only retain names of toolchain elements, excluding toolchain name
         toolchain_definition = set([e for es in self.definition().values() for e in es if not e == self.name])
 
+        def tc_elem_present(name):
+            """Check whether the specified toolchain element is present in the loaded toolchain module."""
+            # check whether a module for the toolchain element with specified name is present
+            # assumption: the software name is a prefix for either one of the module filepath subdirs, or its filename
+            # for example, when looking for 'BLACS', to following modules are considered to be BLACS modules:
+            # - BLACS/1.1-gompi-1.1.0-no-OFED
+            # - apps/blacs/1.1
+            # - lib/math/BLACS-stable/1.1
+            # the following ones are NOT consider BLACS modules, even though the substring 'blacs' is included in the module name
+            # - ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1
+            # - apps/math-blacs/1.1
+            modname_regex = re.compile('(?:^|/)%s' % name.lower())
+            return any([modname_regex.search(m.lower()) for m in self.toolchain_dep_mods])
+
         # filter out optional toolchain elements if they're not used in the module
-        for mod_name in toolchain_definition.copy():
-            if not self.is_required(mod_name):
-                if not mod_name in toolchain_module_deps:
-                    self.log.debug("Removing optional module %s from list of toolchain elements." % mod_name)
-                    toolchain_definition.remove(mod_name)
+        for elem_name in toolchain_definition.copy():
+            if not self.is_required(elem_name):
+                if not tc_elem_present(elem_name):
+                    self.log.debug("Removing %s from list of optional toolchain elements." % elem_name)
+                    toolchain_definition.remove(elem_name)
 
-        self.log.debug("List of toolchain dependencies from toolchain module: %s" % toolchain_module_deps)
+        self.log.debug("List of toolchain dependencies from toolchain module: %s" % self.toolchain_dep_mods)
         self.log.debug("List of toolchain elements from toolchain definition: %s" % toolchain_definition)
 
-        if toolchain_module_deps == toolchain_definition:
+        if all([tc_elem_present(e) for e in toolchain_definition]):
             self.log.info("List of toolchain dependency modules and toolchain definition match!")
         else:
             self.log.error("List of toolchain dependency modules and toolchain definition do not match " \
-                           "(%s vs %s)" % (toolchain_module_deps, toolchain_definition))
+                           "(%s vs %s)" % (self.toolchain_dep_mods, toolchain_definition))
 
         # Generate the variables to be set
         self.set_variables()

From 03820bedfdfba9d22fd19568edc23d6fca0b04be Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 22 Aug 2014 16:27:16 +0200
Subject: [PATCH 0095/1356] fix minor remark wrt sorted imports

---
 easybuild/framework/easyblock.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 358a844f03..7f907651f1 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -55,8 +55,8 @@
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP
 from easybuild.tools.build_details import get_build_stats
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
-from easybuild.tools.config import build_path, get_log_filename, get_repository, get_repositorypath, install_path
-from easybuild.tools.config import log_path, read_only_installdir, source_paths, build_option, install_path
+from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
+from easybuild.tools.config import install_path, log_path, read_only_installdir, source_paths
 from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import DEFAULT_CHECKSUM
 from easybuild.tools.filetools import adjust_permissions, apply_patch, convert_name, download_file, encode_class_name

From 52057078d15e0838f07db4badea1311d4559acd4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 22 Aug 2014 23:14:44 +0200
Subject: [PATCH 0096/1356] add support for only (re)generating module file

---
 easybuild/framework/easyblock.py | 15 +++++++++++++--
 easybuild/main.py                |  1 +
 easybuild/tools/config.py        |  1 +
 easybuild/tools/options.py       |  1 +
 4 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 42cf3e6af5..0e442a0cbf 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1687,9 +1687,20 @@ def run_step(self, step, methods, skippable=False):
         """
         Run step, returns false when execution should be stopped
         """
-        if skippable and (self.skip or step in self.cfg['skipsteps']):
+        skip = False
+        # skip step if specified, either as individual (skippable) step, or when only generating module file
+        # still run sanity check when only generating module
+        skip_individual_step = skippable and (self.skip or step in self.cfg['skipsteps'])
+        only_module_skip = build_option('only_module') and not step in ['sanitycheck', 'module']
+        if skip_individual_step or only_module_skip:
             self.log.info("Skipping %s step" % step)
-        else:
+            skip = True
+        # allow skipping sanity check too when only generating module via --force
+        elif build_option('only_module') and step == 'sanitycheck' and build_option('force'):
+            self.log.info("Skipping %s step, due to combo of --only-module and --force" in ['sanitycheck'])
+            skip = True
+
+        if not skip:
             self.log.info("Starting %s step" % step)
             # update the config templates
             self.update_config_template_run_step()
diff --git a/easybuild/main.py b/easybuild/main.py
index acb69b15d4..965adadbff 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -251,6 +251,7 @@ def main(testing_data=(None, None, None)):
         'ignore_dirs': options.ignore_dirs,
         'modules_footer': options.modules_footer,
         'only_blocks': options.only_blocks,
+        'only_module': options.only_module,
         'optarch': options.optarch,
         'recursive_mod_unload': options.recursive_module_unload,
         'regtest_output_dir': options.regtest_output_dir,
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index d595b79803..b3cab8d3e8 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -86,6 +86,7 @@
     'ignore_dirs': None,
     'modules_footer': None,
     'only_blocks': None,
+    'only_module': None,
     'optarch': None,
     'recursive_mod_unload': False,
     'regtest_output_dir': None,
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ee44159a30..8060c51f3b 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -169,6 +169,7 @@ def override_options(self):
                             str, 'extend', None),
             'oldstyleconfig':   ("Look for and use the oldstyle configuration file.",
                                  None, 'store_true', True),
+            'only-module': ("Only (re)generate module file", None, 'store_true', False),
             'pretend': (("Does the build/installation in a test directory located in $HOME/easybuildinstall"),
                          None, 'store_true', False, 'p'),
             'set-gid-bit': ("Set group ID bit on newly created directories", None, 'store_true', False),

From 0fbae65de2f08809027b27a2dff4c5e274172cdd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 22 Aug 2014 23:36:23 +0200
Subject: [PATCH 0097/1356] improve error message generated for a missing
 easyconfig file

---
 easybuild/framework/easyconfig/easyconfig.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 094770d207..40497f507b 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1032,7 +1032,8 @@ def check_ec_type(self, ec):
                     self.log.debug("Full list of parsed easyconfigs: %s" % parsed_ec)
                 ec = parsed_ec[0]['ec']
             else:
-                self.log.error("Failed to find an easyconfig file when determining module name for: %s" % ec)
+                tup = (ec['name'], det_full_ec_version(ec), ec)
+                self.log.error("Failed to find easyconfig file '%s-%s.eb' when determining module name for: %s" % tup)
 
         return ec
 

From fd90cb2139308faa3b94d961dd83237815ebeb68 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 23 Aug 2014 21:51:20 +0200
Subject: [PATCH 0098/1356] make checking of module path extensions in
 make_module_dep symlink-safe

---
 easybuild/framework/easyblock.py | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 7f907651f1..6c41c73d52 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -46,6 +46,7 @@
 import traceback
 from distutils.version import LooseVersion
 from vsc.utils import fancylogger
+from vsc.utils.missing import any
 
 import easybuild.tools.environment as env
 from easybuild.tools import config, filetools
@@ -795,34 +796,35 @@ def make_module_dep(self):
         self.log.debug("Full list of dependencies: %s" % deps)
 
         # determine full module path extensions for each of the modules
-        modpaths = os.environ['MODULEPATH'].split(os.pathsep)
-        mod_install_path = os.path.join(install_path('mod'), build_option('suffix_modules_path')).rstrip(os.path.sep)
-        full_mod_subdir = os.path.join(mod_install_path, self.cfg.mod_subdir).rstrip(os.path.sep)
+        modpaths = [os.path.realpath(p) for p in os.environ['MODULEPATH'].split(os.pathsep) if os.path.exists(p)]
+        mod_install_path = os.path.realpath(os.path.join(install_path('mod'), build_option('suffix_modules_path')))
+        full_mod_subdir = os.path.join(mod_install_path, self.cfg.mod_subdir)
         all_modpath_exts = {}
-        if full_mod_subdir != mod_install_path:
+        if not os.path.samefile(full_mod_subdir, mod_install_path):
             for dep in deps:
                 all_modpath_exts.update({dep: []})
-                for full_modpath_ext in self.modules_tool.modpath_extensions_for(dep):
+                full_modpath_exts = [os.path.realpath(p) for p in self.modules_tool.modpath_extensions_for(dep)]
+                for full_modpath_ext in full_modpath_exts:
                     for modpath in modpaths:
-                        if full_modpath_ext.startswith(modpath):
+                        trimmed_modpath_ext = full_modpath_ext[:len(modpath)+1]
+                        if os.path.exists(trimmed_modpath_ext) and os.path.samefile(trimmed_modpath_ext, modpath):
                             modpath_ext = full_modpath_ext[len(modpath)+1:]
                             if modpath_ext:
                                 all_modpath_exts[dep].append(modpath_ext)
-            self.log.debug("Module path extensions for dependencies: %s" % all_modpath_exts)
+        self.log.debug("Module path extensions for dependencies: %s" % all_modpath_exts)
 
         # determine dependencies to exclude based on their $MODULEPATH extensions, recursively
         excluded_deps = []
         extended = True
-        while full_mod_subdir != mod_install_path and extended:
+        while extended and not os.path.samefile(full_mod_subdir, mod_install_path):
             extended = False
             self.log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
             for dep, modpath_exts in all_modpath_exts.items():
-                # if $MODULEPATH extension is identical to where this module will be installed, we have a hit
-                full_modpath_exts = [os.path.join(mod_install_path, e).rstrip(os.path.sep) for e in modpath_exts]
-                if full_mod_subdir in full_modpath_exts:
+                # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
+                if any([os.path.samefile(full_mod_subdir, os.path.join(mod_install_path, e)) for e in modpath_exts]):
                     # figure out module subdir for this dep, so we can recurse
                     modfile_path = self.modules_tool.modulefile_path(dep)
-                    full_mod_subdir = modfile_path[:-len(dep)].rstrip(os.path.sep)
+                    full_mod_subdir = modfile_path[:-len(dep)]
                     excluded_deps.append(dep)
                     extended = True
                     tup = (dep, full_mod_subdir, all_modpath_exts.pop(dep))

From 912c075d5b3abc19f9e7021394467c32a8a92c62 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 24 Aug 2014 14:48:23 +0200
Subject: [PATCH 0099/1356] add unit test for installing toolchain under
 HierarchicalMNS

---
 test/framework/toy_build.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 4fa3a16ae6..3268b813a1 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -44,6 +44,7 @@
 import easybuild.tools.module_naming_scheme  # required to dynamically load test module naming scheme(s)
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import mkdir, read_file, write_file
+from easybuild.tools.modules import modules_tool
 
 
 class ToyBuildTest(EnhancedTestCase):
@@ -521,6 +522,10 @@ def test_toy_hierarchical(self):
 
         mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
 
+        # make sure only modules in a hierarchical scheme are available, mixing modules installed with
+        # a flat scheme like EasyBuildMNS and a hierarhical one like HierarchicalMNS doesn't work
+        os.environ['MODULEPATH'] = os.path.join(mod_prefix, 'Core')
+
         # simply copy module files under 'Core' and 'Compiler' to test install path
         # EasyBuild is responsible for making sure that the toolchain can be loaded using the short module name
         mkdir(mod_prefix, parents=True)
@@ -649,6 +654,11 @@ def test_toy_hierarchical(self):
         self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
         os.remove(toy_module_path)
 
+        # building a toolchain module should also work
+        args = ['gompi-1.4.10.eb'] + args[1:]
+        modules_tool().purge()
+        self.eb_main(args, logfile=self.dummylogfn, do_build=True, verbose=True, raise_error=True)
+
     def test_toy_advanced(self):
         """Test toy build with extensions and non-dummy toolchain."""
         test_dir = os.path.abspath(os.path.dirname(__file__))

From 93c77231a6251ebcbe3a3e299a5a0cc4a09af18e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 24 Aug 2014 14:48:27 +0200
Subject: [PATCH 0100/1356] load dependencies one-by-one when determining
 $MODULEPATH extensions, simplify (and correct) code by checking extensions
 full path

---
 easybuild/framework/easyblock.py | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 6c41c73d52..5c6d7de66a 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -795,22 +795,21 @@ def make_module_dep(self):
 
         self.log.debug("Full list of dependencies: %s" % deps)
 
-        # determine full module path extensions for each of the modules
+        # determine full module path extensions for each of the dependency modules
         modpaths = [os.path.realpath(p) for p in os.environ['MODULEPATH'].split(os.pathsep) if os.path.exists(p)]
         mod_install_path = os.path.realpath(os.path.join(install_path('mod'), build_option('suffix_modules_path')))
         full_mod_subdir = os.path.join(mod_install_path, self.cfg.mod_subdir)
         all_modpath_exts = {}
         if not os.path.samefile(full_mod_subdir, mod_install_path):
+            modtool = modules_tool()
             for dep in deps:
-                all_modpath_exts.update({dep: []})
                 full_modpath_exts = [os.path.realpath(p) for p in self.modules_tool.modpath_extensions_for(dep)]
-                for full_modpath_ext in full_modpath_exts:
-                    for modpath in modpaths:
-                        trimmed_modpath_ext = full_modpath_ext[:len(modpath)+1]
-                        if os.path.exists(trimmed_modpath_ext) and os.path.samefile(trimmed_modpath_ext, modpath):
-                            modpath_ext = full_modpath_ext[len(modpath)+1:]
-                            if modpath_ext:
-                                all_modpath_exts[dep].append(modpath_ext)
+                all_modpath_exts.update({dep: full_modpath_exts})
+
+                # load this dependency, since it may extend $MODULEPATH to make other dependencies available,
+                # which is required to obtain the list of $MODULEPATH extensions they make (via 'show')
+                modtool.load([dep])
+
         self.log.debug("Module path extensions for dependencies: %s" % all_modpath_exts)
 
         # determine dependencies to exclude based on their $MODULEPATH extensions, recursively
@@ -819,9 +818,9 @@ def make_module_dep(self):
         while extended and not os.path.samefile(full_mod_subdir, mod_install_path):
             extended = False
             self.log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
-            for dep, modpath_exts in all_modpath_exts.items():
+            for dep, full_modpath_exts in all_modpath_exts.items():
                 # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
-                if any([os.path.samefile(full_mod_subdir, os.path.join(mod_install_path, e)) for e in modpath_exts]):
+                if any([os.path.samefile(full_mod_subdir, e) for e in full_modpath_exts]):
                     # figure out module subdir for this dep, so we can recurse
                     modfile_path = self.modules_tool.modulefile_path(dep)
                     full_mod_subdir = modfile_path[:-len(dep)]

From faafb2adef3eba3626459441a6d936980591c81f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 24 Aug 2014 20:06:03 +0200
Subject: [PATCH 0101/1356] only use 'show' for hidden modules

---
 easybuild/tools/modules.py | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index e5956b10cd..abbf47b15f 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -337,20 +337,13 @@ def exist(self, mod_names):
         """
         Check if modules with specified names exists.
         """
-        # resort to use 'show' for short lists of module names (3 or less)
-        use_show = False
-        avail_mod_names = None
-        if len(mod_names) <= 3:
-            use_show = True
-        else:
-            avail_mod_names = self.available()
-
+        avail_mod_names = self.available()
         # differentiate between hidden and visible modules
         mod_names = [(mod_name, not os.path.basename(mod_name).startswith('.')) for mod_name in mod_names]
 
         mods_exist = []
         for (mod_name, visible) in mod_names:
-            if visible and not use_show:
+            if visible:
                 mods_exist.append(mod_name in avail_mod_names)
             else:
                 # hidden modules are not visible in 'avail', need to use 'show' instead

From 4e4bbdb03d9f5b00278bb9c9fbe07d355122ade8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 25 Aug 2014 11:12:27 +0200
Subject: [PATCH 0102/1356] fix bug causing --from-pr to crash hard unless
 --robot is used

---
 easybuild/framework/easyblock.py | 2 +-
 easybuild/main.py                | 4 +---
 easybuild/tools/options.py       | 2 +-
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 42cf3e6af5..03025fd5d8 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -473,7 +473,7 @@ def obtain_file(self, filename, extension=False, urls=None):
 
             # always consider robot + easyconfigs install paths as a fall back (e.g. for patch files, test cases, ...)
             common_filepaths = []
-            if self.robot_path is not None:
+            if self.robot_path:
                 common_filepaths.extend(self.robot_path)
             common_filepaths.extend(get_paths_for("easyconfigs", robot_path=self.robot_path))
 
diff --git a/easybuild/main.py b/easybuild/main.py
index acb69b15d4..4697653f37 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -188,7 +188,7 @@ def main(testing_data=(None, None, None)):
             _log.error("No robot paths specified, and unable to determine easybuild-easyconfigs install path.")
 
     # do not pass options.robot, it's not a list instance (and it shouldn't be modified)
-    robot_path = None
+    robot_path = []
     if options.robot:
         robot_path = list(options.robot)
 
@@ -206,8 +206,6 @@ def main(testing_data=(None, None, None)):
     # specified robot paths are preferred over installed easyconfig files
     # --try-X and --dep-graph both require --robot, so enable it with path of installed easyconfigs
     if robot_path or try_to_generate or options.dep_graph:
-        if robot_path is None:
-            robot_path = []
         robot_path.extend(easyconfigs_paths)
         easyconfigs_paths = robot_path[:]
         _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ee44159a30..099879b796 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -84,7 +84,7 @@ def basic_options(self):
             default_robot_path = get_paths_for("easyconfigs", robot_path=None)[0]
         except:
             self.log.warning("basic_options: unable to determine default easyconfig path")
-            default_robot_path = False  # False as opposed to None, since None is used for indicating that --robot was not used
+            default_robot_path = False  # False as opposed to None, since None is used for indicating that --robot was used
 
         descr = ("Basic options", "Basic runtime options for EasyBuild.")
 

From 14148255a569548e27a61dfbd82be5295d518585 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 25 Aug 2014 15:38:26 +0200
Subject: [PATCH 0103/1356] fix checking whether --robot was used in
 robot_find_easyconfig

---
 easybuild/framework/easyconfig/easyconfig.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 40497f507b..c46c2d2662 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -978,9 +978,9 @@ def robot_find_easyconfig(name, version):
         _log.debug("Obtained easyconfig path from cache for %s: %s" % (key, _easyconfig_files_cache[key]))
         return _easyconfig_files_cache[key]
     paths = build_option('robot_path')
+    if not paths:
+        _log.error("No robot path specified, which is required when looking for easyconfigs (use --robot)")
     if not isinstance(paths, (list, tuple)):
-        if paths is None:
-            _log.error("No robot path specified, which is required when looking for easyconfigs (use --robot)")
         paths = [paths]
     # candidate easyconfig paths
     for path in paths:

From 9badf958a6d027337b2a5ea44424b0cedc7ddc92 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 25 Aug 2014 17:20:57 +0200
Subject: [PATCH 0104/1356] fix remarks

---
 easybuild/framework/easyblock.py | 15 ++++++++++++++-
 easybuild/tools/modules.py       |  2 +-
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 5c6d7de66a..0b8ee98c50 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -813,6 +813,14 @@ def make_module_dep(self):
         self.log.debug("Module path extensions for dependencies: %s" % all_modpath_exts)
 
         # determine dependencies to exclude based on their $MODULEPATH extensions, recursively
+        # example, when building HPL/2.1 with gompi toolchain in a Core/Compiler/MPI hierarchy:
+        # before start of while loop: full_mod_subdir for HPL/2.1 == 'MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.4'
+        # 1st iteration: find & exclude module that extends $MODULEPATH with MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.4,
+        #                => OpenMPI/1.6.4 (in 'Compiler/GCC/4.8.2' subdir);
+        #                recurse with full_mod_subdir = 'Compiler/GCC/4.8.2'
+        # 2nd iteration: find & exclude module that extends $MODULEPATH with Compiler/GCC/4.8.2
+        #                => GCC/4.8.2 (in 'Core' subdir; recurse with full_mod_subdir = 'Core'
+        # 3rd iteration: try to find module that extends $MODULEPATH with Core => no such module, so exit while loop
         excluded_deps = []
         extended = True
         while extended and not os.path.samefile(full_mod_subdir, mod_install_path):
@@ -823,10 +831,15 @@ def make_module_dep(self):
                 if any([os.path.samefile(full_mod_subdir, e) for e in full_modpath_exts]):
                     # figure out module subdir for this dep, so we can recurse
                     modfile_path = self.modules_tool.modulefile_path(dep)
+                    # full path to module subdir is simply path to module file without (short) module name
                     full_mod_subdir = modfile_path[:-len(dep)]
+
+                    # mark dep as to-be-exlucded, and remove it from dict with all modpath exts, no longer relevant
                     excluded_deps.append(dep)
                     extended = True
-                    tup = (dep, full_mod_subdir, all_modpath_exts.pop(dep))
+                    dep_modpath_exts = all_modpath_exts.pop(dep)
+
+                    tup = (dep, full_mod_subdir, dep_modpath_exts)
                     self.log.debug("Excluded dependency %s (subdir: %s) with module path extensions %s" % tup)
                     break
 
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 4b4ce32db6..cf4507233f 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -578,7 +578,7 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
         Obtain a list of dependencies for the given module, determined recursively, up to a specified depth (optionally)
         """
         modtxt = self.read_module_file(mod_name)
-        loadregex = re.compile(r"^\s+module load\s+(.*)$", re.M)
+        loadregex = re.compile(r"^\s*module load\s+(.*)$", re.M)
         mods = loadregex.findall(modtxt)
 
         if depth > 0:

From a36bc8085d9f6399ecfd4c703491e69fc771873e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 25 Aug 2014 17:22:56 +0200
Subject: [PATCH 0105/1356] include 'hidden' in key for easyconfigs cache

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index c46c2d2662..3c48a45779 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -886,7 +886,7 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False,
     # only cache when no build specifications are involved (since those can't be part of a dict key)
     cache_key = None
     if build_specs is None:
-        cache_key = (path, validate, parse_only)
+        cache_key = (path, validate, hidden, parse_only)
         if cache_key in _easyconfigs_cache:
             return copy.deepcopy(_easyconfigs_cache[cache_key])
 

From 738ea032e7fe388a8d403caf57423cffd0ec8a6b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 14:27:34 +0200
Subject: [PATCH 0106/1356] fix remarks

---
 easybuild/framework/easyblock.py    | 25 +++++++------------------
 easybuild/tools/module_generator.py |  4 ++--
 easybuild/tools/modules.py          | 29 ++++++++++++++++++++++-------
 test/framework/module_generator.py  |  5 +++--
 4 files changed, 34 insertions(+), 29 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 0b8ee98c50..21a59f2908 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -140,9 +140,6 @@ def __init__(self, ec):
         if modules_footer_path is not None:
             self.modules_footer = read_file(modules_footer_path)
 
-        # recursive unloading in modules
-        self.recursive_mod_unload = build_option('recursive_mod_unload')
-
         # easyconfig for this application
         if isinstance(ec, EasyConfig):
             self.cfg = ec
@@ -747,7 +744,7 @@ def make_devel_module(self, create_in_builddir=False):
                     path = os.environ[key]
                     if os.path.isfile(path):
                         mod_name = path.rsplit(os.path.sep, 1)[-1]
-                        load_txt += mod_gen.load_module(mod_name, recursive_unload=self.recursive_mod_unload)
+                        load_txt += mod_gen.load_module(mod_name)
 
         if create_in_builddir:
             output_dir = self.builddir
@@ -796,20 +793,11 @@ def make_module_dep(self):
         self.log.debug("Full list of dependencies: %s" % deps)
 
         # determine full module path extensions for each of the dependency modules
-        modpaths = [os.path.realpath(p) for p in os.environ['MODULEPATH'].split(os.pathsep) if os.path.exists(p)]
-        mod_install_path = os.path.realpath(os.path.join(install_path('mod'), build_option('suffix_modules_path')))
+        mod_install_path = os.path.join(install_path('mod'), build_option('suffix_modules_path'))
         full_mod_subdir = os.path.join(mod_install_path, self.cfg.mod_subdir)
-        all_modpath_exts = {}
+        all_modpath_exts = None
         if not os.path.samefile(full_mod_subdir, mod_install_path):
-            modtool = modules_tool()
-            for dep in deps:
-                full_modpath_exts = [os.path.realpath(p) for p in self.modules_tool.modpath_extensions_for(dep)]
-                all_modpath_exts.update({dep: full_modpath_exts})
-
-                # load this dependency, since it may extend $MODULEPATH to make other dependencies available,
-                # which is required to obtain the list of $MODULEPATH extensions they make (via 'show')
-                modtool.load([dep])
-
+            all_modpath_exts = self.modules_tool.modpath_extensions_for(deps)
         self.log.debug("Module path extensions for dependencies: %s" % all_modpath_exts)
 
         # determine dependencies to exclude based on their $MODULEPATH extensions, recursively
@@ -828,6 +816,7 @@ def make_module_dep(self):
             self.log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
             for dep, full_modpath_exts in all_modpath_exts.items():
                 # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
+                # use os.path.samefile when comparing paths to avoid issues with resolved symlinks
                 if any([os.path.samefile(full_mod_subdir, e) for e in full_modpath_exts]):
                     # figure out module subdir for this dep, so we can recurse
                     modfile_path = self.modules_tool.modulefile_path(dep)
@@ -845,8 +834,8 @@ def make_module_dep(self):
 
         deps = [d for d in deps if d not in excluded_deps]
         self.log.debug("List of retained dependencies: %s" % deps)
-        loads = [self.moduleGenerator.load_module(d, recursive_unload=self.recursive_mod_unload) for d in deps]
-        unloads = [self.moduleGenerator.unload_module(d) for d in deps]
+        loads = [self.moduleGenerator.load_module(d) for d in deps]
+        unloads = [self.moduleGenerator.unload_module(d) for d in deps[::-1]]
 
         # Force unloading any other modules
         if self.cfg['moduleforceunload']:
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 40553d1915..8d3d2a47ea 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -134,11 +134,11 @@ def get_description(self, conflict=True):
 
         return txt
 
-    def load_module(self, mod_name, recursive_unload=False):
+    def load_module(self, mod_name):
         """
         Generate load statements for module.
         """
-        if recursive_unload:
+        if build_option('recursive_mod_unload'):
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the depedency "module load" is present,
             # it will get translated to "module unload"
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index cf4507233f..9540cdc94a 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -572,10 +572,10 @@ def read_module_file(self, mod_name):
 
         return read_file(modfilepath)
 
-    # depth=sys.maxint should be equivalent to infinite recursion depth
     def dependencies_for(self, mod_name, depth=sys.maxint):
         """
         Obtain a list of dependencies for the given module, determined recursively, up to a specified depth (optionally)
+        @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
         """
         modtxt = self.read_module_file(mod_name)
         loadregex = re.compile(r"^\s*module load\s+(.*)$", re.M)
@@ -596,15 +596,30 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
 
         return mods
 
-    def modpath_extensions_for(self, mod_name):
+    def modpath_extensions_for(self, mod_names):
         """
-        Determine list of $MODULEPATH extensions for specified module.
+        Determine dictionary with $MODULEPATH extensions for specified modules.
         """
-        modtxt = self.read_module_file(mod_name)
-        useregex = re.compile(r"^\s*module use\s+(.*)$", re.M)
-        exts = useregex.findall(modtxt)
+        # copy environment so we can restore it
+        orig_env = os.environ.copy()
+
+        modpath_exts = {}
+        for mod_name in mod_names:
+            modtxt = self.read_module_file(mod_name)
+            useregex = re.compile(r"^\s*module use\s+(.*)$", re.M)
+            exts = useregex.findall(modtxt)
+
+            modpath_exts.update({mod_name: exts})
+
+            # load this module, since it may extend $MODULEPATH to make other modules available
+            # this is required to obtain the list of $MODULEPATH extensions they make (via 'show')
+            self.load([mod_name])
+
+        # purge loaded modules and restore original environment
+        self.purge()
+        modify_env(os.environ, orig_env)
 
-        return exts
+        return modpath_exts
 
     def update(self):
         """Update after new modules were added."""
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index c101271674..e7b00db95f 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -46,7 +46,7 @@
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS
 from easybuild.tools.build_log import EasyBuildError
-from test.framework.utilities import find_full_path
+from test.framework.utilities import find_full_path, init_config
 
 
 class ModuleGeneratorTest(EnhancedTestCase):
@@ -108,12 +108,13 @@ def test_load(self):
         self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
 
         # with recursive unloading: no if is-loaded guard
+        init_config(build_options={'recursive_mod_unload': True})
         expected = [
             "",
             "module load mod_name",
             "",
         ]
-        self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name", recursive_unload=True))
+        self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
 
     def test_unload(self):
         """Test unload part in generated module file."""

From 2ba3a6681560d9895ee3c6a9cce19d5f5618f47f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 17:32:22 +0200
Subject: [PATCH 0107/1356] fix remarks

---
 .../module_naming_scheme/hierarchical_mns.py  | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index bbf1e6d7e8..e8cfffc577 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -40,6 +40,9 @@
 COMPILER = 'Compiler'
 MPI = 'MPI'
 
+MODULECLASS_COMPILER = 'compiler'
+MODULECLASS_MPI = 'mpi'
+
 
 class HierarchicalMNS(ModuleNamingScheme):
     """Class implementing an example hierarchical module naming scheme."""
@@ -124,24 +127,24 @@ def det_modpath_extensions(self, ec):
         modclass = ec['moduleclass']
 
         paths = []
-        if modclass == 'compiler':
+        if modclass == MODULECLASS_COMPILER:
             if ec['name'] in ['icc', 'ifort']:
                 compdir = 'intel'
             else:
                 compdir = ec['name']
             paths.append(os.path.join(COMPILER, compdir, ec['version']))
-        elif modclass == 'mpi':
+        elif modclass == MODULECLASS_MPI:
             tc_comps = det_toolchain_compilers(ec)
             tc_comp_info = self.det_toolchain_compilers_name_version(tc_comps)
-            if not tc_comp_info is None:
+            if tc_comp_info is None:
+                tup = (ec['toolchain'], ec['name'], ec['version'])
+                error_msg = ("No compiler available in toolchain %s used to install MPI library %s v%s, "
+                             "which is required by the active module naming scheme.") % tup
+                self.log.error(error_msg)
+            else:
                 tc_comp_name, tc_comp_ver = tc_comp_info
                 fullver = ec['version'] + ec['versionsuffix']
                 paths.append(os.path.join(MPI, tc_comp_name, tc_comp_ver, ec['name'], fullver))
-            else:
-                tup = (ec['toolchain'], ec['name'], ec['version'])
-                error_msg = "No compiler available in toolchain %s used to install MPI library %s v%s, " % tup
-                error_msg += "which is required by the active module naming scheme %s." % self.__class__.__name__
-                self.log.error(error_msg)
 
         return paths
 

From 53dd32dd5471a16529f6f6307655559e9956ecbd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 17:34:00 +0200
Subject: [PATCH 0108/1356] enhance unit tests to catch issues with
 HierarchicalMNS and Intel MPI

---
 test/framework/module_generator.py | 54 +++++++++++++++++++-----------
 1 file changed, 34 insertions(+), 20 deletions(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 8c5f9167c9..11c4d3ad89 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -343,7 +343,8 @@ def test_mod_name_validation(self):
 
     def test_hierarchical_mns(self):
         """Test hierarchical module naming scheme."""
-        ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
+
+        ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         all_stops = [x[0] for x in EasyBlock.get_steps()]
         build_options = {
             'check_osdeps': False,
@@ -351,33 +352,46 @@ def test_hierarchical_mns(self):
             'valid_stops': all_stops,
             'validate': False,
         }
+
+        def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
+            """Test whether active module naming scheme returns expected values."""
+            ec = EasyConfig(os.path.join(ecs_dir, ecfile))
+            self.assertEqual(ActiveMNS().det_full_module_name(ec), os.path.join(mod_subdir, short_modname))
+            self.assertEqual(ActiveMNS().det_short_module_name(ec), short_modname)
+            self.assertEqual(ActiveMNS().det_module_subdir(ec), mod_subdir)
+            self.assertEqual(ActiveMNS().det_modpath_extensions(ec), modpath_exts)
+            self.assertEqual(ActiveMNS().det_init_modulepaths(ec), init_modpaths)
+
         os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
         init_config(build_options=build_options)
 
-        ec = EasyConfig(os.path.join(ecs_dir, 'GCC-4.7.2.eb'))
-        self.assertEqual(ActiveMNS().det_full_module_name(ec), 'Core/GCC/4.7.2')
-        self.assertEqual(ActiveMNS().det_short_module_name(ec), 'GCC/4.7.2')
-        self.assertEqual(ActiveMNS().det_module_subdir(ec), 'Core')
-        self.assertEqual(ActiveMNS().det_modpath_extensions(ec), ['Compiler/GCC/4.7.2'])
-        self.assertEqual(ActiveMNS().det_init_modulepaths(ec), ['Core'])
-
-        ec = EasyConfig(os.path.join(ecs_dir, 'OpenMPI-1.6.4-GCC-4.7.2.eb'))
-        self.assertEqual(ActiveMNS().det_full_module_name(ec), 'Compiler/GCC/4.7.2/OpenMPI/1.6.4')
-        self.assertEqual(ActiveMNS().det_short_module_name(ec), 'OpenMPI/1.6.4')
-        self.assertEqual(ActiveMNS().det_module_subdir(ec), 'Compiler/GCC/4.7.2')
-        self.assertEqual(ActiveMNS().det_modpath_extensions(ec), ['MPI/GCC/4.7.2/OpenMPI/1.6.4'])
-        self.assertEqual(ActiveMNS().det_init_modulepaths(ec), ['Core'])
+        # format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions)
+        test_ecs = {
+            'GCC-4.7.2.eb': ('GCC/4.7.2', 'Core', ['Compiler/GCC/4.7.2'], ['Core']),
+            'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2', ['MPI/GCC/4.7.2/OpenMPI/1.6.4'], ['Core']),
+            'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5', 'MPI/GCC/4.7.2/OpenMPI/1.6.4', [], ['Core']),
+            'goolf-1.4.10.eb': ('goolf/1.4.10', 'Core', [], ['Core']),
+        }
+        for ecfile, mns_vals in test_ecs.items():
+            test_ec(ecfile, *mns_vals)
 
-        ec = EasyConfig(os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
-        self.assertEqual(ActiveMNS().det_full_module_name(ec), 'MPI/GCC/4.7.2/OpenMPI/1.6.4/gzip/1.5')
-        self.assertEqual(ActiveMNS().det_short_module_name(ec), 'gzip/1.5')
-        self.assertEqual(ActiveMNS().det_module_subdir(ec), 'MPI/GCC/4.7.2/OpenMPI/1.6.4')
-        self.assertEqual(ActiveMNS().det_modpath_extensions(ec), [])
-        self.assertEqual(ActiveMNS().det_init_modulepaths(ec), ['Core'])
+        # impi with dummy toolchain, which doesn't make sense in a hierarchical context
+        ec = EasyConfig(os.path.join(ecs_dir, 'impi-4.1.3.049.eb'))
+        self.assertErrorRegex(EasyBuildError, 'No compiler available.*MPI lib', ActiveMNS().det_modpath_extensions, ec)
 
         os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
         init_config(build_options=build_options)
 
+        test_ecs = {
+            'GCC-4.7.2.eb': ('GCC/4.7.2', '', [], []),
+            'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4-GCC-4.7.2', '', [], []),
+            'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5-goolf-1.4.10', '', [], []),
+            'goolf-1.4.10.eb': ('goolf/1.4.10', '', [], []),
+            'impi-4.1.3.049.eb': ('impi/4.1.3.049', '', [], []),
+        }
+        for ecfile, mns_vals in test_ecs.items():
+            test_ec(ecfile, *mns_vals)
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(ModuleGeneratorTest)

From 5243a8e3986630f75296c872c5793a25ff47fcfd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 17:34:42 +0200
Subject: [PATCH 0109/1356] add additional easyconfig for testing

---
 test/framework/easyconfigs/impi-4.1.3.049.eb | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 test/framework/easyconfigs/impi-4.1.3.049.eb

diff --git a/test/framework/easyconfigs/impi-4.1.3.049.eb b/test/framework/easyconfigs/impi-4.1.3.049.eb
new file mode 100644
index 0000000000..e55725a62a
--- /dev/null
+++ b/test/framework/easyconfigs/impi-4.1.3.049.eb
@@ -0,0 +1,19 @@
+name = 'impi'
+version = '4.1.3.049'
+
+homepage = 'http://software.intel.com/en-us/intel-mpi-library/'
+description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message
+ passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for
+ Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['l_mpi_p_%(version)s.tgz']
+
+dontcreateinstalldir = 'True'
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
+
+moduleclass = 'mpi'

From 4bbf634daa25b71609167006fc29822e892aaa06 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 18:18:33 +0200
Subject: [PATCH 0110/1356] fix test_generate_software_list after adding an
 extra test easyconfig

---
 test/framework/scripts.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 527b7e274a..b13cf8b3a9 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -66,13 +66,13 @@ def test_generate_software_list(self):
         out, ec = run_cmd(cmd, simple=False)
 
         # make sure output is kind of what we expect it to be
-        regex = r"Supported Packages \(11 "
+        regex = r"Supported Packages \(12 "
         self.assertTrue(re.search(regex, out), "Pattern '%s' found in output: %s" % (regex, out))
         per_letter = {
             'F': '1',  # FFTW
             'G': '4',  # GCC, gompi, goolf, gzip
             'H': '1',  # hwloc
-            'I': '1',  # ictce
+            'I': '2',  # ictce, impi
             'O': '2',  # OpenMPI, OpenBLAS
             'S': '1',  # ScaLAPACK
             'T': '1',  # toy

From 3cd0b0ede86e1c299749ccb6e76e3332cc62bd29 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 21:52:48 +0200
Subject: [PATCH 0111/1356] determine dependencies to exclude from generated
 module file using recursive ModulesTool method path_to_top_of_module_tree

---
 easybuild/framework/easyblock.py | 41 ++--------------------
 easybuild/tools/modules.py       | 58 +++++++++++++++++++++++++++++++-
 2 files changed, 60 insertions(+), 39 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 21a59f2908..c7c62345ba 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -765,12 +765,12 @@ def make_module_dep(self):
         Make the dependencies for the module file.
         """
         deps = []
+        mns = ActiveMNS()
 
         # include load statements for toolchain, either directly or for toolchain dependencies
         # purposely after dependencies which may be critical,
         # e.g. when unloading a module in a hierarchical naming scheme
         if self.toolchain.name != DUMMY_TOOLCHAIN_NAME:
-            mns = ActiveMNS()
             if mns.expand_toolchain_load():
                 mod_names = self.toolchain.toolchain_dependencies
                 deps.extend(mod_names)
@@ -792,45 +792,10 @@ def make_module_dep(self):
 
         self.log.debug("Full list of dependencies: %s" % deps)
 
-        # determine full module path extensions for each of the dependency modules
+        # exclude dependencies that form the path to the top of the module tree (if any)
         mod_install_path = os.path.join(install_path('mod'), build_option('suffix_modules_path'))
         full_mod_subdir = os.path.join(mod_install_path, self.cfg.mod_subdir)
-        all_modpath_exts = None
-        if not os.path.samefile(full_mod_subdir, mod_install_path):
-            all_modpath_exts = self.modules_tool.modpath_extensions_for(deps)
-        self.log.debug("Module path extensions for dependencies: %s" % all_modpath_exts)
-
-        # determine dependencies to exclude based on their $MODULEPATH extensions, recursively
-        # example, when building HPL/2.1 with gompi toolchain in a Core/Compiler/MPI hierarchy:
-        # before start of while loop: full_mod_subdir for HPL/2.1 == 'MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.4'
-        # 1st iteration: find & exclude module that extends $MODULEPATH with MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.4,
-        #                => OpenMPI/1.6.4 (in 'Compiler/GCC/4.8.2' subdir);
-        #                recurse with full_mod_subdir = 'Compiler/GCC/4.8.2'
-        # 2nd iteration: find & exclude module that extends $MODULEPATH with Compiler/GCC/4.8.2
-        #                => GCC/4.8.2 (in 'Core' subdir; recurse with full_mod_subdir = 'Core'
-        # 3rd iteration: try to find module that extends $MODULEPATH with Core => no such module, so exit while loop
-        excluded_deps = []
-        extended = True
-        while extended and not os.path.samefile(full_mod_subdir, mod_install_path):
-            extended = False
-            self.log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
-            for dep, full_modpath_exts in all_modpath_exts.items():
-                # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
-                # use os.path.samefile when comparing paths to avoid issues with resolved symlinks
-                if any([os.path.samefile(full_mod_subdir, e) for e in full_modpath_exts]):
-                    # figure out module subdir for this dep, so we can recurse
-                    modfile_path = self.modules_tool.modulefile_path(dep)
-                    # full path to module subdir is simply path to module file without (short) module name
-                    full_mod_subdir = modfile_path[:-len(dep)]
-
-                    # mark dep as to-be-exlucded, and remove it from dict with all modpath exts, no longer relevant
-                    excluded_deps.append(dep)
-                    extended = True
-                    dep_modpath_exts = all_modpath_exts.pop(dep)
-
-                    tup = (dep, full_mod_subdir, dep_modpath_exts)
-                    self.log.debug("Excluded dependency %s (subdir: %s) with module path extensions %s" % tup)
-                    break
+        excluded_deps = self.modules_tool.path_to_top_of_module_tree(self.cfg.short_mod_name, full_mod_subdir, deps)
 
         deps = [d for d in deps if d not in excluded_deps]
         self.log.debug("List of retained dependencies: %s" % deps)
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 9540cdc94a..4844ce147b 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -612,7 +612,7 @@ def modpath_extensions_for(self, mod_names):
             modpath_exts.update({mod_name: exts})
 
             # load this module, since it may extend $MODULEPATH to make other modules available
-            # this is required to obtain the list of $MODULEPATH extensions they make (via 'show')
+            # this is required to obtain the list of $MODULEPATH extensions they make (via 'module show')
             self.load([mod_name])
 
         # purge loaded modules and restore original environment
@@ -621,6 +621,62 @@ def modpath_extensions_for(self, mod_names):
 
         return modpath_exts
 
+    def path_to_top_of_module_tree(self, mod_name, full_mod_subdir, deps, modpath_exts=None):
+        """
+        Recursively determine path to the top of the module tree,
+        for given module, module subdir and list of $MODULEPATH extensions per dependency module.
+        """
+        # example, when building HPL/2.1 with gompi toolchain in a Core/Compiler/MPI hierarchy:
+        # before start of while loop: full_mod_subdir for HPL/2.1 == 'MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.4'
+        # 1st iteration: find & exclude module that extends $MODULEPATH with MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.4,
+        #                => OpenMPI/1.6.4 (in 'Compiler/GCC/4.8.2' subdir);
+        #                recurse with full_mod_subdir = 'Compiler/GCC/4.8.2'
+        # 2nd iteration: find & exclude module that extends $MODULEPATH with Compiler/GCC/4.8.2
+        #                => GCC/4.8.2 (in 'Core' subdir; recurse with full_mod_subdir = 'Core'
+        # 3rd iteration: try to find module that extends $MODULEPATH with Core => no such module, so exit while loop
+        # copy environment so we can restore it
+        orig_env = os.environ.copy()
+
+        path = []
+        if modpath_exts is None:
+            modpath_exts = self.modpath_extensions_for(deps)
+            _log.debug("Module path extensions for dependencies: %s" % modpath_exts)
+
+        _log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
+
+        for dep in deps:
+            # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
+            # use os.path.samefile when comparing paths to avoid issues with resolved symlinks
+            full_modpath_exts = modpath_exts[dep]
+            if any([os.path.samefile(full_mod_subdir, e) for e in full_modpath_exts]):
+                # figure out module subdir for this dep, so we can recurse
+                modfile_path = self.modulefile_path(dep)
+                # full path to module subdir is simply path to module file without (short) module name
+                full_mod_subdir = modfile_path[:-len(dep)-1]
+
+                path.append(dep)
+                tup = (dep, full_mod_subdir, modpath_exts[dep])
+                _log.debug("Excluded dependency %s (subdir: %s) with module path extensions %s" % tup)
+
+                break
+
+            # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
+            # this is required to obtain the corresponding module file paths (via 'module show')
+            self.load([dep])
+
+        # recurse if we've found another step up to the top; if not, we must have reached the top
+        if path:
+            _log.debug("Path to top from %s extended to %s, so recursing to find way to the top" % (mod_name, path))
+            path.extend(self.path_to_top_of_module_tree(path[-1], full_mod_subdir, deps, modpath_exts=modpath_exts))
+        else:
+            _log.debug("Path not extended, we must have reached the top of the module tree")
+
+        self.purge()
+        modify_env(os.environ, orig_env)
+
+        _log.debug("Path to top of module tree from %s: %s" % (mod_name, path))
+        return path
+
     def update(self):
         """Update after new modules were added."""
         raise NotImplementedError

From a54bd4041a3aa09319cf364d1ccf36b6f5512c15 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 21:53:28 +0200
Subject: [PATCH 0112/1356] add unit test for path_to_top_of_module_tree +
 factor out common code to test utilities module

---
 test/framework/modules.py   | 42 +++++++++++++++++++++++++++++++++++++
 test/framework/toy_build.py | 28 +------------------------
 test/framework/utilities.py | 34 +++++++++++++++++++++++++++++-
 3 files changed, 76 insertions(+), 28 deletions(-)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index ee97938ab8..6c8602101c 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -37,6 +37,7 @@
 from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader, main
 
+from easybuild.framework.easyblock import EasyBlock
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.modules import get_software_root, get_software_version, get_software_libdir, modules_tool
 
@@ -245,6 +246,47 @@ def test_wrong_modulepath(self):
         self.assertEqual(modtool.mod_paths[1], test_modules_path)
         self.assertTrue(len(modtool.available()) > 0)
 
+    def test_path_to_top_of_module_tree(self):
+        """Test function to determine path to top of the module tree."""
+
+        modtool = modules_tool()
+
+        path = modtool.path_to_top_of_module_tree('gompi/1.3.12', '', ['GCC/4.6.4', 'OpenMPI/1.6.4-GCC-4.6.4'])
+        self.assertEqual(path, [])
+        path = modtool.path_to_top_of_module_tree('toy/.0.0-deps', '', ['gompi/1.3.12'])
+        self.assertEqual(path, [])
+        path = modtool.path_to_top_of_module_tree('toy/0.0', '', [])
+        self.assertEqual(path, [])
+
+        ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
+        all_stops = [x[0] for x in EasyBlock.get_steps()]
+        build_options = {
+            'check_osdeps': False,
+            'robot_path': [ecs_dir],
+            'valid_stops': all_stops,
+            'validate': False,
+        }
+        os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
+        init_config(build_options=build_options)
+        self.setup_hierarchical_modules()
+        modtool = modules_tool()
+        mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
+
+        deps = ['GCC/4.7.2', 'OpenMPI/1.6.4', 'FFTW/3.3.3', 'OpenBLAS/0.2.6-LAPACK-3.4.2',
+                'ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2']
+        path = modtool.path_to_top_of_module_tree('goolf/1.4.10', os.path.join(mod_prefix, 'Core'), deps)
+        self.assertEqual(path, [])
+        path = modtool.path_to_top_of_module_tree('GCC/4.7.2', os.path.join(mod_prefix, 'Core'), [])
+        self.assertEqual(path, [])
+        full_mod_subdir = os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2')
+        deps = ['GCC/4.7.2', 'hwloc/1.6.2']
+        path = modtool.path_to_top_of_module_tree('OpenMPI/1.6.4', full_mod_subdir, deps) 
+        self.assertEqual(path, ['GCC/4.7.2'])
+        full_mod_subdir = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
+        deps = ['GCC/4.7.2', 'OpenMPI/1.6.4']
+        path = modtool.path_to_top_of_module_tree('FFTW/3.3.3', full_mod_subdir, deps) 
+        self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(ModulesTest)
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 3268b813a1..56c66876b9 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -27,7 +27,6 @@
 
 @author: Kenneth Hoste (Ghent University)
 """
-import fileinput
 import glob
 import grp
 import os
@@ -520,34 +519,9 @@ def test_allow_system_deps(self):
     def test_toy_hierarchical(self):
         """Test toy build under example hierarchical module naming scheme."""
 
+        self.setup_hierarchical_modules()
         mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
 
-        # make sure only modules in a hierarchical scheme are available, mixing modules installed with
-        # a flat scheme like EasyBuildMNS and a hierarhical one like HierarchicalMNS doesn't work
-        os.environ['MODULEPATH'] = os.path.join(mod_prefix, 'Core')
-
-        # simply copy module files under 'Core' and 'Compiler' to test install path
-        # EasyBuild is responsible for making sure that the toolchain can be loaded using the short module name
-        mkdir(mod_prefix, parents=True)
-        for mod_subdir in ['Core', 'Compiler', 'MPI']:
-            src_mod_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'modules', mod_subdir)
-            shutil.copytree(src_mod_path, os.path.join(mod_prefix, mod_subdir))
-
-        # tweak use statements in GCC/OpenMPI modules to ensure correct paths
-        mpi_pref = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
-        for modfile in [
-            os.path.join(mod_prefix, 'Core', 'GCC', '4.7.2'),
-            os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'),
-            os.path.join(mpi_pref, 'FFTW', '3.3.3'),
-            os.path.join(mpi_pref, 'OpenBLAS', '0.2.6-LAPACK-3.4.2'),
-            os.path.join(mpi_pref, 'ScaLAPACK', '2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2'),
-        ]:
-            for line in fileinput.input(modfile, inplace=1):
-                line = re.sub(r"(module\s*use\s*)/tmp/modules/all",
-                              r"\1%s/modules/all" % self.test_installpath,
-                              line)
-                sys.stdout.write(line)
-
         args = [
             os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb'),
             '--sourcepath=%s' % self.test_sourcepath,
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 5674f4e4fc..db69e96eb5 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -28,6 +28,7 @@
 @author: Kenneth Hoste (Ghent University)
 """
 import copy
+import fileinput
 import os
 import re
 import shutil
@@ -46,7 +47,7 @@
 from easybuild.tools import config
 from easybuild.tools.config import module_classes
 from easybuild.tools.environment import modify_env
-from easybuild.tools.filetools import read_file
+from easybuild.tools.filetools import mkdir, read_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.modules import modules_tool
 
@@ -172,6 +173,36 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
         else:
             return read_file(self.logfile)
 
+    def setup_hierarchical_modules(self):
+        """Setup hierarchical modules to run tests on."""
+        mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
+
+        # make sure only modules in a hierarchical scheme are available, mixing modules installed with
+        # a flat scheme like EasyBuildMNS and a hierarhical one like HierarchicalMNS doesn't work
+        os.environ['MODULEPATH'] = os.path.join(mod_prefix, 'Core')
+
+        # simply copy module files under 'Core' and 'Compiler' to test install path
+        # EasyBuild is responsible for making sure that the toolchain can be loaded using the short module name
+        mkdir(mod_prefix, parents=True)
+        for mod_subdir in ['Core', 'Compiler', 'MPI']:
+            src_mod_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'modules', mod_subdir)
+            shutil.copytree(src_mod_path, os.path.join(mod_prefix, mod_subdir))
+
+        # tweak use statements in GCC/OpenMPI modules to ensure correct paths
+        mpi_pref = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
+        for modfile in [
+            os.path.join(mod_prefix, 'Core', 'GCC', '4.7.2'),
+            os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'),
+            os.path.join(mpi_pref, 'FFTW', '3.3.3'),
+            os.path.join(mpi_pref, 'OpenBLAS', '0.2.6-LAPACK-3.4.2'),
+            os.path.join(mpi_pref, 'ScaLAPACK', '2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2'),
+        ]:
+            for line in fileinput.input(modfile, inplace=1):
+                line = re.sub(r"(module\s*use\s*)/tmp/modules/all",
+                              r"\1%s/modules/all" % self.test_installpath,
+                              line)
+                sys.stdout.write(line)
+
 
 def cleanup():
     """Perform cleanup of singletons and caches."""
@@ -205,6 +236,7 @@ def init_config(args=None, build_options=None):
 
     return eb_go.options
 
+
 def find_full_path(base_path, trim=(lambda x: x)):
     """
     Determine full path for given base path by looking in sys.path and PYTHONPATH.

From e21ca4758dd5e5cdcb723911a4a27e8cd31ec997 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 22:19:45 +0200
Subject: [PATCH 0113/1356] add check for top of module tree in
 path_to_top_of_module_tree

---
 easybuild/framework/easyblock.py |  5 +++-
 easybuild/tools/modules.py       | 51 ++++++++++++++++++--------------
 2 files changed, 32 insertions(+), 24 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index c7c62345ba..9b9ca88986 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -795,7 +795,10 @@ def make_module_dep(self):
         # exclude dependencies that form the path to the top of the module tree (if any)
         mod_install_path = os.path.join(install_path('mod'), build_option('suffix_modules_path'))
         full_mod_subdir = os.path.join(mod_install_path, self.cfg.mod_subdir)
-        excluded_deps = self.modules_tool.path_to_top_of_module_tree(self.cfg.short_mod_name, full_mod_subdir, deps)
+        init_modpaths = mns.det_init_modulepaths(self.cfg)
+        top_paths = [mod_install_path] + [os.path.join(mod_install_path, p) for p in init_modpaths]
+        excluded_deps = self.modules_tool.path_to_top_of_module_tree(top_paths, self.cfg.short_mod_name,
+                                                                     full_mod_subdir, deps)
 
         deps = [d for d in deps if d not in excluded_deps]
         self.log.debug("List of retained dependencies: %s" % deps)
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 4844ce147b..4f98bc3e1a 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -621,7 +621,7 @@ def modpath_extensions_for(self, mod_names):
 
         return modpath_exts
 
-    def path_to_top_of_module_tree(self, mod_name, full_mod_subdir, deps, modpath_exts=None):
+    def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps, modpath_exts=None):
         """
         Recursively determine path to the top of the module tree,
         for given module, module subdir and list of $MODULEPATH extensions per dependency module.
@@ -644,36 +644,41 @@ def path_to_top_of_module_tree(self, mod_name, full_mod_subdir, deps, modpath_ex
 
         _log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
 
-        for dep in deps:
-            # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
-            # use os.path.samefile when comparing paths to avoid issues with resolved symlinks
-            full_modpath_exts = modpath_exts[dep]
-            if any([os.path.samefile(full_mod_subdir, e) for e in full_modpath_exts]):
-                # figure out module subdir for this dep, so we can recurse
-                modfile_path = self.modulefile_path(dep)
-                # full path to module subdir is simply path to module file without (short) module name
-                full_mod_subdir = modfile_path[:-len(dep)-1]
-
-                path.append(dep)
-                tup = (dep, full_mod_subdir, modpath_exts[dep])
-                _log.debug("Excluded dependency %s (subdir: %s) with module path extensions %s" % tup)
-
-                break
+        mod_install_path = os.path.join(install_path('mod'), build_option('suffix_modules_path'))
+        if any([os.path.samefile(full_mod_subdir, p) for p in top_paths]):
+            self.log.debug("Top of module tree reached with %s (module subdir: %s)" % (mod_name, full_mod_subdir))
+        else:
+            for dep in deps:
+                # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
+                # use os.path.samefile when comparing paths to avoid issues with resolved symlinks
+                full_modpath_exts = modpath_exts[dep]
+                if any([os.path.samefile(full_mod_subdir, e) for e in full_modpath_exts]):
+                    # figure out module subdir for this dep, so we can recurse
+                    modfile_path = self.modulefile_path(dep)
+                    # full path to module subdir is simply path to module file without (short) module name
+                    full_mod_subdir = modfile_path[:-len(dep)-1]
+
+                    path.append(dep)
+                    tup = (dep, full_mod_subdir, modpath_exts[dep])
+                    _log.debug("Excluded dependency %s (subdir: %s) with module path extensions %s" % tup)
+
+                    break
+
+                # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
+                # this is required to obtain the corresponding module file paths (via 'module show')
+                self.load([dep])
 
-            # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
-            # this is required to obtain the corresponding module file paths (via 'module show')
-            self.load([dep])
+            self.purge()
+            modify_env(os.environ, orig_env)
 
         # recurse if we've found another step up to the top; if not, we must have reached the top
         if path:
             _log.debug("Path to top from %s extended to %s, so recursing to find way to the top" % (mod_name, path))
-            path.extend(self.path_to_top_of_module_tree(path[-1], full_mod_subdir, deps, modpath_exts=modpath_exts))
+            path.extend(self.path_to_top_of_module_tree(top_paths, path[-1], full_mod_subdir, deps,
+                                                        modpath_exts=modpath_exts))
         else:
             _log.debug("Path not extended, we must have reached the top of the module tree")
 
-        self.purge()
-        modify_env(os.environ, orig_env)
-
         _log.debug("Path to top of module tree from %s: %s" % (mod_name, path))
         return path
 

From c3f0960d0b84a61f5783bd08b2ce29aa0e19f06e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 22:47:23 +0200
Subject: [PATCH 0114/1356] fix unit test for
 modtool.path_to_top_of_module_tree

---
 test/framework/modules.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 6c8602101c..02bc379318 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -251,11 +251,11 @@ def test_path_to_top_of_module_tree(self):
 
         modtool = modules_tool()
 
-        path = modtool.path_to_top_of_module_tree('gompi/1.3.12', '', ['GCC/4.6.4', 'OpenMPI/1.6.4-GCC-4.6.4'])
+        path = modtool.path_to_top_of_module_tree([], 'gompi/1.3.12', '', ['GCC/4.6.4', 'OpenMPI/1.6.4-GCC-4.6.4'])
         self.assertEqual(path, [])
-        path = modtool.path_to_top_of_module_tree('toy/.0.0-deps', '', ['gompi/1.3.12'])
+        path = modtool.path_to_top_of_module_tree([], 'toy/.0.0-deps', '', ['gompi/1.3.12'])
         self.assertEqual(path, [])
-        path = modtool.path_to_top_of_module_tree('toy/0.0', '', [])
+        path = modtool.path_to_top_of_module_tree([], 'toy/0.0', '', [])
         self.assertEqual(path, [])
 
         ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
@@ -271,20 +271,21 @@ def test_path_to_top_of_module_tree(self):
         self.setup_hierarchical_modules()
         modtool = modules_tool()
         mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
+        init_modpaths = [os.path.join(mod_prefix, 'Core')]
 
         deps = ['GCC/4.7.2', 'OpenMPI/1.6.4', 'FFTW/3.3.3', 'OpenBLAS/0.2.6-LAPACK-3.4.2',
                 'ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2']
-        path = modtool.path_to_top_of_module_tree('goolf/1.4.10', os.path.join(mod_prefix, 'Core'), deps)
+        path = modtool.path_to_top_of_module_tree(init_modpaths, 'goolf/1.4.10', os.path.join(mod_prefix, 'Core'), deps)
         self.assertEqual(path, [])
-        path = modtool.path_to_top_of_module_tree('GCC/4.7.2', os.path.join(mod_prefix, 'Core'), [])
+        path = modtool.path_to_top_of_module_tree(init_modpaths, 'GCC/4.7.2', os.path.join(mod_prefix, 'Core'), [])
         self.assertEqual(path, [])
         full_mod_subdir = os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2')
         deps = ['GCC/4.7.2', 'hwloc/1.6.2']
-        path = modtool.path_to_top_of_module_tree('OpenMPI/1.6.4', full_mod_subdir, deps) 
+        path = modtool.path_to_top_of_module_tree(init_modpaths, 'OpenMPI/1.6.4', full_mod_subdir, deps)
         self.assertEqual(path, ['GCC/4.7.2'])
         full_mod_subdir = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
         deps = ['GCC/4.7.2', 'OpenMPI/1.6.4']
-        path = modtool.path_to_top_of_module_tree('FFTW/3.3.3', full_mod_subdir, deps) 
+        path = modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
         self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
 
 def suite():

From 4720b5f32f9b6e3f3ae0867efd408d8b831396dd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Aug 2014 23:51:26 +0200
Subject: [PATCH 0115/1356] fix remarks

---
 easybuild/tools/modules.py | 81 +++++++++++++++++++++++++-------------
 1 file changed, 53 insertions(+), 28 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 4f98bc3e1a..87d2d07d45 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -599,6 +599,7 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
     def modpath_extensions_for(self, mod_names):
         """
         Determine dictionary with $MODULEPATH extensions for specified modules.
+        Modules with an empty list of $MODULEPATH extensions are included.
         """
         # copy environment so we can restore it
         orig_env = os.environ.copy()
@@ -611,9 +612,10 @@ def modpath_extensions_for(self, mod_names):
 
             modpath_exts.update({mod_name: exts})
 
-            # load this module, since it may extend $MODULEPATH to make other modules available
-            # this is required to obtain the list of $MODULEPATH extensions they make (via 'module show')
-            self.load([mod_name])
+            if exts:
+                # load this module, since it may extend $MODULEPATH to make other modules available
+                # this is required to obtain the list of $MODULEPATH extensions they make (via 'module show')
+                self.load([mod_name])
 
         # purge loaded modules and restore original environment
         self.purge()
@@ -625,43 +627,64 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
         """
         Recursively determine path to the top of the module tree,
         for given module, module subdir and list of $MODULEPATH extensions per dependency module.
-        """
-        # example, when building HPL/2.1 with gompi toolchain in a Core/Compiler/MPI hierarchy:
-        # before start of while loop: full_mod_subdir for HPL/2.1 == 'MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.4'
-        # 1st iteration: find & exclude module that extends $MODULEPATH with MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.4,
-        #                => OpenMPI/1.6.4 (in 'Compiler/GCC/4.8.2' subdir);
-        #                recurse with full_mod_subdir = 'Compiler/GCC/4.8.2'
-        # 2nd iteration: find & exclude module that extends $MODULEPATH with Compiler/GCC/4.8.2
-        #                => GCC/4.8.2 (in 'Core' subdir; recurse with full_mod_subdir = 'Core'
-        # 3rd iteration: try to find module that extends $MODULEPATH with Core => no such module, so exit while loop
-        # copy environment so we can restore it
-        orig_env = os.environ.copy()
 
+        For example, when to determine the path to the top of the module tree for the HPL/2.1 module being
+        installed with a goolf/1.5.14 toolchain in a Core/Compiler/MPI hierarchy (HierarchicalMNS):
+
+        * starting point:
+            top_paths = ['<prefix>', '<prefix>/Core']
+            mod_name = 'HPL/2.1'
+            full_mod_subdir = '<prefix>/MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.5'
+            deps = ['GCC/4.8.2', 'OpenMPI/1.6.5', 'OpenBLAS/0.2.8-LAPACK-3.5.0', 'FFTW/3.3.4', 'ScaLAPACK/...']
+
+        * 1st iteration: find module that extends $MODULEPATH with '<prefix>/MPI/Compiler/GCC/4.8.2/OpenMPI/1.6.5',
+                         => OpenMPI/1.6.5 (in '<prefix>/Compiler/GCC/4.8.2' subdir);
+                         recurse with mod_name = 'OpenMPI/1.6.5' and full_mod_subdir = '<prefix>/Compiler/GCC/4.8.2'
+
+        * 2nd iteration: find module that extends $MODULEPATH with '<prefix>/Compiler/GCC/4.8.2'
+                         => GCC/4.8.2 (in '<prefix>/Core' subdir);
+                         recurse with mod_name = 'GCC/4.8.2' and full_mod_subdir = '<prefix>/Core'
+
+        * 3rd iteration: try to find module that extends $MODULEPATH with '<prefix>/Core'
+                         => '<prefix>/Core' is in top_paths, so stop recursion
+
+        @param top_paths: list of potentation 'top of module tree' (absolute) paths
+        @param mod_name: (short) module name for starting point (only used in log messages)
+        @param full_mod_subdir: absolute path to module subdirectory for starting point
+        @param deps: list of dependency modules for module at starting point
+        @param modpath_exts: list of module path extensions for each of the dependency modules
+        """
         path = []
         if modpath_exts is None:
             modpath_exts = self.modpath_extensions_for(deps)
-            _log.debug("Module path extensions for dependencies: %s" % modpath_exts)
+            # only retain dependencies that have a non-empty lists of $MODULEPATH extensions
+            for dep in modpath_exts.keys():
+                if not modpath_exts[dep]:
+                    modpath_exts.pop(dep)
+            self.log.debug("Non-empty lists of module path extensions for dependencies: %s" % modpath_exts)
 
-        _log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
+        self.log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
 
         mod_install_path = os.path.join(install_path('mod'), build_option('suffix_modules_path'))
         if any([os.path.samefile(full_mod_subdir, p) for p in top_paths]):
             self.log.debug("Top of module tree reached with %s (module subdir: %s)" % (mod_name, full_mod_subdir))
         else:
-            for dep in deps:
+            # copy environment so we can restore it
+            orig_env = os.environ.copy()
+
+            for dep in modpath_exts:
                 # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
                 # use os.path.samefile when comparing paths to avoid issues with resolved symlinks
                 full_modpath_exts = modpath_exts[dep]
                 if any([os.path.samefile(full_mod_subdir, e) for e in full_modpath_exts]):
-                    # figure out module subdir for this dep, so we can recurse
-                    modfile_path = self.modulefile_path(dep)
-                    # full path to module subdir is simply path to module file without (short) module name
-                    full_mod_subdir = modfile_path[:-len(dep)-1]
+                    # full path to module subdir of dependency is simply path to module file without (short) module name
+                    full_mod_subdir = self.modulefile_path(dep)[:-len(dep)-1]
 
                     path.append(dep)
-                    tup = (dep, full_mod_subdir, modpath_exts[dep])
-                    _log.debug("Excluded dependency %s (subdir: %s) with module path extensions %s" % tup)
+                    tup = (dep, full_mod_subdir, full_modpath_exts)
+                    self.log.debug("Found module to top of module tree: %s (subdir: %s, modpath extensions %s)" % tup)
 
+                    # no need to continue further, we found the module that extends $MODULEPATH with module subdir
                     break
 
                 # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
@@ -671,15 +694,17 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
             self.purge()
             modify_env(os.environ, orig_env)
 
-        # recurse if we've found another step up to the top; if not, we must have reached the top
         if path:
-            _log.debug("Path to top from %s extended to %s, so recursing to find way to the top" % (mod_name, path))
-            path.extend(self.path_to_top_of_module_tree(top_paths, path[-1], full_mod_subdir, deps,
+            # remove retained dependency from the list, since we're climbing up the module tree
+            modpath_exts.pop(path[-1])
+
+            self.log.debug("Path to top from %s extended to %s, so recursing to find way to the top" % (mod_name, path))
+            path.extend(self.path_to_top_of_module_tree(top_paths, path[-1], full_mod_subdir, None,
                                                         modpath_exts=modpath_exts))
         else:
-            _log.debug("Path not extended, we must have reached the top of the module tree")
+            self.log.debug("Path not extended, we must have reached the top of the module tree")
 
-        _log.debug("Path to top of module tree from %s: %s" % (mod_name, path))
+        self.log.debug("Path to top of module tree from %s: %s" % (mod_name, path))
         return path
 
     def update(self):

From 46833b6e7ed3ff935af2a4bcd1ee202cf4361edf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 27 Aug 2014 00:07:01 +0200
Subject: [PATCH 0116/1356] fix remarks

---
 easybuild/tools/toolchain/toolchain.py | 39 +++++++++++++-------------
 1 file changed, 20 insertions(+), 19 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index ea48abae1b..184fddf58c 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -315,6 +315,20 @@ def definition(self):
         _log.debug("Toolchain definition for %s: %s" % (self.as_dict(), tc_elems))
         return tc_elems
 
+    def is_dep_in_toolchain_module(self, name):
+        """Check whether a specific software name is listed as a dependency in the module for this toolchain."""
+        # check whether a module for the toolchain element with specified name is present
+        # assumption: the software name is a prefix for either one of the module filepath subdirs, or its filename
+        # for example, when looking for 'BLACS', to following modules are considered to be BLACS modules:
+        # - BLACS/1.1-gompi-1.1.0-no-OFED
+        # - apps/blacs/1.1
+        # - lib/math/BLACS-stable/1.1
+        # the following ones are NOT consider BLACS modules, even though the substring 'blacs' is included in the module name
+        # - ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1
+        # - apps/math-blacs/1.1
+        modname_regex = re.compile('(?:^|/)%s' % name, re.I)
+        return any(map(modname_regex.search, self.toolchain_dep_mods))
+
     def prepare(self, onlymod=None):
         """
         Prepare a set of environment parameters based on name/version of toolchain
@@ -357,31 +371,18 @@ def prepare(self, onlymod=None):
         # only retain names of toolchain elements, excluding toolchain name
         toolchain_definition = set([e for es in self.definition().values() for e in es if not e == self.name])
 
-        def tc_elem_present(name):
-            """Check whether the specified toolchain element is present in the loaded toolchain module."""
-            # check whether a module for the toolchain element with specified name is present
-            # assumption: the software name is a prefix for either one of the module filepath subdirs, or its filename
-            # for example, when looking for 'BLACS', to following modules are considered to be BLACS modules:
-            # - BLACS/1.1-gompi-1.1.0-no-OFED
-            # - apps/blacs/1.1
-            # - lib/math/BLACS-stable/1.1
-            # the following ones are NOT consider BLACS modules, even though the substring 'blacs' is included in the module name
-            # - ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1
-            # - apps/math-blacs/1.1
-            modname_regex = re.compile('(?:^|/)%s' % name.lower())
-            return any([modname_regex.search(m.lower()) for m in self.toolchain_dep_mods])
-
         # filter out optional toolchain elements if they're not used in the module
         for elem_name in toolchain_definition.copy():
-            if not self.is_required(elem_name):
-                if not tc_elem_present(elem_name):
-                    self.log.debug("Removing %s from list of optional toolchain elements." % elem_name)
-                    toolchain_definition.remove(elem_name)
+            if self.is_required(elem_name) or self.is_dep_in_toolchain_module(elem_name):
+                continue
+            # not required and missing: remove from toolchain definition
+            self.log.debug("Removing %s from list of optional toolchain elements." % elem_name)
+            toolchain_definition.remove(elem_name)
 
         self.log.debug("List of toolchain dependencies from toolchain module: %s" % self.toolchain_dep_mods)
         self.log.debug("List of toolchain elements from toolchain definition: %s" % toolchain_definition)
 
-        if all([tc_elem_present(e) for e in toolchain_definition]):
+        if all(map(self.is_dep_in_toolchain_module, toolchain_definition)):
             self.log.info("List of toolchain dependency modules and toolchain definition match!")
         else:
             self.log.error("List of toolchain dependency modules and toolchain definition do not match " \

From 273fbaa724881ea6d7539275cbcc757983ec47bb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 29 Aug 2014 09:32:26 +0200
Subject: [PATCH 0117/1356] fix remark w.r.t. regex for 'module load'

---
 easybuild/tools/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 33d4a5c060..7389c2da23 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -569,7 +569,7 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
 
         modtxt = read_file(modfilepath)
 
-        loadregex = re.compile(r"^\s+module load\s+(.*)$", re.M)
+        loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
         mods = loadregex.findall(modtxt)
 
         if depth > 0:

From 1a557534d25a844cc5efc3a488e6610765b59380 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 29 Aug 2014 09:33:26 +0200
Subject: [PATCH 0118/1356] fix remark w.r.t. regex for 'module X'

---
 easybuild/tools/modules.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 87d2d07d45..d64ae93b3b 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -578,7 +578,7 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
         @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
         """
         modtxt = self.read_module_file(mod_name)
-        loadregex = re.compile(r"^\s*module load\s+(.*)$", re.M)
+        loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
         mods = loadregex.findall(modtxt)
 
         if depth > 0:
@@ -607,7 +607,7 @@ def modpath_extensions_for(self, mod_names):
         modpath_exts = {}
         for mod_name in mod_names:
             modtxt = self.read_module_file(mod_name)
-            useregex = re.compile(r"^\s*module use\s+(.*)$", re.M)
+            useregex = re.compile(r"^\s*module\s+use\s+(\S+)", re.M)
             exts = useregex.findall(modtxt)
 
             modpath_exts.update({mod_name: exts})

From 297ceec5392ee83ab349289358f18a345ed7c652 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 1 Sep 2014 12:30:47 +0200
Subject: [PATCH 0119/1356] fix remarks

---
 easybuild/framework/easyblock.py |  2 +-
 easybuild/tools/filetools.py     |  7 +++-
 easybuild/tools/modules.py       | 66 +++++++++++++++-----------------
 3 files changed, 38 insertions(+), 37 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 9b9ca88986..d4d913af62 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -792,7 +792,7 @@ def make_module_dep(self):
 
         self.log.debug("Full list of dependencies: %s" % deps)
 
-        # exclude dependencies that form the path to the top of the module tree (if any)
+        # exclude dependencies that extend $MODULEPATH and form the path to the top of the module tree (if any)
         mod_install_path = os.path.join(install_path('mod'), build_option('suffix_modules_path'))
         full_mod_subdir = os.path.join(mod_install_path, self.cfg.mod_subdir)
         init_modpaths = mns.det_init_modulepaths(self.cfg)
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index f15d93c060..91b417fddb 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -42,7 +42,7 @@
 import urllib
 import zlib
 from vsc.utils import fancylogger
-from vsc.utils.missing import all
+from vsc.utils.missing import all, any
 
 import easybuild.tools.environment as env
 from easybuild.tools.build_log import print_msg  # import build_log must stay, to activate use of EasyBuildLog
@@ -819,6 +819,11 @@ def mkdir(path, parents=False, set_gid=None, sticky=None):
         _log.debug("Not creating existing path %s" % path)
 
 
+def path_matches(path, paths):
+    """Check whether given path matches any of the provided paths."""
+    return any([os.path.samefile(path, p) for p in paths])
+
+
 def rmtree2(path, n=3):
     """Wrapper around shutil.rmtree to make it more robust when used on NFS mounted file systems."""
 
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index d64ae93b3b..6ad650608e 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -48,7 +48,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_modules_tool, install_path
 from easybuild.tools.environment import modify_env
-from easybuild.tools.filetools import convert_name, mkdir, read_file, which
+from easybuild.tools.filetools import convert_name, mkdir, read_file, path_matches, which
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.run import run_cmd
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
@@ -617,8 +617,7 @@ def modpath_extensions_for(self, mod_names):
                 # this is required to obtain the list of $MODULEPATH extensions they make (via 'module show')
                 self.load([mod_name])
 
-        # purge loaded modules and restore original environment
-        self.purge()
+        # restore original environment (modules may have been loaded above)
         modify_env(os.environ, orig_env)
 
         return modpath_exts
@@ -654,45 +653,39 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
         @param deps: list of dependency modules for module at starting point
         @param modpath_exts: list of module path extensions for each of the dependency modules
         """
-        path = []
-        if modpath_exts is None:
-            modpath_exts = self.modpath_extensions_for(deps)
-            # only retain dependencies that have a non-empty lists of $MODULEPATH extensions
-            for dep in modpath_exts.keys():
-                if not modpath_exts[dep]:
-                    modpath_exts.pop(dep)
-            self.log.debug("Non-empty lists of module path extensions for dependencies: %s" % modpath_exts)
-
-        self.log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
+        # copy environment so we can restore it
+        orig_env = os.environ.copy()
 
-        mod_install_path = os.path.join(install_path('mod'), build_option('suffix_modules_path'))
-        if any([os.path.samefile(full_mod_subdir, p) for p in top_paths]):
+        if path_matches(full_mod_subdir, top_paths):
             self.log.debug("Top of module tree reached with %s (module subdir: %s)" % (mod_name, full_mod_subdir))
-        else:
-            # copy environment so we can restore it
-            orig_env = os.environ.copy()
+            return []
 
-            for dep in modpath_exts:
-                # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
-                # use os.path.samefile when comparing paths to avoid issues with resolved symlinks
-                full_modpath_exts = modpath_exts[dep]
-                if any([os.path.samefile(full_mod_subdir, e) for e in full_modpath_exts]):
-                    # full path to module subdir of dependency is simply path to module file without (short) module name
-                    full_mod_subdir = self.modulefile_path(dep)[:-len(dep)-1]
+        self.log.debug("Checking for dependency that extends $MODULEPATH with %s" % full_mod_subdir)
 
-                    path.append(dep)
-                    tup = (dep, full_mod_subdir, full_modpath_exts)
-                    self.log.debug("Found module to top of module tree: %s (subdir: %s, modpath extensions %s)" % tup)
+        if modpath_exts is None:
+            # only retain dependencies that have a non-empty lists of $MODULEPATH extensions
+            modpath_exts = dict([(k, v) for k, v in self.modpath_extensions_for(deps).items() if v])
+            self.log.debug("Non-empty lists of module path extensions for dependencies: %s" % modpath_exts)
 
-                    # no need to continue further, we found the module that extends $MODULEPATH with module subdir
-                    break
+        path = []
+        for dep in modpath_exts:
+            # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
+            # use os.path.samefile when comparing paths to avoid issues with resolved symlinks
+            full_modpath_exts = modpath_exts[dep]
+            if path_matches(full_mod_subdir, full_modpath_exts):
+                # full path to module subdir of dependency is simply path to module file without (short) module name
+                full_mod_subdir = self.modulefile_path(dep)[:-len(dep)-1]
 
-                # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
-                # this is required to obtain the corresponding module file paths (via 'module show')
-                self.load([dep])
+                path.append(dep)
+                tup = (dep, full_mod_subdir, full_modpath_exts)
+                self.log.debug("Found module to top of module tree: %s (subdir: %s, modpath extensions %s)" % tup)
 
-            self.purge()
-            modify_env(os.environ, orig_env)
+                # no need to continue further, we found the module that extends $MODULEPATH with module subdir
+                break
+
+            # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
+            # this is required to obtain the corresponding module file paths (via 'module show')
+            self.load([dep])
 
         if path:
             # remove retained dependency from the list, since we're climbing up the module tree
@@ -704,6 +697,9 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
         else:
             self.log.debug("Path not extended, we must have reached the top of the module tree")
 
+        # restore original environment (modules may have been loaded above)
+        modify_env(os.environ, orig_env)
+
         self.log.debug("Path to top of module tree from %s: %s" % (mod_name, path))
         return path
 

From 2bc9b5ac33a5e5598bfc1c5d7de23334819208d1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 1 Sep 2014 13:12:20 +0200
Subject: [PATCH 0120/1356] remove senseless comment

---
 easybuild/framework/easyblock.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index d4d913af62..09175b16d1 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -768,8 +768,6 @@ def make_module_dep(self):
         mns = ActiveMNS()
 
         # include load statements for toolchain, either directly or for toolchain dependencies
-        # purposely after dependencies which may be critical,
-        # e.g. when unloading a module in a hierarchical naming scheme
         if self.toolchain.name != DUMMY_TOOLCHAIN_NAME:
             if mns.expand_toolchain_load():
                 mod_names = self.toolchain.toolchain_dependencies

From 456182ba17e0ab38fe23ce5e78d21ee93c9c17ce Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 1 Sep 2014 13:15:27 +0200
Subject: [PATCH 0121/1356] remove unused import of 'any'

---
 easybuild/framework/easyblock.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 09175b16d1..bbefc50f13 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -46,7 +46,6 @@
 import traceback
 from distutils.version import LooseVersion
 from vsc.utils import fancylogger
-from vsc.utils.missing import any
 
 import easybuild.tools.environment as env
 from easybuild.tools import config, filetools

From 416b48f972809fa4091770dea4155390f2963f97 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 1 Sep 2014 13:20:50 +0200
Subject: [PATCH 0122/1356] only load modules that include $MODULEPATH
 extensions

---
 easybuild/tools/modules.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 6ad650608e..eeaa17307e 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -683,9 +683,10 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
                 # no need to continue further, we found the module that extends $MODULEPATH with module subdir
                 break
 
-            # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
-            # this is required to obtain the corresponding module file paths (via 'module show')
-            self.load([dep])
+            if full_modpath_exts:
+                # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
+                # this is required to obtain the corresponding module file paths (via 'module show')
+                self.load([dep])
 
         if path:
             # remove retained dependency from the list, since we're climbing up the module tree

From 24ac4eb8c653a1abb710dd03f2f6af13d510fd11 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 1 Sep 2014 14:12:27 +0200
Subject: [PATCH 0123/1356] fix small remark w.r.t. log error in
 HierarchicalMNS

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 48a4bc9e05..17f6beb061 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -86,8 +86,7 @@ def det_toolchain_compilers_name_version(self, tc_comps):
                 else:
                     _log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
             else:
-                mns = self.__class__.__name__
-                _log.error("Unknown set of toolchain compilers, %s needs to be enhanced first." % mns)
+                self.log.error("Unknown set of toolchain compilers, module naming scheme needs to be enhanced first.")
         return tc_comp_name, tc_comp_ver
 
     def det_module_subdir(self, ec):

From a12675ecef0b4b9e6e88bb4a73b81325a33d7bed Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 1 Sep 2014 15:47:31 +0200
Subject: [PATCH 0124/1356] fix merge conflict resolution failure

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index aa6229099a..d88f794aae 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -89,7 +89,8 @@ def det_toolchain_compilers_name_version(self, tc_comps):
                     self.log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
             else:
                 self.log.error("Unknown set of toolchain compilers, module naming scheme needs to be enhanced first.")
-        return tc_comp_name, tc_comp_ver
+            res = (tc_comp_name, tc_comp_ver)
+        return res
 
     def det_module_subdir(self, ec):
         """

From a40a3216338a687dc689752d160f6505f2db4756 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@ugent.be>
Date: Tue, 2 Sep 2014 10:49:06 +0200
Subject: [PATCH 0125/1356] fixes for tests and build_log

---
 easybuild/tools/build_log.py | 6 ++++--
 test/framework/scripts.py    | 4 ++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index e74931ff61..c08ffbf71c 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -80,6 +80,8 @@ def caller_info(self):
                 filepath_dirs.remove(dirName)
             else:
                 break
+            if not filepath_dirs:
+                filepath_dirs = ['?']
         return "(at %s:%s in %s)" % (os.path.join(*filepath_dirs), line, function_name)
 
     def experimental(self, msg, *args, **kwargs):
@@ -155,6 +157,7 @@ def print_msg(msg, log=None, silent=False, prefix=True):
         else:
             print msg
 
+
 def print_error(message, log=None, exitCode=1, opt_parser=None, exit_on_error=True, silent=False):
     """
     Print error message and exit EasyBuild
@@ -169,10 +172,9 @@ def print_error(message, log=None, exitCode=1, opt_parser=None, exit_on_error=Tr
     elif log is not None:
         log.error(message)
 
+
 def print_warning(message, silent=False):
     """
     Print warning message.
     """
     print_msg("WARNING: %s\n" % message, silent=silent)
-
-
diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index b13cf8b3a9..f9704b7937 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -30,7 +30,6 @@
 import os
 import re
 import shutil
-import sys
 import tempfile
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
@@ -46,7 +45,7 @@ def test_generate_software_list(self):
 
         # adjust $PYTHONPATH such that test easyblocks are found by the script
         eb_blocks_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'sandbox'))
-        pythonpath = os.environ['PYTHONPATH']
+        pythonpath = os.environ.get('PYTHONPATH', '.')
         os.environ['PYTHONPATH'] = "%s:%s" % (pythonpath, eb_blocks_path)
 
         testdir = os.path.dirname(__file__)
@@ -90,6 +89,7 @@ def test_generate_software_list(self):
         shutil.rmtree(tmpdir)
         os.environ['PYTHONPATH'] = pythonpath
 
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(ScriptsTest)

From 8193b23f11cc0d5a66ba90729594e8aef941e96e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 11:05:10 +0200
Subject: [PATCH 0126/1356] Revert "also include libgomp.a in list of libraries
 for multithreading for GCC"

---
 easybuild/toolchains/compiler/gcc.py | 2 +-
 test/framework/toolchain.py          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py
index 4889746920..e47a9c4778 100644
--- a/easybuild/toolchains/compiler/gcc.py
+++ b/easybuild/toolchains/compiler/gcc.py
@@ -77,7 +77,7 @@ class Gcc(Compiler):
     COMPILER_F90 = 'gfortran'
     COMPILER_F_UNIQUE_FLAGS = ['f2c']
 
-    LIB_MULTITHREAD = ['gomp', 'pthread']
+    LIB_MULTITHREAD = ['pthread']
     LIB_MATH = ['m']
 
     def _set_compiler_vars(self):
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 8056c71d12..45eefd7ad8 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -381,7 +381,7 @@ def test_goolfc(self):
         nvcc_flags = r' '.join([
             r'-Xcompiler="-O2 -march=native"',
             # the use of -lcudart in -Xlinker is a bit silly but hard to avoid
-            r'-Xlinker=".* -lm -lrt -lcudart -lgomp -lpthread"',
+            r'-Xlinker=".* -lm -lrt -lcudart -lpthread"',
             r' '.join(["-gencode %s" % x for x in opts['cuda_gencode']]),
         ])
 

From ba2ea70f1925e4b0c7624dd32761e63c208c2b3b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Sep 2014 11:40:32 +0200
Subject: [PATCH 0127/1356] specify location to generate tweaked easyconfigs in

---
 easybuild/framework/easyconfig/tweak.py | 10 ++++++----
 easybuild/main.py                       |  2 +-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index e5b346d13c..23e48ff647 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -69,7 +69,7 @@ def ec_filename_for(path):
     return fn
 
 
-def tweak(easyconfigs, build_specs):
+def tweak(easyconfigs, build_specs, targetdir=None):
     """Tweak list of easyconfigs according to provided build specifications."""
 
     # make sure easyconfigs all feature the same toolchain (otherwise we *will* run into trouble)
@@ -93,14 +93,14 @@ def tweak(easyconfigs, build_specs):
     # generate tweaked easyconfigs, and continue with those instead
     easyconfigs = []
     for orig_ec in orig_ecs:
-        new_ec_file = tweak_one(orig_ec['spec'], None, build_specs)
+        new_ec_file = tweak_one(orig_ec['spec'], None, build_specs, targetdir=targetdir)
         new_ecs = process_easyconfig(new_ec_file, build_specs=build_specs)
         easyconfigs.extend(new_ecs)
 
     return easyconfigs
 
 
-def tweak_one(src_fn, target_fn, tweaks):
+def tweak_one(src_fn, target_fn, tweaks, targetdir=None):
     """
     Tweak an easyconfig file with the given list of tweaks, using replacement via regular expressions.
     Note: this will only work 'well-written' easyconfig files, i.e. ones that e.g. set the version
@@ -222,7 +222,9 @@ def __repr__(self):
         except OSError, err:
             _log.error("Failed to determine suiting filename for tweaked easyconfig file: %s" % err)
 
-        target_fn = os.path.join(tempfile.gettempdir(), fn)
+        if targetdir is None:
+            targetdir = tempfile.gettempdir()
+        target_fn = os.path.join(targetdir, fn)
         _log.debug("Generated file name for tweaked easyconfig file: %s" % target_fn)
 
     # write out tweaked easyconfig file
diff --git a/easybuild/main.py b/easybuild/main.py
index 4697653f37..bd3db3a92f 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -374,7 +374,7 @@ def main(testing_data=(None, None, None)):
     # don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
     # if easyconfig files for the dependencies are not available
     if try_to_generate and build_specs and not generated_ecs:
-        easyconfigs = tweak(easyconfigs, build_specs)
+        easyconfigs = tweak(easyconfigs, build_specs, targetdir=os.path.join(eb_tmpdir, 'tweak'))
 
     # before building starts, take snapshot of environment (watch out -t option!)
     os.chdir(os.environ['PWD'])

From 0ca7f37483fbfc9aa29cca0a1b5c6c6313433161 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 09:06:03 +0200
Subject: [PATCH 0128/1356] fix bug with repositorypath not honoring --prefix

---
 easybuild/tools/config.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index d595b79803..bab24b21af 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -47,6 +47,7 @@
 import easybuild.tools.environment as env
 from easybuild.tools.environment import read_environment as _read_environment
 from easybuild.tools.run import run_cmd
+from easybuild.tools.repository.repository import init_repository
 
 
 _log = fancylogger.getLogger('config', fname=False)
@@ -351,6 +352,19 @@ def init(options, config_options_dict):
     _log.debug("Updating config variables with generaloption dict %s" % config_options_dict)
     tmpdict.update(config_options_dict)
 
+    # if the repository path has changed (e.g. via --prefix), we need to reinitialise the repository instance
+    repositorypath = tmpdict['repositorypath']
+    repositoryspecs = tmpdict['repositorypath']
+    if isinstance(repositorypath, (list, tuple)):
+        repositorypath = tmpdict['repositorypath'][0]
+    else:
+        repositoryspecs = [repositoryspecs]
+    if repositorypath != tmpdict['repository'].repo:
+        tup = (tmpdict['repository'].repo, tmpdict['repositorypath'])
+        _log.debug("Reinitialising 'repository' since repository path has changed from %s to %s" % tup)
+        # we can't use init_repository yet, since we're not done configuring
+        tmpdict['repository'] = tmpdict['repository'].__class__(*repositoryspecs)
+
     # make sure source path is a list
     sourcepath = tmpdict['sourcepath']
     if isinstance(sourcepath, basestring):

From 8329857d4c8532010011bd8879f0779ca775fe4b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 10:12:20 +0200
Subject: [PATCH 0129/1356] only reinitialize 'repository' if it is a
 repository already

---
 easybuild/tools/config.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index bab24b21af..63ef41d9d1 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -47,7 +47,7 @@
 import easybuild.tools.environment as env
 from easybuild.tools.environment import read_environment as _read_environment
 from easybuild.tools.run import run_cmd
-from easybuild.tools.repository.repository import init_repository
+from easybuild.tools.repository.repository import Repository, init_repository
 
 
 _log = fancylogger.getLogger('config', fname=False)
@@ -359,7 +359,7 @@ def init(options, config_options_dict):
         repositorypath = tmpdict['repositorypath'][0]
     else:
         repositoryspecs = [repositoryspecs]
-    if repositorypath != tmpdict['repository'].repo:
+    if isinstance(tmpdict['repository'], Repository) and repositorypath != tmpdict['repository'].repo:
         tup = (tmpdict['repository'].repo, tmpdict['repositorypath'])
         _log.debug("Reinitialising 'repository' since repository path has changed from %s to %s" % tup)
         # we can't use init_repository yet, since we're not done configuring

From 5499b785924a452cd957e5eabed177eca2b8efb2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 09:45:29 +0200
Subject: [PATCH 0130/1356] also set prefix configuration option in unit test
 setup

---
 test/framework/utilities.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index db69e96eb5..3f6b1fbf71 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -99,6 +99,8 @@ def setUp(self):
 
         self.test_sourcepath = os.path.join(testdir, 'sandbox', 'sources')
         os.environ['EASYBUILD_SOURCEPATH'] = self.test_sourcepath
+        self.test_prefix = tempfile.mkdtemp()
+        os.environ['EASYBUILD_PREFIX'] = self.test_prefix
         self.test_buildpath = tempfile.mkdtemp()
         os.environ['EASYBUILD_BUILDPATH'] = self.test_buildpath
         self.test_installpath = tempfile.mkdtemp()
@@ -130,7 +132,7 @@ def tearDown(self):
         # restore original Python search path
         sys.path = self.orig_sys_path
 
-        for path in [self.test_buildpath, self.test_installpath]:
+        for path in [self.test_buildpath, self.test_installpath, self.test_prefix]:
             try:
                 shutil.rmtree(path)
             except OSError, err:

From 52482edbe8f9e8cb254fb473dd4a3e9bf9d87123 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 10:12:47 +0200
Subject: [PATCH 0131/1356] unset $EASYBUILD_PREFIX for config unit tests

---
 test/framework/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index 2ce0946dbd..e0c5c85953 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -59,7 +59,7 @@ def setUp(self):
 
     def purge_environment(self):
         """Remove any leftover easybuild variables"""
-        for path in ['buildpath', 'installpath', 'sourcepath']:
+        for path in ['buildpath', 'installpath', 'sourcepath', 'prefix']:
             var = 'EASYBUILD_%s' % path.upper()
             if var in os.environ:
                 del os.environ[var]

From af90d58220eba27c4fc64dd2719fa47246eee897 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 09:05:37 +0200
Subject: [PATCH 0132/1356] properly quote GCC version info to ensure parseable
 archived easyconfig

---
 easybuild/tools/systemtools.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 7cd2babc04..b47fb946e2 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -44,6 +44,7 @@
 
 from easybuild.tools.filetools import read_file, which
 from easybuild.tools.run import run_cmd
+from easybuild.tools.utilities import quote_str
 
 
 _log = fancylogger.getLogger('systemtools', fname=False)
@@ -461,7 +462,7 @@ def get_system_info():
         'cpu_model': get_cpu_model(),
         'cpu_speed': get_cpu_speed(),
         'cpu_vendor': get_cpu_vendor(),
-        'gcc_version': get_tool_version('gcc', version_option='-v'),
+        'gcc_version': quote_str(get_tool_version('gcc', version_option='-v')),
         'hostname': gethostname(),
         'glibc_version': get_glibc_version(),
         'kernel_name': get_kernel_name(),

From f2659131a57d51e32199573ab58710e36556f227 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 09:06:40 +0200
Subject: [PATCH 0133/1356] change filename for archived easyconfig, to include
 software name as well

---
 easybuild/tools/repository/filerepo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/repository/filerepo.py b/easybuild/tools/repository/filerepo.py
index 06e67f76bc..7e1b2f792e 100644
--- a/easybuild/tools/repository/filerepo.py
+++ b/easybuild/tools/repository/filerepo.py
@@ -78,7 +78,7 @@ def add_easyconfig(self, cfg, name, version, stats, previous):
         mkdir(full_path, parents=True)
 
         # destination
-        dest = os.path.join(full_path, "%s.eb" % version)
+        dest = os.path.join(full_path, "%s-%s.eb" % (name, version))
 
         txt = "# Built with EasyBuild version %s on %s\n" % (VERBOSE_VERSION, time.strftime("%Y-%m-%d_%H-%M-%S"))
 

From 53a989a5e22ecff194c5001636d0a6c68832f054 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 10:13:03 +0200
Subject: [PATCH 0134/1356] add unit test for parsing archived easyconfig

---
 test/framework/toy_build.py | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 56c66876b9..43d81c347d 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -41,6 +41,7 @@
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 
 import easybuild.tools.module_naming_scheme  # required to dynamically load test module naming scheme(s)
+from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.modules import modules_tool
@@ -142,6 +143,8 @@ def test_toy_build(self, extra_args=None, ec_file=None, tmpdir=None, verify=True
                                   raise_error=raise_error)
         except Exception, err:
             myerr = err
+            if raise_error:
+                raise myerr
 
         if verify:
             self.check_toy(self.test_installpath, outtxt, versionsuffix=versionsuffix)
@@ -173,9 +176,6 @@ def test_toy_build(self, extra_args=None, ec_file=None, tmpdir=None, verify=True
                 msg = "Pattern %s found in full test report: %s" % (regex.pattern, test_report_txt)
                 self.assertTrue(regex.search(test_report_txt), msg)
 
-        if raise_error and (myerr is not None):
-            raise myerr
-
         return outtxt
 
     def test_toy_broken(self):
@@ -681,6 +681,16 @@ def test_module_filepath_tweaking(self):
         self.assertTrue(os.path.exists(os.path.join(mod_file_prefix, 't', 'toy', '0.0')))
         self.assertTrue(os.path.islink(os.path.join(mod_file_prefix, 't', 'toy', '0.0')))
 
+    def test_toy_archived_easyconfig(self):
+        """Test archived easyconfig for a succesful build."""
+        self.test_toy_build(raise_error=True, extra_args=['--prefix=%s' % self.test_prefix])
+
+        archived_ec = os.path.join(self.test_prefix, 'ebfiles_repo', 'toy', 'toy-0.0.eb')
+        self.assertTrue(os.path.exists(archived_ec))
+        ec = EasyConfig(archived_ec)
+        self.assertEqual(ec.name, 'toy')
+        self.assertEqual(ec.version, '0.0')
+
 def suite():
     """ return all the tests in this file """
     return TestLoader().loadTestsFromTestCase(ToyBuildTest)

From e63b932e77a0ea42445a7700cb3eff3b159aae50 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 18:37:26 +0200
Subject: [PATCH 0135/1356] use quote_str in stats_to_str rather than in
 get_system_info

---
 easybuild/framework/easyconfig/tools.py | 12 ++----------
 easybuild/tools/systemtools.py          |  3 +--
 test/framework/easyconfig.py            |  1 +
 3 files changed, 4 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index b491fa9501..09154955ee 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -74,6 +74,7 @@
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version, det_hidden_modname
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.ordereddict import OrderedDict
+from easybuild.tools.utilities import quote_str
 
 _log = fancylogger.getLogger('easyconfig.tools', fname=False)
 
@@ -388,17 +389,8 @@ def stats_to_str(stats):
         _log.error("Can only pretty print build stats in dictionary form, not of type %s" % type(stats))
 
     txt = "{\n"
-
     pref = "    "
-
-    def tostr(x):
-        if isinstance(x, basestring):
-            return "'%s'" % x
-        else:
-            return str(x)
-
     for (k, v) in stats.items():
-        txt += "%s%s: %s,\n" % (pref, tostr(k), tostr(v))
-
+        txt += "%s%s: %s,\n" % (pref, quote_str(k), quote_str(v))
     txt += "}"
     return txt
diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index b47fb946e2..c507fb207e 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -44,7 +44,6 @@
 
 from easybuild.tools.filetools import read_file, which
 from easybuild.tools.run import run_cmd
-from easybuild.tools.utilities import quote_str
 
 
 _log = fancylogger.getLogger('systemtools', fname=False)
@@ -462,7 +461,7 @@ def get_system_info():
         'cpu_model': get_cpu_model(),
         'cpu_speed': get_cpu_speed(),
         'cpu_vendor': get_cpu_vendor(),
-        'gcc_version': quote_str(get_tool_version('gcc', version_option='-v')),
+        'gcc_version': get_tool_version('gcc', version_option='-v')
         'hostname': gethostname(),
         'glibc_version': get_glibc_version(),
         'kernel_name': get_kernel_name(),
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 4c89afe53a..c78ec426a3 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -952,6 +952,7 @@ def test_filter_deps(self):
         opts = init_config(args=['--filter-deps=zlib,ncurses'])
         self.assertEqual(opts.filter_deps, ['zlib', 'ncurses'])
 
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(EasyConfigTest)

From 289fb828aa4ecee23323b4fba074c18099d243ab Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Sep 2014 18:41:04 +0200
Subject: [PATCH 0136/1356] fix typo

---
 easybuild/tools/systemtools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index c507fb207e..7cd2babc04 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -461,7 +461,7 @@ def get_system_info():
         'cpu_model': get_cpu_model(),
         'cpu_speed': get_cpu_speed(),
         'cpu_vendor': get_cpu_vendor(),
-        'gcc_version': get_tool_version('gcc', version_option='-v')
+        'gcc_version': get_tool_version('gcc', version_option='-v'),
         'hostname': gethostname(),
         'glibc_version': get_glibc_version(),
         'kernel_name': get_kernel_name(),

From 5bec24fc69cd37d8188a996a1f78072fd5cb1446 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Sep 2014 11:49:08 +0200
Subject: [PATCH 0137/1356] use --repositorypath directly rather than relying
 on --prefix

---
 test/framework/toy_build.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 43d81c347d..09b16d6ad9 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -683,9 +683,14 @@ def test_module_filepath_tweaking(self):
 
     def test_toy_archived_easyconfig(self):
         """Test archived easyconfig for a succesful build."""
-        self.test_toy_build(raise_error=True, extra_args=['--prefix=%s' % self.test_prefix])
+        repositorypath = os.path.join(self.test_installpath, 'easyconfigs_archive')
+        extra_args = [
+            '--repository=FileRepository',
+            '--repositorypath=%s' % repositorypath,
+        ]
+        self.test_toy_build(raise_error=True, extra_args=extra_args)
 
-        archived_ec = os.path.join(self.test_prefix, 'ebfiles_repo', 'toy', 'toy-0.0.eb')
+        archived_ec = os.path.join(repositorypath, 'toy', 'toy-0.0.eb')
         self.assertTrue(os.path.exists(archived_ec))
         ec = EasyConfig(archived_ec)
         self.assertEqual(ec.name, 'toy')

From c506f1573c06ef5027716048d3094305b2b30984 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Sep 2014 12:18:58 +0200
Subject: [PATCH 0138/1356] fix forcing reinitialisation of repository in
 options.py rather than in config.py

---
 easybuild/tools/config.py  | 14 --------------
 easybuild/tools/options.py |  5 +++--
 2 files changed, 3 insertions(+), 16 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 63ef41d9d1..d595b79803 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -47,7 +47,6 @@
 import easybuild.tools.environment as env
 from easybuild.tools.environment import read_environment as _read_environment
 from easybuild.tools.run import run_cmd
-from easybuild.tools.repository.repository import Repository, init_repository
 
 
 _log = fancylogger.getLogger('config', fname=False)
@@ -352,19 +351,6 @@ def init(options, config_options_dict):
     _log.debug("Updating config variables with generaloption dict %s" % config_options_dict)
     tmpdict.update(config_options_dict)
 
-    # if the repository path has changed (e.g. via --prefix), we need to reinitialise the repository instance
-    repositorypath = tmpdict['repositorypath']
-    repositoryspecs = tmpdict['repositorypath']
-    if isinstance(repositorypath, (list, tuple)):
-        repositorypath = tmpdict['repositorypath'][0]
-    else:
-        repositoryspecs = [repositoryspecs]
-    if isinstance(tmpdict['repository'], Repository) and repositorypath != tmpdict['repository'].repo:
-        tup = (tmpdict['repository'].repo, tmpdict['repositorypath'])
-        _log.debug("Reinitialising 'repository' since repository path has changed from %s to %s" % tup)
-        # we can't use init_repository yet, since we're not done configuring
-        tmpdict['repository'] = tmpdict['repository'].__class__(*repositoryspecs)
-
     # make sure source path is a list
     sourcepath = tmpdict['sourcepath']
     if isinstance(sourcepath, basestring):
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 099879b796..893b121318 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -216,7 +216,6 @@ def config_options(self):
                              'choice', 'store', oldstyle_defaults['modules_tool'],
                              sorted(avail_modules_tools().keys())),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
-                        "(repositorypath prefix is only relevant in case of FileRepository repository) "
                         "(used prefix for defaults %s)" % oldstyle_defaults['prefix']),
                         None, 'store', None),
             'recursive-module-unload': ("Enable generating of modules that unload recursively.",
@@ -398,7 +397,9 @@ def _postprocess_config(self):
         """Postprocessing of configuration options"""
         if self.options.prefix is not None:
             changed_defaults = get_default_oldstyle_configfile_defaults(self.options.prefix)
-            for dest in ['installpath', 'buildpath', 'sourcepath', 'repositorypath']:
+            # prefix applies to all paths, and repository has to be reinitialised to take new repositorypath into account
+            # in the legacy-style configuration, repository is initialised in configuration file itself
+            for dest in ['installpath', 'buildpath', 'sourcepath', 'repository', 'repositorypath']:
                 if not self.options._action_taken.get(dest, False):
                     new_def = changed_defaults[dest]
                     if dest == 'repositorypath':

From 9426e74e95ca9cb8ca1cc0413ead16bfa57894a6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Sep 2014 12:19:16 +0200
Subject: [PATCH 0139/1356] add unit test to check whether generaloption-style
 configuration overrides legacy style

---
 test/framework/config.py | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/test/framework/config.py b/test/framework/config.py
index e0c5c85953..a6c5eee8e6 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -107,6 +107,36 @@ def test_default_config(self):
         self.assertEqual(config_options['logfile_format'][1], "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
         self.assertEqual(config_options['tmp_logdir'], tempfile.gettempdir())
 
+    def test_generaloption_overrides_legacy(self):
+        """Test whether generaloption overrides legacy configuration."""
+        self.purge_environment()
+        # if both legacy and generaloption style configuration is mixed, generaloption wins
+        legacy_prefix = os.path.join(self.tmpdir, 'legacy')
+        go_prefix = os.path.join(self.tmpdir, 'generaloption')
+
+        # legacy env vars
+        os.environ['EASYBUILDPREFIX'] = legacy_prefix
+        os.environ['EASYBUILDBUILDPATH'] = os.path.join(legacy_prefix, 'build')
+        # generaloption env vars
+        os.environ['EASYBUILD_INSTALLPATH'] = go_prefix
+        init_config()
+        self.assertEqual(build_path(), os.path.join(legacy_prefix, 'build'))
+        self.assertEqual(install_path(), os.path.join(go_prefix, 'software'))
+        repo = init_repository(get_repository(), get_repositorypath())
+        self.assertEqual(repo.repo, os.path.join(legacy_prefix, 'ebfiles_repo'))
+        del os.environ['EASYBUILDPREFIX']
+
+        # legacy env vars
+        os.environ['EASYBUILDBUILDPATH'] = os.path.join(legacy_prefix, 'buildagain')
+        # generaloption env vars
+        os.environ['EASYBUILD_PREFIX'] = go_prefix
+        init_config()
+        self.assertEqual(build_path(), os.path.join(go_prefix, 'build'))
+        self.assertEqual(install_path(), os.path.join(go_prefix, 'software'))
+        repo = init_repository(get_repository(), get_repositorypath())
+        self.assertEqual(repo.repo, os.path.join(go_prefix, 'ebfiles_repo'))
+        del os.environ['EASYBUILDBUILDPATH']
+
     def test_legacy_env_vars(self):
         """Test legacy environment variables."""
         self.purge_environment()
@@ -167,6 +197,7 @@ def test_legacy_env_vars(self):
         repo = init_repository(get_repository(), get_repositorypath())
         self.assertTrue(isinstance(repo, FileRepository))
         self.assertEqual(repo.repo, os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['repositorypath']))
+        del os.environ['EASYBUILDPREFIX']
 
         # build/source/install path overrides prefix
         init_config()
@@ -206,6 +237,7 @@ def test_legacy_env_vars(self):
         repo = init_repository(get_repository(), get_repositorypath())
         self.assertTrue(isinstance(repo, FileRepository))
         self.assertEqual(repo.repo, os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['repositorypath']))
+        del os.environ['EASYBUILDINSTALLPATH']
 
     def test_legacy_config_file(self):
         """Test finding/using legacy configuration files."""

From c3a2592c1709258a8171363784b802c038d274aa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Sep 2014 13:07:12 +0200
Subject: [PATCH 0140/1356] fix config.py unit test by not unsetting
 $EASYBUILDPREFIX too early

---
 test/framework/config.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index a6c5eee8e6..b28ec141cf 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -197,7 +197,7 @@ def test_legacy_env_vars(self):
         repo = init_repository(get_repository(), get_repositorypath())
         self.assertTrue(isinstance(repo, FileRepository))
         self.assertEqual(repo.repo, os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['repositorypath']))
-        del os.environ['EASYBUILDPREFIX']
+        # purposely not unsetting $EASYBUILDPREFIX yet here
 
         # build/source/install path overrides prefix
         init_config()
@@ -237,6 +237,7 @@ def test_legacy_env_vars(self):
         repo = init_repository(get_repository(), get_repositorypath())
         self.assertTrue(isinstance(repo, FileRepository))
         self.assertEqual(repo.repo, os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['repositorypath']))
+        del os.environ['EASYBUILDPREFIX']
         del os.environ['EASYBUILDINSTALLPATH']
 
     def test_legacy_config_file(self):

From 66a2ffd6ba17b23347cd52e75a4e241096373333 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Sep 2014 17:11:22 +0200
Subject: [PATCH 0141/1356] include path where tweaked easyconfigs are placed
 in robot path to fix --try-toolchain --robot
 --module-naming-scheme=HierarchicalMNS scenario

---
 easybuild/main.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index bd3db3a92f..cc5b42ec15 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -210,6 +210,11 @@ def main(testing_data=(None, None, None)):
         easyconfigs_paths = robot_path[:]
         _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
 
+    # prepend robot path with location where tweaked easyconfigs will be placed
+    if try_to_generate and build_specs:
+        tweaked_ecs_path = os.path.join(eb_tmpdir, 'tweaked_easyconfigs')
+        robot_path.insert(0, tweaked_ecs_path)
+
     # initialise the easybuild configuration
     config.init(options, eb_go.get_options_by_section('config'))
 
@@ -374,7 +379,7 @@ def main(testing_data=(None, None, None)):
     # don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
     # if easyconfig files for the dependencies are not available
     if try_to_generate and build_specs and not generated_ecs:
-        easyconfigs = tweak(easyconfigs, build_specs, targetdir=os.path.join(eb_tmpdir, 'tweak'))
+        easyconfigs = tweak(easyconfigs, build_specs, targetdir=tweaked_ecs_path)
 
     # before building starts, take snapshot of environment (watch out -t option!)
     os.chdir(os.environ['PWD'])

From 2df7d659069d5e94a39cdf5d150364e4359e5e83 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Sep 2014 17:11:47 +0200
Subject: [PATCH 0142/1356] enhance unit test to capture issue with tweaked
 easyconfigs not being part of robot path

---
 test/framework/options.py | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 6ec2cc012f..46d8a15f9f 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -982,18 +982,21 @@ def test_recursive_try(self):
             '--ignore-osdeps',
             '--dry-run',
         ]
-        outtxt = self.eb_main(args, do_build=True, verbose=True, raise_error=True)
 
-        # toolchain gompi/1.4.10 should be listed
-        tc_regex = re.compile("^\s*\*\s*\[.\]\s*\S*%s/gompi-1.4.10.eb\s\(module: gompi/1.4.10\)\s*$" % ecs_path, re.M)
-        self.assertTrue(tc_regex.search(outtxt), "Pattern %s found in %s" % (tc_regex.pattern, outtxt))
+        for extra_args in [[], ['--module-naming-scheme=HierarchicalMNS']]:
+
+            outtxt = self.eb_main(args + extra_args, do_build=True, verbose=True, raise_error=True)
+
+            # toolchain gompi/1.4.10 should be listed
+            tc_regex = re.compile("^\s*\*\s*\[.\]\s*\S*%s/gompi-1.4.10.eb\s\(module: gompi/1.4.10\)\s*$" % ecs_path, re.M)
+            self.assertTrue(tc_regex.search(outtxt), "Pattern %s found in %s" % (tc_regex.pattern, outtxt))
 
-        # both toy and gzip dependency should be listed with gompi/1.4.10 toolchain
-        for ec_name in ['gzip-1.4', 'toy-0.0']:
-            ec = '%s-gompi-1.4.10.eb' % ec_name
-            mod = '%s-gompi-1.4.10' % ec_name.replace('-', '/')
-            mod_regex = re.compile("^\s*\*\s*\[.\]\s*\S*/easybuild-\S*/%s\s\(module: %s\)\s*$" % (ec, mod), re.M)
-            self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
+            # both toy and gzip dependency should be listed with gompi/1.4.10 toolchain
+            for ec_name in ['gzip-1.4', 'toy-0.0']:
+                ec = '%s-gompi-1.4.10.eb' % ec_name
+                mod = '%s-gompi-1.4.10' % ec_name.replace('-', '/')
+                mod_regex = re.compile("^\s*\*\s*\[.\]\s*\S*/easybuild-\S*/%s\s\(module: %s\)\s*$" % (ec, mod), re.M)
+                self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 
     def test_cleanup_builddir(self):
         """Test cleaning up of build dir and --disable-cleanup-builddir."""

From 6f1015106db7e04c9c6bb36eda95b67cfd07ffe6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Sep 2014 17:23:59 +0200
Subject: [PATCH 0143/1356] fix minor remark

---
 easybuild/main.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/main.py b/easybuild/main.py
index cc5b42ec15..b250876641 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -211,6 +211,7 @@ def main(testing_data=(None, None, None)):
         _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
 
     # prepend robot path with location where tweaked easyconfigs will be placed
+    tweaked_ecs_path = None
     if try_to_generate and build_specs:
         tweaked_ecs_path = os.path.join(eb_tmpdir, 'tweaked_easyconfigs')
         robot_path.insert(0, tweaked_ecs_path)

From 9a177fb5e83350ab1dc40b9d0bb656ef8db44789 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 09:52:03 +0200
Subject: [PATCH 0144/1356] set $MODULEPATH in unit tests via 'module use'

---
 test/framework/utilities.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 3f6b1fbf71..878964ee54 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -117,11 +117,13 @@ def setUp(self):
         reload(easybuild.easyblocks.generic)
         reload(easybuild.tools.module_naming_scheme)  # required to run options unit tests stand-alone
 
+        modtool = modules_tool()
+
         # set MODULEPATH to included test modules
-        os.environ['MODULEPATH'] = os.path.join(testdir, 'modules')
+        modtool.use(os.path.join(testdir, 'modules'))
 
         # purge out any loaded modules with original $MODULEPATH before running each test
-        modules_tool().purge()
+        modtool.purge()
 
     def tearDown(self):
         """Clean up after running testcase."""
@@ -179,10 +181,6 @@ def setup_hierarchical_modules(self):
         """Setup hierarchical modules to run tests on."""
         mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
 
-        # make sure only modules in a hierarchical scheme are available, mixing modules installed with
-        # a flat scheme like EasyBuildMNS and a hierarhical one like HierarchicalMNS doesn't work
-        os.environ['MODULEPATH'] = os.path.join(mod_prefix, 'Core')
-
         # simply copy module files under 'Core' and 'Compiler' to test install path
         # EasyBuild is responsible for making sure that the toolchain can be loaded using the short module name
         mkdir(mod_prefix, parents=True)
@@ -190,6 +188,10 @@ def setup_hierarchical_modules(self):
             src_mod_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'modules', mod_subdir)
             shutil.copytree(src_mod_path, os.path.join(mod_prefix, mod_subdir))
 
+        # make sure only modules in a hierarchical scheme are available, mixing modules installed with
+        # a flat scheme like EasyBuildMNS and a hierarhical one like HierarchicalMNS doesn't work
+        modules_tool().use(os.path.join(mod_prefix, 'Core'))
+
         # tweak use statements in GCC/OpenMPI modules to ensure correct paths
         mpi_pref = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
         for modfile in [

From afa46aa51ec31665a914538dae5e0e2f59e62d0c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 12:13:41 +0200
Subject: [PATCH 0145/1356] indicate which builds will be forced in the output
 of --dry-run by marking them as 'F'

---
 easybuild/framework/easyconfig/tools.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index b491fa9501..29b81c95d0 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -258,6 +258,8 @@ def print_dry_run(easyconfigs, short=False, build_specs=None):
     unbuilt_specs = skip_available(all_specs, testing=True)
     dry_run_fmt = " * [%1s] %s (module: %s)"  # markdown compatible (list of items with checkboxes in front)
 
+    listed_ec_paths = [spec['spec'] for spec in easyconfigs]
+
     var_name = 'CFGS'
     common_prefix = det_common_path_prefix([spec['spec'] for spec in all_specs])
     # only allow short if common prefix is long enough
@@ -265,6 +267,8 @@ def print_dry_run(easyconfigs, short=False, build_specs=None):
     for spec in all_specs:
         if spec in unbuilt_specs:
             ans = ' '
+        elif build_option('force') and spec['spec'] in listed_ec_paths:
+            ans = 'F'
         else:
             ans = 'x'
 

From ddea4c94ae3dc5b4a1cc16355a442d72a5b9daba Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 13:30:39 +0200
Subject: [PATCH 0146/1356] fix unit tests w.r.t. dry-run and also check for
 forced builds listed in --dry-run output

---
 test/framework/options.py   | 65 ++++++++++++++++++++++---------------
 test/framework/utilities.py |  3 ++
 2 files changed, 41 insertions(+), 27 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 46d8a15f9f..9c63726ac9 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -566,11 +566,11 @@ def test_dry_run(self):
         info_msg = r"Dry run: printing build status of easyconfigs and dependencies"
         self.assertTrue(re.search(info_msg, outtxt, re.M), "Info message dry running in '%s'" % outtxt)
         ecs_mods = [
-            ("gzip-1.4-GCC-4.6.3.eb", "gzip/1.4-GCC-4.6.3"),
-            ("GCC-4.6.3.eb", "GCC/4.6.3"),
+            ("gzip-1.4-GCC-4.6.3.eb", "gzip/1.4-GCC-4.6.3", ' '),
+            ("GCC-4.6.3.eb", "GCC/4.6.3", 'x'),
         ]
-        for ec, mod in ecs_mods:
-            regex = re.compile(r" \* \[.\] \S+%s \(module: %s\)" % (ec, mod), re.M)
+        for ec, mod, mark in ecs_mods:
+            regex = re.compile(r" \* \[%s\] \S+%s \(module: %s\)" % (mark, ec, mod), re.M)
             self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
 
         for dry_run_arg in ['-D', '--dry-run-short']:
@@ -587,11 +587,11 @@ def test_dry_run(self):
             self.assertTrue(re.search(info_msg, outtxt, re.M), "Info message dry running in '%s'" % outtxt)
             self.assertTrue(re.search('CFGS=', outtxt), "CFGS line message found in '%s'" % outtxt)
             ecs_mods = [
-                ("gzip-1.4-GCC-4.6.3.eb", "gzip/1.4-GCC-4.6.3"),
-                ("GCC-4.6.3.eb", "GCC/4.6.3"),
+                ("gzip-1.4-GCC-4.6.3.eb", "gzip/1.4-GCC-4.6.3", ' '),
+                ("GCC-4.6.3.eb", "GCC/4.6.3", 'x'),
             ]
-            for ec, mod in ecs_mods:
-                regex = re.compile(r" \* \[.\] \$CFGS\S+%s \(module: %s\)" % (ec, mod), re.M)
+            for ec, mod, mark in ecs_mods:
+                regex = re.compile(r" \* \[%s\] \$CFGS\S+%s \(module: %s\)" % (mark, ec, mod), re.M)
                 self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
 
         if os.path.exists(dummylogfn):
@@ -602,12 +602,15 @@ def test_dry_run_hierarchical(self):
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
+        test_ecs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         args = [
-            os.path.join(os.path.dirname(__file__), 'easyconfigs', 'gzip-1.5-goolf-1.4.10.eb'),
+            os.path.join(test_ecs, 'gzip-1.5-goolf-1.4.10.eb'),
+            os.path.join(test_ecs, 'GCC-4.7.2.eb'),
             '--dry-run',
             '--unittest-file=%s' % self.logfile,
             '--module-naming-scheme=HierarchicalMNS',
             '--ignore-osdeps',
+            '--force',
         ]
         errmsg = r"No robot path specified, which is required when looking for easyconfigs \(use --robot\)"
         self.assertErrorRegex(EasyBuildError, errmsg, self.eb_main, args, logfile=dummylogfn, raise_error=True)
@@ -617,20 +620,20 @@ def test_dry_run_hierarchical(self):
 
         ecs_mods = [
             # easyconfig, module subdir, (short) module name
-            ("GCC-4.7.2.eb", "Core", "GCC/4.7.2"),
-            ("hwloc-1.6.2-GCC-4.7.2.eb", "Compiler/GCC/4.7.2", "hwloc/1.6.2"),
-            ("OpenMPI-1.6.4-GCC-4.7.2.eb", "Compiler/GCC/4.7.2", "OpenMPI/1.6.4"),
-            ("gompi-1.4.10.eb", "Core", "gompi/1.4.10"),
+            ("GCC-4.7.2.eb", "Core", "GCC/4.7.2", 'F'),  # already present and listed, so 'F'
+            ("hwloc-1.6.2-GCC-4.7.2.eb", "Compiler/GCC/4.7.2", "hwloc/1.6.2", 'x'),
+            ("OpenMPI-1.6.4-GCC-4.7.2.eb", "Compiler/GCC/4.7.2", "OpenMPI/1.6.4", 'x'),
+            ("gompi-1.4.10.eb", "Core", "gompi/1.4.10", 'x'),
             ("OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4",
-             "OpenBLAS/0.2.6-LAPACK-3.4.2"),
-            ("FFTW-3.3.3-gompi-1.4.10.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4", "FFTW/3.3.3"),
+             "OpenBLAS/0.2.6-LAPACK-3.4.2", 'x'),
+            ("FFTW-3.3.3-gompi-1.4.10.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4", "FFTW/3.3.3", 'x'),
             ("ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4",
-             "ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2"),
-            ("goolf-1.4.10.eb", "Core", "goolf/1.4.10"),
-            ("gzip-1.5-goolf-1.4.10.eb", "MPI/GCC/4.8.2/OpenMPI/1.6.5", "gzip/1.5"),
+             "ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2", 'x'),
+            ("goolf-1.4.10.eb", "Core", "goolf/1.4.10", 'x'),
+            ("gzip-1.5-goolf-1.4.10.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4", "gzip/1.5", ' '),  # listed but not there: ' '
         ]
-        for ec, mod_subdir, mod_name in ecs_mods:
-            regex = re.compile(r" \* \[.\] \S+%s \(module: %s | %s\)" % (ec, mod_subdir, mod_name), re.M)
+        for ec, mod_subdir, mod_name, mark in ecs_mods:
+            regex = re.compile("^ \* \[%s\] \S+%s \(module: %s \| %s\)$" % (mark, ec, mod_subdir, mod_name), re.M)
             self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
 
         if os.path.exists(dummylogfn):
@@ -962,9 +965,9 @@ def test_allow_modules_tool_mismatch(self):
         else:
             del os.environ['module']
 
-    def test_recursive_try(self):
+    def test_recursive_try_toolchain(self):
         """Test whether recursive --try-X works."""
-        ecs_path = os.path.join(os.path.dirname(__file__), 'easyconfigs')
+        ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         tweaked_toy_ec = os.path.join(self.test_buildpath, 'toy-0.0-tweaked.eb')
         shutil.copy2(os.path.join(ecs_path, 'toy-0.0.eb'), tweaked_toy_ec)
         f = open(tweaked_toy_ec, 'a')
@@ -985,17 +988,25 @@ def test_recursive_try(self):
 
         for extra_args in [[], ['--module-naming-scheme=HierarchicalMNS']]:
 
-            outtxt = self.eb_main(args + extra_args, do_build=True, verbose=True, raise_error=True)
+            outtxt = self.eb_main(args + extra_args, do_build=True, verbose=False, raise_error=True)
 
-            # toolchain gompi/1.4.10 should be listed
-            tc_regex = re.compile("^\s*\*\s*\[.\]\s*\S*%s/gompi-1.4.10.eb\s\(module: gompi/1.4.10\)\s*$" % ecs_path, re.M)
+            # toolchain gompi/1.4.10 should be listed (but not present yet)
+            if extra_args:
+                mark = 'x'
+            else:
+                mark = ' '
+            tc_regex = re.compile("^ \* \[%s\] %s/gompi-1.4.10.eb \(module: .*gompi/1.4.10\)$" % (mark, ecs_path), re.M)
             self.assertTrue(tc_regex.search(outtxt), "Pattern %s found in %s" % (tc_regex.pattern, outtxt))
 
             # both toy and gzip dependency should be listed with gompi/1.4.10 toolchain
             for ec_name in ['gzip-1.4', 'toy-0.0']:
                 ec = '%s-gompi-1.4.10.eb' % ec_name
-                mod = '%s-gompi-1.4.10' % ec_name.replace('-', '/')
-                mod_regex = re.compile("^\s*\*\s*\[.\]\s*\S*/easybuild-\S*/%s\s\(module: %s\)\s*$" % (ec, mod), re.M)
+                if extra_args:
+                    mod = ec_name.replace('-', '/')
+                else:
+                    mod = '%s-gompi-1.4.10' % ec_name.replace('-', '/')
+                mod_regex = re.compile("^ \* \[ \] \S+/easybuild-\S+/%s \(module: .*%s\)$" % (ec, mod), re.M)
+                #mod_regex = re.compile("%s \(module: .*%s\)$" % (ec, mod), re.M)
                 self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 
     def test_cleanup_builddir(self):
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index db69e96eb5..b09490d335 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -151,6 +151,9 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
         myerr = False
         if logfile is None:
             logfile = self.logfile
+        # clear log file
+        open(logfile, 'w').write('')
+
         try:
             main((args, logfile, do_build))
         except SystemExit:

From a17a1fe4425bbe12cc700231e09f44a6a6689b96 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 14:32:08 +0200
Subject: [PATCH 0147/1356] fix breaking in unit tests

---
 test/framework/modules.py   |  7 +------
 test/framework/utilities.py | 15 ++++++++++-----
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 02bc379318..6de1c2e998 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -58,12 +58,7 @@ def init_testmods(self, test_modules_paths=None):
         """Initialize set of test modules for test."""
         if test_modules_paths is None:
             test_modules_paths = [os.path.abspath(os.path.join(os.path.dirname(__file__), 'modules'))]
-        mod_paths = self.testmods.mod_paths[:]
-        for path in test_modules_paths:
-            self.testmods.prepend_module_path(path)
-        for path in mod_paths:
-            if path not in test_modules_paths:
-                self.testmods.remove_module_path(path)
+        self.reset_modulepath(test_modules_paths)
 
     # for Lmod, this test has to run first, to avoid that it fails;
     # no modules are found if another test ran before it, but using a (very) long module path works fine interactively
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 878964ee54..ad250c2104 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -118,10 +118,7 @@ def setUp(self):
         reload(easybuild.tools.module_naming_scheme)  # required to run options unit tests stand-alone
 
         modtool = modules_tool()
-
-        # set MODULEPATH to included test modules
-        modtool.use(os.path.join(testdir, 'modules'))
-
+        self.reset_modulepath([os.path.join(testdir, 'modules')])
         # purge out any loaded modules with original $MODULEPATH before running each test
         modtool.purge()
 
@@ -148,6 +145,14 @@ def tearDown(self):
                     del os.environ['EASYBUILD_%s' % path.upper()]
         init_config()
 
+    def reset_modulepath(self, modpaths):
+        """Reset $MODULEPATH with specified paths."""
+        modtool = modules_tool()
+        for modpath in os.environ.get('MODULEPATH', '').split(os.pathsep):
+            modtool.remove_module_path(modpath)
+        for modpath in modpaths:
+            modtool.add_module_path(modpath)
+
     def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbose=False, raise_error=False):
         """Helper method to call EasyBuild main function."""
         cleanup()
@@ -190,7 +195,7 @@ def setup_hierarchical_modules(self):
 
         # make sure only modules in a hierarchical scheme are available, mixing modules installed with
         # a flat scheme like EasyBuildMNS and a hierarhical one like HierarchicalMNS doesn't work
-        modules_tool().use(os.path.join(mod_prefix, 'Core'))
+        self.reset_modulepath([os.path.join(mod_prefix, 'Core')])
 
         # tweak use statements in GCC/OpenMPI modules to ensure correct paths
         mpi_pref = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')

From e9216febbc026920255eda7c7741391e9acdeacf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 14:48:30 +0200
Subject: [PATCH 0148/1356] enhance unit test to check --dry-run --force
 --module-naming-scheme combo

---
 test/framework/options.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 9c63726ac9..e185bcaabd 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -605,12 +605,13 @@ def test_dry_run_hierarchical(self):
         test_ecs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         args = [
             os.path.join(test_ecs, 'gzip-1.5-goolf-1.4.10.eb'),
-            os.path.join(test_ecs, 'GCC-4.7.2.eb'),
+            os.path.join(test_ecs, 'OpenMPI-1.6.4-GCC-4.7.2.eb'),
             '--dry-run',
             '--unittest-file=%s' % self.logfile,
             '--module-naming-scheme=HierarchicalMNS',
             '--ignore-osdeps',
             '--force',
+            '--debug',
         ]
         errmsg = r"No robot path specified, which is required when looking for easyconfigs \(use --robot\)"
         self.assertErrorRegex(EasyBuildError, errmsg, self.eb_main, args, logfile=dummylogfn, raise_error=True)
@@ -620,9 +621,9 @@ def test_dry_run_hierarchical(self):
 
         ecs_mods = [
             # easyconfig, module subdir, (short) module name
-            ("GCC-4.7.2.eb", "Core", "GCC/4.7.2", 'F'),  # already present and listed, so 'F'
+            ("GCC-4.7.2.eb", "Core", "GCC/4.7.2", 'x'),  # already present but not listed, so 'x'
             ("hwloc-1.6.2-GCC-4.7.2.eb", "Compiler/GCC/4.7.2", "hwloc/1.6.2", 'x'),
-            ("OpenMPI-1.6.4-GCC-4.7.2.eb", "Compiler/GCC/4.7.2", "OpenMPI/1.6.4", 'x'),
+            ("OpenMPI-1.6.4-GCC-4.7.2.eb", "Compiler/GCC/4.7.2", "OpenMPI/1.6.4", 'F'),  # already present and listed, so 'F'
             ("gompi-1.4.10.eb", "Core", "gompi/1.4.10", 'x'),
             ("OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4",
              "OpenBLAS/0.2.6-LAPACK-3.4.2", 'x'),

From 7d19f423b57ff730f71400af3bfdb062404b14cc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 16:01:45 +0200
Subject: [PATCH 0149/1356] make very sure $MODULEPATH is empty before
 redefining it in unit tests

---
 test/framework/utilities.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index ad250c2104..0b57dc2a26 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -150,6 +150,10 @@ def reset_modulepath(self, modpaths):
         modtool = modules_tool()
         for modpath in os.environ.get('MODULEPATH', '').split(os.pathsep):
             modtool.remove_module_path(modpath)
+        # make very sure $MODULEPATH is totally empty
+        # some paths may be left behind, e.g. when they contain environment variables
+        # example: "module unuse Modules/$MODULE_VERSION/modulefiles" may not yield the desired result
+        os.environ['MODULEPATH'] = ''
         for modpath in modpaths:
             modtool.add_module_path(modpath)
 

From 895d46a15d38fa8a45ed131ef5745bb860b232cf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 16:15:54 +0200
Subject: [PATCH 0150/1356] fix --try --force combo behavior by only returning
 tweaked easyconfigs for easyconfigs that were listed originally

---
 easybuild/framework/easyconfig/tweak.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 23e48ff647..0ebe42065f 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -77,6 +77,9 @@ def tweak(easyconfigs, build_specs, targetdir=None):
     if len(toolchains) > 1:
         _log.error("Multiple toolchains featured in easyconfigs, --try-X not supported in that case: %s" % toolchains)
 
+    # keep track of originally listed easyconfigs (via their path)
+    listed_ec_paths = [ec['spec'] for ec in easyconfigs]
+
     # obtain full dependency graph for specified easyconfigs
     # easyconfigs will be ordered 'top-to-bottom': toolchain dependencies and toolchain first
     orig_ecs = resolve_dependencies(easyconfigs, retain_all_deps=True)
@@ -91,13 +94,16 @@ def tweak(easyconfigs, build_specs, targetdir=None):
             orig_ecs = orig_ecs[1:]
 
     # generate tweaked easyconfigs, and continue with those instead
-    easyconfigs = []
+    tweaked_easyconfigs = []
     for orig_ec in orig_ecs:
         new_ec_file = tweak_one(orig_ec['spec'], None, build_specs, targetdir=targetdir)
-        new_ecs = process_easyconfig(new_ec_file, build_specs=build_specs)
-        easyconfigs.extend(new_ecs)
+        # only return tweaked easyconfigs for easyconfigs which were listed originally
+        # easyconfig files for dependencies are also generated but not included, and will be resolved via --robot
+        if orig_ec['spec'] in listed_ec_paths:
+            new_ecs = process_easyconfig(new_ec_file, build_specs=build_specs)
+            tweaked_easyconfigs.extend(new_ecs)
 
-    return easyconfigs
+    return tweaked_easyconfigs
 
 
 def tweak_one(src_fn, target_fn, tweaks, targetdir=None):

From 3b2ff14c27ec2333cd148acdc4d14913935f3fae Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 16:16:04 +0200
Subject: [PATCH 0151/1356] add unit test for --try --robot --force combination

---
 test/framework/options.py | 44 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 46d8a15f9f..a482247a84 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -597,6 +597,50 @@ def test_dry_run(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
+    def test_try_robot_force(self):
+        """
+        Test correct behavior for combination of --try-toolchain --robot --force.
+        Only the listed easyconfigs should be forced, resolved dependencies should not (even if tweaked).
+        """
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        # use toy-0.0.eb easyconfig file that comes with the tests
+        test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        eb_file1 = os.path.join(test_ecs_dir, 'FFTW-3.3.3-gompi-1.4.10.eb')
+        eb_file2 = os.path.join(test_ecs_dir, 'ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb')
+
+        # check log message with --skip for existing module
+        args = [
+            eb_file1,
+            eb_file2,
+            '--sourcepath=%s' % self.test_sourcepath,
+            '--buildpath=%s' % self.test_buildpath,
+            '--installpath=%s' % self.test_installpath,
+            '--debug',
+            '--force',
+            '--robot=%s' % test_ecs_dir,
+            '--try-toolchain=gompi,1.3.12',
+            '--dry-run',
+            '--unittest-file=%s' % self.logfile,
+        ]
+        outtxt = self.eb_main(args, logfile=dummylogfn)
+
+        scalapack_ver = '2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2'
+        ecs_mods = [
+            # GCC/OpenMPI dependencies are there, but part of toolchain => 'x'
+            ("GCC-4.6.4.eb", "GCC/4.6.4", 'x'),
+            ("OpenMPI-1.6.4-GCC-4.6.4.eb", "OpenMPI/1.6.4-GCC-4.6.4", 'x'),
+            # OpenBLAS dependency is there, but not listed => 'x'
+            ("OpenBLAS-0.2.6-gompi-1.3.12-LAPACK-3.4.2.eb", "OpenBLAS/0.2.6-gompi-1.3.12-LAPACK-3.4.2", 'x'),
+            # both FFTW and ScaLAPACK are listed => 'F'
+            ("ScaLAPACK-%s.eb" % scalapack_ver, "ScaLAPACK/%s" % scalapack_ver, 'F'),
+            ("FFTW-3.3.3-gompi-1.3.12.eb", "FFTW/3.3.3-gompi-1.3.12", 'F'),
+        ]
+        for ec, mod, mark in ecs_mods:
+            regex = re.compile("^ \* \[%s\] \S+%s \(module: %s\)$" % (mark, ec, mod), re.M)
+            self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
+
     def test_dry_run_hierarchical(self):
         """Test dry run using a hierarchical module naming scheme."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')

From d7f3acab8fdd3603c00316186f414b5dbb795edf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 17:44:29 +0200
Subject: [PATCH 0152/1356] add --(try-)software cmdline options, don't recurse
 when --try-software(-X) is used

---
 easybuild/framework/easyconfig/tweak.py | 13 ++++--
 easybuild/tools/options.py              | 59 ++++++++++++++-----------
 2 files changed, 43 insertions(+), 29 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 23e48ff647..ce147fb584 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -77,9 +77,16 @@ def tweak(easyconfigs, build_specs, targetdir=None):
     if len(toolchains) > 1:
         _log.error("Multiple toolchains featured in easyconfigs, --try-X not supported in that case: %s" % toolchains)
 
-    # obtain full dependency graph for specified easyconfigs
-    # easyconfigs will be ordered 'top-to-bottom': toolchain dependencies and toolchain first
-    orig_ecs = resolve_dependencies(easyconfigs, retain_all_deps=True)
+
+    if 'name' in build_specs or 'version' in build_specs:
+        # no recursion if software name/version build specification are included
+        # in that case, do not construct full dependency graph
+        orig_ecs = easyconfigs
+    else:
+        # build specifications should be applied to the whole dependency graph
+        # obtain full dependency graph for specified easyconfigs
+        # easyconfigs will be ordered 'top-to-bottom': toolchain dependencies and toolchain first
+        orig_ecs = resolve_dependencies(easyconfigs, retain_all_deps=True)
 
     # determine toolchain based on last easyconfigs
     toolchain = orig_ecs[-1]['ec']['toolchain']
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 893b121318..f20554ad1c 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -49,7 +49,6 @@
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
-from easybuild.tools.build_log import print_warning
 from easybuild.tools.config import get_default_configfiles, get_pretend_installpath
 from easybuild.tools.config import get_default_oldstyle_configfile_defaults, DEFAULT_MODULECLASSES
 from easybuild.tools.convert import ListOfStrings
@@ -66,6 +65,9 @@
 from vsc.utils.missing import any
 
 
+_log = fancylogger.getLogger('tools.options', fname=False)
+
+
 class EasyBuildOptions(GeneralOption):
     """Easybuild generaloption class"""
     VERSION = this_is_easybuild()
@@ -121,15 +123,17 @@ def software_options(self):
             'amend':(("Specify additional search and build parameters (can be used multiple times); "
                       "for example: versionprefix=foo or patches=one.patch,two.patch)"),
                       None, 'append', None, {'metavar': 'VAR=VALUE[,VALUE]'}),
-            'software-name': ("Search and build software with name",
+            'software': ("Search and build software with given name and version",
+                              None, 'extend', None, {'metavar': 'NAME,VERSION'}),
+            'software-name': ("Search and build software with given name",
                               None, 'store', None, {'metavar': 'NAME'}),
-            'software-version': ("Search and build software with version",
+            'software-version': ("Search and build software with given version",
                                  None, 'store', None, {'metavar': 'VERSION'}),
-            'toolchain': ("Search and build with toolchain (name and version)",
+            'toolchain': ("Search and build with given toolchain (name and version)",
                           None, 'extend', None, {'metavar': 'NAME,VERSION'}),
-            'toolchain-name': ("Search and build with toolchain name",
+            'toolchain-name': ("Search and build with given toolchain name",
                                None, 'store', None, {'metavar': 'NAME'}),
-            'toolchain-version': ("Search and build with toolchain version",
+            'toolchain-version': ("Search and build with given toolchain version",
                                   None, 'store', None, {'metavar': 'VERSION'}),
         })
 
@@ -330,12 +334,10 @@ def validate(self):
         """Additional validation of options"""
         stop_msg = []
 
-        if self.options.toolchain and not len(self.options.toolchain) == 2:
-            stop_msg.append('--toolchain requires NAME,VERSION (given %s)' %
-                            (','.join(self.options.toolchain)))
-        if self.options.try_toolchain and not len(self.options.try_toolchain) == 2:
-            stop_msg.append('--try-toolchain requires NAME,VERSION (given %s)' %
-                            (','.join(self.options.try_toolchain)))
+        for opt in ['software', 'try-software', 'toolchain', 'try-toolchain']:
+            val = getattr(self.options, opt.replace('-', '_'))
+            if val and len(val) != 2:
+                stop_msg.append('--%s requires NAME,VERSION (given %s)' % (opt, ','.join(val)))
 
         if self.options.umask:
             umask_regex = re.compile('^[0-7]{3}$')
@@ -346,8 +348,7 @@ def validate(self):
             indent = " "*2
             stop_msg = ['%s%s' % (indent, x) for x in stop_msg]
             stop_msg.insert(0, 'ERROR: Found %s problems validating the options:' % len(stop_msg))
-            print "\n".join(stop_msg)
-            sys.exit(1)
+            _log.error('\n'.join(stop_msg))
 
     def postprocess(self):
         """Do some postprocessing, in particular print stuff"""
@@ -671,17 +672,23 @@ def process_software_build_specs(options):
             # only when a try option is set do we enable generating easyconfigs
             try_to_generate = True
 
-    # process --toolchain --try-toolchain (sanity check done in tools.options)
-    tc = options.toolchain or options.try_toolchain
-    if tc:
-        if options.toolchain and options.try_toolchain:
-            print_warning("Ignoring --try-toolchain, only using --toolchain specification.")
-        elif options.try_toolchain:
-            try_to_generate = True
-        build_specs.update({
-            'toolchain_name': tc[0],
-            'toolchain_version': tc[1],
-        })
+    # process --(try-)software/toolchain
+    for opt in ['software', 'toolchain']:
+        val = getattr(options, opt)
+        tryval = getattr(options, 'try_%s' % opt)
+        if val or tryval:
+            if val and tryval:
+                _log.warning("Ignoring --try-%(opt)s, only using --%(opt)s specification" % {'opt': opt})
+            elif tryval:
+                try_to_generate = True
+            val = val or tryval  # --try-X value is overridden by --X
+            key_prefix = ''
+            if opt == 'toolchain':
+                key_prefix = 'toolchain_'
+            build_specs.update({
+                '%sname' % key_prefix: val[0],
+                '%sversion' % key_prefix: val[1],
+            })
 
     # provide both toolchain and toolchain_name/toolchain_version keys
     if 'toolchain_name' in build_specs:
@@ -697,7 +704,7 @@ def process_software_build_specs(options):
         if options.amend:
             amends += options.amend
             if options.try_amend:
-                print_warning("Ignoring options passed via --try-amend, only using those passed via --amend.")
+                _log.warning("Ignoring options passed via --try-amend, only using those passed via --amend.")
         if options.try_amend:
             amends += options.try_amend
             try_to_generate = True

From 40431efd5af4ef316804d1f6b4bef4a68fb0c2ee Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 17:44:47 +0200
Subject: [PATCH 0153/1356] add unit test for --try-X cmdline options

---
 test/framework/options.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 46d8a15f9f..6cadc3e2fb 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -962,6 +962,44 @@ def test_allow_modules_tool_mismatch(self):
         else:
             del os.environ['module']
 
+    def test_try(self):
+        """Test whether --try options are taken into account."""
+        ec_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb')
+        args = [
+            ec_file,
+            '--sourcepath=%s' % self.test_sourcepath,
+            '--buildpath=%s' % self.test_buildpath,
+            '--installpath=%s' % self.test_installpath,
+            '--dry-run',
+        ]
+
+        test_cases = [
+            ([], 'toy/0.0'),
+            (['--try-software=foo,1.2.3', '--try-toolchain=gompi,1.4.10'], 'foo/1.2.3-gompi-1.4.10'),
+            (['--try-toolchain-name=gompi', '--try-toolchain-version=1.4.10'], 'toy/0.0-gompi-1.4.10'),
+            (['--try-software-name=foo', '--try-software-version=1.2.3'], 'foo/1.2.3'),
+            (['--try-toolchain-name=gompi', '--try-toolchain-version=1.4.10'], 'toy/0.0-gompi-1.4.10'),
+            (['--try-software-version=1.2.3', '--try-toolchain=gompi,1.4.10'], 'toy/1.2.3-gompi-1.4.10'),
+            (['--try-amend=versionsuffix=-test'], 'toy/0.0-test'),
+            # only --try causes other build specs to be included too
+            (['--try-software=foo,1.2.3', '--toolchain=gompi,1.4.10'], 'foo/1.2.3-gompi-1.4.10'),
+            (['--software=foo,1.2.3', '--try-toolchain=gompi,1.4.10'], 'foo/1.2.3-gompi-1.4.10'),
+            (['--software=foo,1.2.3', '--try-amend=versionsuffix=-test'], 'foo/1.2.3-test'),
+        ]
+
+        for extra_args, mod in test_cases:
+            outtxt = self.eb_main(args + extra_args, verbose=True, raise_error=True)
+            mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
+            self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
+
+        for extra_arg in ['--try-software=foo', '--try-toolchain=gompi', '--try-toolchain=gomp,1.4.10,-no-OFED']:
+            allargs = args + [extra_arg]
+            self.assertErrorRegex(EasyBuildError, "requires NAME,VERSION", self.eb_main, allargs, raise_error=True)
+
+        # no --try used, so no tweaked easyconfig files are generated
+        allargs = args + ['--software-version=1.2.3', '--toolchain=gompi,1.4.10']
+        self.assertErrorRegex(EasyBuildError, "version .* not available", self.eb_main, allargs, raise_error=True)
+
     def test_recursive_try(self):
         """Test whether recursive --try-X works."""
         ecs_path = os.path.join(os.path.dirname(__file__), 'easyconfigs')

From eae8bf4202356d7d148903e6da2b81bbaa6623fe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 17:55:20 +0200
Subject: [PATCH 0154/1356] test that --try-software options are *not* applied
 recursively

---
 test/framework/options.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 6cadc3e2fb..b58b4d3a1a 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1023,7 +1023,7 @@ def test_recursive_try(self):
 
         for extra_args in [[], ['--module-naming-scheme=HierarchicalMNS']]:
 
-            outtxt = self.eb_main(args + extra_args, do_build=True, verbose=True, raise_error=True)
+            outtxt = self.eb_main(args + extra_args, verbose=True, raise_error=True)
 
             # toolchain gompi/1.4.10 should be listed
             tc_regex = re.compile("^\s*\*\s*\[.\]\s*\S*%s/gompi-1.4.10.eb\s\(module: gompi/1.4.10\)\s*$" % ecs_path, re.M)
@@ -1036,6 +1036,15 @@ def test_recursive_try(self):
                 mod_regex = re.compile("^\s*\*\s*\[.\]\s*\S*/easybuild-\S*/%s\s\(module: %s\)\s*$" % (ec, mod), re.M)
                 self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 
+        # no recursive try for --try-software(-X)
+        outtxt = self.eb_main(args + ['--try-software-version=1.2.3'], raise_error=True)
+        for mod in ['toy/1.2.3-gompi-1.4.10', 'gzip/1.4-gompi-1.4.10', 'gompi/1.4.10', 'GCC/4.7.2']:
+            mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
+            self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
+        for mod in ['gzip/1.2.3-gompi-1.4.10']:
+            mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
+            self.assertFalse(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
+
     def test_cleanup_builddir(self):
         """Test cleaning up of build dir and --disable-cleanup-builddir."""
         toy_ec = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')

From b005d5316d5ab51c6702f0c7b89aba98adea07c0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 18:15:37 +0200
Subject: [PATCH 0155/1356] extend testcase for no recursion when --software is
 involved

---
 test/framework/options.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index b58b4d3a1a..c53dd89b75 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1036,14 +1036,15 @@ def test_recursive_try(self):
                 mod_regex = re.compile("^\s*\*\s*\[.\]\s*\S*/easybuild-\S*/%s\s\(module: %s\)\s*$" % (ec, mod), re.M)
                 self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 
-        # no recursive try for --try-software(-X)
-        outtxt = self.eb_main(args + ['--try-software-version=1.2.3'], raise_error=True)
-        for mod in ['toy/1.2.3-gompi-1.4.10', 'gzip/1.4-gompi-1.4.10', 'gompi/1.4.10', 'GCC/4.7.2']:
-            mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
-            self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
-        for mod in ['gzip/1.2.3-gompi-1.4.10']:
-            mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
-            self.assertFalse(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
+        # no recursive try if --(try-)software(-X) is involved
+        for extra_args in [['--try-software-version=1.2.3'], ['--software-version=1.2.3']]:
+            outtxt = self.eb_main(args + extra_args, raise_error=True)
+            for mod in ['toy/1.2.3-gompi-1.4.10', 'gzip/1.4-gompi-1.4.10', 'gompi/1.4.10', 'GCC/4.7.2']:
+                mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
+                self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
+            for mod in ['gzip/1.2.3-gompi-1.4.10']:
+                mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
+                self.assertFalse(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 
     def test_cleanup_builddir(self):
         """Test cleaning up of build dir and --disable-cleanup-builddir."""

From 7726971b69092310e2c92344d6cda1a08b0e8885 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 20:03:42 +0200
Subject: [PATCH 0156/1356] add is_module_for method to module naming scheme
 API, and use it to verify toolchain definition based on module names

---
 easybuild/framework/easyconfig/easyconfig.py | 14 ++++++++++++-
 easybuild/tools/module_naming_scheme/mns.py  | 15 ++++++++++++++
 easybuild/tools/toolchain/toolchain.py       | 21 ++++++--------------
 3 files changed, 34 insertions(+), 16 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 3c48a45779..7a170f1099 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -456,7 +456,7 @@ def toolchain(self):
         returns the Toolchain used
         """
         if self._toolchain is None:
-            self._toolchain = get_toolchain(self['toolchain'], self['toolchainopts'], ActiveMNS())
+            self._toolchain = get_toolchain(self['toolchain'], self['toolchainopts'], mns=ActiveMNS())
             tc_dict = self._toolchain.as_dict()
             self.log.debug("Initialized toolchain: %s (opts: %s)" % (tc_dict, self['toolchainopts']))
         return self._toolchain
@@ -1082,6 +1082,12 @@ def det_short_module_name(self, ec, force_visible=False):
         self.log.debug("Determining short module name for %s (force_visible: %s)" % (ec, force_visible))
         mod_name = self._det_module_name_with(self.mns.det_short_module_name, ec, force_visible=force_visible)
         self.log.debug("Obtained valid short module name %s" % mod_name)
+
+        # sanity check: obtained module name should pass the 'is_module_for' check
+        if not self.is_module_for(mod_name, ec['name']):
+            tup = (mod_name, ec['name'])
+            self.log.error("is_module_for('%s', '%s') for active module naming scheme returns False" % tup)
+
         return mod_name
 
     def det_module_subdir(self, ec):
@@ -1117,3 +1123,9 @@ def expand_toolchain_load(self):
         This is useful when toolchains are not exposed to users.
         """
         return self.mns.expand_toolchain_load()
+
+    def is_module_for(self, modname, name):
+        """
+        Determine whether the specified (short) module name is a module for software with the specified name.
+        """
+        return self.mns.is_module_for(modname, name)
diff --git a/easybuild/tools/module_naming_scheme/mns.py b/easybuild/tools/module_naming_scheme/mns.py
index 48da9c8a8d..f9eb8e0a19 100644
--- a/easybuild/tools/module_naming_scheme/mns.py
+++ b/easybuild/tools/module_naming_scheme/mns.py
@@ -28,6 +28,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
+import re
 from vsc.utils import fancylogger
 from vsc.utils.patterns import Singleton
 
@@ -123,3 +124,17 @@ def expand_toolchain_load(self):
         """
         # by default: just include a load statement for the toolchain
         return False
+
+    def is_module_for(self, modname, name):
+        """
+        Determine whether the specified (short) module name is a module for software with the specified name.
+        Default implementation checks via a strict regex pattern, and assumes short module names are of the form:
+            <name>/<version>[-<toolchain>]
+        """
+        modname_regex = re.compile('^%s/\S+$' % name)
+        res = bool(modname_regex.match(modname))
+
+        tup = (modname, name, modname_regex.pattern, res)
+        self.log.debug("Checking whether '%s' is a module name for software with name '%s' via regex %s: %s" % tup)
+
+        return res
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 184fddf58c..495268f543 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -94,16 +94,17 @@ def __init__(self, name=None, version=None, mns=None):
         self.vars = None
 
         self.modules_tool = modules_tool()
+        self.mns = mns
         self.mod_full_name = None
         self.mod_short_name = None
         self.init_modpaths = None
         if self.name != DUMMY_TOOLCHAIN_NAME:
             # sometimes no module naming scheme class instance can/will be provided, e.g. with --list-toolchains
-            if mns is not None:
+            if self.mns is not None:
                 tc_dict = self.as_dict()
-                self.mod_full_name = mns.det_full_module_name(tc_dict)
-                self.mod_short_name = mns.det_short_module_name(tc_dict)
-                self.init_modpaths = mns.det_init_modulepaths(tc_dict)
+                self.mod_full_name = self.mns.det_full_module_name(tc_dict)
+                self.mod_short_name = self.mns.det_short_module_name(tc_dict)
+                self.init_modpaths = self.mns.det_init_modulepaths(tc_dict)
 
     def base_init(self):
         if not hasattr(self, 'log'):
@@ -317,17 +318,7 @@ def definition(self):
 
     def is_dep_in_toolchain_module(self, name):
         """Check whether a specific software name is listed as a dependency in the module for this toolchain."""
-        # check whether a module for the toolchain element with specified name is present
-        # assumption: the software name is a prefix for either one of the module filepath subdirs, or its filename
-        # for example, when looking for 'BLACS', to following modules are considered to be BLACS modules:
-        # - BLACS/1.1-gompi-1.1.0-no-OFED
-        # - apps/blacs/1.1
-        # - lib/math/BLACS-stable/1.1
-        # the following ones are NOT consider BLACS modules, even though the substring 'blacs' is included in the module name
-        # - ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1
-        # - apps/math-blacs/1.1
-        modname_regex = re.compile('(?:^|/)%s' % name, re.I)
-        return any(map(modname_regex.search, self.toolchain_dep_mods))
+        return any(map(lambda m: self.mns.is_module_for(m, name), self.toolchain_dep_mods))
 
     def prepare(self, onlymod=None):
         """

From 6b6cb7dffe2e5961f62186c976797232f773c931 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 20:04:05 +0200
Subject: [PATCH 0157/1356] add unit test for is_module_for method, fix test
 module naming schemes

---
 test/framework/module_generator.py            | 20 +++++++++++++++++++
 .../test_module_naming_scheme.py              |  6 ++++++
 .../test_module_naming_scheme_more.py         |  6 ++++++
 3 files changed, 32 insertions(+)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 3b720e2a9e..5323e9e1fe 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -347,6 +347,26 @@ def test_mod_name_validation(self):
         self.assertTrue(is_valid_module_name('foo-bar/1.2.3'))
         self.assertTrue(is_valid_module_name('ictce'))
 
+    def test_is_module_for(self):
+        """Test is_module_for method of module naming schemes."""
+        test_cases = [
+            ('GCC/4.7.2', 'GCC', True),
+            ('gzip/1.6-gompi-1.4.10', 'gzip', True),
+            ('OpenMPI/1.6.4-GCC-4.7.2-no-OFED', 'OpenMPI', True),
+            ('BLACS/1.1-gompi-1.1.0-no-OFED', 'BLACS', True),
+            ('ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1', 'ScaLAPACK', True),
+            ('gcc/4.7.2', 'GCC', False),
+            ('ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1', 'BLACS', False),
+            ('apps/blacs/1.1', 'BLACS', False),
+            ('lib/math/BLACS-stable/1.1', 'BLACS', False),
+        ]
+        for modname, softname, res in test_cases:
+            if res:
+                errormsg = "%s is recognised as a module for '%s'" % (modname, softname)
+            else:
+                errormsg = "%s is NOT recognised as a module for '%s'" % (modname, softname)
+            self.assertEqual(ActiveMNS().is_module_for(modname, softname), res, errormsg)
+
     def test_hierarchical_mns(self):
         """Test hierarchical module naming scheme."""
 
diff --git a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py
index 2b682a72b1..a705da1f77 100644
--- a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py
+++ b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py
@@ -61,3 +61,9 @@ def det_module_symlink_paths(self, ec):
         Determine list of paths in which symlinks to module files must be created.
         """
         return [ec['moduleclass'].upper(), ec['name'].lower()[0]]
+
+    def is_module_for(self, modname, name):
+        """
+        Determine whether the specified (short) module name is a module for software with the specified name.
+        """
+        return modname.find('%s' % name)!= -1
diff --git a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py
index d7ba785468..7b7c49c115 100644
--- a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py
+++ b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py
@@ -70,3 +70,9 @@ def det_full_module_name(self, ec):
         ec_sha1 = sha1(res).hexdigest()
         _log.debug("SHA1 for string '%s' obtained for %s: %s" % (res, ec, ec_sha1))
         return os.path.join(ec['name'], ec_sha1)
+
+    def is_module_for(self, modname, name):
+        """
+        Determine whether the specified (short) module name is a module for software with the specified name.
+        """
+        return modname.startswith(name)

From 8a327e370f3bd9ecaaed54c1d3ba248e3717c613 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 22:02:32 +0200
Subject: [PATCH 0158/1356] fix remark w.r.t. name of method, renamed to
 is_short_modname_for

---
 easybuild/framework/easyconfig/easyconfig.py | 10 +++++-----
 easybuild/tools/module_naming_scheme/mns.py  |  6 +++---
 easybuild/tools/toolchain/toolchain.py       |  2 +-
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 7a170f1099..3fea3e6c3e 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1083,10 +1083,10 @@ def det_short_module_name(self, ec, force_visible=False):
         mod_name = self._det_module_name_with(self.mns.det_short_module_name, ec, force_visible=force_visible)
         self.log.debug("Obtained valid short module name %s" % mod_name)
 
-        # sanity check: obtained module name should pass the 'is_module_for' check
-        if not self.is_module_for(mod_name, ec['name']):
+        # sanity check: obtained module name should pass the 'is_short_modname_for' check
+        if not self.is_short_modname_for(mod_name, ec['name']):
             tup = (mod_name, ec['name'])
-            self.log.error("is_module_for('%s', '%s') for active module naming scheme returns False" % tup)
+            self.log.error("is_short_modname_for('%s', '%s') for active module naming scheme returns False" % tup)
 
         return mod_name
 
@@ -1124,8 +1124,8 @@ def expand_toolchain_load(self):
         """
         return self.mns.expand_toolchain_load()
 
-    def is_module_for(self, modname, name):
+    def is_short_modname_for(self, short_modname, name):
         """
         Determine whether the specified (short) module name is a module for software with the specified name.
         """
-        return self.mns.is_module_for(modname, name)
+        return self.mns.is_short_modname_for(short_modname, name)
diff --git a/easybuild/tools/module_naming_scheme/mns.py b/easybuild/tools/module_naming_scheme/mns.py
index f9eb8e0a19..2d84760729 100644
--- a/easybuild/tools/module_naming_scheme/mns.py
+++ b/easybuild/tools/module_naming_scheme/mns.py
@@ -125,16 +125,16 @@ def expand_toolchain_load(self):
         # by default: just include a load statement for the toolchain
         return False
 
-    def is_module_for(self, modname, name):
+    def is_short_modname_for(self, short_modname, name):
         """
         Determine whether the specified (short) module name is a module for software with the specified name.
         Default implementation checks via a strict regex pattern, and assumes short module names are of the form:
             <name>/<version>[-<toolchain>]
         """
         modname_regex = re.compile('^%s/\S+$' % name)
-        res = bool(modname_regex.match(modname))
+        res = bool(modname_regex.match(short_modname))
 
-        tup = (modname, name, modname_regex.pattern, res)
+        tup = (short_modname, name, modname_regex.pattern, res)
         self.log.debug("Checking whether '%s' is a module name for software with name '%s' via regex %s: %s" % tup)
 
         return res
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 495268f543..75c5a29c85 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -318,7 +318,7 @@ def definition(self):
 
     def is_dep_in_toolchain_module(self, name):
         """Check whether a specific software name is listed as a dependency in the module for this toolchain."""
-        return any(map(lambda m: self.mns.is_module_for(m, name), self.toolchain_dep_mods))
+        return any(map(lambda m: self.mns.is_short_modname_for(m, name), self.toolchain_dep_mods))
 
     def prepare(self, onlymod=None):
         """

From 5b8dad1835f158a2675fb4b7f25db5867eb75c89 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 22:16:53 +0200
Subject: [PATCH 0159/1356] rename mns method to is_short_modname_for

---
 test/framework/module_generator.py                          | 6 +++---
 .../tools/module_naming_scheme/test_module_naming_scheme.py | 2 +-
 .../module_naming_scheme/test_module_naming_scheme_more.py  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 5323e9e1fe..48a178f4b8 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -347,8 +347,8 @@ def test_mod_name_validation(self):
         self.assertTrue(is_valid_module_name('foo-bar/1.2.3'))
         self.assertTrue(is_valid_module_name('ictce'))
 
-    def test_is_module_for(self):
-        """Test is_module_for method of module naming schemes."""
+    def test_is_short_modname_for(self):
+        """Test is_short_modname_for method of module naming schemes."""
         test_cases = [
             ('GCC/4.7.2', 'GCC', True),
             ('gzip/1.6-gompi-1.4.10', 'gzip', True),
@@ -365,7 +365,7 @@ def test_is_module_for(self):
                 errormsg = "%s is recognised as a module for '%s'" % (modname, softname)
             else:
                 errormsg = "%s is NOT recognised as a module for '%s'" % (modname, softname)
-            self.assertEqual(ActiveMNS().is_module_for(modname, softname), res, errormsg)
+            self.assertEqual(ActiveMNS().is_short_modname_for(modname, softname), res, errormsg)
 
     def test_hierarchical_mns(self):
         """Test hierarchical module naming scheme."""
diff --git a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py
index a705da1f77..1fa5865941 100644
--- a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py
+++ b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py
@@ -62,7 +62,7 @@ def det_module_symlink_paths(self, ec):
         """
         return [ec['moduleclass'].upper(), ec['name'].lower()[0]]
 
-    def is_module_for(self, modname, name):
+    def is_short_modname_for(self, modname, name):
         """
         Determine whether the specified (short) module name is a module for software with the specified name.
         """
diff --git a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py
index 7b7c49c115..8e8d74e0c8 100644
--- a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py
+++ b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py
@@ -71,7 +71,7 @@ def det_full_module_name(self, ec):
         _log.debug("SHA1 for string '%s' obtained for %s: %s" % (res, ec, ec_sha1))
         return os.path.join(ec['name'], ec_sha1)
 
-    def is_module_for(self, modname, name):
+    def is_short_modname_for(self, modname, name):
         """
         Determine whether the specified (short) module name is a module for software with the specified name.
         """

From 71df7f01ec6618de8afeb5acc7abdbe3819be418 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 23:17:00 +0200
Subject: [PATCH 0160/1356] fix remarks

---
 easybuild/framework/easyconfig/tweak.py |  3 ++-
 easybuild/tools/options.py              | 27 +++++++++++++------------
 test/framework/options.py               |  2 +-
 3 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index ce147fb584..931b9a46d5 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -77,15 +77,16 @@ def tweak(easyconfigs, build_specs, targetdir=None):
     if len(toolchains) > 1:
         _log.error("Multiple toolchains featured in easyconfigs, --try-X not supported in that case: %s" % toolchains)
 
-
     if 'name' in build_specs or 'version' in build_specs:
         # no recursion if software name/version build specification are included
         # in that case, do not construct full dependency graph
         orig_ecs = easyconfigs
+        _log.debug("Software name/version found, so not applying build specifications recursively: %s" % build_specs)
     else:
         # build specifications should be applied to the whole dependency graph
         # obtain full dependency graph for specified easyconfigs
         # easyconfigs will be ordered 'top-to-bottom': toolchain dependencies and toolchain first
+        _log.debug("Applying build specifications recursively (no software name/version found): %s" % build_specs)
         orig_ecs = resolve_dependencies(easyconfigs, retain_all_deps=True)
 
     # determine toolchain based on last easyconfigs
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index f20554ad1c..a97ba1707b 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -65,9 +65,6 @@
 from vsc.utils.missing import any
 
 
-_log = fancylogger.getLogger('tools.options', fname=False)
-
-
 class EasyBuildOptions(GeneralOption):
     """Easybuild generaloption class"""
     VERSION = this_is_easybuild()
@@ -77,6 +74,11 @@ class EasyBuildOptions(GeneralOption):
 
     ALLOPTSMANDATORY = False  # allow more than one argument
 
+    def __init__(self, *args, **kwargs):
+        """EasyBuildOptions constructor."""
+        super(EasyBuildOptions, self).__init__(*args, **kwargs)
+        self.log = fancylogger.getLogger(name=self.__class__.__name__, fname=False)
+
     def basic_options(self):
         """basic runtime options"""
         all_stops = [x[0] for x in EasyBlock.get_steps()]
@@ -332,23 +334,22 @@ def unittest_options(self):
 
     def validate(self):
         """Additional validation of options"""
-        stop_msg = []
+        error_cnt = 0
 
         for opt in ['software', 'try-software', 'toolchain', 'try-toolchain']:
             val = getattr(self.options, opt.replace('-', '_'))
             if val and len(val) != 2:
-                stop_msg.append('--%s requires NAME,VERSION (given %s)' % (opt, ','.join(val)))
+                self.log.warning('--%s requires NAME,VERSION (given %s)' % (opt, ','.join(val)))
+                error_cnt += 1
 
         if self.options.umask:
             umask_regex = re.compile('^[0-7]{3}$')
             if not umask_regex.match(self.options.umask):
-                stop_msg.append("--umask value should be 3 digits (0-7) (regex pattern '%s')" % umask_regex.pattern)
+                self.log.warning("--umask value should be 3 digits (0-7) (regex pattern '%s')" % umask_regex.pattern)
+                error_cnt += 1
 
-        if len(stop_msg) > 0:
-            indent = " "*2
-            stop_msg = ['%s%s' % (indent, x) for x in stop_msg]
-            stop_msg.insert(0, 'ERROR: Found %s problems validating the options:' % len(stop_msg))
-            _log.error('\n'.join(stop_msg))
+        if error_cnt > 0:
+            self.log.error("Found %s problems validating the options, treating warnings as fatal." % error_cnt)
 
     def postprocess(self):
         """Do some postprocessing, in particular print stuff"""
@@ -678,7 +679,7 @@ def process_software_build_specs(options):
         tryval = getattr(options, 'try_%s' % opt)
         if val or tryval:
             if val and tryval:
-                _log.warning("Ignoring --try-%(opt)s, only using --%(opt)s specification" % {'opt': opt})
+                self.log.warning("Ignoring --try-%(opt)s, only using --%(opt)s specification" % {'opt': opt})
             elif tryval:
                 try_to_generate = True
             val = val or tryval  # --try-X value is overridden by --X
@@ -704,7 +705,7 @@ def process_software_build_specs(options):
         if options.amend:
             amends += options.amend
             if options.try_amend:
-                _log.warning("Ignoring options passed via --try-amend, only using those passed via --amend.")
+                self.log.warning("Ignoring options passed via --try-amend, only using those passed via --amend.")
         if options.try_amend:
             amends += options.try_amend
             try_to_generate = True
diff --git a/test/framework/options.py b/test/framework/options.py
index 60b50110ee..07278259c2 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -998,7 +998,7 @@ def test_try(self):
 
         for extra_arg in ['--try-software=foo', '--try-toolchain=gompi', '--try-toolchain=gomp,1.4.10,-no-OFED']:
             allargs = args + [extra_arg]
-            self.assertErrorRegex(EasyBuildError, "requires NAME,VERSION", self.eb_main, allargs, raise_error=True)
+            self.assertErrorRegex(EasyBuildError, "problems validating the options", self.eb_main, allargs, raise_error=True)
 
         # no --try used, so no tweaked easyconfig files are generated
         allargs = args + ['--software-version=1.2.3', '--toolchain=gompi,1.4.10']

From e81cf8e08bc127afa42300af378f514c2628c560 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Sep 2014 23:39:31 +0200
Subject: [PATCH 0161/1356] use self.log provided via GeneralOption

---
 easybuild/tools/options.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index a97ba1707b..4d15565caf 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -74,11 +74,6 @@ class EasyBuildOptions(GeneralOption):
 
     ALLOPTSMANDATORY = False  # allow more than one argument
 
-    def __init__(self, *args, **kwargs):
-        """EasyBuildOptions constructor."""
-        super(EasyBuildOptions, self).__init__(*args, **kwargs)
-        self.log = fancylogger.getLogger(name=self.__class__.__name__, fname=False)
-
     def basic_options(self):
         """basic runtime options"""
         all_stops = [x[0] for x in EasyBlock.get_steps()]
@@ -349,7 +344,7 @@ def validate(self):
                 error_cnt += 1
 
         if error_cnt > 0:
-            self.log.error("Found %s problems validating the options, treating warnings as fatal." % error_cnt)
+            self.log.error("Found %s problems validating the options, treating warnings above as fatal." % error_cnt)
 
     def postprocess(self):
         """Do some postprocessing, in particular print stuff"""

From 66ad64474c16339012e8a00074428714cb15b64b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 6 Sep 2014 00:43:22 +0200
Subject: [PATCH 0162/1356] enhance unit test for is_short_modname_for

---
 test/framework/module_generator.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 48a178f4b8..4e12e71427 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -355,6 +355,7 @@ def test_is_short_modname_for(self):
             ('OpenMPI/1.6.4-GCC-4.7.2-no-OFED', 'OpenMPI', True),
             ('BLACS/1.1-gompi-1.1.0-no-OFED', 'BLACS', True),
             ('ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1', 'ScaLAPACK', True),
+            ('netCDF-C++/4.2-goolf-1.4.10', 'netCDF-C++', True),
             ('gcc/4.7.2', 'GCC', False),
             ('ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1', 'BLACS', False),
             ('apps/blacs/1.1', 'BLACS', False),

From e0712407b9096585271db54f7cec9b1a03a70254 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 6 Sep 2014 00:44:09 +0200
Subject: [PATCH 0163/1356] escape software name before using it in regex in
 is_short_modname_for

---
 easybuild/tools/module_naming_scheme/mns.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/mns.py b/easybuild/tools/module_naming_scheme/mns.py
index 2d84760729..ce6de596c1 100644
--- a/easybuild/tools/module_naming_scheme/mns.py
+++ b/easybuild/tools/module_naming_scheme/mns.py
@@ -131,7 +131,7 @@ def is_short_modname_for(self, short_modname, name):
         Default implementation checks via a strict regex pattern, and assumes short module names are of the form:
             <name>/<version>[-<toolchain>]
         """
-        modname_regex = re.compile('^%s/\S+$' % name)
+        modname_regex = re.compile('^%s/\S+$' % re.escape(name))
         res = bool(modname_regex.match(short_modname))
 
         tup = (short_modname, name, modname_regex.pattern, res)

From c5bde28697bb5bbafef1bb8be70b55abc513eb58 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 9 Sep 2014 17:56:51 +0200
Subject: [PATCH 0164/1356] sync with latest vsc-base version

---
 vsc/README.md              |  2 +-
 vsc/utils/fancylogger.py   | 23 +++++++++++-
 vsc/utils/generaloption.py | 74 ++++++++++++++++++++++++++++++--------
 vsc/utils/rest.py          | 18 +++++++++-
 4 files changed, 99 insertions(+), 18 deletions(-)

diff --git a/vsc/README.md b/vsc/README.md
index 77be7da954..c2fac06881 100644
--- a/vsc/README.md
+++ b/vsc/README.md
@@ -1,3 +1,3 @@
 Code from https://github.com/hpcugent/vsc-base
 
-based on a15bb01eb06b385144325a8d9be20184b1044259 (vsc-base v1.9.2)
+based on 95c2174a243874227dcc895d3e26c1b3b949ba22 (vsc-base v1.9.5)
diff --git a/vsc/utils/fancylogger.py b/vsc/utils/fancylogger.py
index 56a2ded26f..b9576bbd68 100644
--- a/vsc/utils/fancylogger.py
+++ b/vsc/utils/fancylogger.py
@@ -95,9 +95,10 @@
 
 # register new loglevelname
 logging.addLevelName(logging.CRITICAL * 2 + 1, 'APOCALYPTIC')
-# register EXCEPTION and FATAL alias
+# register QUIET, EXCEPTION and FATAL alias
 logging._levelNames['EXCEPTION'] = logging.ERROR
 logging._levelNames['FATAL'] = logging.CRITICAL
+logging._levelNames['QUIET'] = logging.WARNING
 
 
 # mpi rank support
@@ -677,3 +678,23 @@ def disableDefaultHandlers():
 def enableDefaultHandlers():
     """(re)Enable the default handlers on all fancyloggers"""
     _enable_disable_default_handlers(True)
+
+
+def getDetailsLogLevels(fancy=True):
+    """
+    Return list of (name,loglevelname) pairs of existing loggers
+    
+    @param fancy: if True, returns only Fancylogger; if False, returns non-FancyLoggers, 
+                  anything else, return all loggers
+    """
+    func_map = {
+        True: getAllFancyloggers,
+        False: getAllNonFancyloggers,
+    }
+    func = func_map.get(fancy, getAllExistingLoggers)
+    res = []
+    for name, logger in func():
+        # PlaceHolder instances have no level attribute set
+        level_name = logging.getLevelName(getattr(logger, 'level', logging.NOTSET))
+        res.append((name, level_name))
+    return res
diff --git a/vsc/utils/generaloption.py b/vsc/utils/generaloption.py
index c3b94ee983..2dd49ed8ce 100644
--- a/vsc/utils/generaloption.py
+++ b/vsc/utils/generaloption.py
@@ -46,10 +46,11 @@
 from optparse import SUPPRESS_HELP as nohelp  # supported in optparse of python v2.4
 from optparse import _ as _gettext  # this is gettext normally
 from vsc.utils.dateandtime import date_parser, datetime_parser
-from vsc.utils.fancylogger import getLogger, setLogLevel
+from vsc.utils.fancylogger import getLogger, setLogLevel, getDetailsLogLevels
 from vsc.utils.missing import shell_quote, nub
 from vsc.utils.optcomplete import autocomplete, CompleterOption
 
+
 def set_columns(cols=None):
     """Set os.environ COLUMNS variable
         - only if it is not set already
@@ -126,6 +127,11 @@ class ExtOption(CompleterOption):
     TYPES = tuple(['strlist', 'strtuple'] + list(Option.TYPES))
     BOOLEAN_ACTIONS = ('store_true', 'store_false',) + EXTOPTION_LOG
 
+    def __init__(self, *args, **kwargs):
+        """Add logger to init"""
+        CompleterOption.__init__(self, *args, **kwargs)
+        self.log = getLogger(self.__class__.__name__)
+
     def _set_attrs(self, attrs):
         """overwrite _set_attrs to allow store_or callbacks"""
         Option._set_attrs(self, attrs)
@@ -184,9 +190,16 @@ def take_action(self, action, dest, opt, value, values, parser):
                     action = 'store_true'
 
             if orig_action in self.EXTOPTION_LOG and action == 'store_true':
-                setLogLevel(orig_action.split('_')[1][:-3].upper())
+                newloglevel = orig_action.split('_')[1][:-3].upper()
+                logstate = ", ".join(["(%s, %s)" % (n, l) for n, l in getDetailsLogLevels()])
+                self.log.debug("changing loglevel to %s, current state: %s" % (newloglevel, logstate))
+                setLogLevel(newloglevel)
+                self.log.debug("changed loglevel to %s, previous state: %s" % (newloglevel, logstate))
+                if hasattr(values, '_logaction_taken'):
+                    values._logaction_taken[dest] = True
 
             Option.take_action(self, action, dest, opt, value, values, parser)
+
         elif action in self.EXTOPTION_EXTRA_OPTIONS:
             if action == "extend":
                 # comma separated list convert in list
@@ -324,6 +337,7 @@ def __init__(self, *args, **kwargs):
         self.help_to_string = kwargs.pop('help_to_string', None)
         self.help_to_file = kwargs.pop('help_to_file', None)
         self.envvar_prefix = kwargs.pop('envvar_prefix', None)
+        self.process_env_options = kwargs.pop('process_env_options', True)
 
         # py2.4 epilog compatibilty with py2.7 / optparse 1.5.3
         self.epilog = kwargs.pop('epilog', None)
@@ -344,6 +358,9 @@ def __init__(self, *args, **kwargs):
             epilogtxt += ' e.g. option --someopt also supports --disable-someopt.'
             self.epilog.append(epilogtxt % {'disable': self.option_class.DISABLE})
 
+        self.environment_arguments = None
+        self.commandline_arguments = None
+
     def set_description_docstring(self):
         """Try to find the main docstring and add it if description is not None"""
         stack = inspect.stack()[-1]
@@ -400,12 +417,15 @@ def set_usage(self, usage):
     def get_default_values(self):
         """Introduce the ExtValues class with class constant
             - make it dynamic, otherwise the class constant is shared between multiple instances
-            - class constant is used to avoid _taken_action as option in the __dict__
+            - class constant is used to avoid _action_taken as option in the __dict__ 
+                - only works by using reference to object
+                - same for _logaction_taken
         """
         values = OptionParser.get_default_values(self)
 
         class ExtValues(self.VALUES_CLASS):
             _action_taken = {}
+            _logaction_taken = {}
 
         newvalues = ExtValues()
         newvalues.__dict__ = values.__dict__.copy()
@@ -524,9 +544,9 @@ def _add_help_option(self):
 
     def _get_args(self, args):
         """Prepend the options set through the environment"""
-        regular_args = OptionParser._get_args(self, args)
-        env_args = self.get_env_options()
-        return env_args + regular_args  # prepend the environment options as longopts
+        self.commandline_arguments = OptionParser._get_args(self, args)
+        self.get_env_options()
+        return self.environment_arguments + self.commandline_arguments  # prepend the environment options as longopts
 
     def get_env_options_prefix(self):
         """Return the prefix to use for options passed through the environment"""
@@ -537,7 +557,12 @@ def get_env_options_prefix(self):
 
     def get_env_options(self):
         """Retrieve options from the environment: prefix_longopt.upper()"""
-        env_long_opts = []
+        self.environment_arguments = []
+
+        if not self.process_env_options:
+            self.log.debug("Not processing environment for options")
+            return
+
         if self.envvar_prefix is None:
             self.get_env_options_prefix()
 
@@ -556,16 +581,16 @@ def get_env_options(self):
                 val = os.environ.get(env_opt_name, None)
                 if not val is None:
                     if opt.action in opt.TYPED_ACTIONS:  # not all typed actions are mandatory, but let's assume so
-                        env_long_opts.append("%s=%s" % (lo, val))
+                        self.environment_arguments.append("%s=%s" % (lo, val))
                     else:
                         # interpretation of values: 0/no/false means: don't set it
                         if not ("%s" % val).lower() in ("0", "no", "false",):
-                            env_long_opts.append("%s" % lo)
+                            self.environment_arguments.append("%s" % lo)
                 else:
                     self.log.debug("Environment variable %s is not set" % env_opt_name)
 
-        self.log.debug("Environment variable options with prefix %s: %s" % (self.envvar_prefix, env_long_opts))
-        return env_long_opts
+        self.log.debug("Environment variable options with prefix %s: %s" % (self.envvar_prefix, self.environment_arguments))
+        return self.environment_arguments
 
     def get_option_by_long_name(self, name):
         """Return the option matching the long option name"""
@@ -719,7 +744,7 @@ def _make_debug_options(self):
         self._logopts = {
             'debug': ("Enable debug log mode", None, "store_debuglog", False, 'd'),
             'info': ("Enable info log mode", None, "store_infolog", False),
-            'quiet': ("Enable info quiet/warning mode", None, "store_warninglog", False),
+            'quiet': ("Enable quiet/warning log mode", None, "store_warninglog", False),
         }
 
         descr = ['Debug and logging options', '']
@@ -970,6 +995,9 @@ def parseoptions(self, options_list=None):
             else:
                 sys.exit(err.code)
 
+        self.log.debug("parseoptions: options from environment %s" % (self.parser.environment_arguments))
+        self.log.debug("parseoptions: options from commandline %s" % (self.parser.commandline_arguments))
+
         # args should be empty, since everything is optional
         if len(self.args) > 1:
             self.log.debug("Found remaining args %s" % self.args)
@@ -1045,8 +1073,8 @@ def parseconfigfiles(self):
             if section not in cfg_sections_flat:
                 self.log.debug("parseconfigfiles: found section %s, adding to remainder" % section)
                 remainder = self.configfile_remainder.setdefault(section, {})
-                # parse te remaining options, sections starting with 'raw_' as their name will be considered raw sections
-
+                # parse te remaining options, sections starting with 'raw_'
+                # as their name will be considered raw sections
                 for opt, val in self.configfile_parser.items(section, raw=(section.startswith('raw_'))):
                     remainder[opt] = val
 
@@ -1075,7 +1103,17 @@ def parseconfigfiles(self):
 
                     configfile_options_default[opt_dest] = actual_option.default
 
-                    if actual_option.action in ExtOption.BOOLEAN_ACTIONS:
+                    # log actions require special care
+                    # if any log action was already taken before, it would precede the one from the configfile
+                    # however, multiple logactions in a configfile (or environment for that matter) have
+                    # undefined behaviour
+                    is_log_action = actual_option.action in ExtOption.EXTOPTION_LOG
+                    log_action_taken = getattr(self.options, '_logaction_taken', False)
+                    if is_log_action and log_action_taken:
+                        # value set through take_action. do not modify by configfile
+                        self.log.debug(('parseconfigfiles: log action %s (value %s) found,'
+                                        ' but log action already taken. Ignoring.') % (opt_dest, val))
+                    elif actual_option.action in ExtOption.BOOLEAN_ACTIONS:
                         try:
                             newval = self.configfile_parser.getboolean(section, opt)
                             self.log.debug(('parseconfigfiles: getboolean for option %s value %s '
@@ -1102,11 +1140,17 @@ def parseconfigfiles(self):
         # reparse
         self.log.debug('parseconfigfiles: going to parse options through cmdline %s' % configfile_cmdline)
         try:
+            # can't reprocress the environment, since we are not reporcessing the commandline either
+            self.parser.process_env_options = False
             (parsed_configfile_options, parsed_configfile_args) = self.parser.parse_args(configfile_cmdline)
+            self.parser.process_env_options = True
         except:
             self.log.raiseException('parseconfigfiles: failed to parse options through cmdline %s' %
                                     configfile_cmdline)
 
+        # re-report the options as parsed via parser
+        self.log.debug("parseconfigfiles: options from configfile %s" % (self.parser.commandline_arguments))
+
         if len(parsed_configfile_args) > 0:
             self.log.raiseException('parseconfigfiles: not all options were parsed: %s' % parsed_configfile_args)
 
diff --git a/vsc/utils/rest.py b/vsc/utils/rest.py
index a7e87ec001..82d5835eee 100644
--- a/vsc/utils/rest.py
+++ b/vsc/utils/rest.py
@@ -65,7 +65,7 @@ class Client(object):
 
     USER_AGENT = 'vsc-rest-client'
 
-    def __init__(self, url, username=None, password=None, token=None, token_type='Token', user_agent=None):
+    def __init__(self, url, username=None, password=None, token=None, token_type='Token', user_agent=None, append_slash=False):
         """
         Create a Client object,
         this client can consume a REST api hosted at host/endpoint
@@ -78,6 +78,7 @@ def __init__(self, url, username=None, password=None, token=None, token_type='To
         self.auth_header = None
         self.username = username
         self.url = url
+        self.append_slash = append_slash
 
         if not user_agent:
             self.user_agent = self.USER_AGENT
@@ -103,6 +104,8 @@ def get(self, url, headers={}, **params):
         Do a http get request on the given url with given headers and parameters
         Parameters is a dictionary that will will be urlencoded
         """
+        if self.append_slash:
+            url += '/'
         url += self.urlencode(params)
         return self.request(self.GET, url, None, headers)
 
@@ -111,6 +114,8 @@ def head(self, url, headers={}, **params):
         Do a http head request on the given url with given headers and parameters
         Parameters is a dictionary that will will be urlencoded
         """
+        if self.append_slash:
+            url += '/'
         url += self.urlencode(params)
         return self.request(self.HEAD, url, None, headers)
 
@@ -119,6 +124,8 @@ def delete(self, url, headers={}, **params):
         Do a http delete request on the given url with given headers and parameters
         Parameters is a dictionary that will will be urlencoded
         """
+        if self.append_slash:
+            url += '/'
         url += self.urlencode(params)
         return self.request(self.DELETE, url, None, headers)
 
@@ -127,7 +134,10 @@ def post(self, url, body=None, headers={}, **params):
         Do a http post request on the given url with given body, headers and parameters
         Parameters is a dictionary that will will be urlencoded
         """
+        if self.append_slash:
+            url += '/'
         url += self.urlencode(params)
+        headers['Content-Type'] = 'application/json'
         return self.request(self.POST, url, json.dumps(body), headers)
 
     def put(self, url, body=None, headers={}, **params):
@@ -135,7 +145,10 @@ def put(self, url, body=None, headers={}, **params):
         Do a http put request on the given url with given body, headers and parameters
         Parameters is a dictionary that will will be urlencoded
         """
+        if self.append_slash:
+            url += '/'
         url += self.urlencode(params)
+        headers['Content-Type'] = 'application/json'
         return self.request(self.PUT, url, json.dumps(body), headers)
 
     def patch(self, url, body=None, headers={}, **params):
@@ -143,7 +156,10 @@ def patch(self, url, body=None, headers={}, **params):
         Do a http patch request on the given url with given body, headers and parameters
         Parameters is a dictionary that will will be urlencoded
         """
+        if self.append_slash:
+            url += '/'
         url += self.urlencode(params)
+        headers['Content-Type'] = 'application/json'
         return self.request(self.PATCH, url, json.dumps(body), headers)
 
     def request(self, method, url, body, headers):

From 8a24a2969179c480cc5a3b11a13b403d3cf08a00 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 10 Sep 2014 13:34:04 +0200
Subject: [PATCH 0165/1356] increase # commits per page for --from-pr

---
 easybuild/tools/github.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 5e0f1f0729..8b272661e4 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -248,7 +248,8 @@ def download(url, path=None):
     _log.debug("List of patches files: %s" % patched_files)
 
     # obtain last commit
-    status, commits_data = pr_url.commits.get()
+    # get all commits, increase to (max of) 100 per page
+    status, commits_data = pr_url.commits.get(per_page=100)
     last_commit = commits_data[-1]
     _log.debug("Commits: %s" % commits_data)
 

From 55744cea8539408252254ca5f8c84de6be0cac70 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 10 Sep 2014 14:10:01 +0200
Subject: [PATCH 0166/1356] issue error when more than 100 commits are detected
 in PR

---
 easybuild/tools/github.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 8b272661e4..ae544e28b4 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -64,6 +64,7 @@
 GITHUB_EB_MAIN = 'hpcugent'
 GITHUB_EASYCONFIGS_REPO = 'easybuild-easyconfigs'
 GITHUB_FILE_TYPE = u'file'
+GITHUB_MAX_PER_PAGE = 100
 GITHUB_MERGEABLE_STATE_CLEAN = 'clean'
 GITHUB_RAW = 'https://raw.githubusercontent.com'
 GITHUB_STATE_CLOSED = 'closed'
@@ -249,9 +250,11 @@ def download(url, path=None):
 
     # obtain last commit
     # get all commits, increase to (max of) 100 per page
-    status, commits_data = pr_url.commits.get(per_page=100)
+    if pr_data['commits'] > GITHUB_MAX_PER_PAGE:
+        _log.error("PR #%s contains more than %s commits, can't obtain last commit" % (pr, GITHUB_MAX_PER_PAGE))
+    status, commits_data = pr_url.commits.get(per_page=GITHUB_MAX_PER_PAGE)
     last_commit = commits_data[-1]
-    _log.debug("Commits: %s" % commits_data)
+    _log.debug("Commits: %s, last commit: %s" % (commits_data, last_commit['sha']))
 
     # obtain most recent version of patched files
     for patched_file in patched_files:

From 6ed3d20fb51b8f06fefd9f9ce8ee46b60cdf02ea Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 10 Sep 2014 14:10:14 +0200
Subject: [PATCH 0167/1356] add unit test for fetch_easyconfigs_from_pr

---
 test/framework/github.py | 25 +++++++++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/test/framework/github.py b/test/framework/github.py
index 109abf5901..588bc7240f 100644
--- a/test/framework/github.py
+++ b/test/framework/github.py
@@ -29,12 +29,17 @@
 """
 
 import os
+import shutil
+import tempfile
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
 
-from easybuild.tools.github import Githubfs, fetch_github_token
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.github import Githubfs, fetch_github_token, fetch_easyconfigs_from_pr
 
 
+# test account, for which a token is available
+GITHUB_TEST_ACCOUNT = 'easybuild_test'
 # the user who's repo to test
 GITHUB_USER = "hpcugent"
 # the repo of this user to use in this test
@@ -50,7 +55,7 @@ class GithubTest(EnhancedTestCase):
     def setUp(self):
         """setup"""
         super(GithubTest, self).setUp()
-        github_user = 'easybuild_test'
+        github_user = GITHUB_TEST_ACCOUNT
         github_token = fetch_github_token(github_user)
         if github_token is None:
             self.ghfs = None
@@ -93,6 +98,22 @@ def test_read(self):
         else:
             print "Skipping test_read, no GitHub token available?"
 
+    def test_fetch_easyconfigs_from_pr(self):
+        """Test fetch_easyconfigs_from_pr function."""
+        tmpdir = tempfile.mkdtemp()
+        # PR for ictce/6.2.5, see https://github.com/hpcugent/easybuild-easyconfigs/pull/726/files
+        all_ecs = ['gzip-1.6-ictce-6.2.5.eb', 'icc-2013_sp1.2.144.eb', 'ictce-6.2.5.eb', 'ifort-2013_sp1.2.144.eb',
+                   'imkl-11.1.2.144.eb', 'impi-4.1.3.049.eb']
+        ec_files = fetch_easyconfigs_from_pr(726, path=tmpdir, github_user=GITHUB_TEST_ACCOUNT)
+        self.assertEqual(all_ecs, sorted([os.path.basename(f) for f in ec_files]))
+        self.assertEqual(all_ecs, sorted(os.listdir(tmpdir)))
+        shutil.rmtree(tmpdir)
+
+        # PR for EasyBuild v1.13.0 release (250+ commits, 218 files changed)
+        err_msg = "PR #897 contains more than .* commits, can't obtain last commit"
+        self.assertErrorRegex(EasyBuildError, err_msg, fetch_easyconfigs_from_pr, 897, github_user=GITHUB_TEST_ACCOUNT)
+
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(GithubTest)

From 3941530a703778adc89a3670ba0e45f92de63021 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 11 Sep 2014 15:32:19 +0200
Subject: [PATCH 0168/1356] bump version to v1.15.0 and update release notes

---
 RELEASE_NOTES              | 34 ++++++++++++++++++++++++++++++++++
 easybuild/tools/version.py |  2 +-
 2 files changed, 35 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 3b7a82b7fd..2186d01915 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -1,6 +1,40 @@
 This file contains a description of the major changes to the easybuild-framework EasyBuild package.
 For more detailed information, please see the git log.
 
+v1.15.0 (September 12th 2014)
+-----------------------------
+
+feature + bugfix release
+- various other enhancements, including:
+    - fetch extension sources in fetch_step to enhance --stop=fetch (#978)
+    - add iimpi toolchain definition (#993)
+    - prepend robot path with download location of files when --from-pr is used (#995)
+    - add support for excluding module path extensions from generated modules (#1003)
+        - see 'include_modpath_extensions' easyconfig parameter
+    - add support for installing hidden modules and using them as dependencies (#1009, #1021, #1023)
+        - see --hidden and 'hiddendependencies' easyconfig parameter
+    - stop relying on 'conflict' statement in module files to determine software name of toolchain components (#1017, #1037)
+        - instead, the 'is_short_modname_for' method defined by the module naming scheme implementation is queried
+    - improve error message generated for a missing easyconfig file (#1019)
+    - include path where tweaked easyconfigs are placed in robot path (#1032)
+    - indicate forced builds in --dry-run output (#1034)
+    - fix interaction between --force and --try-toolchain --robot (#1035)
+    - add --software option, disable recursion for --try-software(-X) (#1036)
+- various bug fixes, including:
+    - fix HierarchicalMNS crashing when MPI library is installed with a dummy toolchain (#986)
+    - fix list of FFTW wrapper libraries for Intel MKL (#987)
+    - fix stability of unit tests (#988, #1027, #1033)
+    - make sure $SCALAPACK_INC_DIR (and $SCALAPACK_LIB_DIR) are defined when using imkl (#990)
+    - fix error message on missing FFTW wrapper libs (#992)
+    - fix duplicate toolchain elements in --list-toolchains output (#993)
+    - filter out load statements that extend the $MODULEPATH to make the module being installed available (#1016)
+    - fix conflict specification included in module files (#1017)
+    - avoid --from-pr crashing hard unless --robot is used (#1022)
+    - properly quote GCC version string in archived easyconfig (#1028)
+    - fix issue with --repositorypath not honoring --prefix (#1031)
+    - sync with latest vsc-base version to fix log order (#1039)
+    - increase # commits per page for --from-pr (#1040)
+
 v1.14.0 (July 9th 2014)
 -----------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 8528cee3ad..d9dc51628d 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.15.0dev")
+VERSION = LooseVersion("1.15.0")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 66a5f3cadb974a639cd5fc63ccb4032daccfeebe Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Thu, 11 Sep 2014 16:52:15 +0200
Subject: [PATCH 0169/1356] clean_gists: fix bug when description is empty

---
 easybuild/scripts/clean_gists.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/scripts/clean_gists.py b/easybuild/scripts/clean_gists.py
index ba847e6198..5a7933d038 100755
--- a/easybuild/scripts/clean_gists.py
+++ b/easybuild/scripts/clean_gists.py
@@ -86,6 +86,8 @@ def main():
     num_deleted = 0
 
     for gist in gists:
+        if not gist["description"]:
+            continue
         re_pr_num = regex.search(gist["description"])
         delete_gist = False
 

From a6ffb5b6074b1ec3cbbcaf0a315d6b479284ed6a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Sep 2014 17:14:17 +0200
Subject: [PATCH 0170/1356] bump version to v1.15.1dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index d9dc51628d..e035b9849c 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.15.0")
+VERSION = LooseVersion("1.15.1dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 55dc0025369639427322356f3131bf3d474af9d8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Sep 2014 17:14:39 +0200
Subject: [PATCH 0171/1356] bump version to v1.16.0dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index e035b9849c..f527eaecee 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.15.1dev")
+VERSION = LooseVersion("1.16.0dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From f3db58ed33b600bbdb60997e3d8c187b930764cd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Sep 2014 17:34:41 +0200
Subject: [PATCH 0172/1356] fix get_cpu_model in case /proc/cpuinfo doesn't
 list a model name

---
 easybuild/tools/systemtools.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 7cd2babc04..f908673ae0 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -190,13 +190,16 @@ def get_cpu_model():
     returns cpu model
     f.ex Intel(R) Core(TM) i5-2540M CPU @ 2.60GHz
     """
+    model = UNKNOWN
     os_type = get_os_type()
     if os_type == LINUX:
         regexp = re.compile(r"^model name\s+:\s*(?P<modelname>.+)\s*$", re.M)
         try:
             txt = read_file('/proc/cpuinfo', log_error=False)
             if txt is not None:
-                return regexp.search(txt).groupdict()['modelname'].strip()
+                res = regexp.search(txt)
+                if res is not None:
+                    model = res.group('modelname').strip()
         except IOError, err:
             raise SystemToolsException("An error occured when determining CPU model: %s" % err)
 
@@ -204,9 +207,9 @@ def get_cpu_model():
         out, exitcode = run_cmd("sysctl -n machdep.cpu.brand_string")
         out = out.strip()
         if not exitcode:
-            return out
+            model = out
 
-    return UNKNOWN
+    return model
 
 
 def get_cpu_speed():

From b2ab456a3adf0a3ee2b29e6c53ce9e16a8e1ee0f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Sep 2014 19:09:33 +0200
Subject: [PATCH 0173/1356] enhance get_cpu_speed to also support determining
 CPU frequency on POWER, and clean things up

---
 easybuild/tools/systemtools.py | 26 ++++++++++++++++++--------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index f908673ae0..3f9c24e807 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -222,30 +222,40 @@ def get_cpu_speed():
         try:
             # Linux with cpu scaling
             max_freq_fp = '/sys/devices/system/cpu/cpu0/cpufreq/scaling_max_freq'
+            _log.debug("Trying to determine CPU frequency via %s" % max_freq_fp)
             try:
                 f = open(max_freq_fp, 'r')
                 cpu_freq = float(f.read())/1000
                 f.close()
                 return cpu_freq
             except IOError, err:
-                _log.warning("Failed to read %s to determine max. CPU clock frequency with CPU scaling: %s" % (max_freq_fp, err))
+                _log.debug("Failed to read %s to determine max. CPU clock frequency with CPU scaling: %s" % (max_freq_fp, err))
 
             # Linux without cpu scaling
             cpuinfo_fp = '/proc/cpuinfo'
+            _log.debug("Trying to determine CPU frequency via %s" % cpuinfo_fp)
             try:
                 cpu_freq = None
-                f = open(cpuinfo_fp, 'r')
-                for line in f:
-                    cpu_freq = re.match("^cpu MHz\s*:\s*([0-9.]+)", line)
-                    if cpu_freq is not None:
+                cpuinfo_txt = open(cpuinfo_fp, 'r').read()
+                cpu_freq_patterns = [
+                    r"^cpu MHz\s*:\s*(?P<cpu_freq>[0-9.]+)",  # Linux x86 & more
+                    r"^clock\s*:\s*(?P<cpu_freq>[0-9.]+)",  # Linux on POWER
+                ]
+                for cpu_freq_pattern in cpu_freq_patterns:
+                    cpu_freq_re = re.compile(cpu_freq_pattern, re.M)
+                    res = cpu_freq_re.search(cpuinfo_txt)
+                    if res:
+                        cpu_freq = res.group('cpu_freq')
+                        _log.debug("Found CPU frequency using regex '%s': %s" % (cpu_freq_pattern, cpu_freq))
                         break
-                f.close()
+                    else:
+                        _log.debug("Failed to determine CPU frequency using regex '%s'" % cpu_freq_re.pattern)
                 if cpu_freq is None:
                     raise SystemToolsException("Failed to determine CPU frequency from %s" % cpuinfo_fp)
                 else:
-                    return float(cpu_freq.group(1))
+                    return float(cpu_freq)
             except IOError, err:
-                _log.warning("Failed to read %s to determine CPU clock frequency: %s" % (cpuinfo_fp, err))
+                _log.debug("Failed to read %s to determine CPU clock frequency: %s" % (cpuinfo_fp, err))
 
         except (IOError, OSError), err:
             raise SystemToolsException("Determining CPU speed failed, exception occured: %s" % err)

From cfbc988cf57a26dd4fb29e71766f77f0c8cbd15f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Sep 2014 10:32:15 +0200
Subject: [PATCH 0174/1356] add debug logging in modpath_extensions_for

---
 easybuild/tools/modules.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index d0083bc294..52ef1d54d9 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -590,6 +590,8 @@ def modpath_extensions_for(self, mod_names):
         Determine dictionary with $MODULEPATH extensions for specified modules.
         Modules with an empty list of $MODULEPATH extensions are included.
         """
+        self.log.debug("Determining $MODULEPATH extensions for modules %s" % mod_names)
+
         # copy environment so we can restore it
         orig_env = os.environ.copy()
 
@@ -599,6 +601,7 @@ def modpath_extensions_for(self, mod_names):
             useregex = re.compile(r"^\s*module\s+use\s+(\S+)", re.M)
             exts = useregex.findall(modtxt)
 
+            self.log.debug("Found $MODULEPATH extensions for %s: %s" % (mod_name, exts))
             modpath_exts.update({mod_name: exts})
 
             if exts:

From 918230596b98d3a72f1e51be6cd0b486707b968e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Sep 2014 16:20:36 +0200
Subject: [PATCH 0175/1356] add Python version check in 'eb' command

---
 eb | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/eb b/eb
index 4bb70df087..c67fe08284 100755
--- a/eb
+++ b/eb
@@ -39,6 +39,37 @@
 # @author: Pieter De Baets (Ghent University)
 # @author: Jens Timmerman (Ghent University)
 
+# Python 2.4 or more recent 2.x required
+REQ_MAJ_PYVER=2
+REQ_MIN_PYVER=4
+REQ_PYVER=${REQ_MAJ_PYVER}.${REQ_MIN_PYVER}
+
+# make sure Python version being used is compatible
+pyver=`python -V 2>&1 | cut -f2 -d' '`
+pyver_maj=`echo $pyver | cut -f1 -d'.'`
+pyver_min=`echo $pyver | cut -f2 -d'.'`
+
+if [ $pyver_maj -ne $REQ_MAJ_PYVER ]
+then
+    echo "ERROR: EasyBuild is currently only compatible with Python v${REQ_MAJ_PYVER}.x, found v${pyver}" 1>&2
+    exit 1
+fi
+if [ $pyver_min -lt $REQ_MIN_PYVER ]
+then
+    echo "ERROR: EasyBuild requires Python v${REQ_PYVER} or a more recent v${REQ_MAJ_PYVER}.x, found v${pyver}." 1>&2
+    exit 2
+fi
+
+# support for Python versions older than v2.6 is deprecated
+OK_MIN_PYVER=6
+if [ $pyver_min -lt $OK_MIN_PYVER ]
+then
+    OK_PYVER=${REQ_MAJ_PYVER}.${OK_MIN_PYVER}
+    echo -n "WARNING: Running EasyBuild with a Python version prior to v${OK_PYVER} is deprecated, " 1>&2
+    echo "found Python v$pyver which will no longer be supported in EasyBuild v2.0." 1>&2
+fi
+
+
 main_script_base_path="easybuild/main.py"
 python_search_path_cmd="python -c \"import sys; print ' '.join(sys.path)\""
 

From 022409a8862ad7de996ae046c342f3a3800040e7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 20 Sep 2014 00:25:27 +0200
Subject: [PATCH 0176/1356] fix path_to_top_of_module_tree to consider multiple
 paths to the top of the module tree

---
 easybuild/tools/modules.py | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 52ef1d54d9..b2e75295b2 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -659,40 +659,40 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
             modpath_exts = dict([(k, v) for k, v in self.modpath_extensions_for(deps).items() if v])
             self.log.debug("Non-empty lists of module path extensions for dependencies: %s" % modpath_exts)
 
-        path = []
+        mods_to_top = []
+        full_mod_subdirs = []
         for dep in modpath_exts:
             # if a $MODULEPATH extension is identical to where this module will be installed, we have a hit
             # use os.path.samefile when comparing paths to avoid issues with resolved symlinks
             full_modpath_exts = modpath_exts[dep]
             if path_matches(full_mod_subdir, full_modpath_exts):
                 # full path to module subdir of dependency is simply path to module file without (short) module name
-                full_mod_subdir = self.modulefile_path(dep)[:-len(dep)-1]
+                full_mod_subdirs.append(self.modulefile_path(dep)[:-len(dep)-1])
 
-                path.append(dep)
-                tup = (dep, full_mod_subdir, full_modpath_exts)
+                mods_to_top.append(dep)
+                tup = (dep, full_mod_subdirs[-1], full_modpath_exts)
                 self.log.debug("Found module to top of module tree: %s (subdir: %s, modpath extensions %s)" % tup)
 
-                # no need to continue further, we found the module that extends $MODULEPATH with module subdir
-                break
-
             if full_modpath_exts:
                 # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
                 # this is required to obtain the corresponding module file paths (via 'module show')
                 self.load([dep])
 
-        if path:
-            # remove retained dependency from the list, since we're climbing up the module tree
-            modpath_exts.pop(path[-1])
+        # restore original environment (modules may have been loaded above)
+        modify_env(os.environ, orig_env)
+
+        path = mods_to_top[:]
+        if mods_to_top:
+            # remove retained dependencies from the list, since we're climbing up the module tree
+            remaining_modpath_exts = dict([(m, modpath_exts[m]) for m in modpath_exts if not m in mods_to_top])
 
-            self.log.debug("Path to top from %s extended to %s, so recursing to find way to the top" % (mod_name, path))
-            path.extend(self.path_to_top_of_module_tree(top_paths, path[-1], full_mod_subdir, None,
-                                                        modpath_exts=modpath_exts))
+            self.log.debug("Path to top from %s extended to %s, so recursing to find way to the top" % (mod_name, mods_to_top))
+            for mod_name, full_mod_subdir in zip(mods_to_top, full_mod_subdirs):
+                path.extend(self.path_to_top_of_module_tree(top_paths, mod_name, full_mod_subdir, None,
+                                                            modpath_exts=remaining_modpath_exts))
         else:
             self.log.debug("Path not extended, we must have reached the top of the module tree")
 
-        # restore original environment (modules may have been loaded above)
-        modify_env(os.environ, orig_env)
-
         self.log.debug("Path to top of module tree from %s: %s" % (mod_name, path))
         return path
 

From 0dcde88ce3926a94c3be11fe64f081174a2190a1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 20 Sep 2014 01:57:24 +0200
Subject: [PATCH 0177/1356] add unit test for checking load statements in imkl
 module under HierarchicalMNS

---
 test/framework/easyblock.py                   | 44 ++++++++++++++++++-
 test/framework/easyconfigs/GCC-4.8.3.eb       | 28 ++++++++++++
 .../easyconfigs/icc-2013.5.192-GCC-4.8.3.eb   | 23 ++++++++++
 .../iccifort-2013.5.192-GCC-4.8.3.eb          | 17 +++++++
 .../easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb | 23 ++++++++++
 .../easyconfigs/iimpi-5.5.3-GCC-4.8.3.eb      | 21 +++++++++
 .../imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb  | 22 ++++++++++
 ...4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb | 19 ++++++++
 test/framework/module_generator.py            |  1 +
 test/framework/modules.py                     |  1 +
 .../Compiler/intel/2013.5.192/impi/4.1.3.049  | 30 +++++++++++++
 test/framework/modules/Core/GCC/4.8.3         | 30 +++++++++++++
 .../modules/Core/icc/2013.5.192-GCC-4.8.3     | 31 +++++++++++++
 .../Core/iccifort/2013.5.192-GCC-4.8.3        | 24 ++++++++++
 .../modules/Core/ifort/2013.5.192-GCC-4.8.3   | 31 +++++++++++++
 .../modules/Core/iimpi/5.5.3-GCC-4.8.3        | 26 +++++++++++
 test/framework/utilities.py                   |  8 +++-
 17 files changed, 376 insertions(+), 3 deletions(-)
 create mode 100644 test/framework/easyconfigs/GCC-4.8.3.eb
 create mode 100644 test/framework/easyconfigs/icc-2013.5.192-GCC-4.8.3.eb
 create mode 100644 test/framework/easyconfigs/iccifort-2013.5.192-GCC-4.8.3.eb
 create mode 100644 test/framework/easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb
 create mode 100644 test/framework/easyconfigs/iimpi-5.5.3-GCC-4.8.3.eb
 create mode 100644 test/framework/easyconfigs/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb
 create mode 100644 test/framework/easyconfigs/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb
 create mode 100644 test/framework/modules/Compiler/intel/2013.5.192/impi/4.1.3.049
 create mode 100644 test/framework/modules/Core/GCC/4.8.3
 create mode 100644 test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
 create mode 100644 test/framework/modules/Core/iccifort/2013.5.192-GCC-4.8.3
 create mode 100644 test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
 create mode 100644 test/framework/modules/Core/iimpi/5.5.3-GCC-4.8.3

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 6dcd861e96..1107f8049b 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -44,7 +44,9 @@
 from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
 from easybuild.tools import config
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import mkdir, write_file
+from easybuild.tools.environment import modify_env
+from easybuild.tools.filetools import mkdir, read_file, write_file
+from easybuild.tools.modules import modules_tool
 
 
 class EasyBlockTest(EnhancedTestCase):
@@ -465,6 +467,46 @@ def test_check_readiness(self):
 
         shutil.rmtree(tmpdir)
 
+    def test_exclude_path_to_top_of_module_tree(self):
+        """
+        Make sure that modules under the HierarchicalMNS are correct,
+        w.r.t. not including any load statements for modules that build up the path to the top of the module tree.
+        """
+        self.orig_module_naming_scheme = config.get_module_naming_scheme()
+        test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        all_stops = [x[0] for x in EasyBlock.get_steps()]
+        build_options = {
+            'check_osdeps': False,
+            'robot_path': [test_ecs_path],
+            'valid_stops': all_stops,
+            'validate': False,
+        }
+        os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
+        init_config(build_options=build_options)
+        self.setup_hierarchical_modules()
+        modtool = modules_tool()
+
+        ec = EasyConfig(os.path.join(test_ecs_path, 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'))
+        eb = EasyBlock(ec)
+
+        modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all', 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl')
+        mkdir(os.path.dirname(modfile_prefix), parents=True)
+        eb.toolchain.prepare()
+        modpath = eb.make_module_step()
+        modfile_path = os.path.join(modpath, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
+        modtxt = read_file(modfile_path)
+
+        # for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included at all
+        # not for the toolchain or any of the toolchain components,
+        # since both icc/ifort and impi form the path to the top of the module tree
+        for imkl_dep in ['icc', 'ifort', 'impi', 'iccifort', 'iimpi']:
+            tup = (imkl_dep, modfile_path, modtxt)
+            failmsg = "No 'module load' statement found for '%s' not found in module %s: %s" % tup
+            self.assertFalse(re.search("module load %s" % imkl_dep, modtxt), failmsg)
+
+        os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
+        init_config(build_options=build_options)
+
     def tearDown(self):
         """ make sure to remove the temporary file """
         super(EasyBlockTest, self).tearDown()
diff --git a/test/framework/easyconfigs/GCC-4.8.3.eb b/test/framework/easyconfigs/GCC-4.8.3.eb
new file mode 100644
index 0000000000..c62aa710d1
--- /dev/null
+++ b/test/framework/easyconfigs/GCC-4.8.3.eb
@@ -0,0 +1,28 @@
+name = "GCC"
+version = '4.8.3'
+
+homepage = 'http://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = [
+    'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s',  # GCC auto-resolving HTTP mirror
+    'http://ftpmirror.gnu.org/gmp',  # idem for GMP
+    'http://ftpmirror.gnu.org/mpfr',  # idem for MPFR
+    'http://www.multiprecision.org/mpc/download',  # MPC official
+]
+sources = [
+    SOURCELOWER_TAR_GZ,
+    'gmp-5.1.3.tar.bz2',
+    'mpfr-3.1.2.tar.gz',
+    'mpc-1.0.1.tar.gz',
+]
+
+languages = ['c', 'c++', 'fortran', 'lto']
+
+# building GCC sometimes fails if make parallelism is too high, so let's limit it
+maxparallel = 4
+
+moduleclass = 'compiler'
diff --git a/test/framework/easyconfigs/icc-2013.5.192-GCC-4.8.3.eb b/test/framework/easyconfigs/icc-2013.5.192-GCC-4.8.3.eb
new file mode 100644
index 0000000000..23b5d632b0
--- /dev/null
+++ b/test/framework/easyconfigs/icc-2013.5.192-GCC-4.8.3.eb
@@ -0,0 +1,23 @@
+name = 'icc'
+version = '2013.5.192'
+
+homepage = 'http://software.intel.com/en-us/intel-compilers/'
+description = "C and C++ compiler from Intel"
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['l_ccompxe_%(version)s.tgz']
+
+gcc = 'GCC'
+gccver = '4.8.3'
+versionsuffix = '-%s-%s' % (gcc, gccver)
+
+dependencies = [(gcc, gccver)]
+
+dontcreateinstalldir = 'True'
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
+
+moduleclass = 'compiler'
diff --git a/test/framework/easyconfigs/iccifort-2013.5.192-GCC-4.8.3.eb b/test/framework/easyconfigs/iccifort-2013.5.192-GCC-4.8.3.eb
new file mode 100644
index 0000000000..9a152f81fe
--- /dev/null
+++ b/test/framework/easyconfigs/iccifort-2013.5.192-GCC-4.8.3.eb
@@ -0,0 +1,17 @@
+easyblock = "Toolchain"
+
+name = 'iccifort'
+version = '2013.5.192'
+versionsuffix = '-GCC-4.8.3'
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel C, C++ and Fortran compilers"""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+dependencies = [
+    ('icc', version, versionsuffix),
+    ('ifort', version, versionsuffix),
+]
+
+moduleclass = 'toolchain'
diff --git a/test/framework/easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb b/test/framework/easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb
new file mode 100644
index 0000000000..cba97b45a2
--- /dev/null
+++ b/test/framework/easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb
@@ -0,0 +1,23 @@
+name = 'ifort'
+version = '2013.5.192'
+
+homepage = 'http://software.intel.com/en-us/intel-compilers/'
+description = "Fortran compiler from Intel"
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['l_fcompxe_%(version)s.tgz']
+
+gcc = 'GCC'
+gccver = '4.8.3'
+versionsuffix = '-%s-%s' % (gcc, gccver)
+
+dependencies = [(gcc, gccver)]
+
+dontcreateinstalldir = 'True'
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
+
+moduleclass = 'compiler'
diff --git a/test/framework/easyconfigs/iimpi-5.5.3-GCC-4.8.3.eb b/test/framework/easyconfigs/iimpi-5.5.3-GCC-4.8.3.eb
new file mode 100644
index 0000000000..221f1fb36d
--- /dev/null
+++ b/test/framework/easyconfigs/iimpi-5.5.3-GCC-4.8.3.eb
@@ -0,0 +1,21 @@
+easyblock = "Toolchain"
+
+name = 'iimpi'
+version = '5.5.3'
+versionsuffix = '-GCC-4.8.3'
+
+homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/'
+description = """Intel C/C++ and Fortran compilers, alongside Intel MPI."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+suff = '5.192'
+compver = '2013.%s' % suff
+
+dependencies = [                                                                 # version/released
+    ('icc', compver, versionsuffix),                                             # 28 Apr 2014
+    ('ifort', compver, versionsuffix),                                           # 28 Apr 2014
+    ('impi', '4.1.3.049', '', ('iccifort', '%s%s' % (compver, versionsuffix))),  # 06 Mar 2014
+]
+
+moduleclass = 'toolchain'
diff --git a/test/framework/easyconfigs/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb b/test/framework/easyconfigs/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb
new file mode 100644
index 0000000000..2114374474
--- /dev/null
+++ b/test/framework/easyconfigs/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb
@@ -0,0 +1,22 @@
+name = 'imkl'
+version = '11.1.2.144'
+
+homepage = 'http://software.intel.com/en-us/intel-mkl/'
+description = """Intel Math Kernel Library is a library of highly optimized,
+ extensively threaded math routines for science, engineering, and financial
+ applications that require maximum performance. Core math functions include
+ BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more."""
+
+toolchain = {'name': 'iimpi', 'version': '5.5.3-GCC-4.8.3'}
+
+sources = ['l_mkl_%(version)s.tgz']
+
+dontcreateinstalldir = 'True'
+
+interfaces = True
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
+
+moduleclass = 'numlib'
diff --git a/test/framework/easyconfigs/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/test/framework/easyconfigs/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb
new file mode 100644
index 0000000000..ddba0fe1d6
--- /dev/null
+++ b/test/framework/easyconfigs/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb
@@ -0,0 +1,19 @@
+name = 'impi'
+version = '4.1.3.049'
+
+homepage = 'http://software.intel.com/en-us/intel-mpi-library/'
+description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric message
+ passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for
+ Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification."""
+
+toolchain = {'name': 'iccifort', 'version': '2013.5.192-GCC-4.8.3'}
+
+sources = ['l_mpi_p_%(version)s.tgz']
+
+dontcreateinstalldir = 'True'
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
+
+moduleclass = 'mpi'
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 4e12e71427..9d0c46188b 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -419,6 +419,7 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
         for ecfile, mns_vals in test_ecs.items():
             test_ec(ecfile, *mns_vals)
 
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(ModuleGeneratorTest)
diff --git a/test/framework/modules.py b/test/framework/modules.py
index ae8ab63f6f..46b7453ba8 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -283,6 +283,7 @@ def test_path_to_top_of_module_tree(self):
         path = modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
         self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
 
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(ModulesTest)
diff --git a/test/framework/modules/Compiler/intel/2013.5.192/impi/4.1.3.049 b/test/framework/modules/Compiler/intel/2013.5.192/impi/4.1.3.049
new file mode 100644
index 0000000000..6b65daae4f
--- /dev/null
+++ b/test/framework/modules/Compiler/intel/2013.5.192/impi/4.1.3.049
@@ -0,0 +1,30 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   The Intel(R) MPI Library for Linux* OS is a multi-fabric message
+ passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for
+ Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. - Homepage: http://software.intel.com/en-us/intel-mpi-library/
+    }
+}
+
+module-whatis {Description: The Intel(R) MPI Library for Linux* OS is a multi-fabric message
+ passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for
+ Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. - Homepage: http://software.intel.com/en-us/intel-mpi-library/}
+
+set root    /tmp/software/Compiler/intel/2013.5.192/impi/4.1.3.049
+
+conflict impi
+module use /tmp/modules/all/MPI/intel/2013.5.192/impi/4.1.3.049
+prepend-path	CPATH		$root/include64
+prepend-path	LD_LIBRARY_PATH		$root/lib64
+prepend-path	LIBRARY_PATH		$root/lib64
+prepend-path	PATH		$root/bin64
+
+setenv	EBROOTIMPI		"$root"
+setenv	EBVERSIONIMPI		"4.1.3.049"
+setenv	EBDEVELIMPI		"$root/easybuild/Compiler-intel-2013.5.192-impi-4.1.3.049-easybuild-devel"
+
+prepend-path	INTEL_LICENSE_FILE		/tmp/license.lic
+setenv	I_MPI_ROOT		$root
+
+# Built with EasyBuild version 1.16.0dev
diff --git a/test/framework/modules/Core/GCC/4.8.3 b/test/framework/modules/Core/GCC/4.8.3
new file mode 100644
index 0000000000..dded358b87
--- /dev/null
+++ b/test/framework/modules/Core/GCC/4.8.3
@@ -0,0 +1,30 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/
+    }
+}
+
+module-whatis {Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/}
+
+set root    /tmp/problem1086/software/Core/GCC/4.8.3
+
+conflict GCC
+module use /tmp/problem1086/modules/all/Compiler/GCC/4.8.3
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+prepend-path	LD_LIBRARY_PATH		$root/lib64
+prepend-path	LD_LIBRARY_PATH		$root/lib/gcc/x86_64-unknown-linux-gnu/4.8.3
+prepend-path	LIBRARY_PATH		$root/lib
+prepend-path	LIBRARY_PATH		$root/lib64
+prepend-path	MANPATH		$root/share/man
+prepend-path	PATH		$root/bin
+
+setenv	EBROOTGCC		"$root"
+setenv	EBVERSIONGCC		"4.8.3"
+setenv	EBDEVELGCC		"$root/easybuild/Core-GCC-4.8.3-easybuild-devel"
+
+
+# Built with EasyBuild version 1.16.0dev
diff --git a/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
new file mode 100644
index 0000000000..6ae62b5684
--- /dev/null
+++ b/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
@@ -0,0 +1,31 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   C and C++ compiler from Intel - Homepage: http://software.intel.com/en-us/intel-compilers/
+    }
+}
+
+module-whatis {Description: C and C++ compiler from Intel - Homepage: http://software.intel.com/en-us/intel-compilers/}
+
+set root    /tmp/software/Core/icc/2013.5.192-GCC-4.8.3
+
+conflict icc
+module use /tmp/modules/all/Compiler/intel/2013.5.192
+module load GCC/4.8.3
+
+prepend-path	IDB_HOME		$root/bin/intel64
+prepend-path	LD_LIBRARY_PATH		$root/compiler/lib
+prepend-path	LD_LIBRARY_PATH		$root/compiler/lib/intel64
+prepend-path	MANPATH		$root/man
+prepend-path	MANPATH		$root/man/en_US
+prepend-path	PATH		$root/bin
+prepend-path	PATH		$root/bin/intel64
+
+setenv	EBROOTICC		"$root"
+setenv	EBVERSIONICC		"2013.5.192"
+setenv	EBDEVELICC		"$root/easybuild/Core-icc-2013.5.192-GCC-4.8.3-easybuild-devel"
+
+prepend-path	INTEL_LICENSE_FILE		/tmp/license.lic
+prepend-path	NLSPATH		$root/idb/intel64/locale/%l_%t/%N
+
+# Built with EasyBuild version 1.16.0dev
diff --git a/test/framework/modules/Core/iccifort/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/iccifort/2013.5.192-GCC-4.8.3
new file mode 100644
index 0000000000..db05126002
--- /dev/null
+++ b/test/framework/modules/Core/iccifort/2013.5.192-GCC-4.8.3
@@ -0,0 +1,24 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   Intel C, C++ and Fortran compilers - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
+    }
+}
+
+module-whatis {Description: Intel C, C++ and Fortran compilers - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/}
+
+set root    /tmp/software/Core/iccifort/2013.5.192-GCC-4.8.3
+
+conflict iccifort
+
+module load icc/2013.5.192-GCC-4.8.3
+
+module load ifort/2013.5.192-GCC-4.8.3
+
+
+setenv	EBROOTICCIFORT		"$root"
+setenv	EBVERSIONICCIFORT		"2013.5.192"
+setenv	EBDEVELICCIFORT		"$root/easybuild/Core-iccifort-2013.5.192-GCC-4.8.3-easybuild-devel"
+
+
+# Built with EasyBuild version 1.16.0dev
diff --git a/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
new file mode 100644
index 0000000000..192c8082f9
--- /dev/null
+++ b/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
@@ -0,0 +1,31 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   Fortran compiler from Intel - Homepage: http://software.intel.com/en-us/intel-compilers/
+    }
+}
+
+module-whatis {Description: Fortran compiler from Intel - Homepage: http://software.intel.com/en-us/intel-compilers/}
+
+set root    /tmp/software/Core/ifort/2013.5.192-GCC-4.8.3
+
+conflict ifort
+module use /tmp/modules/all/Compiler/intel/2013.5.192
+module load GCC/4.8.3
+
+prepend-path	IDB_HOME		$root/bin/intel64
+prepend-path	LD_LIBRARY_PATH		$root/compiler/lib
+prepend-path	LD_LIBRARY_PATH		$root/compiler/lib/intel64
+prepend-path	MANPATH		$root/man
+prepend-path	MANPATH		$root/man/en_US
+prepend-path	PATH		$root/bin
+prepend-path	PATH		$root/bin/intel64
+
+setenv	EBROOTIFORT		"$root"
+setenv	EBVERSIONIFORT		"2013.5.192"
+setenv	EBDEVELIFORT		"$root/easybuild/Core-ifort-2013.5.192-GCC-4.8.3-easybuild-devel"
+
+prepend-path	INTEL_LICENSE_FILE		/tmp/license.lic
+prepend-path	NLSPATH		$root/idb/intel64/locale/%l_%t/%N
+
+# Built with EasyBuild version 1.16.0dev
diff --git a/test/framework/modules/Core/iimpi/5.5.3-GCC-4.8.3 b/test/framework/modules/Core/iimpi/5.5.3-GCC-4.8.3
new file mode 100644
index 0000000000..ad5b080f00
--- /dev/null
+++ b/test/framework/modules/Core/iimpi/5.5.3-GCC-4.8.3
@@ -0,0 +1,26 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   Intel C/C++ and Fortran compilers, alongside Intel MPI. - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
+    }
+}
+
+module-whatis {Description: Intel C/C++ and Fortran compilers, alongside Intel MPI. - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/}
+
+set root    /tmp/software/Core/iimpi/5.5.3-GCC-4.8.3
+
+conflict iimpi
+
+module load icc/2013.5.192-GCC-4.8.3
+
+module load ifort/2013.5.192-GCC-4.8.3
+
+module load impi/4.1.3.049
+
+
+setenv	EBROOTIIMPI		"$root"
+setenv	EBVERSIONIIMPI		"5.5.3"
+setenv	EBDEVELIIMPI		"$root/easybuild/Core-iimpi-5.5.3-GCC-4.8.3-easybuild-devel"
+
+
+# Built with EasyBuild version 1.16.0dev
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 0aa37bdd63..e4237bc05c 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -202,13 +202,17 @@ def setup_hierarchical_modules(self):
 
         # make sure only modules in a hierarchical scheme are available, mixing modules installed with
         # a flat scheme like EasyBuildMNS and a hierarhical one like HierarchicalMNS doesn't work
-        self.reset_modulepath([os.path.join(mod_prefix, 'Core')])
+        self.reset_modulepath([mod_prefix, os.path.join(mod_prefix, 'Core')])
 
-        # tweak use statements in GCC/OpenMPI modules to ensure correct paths
+        # tweak use statements in modules to ensure correct paths
         mpi_pref = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
         for modfile in [
             os.path.join(mod_prefix, 'Core', 'GCC', '4.7.2'),
+            os.path.join(mod_prefix, 'Core', 'GCC', '4.8.3'),
+            os.path.join(mod_prefix, 'Core', 'icc', '2013.5.192-GCC-4.8.3'),
+            os.path.join(mod_prefix, 'Core', 'ifort', '2013.5.192-GCC-4.8.3'),
             os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'),
+            os.path.join(mod_prefix, 'Compiler', 'intel', '2013.5.192', 'impi', '4.1.3.049'),
             os.path.join(mpi_pref, 'FFTW', '3.3.3'),
             os.path.join(mpi_pref, 'OpenBLAS', '0.2.6-LAPACK-3.4.2'),
             os.path.join(mpi_pref, 'ScaLAPACK', '2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2'),

From 502384fe76b1669efd37e808838180b6601b1ffb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 20 Sep 2014 09:35:58 +0200
Subject: [PATCH 0178/1356] fix added unit test for Tcl-based module tools:
 don't use test modules that unload recursively and make 'purge' fail

---
 test/framework/easyblock.py                          |  4 ++--
 test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3 |  5 ++++-
 .../modules/Core/iccifort/2013.5.192-GCC-4.8.3       |  8 ++++++--
 .../modules/Core/ifort/2013.5.192-GCC-4.8.3          |  5 ++++-
 test/framework/modules/Core/iimpi/5.5.3-GCC-4.8.3    | 12 +++++++++---
 5 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 1107f8049b..80a3a6e51a 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -489,8 +489,8 @@ def test_exclude_path_to_top_of_module_tree(self):
         ec = EasyConfig(os.path.join(test_ecs_path, 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'))
         eb = EasyBlock(ec)
 
-        modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all', 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl')
-        mkdir(os.path.dirname(modfile_prefix), parents=True)
+        modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all', 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049')
+        mkdir(modfile_prefix, parents=True)
         eb.toolchain.prepare()
         modpath = eb.make_module_step()
         modfile_path = os.path.join(modpath, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
diff --git a/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
index 6ae62b5684..d01107fd85 100644
--- a/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
+++ b/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
@@ -11,7 +11,10 @@ set root    /tmp/software/Core/icc/2013.5.192-GCC-4.8.3
 
 conflict icc
 module use /tmp/modules/all/Compiler/intel/2013.5.192
-module load GCC/4.8.3
+
+if { ![is-loaded GCC/4.8.3] } {
+    module load GCC/4.8.3
+}
 
 prepend-path	IDB_HOME		$root/bin/intel64
 prepend-path	LD_LIBRARY_PATH		$root/compiler/lib
diff --git a/test/framework/modules/Core/iccifort/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/iccifort/2013.5.192-GCC-4.8.3
index db05126002..2375404a69 100644
--- a/test/framework/modules/Core/iccifort/2013.5.192-GCC-4.8.3
+++ b/test/framework/modules/Core/iccifort/2013.5.192-GCC-4.8.3
@@ -11,9 +11,13 @@ set root    /tmp/software/Core/iccifort/2013.5.192-GCC-4.8.3
 
 conflict iccifort
 
-module load icc/2013.5.192-GCC-4.8.3
+if { ![is-loaded icc/2013.5.192-GCC-4.8.3] } {
+    module load icc/2013.5.192-GCC-4.8.3
+}
 
-module load ifort/2013.5.192-GCC-4.8.3
+if { ![is-loaded ifort/2013.5.192-GCC-4.8.3] } {
+    module load ifort/2013.5.192-GCC-4.8.3
+}
 
 
 setenv	EBROOTICCIFORT		"$root"
diff --git a/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
index 192c8082f9..02c64f8bf8 100644
--- a/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
+++ b/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
@@ -11,7 +11,10 @@ set root    /tmp/software/Core/ifort/2013.5.192-GCC-4.8.3
 
 conflict ifort
 module use /tmp/modules/all/Compiler/intel/2013.5.192
-module load GCC/4.8.3
+
+if { ![is-loaded GCC/4.8.3] } {
+    module load GCC/4.8.3
+}
 
 prepend-path	IDB_HOME		$root/bin/intel64
 prepend-path	LD_LIBRARY_PATH		$root/compiler/lib
diff --git a/test/framework/modules/Core/iimpi/5.5.3-GCC-4.8.3 b/test/framework/modules/Core/iimpi/5.5.3-GCC-4.8.3
index ad5b080f00..3bb0b860cb 100644
--- a/test/framework/modules/Core/iimpi/5.5.3-GCC-4.8.3
+++ b/test/framework/modules/Core/iimpi/5.5.3-GCC-4.8.3
@@ -11,11 +11,17 @@ set root    /tmp/software/Core/iimpi/5.5.3-GCC-4.8.3
 
 conflict iimpi
 
-module load icc/2013.5.192-GCC-4.8.3
+if { ![is-loaded icc/2013.5.192-GCC-4.8.3] } {
+    module load icc/2013.5.192-GCC-4.8.3
+}
 
-module load ifort/2013.5.192-GCC-4.8.3
+if { ![is-loaded ifort/2013.5.192-GCC-4.8.3] } {
+    module load ifort/2013.5.192-GCC-4.8.3
+}
 
-module load impi/4.1.3.049
+if { ![is-loaded impi/4.1.3.049] } {
+    module load impi/4.1.3.049
+}
 
 
 setenv	EBROOTIIMPI		"$root"

From 99bdab5c65e6cb3e3fbc4c7373ab21b2f1d120e8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 20 Sep 2014 10:03:52 +0200
Subject: [PATCH 0179/1356] fix broken tests

---
 test/framework/easyblock.py | 5 +++--
 test/framework/modules.py   | 2 +-
 test/framework/scripts.py   | 4 ++--
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 80a3a6e51a..f5c4401fb3 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -489,8 +489,9 @@ def test_exclude_path_to_top_of_module_tree(self):
         ec = EasyConfig(os.path.join(test_ecs_path, 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'))
         eb = EasyBlock(ec)
 
-        modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all', 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049')
-        mkdir(modfile_prefix, parents=True)
+        modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all')
+        mkdir(os.path.join(modfile_prefix, 'Compiler', 'GCC', '4.8.3'), parents=True)
+        mkdir(os.path.join(modfile_prefix, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049'), parents=True)
         eb.toolchain.prepare()
         modpath = eb.make_module_step()
         modfile_path = os.path.join(modpath, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
diff --git a/test/framework/modules.py b/test/framework/modules.py
index 46b7453ba8..21f0a5407c 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -43,7 +43,7 @@
 
 
 # number of modules included for testing purposes
-TEST_MODULES_COUNT = 44
+TEST_MODULES_COUNT = 50
 
 
 class ModulesTest(EnhancedTestCase):
diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index f9704b7937..9712938abf 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -65,13 +65,13 @@ def test_generate_software_list(self):
         out, ec = run_cmd(cmd, simple=False)
 
         # make sure output is kind of what we expect it to be
-        regex = r"Supported Packages \(12 "
+        regex = r"Supported Packages \(17 "
         self.assertTrue(re.search(regex, out), "Pattern '%s' found in output: %s" % (regex, out))
         per_letter = {
             'F': '1',  # FFTW
             'G': '4',  # GCC, gompi, goolf, gzip
             'H': '1',  # hwloc
-            'I': '2',  # ictce, impi
+            'I': '7',  # icc, iccifort, ictce, ifort, iimpi, imkl, impi
             'O': '2',  # OpenMPI, OpenBLAS
             'S': '1',  # ScaLAPACK
             'T': '1',  # toy

From 591725c45dd484aa0d5097465add1cf0a695b00c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 20 Sep 2014 10:05:29 +0200
Subject: [PATCH 0180/1356] cleanup in GCC test module

---
 test/framework/modules/Core/GCC/4.8.3 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/modules/Core/GCC/4.8.3 b/test/framework/modules/Core/GCC/4.8.3
index dded358b87..4c88e02254 100644
--- a/test/framework/modules/Core/GCC/4.8.3
+++ b/test/framework/modules/Core/GCC/4.8.3
@@ -9,10 +9,10 @@ proc ModulesHelp { } {
 module-whatis {Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
  as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/}
 
-set root    /tmp/problem1086/software/Core/GCC/4.8.3
+set root    /tmp/gsoftware/Core/GCC/4.8.3
 
 conflict GCC
-module use /tmp/problem1086/modules/all/Compiler/GCC/4.8.3
+module use /tmp/gmodules/all/Compiler/GCC/4.8.3
 prepend-path	CPATH		$root/include
 prepend-path	LD_LIBRARY_PATH		$root/lib
 prepend-path	LD_LIBRARY_PATH		$root/lib64

From 27dc61e3f2e49c80a80c94cb02b62ac46b67bbd4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 20 Sep 2014 10:22:33 +0200
Subject: [PATCH 0181/1356] fix typo in GCC test module

---
 test/framework/modules/Core/GCC/4.8.3 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/modules/Core/GCC/4.8.3 b/test/framework/modules/Core/GCC/4.8.3
index 4c88e02254..4ddfb7dc18 100644
--- a/test/framework/modules/Core/GCC/4.8.3
+++ b/test/framework/modules/Core/GCC/4.8.3
@@ -9,10 +9,10 @@ proc ModulesHelp { } {
 module-whatis {Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
  as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/}
 
-set root    /tmp/gsoftware/Core/GCC/4.8.3
+set root    /tmp/software/Core/GCC/4.8.3
 
 conflict GCC
-module use /tmp/gmodules/all/Compiler/GCC/4.8.3
+module use /tmp/modules/all/Compiler/GCC/4.8.3
 prepend-path	CPATH		$root/include
 prepend-path	LD_LIBRARY_PATH		$root/lib
 prepend-path	LD_LIBRARY_PATH		$root/lib64

From c24cb0fccc9001273660fc0f5b19bf88700cdd50 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 22 Sep 2014 18:26:52 +0200
Subject: [PATCH 0182/1356] fix remarks

---
 easybuild/framework/easyblock.py |  8 ++++----
 easybuild/tools/environment.py   |  8 +++++++-
 easybuild/tools/modules.py       | 15 ++++++++-------
 3 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3a5bf95e63..32bbe6a4a9 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -57,7 +57,7 @@
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
 from easybuild.tools.config import install_path, log_path, read_only_installdir, source_paths
-from easybuild.tools.environment import modify_env
+from easybuild.tools.environment import restore_env
 from easybuild.tools.filetools import DEFAULT_CHECKSUM
 from easybuild.tools.filetools import adjust_permissions, apply_patch, convert_name, download_file, encode_class_name
 from easybuild.tools.filetools import extract_file, mkdir, read_file, rmtree2
@@ -997,7 +997,7 @@ def clean_up_fake_module(self, fake_mod_data):
             self.log.warning("Not unloading module, since self.full_mod_name is not set.")
 
         # restore original environment
-        modify_env(os.environ, orig_env)
+        restore_env(orig_env)
 
     def load_dependency_modules(self):
         """Load dependency modules."""
@@ -1851,7 +1851,7 @@ def build_and_install_one(module, orig_environ):
     # restore original environment
     _log.info("Resetting environment")
     filetools.errors_found_in_log = 0
-    modify_env(os.environ, orig_environ)
+    restore_env(orig_environ)
 
     cwd = os.getcwd()
 
@@ -2054,7 +2054,7 @@ def perform_step(step, obj, method, logfile):
 
             # start with a clean slate
             os.chdir(base_dir)
-            modify_env(os.environ, base_env)
+            restore_env(base_env)
 
             steps = EasyBlock.get_steps(iteration_count=app.det_iter_cnt())
 
diff --git a/easybuild/tools/environment.py b/easybuild/tools/environment.py
index 073c43829d..384c65febd 100644
--- a/easybuild/tools/environment.py
+++ b/easybuild/tools/environment.py
@@ -102,7 +102,6 @@ def restore_env_vars(env_keys):
     """
     Restore the environment by setting the keys in the env_keys dict again with their old value
     """
-
     for key in env_keys:
         if env_keys[key] is not None:
             _log.info("Restoring environment variable %s (value: %s)" % (key, env_keys[key]))
@@ -150,3 +149,10 @@ def modify_env(old, new):
             _log.debug("Key in old environment found that is not in new one: %s (%s)" % (key, old[key]))
             os.unsetenv(key)
             del os.environ[key]
+
+
+def restore_env(env):
+    """
+    Restore active environment based on specified dictionary.
+    """
+    modify_env(os.environ, env)
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index b2e75295b2..8dbef28852 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -47,7 +47,7 @@
 
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_modules_tool, install_path
-from easybuild.tools.environment import modify_env
+from easybuild.tools.environment import restore_env
 from easybuild.tools.filetools import convert_name, mkdir, read_file, path_matches, which
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.run import run_cmd
@@ -377,7 +377,7 @@ def load(self, modules, mod_paths=None, purge=False, orig_env=None):
             self.purge()
             # restore original environment if provided
             if orig_env is not None:
-                modify_env(os.environ, orig_env)
+                restore_env(orig_env)
 
         # make sure $MODULEPATH is set correctly after purging
         self.check_module_path()
@@ -610,7 +610,7 @@ def modpath_extensions_for(self, mod_names):
                 self.load([mod_name])
 
         # restore original environment (modules may have been loaded above)
-        modify_env(os.environ, orig_env)
+        restore_env(orig_env)
 
         return modpath_exts
 
@@ -667,10 +667,11 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
             full_modpath_exts = modpath_exts[dep]
             if path_matches(full_mod_subdir, full_modpath_exts):
                 # full path to module subdir of dependency is simply path to module file without (short) module name
-                full_mod_subdirs.append(self.modulefile_path(dep)[:-len(dep)-1])
+                full_mod_subdir = self.modulefile_path(dep)[:-len(dep)-1]
+                full_mod_subdirs.append(full_mod_subdir)
 
                 mods_to_top.append(dep)
-                tup = (dep, full_mod_subdirs[-1], full_modpath_exts)
+                tup = (dep, full_mod_subdir, full_modpath_exts)
                 self.log.debug("Found module to top of module tree: %s (subdir: %s, modpath extensions %s)" % tup)
 
             if full_modpath_exts:
@@ -679,12 +680,12 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
                 self.load([dep])
 
         # restore original environment (modules may have been loaded above)
-        modify_env(os.environ, orig_env)
+        restore_env(orig_env)
 
         path = mods_to_top[:]
         if mods_to_top:
             # remove retained dependencies from the list, since we're climbing up the module tree
-            remaining_modpath_exts = dict([(m, modpath_exts[m]) for m in modpath_exts if not m in mods_to_top])
+            remaining_modpath_exts = dict([m for m in modpath_exts.items() if not m[0] in mods_to_top])
 
             self.log.debug("Path to top from %s extended to %s, so recursing to find way to the top" % (mod_name, mods_to_top))
             for mod_name, full_mod_subdir in zip(mods_to_top, full_mod_subdirs):

From 38302bc7bdea368500528b53be62e66d60d8b299 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 22 Sep 2014 20:04:34 +0200
Subject: [PATCH 0183/1356] bump version to v1.15.1, update release notes

---
 RELEASE_NOTES              | 9 +++++++++
 easybuild/tools/version.py | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 2186d01915..6e7de30e18 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -1,6 +1,15 @@
 This file contains a description of the major changes to the easybuild-framework EasyBuild package.
 For more detailed information, please see the git log.
 
+v1.15.1 (September 23rd 2014)
+-----------------------------
+
+bugfix release
+- take into account that multiple modules may be extending $MODULEPATH with the same path,
+  when determining path to top of module tree (see #1047)
+        - this bug caused a load statement for either icc or ifort to be included in higher-level
+          modules installed with an Intel-based compiler toolchain, under the HierarchicalMNS module naming scheme
+
 v1.15.0 (September 12th 2014)
 -----------------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index f527eaecee..dcdeea01fd 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.16.0dev")
+VERSION = LooseVersion("1.15.1")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 6b141bbd2ae308c28eabb692feef5d280af21723 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 Sep 2014 15:18:05 +0200
Subject: [PATCH 0184/1356] fix HierarchicalMNS for cgoolf and goolfc
 toolchains

---
 .../tools/module_naming_scheme/hierarchical_mns.py  | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index d88f794aae..62dde03264 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -80,15 +80,22 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         elif len(tc_comps) == 1:
             res = (tc_comps[0]['name'], tc_comps[0]['version'])
         else:
-            tc_comp_names = [comp['name'] for comp in tc_comps]
-            if set(tc_comp_names) == set(['icc', 'ifort']):
+            comp_versions = dict([(comp['name'], comp['version']) for comp in tc_comps])
+            comp_names = comp_versions.keys()
+            if set(comp_names) == set(['icc', 'ifort']):
                 tc_comp_name = 'intel'
                 if tc_comps[0]['version'] == tc_comps[1]['version']:
                     tc_comp_ver = tc_comps[0]['version']
                 else:
                     self.log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
+            elif set(comp_names) == set(['Clang', 'GCC']):
+                tc_comp_name = 'ClangGCC'
+                tc_comp_ver = '%s-%s' % (comp_versions['Clang'], comp_versions['GCC'])
+            elif set(comp_names) == set(['GCC', 'CUDA']):
+                tc_comp_name = 'GCC-CUDA'
+                tc_comp_ver = '%s-%s' % (comp_versions['GCC'], comp_versions['CUDA'])
             else:
-                self.log.error("Unknown set of toolchain compilers, module naming scheme needs to be enhanced first.")
+                self.log.error("Unknown set of toolchain compilers, module naming scheme needs work: %s" % comp_names)
             res = (tc_comp_name, tc_comp_ver)
         return res
 

From f76e1a58a54db345a6def5a8148f1e8cebcf4048 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 Sep 2014 15:18:10 +0200
Subject: [PATCH 0185/1356] add definition of iompi toolchain

---
 easybuild/toolchains/iompi.py | 40 +++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/toolchains/iompi.py

diff --git a/easybuild/toolchains/iompi.py b/easybuild/toolchains/iompi.py
new file mode 100644
index 0000000000..fd757a3c92
--- /dev/null
+++ b/easybuild/toolchains/iompi.py
@@ -0,0 +1,40 @@
+##
+# Copyright 2012-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for iompi compiler toolchain (includes Intel compilers (icc, ifort) and OpenMPI.
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+"""
+
+from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.toolchains.mpi.openmpi import OpenMPI
+
+
+class Iompi(IntelIccIfort, OpenMPI):
+    """
+    Compiler toolchain with Intel compilers (icc/ifort) and OpenMPI.
+    """
+    NAME = 'iompi'

From 6ea8bbb1726557ce21794044f05b19085d6971ec Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 Sep 2014 17:28:36 +0200
Subject: [PATCH 0186/1356] clean up code in
 HierarchicalMNS.det_toolchain_compilers_name_version

---
 .../module_naming_scheme/hierarchical_mns.py  | 21 ++++++++-----------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 62dde03264..f4113fbe71 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -82,18 +82,15 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         else:
             comp_versions = dict([(comp['name'], comp['version']) for comp in tc_comps])
             comp_names = comp_versions.keys()
-            if set(comp_names) == set(['icc', 'ifort']):
-                tc_comp_name = 'intel'
-                if tc_comps[0]['version'] == tc_comps[1]['version']:
-                    tc_comp_ver = tc_comps[0]['version']
-                else:
-                    self.log.error("Bumped into different versions for toolchain compilers: %s" % tc_comps)
-            elif set(comp_names) == set(['Clang', 'GCC']):
-                tc_comp_name = 'ClangGCC'
-                tc_comp_ver = '%s-%s' % (comp_versions['Clang'], comp_versions['GCC'])
-            elif set(comp_names) == set(['GCC', 'CUDA']):
-                tc_comp_name = 'GCC-CUDA'
-                tc_comp_ver = '%s-%s' % (comp_versions['GCC'], comp_versions['CUDA'])
+            name_version_templates = {
+                'icc,ifort': ('intel', '%(icc)s'),
+                'Clang,GCC': ('Clang-GCC', '%(Clang)s-%(GCC)s'),
+                'CUDA,GCC': ('GCC-CUDA', '%(GCC)s-%(CUDA)s'),
+            }
+            key = ','.join(sorted(comp_names))
+            if key in name_version_templates:
+                tc_comp_name, tc_comp_ver_tmpl = name_version_templates[key]
+                tc_comp_ver = tc_comp_ver_tmpl % comp_versions
             else:
                 self.log.error("Unknown set of toolchain compilers, module naming scheme needs work: %s" % comp_names)
             res = (tc_comp_name, tc_comp_ver)

From 0775a2139d152a23ae37ea9ab62415969b5a26d6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 Sep 2014 17:57:25 +0200
Subject: [PATCH 0187/1356] fix remarks

---
 .../module_naming_scheme/hierarchical_mns.py  | 20 ++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index f4113fbe71..5efc55a2ee 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -43,6 +43,13 @@
 MODULECLASS_COMPILER = 'compiler'
 MODULECLASS_MPI = 'mpi'
 
+# note: names in keys are ordered alphabetically
+COMP_NAME_VERSION_TEMPLATES = {
+    'icc,ifort': ('intel', '%(icc)s'),
+    'Clang,GCC': ('Clang-GCC', '%(Clang)s-%(GCC)s'),
+    'CUDA,GCC': ('GCC-CUDA', '%(GCC)s-%(CUDA)s'),
+}
+
 
 class HierarchicalMNS(ModuleNamingScheme):
     """Class implementing an example hierarchical module naming scheme."""
@@ -82,15 +89,14 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         else:
             comp_versions = dict([(comp['name'], comp['version']) for comp in tc_comps])
             comp_names = comp_versions.keys()
-            name_version_templates = {
-                'icc,ifort': ('intel', '%(icc)s'),
-                'Clang,GCC': ('Clang-GCC', '%(Clang)s-%(GCC)s'),
-                'CUDA,GCC': ('GCC-CUDA', '%(GCC)s-%(CUDA)s'),
-            }
             key = ','.join(sorted(comp_names))
-            if key in name_version_templates:
-                tc_comp_name, tc_comp_ver_tmpl = name_version_templates[key]
+            if key in COMP_NAME_VERSION_TEMPLATES:
+                tc_comp_name, tc_comp_ver_tmpl = COMP_NAME_VERSION_TEMPLATES[key]
                 tc_comp_ver = tc_comp_ver_tmpl % comp_versions
+                # make sure that icc/ifort versions match
+                if tc_comp_name == 'intel':
+                    if comp_versions['icc'] != comp_versions['ifort']:
+                        self.log.error("Bumped into different versions for Intel compilers: %s" % comp_versions)
             else:
                 self.log.error("Unknown set of toolchain compilers, module naming scheme needs work: %s" % comp_names)
             res = (tc_comp_name, tc_comp_ver)

From 14e489df1c09b465adc3e6e80f15cfde799ff76d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 Sep 2014 18:05:38 +0200
Subject: [PATCH 0188/1356] fix minor remark

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 5efc55a2ee..420fb67a38 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -94,8 +94,7 @@ def det_toolchain_compilers_name_version(self, tc_comps):
                 tc_comp_name, tc_comp_ver_tmpl = COMP_NAME_VERSION_TEMPLATES[key]
                 tc_comp_ver = tc_comp_ver_tmpl % comp_versions
                 # make sure that icc/ifort versions match
-                if tc_comp_name == 'intel':
-                    if comp_versions['icc'] != comp_versions['ifort']:
+                if tc_comp_name == 'intel' and comp_versions['icc'] != comp_versions['ifort']:
                         self.log.error("Bumped into different versions for Intel compilers: %s" % comp_versions)
             else:
                 self.log.error("Unknown set of toolchain compilers, module naming scheme needs work: %s" % comp_names)

From db628f4f0016dff998dc9576e60c3b5d4d846160 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 Sep 2014 19:22:31 +0200
Subject: [PATCH 0189/1356] fix indent

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 420fb67a38..c415d61d72 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -95,7 +95,7 @@ def det_toolchain_compilers_name_version(self, tc_comps):
                 tc_comp_ver = tc_comp_ver_tmpl % comp_versions
                 # make sure that icc/ifort versions match
                 if tc_comp_name == 'intel' and comp_versions['icc'] != comp_versions['ifort']:
-                        self.log.error("Bumped into different versions for Intel compilers: %s" % comp_versions)
+                    self.log.error("Bumped into different versions for Intel compilers: %s" % comp_versions)
             else:
                 self.log.error("Unknown set of toolchain compilers, module naming scheme needs work: %s" % comp_names)
             res = (tc_comp_name, tc_comp_ver)

From fa33d36a0f839f4ad3ea05ec6cec7d3bc57ac7b6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 24 Sep 2014 10:10:37 +0200
Subject: [PATCH 0190/1356] extend release notes w.r.t. PR #1049

---
 RELEASE_NOTES | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 6e7de30e18..7c587db954 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -9,6 +9,8 @@ bugfix release
   when determining path to top of module tree (see #1047)
         - this bug caused a load statement for either icc or ifort to be included in higher-level
           modules installed with an Intel-based compiler toolchain, under the HierarchicalMNS module naming scheme
+- make HierarchicalMNS module naming scheme compatible with cgoolf and goolfc toolchain (#1049)
+- add definition of iompi (sub)toolchain to make iomkl toolchain compatible with HierarchicalMNS (#1049)
 
 v1.15.0 (September 12th 2014)
 -----------------------------

From 77d499b6e3cb5e84a88589a7f17aef3477cf5fbd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 25 Sep 2014 15:32:02 +0200
Subject: [PATCH 0191/1356] fix version to v1.16.0dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index dcdeea01fd..f527eaecee 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.15.1")
+VERSION = LooseVersion("1.16.0dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From e6b477781c9c1f7fb6c9ea4fb128d689693f04f2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Oct 2014 17:16:04 +0200
Subject: [PATCH 0192/1356] fix $MODULEPATH extensions for Clang/CUDA, include
 versionsuffix in module subdir

---
 .../module_naming_scheme/hierarchical_mns.py  | 36 +++++++++++++++----
 .../easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb      | 29 +++++++++++++++
 test/framework/easyconfigs/GCC-4.8.2.eb       | 28 +++++++++++++++
 .../framework/easyconfigs/ifort-2013.3.163.eb | 17 +++++++++
 test/framework/module_generator.py            |  4 +++
 5 files changed, 107 insertions(+), 7 deletions(-)
 create mode 100644 test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
 create mode 100644 test/framework/easyconfigs/GCC-4.8.2.eb
 create mode 100644 test/framework/easyconfigs/ifort-2013.3.163.eb

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index c415d61d72..27ba3de274 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -30,6 +30,7 @@
 """
 
 import os
+import re
 from vsc.utils import fancylogger
 
 from easybuild.tools.module_naming_scheme import ModuleNamingScheme
@@ -132,17 +133,38 @@ def det_modpath_extensions(self, ec):
         Examples: Compiler/GCC/4.8.3 (for GCC/4.8.3 module), MPI/GCC/4.8.3/OpenMPI/1.6.5 (for OpenMPI/1.6.5 module)
         """
         modclass = ec['moduleclass']
+        tc_comps = det_toolchain_compilers(ec)
+        tc_comp_info = self.det_toolchain_compilers_name_version(tc_comps)
 
         paths = []
-        if modclass == MODULECLASS_COMPILER:
-            if ec['name'] in ['icc', 'ifort']:
-                compdir = 'intel'
+        if modclass == MODULECLASS_COMPILER or ec['name'] in ['CUDA']:
+            # obtain list of compilers based on that extend $MODULEPATH in some way other than <name>/<version>
+            extend_comps = []
+            # exclude GCC for which <name>/<version> is used as $MODULEPATH extension
+            excluded_comps = ['GCC']
+            for comps in COMP_NAME_VERSION_TEMPLATES.keys():
+                extend_comps.extend([comp for comp in comps.split(',') if comp not in excluded_comps])
+
+            comp_name_ver = None
+            if ec['name'] in extend_comps:
+                for key in COMP_NAME_VERSION_TEMPLATES:
+                    if re.search(".*%s.*" % ec['name'], key):
+                        comp_name, comp_ver_tmpl = COMP_NAME_VERSION_TEMPLATES[key]
+                        comp_versions = {ec['name']: ec['version'] + ec['versionsuffix']}
+                        if ec['name'] == 'ifort':
+                            # 'icc' key should be provided since it's the only one used in the template
+                            comp_versions.update({'icc': ec['version'] + ec['versionsuffix']})
+                        if tc_comp_info is not None:
+                            # also provide toolchain version for non-dummy toolchains
+                            comp_versions.update({tc_comp_info[0]: tc_comp_info[1]})
+                        comp_name_ver = [comp_name, comp_ver_tmpl % comp_versions]
+                        break
             else:
-                compdir = ec['name']
-            paths.append(os.path.join(COMPILER, compdir, ec['version']))
+                comp_name_ver = [ec['name'], ec['version'] + ec['versionsuffix']]
+
+            paths.append(os.path.join(COMPILER, *comp_name_ver))
+
         elif modclass == MODULECLASS_MPI:
-            tc_comps = det_toolchain_compilers(ec)
-            tc_comp_info = self.det_toolchain_compilers_name_version(tc_comps)
             if tc_comp_info is None:
                 tup = (ec['toolchain'], ec['name'], ec['version'])
                 error_msg = ("No compiler available in toolchain %s used to install MPI library %s v%s, "
diff --git a/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
new file mode 100644
index 0000000000..a8e69945a9
--- /dev/null
+++ b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
@@ -0,0 +1,29 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University
+# Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis.georgatos@uni.lu>, Kenneth Hoste
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html
+##
+
+name = 'CUDA'
+version = '5.5.22'
+
+homepage = 'https://developer.nvidia.com/cuda-toolkit'
+description = """CUDA (formerly Compute Unified Device Architecture) is a parallel
+ computing platform and programming model created by NVIDIA and implemented by the
+ graphics processing units (GPUs) that they produce. CUDA gives developers access
+ to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs."""
+
+toolchain = {'name': 'GCC', 'version': '4.8.2'}
+
+# eg. http://developer.download.nvidia.com/compute/cuda/5_5/rel/installers/cuda_5.5.22_linux_64.run
+source_urls = ['http://developer.download.nvidia.com/compute/cuda/5_5/rel/installers/']
+
+sources = ['%(namelower)s_%(version)s_linux_64.run']
+
+moduleclass = 'system'
diff --git a/test/framework/easyconfigs/GCC-4.8.2.eb b/test/framework/easyconfigs/GCC-4.8.2.eb
new file mode 100644
index 0000000000..cef0802601
--- /dev/null
+++ b/test/framework/easyconfigs/GCC-4.8.2.eb
@@ -0,0 +1,28 @@
+name = "GCC"
+version = '4.8.2'
+
+homepage = 'http://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = [
+    'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s',  # GCC auto-resolving HTTP mirror
+    'http://ftpmirror.gnu.org/gmp',  # idem for GMP
+    'http://ftpmirror.gnu.org/mpfr',  # idem for MPFR
+    'http://www.multiprecision.org/mpc/download',  # MPC official
+]
+sources = [
+    SOURCELOWER_TAR_GZ,
+    'gmp-5.1.3.tar.bz2',
+    'mpfr-3.1.2.tar.gz',
+    'mpc-1.0.1.tar.gz',
+]
+
+languages = ['c', 'c++', 'fortran', 'lto']
+
+# building GCC sometimes fails if make parallelism is too high, so let's limit it
+maxparallel = 4
+
+moduleclass = 'compiler'
diff --git a/test/framework/easyconfigs/ifort-2013.3.163.eb b/test/framework/easyconfigs/ifort-2013.3.163.eb
new file mode 100644
index 0000000000..4efd890d23
--- /dev/null
+++ b/test/framework/easyconfigs/ifort-2013.3.163.eb
@@ -0,0 +1,17 @@
+name = 'ifort'
+version = '2013.3.163'
+
+homepage = 'http://software.intel.com/en-us/intel-compilers/'
+description = "Fortran compiler from Intel"
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['l_fcompxe_%s.tgz' % version]
+
+dontcreateinstalldir = 'True'
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
+
+moduleclass = 'compiler'
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 9d0c46188b..cd8cddb439 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -393,11 +393,15 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
         init_config(build_options=build_options)
 
         # format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions)
+        iccver = '2013.5.192-GCC-4.8.3'
         test_ecs = {
             'GCC-4.7.2.eb': ('GCC/4.7.2', 'Core', ['Compiler/GCC/4.7.2'], ['Core']),
             'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2', ['MPI/GCC/4.7.2/OpenMPI/1.6.4'], ['Core']),
             'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5', 'MPI/GCC/4.7.2/OpenMPI/1.6.4', [], ['Core']),
             'goolf-1.4.10.eb': ('goolf/1.4.10', 'Core', [], ['Core']),
+            'icc-2013.5.192-GCC-4.8.3.eb': ('icc/%s' % iccver, 'Core', ['Compiler/intel/%s' % iccver], ['Core']),
+            'ifort-2013.3.163.eb': ('ifort/2013.3.163', 'Core', ['Compiler/intel/2013.3.163'], ['Core']),
+            'CUDA-5.5.22-GCC-4.8.2.eb': ('CUDA/5.5.22', 'Compiler/GCC/4.8.2', ['Compiler/GCC-CUDA/4.8.2-5.5.22'], ['Core']),
         }
         for ecfile, mns_vals in test_ecs.items():
             test_ec(ecfile, *mns_vals)

From 17d548a7a36410be55b4d1c5c4c4b2920613a42d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 12:17:04 +0200
Subject: [PATCH 0193/1356] fix tiny remark

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 27ba3de274..184c596c43 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -157,6 +157,7 @@ def det_modpath_extensions(self, ec):
                         if tc_comp_info is not None:
                             # also provide toolchain version for non-dummy toolchains
                             comp_versions.update({tc_comp_info[0]: tc_comp_info[1]})
+
                         comp_name_ver = [comp_name, comp_ver_tmpl % comp_versions]
                         break
             else:

From 0b2066221329e6644f37953080a3178f006d7671 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 12:17:50 +0200
Subject: [PATCH 0194/1356] fix unit tests broken due to shellshock patch

---
 easybuild/tools/modules.py    | 18 +++++++++++++-----
 test/framework/modulestool.py | 17 ++++++++---------
 2 files changed, 21 insertions(+), 14 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 8dbef28852..c3c2c2b81a 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -137,12 +137,14 @@ class ModulesTool(object):
 
     __metaclass__ = Singleton
 
-    def __init__(self, mod_paths=None):
+    def __init__(self, mod_paths=None, testing=False):
         """
         Create a ModulesTool object
         @param mod_paths: A list of paths where the modules can be located
         @type mod_paths: list
         """
+        # this can/should be set to True during testing
+        self.testing = testing
 
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
         self.mod_paths = None
@@ -172,9 +174,6 @@ def __init__(self, mod_paths=None):
         self.check_module_function(allow_mismatch=build_option('allow_modules_tool_mismatch'))
         self.set_and_check_version()
 
-        # this can/should be set to True during testing
-        self.testing = False
-
     def buildstats(self):
         """Return tuple with data to be included in buildstats"""
         return (self.__class__.__name__, self.cmd, self.version)
@@ -229,11 +228,20 @@ def check_cmd_avail(self):
 
     def check_module_function(self, allow_mismatch=False, regex=None):
         """Check whether selected module tool matches 'module' function definition."""
-        out, ec = run_cmd("type module", simple=False, log_ok=False, log_all=False)
+        if self.testing:
+            # grab 'module' function definition from environment if it's there; only during testing
+            if 'module' in os.environ:
+                out, ec = os.environ['module'], 0
+            else:
+                out, ec = None, 1
+        else:
+            out, ec = run_cmd("type module", simple=False, log_ok=False, log_all=False)
+
         if regex is None:
             regex = r".*%s" % os.path.basename(self.cmd)
         mod_cmd_re = re.compile(regex, re.M)
         mod_details = "pattern '%s' (%s)" % (mod_cmd_re.pattern, self.__class__.__name__)
+
         if ec == 0:
             if mod_cmd_re.search(out):
                 self.log.debug("Found pattern '%s' in defined 'module' function." % mod_cmd_re.pattern)
diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index ad8c28de27..82e6cf39d4 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -76,7 +76,7 @@ def test_mock(self):
         os.environ['module'] = "() {  eval `/bin/echo $*`\n}"
 
         # ue empty mod_path list, otherwise the install_path is called
-        mmt = MockModulesTool(mod_paths=[])
+        mmt = MockModulesTool(mod_paths=[], testing=True)
 
         # the version of the MMT is the commandline option
         self.assertEqual(mmt.version, StrictVersion(MockModulesTool.VERSION_OPTION))
@@ -91,7 +91,7 @@ def test_environment_command(self):
         os.environ['module'] = "() { %s $*\n}" % BrokenMockModulesTool.COMMAND
 
         try:
-            bmmt = BrokenMockModulesTool(mod_paths=[])
+            bmmt = BrokenMockModulesTool(mod_paths=[], testing=True)
             # should never get here
             self.assertTrue(False, 'BrokenMockModulesTool should fail')
         except EasyBuildError, err:
@@ -100,7 +100,7 @@ def test_environment_command(self):
         os.environ[BrokenMockModulesTool.COMMAND_ENVIRONMENT] = MockModulesTool.COMMAND
         os.environ['module'] = "() { /bin/echo $*\n}"
         BrokenMockModulesTool._instances.pop(BrokenMockModulesTool, None)
-        bmmt = BrokenMockModulesTool(mod_paths=[])
+        bmmt = BrokenMockModulesTool(mod_paths=[], testing=True)
         cmd_abspath = which(MockModulesTool.COMMAND)
 
         self.assertEqual(bmmt.version, StrictVersion(MockModulesTool.VERSION_OPTION))
@@ -112,7 +112,7 @@ def test_environment_command(self):
     def test_module_mismatch(self):
         """Test whether mismatch detection between modules tool and 'module' function works."""
         # redefine 'module' function (deliberate mismatch with used module command in MockModulesTool)
-        os.environ['module'] = "() {  eval `/Users/kehoste/Modules/$MODULE_VERSION/bin/modulecmd bash $*`\n}"
+        os.environ['module'] = "() {  eval `/tmp/Modules/$MODULE_VERSION/bin/modulecmd bash $*`\n}"
         self.assertErrorRegex(EasyBuildError, ".*pattern .* not found in defined 'module' function", MockModulesTool)
 
         # check whether escaping error by allowing mismatch via build options works
@@ -123,7 +123,7 @@ def test_module_mismatch(self):
 
         fancylogger.logToFile(self.logfile)
 
-        mt = MockModulesTool()
+        mt = MockModulesTool(testing=True)
         f = open(self.logfile, 'r')
         logtxt = f.read()
         f.close()
@@ -133,13 +133,13 @@ def test_module_mismatch(self):
         # redefine 'module' function with correct module command
         os.environ['module'] = "() {  eval `/bin/echo $*`\n}"
         MockModulesTool._instances.pop(MockModulesTool)
-        mt = MockModulesTool()
+        mt = MockModulesTool(testing=True)
         self.assertTrue(isinstance(mt.loaded_modules(), list))  # dummy usage
 
         # a warning should be logged if the 'module' function is undefined
         del os.environ['module']
         MockModulesTool._instances.pop(MockModulesTool)
-        mt = MockModulesTool()
+        mt = MockModulesTool(testing=True)
         f = open(self.logfile, 'r')
         logtxt = f.read()
         f.close()
@@ -173,8 +173,7 @@ def test_lmod_specific(self):
 
             # initialize Lmod modules tool, pass full path to 'lmod' via $LMOD_CMD
             os.environ['LMOD_CMD'] = lmod_abspath
-            lmod = Lmod()
-            lmod.testing = True
+            lmod = Lmod(testing=True)
 
             # obtain list of availabe modules, should be non-empty
             self.assertTrue(lmod.available(), "List of available modules obtained using Lmod is non-empty")

From 30063544c538c4e49a4289535a4477780f629f7e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 12:20:57 +0200
Subject: [PATCH 0195/1356] fix broken test

---
 test/framework/scripts.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 9712938abf..1776f8cdc1 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -65,9 +65,10 @@ def test_generate_software_list(self):
         out, ec = run_cmd(cmd, simple=False)
 
         # make sure output is kind of what we expect it to be
-        regex = r"Supported Packages \(17 "
+        regex = r"Supported Packages \(18 "
         self.assertTrue(re.search(regex, out), "Pattern '%s' found in output: %s" % (regex, out))
         per_letter = {
+            'C': '1',  # CUDA
             'F': '1',  # FFTW
             'G': '4',  # GCC, gompi, goolf, gzip
             'H': '1',  # hwloc

From 0aab07da44463597bdf700a8e19e20ae3a3fb3d5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 13:23:23 +0200
Subject: [PATCH 0196/1356] fix case where testing is not enabled in
 modulestool.py tests

---
 test/framework/modulestool.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index 82e6cf39d4..80c745fb31 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -113,7 +113,7 @@ def test_module_mismatch(self):
         """Test whether mismatch detection between modules tool and 'module' function works."""
         # redefine 'module' function (deliberate mismatch with used module command in MockModulesTool)
         os.environ['module'] = "() {  eval `/tmp/Modules/$MODULE_VERSION/bin/modulecmd bash $*`\n}"
-        self.assertErrorRegex(EasyBuildError, ".*pattern .* not found in defined 'module' function", MockModulesTool)
+        self.assertErrorRegex(EasyBuildError, ".*pattern .* not found in defined 'module' function", MockModulesTool, testing=True)
 
         # check whether escaping error by allowing mismatch via build options works
         build_options = {

From b092c5f8ef52c0f6efe8384046a6af9acadaec59 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 14:05:09 +0200
Subject: [PATCH 0197/1356] fix long line

---
 test/framework/modulestool.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index 80c745fb31..5b92f8822a 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -113,7 +113,8 @@ def test_module_mismatch(self):
         """Test whether mismatch detection between modules tool and 'module' function works."""
         # redefine 'module' function (deliberate mismatch with used module command in MockModulesTool)
         os.environ['module'] = "() {  eval `/tmp/Modules/$MODULE_VERSION/bin/modulecmd bash $*`\n}"
-        self.assertErrorRegex(EasyBuildError, ".*pattern .* not found in defined 'module' function", MockModulesTool, testing=True)
+        error_regex = ".*pattern .* not found in defined 'module' function"
+        self.assertErrorRegex(EasyBuildError, error_regex, MockModulesTool, testing=True)
 
         # check whether escaping error by allowing mismatch via build options works
         build_options = {

From 49da67ceb96340b22a3884a4486b97631caecaf6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 14:06:01 +0200
Subject: [PATCH 0198/1356] fix broken test that verifies mismatch on 'module'
 function

---
 easybuild/main.py          | 2 +-
 easybuild/tools/modules.py | 4 ++--
 easybuild/tools/testing.py | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index b250876641..a572ac2c05 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -276,7 +276,7 @@ def main(testing_data=(None, None, None)):
     })
 
     # obtain list of loaded modules, build options must be initialized first
-    modlist = session_module_list()
+    modlist = session_module_list(testing=testing)
     init_session_state.update({'module_list': modlist})
     _log.debug("Initial session state: %s" % init_session_state)
 
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index c3c2c2b81a..7111fd872b 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -973,7 +973,7 @@ def avail_modules_tools():
     return class_dict
 
 
-def modules_tool(mod_paths=None):
+def modules_tool(mod_paths=None, testing=False):
     """
     Return interface to modules tool (environment modules (C, Tcl), or Lmod)
     """
@@ -981,7 +981,7 @@ def modules_tool(mod_paths=None):
     modules_tool = get_modules_tool()
     if modules_tool is not None:
         modules_tool_class = avail_modules_tools().get(modules_tool)
-        return modules_tool_class(mod_paths=mod_paths)
+        return modules_tool_class(mod_paths=mod_paths, testing=testing)
     else:
         return None
 
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index b572921f7e..fa579e2107 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -157,9 +157,9 @@ def session_state():
     }
 
 
-def session_module_list():
+def session_module_list(testing=False):
     """Get list of loaded modules ('module list')."""
-    modtool = modules_tool()
+    modtool = modules_tool(testing=testing)
     return modtool.list()
 
 

From 4b19da1ab4451f58f2f7283c855d58c6648aec10 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 14:08:09 +0200
Subject: [PATCH 0199/1356] fix remark

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 184c596c43..9eee1439cc 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -148,7 +148,7 @@ def det_modpath_extensions(self, ec):
             comp_name_ver = None
             if ec['name'] in extend_comps:
                 for key in COMP_NAME_VERSION_TEMPLATES:
-                    if re.search(".*%s.*" % ec['name'], key):
+                    if ec['name'] in key.split(','):
                         comp_name, comp_ver_tmpl = COMP_NAME_VERSION_TEMPLATES[key]
                         comp_versions = {ec['name']: ec['version'] + ec['versionsuffix']}
                         if ec['name'] == 'ifort':

From 178769b065ff15e7bd91f4a79cba27b1642bcb01 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 12:17:50 +0200
Subject: [PATCH 0200/1356] fix unit tests broken due to shellshock patch

---
 easybuild/tools/modules.py    | 18 +++++++++++++-----
 test/framework/modulestool.py | 17 ++++++++---------
 2 files changed, 21 insertions(+), 14 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 8dbef28852..c3c2c2b81a 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -137,12 +137,14 @@ class ModulesTool(object):
 
     __metaclass__ = Singleton
 
-    def __init__(self, mod_paths=None):
+    def __init__(self, mod_paths=None, testing=False):
         """
         Create a ModulesTool object
         @param mod_paths: A list of paths where the modules can be located
         @type mod_paths: list
         """
+        # this can/should be set to True during testing
+        self.testing = testing
 
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
         self.mod_paths = None
@@ -172,9 +174,6 @@ def __init__(self, mod_paths=None):
         self.check_module_function(allow_mismatch=build_option('allow_modules_tool_mismatch'))
         self.set_and_check_version()
 
-        # this can/should be set to True during testing
-        self.testing = False
-
     def buildstats(self):
         """Return tuple with data to be included in buildstats"""
         return (self.__class__.__name__, self.cmd, self.version)
@@ -229,11 +228,20 @@ def check_cmd_avail(self):
 
     def check_module_function(self, allow_mismatch=False, regex=None):
         """Check whether selected module tool matches 'module' function definition."""
-        out, ec = run_cmd("type module", simple=False, log_ok=False, log_all=False)
+        if self.testing:
+            # grab 'module' function definition from environment if it's there; only during testing
+            if 'module' in os.environ:
+                out, ec = os.environ['module'], 0
+            else:
+                out, ec = None, 1
+        else:
+            out, ec = run_cmd("type module", simple=False, log_ok=False, log_all=False)
+
         if regex is None:
             regex = r".*%s" % os.path.basename(self.cmd)
         mod_cmd_re = re.compile(regex, re.M)
         mod_details = "pattern '%s' (%s)" % (mod_cmd_re.pattern, self.__class__.__name__)
+
         if ec == 0:
             if mod_cmd_re.search(out):
                 self.log.debug("Found pattern '%s' in defined 'module' function." % mod_cmd_re.pattern)
diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index ad8c28de27..82e6cf39d4 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -76,7 +76,7 @@ def test_mock(self):
         os.environ['module'] = "() {  eval `/bin/echo $*`\n}"
 
         # ue empty mod_path list, otherwise the install_path is called
-        mmt = MockModulesTool(mod_paths=[])
+        mmt = MockModulesTool(mod_paths=[], testing=True)
 
         # the version of the MMT is the commandline option
         self.assertEqual(mmt.version, StrictVersion(MockModulesTool.VERSION_OPTION))
@@ -91,7 +91,7 @@ def test_environment_command(self):
         os.environ['module'] = "() { %s $*\n}" % BrokenMockModulesTool.COMMAND
 
         try:
-            bmmt = BrokenMockModulesTool(mod_paths=[])
+            bmmt = BrokenMockModulesTool(mod_paths=[], testing=True)
             # should never get here
             self.assertTrue(False, 'BrokenMockModulesTool should fail')
         except EasyBuildError, err:
@@ -100,7 +100,7 @@ def test_environment_command(self):
         os.environ[BrokenMockModulesTool.COMMAND_ENVIRONMENT] = MockModulesTool.COMMAND
         os.environ['module'] = "() { /bin/echo $*\n}"
         BrokenMockModulesTool._instances.pop(BrokenMockModulesTool, None)
-        bmmt = BrokenMockModulesTool(mod_paths=[])
+        bmmt = BrokenMockModulesTool(mod_paths=[], testing=True)
         cmd_abspath = which(MockModulesTool.COMMAND)
 
         self.assertEqual(bmmt.version, StrictVersion(MockModulesTool.VERSION_OPTION))
@@ -112,7 +112,7 @@ def test_environment_command(self):
     def test_module_mismatch(self):
         """Test whether mismatch detection between modules tool and 'module' function works."""
         # redefine 'module' function (deliberate mismatch with used module command in MockModulesTool)
-        os.environ['module'] = "() {  eval `/Users/kehoste/Modules/$MODULE_VERSION/bin/modulecmd bash $*`\n}"
+        os.environ['module'] = "() {  eval `/tmp/Modules/$MODULE_VERSION/bin/modulecmd bash $*`\n}"
         self.assertErrorRegex(EasyBuildError, ".*pattern .* not found in defined 'module' function", MockModulesTool)
 
         # check whether escaping error by allowing mismatch via build options works
@@ -123,7 +123,7 @@ def test_module_mismatch(self):
 
         fancylogger.logToFile(self.logfile)
 
-        mt = MockModulesTool()
+        mt = MockModulesTool(testing=True)
         f = open(self.logfile, 'r')
         logtxt = f.read()
         f.close()
@@ -133,13 +133,13 @@ def test_module_mismatch(self):
         # redefine 'module' function with correct module command
         os.environ['module'] = "() {  eval `/bin/echo $*`\n}"
         MockModulesTool._instances.pop(MockModulesTool)
-        mt = MockModulesTool()
+        mt = MockModulesTool(testing=True)
         self.assertTrue(isinstance(mt.loaded_modules(), list))  # dummy usage
 
         # a warning should be logged if the 'module' function is undefined
         del os.environ['module']
         MockModulesTool._instances.pop(MockModulesTool)
-        mt = MockModulesTool()
+        mt = MockModulesTool(testing=True)
         f = open(self.logfile, 'r')
         logtxt = f.read()
         f.close()
@@ -173,8 +173,7 @@ def test_lmod_specific(self):
 
             # initialize Lmod modules tool, pass full path to 'lmod' via $LMOD_CMD
             os.environ['LMOD_CMD'] = lmod_abspath
-            lmod = Lmod()
-            lmod.testing = True
+            lmod = Lmod(testing=True)
 
             # obtain list of availabe modules, should be non-empty
             self.assertTrue(lmod.available(), "List of available modules obtained using Lmod is non-empty")

From 92e7764c8719bf10cc5450ece75a96e39c11a315 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 13:23:23 +0200
Subject: [PATCH 0201/1356] fix case where testing is not enabled in
 modulestool.py tests

---
 test/framework/modulestool.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index 82e6cf39d4..80c745fb31 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -113,7 +113,7 @@ def test_module_mismatch(self):
         """Test whether mismatch detection between modules tool and 'module' function works."""
         # redefine 'module' function (deliberate mismatch with used module command in MockModulesTool)
         os.environ['module'] = "() {  eval `/tmp/Modules/$MODULE_VERSION/bin/modulecmd bash $*`\n}"
-        self.assertErrorRegex(EasyBuildError, ".*pattern .* not found in defined 'module' function", MockModulesTool)
+        self.assertErrorRegex(EasyBuildError, ".*pattern .* not found in defined 'module' function", MockModulesTool, testing=True)
 
         # check whether escaping error by allowing mismatch via build options works
         build_options = {

From c081f928631354ccf9a436c1bbbeae9dabc980b6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 14:05:09 +0200
Subject: [PATCH 0202/1356] fix long line

---
 test/framework/modulestool.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index 80c745fb31..5b92f8822a 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -113,7 +113,8 @@ def test_module_mismatch(self):
         """Test whether mismatch detection between modules tool and 'module' function works."""
         # redefine 'module' function (deliberate mismatch with used module command in MockModulesTool)
         os.environ['module'] = "() {  eval `/tmp/Modules/$MODULE_VERSION/bin/modulecmd bash $*`\n}"
-        self.assertErrorRegex(EasyBuildError, ".*pattern .* not found in defined 'module' function", MockModulesTool, testing=True)
+        error_regex = ".*pattern .* not found in defined 'module' function"
+        self.assertErrorRegex(EasyBuildError, error_regex, MockModulesTool, testing=True)
 
         # check whether escaping error by allowing mismatch via build options works
         build_options = {

From b0c9a06b98e116108d5f5bd7ecdfedc7f7f47733 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 14:06:01 +0200
Subject: [PATCH 0203/1356] fix broken test that verifies mismatch on 'module'
 function

---
 easybuild/main.py          | 2 +-
 easybuild/tools/modules.py | 4 ++--
 easybuild/tools/testing.py | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index b250876641..a572ac2c05 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -276,7 +276,7 @@ def main(testing_data=(None, None, None)):
     })
 
     # obtain list of loaded modules, build options must be initialized first
-    modlist = session_module_list()
+    modlist = session_module_list(testing=testing)
     init_session_state.update({'module_list': modlist})
     _log.debug("Initial session state: %s" % init_session_state)
 
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index c3c2c2b81a..7111fd872b 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -973,7 +973,7 @@ def avail_modules_tools():
     return class_dict
 
 
-def modules_tool(mod_paths=None):
+def modules_tool(mod_paths=None, testing=False):
     """
     Return interface to modules tool (environment modules (C, Tcl), or Lmod)
     """
@@ -981,7 +981,7 @@ def modules_tool(mod_paths=None):
     modules_tool = get_modules_tool()
     if modules_tool is not None:
         modules_tool_class = avail_modules_tools().get(modules_tool)
-        return modules_tool_class(mod_paths=mod_paths)
+        return modules_tool_class(mod_paths=mod_paths, testing=testing)
     else:
         return None
 
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index b572921f7e..fa579e2107 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -157,9 +157,9 @@ def session_state():
     }
 
 
-def session_module_list():
+def session_module_list(testing=False):
     """Get list of loaded modules ('module list')."""
-    modtool = modules_tool()
+    modtool = modules_tool(testing=testing)
     return modtool.list()
 
 

From ab1b84d735314e59a11e0d6017e85c3292b53a12 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 10:53:15 +0200
Subject: [PATCH 0204/1356] add definition of gimpi toolchain

---
 easybuild/tools/gimpi.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/tools/gimpi.py

diff --git a/easybuild/tools/gimpi.py b/easybuild/tools/gimpi.py
new file mode 100644
index 0000000000..0ac2345266
--- /dev/null
+++ b/easybuild/tools/gimpi.py
@@ -0,0 +1,38 @@
+##
+# Copyright 2012-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for gimpi compiler toolchain (includes GCC and Intel MPI).
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+"""
+
+from easybuild.toolchains.compiler.gcc import Gcc
+from easybuild.toolchains.mpi.intelmpi import IntelMPI
+
+
+class Gimpi(Gcc, IntelMPI):
+    """Compiler toolchain with GCC and Intel MPI."""
+    NAME = 'gimpi'

From 5d213ca479e1b49a643638ed2d50f5e84c1f6395 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 11:06:08 +0200
Subject: [PATCH 0205/1356] move gimpi toolchain definition to correct location

---
 easybuild/{tools => toolchains}/gimpi.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/{tools => toolchains}/gimpi.py (100%)

diff --git a/easybuild/tools/gimpi.py b/easybuild/toolchains/gimpi.py
similarity index 100%
rename from easybuild/tools/gimpi.py
rename to easybuild/toolchains/gimpi.py

From 20423602cd5f08fd70dcbfdd21a95a08ccfbc59b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 14:13:53 +0200
Subject: [PATCH 0206/1356] don't override COMPILER_MODULE_NAME obtained from
 ClangGCC in Clang-based toolchains

---
 easybuild/toolchains/cgmpich.py    | 1 -
 easybuild/toolchains/cgmvapich2.py | 1 -
 easybuild/toolchains/cgompi.py     | 1 -
 3 files changed, 3 deletions(-)

diff --git a/easybuild/toolchains/cgmpich.py b/easybuild/toolchains/cgmpich.py
index a85f500257..af3a4e9dbf 100644
--- a/easybuild/toolchains/cgmpich.py
+++ b/easybuild/toolchains/cgmpich.py
@@ -38,4 +38,3 @@
 class Cgmpich(ClangGcc, Mpich):
     """Compiler toolchain with Clang, GFortran and MPICH."""
     NAME = 'cgmpich'
-    COMPILER_MODULE_NAME = ['ClangGCC']
diff --git a/easybuild/toolchains/cgmvapich2.py b/easybuild/toolchains/cgmvapich2.py
index d3a4b596c2..61a764c40e 100644
--- a/easybuild/toolchains/cgmvapich2.py
+++ b/easybuild/toolchains/cgmvapich2.py
@@ -38,4 +38,3 @@
 class Cgmvapich2(ClangGcc, Mvapich2):
     """Compiler toolchain with Clang, GFortran and MVAPICH2."""
     NAME = 'cgmvapich2'
-    COMPILER_MODULE_NAME = ['ClangGCC']
diff --git a/easybuild/toolchains/cgompi.py b/easybuild/toolchains/cgompi.py
index 9fe8105313..b39c6a0c23 100644
--- a/easybuild/toolchains/cgompi.py
+++ b/easybuild/toolchains/cgompi.py
@@ -38,4 +38,3 @@
 class Cgompi(ClangGcc, OpenMPI):
     """Compiler toolchain with Clang, GFortran and OpenMPI."""
     NAME = 'cgompi'
-    COMPILER_MODULE_NAME = ['ClangGCC']

From fc91b81821fe0d90b7adfa876a2fbaadc5a1832c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 15:49:57 +0200
Subject: [PATCH 0207/1356] fix Clang-based test modules

---
 test/framework/modules/cgompi/1.1.6 | 8 ++++++--
 test/framework/modules/cgoolf/1.1.6 | 8 ++++++--
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/test/framework/modules/cgompi/1.1.6 b/test/framework/modules/cgompi/1.1.6
index 22bd608d51..33367e0a50 100644
--- a/test/framework/modules/cgompi/1.1.6
+++ b/test/framework/modules/cgompi/1.1.6
@@ -13,8 +13,12 @@ set root    /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge
 
 conflict    cgompi
 
-if { ![is-loaded ClangGCC/1.1.2] } {
-    module load ClangGCC/1.1.2
+if { ![is-loaded GCC/4.7.2] } {
+    module load GCC/4.7.2
+}
+
+if { ![is-loaded Clang/3.2-GCC-4.7.2] } {
+    module load Clang/3.2-GCC-4.7.2
 }
 
 if { ![is-loaded OpenMPI/1.6.4-ClangGCC-1.1.2] } {
diff --git a/test/framework/modules/cgoolf/1.1.6 b/test/framework/modules/cgoolf/1.1.6
index 477da80d19..7ce5aa2cc0 100644
--- a/test/framework/modules/cgoolf/1.1.6
+++ b/test/framework/modules/cgoolf/1.1.6
@@ -13,8 +13,12 @@ set root    /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge
 
 conflict    cgoolf
 
-if { ![is-loaded ClangGCC/1.1.2] } {
-    module load ClangGCC/1.1.2
+if { ![is-loaded GCC/4.7.2] } {
+    module load GCC/4.7.2
+}
+
+if { ![is-loaded Clang/3.2-GCC-4.7.2] } {
+    module load Clang/3.2-GCC-4.7.2
 }
 
 if { ![is-loaded OpenMPI/1.6.4-ClangGCC-1.1.2] } {

From 5ceb479a3afacae53999eb718be602d1049cb2c5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 10:53:15 +0200
Subject: [PATCH 0208/1356] add definition of gimpi toolchain

---
 easybuild/tools/gimpi.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/tools/gimpi.py

diff --git a/easybuild/tools/gimpi.py b/easybuild/tools/gimpi.py
new file mode 100644
index 0000000000..0ac2345266
--- /dev/null
+++ b/easybuild/tools/gimpi.py
@@ -0,0 +1,38 @@
+##
+# Copyright 2012-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for gimpi compiler toolchain (includes GCC and Intel MPI).
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+"""
+
+from easybuild.toolchains.compiler.gcc import Gcc
+from easybuild.toolchains.mpi.intelmpi import IntelMPI
+
+
+class Gimpi(Gcc, IntelMPI):
+    """Compiler toolchain with GCC and Intel MPI."""
+    NAME = 'gimpi'

From 7bc6ea3f0a372cd54f1a844c70fbfed682fb57cc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 11:06:08 +0200
Subject: [PATCH 0209/1356] move gimpi toolchain definition to correct location

---
 easybuild/{tools => toolchains}/gimpi.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/{tools => toolchains}/gimpi.py (100%)

diff --git a/easybuild/tools/gimpi.py b/easybuild/toolchains/gimpi.py
similarity index 100%
rename from easybuild/tools/gimpi.py
rename to easybuild/toolchains/gimpi.py

From 0472c7148a0e3560f40485db4ca153578c2f04f6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 17:52:18 +0200
Subject: [PATCH 0210/1356] fix blatently wrong code in
 path_to_top_of_module_tree function

---
 easybuild/tools/modules.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 7111fd872b..30893436b9 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -675,11 +675,11 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
             full_modpath_exts = modpath_exts[dep]
             if path_matches(full_mod_subdir, full_modpath_exts):
                 # full path to module subdir of dependency is simply path to module file without (short) module name
-                full_mod_subdir = self.modulefile_path(dep)[:-len(dep)-1]
-                full_mod_subdirs.append(full_mod_subdir)
+                dep_full_mod_subdir = self.modulefile_path(dep)[:-len(dep)-1]
+                full_mod_subdirs.append(dep_full_mod_subdir)
 
                 mods_to_top.append(dep)
-                tup = (dep, full_mod_subdir, full_modpath_exts)
+                tup = (dep, dep_full_mod_subdir, full_modpath_exts)
                 self.log.debug("Found module to top of module tree: %s (subdir: %s, modpath extensions %s)" % tup)
 
             if full_modpath_exts:

From 192b989b15e590d01e96b1346a084bc1af899541 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 18:20:19 +0200
Subject: [PATCH 0211/1356] enhance unit test to catch missed bug

---
 test/framework/easyblock.py | 32 ++++++++++++++++++++------------
 1 file changed, 20 insertions(+), 12 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index f5c4401fb3..b6281e965e 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -486,24 +486,32 @@ def test_exclude_path_to_top_of_module_tree(self):
         self.setup_hierarchical_modules()
         modtool = modules_tool()
 
-        ec = EasyConfig(os.path.join(test_ecs_path, 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'))
-        eb = EasyBlock(ec)
-
         modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all')
         mkdir(os.path.join(modfile_prefix, 'Compiler', 'GCC', '4.8.3'), parents=True)
         mkdir(os.path.join(modfile_prefix, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049'), parents=True)
-        eb.toolchain.prepare()
-        modpath = eb.make_module_step()
-        modfile_path = os.path.join(modpath, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
-        modtxt = read_file(modfile_path)
 
-        # for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included at all
+        impi_modfile_path = os.path.join('Compiler', 'intel', '2013.5.192', 'impi', '4.1.3.049')
+        imkl_modfile_path = os.path.join('MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
+
+        # example: for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included
         # not for the toolchain or any of the toolchain components,
         # since both icc/ifort and impi form the path to the top of the module tree
-        for imkl_dep in ['icc', 'ifort', 'impi', 'iccifort', 'iimpi']:
-            tup = (imkl_dep, modfile_path, modtxt)
-            failmsg = "No 'module load' statement found for '%s' not found in module %s: %s" % tup
-            self.assertFalse(re.search("module load %s" % imkl_dep, modtxt), failmsg)
+        tests = [
+            ('impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb', impi_modfile_path, ['icc', 'ifort', 'iccifort']),
+            ('imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb', imkl_modfile_path, ['icc', 'ifort', 'impi', 'iccifort', 'iimpi']),
+        ]
+        for ec_file, modfile_path, excluded_deps in tests:
+            ec = EasyConfig(os.path.join(test_ecs_path, ec_file))
+            eb = EasyBlock(ec)
+            eb.toolchain.prepare()
+            modpath = eb.make_module_step()
+            modfile_path = os.path.join(modpath, modfile_path)
+            modtxt = read_file(modfile_path)
+
+            for imkl_dep in excluded_deps:
+                tup = (imkl_dep, modfile_path, modtxt)
+                failmsg = "No 'module load' statement found for '%s' not found in module %s: %s" % tup
+                self.assertFalse(re.search("module load %s" % imkl_dep, modtxt), failmsg)
 
         os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
         init_config(build_options=build_options)

From 629c090fab13959724a2768685b90b556f1dd674 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 17:52:18 +0200
Subject: [PATCH 0212/1356] fix blatently wrong code in
 path_to_top_of_module_tree function

---
 easybuild/tools/modules.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 7111fd872b..30893436b9 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -675,11 +675,11 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
             full_modpath_exts = modpath_exts[dep]
             if path_matches(full_mod_subdir, full_modpath_exts):
                 # full path to module subdir of dependency is simply path to module file without (short) module name
-                full_mod_subdir = self.modulefile_path(dep)[:-len(dep)-1]
-                full_mod_subdirs.append(full_mod_subdir)
+                dep_full_mod_subdir = self.modulefile_path(dep)[:-len(dep)-1]
+                full_mod_subdirs.append(dep_full_mod_subdir)
 
                 mods_to_top.append(dep)
-                tup = (dep, full_mod_subdir, full_modpath_exts)
+                tup = (dep, dep_full_mod_subdir, full_modpath_exts)
                 self.log.debug("Found module to top of module tree: %s (subdir: %s, modpath extensions %s)" % tup)
 
             if full_modpath_exts:

From b1c7a37fcd57ecb3d0e22946d8d5a000110a1faa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 18:20:19 +0200
Subject: [PATCH 0213/1356] enhance unit test to catch missed bug

---
 test/framework/easyblock.py | 32 ++++++++++++++++++++------------
 1 file changed, 20 insertions(+), 12 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index f5c4401fb3..b6281e965e 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -486,24 +486,32 @@ def test_exclude_path_to_top_of_module_tree(self):
         self.setup_hierarchical_modules()
         modtool = modules_tool()
 
-        ec = EasyConfig(os.path.join(test_ecs_path, 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'))
-        eb = EasyBlock(ec)
-
         modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all')
         mkdir(os.path.join(modfile_prefix, 'Compiler', 'GCC', '4.8.3'), parents=True)
         mkdir(os.path.join(modfile_prefix, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049'), parents=True)
-        eb.toolchain.prepare()
-        modpath = eb.make_module_step()
-        modfile_path = os.path.join(modpath, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
-        modtxt = read_file(modfile_path)
 
-        # for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included at all
+        impi_modfile_path = os.path.join('Compiler', 'intel', '2013.5.192', 'impi', '4.1.3.049')
+        imkl_modfile_path = os.path.join('MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
+
+        # example: for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included
         # not for the toolchain or any of the toolchain components,
         # since both icc/ifort and impi form the path to the top of the module tree
-        for imkl_dep in ['icc', 'ifort', 'impi', 'iccifort', 'iimpi']:
-            tup = (imkl_dep, modfile_path, modtxt)
-            failmsg = "No 'module load' statement found for '%s' not found in module %s: %s" % tup
-            self.assertFalse(re.search("module load %s" % imkl_dep, modtxt), failmsg)
+        tests = [
+            ('impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb', impi_modfile_path, ['icc', 'ifort', 'iccifort']),
+            ('imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb', imkl_modfile_path, ['icc', 'ifort', 'impi', 'iccifort', 'iimpi']),
+        ]
+        for ec_file, modfile_path, excluded_deps in tests:
+            ec = EasyConfig(os.path.join(test_ecs_path, ec_file))
+            eb = EasyBlock(ec)
+            eb.toolchain.prepare()
+            modpath = eb.make_module_step()
+            modfile_path = os.path.join(modpath, modfile_path)
+            modtxt = read_file(modfile_path)
+
+            for imkl_dep in excluded_deps:
+                tup = (imkl_dep, modfile_path, modtxt)
+                failmsg = "No 'module load' statement found for '%s' not found in module %s: %s" % tup
+                self.assertFalse(re.search("module load %s" % imkl_dep, modtxt), failmsg)
 
         os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
         init_config(build_options=build_options)

From bf1ba6c649e0d9cadafa7becd59e0b5dec62c3a4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Oct 2014 17:16:04 +0200
Subject: [PATCH 0214/1356] fix $MODULEPATH extensions for Clang/CUDA, include
 versionsuffix in module subdir

---
 .../module_naming_scheme/hierarchical_mns.py  | 36 +++++++++++++++----
 .../easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb      | 29 +++++++++++++++
 test/framework/easyconfigs/GCC-4.8.2.eb       | 28 +++++++++++++++
 .../framework/easyconfigs/ifort-2013.3.163.eb | 17 +++++++++
 test/framework/module_generator.py            |  4 +++
 5 files changed, 107 insertions(+), 7 deletions(-)
 create mode 100644 test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
 create mode 100644 test/framework/easyconfigs/GCC-4.8.2.eb
 create mode 100644 test/framework/easyconfigs/ifort-2013.3.163.eb

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index c415d61d72..27ba3de274 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -30,6 +30,7 @@
 """
 
 import os
+import re
 from vsc.utils import fancylogger
 
 from easybuild.tools.module_naming_scheme import ModuleNamingScheme
@@ -132,17 +133,38 @@ def det_modpath_extensions(self, ec):
         Examples: Compiler/GCC/4.8.3 (for GCC/4.8.3 module), MPI/GCC/4.8.3/OpenMPI/1.6.5 (for OpenMPI/1.6.5 module)
         """
         modclass = ec['moduleclass']
+        tc_comps = det_toolchain_compilers(ec)
+        tc_comp_info = self.det_toolchain_compilers_name_version(tc_comps)
 
         paths = []
-        if modclass == MODULECLASS_COMPILER:
-            if ec['name'] in ['icc', 'ifort']:
-                compdir = 'intel'
+        if modclass == MODULECLASS_COMPILER or ec['name'] in ['CUDA']:
+            # obtain list of compilers based on that extend $MODULEPATH in some way other than <name>/<version>
+            extend_comps = []
+            # exclude GCC for which <name>/<version> is used as $MODULEPATH extension
+            excluded_comps = ['GCC']
+            for comps in COMP_NAME_VERSION_TEMPLATES.keys():
+                extend_comps.extend([comp for comp in comps.split(',') if comp not in excluded_comps])
+
+            comp_name_ver = None
+            if ec['name'] in extend_comps:
+                for key in COMP_NAME_VERSION_TEMPLATES:
+                    if re.search(".*%s.*" % ec['name'], key):
+                        comp_name, comp_ver_tmpl = COMP_NAME_VERSION_TEMPLATES[key]
+                        comp_versions = {ec['name']: ec['version'] + ec['versionsuffix']}
+                        if ec['name'] == 'ifort':
+                            # 'icc' key should be provided since it's the only one used in the template
+                            comp_versions.update({'icc': ec['version'] + ec['versionsuffix']})
+                        if tc_comp_info is not None:
+                            # also provide toolchain version for non-dummy toolchains
+                            comp_versions.update({tc_comp_info[0]: tc_comp_info[1]})
+                        comp_name_ver = [comp_name, comp_ver_tmpl % comp_versions]
+                        break
             else:
-                compdir = ec['name']
-            paths.append(os.path.join(COMPILER, compdir, ec['version']))
+                comp_name_ver = [ec['name'], ec['version'] + ec['versionsuffix']]
+
+            paths.append(os.path.join(COMPILER, *comp_name_ver))
+
         elif modclass == MODULECLASS_MPI:
-            tc_comps = det_toolchain_compilers(ec)
-            tc_comp_info = self.det_toolchain_compilers_name_version(tc_comps)
             if tc_comp_info is None:
                 tup = (ec['toolchain'], ec['name'], ec['version'])
                 error_msg = ("No compiler available in toolchain %s used to install MPI library %s v%s, "
diff --git a/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
new file mode 100644
index 0000000000..a8e69945a9
--- /dev/null
+++ b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
@@ -0,0 +1,29 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University
+# Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis.georgatos@uni.lu>, Kenneth Hoste
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html
+##
+
+name = 'CUDA'
+version = '5.5.22'
+
+homepage = 'https://developer.nvidia.com/cuda-toolkit'
+description = """CUDA (formerly Compute Unified Device Architecture) is a parallel
+ computing platform and programming model created by NVIDIA and implemented by the
+ graphics processing units (GPUs) that they produce. CUDA gives developers access
+ to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs."""
+
+toolchain = {'name': 'GCC', 'version': '4.8.2'}
+
+# eg. http://developer.download.nvidia.com/compute/cuda/5_5/rel/installers/cuda_5.5.22_linux_64.run
+source_urls = ['http://developer.download.nvidia.com/compute/cuda/5_5/rel/installers/']
+
+sources = ['%(namelower)s_%(version)s_linux_64.run']
+
+moduleclass = 'system'
diff --git a/test/framework/easyconfigs/GCC-4.8.2.eb b/test/framework/easyconfigs/GCC-4.8.2.eb
new file mode 100644
index 0000000000..cef0802601
--- /dev/null
+++ b/test/framework/easyconfigs/GCC-4.8.2.eb
@@ -0,0 +1,28 @@
+name = "GCC"
+version = '4.8.2'
+
+homepage = 'http://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = [
+    'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s',  # GCC auto-resolving HTTP mirror
+    'http://ftpmirror.gnu.org/gmp',  # idem for GMP
+    'http://ftpmirror.gnu.org/mpfr',  # idem for MPFR
+    'http://www.multiprecision.org/mpc/download',  # MPC official
+]
+sources = [
+    SOURCELOWER_TAR_GZ,
+    'gmp-5.1.3.tar.bz2',
+    'mpfr-3.1.2.tar.gz',
+    'mpc-1.0.1.tar.gz',
+]
+
+languages = ['c', 'c++', 'fortran', 'lto']
+
+# building GCC sometimes fails if make parallelism is too high, so let's limit it
+maxparallel = 4
+
+moduleclass = 'compiler'
diff --git a/test/framework/easyconfigs/ifort-2013.3.163.eb b/test/framework/easyconfigs/ifort-2013.3.163.eb
new file mode 100644
index 0000000000..4efd890d23
--- /dev/null
+++ b/test/framework/easyconfigs/ifort-2013.3.163.eb
@@ -0,0 +1,17 @@
+name = 'ifort'
+version = '2013.3.163'
+
+homepage = 'http://software.intel.com/en-us/intel-compilers/'
+description = "Fortran compiler from Intel"
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['l_fcompxe_%s.tgz' % version]
+
+dontcreateinstalldir = 'True'
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
+
+moduleclass = 'compiler'
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 9d0c46188b..cd8cddb439 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -393,11 +393,15 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
         init_config(build_options=build_options)
 
         # format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions)
+        iccver = '2013.5.192-GCC-4.8.3'
         test_ecs = {
             'GCC-4.7.2.eb': ('GCC/4.7.2', 'Core', ['Compiler/GCC/4.7.2'], ['Core']),
             'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2', ['MPI/GCC/4.7.2/OpenMPI/1.6.4'], ['Core']),
             'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5', 'MPI/GCC/4.7.2/OpenMPI/1.6.4', [], ['Core']),
             'goolf-1.4.10.eb': ('goolf/1.4.10', 'Core', [], ['Core']),
+            'icc-2013.5.192-GCC-4.8.3.eb': ('icc/%s' % iccver, 'Core', ['Compiler/intel/%s' % iccver], ['Core']),
+            'ifort-2013.3.163.eb': ('ifort/2013.3.163', 'Core', ['Compiler/intel/2013.3.163'], ['Core']),
+            'CUDA-5.5.22-GCC-4.8.2.eb': ('CUDA/5.5.22', 'Compiler/GCC/4.8.2', ['Compiler/GCC-CUDA/4.8.2-5.5.22'], ['Core']),
         }
         for ecfile, mns_vals in test_ecs.items():
             test_ec(ecfile, *mns_vals)

From cab3ccd7d2c44be64c1d82b66150c2b188ab7f16 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 12:17:04 +0200
Subject: [PATCH 0215/1356] fix tiny remark

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 27ba3de274..184c596c43 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -157,6 +157,7 @@ def det_modpath_extensions(self, ec):
                         if tc_comp_info is not None:
                             # also provide toolchain version for non-dummy toolchains
                             comp_versions.update({tc_comp_info[0]: tc_comp_info[1]})
+
                         comp_name_ver = [comp_name, comp_ver_tmpl % comp_versions]
                         break
             else:

From 671108be46c99096846aa5552d56217a88029822 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 12:20:57 +0200
Subject: [PATCH 0216/1356] fix broken test

---
 test/framework/scripts.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 9712938abf..1776f8cdc1 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -65,9 +65,10 @@ def test_generate_software_list(self):
         out, ec = run_cmd(cmd, simple=False)
 
         # make sure output is kind of what we expect it to be
-        regex = r"Supported Packages \(17 "
+        regex = r"Supported Packages \(18 "
         self.assertTrue(re.search(regex, out), "Pattern '%s' found in output: %s" % (regex, out))
         per_letter = {
+            'C': '1',  # CUDA
             'F': '1',  # FFTW
             'G': '4',  # GCC, gompi, goolf, gzip
             'H': '1',  # hwloc

From bd0a01604d0401ae5540a89a9485fbd7b168b771 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Oct 2014 14:08:09 +0200
Subject: [PATCH 0217/1356] fix remark

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 184c596c43..9eee1439cc 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -148,7 +148,7 @@ def det_modpath_extensions(self, ec):
             comp_name_ver = None
             if ec['name'] in extend_comps:
                 for key in COMP_NAME_VERSION_TEMPLATES:
-                    if re.search(".*%s.*" % ec['name'], key):
+                    if ec['name'] in key.split(','):
                         comp_name, comp_ver_tmpl = COMP_NAME_VERSION_TEMPLATES[key]
                         comp_versions = {ec['name']: ec['version'] + ec['versionsuffix']}
                         if ec['name'] == 'ifort':

From 6fd20c792cc1b75f84ca5bbfea5c62cb71bf35b5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 14:13:53 +0200
Subject: [PATCH 0218/1356] don't override COMPILER_MODULE_NAME obtained from
 ClangGCC in Clang-based toolchains

---
 easybuild/toolchains/cgmpich.py    | 1 -
 easybuild/toolchains/cgmvapich2.py | 1 -
 easybuild/toolchains/cgompi.py     | 1 -
 3 files changed, 3 deletions(-)

diff --git a/easybuild/toolchains/cgmpich.py b/easybuild/toolchains/cgmpich.py
index a85f500257..af3a4e9dbf 100644
--- a/easybuild/toolchains/cgmpich.py
+++ b/easybuild/toolchains/cgmpich.py
@@ -38,4 +38,3 @@
 class Cgmpich(ClangGcc, Mpich):
     """Compiler toolchain with Clang, GFortran and MPICH."""
     NAME = 'cgmpich'
-    COMPILER_MODULE_NAME = ['ClangGCC']
diff --git a/easybuild/toolchains/cgmvapich2.py b/easybuild/toolchains/cgmvapich2.py
index d3a4b596c2..61a764c40e 100644
--- a/easybuild/toolchains/cgmvapich2.py
+++ b/easybuild/toolchains/cgmvapich2.py
@@ -38,4 +38,3 @@
 class Cgmvapich2(ClangGcc, Mvapich2):
     """Compiler toolchain with Clang, GFortran and MVAPICH2."""
     NAME = 'cgmvapich2'
-    COMPILER_MODULE_NAME = ['ClangGCC']
diff --git a/easybuild/toolchains/cgompi.py b/easybuild/toolchains/cgompi.py
index 9fe8105313..b39c6a0c23 100644
--- a/easybuild/toolchains/cgompi.py
+++ b/easybuild/toolchains/cgompi.py
@@ -38,4 +38,3 @@
 class Cgompi(ClangGcc, OpenMPI):
     """Compiler toolchain with Clang, GFortran and OpenMPI."""
     NAME = 'cgompi'
-    COMPILER_MODULE_NAME = ['ClangGCC']

From 8899c3c7af6e20637fdc191833291d1820db9075 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Oct 2014 15:49:57 +0200
Subject: [PATCH 0219/1356] fix Clang-based test modules

---
 test/framework/modules/cgompi/1.1.6 | 8 ++++++--
 test/framework/modules/cgoolf/1.1.6 | 8 ++++++--
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/test/framework/modules/cgompi/1.1.6 b/test/framework/modules/cgompi/1.1.6
index 22bd608d51..33367e0a50 100644
--- a/test/framework/modules/cgompi/1.1.6
+++ b/test/framework/modules/cgompi/1.1.6
@@ -13,8 +13,12 @@ set root    /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge
 
 conflict    cgompi
 
-if { ![is-loaded ClangGCC/1.1.2] } {
-    module load ClangGCC/1.1.2
+if { ![is-loaded GCC/4.7.2] } {
+    module load GCC/4.7.2
+}
+
+if { ![is-loaded Clang/3.2-GCC-4.7.2] } {
+    module load Clang/3.2-GCC-4.7.2
 }
 
 if { ![is-loaded OpenMPI/1.6.4-ClangGCC-1.1.2] } {
diff --git a/test/framework/modules/cgoolf/1.1.6 b/test/framework/modules/cgoolf/1.1.6
index 477da80d19..7ce5aa2cc0 100644
--- a/test/framework/modules/cgoolf/1.1.6
+++ b/test/framework/modules/cgoolf/1.1.6
@@ -13,8 +13,12 @@ set root    /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/SL6/sandybridge
 
 conflict    cgoolf
 
-if { ![is-loaded ClangGCC/1.1.2] } {
-    module load ClangGCC/1.1.2
+if { ![is-loaded GCC/4.7.2] } {
+    module load GCC/4.7.2
+}
+
+if { ![is-loaded Clang/3.2-GCC-4.7.2] } {
+    module load Clang/3.2-GCC-4.7.2
 }
 
 if { ![is-loaded OpenMPI/1.6.4-ClangGCC-1.1.2] } {

From fc5f7758d522f04978dae872fcdc0d8afc39446f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 6 Oct 2014 11:57:32 +0200
Subject: [PATCH 0220/1356] bump version to v1.15.2dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index dcdeea01fd..e2b1ab5964 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.15.1")
+VERSION = LooseVersion("1.15.2dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 6d9a6ef628dda83e38fdf1758183c4fe65e7692d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 6 Oct 2014 17:32:52 +0200
Subject: [PATCH 0221/1356] also take verionsuffix into account when
 determining toolchain info

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 9eee1439cc..666dfa1ad0 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -88,7 +88,7 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         elif len(tc_comps) == 1:
             res = (tc_comps[0]['name'], tc_comps[0]['version'])
         else:
-            comp_versions = dict([(comp['name'], comp['version']) for comp in tc_comps])
+            comp_versions = dict([(comp['name'], comp['version'] + comp['versionsuffix']) for comp in tc_comps])
             comp_names = comp_versions.keys()
             key = ','.join(sorted(comp_names))
             if key in COMP_NAME_VERSION_TEMPLATES:

From 97bf3f7712451df01eaaa51a23423df79dfdcffe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 6 Oct 2014 17:45:34 +0200
Subject: [PATCH 0222/1356] enhance unit tests to check on use of versionsuffix
 in module subdirs

---
 test/framework/module_generator.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index cd8cddb439..c67b629db2 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -394,6 +394,8 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
 
         # format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions)
         iccver = '2013.5.192-GCC-4.8.3'
+        impi_ec = 'impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb'
+        imkl_ec = 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'
         test_ecs = {
             'GCC-4.7.2.eb': ('GCC/4.7.2', 'Core', ['Compiler/GCC/4.7.2'], ['Core']),
             'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2', ['MPI/GCC/4.7.2/OpenMPI/1.6.4'], ['Core']),
@@ -402,6 +404,8 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
             'icc-2013.5.192-GCC-4.8.3.eb': ('icc/%s' % iccver, 'Core', ['Compiler/intel/%s' % iccver], ['Core']),
             'ifort-2013.3.163.eb': ('ifort/2013.3.163', 'Core', ['Compiler/intel/2013.3.163'], ['Core']),
             'CUDA-5.5.22-GCC-4.8.2.eb': ('CUDA/5.5.22', 'Compiler/GCC/4.8.2', ['Compiler/GCC-CUDA/4.8.2-5.5.22'], ['Core']),
+            impi_ec: ('impi/4.1.3.049', 'Compiler/intel/%s' % iccver, ['MPI/intel/%s/impi/4.1.3.049' % iccver], ['Core']),
+            imkl_ec: ('imkl/11.1.2.144', 'MPI/intel/%s/impi/4.1.3.049' % iccver, [], ['Core']),
         }
         for ecfile, mns_vals in test_ecs.items():
             test_ec(ecfile, *mns_vals)

From 79a25323ad9c34e3cd4f6f24d1445fd4bbc5ade1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 6 Oct 2014 17:32:52 +0200
Subject: [PATCH 0223/1356] also take verionsuffix into account when
 determining toolchain info

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 9eee1439cc..666dfa1ad0 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -88,7 +88,7 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         elif len(tc_comps) == 1:
             res = (tc_comps[0]['name'], tc_comps[0]['version'])
         else:
-            comp_versions = dict([(comp['name'], comp['version']) for comp in tc_comps])
+            comp_versions = dict([(comp['name'], comp['version'] + comp['versionsuffix']) for comp in tc_comps])
             comp_names = comp_versions.keys()
             key = ','.join(sorted(comp_names))
             if key in COMP_NAME_VERSION_TEMPLATES:

From 4db3050e2732fed13f750f2d8632a37844a13de2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 6 Oct 2014 17:45:34 +0200
Subject: [PATCH 0224/1356] enhance unit tests to check on use of versionsuffix
 in module subdirs

---
 test/framework/module_generator.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index cd8cddb439..c67b629db2 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -394,6 +394,8 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
 
         # format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions)
         iccver = '2013.5.192-GCC-4.8.3'
+        impi_ec = 'impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb'
+        imkl_ec = 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'
         test_ecs = {
             'GCC-4.7.2.eb': ('GCC/4.7.2', 'Core', ['Compiler/GCC/4.7.2'], ['Core']),
             'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2', ['MPI/GCC/4.7.2/OpenMPI/1.6.4'], ['Core']),
@@ -402,6 +404,8 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
             'icc-2013.5.192-GCC-4.8.3.eb': ('icc/%s' % iccver, 'Core', ['Compiler/intel/%s' % iccver], ['Core']),
             'ifort-2013.3.163.eb': ('ifort/2013.3.163', 'Core', ['Compiler/intel/2013.3.163'], ['Core']),
             'CUDA-5.5.22-GCC-4.8.2.eb': ('CUDA/5.5.22', 'Compiler/GCC/4.8.2', ['Compiler/GCC-CUDA/4.8.2-5.5.22'], ['Core']),
+            impi_ec: ('impi/4.1.3.049', 'Compiler/intel/%s' % iccver, ['MPI/intel/%s/impi/4.1.3.049' % iccver], ['Core']),
+            imkl_ec: ('imkl/11.1.2.144', 'MPI/intel/%s/impi/4.1.3.049' % iccver, [], ['Core']),
         }
         for ecfile, mns_vals in test_ecs.items():
             test_ec(ecfile, *mns_vals)

From 94c0fbeb1709485f1df85e324991089eda64509d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 6 Oct 2014 18:40:22 +0200
Subject: [PATCH 0225/1356] correct other tests w.r.t. including versionsuffix
 in module subdir

---
 test/framework/easyblock.py                                 | 6 +++---
 .../{2013.5.192 => 2013.5.192-GCC-4.8.3}/impi/4.1.3.049     | 0
 test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3        | 2 +-
 test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3      | 2 +-
 test/framework/utilities.py                                 | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)
 rename test/framework/modules/Compiler/intel/{2013.5.192 => 2013.5.192-GCC-4.8.3}/impi/4.1.3.049 (100%)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index b6281e965e..ee959f59b6 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -488,10 +488,10 @@ def test_exclude_path_to_top_of_module_tree(self):
 
         modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all')
         mkdir(os.path.join(modfile_prefix, 'Compiler', 'GCC', '4.8.3'), parents=True)
-        mkdir(os.path.join(modfile_prefix, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049'), parents=True)
+        mkdir(os.path.join(modfile_prefix, 'MPI', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049'), parents=True)
 
-        impi_modfile_path = os.path.join('Compiler', 'intel', '2013.5.192', 'impi', '4.1.3.049')
-        imkl_modfile_path = os.path.join('MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
+        impi_modfile_path = os.path.join('Compiler', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049')
+        imkl_modfile_path = os.path.join('MPI', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
 
         # example: for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included
         # not for the toolchain or any of the toolchain components,
diff --git a/test/framework/modules/Compiler/intel/2013.5.192/impi/4.1.3.049 b/test/framework/modules/Compiler/intel/2013.5.192-GCC-4.8.3/impi/4.1.3.049
similarity index 100%
rename from test/framework/modules/Compiler/intel/2013.5.192/impi/4.1.3.049
rename to test/framework/modules/Compiler/intel/2013.5.192-GCC-4.8.3/impi/4.1.3.049
diff --git a/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
index d01107fd85..4428aa9709 100644
--- a/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
+++ b/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
@@ -10,7 +10,7 @@ module-whatis {Description: C and C++ compiler from Intel - Homepage: http://sof
 set root    /tmp/software/Core/icc/2013.5.192-GCC-4.8.3
 
 conflict icc
-module use /tmp/modules/all/Compiler/intel/2013.5.192
+module use /tmp/modules/all/Compiler/intel/2013.5.192-GCC-4.8.3
 
 if { ![is-loaded GCC/4.8.3] } {
     module load GCC/4.8.3
diff --git a/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
index 02c64f8bf8..750f0a4df9 100644
--- a/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
+++ b/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
@@ -10,7 +10,7 @@ module-whatis {Description: Fortran compiler from Intel - Homepage: http://softw
 set root    /tmp/software/Core/ifort/2013.5.192-GCC-4.8.3
 
 conflict ifort
-module use /tmp/modules/all/Compiler/intel/2013.5.192
+module use /tmp/modules/all/Compiler/intel/2013.5.192-GCC-4.8.3
 
 if { ![is-loaded GCC/4.8.3] } {
     module load GCC/4.8.3
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index e4237bc05c..83621c75ea 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -212,7 +212,7 @@ def setup_hierarchical_modules(self):
             os.path.join(mod_prefix, 'Core', 'icc', '2013.5.192-GCC-4.8.3'),
             os.path.join(mod_prefix, 'Core', 'ifort', '2013.5.192-GCC-4.8.3'),
             os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'),
-            os.path.join(mod_prefix, 'Compiler', 'intel', '2013.5.192', 'impi', '4.1.3.049'),
+            os.path.join(mod_prefix, 'Compiler', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049'),
             os.path.join(mpi_pref, 'FFTW', '3.3.3'),
             os.path.join(mpi_pref, 'OpenBLAS', '0.2.6-LAPACK-3.4.2'),
             os.path.join(mpi_pref, 'ScaLAPACK', '2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2'),

From 19057ef1a151bbc9b11cdc4eb93783afe27cca35 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 6 Oct 2014 18:40:22 +0200
Subject: [PATCH 0226/1356] correct other tests w.r.t. including versionsuffix
 in module subdir

---
 test/framework/easyblock.py                                 | 6 +++---
 .../{2013.5.192 => 2013.5.192-GCC-4.8.3}/impi/4.1.3.049     | 0
 test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3        | 2 +-
 test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3      | 2 +-
 test/framework/utilities.py                                 | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)
 rename test/framework/modules/Compiler/intel/{2013.5.192 => 2013.5.192-GCC-4.8.3}/impi/4.1.3.049 (100%)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index b6281e965e..ee959f59b6 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -488,10 +488,10 @@ def test_exclude_path_to_top_of_module_tree(self):
 
         modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all')
         mkdir(os.path.join(modfile_prefix, 'Compiler', 'GCC', '4.8.3'), parents=True)
-        mkdir(os.path.join(modfile_prefix, 'MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049'), parents=True)
+        mkdir(os.path.join(modfile_prefix, 'MPI', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049'), parents=True)
 
-        impi_modfile_path = os.path.join('Compiler', 'intel', '2013.5.192', 'impi', '4.1.3.049')
-        imkl_modfile_path = os.path.join('MPI', 'intel', '2013.5.192', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
+        impi_modfile_path = os.path.join('Compiler', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049')
+        imkl_modfile_path = os.path.join('MPI', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
 
         # example: for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included
         # not for the toolchain or any of the toolchain components,
diff --git a/test/framework/modules/Compiler/intel/2013.5.192/impi/4.1.3.049 b/test/framework/modules/Compiler/intel/2013.5.192-GCC-4.8.3/impi/4.1.3.049
similarity index 100%
rename from test/framework/modules/Compiler/intel/2013.5.192/impi/4.1.3.049
rename to test/framework/modules/Compiler/intel/2013.5.192-GCC-4.8.3/impi/4.1.3.049
diff --git a/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
index d01107fd85..4428aa9709 100644
--- a/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
+++ b/test/framework/modules/Core/icc/2013.5.192-GCC-4.8.3
@@ -10,7 +10,7 @@ module-whatis {Description: C and C++ compiler from Intel - Homepage: http://sof
 set root    /tmp/software/Core/icc/2013.5.192-GCC-4.8.3
 
 conflict icc
-module use /tmp/modules/all/Compiler/intel/2013.5.192
+module use /tmp/modules/all/Compiler/intel/2013.5.192-GCC-4.8.3
 
 if { ![is-loaded GCC/4.8.3] } {
     module load GCC/4.8.3
diff --git a/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3 b/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
index 02c64f8bf8..750f0a4df9 100644
--- a/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
+++ b/test/framework/modules/Core/ifort/2013.5.192-GCC-4.8.3
@@ -10,7 +10,7 @@ module-whatis {Description: Fortran compiler from Intel - Homepage: http://softw
 set root    /tmp/software/Core/ifort/2013.5.192-GCC-4.8.3
 
 conflict ifort
-module use /tmp/modules/all/Compiler/intel/2013.5.192
+module use /tmp/modules/all/Compiler/intel/2013.5.192-GCC-4.8.3
 
 if { ![is-loaded GCC/4.8.3] } {
     module load GCC/4.8.3
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index e4237bc05c..83621c75ea 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -212,7 +212,7 @@ def setup_hierarchical_modules(self):
             os.path.join(mod_prefix, 'Core', 'icc', '2013.5.192-GCC-4.8.3'),
             os.path.join(mod_prefix, 'Core', 'ifort', '2013.5.192-GCC-4.8.3'),
             os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'),
-            os.path.join(mod_prefix, 'Compiler', 'intel', '2013.5.192', 'impi', '4.1.3.049'),
+            os.path.join(mod_prefix, 'Compiler', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049'),
             os.path.join(mpi_pref, 'FFTW', '3.3.3'),
             os.path.join(mpi_pref, 'OpenBLAS', '0.2.6-LAPACK-3.4.2'),
             os.path.join(mpi_pref, 'ScaLAPACK', '2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2'),

From e999c837eb493f178c148a2803deab1764f86041 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Oct 2014 10:30:21 +0200
Subject: [PATCH 0227/1356] bump version to v1.15.2, update release notes

---
 RELEASE_NOTES              | 12 ++++++++++++
 easybuild/tools/version.py |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 7c587db954..fe1835fc19 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -1,6 +1,18 @@
 This file contains a description of the major changes to the easybuild-framework EasyBuild package.
 For more detailed information, please see the git log.
 
+v1.15.2 (October 7th 2014)
+--------------------------
+
+bugfix release
+- fix $MODULEPATH extensions for Clang/CUDA, to make goolfc/cgoolf compatible with HierarchicalMNS (#1050)
+- include versionsuffix in module subdirectory with HierarchicalMNS (#1050, #1055)
+- fix unit tests which were broken with bash patched for ShellShock bug (#1051)
+- add definition of gimpi toolchain, required to make gimkl toolchain compatible with HierarchicalMNS (#1052)
+- don't override COMPILER_MODULE_NAME obtained from ClangGCC in Clang-based toolchains (#1053)
+- fix wrong code in path_to_top_of_module_tree function (#1054)
+    - because of this, load statements for compilers were potentially included in higher-level modules under HierarchicalMNS
+
 v1.15.1 (September 23rd 2014)
 -----------------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index e2b1ab5964..07bd0969ce 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.15.2dev")
+VERSION = LooseVersion("1.15.2")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From cfd4830433a0b657334985eab7380a8e1e9b74a1 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 10 Oct 2014 14:06:09 +0200
Subject: [PATCH 0228/1356] Added support for versionprefix to HMNS

Hopefully, this should cover the support of versionprefix in HMNS
---
 .../module_naming_scheme/hierarchical_mns.py     | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 666dfa1ad0..7c7167ecfc 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -55,7 +55,7 @@
 class HierarchicalMNS(ModuleNamingScheme):
     """Class implementing an example hierarchical module naming scheme."""
 
-    REQUIRED_KEYS = ['name', 'version', 'versionsuffix', 'toolchain', 'moduleclass']
+    REQUIRED_KEYS = ['name', 'versionprefix', 'version', 'versionsuffix', 'toolchain', 'moduleclass']
 
     def requires_toolchain_details(self):
         """
@@ -76,7 +76,7 @@ def det_short_module_name(self, ec):
         Determine short module name, i.e. the name under which modules will be exposed to users.
         Examples: GCC/4.8.3, OpenMPI/1.6.5, OpenBLAS/0.2.9, HPL/2.1, Python/2.7.5
         """
-        return os.path.join(ec['name'], ec['version'] + ec['versionsuffix'])
+        return os.path.join(ec['name'], ec['versionprefix'] + ec['version'] + ec['versionsuffix'])
 
     def det_toolchain_compilers_name_version(self, tc_comps):
         """
@@ -88,7 +88,7 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         elif len(tc_comps) == 1:
             res = (tc_comps[0]['name'], tc_comps[0]['version'])
         else:
-            comp_versions = dict([(comp['name'], comp['version'] + comp['versionsuffix']) for comp in tc_comps])
+            comp_versions = dict([(comp['name'], comp['versionsuffix'] + comp['version'] + comp['versionsuffix']) for comp in tc_comps])
             comp_names = comp_versions.keys()
             key = ','.join(sorted(comp_names))
             if key in COMP_NAME_VERSION_TEMPLATES:
@@ -122,7 +122,7 @@ def det_module_subdir(self, ec):
                 subdir = os.path.join(COMPILER, tc_comp_name, tc_comp_ver)
             else:
                 # compiler-MPI toolchain => MPI/<comp_name>/<comp_version>/<MPI_name>/<MPI_version> namespace
-                tc_mpi_fullver = tc_mpi['version'] + tc_mpi['versionsuffix']
+                tc_mpi_fullver = tc_mpi['versionprefix'] + tc_mpi['version'] + tc_mpi['versionsuffix']
                 subdir = os.path.join(MPI, tc_comp_name, tc_comp_ver, tc_mpi['name'], tc_mpi_fullver)
 
         return subdir
@@ -150,10 +150,10 @@ def det_modpath_extensions(self, ec):
                 for key in COMP_NAME_VERSION_TEMPLATES:
                     if ec['name'] in key.split(','):
                         comp_name, comp_ver_tmpl = COMP_NAME_VERSION_TEMPLATES[key]
-                        comp_versions = {ec['name']: ec['version'] + ec['versionsuffix']}
+                        comp_versions = {ec['name']: ec['versionprefix'] + ec['version'] + ec['versionsuffix']}
                         if ec['name'] == 'ifort':
                             # 'icc' key should be provided since it's the only one used in the template
-                            comp_versions.update({'icc': ec['version'] + ec['versionsuffix']})
+                            comp_versions.update({'icc': ec['versionprefix'] + ec['version'] + ec['versionsuffix']})
                         if tc_comp_info is not None:
                             # also provide toolchain version for non-dummy toolchains
                             comp_versions.update({tc_comp_info[0]: tc_comp_info[1]})
@@ -161,7 +161,7 @@ def det_modpath_extensions(self, ec):
                         comp_name_ver = [comp_name, comp_ver_tmpl % comp_versions]
                         break
             else:
-                comp_name_ver = [ec['name'], ec['version'] + ec['versionsuffix']]
+                comp_name_ver = [ec['name'], ec['versionprefix'] + ec['version'] + ec['versionsuffix']]
 
             paths.append(os.path.join(COMPILER, *comp_name_ver))
 
@@ -173,7 +173,7 @@ def det_modpath_extensions(self, ec):
                 self.log.error(error_msg)
             else:
                 tc_comp_name, tc_comp_ver = tc_comp_info
-                fullver = ec['version'] + ec['versionsuffix']
+                fullver = ec['versionprefix'] + ec['version'] + ec['versionsuffix']
                 paths.append(os.path.join(MPI, tc_comp_name, tc_comp_ver, ec['name'], fullver))
 
         return paths

From a2efe67a156cf69490640b977ef9bf182e9df8ec Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 10 Oct 2014 14:12:43 +0200
Subject: [PATCH 0229/1356] Typo when pasting

suffix should have been prefix
---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 7c7167ecfc..cae623137d 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -88,7 +88,7 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         elif len(tc_comps) == 1:
             res = (tc_comps[0]['name'], tc_comps[0]['version'])
         else:
-            comp_versions = dict([(comp['name'], comp['versionsuffix'] + comp['version'] + comp['versionsuffix']) for comp in tc_comps])
+            comp_versions = dict([(comp['name'], comp['versionprefix'] + comp['version'] + comp['versionsuffix']) for comp in tc_comps])
             comp_names = comp_versions.keys()
             key = ','.join(sorted(comp_names))
             if key in COMP_NAME_VERSION_TEMPLATES:

From 490e8096e3fe38819ddc8438a56fff898c5edad4 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 10 Oct 2014 14:32:50 +0200
Subject: [PATCH 0230/1356] Added utility to determine full version name

Stitch together the version name in utility and replace occurences
---
 .../module_naming_scheme/hierarchical_mns.py  | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index cae623137d..fccf652f1e 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -64,7 +64,10 @@ def requires_toolchain_details(self):
         """
         return True
 
-    def det_full_module_name(self, ec):
+    def det_full_version(self, ec):
+        """Determine full version, taking into account version prefix/suffix."""
+        return ec['versionprefix'] + ec['version'] + ec['versionsuffix']
+        def det_full_module_name(self, ec):
         """
         Determine full module name, relative to the top of the module path.
         Examples: Core/GCC/4.8.3, Compiler/GCC/4.8.3/OpenMPI/1.6.5, MPI/GCC/4.8.3/OpenMPI/1.6.5/HPL/2.1
@@ -76,7 +79,7 @@ def det_short_module_name(self, ec):
         Determine short module name, i.e. the name under which modules will be exposed to users.
         Examples: GCC/4.8.3, OpenMPI/1.6.5, OpenBLAS/0.2.9, HPL/2.1, Python/2.7.5
         """
-        return os.path.join(ec['name'], ec['versionprefix'] + ec['version'] + ec['versionsuffix'])
+        return os.path.join(ec['name'], self.det_full_version(ec))
 
     def det_toolchain_compilers_name_version(self, tc_comps):
         """
@@ -88,7 +91,7 @@ def det_toolchain_compilers_name_version(self, tc_comps):
         elif len(tc_comps) == 1:
             res = (tc_comps[0]['name'], tc_comps[0]['version'])
         else:
-            comp_versions = dict([(comp['name'], comp['versionprefix'] + comp['version'] + comp['versionsuffix']) for comp in tc_comps])
+            comp_versions = dict([(comp['name'], self.det_full_version(comp)) for comp in tc_comps])
             comp_names = comp_versions.keys()
             key = ','.join(sorted(comp_names))
             if key in COMP_NAME_VERSION_TEMPLATES:
@@ -122,7 +125,7 @@ def det_module_subdir(self, ec):
                 subdir = os.path.join(COMPILER, tc_comp_name, tc_comp_ver)
             else:
                 # compiler-MPI toolchain => MPI/<comp_name>/<comp_version>/<MPI_name>/<MPI_version> namespace
-                tc_mpi_fullver = tc_mpi['versionprefix'] + tc_mpi['version'] + tc_mpi['versionsuffix']
+                tc_mpi_fullver = self.det_full_version(tc_mpi)
                 subdir = os.path.join(MPI, tc_comp_name, tc_comp_ver, tc_mpi['name'], tc_mpi_fullver)
 
         return subdir
@@ -150,10 +153,10 @@ def det_modpath_extensions(self, ec):
                 for key in COMP_NAME_VERSION_TEMPLATES:
                     if ec['name'] in key.split(','):
                         comp_name, comp_ver_tmpl = COMP_NAME_VERSION_TEMPLATES[key]
-                        comp_versions = {ec['name']: ec['versionprefix'] + ec['version'] + ec['versionsuffix']}
+                        comp_versions = {ec['name']: self.det_full_version(ec)}
                         if ec['name'] == 'ifort':
                             # 'icc' key should be provided since it's the only one used in the template
-                            comp_versions.update({'icc': ec['versionprefix'] + ec['version'] + ec['versionsuffix']})
+                            comp_versions.update({'icc': self.det_full_version(ec)})
                         if tc_comp_info is not None:
                             # also provide toolchain version for non-dummy toolchains
                             comp_versions.update({tc_comp_info[0]: tc_comp_info[1]})
@@ -161,7 +164,7 @@ def det_modpath_extensions(self, ec):
                         comp_name_ver = [comp_name, comp_ver_tmpl % comp_versions]
                         break
             else:
-                comp_name_ver = [ec['name'], ec['versionprefix'] + ec['version'] + ec['versionsuffix']]
+                comp_name_ver = [ec['name'], self.det_full_version(ec)]
 
             paths.append(os.path.join(COMPILER, *comp_name_ver))
 
@@ -173,7 +176,7 @@ def det_modpath_extensions(self, ec):
                 self.log.error(error_msg)
             else:
                 tc_comp_name, tc_comp_ver = tc_comp_info
-                fullver = ec['versionprefix'] + ec['version'] + ec['versionsuffix']
+                fullver = self.det_full_version(ec)
                 paths.append(os.path.join(MPI, tc_comp_name, tc_comp_ver, ec['name'], fullver))
 
         return paths

From 83c98865b61bcb9ffa20bbd249cc79b54dfe8807 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 10 Oct 2014 14:36:46 +0200
Subject: [PATCH 0231/1356] Typo

---
 .../tools/module_naming_scheme/hierarchical_mns.py    | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index fccf652f1e..d3fd0a490b 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -64,10 +64,7 @@ def requires_toolchain_details(self):
         """
         return True
 
-    def det_full_version(self, ec):
-        """Determine full version, taking into account version prefix/suffix."""
-        return ec['versionprefix'] + ec['version'] + ec['versionsuffix']
-        def det_full_module_name(self, ec):
+    def det_full_module_name(self, ec):
         """
         Determine full module name, relative to the top of the module path.
         Examples: Core/GCC/4.8.3, Compiler/GCC/4.8.3/OpenMPI/1.6.5, MPI/GCC/4.8.3/OpenMPI/1.6.5/HPL/2.1
@@ -81,6 +78,12 @@ def det_short_module_name(self, ec):
         """
         return os.path.join(ec['name'], self.det_full_version(ec))
 
+    def det_full_version(self, ec):
+        """Determine full version, taking into account version prefix/suffix."""
+        
+        return ec['versionprefix'] + ec['version'] + ec['versionsuffix']
+ 
+
     def det_toolchain_compilers_name_version(self, tc_comps):
         """
         Determine toolchain compiler tag, for given list of compilers.

From 198704b9c976e5c12bd48db49e2a068beb2dfd2c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Oct 2014 16:02:56 +0200
Subject: [PATCH 0232/1356] versionprefix is not always available, only use it
 when it's defined

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index d3fd0a490b..42297c1ba2 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -55,7 +55,7 @@
 class HierarchicalMNS(ModuleNamingScheme):
     """Class implementing an example hierarchical module naming scheme."""
 
-    REQUIRED_KEYS = ['name', 'versionprefix', 'version', 'versionsuffix', 'toolchain', 'moduleclass']
+    REQUIRED_KEYS = ['name', 'version', 'versionsuffix', 'toolchain', 'moduleclass']
 
     def requires_toolchain_details(self):
         """
@@ -80,9 +80,9 @@ def det_short_module_name(self, ec):
 
     def det_full_version(self, ec):
         """Determine full version, taking into account version prefix/suffix."""
-        
-        return ec['versionprefix'] + ec['version'] + ec['versionsuffix']
- 
+        # versionprefix is not always available (e.g., for toolchains)
+        versionprefix = ec.get('versionprefix', '')
+        return versionprefix + ec['version'] + ec['versionsuffix']
 
     def det_toolchain_compilers_name_version(self, tc_comps):
         """

From 54bf7bbbe81e507f5a2830b5a21bc8886d2f2f4a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Oct 2014 16:04:36 +0200
Subject: [PATCH 0233/1356] keep 'versionprefix' as a required key

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 42297c1ba2..22a0342965 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -55,7 +55,7 @@
 class HierarchicalMNS(ModuleNamingScheme):
     """Class implementing an example hierarchical module naming scheme."""
 
-    REQUIRED_KEYS = ['name', 'version', 'versionsuffix', 'toolchain', 'moduleclass']
+    REQUIRED_KEYS = ['name', 'versionprefix', 'version', 'versionsuffix', 'toolchain', 'moduleclass']
 
     def requires_toolchain_details(self):
         """

From feda536440d30c8427e9961a6bb4b97ba533a8ac Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 13 Oct 2014 21:54:41 +0200
Subject: [PATCH 0234/1356] refactor main.py, flesh out functions from main
 function

---
 easybuild/framework/easyblock.py |   3 +-
 easybuild/main.py                | 534 ++++++++++++++++++-------------
 easybuild/tools/build_log.py     |  26 ++
 easybuild/tools/config.py        |   8 +
 easybuild/tools/github.py        |   7 +-
 5 files changed, 347 insertions(+), 231 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 32bbe6a4a9..f988295cfe 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -38,7 +38,6 @@
 
 import copy
 import glob
-import re
 import os
 import shutil
 import stat
@@ -74,6 +73,7 @@
 from easybuild.tools.utilities import remove_unwanted_chars
 from easybuild.tools.version import this_is_easybuild, VERBOSE_VERSION, VERSION
 
+
 _log = fancylogger.getLogger('easyblock')
 
 
@@ -1982,6 +1982,7 @@ def build_and_install_one(module, orig_environ):
 
     return (success, application_log, errormsg)
 
+
 def get_easyblock_instance(easyconfig):
     """
     Get an instance for this easyconfig
diff --git a/easybuild/main.py b/easybuild/main.py
index a572ac2c05..bd5e2f0331 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -39,14 +39,12 @@
 import os
 import subprocess
 import sys
-import tempfile
 import traceback
-from vsc.utils import fancylogger
 from vsc.utils.missing import any
 
 # IMPORTANT this has to be the first easybuild import as it customises the logging
 #  expect missing log output when this not the case!
-from easybuild.tools.build_log import EasyBuildError, print_msg, print_error
+from easybuild.tools.build_log import EasyBuildError, init_logging, print_msg, print_error, stop_logging
 
 import easybuild.tools.config as config
 import easybuild.tools.options as eboptions
@@ -55,7 +53,7 @@
 from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, print_dry_run
 from easybuild.framework.easyconfig.tools import resolve_dependencies, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_path, tweak
-from easybuild.tools.config import get_repository, module_classes, get_repositorypath, set_tmpdir
+from easybuild.tools.config import build_option, get_repository, module_classes, get_repositorypath, set_tmpdir
 from easybuild.tools.filetools import cleanup, find_easyconfigs, search_file, write_file
 from easybuild.tools.github import fetch_easyconfigs_from_pr
 from easybuild.tools.options import process_software_build_specs
@@ -63,161 +61,68 @@
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.testing import create_test_report, post_easyconfigs_pr_test_report, upload_test_report_as_gist
 from easybuild.tools.testing import regtest, session_module_list, session_state
-from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.version import this_is_easybuild  # from a single location
 
 
 _log = None
 
 
-def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
-    """Build and install software for all provided parsed easyconfig files."""
-    # obtain a copy of the starting environment so each build can start afresh
-    # we shouldn't use the environment from init_session_state, since relevant env vars might have been set since
-    # e.g. via easyconfig.handle_allowed_system_deps
-    orig_environ = copy.deepcopy(os.environ)
-
-    res = []
-    for ec in ecs:
-        ec_res = {}
-        try:
-            (ec_res['success'], app_log, err) = build_and_install_one(ec, orig_environ)
-            ec_res['log_file'] = app_log
-            if not ec_res['success']:
-                ec_res['err'] = EasyBuildError(err)
-        except Exception, err:
-            # purposely catch all exceptions
-            ec_res['success'] = False
-            ec_res['err'] = err
-            ec_res['traceback'] = traceback.format_exc()
-
-        # keep track of success/total count
-        if ec_res['success']:
-            test_msg = "Successfully built %s" % ec['spec']
-        else:
-            test_msg = "Build of %s failed" % ec['spec']
-            if 'err' in ec_res:
-                test_msg += " (err: %s)" % ec_res['err']
-
-        # dump test report next to log file
-        test_report_txt = create_test_report(test_msg, [(ec, ec_res)], init_session_state)
-        if 'log_file' in ec_res:
-            test_report_fp = "%s_test_report.md" % '.'.join(ec_res['log_file'].split('.')[:-1])
-            write_file(test_report_fp, test_report_txt)
-
-        if not ec_res['success'] and exit_on_failure:
-            if 'traceback' in ec_res:
-                _log.error(ec_res['traceback'])
-            else:
-                _log.error(test_msg)
-
-        res.append((ec, ec_res))
-
-    return res
-
-
-def main(testing_data=(None, None, None)):
-    """
-    Main function:
-    @arg options: a tuple: (options, paths, logger, logfile, hn) as defined in parse_options
-    This function will:
-    - read easyconfig
-    - build software
-    """
-
-    # purposely session state very early, to avoid modules loaded by EasyBuild meddling in
-    init_session_state = session_state()
-
-    # disallow running EasyBuild as root
-    if os.getuid() == 0:
-        sys.stderr.write("ERROR: You seem to be running EasyBuild with root privileges.\n"
-                         "That's not wise, so let's end this here.\n"
-                         "Exiting.\n")
-        sys.exit(1)
-
-    # steer behavior when testing main
-    testing = testing_data[0] is not None
-    args, logfile, do_build = testing_data
-
-    # initialise options
-    eb_go = eboptions.parse_options(args=args)
-    options = eb_go.options
-    orig_paths = eb_go.args
-    eb_config = eb_go.generate_cmd_line(add_default=True)
-    init_session_state.update({'easybuild_configuration': eb_config})
-
-    # set umask (as early as possible)
-    if options.umask is not None:
-        new_umask = int(options.umask, 8)
-        old_umask = os.umask(new_umask)
+def log_start(eb_command_line, eb_tmpdir):
+    """Log startup info."""
+    _log.info(this_is_easybuild())
 
-    # set temporary directory to use
-    eb_tmpdir = set_tmpdir(options.tmpdir)
+    # log used command line
+    _log.info("Command line: %s" % (' '.join(eb_command_line)))
 
-    # initialise logging for main
-    if options.logtostdout:
-        fancylogger.logToScreen(enable=True, stdout=True)
-    else:
-        if logfile is None:
-            # mkstemp returns (fd,filename), fd is from os.open, not regular open!
-            fd, logfile = tempfile.mkstemp(suffix='.log', prefix='easybuild-')
-            os.close(fd)
-
-        fancylogger.logToFile(logfile)
-        print_msg('temporary log file in case of crash %s' % (logfile), log=None, silent=testing)
+    _log.info("Using %s as temporary directory" % eb_tmpdir)
 
-    global _log
-    _log = fancylogger.getLogger(fname=False)
 
-    if options.umask is not None:
-        _log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
+def alt_easyconfig_paths(tmpdir, tweaked_ecs=False, from_pr=False):
+    """Obtain alternative paths for easyconfig files."""
+    # prepend robot path with location where tweaked easyconfigs will be placed
+    tweaked_ecs_path = None
+    if tweaked_ecs:
+        tweaked_ecs_path = os.path.join(tmpdir, 'tweaked_easyconfigs')
 
-    # hello world!
-    _log.info(this_is_easybuild())
+    pr_path = None
+    if from_pr:
+        # extend robot search path with location where files touch in PR will be downloaded to
+        pr_path = os.path.join(tmpdir, "files_pr%s" % from_pr)
 
-    # how was EB called?
-    eb_command_line = eb_go.generate_cmd_line() + eb_go.args
-    _log.info("Command line: %s" % (" ".join(eb_command_line)))
+    return tweaked_ecs_path, pr_path
 
-    _log.info("Using %s as temporary directory" % eb_tmpdir)
 
-    if not options.robot is None:
-        if options.robot:
-            _log.info("Using robot path(s): %s" % options.robot)
+def det_robot_path(robot_option, easyconfigs_paths, tweaked_ecs_path, pr_path, auto_robot=False):
+    """Determine robot path."""
+    # do not use robot option directly, it's not a list instance (and it shouldn't be modified)
+    robot_path = []
+    if not robot_option is None:
+        if robot_option:
+            robot_path = list(robot_option)
+            _log.info("Using robot path(s): %s" % robot_path)
         else:
+            # if options.robot is not None and False, easyconfigs pkg install path could not be found (see options.py)
             _log.error("No robot paths specified, and unable to determine easybuild-easyconfigs install path.")
 
-    # do not pass options.robot, it's not a list instance (and it shouldn't be modified)
-    robot_path = []
-    if options.robot:
-        robot_path = list(options.robot)
-
-    # determine easybuild-easyconfigs package install path
-    easyconfigs_paths = get_paths_for("easyconfigs", robot_path=robot_path)
-    # keep track of paths for install easyconfigs, so we can obtain find specified easyconfigs
-    easyconfigs_pkg_full_paths = easyconfigs_paths[:]
-    if not easyconfigs_paths:
-        _log.warning("Failed to determine install path for easybuild-easyconfigs package.")
-
-    # process software build specifications (if any), i.e.
-    # software name/version, toolchain name/version, extra patches, ...
-    (try_to_generate, build_specs) = process_software_build_specs(options)
-
-    # specified robot paths are preferred over installed easyconfig files
-    # --try-X and --dep-graph both require --robot, so enable it with path of installed easyconfigs
-    if robot_path or try_to_generate or options.dep_graph:
+    if auto_robot:
         robot_path.extend(easyconfigs_paths)
-        easyconfigs_paths = robot_path[:]
         _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
 
-    # prepend robot path with location where tweaked easyconfigs will be placed
-    tweaked_ecs_path = None
-    if try_to_generate and build_specs:
-        tweaked_ecs_path = os.path.join(eb_tmpdir, 'tweaked_easyconfigs')
+    if tweaked_ecs_path is not None:
         robot_path.insert(0, tweaked_ecs_path)
+        _log.info("Prepended list of robot search paths with %s: %s" % (tweaked_ecs_path, robot_path))
+
+    if pr_path is not None:
+        robot_path.insert(0, pr_path)
+        _log.info("Prepended list of robot search paths with %s: %s" % (pr_path, robot_path))
+
+    return robot_path
+
 
+def configure(options, config_options_dict, build_options):
+    """Configure EasyBuild."""
     # initialise the easybuild configuration
-    config.init(options, eb_go.get_options_by_section('config'))
+    config.init(options, config_options_dict)
 
     # building a dependency graph implies force, so that all dependencies are retained
     # and also skips validation of easyconfigs (e.g. checking os dependencies)
@@ -230,22 +135,15 @@ def main(testing_data=(None, None, None)):
     if options.dep_graph or options.dry_run or options.dry_run_short:
         options.ignore_osdeps = True
 
-    pr_path = None
-    if options.from_pr:
-        # extend robot search path with location where files touch in PR will be downloaded to
-        pr_path = os.path.join(eb_tmpdir, "files_pr%s" % options.from_pr)
-        robot_path.insert(0, pr_path)
-        _log.info("Prepended list of robot search paths with %s: %s" % (pr_path, robot_path))
-
-    config.init_build_options({
+    build_options.update({
         'aggregate_regtest': options.aggregate_regtest,
         'allow_modules_tool_mismatch': options.allow_modules_tool_mismatch,
         'check_osdeps': not options.ignore_osdeps,
         'filter_deps': options.filter_deps,
         'cleanup_builddir': options.cleanup_builddir,
-        'command_line': eb_command_line,
         'debug': options.debug,
         'dry_run': options.dry_run or options.dry_run_short,
+        'dump_test_report': options.dump_test_report,
         'easyblock': options.easyblock,
         'experimental': options.experimental,
         'force': options.force,
@@ -259,9 +157,7 @@ def main(testing_data=(None, None, None)):
         'recursive_mod_unload': options.recursive_module_unload,
         'regtest_output_dir': options.regtest_output_dir,
         'retain_all_deps': retain_all_deps,
-        'robot_path': robot_path,
         'sequential': options.sequential,
-        'silent': testing,
         'set_gid_bit': options.set_gid_bit,
         'skip': options.skip,
         'skip_test_cases': options.skip_test_cases,
@@ -270,42 +166,53 @@ def main(testing_data=(None, None, None)):
         'suffix_modules_path': options.suffix_modules_path,
         'test_report_env_filter': options.test_report_env_filter,
         'umask': options.umask,
+        'upload_test_report': options.upload_test_report,
         'valid_module_classes': module_classes(),
         'valid_stops': [x[0] for x in EasyBlock.get_steps()],
         'validate': not options.force,
     })
+    config.init_build_options(build_options)
 
-    # obtain list of loaded modules, build options must be initialized first
-    modlist = session_module_list(testing=testing)
-    init_session_state.update({'module_list': modlist})
-    _log.debug("Initial session state: %s" % init_session_state)
 
-    # search for easyconfigs
-    if options.search or options.search_short:
-        search_path = [os.getcwd()]
-        if easyconfigs_paths:
-            search_path = easyconfigs_paths
-        query = options.search or options.search_short
-        ignore_dirs = config.build_option('ignore_dirs')
-        silent = config.build_option('silent')
-        search_file(search_path, query, short=not options.search, ignore_dirs=ignore_dirs, silent=silent)
+def search(query, short=False):
+    """Search for easyconfigs, if a query is provided."""
+    search_path = [os.getcwd()]
+    robot_path = build_option('robot_path')
+    if robot_path:
+        search_path = robot_path
+    ignore_dirs = config.build_option('ignore_dirs')
+    silent = config.build_option('silent')
+    search_file(search_path, query, short=short, ignore_dirs=ignore_dirs, silent=silent)
+
 
+def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
+    """
+    Determine paths to easyconfig files.
+    @param orig_paths: list of original easyconfig paths
+    @param from_pr: pull request number to fetch easyconfigs from
+    @param easyconfigs_pkg_paths: paths to installed easyconfigs package
+    """
     paths = []
+
+    if easyconfigs_pkg_paths is None:
+        easyconfigs_pkg_paths = []
+    build_specs = build_option('build_specs')
+    ignore_dirs = build_option('ignore_dirs')
+    robot_path = build_option('robot_path')
+    testing = build_option('testing')
+    try_to_generate = build_option('try_to_generate')
+
     if len(orig_paths) == 0:
-        if options.from_pr:
-            pr_files = fetch_easyconfigs_from_pr(options.from_pr, path=pr_path, github_user=options.github_user)
+        if from_pr:
+            pr_files = fetch_easyconfigs_from_pr(from_pr)
             paths = [(path, False) for path in pr_files if path.endswith('.eb')]
         elif 'name' in build_specs:
-            paths = [obtain_path(build_specs, easyconfigs_paths, try_to_generate=try_to_generate,
+            paths = [obtain_path(build_specs, robot_path, try_to_generate=try_to_generate,
                                  exit_on_error=not testing)]
-        elif not any([options.aggregate_regtest, options.search, options.search_short, options.regtest]):
-            print_error(("Please provide one or multiple easyconfig files, or use software build "
-                         "options to make EasyBuild search for easyconfigs"),
-                        log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
     else:
         # look for easyconfigs with relative paths in easybuild-easyconfigs package,
         # unless they were found at the given relative paths
-        if easyconfigs_pkg_full_paths:
+        if easyconfigs_pkg_paths:
             # determine which easyconfigs files need to be found, if any
             ecs_to_find = []
             for idx, orig_path in enumerate(orig_paths):
@@ -314,7 +221,7 @@ def main(testing_data=(None, None, None)):
             _log.debug("List of easyconfig files to find: %s" % ecs_to_find)
 
             # find missing easyconfigs by walking paths with installed easyconfig files
-            for path in easyconfigs_pkg_full_paths:
+            for path in easyconfigs_pkg_paths:
                 _log.debug("Looking for missing easyconfig files (%d left) in %s..." % (len(ecs_to_find), path))
                 for (subpath, dirnames, filenames) in os.walk(path, topdown=True):
                     for idx, orig_path in ecs_to_find[:]:
@@ -330,7 +237,7 @@ def main(testing_data=(None, None, None)):
                         break
 
                     # ignore subdirs specified to be ignored by replacing items in dirnames list used by os.walk
-                    dirnames[:] = [d for d in dirnames if not d in options.ignore_dirs]
+                    dirnames[:] = [d for d in dirnames if not d in ignore_dirs]
 
                 # stop os.walk insanity as soon as we have all we need (paths loop)
                 if len(ecs_to_find) == 0:
@@ -339,22 +246,19 @@ def main(testing_data=(None, None, None)):
         # indicate that specified paths do not contain generated easyconfig files
         paths = [(path, False) for path in orig_paths]
 
-    _log.debug("Paths: %s" % paths)
+    return paths
 
-    # run regtest
-    if options.regtest or options.aggregate_regtest:
-        _log.info("Running regression test")
-        if paths:
-            ec_paths = [path[0] for path in paths]
-        else:  # fallback: easybuild-easyconfigs install path
-            ec_paths = easyconfigs_pkg_full_paths
-        regtest_ok = regtest(ec_paths)
 
-        if not regtest_ok:
-            _log.info("Regression test failed (partially)!")
-            sys.exit(31)  # exit -> 3x1t -> 31
+def read_easyconfigs(paths):
+    """
+    Read/parse easyconfigs
+    @params paths: paths to easyconfigs
+    """
+    build_specs = build_option('build_specs')
+    ignore_dirs = build_option('ignore_dirs')
+    try_to_generate = build_option('try_to_generate')
+    tweaked_ecs_path = build_option('tweaked_ecs_path')
 
-    # read easyconfig files
     easyconfigs = []
     generated_ecs = False
     for (path, generated) in paths:
@@ -363,9 +267,8 @@ def main(testing_data=(None, None, None)):
         generated_ecs |= generated
         if not os.path.exists(path):
             print_error("Can't find path %s" % path)
-
         try:
-            ec_files = find_easyconfigs(path, ignore_dirs=options.ignore_dirs)
+            ec_files = find_easyconfigs(path, ignore_dirs=ignore_dirs)
             for ec_file in ec_files:
                 # only pass build specs when not generating easyconfig files
                 if try_to_generate:
@@ -382,13 +285,222 @@ def main(testing_data=(None, None, None)):
     if try_to_generate and build_specs and not generated_ecs:
         easyconfigs = tweak(easyconfigs, build_specs, targetdir=tweaked_ecs_path)
 
-    # before building starts, take snapshot of environment (watch out -t option!)
-    os.chdir(os.environ['PWD'])
+    return easyconfigs
+
+
+def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
+    """
+    Submit jobs.
+    @param ordered_ecs: list of easyconfigs, in the order they should be processed
+    @param cmd_line_opts: list of command line options (in 'longopt=value' form)
+    """
+    curdir = os.getcwd()
+
+    # the options to ignore (help options can't reach here)
+    ignore_opts = ['robot', 'job']
+
+    # generate_cmd_line returns the options in form --longopt=value
+    opts = [x for x in cmd_line_opts if not x.split('=')[0] in ['--%s' % y for y in ignore_opts]]
+
+    quoted_opts = subprocess.list2cmdline(opts)
+
+    command = "unset TMPDIR && cd %s && eb %%(spec)s %s" % (curdir, quoted_opts)
+    _log.info("Command template for jobs: %s" % command)
+    if not testing:
+        jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
+        txt = ["List of submitted jobs:"]
+        txt.extend(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in jobs])
+        txt.append("(%d jobs submitted)" % len(jobs))
+
+        print_msg("Submitted parallel build jobs, exiting now: %s" % '\n'.join(txt), log=_log)
+
+
+def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
+    """Build and install software for all provided parsed easyconfig files."""
+    # obtain a copy of the starting environment so each build can start afresh
+    # we shouldn't use the environment from init_session_state, since relevant env vars might have been set since
+    # e.g. via easyconfig.handle_allowed_system_deps
+    orig_environ = copy.deepcopy(os.environ)
+
+    res = []
+    for ec in ecs:
+        ec_res = {}
+        try:
+            (ec_res['success'], app_log, err) = build_and_install_one(ec, orig_environ)
+            ec_res['log_file'] = app_log
+            if not ec_res['success']:
+                ec_res['err'] = EasyBuildError(err)
+        except Exception, err:
+            # purposely catch all exceptions
+            ec_res['success'] = False
+            ec_res['err'] = err
+            ec_res['traceback'] = traceback.format_exc()
+
+        # keep track of success/total count
+        if ec_res['success']:
+            test_msg = "Successfully built %s" % ec['spec']
+        else:
+            test_msg = "Build of %s failed" % ec['spec']
+            if 'err' in ec_res:
+                test_msg += " (err: %s)" % ec_res['err']
+
+        # dump test report next to log file
+        test_report_txt = create_test_report(test_msg, [(ec, ec_res)], init_session_state)
+        if 'log_file' in ec_res:
+            test_report_fp = "%s_test_report.md" % '.'.join(ec_res['log_file'].split('.')[:-1])
+            write_file(test_report_fp, test_report_txt)
+
+        if not ec_res['success'] and exit_on_failure:
+            if 'traceback' in ec_res:
+                _log.error(ec_res['traceback'])
+            else:
+                _log.error(test_msg)
+
+        res.append((ec, ec_res))
+
+    return res
+
+
+def test_report(ecs_with_res, orig_cnt, success, msg, init_session_state):
+    """
+    Upload/dump test report
+    @param ecs_with_res: processed easyconfigs with build result (success/failure)
+    @param orig_cnt: number of original easyconfig paths
+    @param success: boolean indicating whether all builds were successful
+    @param msg: message to be included in test report
+    @param init_session_state: initial session state info to include in test report
+    """
+    dump_path = build_option('dump_test_report')
+    pr_nr = build_option('from_pr')
+    upload = build_option('upload_test_report')
+
+    if upload:
+        msg = msg + " (%d easyconfigs in this PR)" % orig_cnt
+        test_report = create_test_report(msg, ecs_with_res, init_session_state, pr_nr=pr_nr, gist_log=True)
+        if pr_nr:
+            # upload test report to gist and issue a comment in the PR to notify
+            msg = post_easyconfigs_pr_test_report(pr_nr, test_report, msg, init_session_state, success)
+            print_msg(msg)
+        else:
+            # only upload test report as a gist
+            gist_url = upload_test_report_as_gist(test_report)
+            print_msg("Test report uploaded to %s" % gist_url)
+    else:
+        test_report = create_test_report(msg, ecs_with_res, init_session_state)
+    _log.debug("Test report: %s" % test_report)
+    if dump_path is not None:
+        write_file(dump_path, test_report)
+        _log.info("Test report dumped to %s" % dump_path)
+
+
+def main(testing_data=(None, None, None)):
+    """
+    Main function: parse command line options, and act accordingly.
+    @param testing_data: tuple with command line arguments, log file and boolean indicating whether or not to build
+    """
+    # purposely session state very early, to avoid modules loaded by EasyBuild meddling in
+    init_session_state = session_state()
+
+    # steer behavior when testing main
+    testing = testing_data[0] is not None
+    args, logfile, do_build = testing_data
+
+    # initialise options
+    eb_go = eboptions.parse_options(args=args)
+    options = eb_go.options
+    orig_paths = eb_go.args
+
+    # set umask (as early as possible)
+    if options.umask is not None:
+        new_umask = int(options.umask, 8)
+        old_umask = os.umask(new_umask)
+
+    # set temporary directory to use
+    eb_tmpdir = set_tmpdir(options.tmpdir)
+
+    # initialise logging for main
+    global _log
+    _log, logfile = init_logging(logfile, logtostdout=options.logtostdout, testing=testing)
+
+    # disallow running EasyBuild as root
+    if os.getuid() == 0:
+        _log.error("You seem to be running EasyBuild with root privileges which is not wise, so let's end this here.")
+
+    # log startup info
+    eb_cmd_line = eb_go.generate_cmd_line() + eb_go.args
+    log_start(eb_cmd_line, eb_tmpdir)
+
+    if options.umask is not None:
+        _log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
+
+    # determine easybuild-easyconfigs package install path
+    easyconfigs_pkg_paths = get_paths_for("easyconfigs")
+    if not easyconfigs_pkg_paths:
+        _log.warning("Failed to determine install path for easybuild-easyconfigs package.")
+
+    # process software build specifications (if any), i.e.
+    # software name/version, toolchain name/version, extra patches, ...
+    (try_to_generate, build_specs) = process_software_build_specs(options)
+
+    # determine robot path
+    # --try-X, --dep-graph, --search use robot path for searching, so enable it with path of installed easyconfigs
+    tweaked_ecs = try_to_generate and build_specs
+    tweaked_ecs_path, pr_path = alt_easyconfig_paths(eb_tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
+    auto_robot = try_to_generate or options.dep_graph or options.search or options.search_short
+    robot_path = det_robot_path(options.robot, easyconfigs_pkg_paths, tweaked_ecs_path, pr_path, auto_robot=auto_robot)
+    _log.debug("Full robot path: %s" % robot_path)
+
+    # configure & initialize build options
+    config_options_dict = eb_go.get_options_by_section('config')
+    build_options = {
+        'build_specs': build_specs,
+        'command_line': eb_cmd_line,
+        'pr_path': pr_path,
+        'robot_path': robot_path,
+        'silent': testing,
+        'testing': testing,
+        'try_to_generate': try_to_generate,
+        'tweaked_ecs_path': tweaked_ecs_path,
+    }
+    configure(options, config_options_dict, build_options)
+
+    # update session state
+    eb_config = eb_go.generate_cmd_line(add_default=True)
+    modlist = session_module_list(testing=testing)  # build options must be initialized first before 'module list' works
+    init_session_state.update({'easybuild_configuration': eb_config})
+    init_session_state.update({'module_list': modlist})
+    _log.debug("Initial session state: %s" % init_session_state)
+
+    # search for easyconfigs, if a query is specified
+    query = options.search or options.search_short
+    if query:
+        search(query, short=not options.search)
+
+    # determine paths to easyconfigs
+    paths = det_easyconfig_paths(orig_paths, options.from_pr, easyconfigs_pkg_paths)
+    if not paths and not any([options.aggregate_regtest, options.search, options.search_short, options.regtest]):
+        print_error(("Please provide one or multiple easyconfig files, or use software build "
+                     "options to make EasyBuild search for easyconfigs"),
+                     log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
+    _log.debug("Paths: %s" % paths)
+
+    # run regtest
+    if options.regtest or options.aggregate_regtest:
+        _log.info("Running regression test")
+        # fallback: easybuild-easyconfigs install path
+        regtest_ok = regtest([path[0] for path in paths] or easyconfigs_pkg_paths)
+        if not regtest_ok:
+            _log.info("Regression test failed (partially)!")
+            sys.exit(31)  # exit -> 3x1t -> 31
+
+    # read easyconfig files
+    easyconfigs = read_easyconfigs(paths)
 
     # dry_run: print all easyconfigs and dependencies, and whether they are already built
     if options.dry_run or options.dry_run_short:
         print_dry_run(easyconfigs, short=not options.dry_run, build_specs=build_specs)
 
+    # cleanup and exit after dry run, searching easyconfigs or submitting regression test
     if any([options.dry_run, options.dry_run_short, options.regtest, options.search, options.search_short]):
         cleanup(logfile, eb_tmpdir, testing)
         sys.exit(0)
@@ -411,27 +523,10 @@ def main(testing_data=(None, None, None)):
         dep_graph(options.dep_graph, ordered_ecs)
         sys.exit(0)
 
-    # submit build as job(s) and exit
+    # submit build as job(s), clean up and exit
     if options.job:
-        curdir = os.getcwd()
-
-        # the options to ignore (help options can't reach here)
-        ignore_opts = ['robot', 'job']
-
-        # generate_cmd_line returns the options in form --longopt=value
-        opts = [x for x in eb_go.generate_cmd_line() if not x.split('=')[0] in ['--%s' % y for y in ignore_opts]]
-
-        quoted_opts = subprocess.list2cmdline(opts)
-
-        command = "unset TMPDIR && cd %s && eb %%(spec)s %s" % (curdir, quoted_opts)
-        _log.info("Command template for jobs: %s" % command)
+        submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
         if not testing:
-            jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
-            txt = ["List of submitted jobs:"]
-            txt.extend(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in jobs])
-            txt.append("(%d jobs submitted)" % len(jobs))
-
-            print_msg("Submitted parallel build jobs, exiting now: %s" % '\n'.join(txt), log=_log)
             cleanup(logfile, eb_tmpdir, testing)
             sys.exit(0)
 
@@ -449,24 +544,8 @@ def main(testing_data=(None, None, None)):
     repo = init_repository(get_repository(), get_repositorypath())
     repo.cleanup()
 
-    # report back in PR in case of testing
-    if options.upload_test_report:
-        msg = success_msg + " (%d easyconfigs in this PR)" % len(paths)
-        test_report = create_test_report(msg, ecs_with_res, init_session_state, pr_nr=options.from_pr, gist_log=True)
-        if options.from_pr:
-            # upload test report to gist and issue a comment in the PR to notify
-            msg = post_easyconfigs_pr_test_report(options.from_pr, test_report, success_msg, init_session_state, overall_success)
-            print_msg(msg)
-        else:
-            # only upload test report as a gist
-            gist_url = upload_test_report_as_gist(test_report)
-            print_msg("Test report uploaded to %s" % gist_url)
-    else:
-        test_report = create_test_report(success_msg, ecs_with_res, init_session_state)
-    _log.debug("Test report: %s" % test_report)
-    if options.dump_test_report is not None:
-        write_file(options.dump_test_report, test_report)
-        _log.info("Test report dumped to %s" % options.dump_test_report)
+    # dump/upload overall test report
+    test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
 
     print_msg(success_msg, log=_log, silent=testing)
 
@@ -475,11 +554,8 @@ def main(testing_data=(None, None, None)):
         if 'original_spec' in ec and os.path.isfile(ec['spec']):
             os.remove(ec['spec'])
 
-    # cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir path)
-    if options.logtostdout:
-        fancylogger.logToScreen(enable=False, stdout=True)
-    else:
-        fancylogger.logToFile(logfile, enable=False)
+    # stop logging and cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir path)
+    stop_logging(logfile, logtostdout=options.logtostdout)
     if overall_success:
         cleanup(logfile, eb_tmpdir, testing)
 
diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index c08ffbf71c..e4873068ae 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -33,6 +33,7 @@
 """
 import os
 import sys
+import tempfile
 from copy import copy
 from vsc.utils import fancylogger
 
@@ -134,6 +135,31 @@ def exception(self, msg, *args):
 _init_easybuildlog = fancylogger.getLogger(fname=False)
 
 
+def init_logging(logfile, logtostdout=False, testing=False):
+    """Initialize logging."""
+    if logtostdout:
+        fancylogger.logToScreen(enable=True, stdout=True)
+    else:
+        if logfile is None:
+            # mkstemp returns (fd,filename), fd is from os.open, not regular open!
+            fd, logfile = tempfile.mkstemp(suffix='.log', prefix='easybuild-')
+            os.close(fd)
+
+        fancylogger.logToFile(logfile)
+        print_msg('temporary log file in case of crash %s' % (logfile), log=None, silent=testing)
+
+    log = fancylogger.getLogger(fname=False)
+
+    return log, logfile
+
+
+def stop_logging(logfile, logtostdout=False):
+    """Stop logging."""
+    if logtostdout:
+        fancylogger.logToScreen(enable=False, stdout=True)
+    fancylogger.logToFile(logfile, enable=False)
+
+
 def get_log(name=None):
     """
     Generate logger object
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index d595b79803..e3f67779f7 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -71,15 +71,18 @@
 DEFAULT_BUILD_OPTIONS = {
     'aggregate_regtest': None,
     'allow_modules_tool_mismatch': False,
+    'build_specs': None,
     'check_osdeps': True,
     'filter_deps': None,
     'cleanup_builddir': True,
     'command_line': None,
     'debug': False,
     'dry_run': False,
+    'dump_test_report': None,
     'easyblock': None,
     'experimental': False,
     'force': False,
+    'from_pr': None,
     'github_user': None,
     'group': None,
     'hidden': False,
@@ -87,6 +90,7 @@
     'modules_footer': None,
     'only_blocks': None,
     'optarch': None,
+    'pr_path': None,
     'recursive_mod_unload': False,
     'regtest_output_dir': None,
     'retain_all_deps': False,
@@ -100,7 +104,11 @@
     'stop': None,
     'suffix_modules_path': None,
     'test_report_env_filter': None,
+    'testing': False,
+    'try_to_generate': False,
+    'tweaked_ecs_path': None,
     'umask': None,
+    'upload_test_report': False,
     'valid_module_classes': None,
     'valid_stops': None,
     'validate': True,
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index ae544e28b4..89319ad2ce 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -30,7 +30,6 @@
 """
 import base64
 import os
-import re
 import socket
 import tempfile
 import urllib
@@ -56,6 +55,7 @@
     _log.warning("Failed to import from 'vsc.utils.rest' Python module: %s" % err)
     HAVE_GITHUB_API = False
 
+from easybuild.tools.config import build_option
 from easybuild.tools.filetools import det_patched_files, mkdir
 
 
@@ -193,6 +193,11 @@ class GithubError(Exception):
 def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
     """Fetch patched easyconfig files for a particular PR."""
 
+    if github_user is None:
+        github_user = build_option('github_user')
+    if path is None:
+        path = build_option('pr_path')
+
     def download(url, path=None):
         """Download file from specified URL to specified path."""
         if path is not None:

From fc4a0cdc90d24a7c22e79eca7c908ce594f16d19 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Oct 2014 11:13:23 +0200
Subject: [PATCH 0235/1356] move function out of main.py, introduce
 easybuild.tools.robot module

---
 easybuild/framework/easyconfig/tools.py | 281 ++++++++------------
 easybuild/framework/easyconfig/tweak.py |   2 +-
 easybuild/main.py                       | 325 +++---------------------
 easybuild/tools/build_log.py            |   3 +-
 easybuild/tools/config.py               |  65 ++++-
 easybuild/tools/filetools.py            |   1 -
 easybuild/tools/options.py              |  15 +-
 easybuild/tools/parallelbuild.py        |  30 ++-
 easybuild/tools/robot.py                | 255 +++++++++++++++++++
 easybuild/tools/testing.py              |  39 ++-
 test/framework/parallelbuild.py         |   3 +-
 test/framework/robot.py                 |  15 +-
 test/framework/utilities.py             |   2 +-
 13 files changed, 548 insertions(+), 488 deletions(-)
 create mode 100644 easybuild/tools/robot.py

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 6a7c48a062..f020231150 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -66,12 +66,11 @@
     graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz")
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
-from easybuild.framework.easyconfig.easyconfig import process_easyconfig, robot_find_easyconfig
-from easybuild.tools.build_log import EasyBuildError, print_msg
+from easybuild.framework.easyconfig.easyconfig import process_easyconfig
+from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import det_common_path_prefix, run_cmd, write_file
-from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS
-from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version, det_hidden_modname
+from easybuild.tools.filetools import find_easyconfigs, run_cmd, search_file, write_file
+from easybuild.tools.github import fetch_easyconfigs_from_pr
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.utilities import quote_str
@@ -123,174 +122,6 @@ def find_resolved_modules(unprocessed, avail_modules):
     return ordered_ecs, new_unprocessed, new_avail_modules
 
 
-def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
-    """
-    Work through the list of easyconfigs to determine an optimal order
-    @param unprocessed: list of easyconfigs
-    @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
-    """
-
-    robot = build_option('robot_path')
-
-    retain_all_deps = build_option('retain_all_deps') or retain_all_deps
-    if retain_all_deps:
-        # assume that no modules are available when forced, to retain all dependencies
-        avail_modules = []
-        _log.info("Forcing all dependencies to be retained.")
-    else:
-        # Get a list of all available modules (format: [(name, installversion), ...])
-        avail_modules = modules_tool().available()
-
-        if len(avail_modules) == 0:
-            _log.warning("No installed modules. Your MODULEPATH is probably incomplete: %s" % os.getenv('MODULEPATH'))
-
-    ordered_ecs = []
-    # all available modules can be used for resolving dependencies except those that will be installed
-    being_installed = [p['full_mod_name'] for p in unprocessed]
-    avail_modules = [m for m in avail_modules if not m in being_installed]
-
-    _log.debug('unprocessed before resolving deps: %s' % unprocessed)
-
-    # resolve all dependencies, put a safeguard in place to avoid an infinite loop (shouldn't occur though)
-    irresolvable = []
-    loopcnt = 0
-    maxloopcnt = 10000
-    while unprocessed:
-        # make sure this stops, we really don't want to get stuck in an infinite loop
-        loopcnt += 1
-        if loopcnt > maxloopcnt:
-            tup = (maxloopcnt, unprocessed, irresolvable)
-            msg = "Maximum loop cnt %s reached, so quitting (unprocessed: %s, irresolvable: %s)" % tup
-            _log.error(msg)
-
-        # first try resolving dependencies without using external dependencies
-        last_processed_count = -1
-        while len(avail_modules) > last_processed_count:
-            last_processed_count = len(avail_modules)
-            more_ecs, unprocessed, avail_modules = find_resolved_modules(unprocessed, avail_modules)
-            for ec in more_ecs:
-                if not ec['full_mod_name'] in [x['full_mod_name'] for x in ordered_ecs]:
-                    ordered_ecs.append(ec)
-
-        # robot: look for existing dependencies, add them
-        if robot and unprocessed:
-
-            # rely on EasyBuild module naming scheme when resolving dependencies, since we know that will
-            # generate sensible module names that include the necessary information for the resolution to work
-            # (name, version, toolchain, versionsuffix)
-            being_installed = [EasyBuildMNS().det_full_module_name(p['ec']) for p in unprocessed]
-
-            additional = []
-            for i, entry in enumerate(unprocessed):
-                # do not choose an entry that is being installed in the current run
-                # if they depend, you probably want to rebuild them using the new dependency
-                deps = entry['dependencies']
-                candidates = [d for d in deps if not EasyBuildMNS().det_full_module_name(d) in being_installed]
-                if len(candidates) > 0:
-                    cand_dep = candidates[0]
-                    # find easyconfig, might not find any
-                    _log.debug("Looking for easyconfig for %s" % str(cand_dep))
-                    # note: robot_find_easyconfig may return None
-                    path = robot_find_easyconfig(cand_dep['name'], det_full_ec_version(cand_dep))
-
-                    if path is None:
-                        # no easyconfig found for dependency, add to list of irresolvable dependencies
-                        if cand_dep not in irresolvable:
-                            _log.debug("Irresolvable dependency found: %s" % cand_dep)
-                            irresolvable.append(cand_dep)
-                        # remove irresolvable dependency from list of dependencies so we can continue
-                        entry['dependencies'].remove(cand_dep)
-                    else:
-                        _log.info("Robot: resolving dependency %s with %s" % (cand_dep, path))
-                        # build specs should not be passed down to resolved dependencies,
-                        # to avoid that e.g. --try-toolchain trickles down into the used toolchain itself
-                        hidden = cand_dep.get('hidden', False)
-                        processed_ecs = process_easyconfig(path, validate=not retain_all_deps, hidden=hidden)
-
-                        # ensure that selected easyconfig provides required dependency
-                        mods = [spec['ec'].full_mod_name for spec in processed_ecs]
-                        dep_mod_name = ActiveMNS().det_full_module_name(cand_dep)
-                        if not dep_mod_name in mods:
-                            tup = (path, dep_mod_name, mods)
-                            _log.error("easyconfig file %s does not contain module %s (mods: %s)" % tup)
-
-                        for ec in processed_ecs:
-                            if not ec in unprocessed + additional:
-                                additional.append(ec)
-                                _log.debug("Added %s as dependency of %s" % (ec, entry))
-                else:
-                    mod_name = EasyBuildMNS().det_full_module_name(entry['ec'])
-                    _log.debug("No more candidate dependencies to resolve for %s" % mod_name)
-
-            # add additional (new) easyconfigs to list of stuff to process
-            unprocessed.extend(additional)
-
-        elif not robot:
-            # no use in continuing if robot is not enabled, dependencies won't be resolved anyway
-            irresolvable = [dep for x in unprocessed for dep in x['dependencies']]
-            break
-
-    if irresolvable:
-        _log.warning("Irresolvable dependencies (details): %s" % irresolvable)
-        irresolvable_mods_eb = [EasyBuildMNS().det_full_module_name(dep) for dep in irresolvable]
-        _log.warning("Irresolvable dependencies (EasyBuild module names): %s" % ', '.join(irresolvable_mods_eb))
-        irresolvable_mods = [ActiveMNS().det_full_module_name(dep) for dep in irresolvable]
-        _log.error('Irresolvable dependencies encountered: %s' % ', '.join(irresolvable_mods))
-
-    _log.info("Dependency resolution complete, building as follows:\n%s" % ordered_ecs)
-    return ordered_ecs
-
-
-def print_dry_run(easyconfigs, short=False, build_specs=None):
-    """
-    Print dry run information
-    @param easyconfigs: list of easyconfig files
-    @param short: print short output (use a variable for the common prefix)
-    @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
-    """
-    lines = []
-    if build_option('robot_path') is None:
-        lines.append("Dry run: printing build status of easyconfigs")
-        all_specs = easyconfigs
-    else:
-        lines.append("Dry run: printing build status of easyconfigs and dependencies")
-        all_specs = resolve_dependencies(easyconfigs, build_specs=build_specs, retain_all_deps=True)
-
-    unbuilt_specs = skip_available(all_specs, testing=True)
-    dry_run_fmt = " * [%1s] %s (module: %s)"  # markdown compatible (list of items with checkboxes in front)
-
-    listed_ec_paths = [spec['spec'] for spec in easyconfigs]
-
-    var_name = 'CFGS'
-    common_prefix = det_common_path_prefix([spec['spec'] for spec in all_specs])
-    # only allow short if common prefix is long enough
-    short = short and common_prefix is not None and len(common_prefix) > len(var_name) * 2
-    for spec in all_specs:
-        if spec in unbuilt_specs:
-            ans = ' '
-        elif build_option('force') and spec['spec'] in listed_ec_paths:
-            ans = 'F'
-        else:
-            ans = 'x'
-
-        if spec['ec'].short_mod_name != spec['ec'].full_mod_name:
-            mod = "%s | %s" % (spec['ec'].mod_subdir, spec['ec'].short_mod_name)
-        else:
-            mod = spec['ec'].full_mod_name
-
-        if short:
-            item = os.path.join('$%s' % var_name, spec['spec'][len(common_prefix) + 1:])
-        else:
-            item = spec['spec']
-        lines.append(dry_run_fmt % (ans, item, mod))
-
-    if short:
-        # insert after 'Dry run:' message
-        lines.insert(1, "%s=%s" % (var_name, common_prefix))
-    silent = build_option('silent')
-    print_msg('\n'.join(lines), log=_log, silent=silent, prefix=False)
-
-
 def _dep_graph(fn, specs, silent=False):
     """
     Create a dependency graph for the given easyconfigs.
@@ -385,6 +216,110 @@ def get_paths_for(subdir="easyconfigs", robot_path=None):
     return paths
 
 
+def alt_easyconfig_paths(tmpdir, tweaked_ecs=False, from_pr=False):
+    """Obtain alternative paths for easyconfig files."""
+    # prepend robot path with location where tweaked easyconfigs will be placed
+    tweaked_ecs_path = None
+    if tweaked_ecs:
+        tweaked_ecs_path = os.path.join(tmpdir, 'tweaked_easyconfigs')
+
+    pr_path = None
+    if from_pr:
+        # extend robot search path with location where files touch in PR will be downloaded to
+        pr_path = os.path.join(tmpdir, "files_pr%s" % from_pr)
+
+    return tweaked_ecs_path, pr_path
+
+
+def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
+    """
+    Determine paths to easyconfig files.
+    @param orig_paths: list of original easyconfig paths
+    @param from_pr: pull request number to fetch easyconfigs from
+    @param easyconfigs_pkg_paths: paths to installed easyconfigs package
+    """
+    paths = []
+
+    if easyconfigs_pkg_paths is None:
+        easyconfigs_pkg_paths = []
+    ignore_dirs = build_option('ignore_dirs')
+
+    if len(orig_paths) == 0:
+        if from_pr:
+            pr_files = fetch_easyconfigs_from_pr(from_pr)
+            paths = [(path, False) for path in pr_files if path.endswith('.eb')]
+    else:
+        # look for easyconfigs with relative paths in easybuild-easyconfigs package,
+        # unless they were found at the given relative paths
+        if easyconfigs_pkg_paths:
+            # determine which easyconfigs files need to be found, if any
+            ecs_to_find = []
+            for idx, orig_path in enumerate(orig_paths):
+                if orig_path == os.path.basename(orig_path) and not os.path.exists(orig_path):
+                    ecs_to_find.append((idx, orig_path))
+            _log.debug("List of easyconfig files to find: %s" % ecs_to_find)
+
+            # find missing easyconfigs by walking paths with installed easyconfig files
+            for path in easyconfigs_pkg_paths:
+                _log.debug("Looking for missing easyconfig files (%d left) in %s..." % (len(ecs_to_find), path))
+                for (subpath, dirnames, filenames) in os.walk(path, topdown=True):
+                    for idx, orig_path in ecs_to_find[:]:
+                        if orig_path in filenames:
+                            full_path = os.path.join(subpath, orig_path)
+                            _log.info("Found %s in %s: %s" % (orig_path, path, full_path))
+                            orig_paths[idx] = full_path
+                            # if file was found, stop looking for it (first hit wins)
+                            ecs_to_find.remove((idx, orig_path))
+
+                    # stop os.walk insanity as soon as we have all we need (os.walk loop)
+                    if len(ecs_to_find) == 0:
+                        break
+
+                    # ignore subdirs specified to be ignored by replacing items in dirnames list used by os.walk
+                    dirnames[:] = [d for d in dirnames if not d in ignore_dirs]
+
+                # stop os.walk insanity as soon as we have all we need (paths loop)
+                if len(ecs_to_find) == 0:
+                    break
+
+        # indicate that specified paths do not contain generated easyconfig files
+        paths = [(path, False) for path in orig_paths]
+
+    return paths
+
+
+def parse_easyconfigs(paths):
+    """
+    Parse easyconfig files
+    @params paths: paths to easyconfigs
+    """
+    build_specs = build_option('build_specs')
+    ignore_dirs = build_option('ignore_dirs')
+    try_to_generate = build_option('try_to_generate')
+
+    easyconfigs = []
+    generated_ecs = False
+    for (path, generated) in paths:
+        path = os.path.abspath(path)
+        # keep track of whether any files were generated
+        generated_ecs |= generated
+        if not os.path.exists(path):
+            print_error("Can't find path %s" % path)
+        try:
+            ec_files = find_easyconfigs(path, ignore_dirs=ignore_dirs)
+            for ec_file in ec_files:
+                # only pass build specs when not generating easyconfig files
+                if try_to_generate:
+                    ecs = process_easyconfig(ec_file)
+                else:
+                    ecs = process_easyconfig(ec_file, build_specs=build_specs)
+                easyconfigs.extend(ecs)
+        except IOError, err:
+            _log.error("Processing easyconfigs in path %s failed: %s" % (path, err))
+
+    return easyconfigs, generated_ecs
+
+
 def stats_to_str(stats):
     """
     Pretty print build statistics to string.
diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index c2bfbe8374..6e0e50c290 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -44,9 +44,9 @@
 
 from easybuild.tools.build_log import print_error, print_msg, print_warning
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, create_paths, process_easyconfig
-from easybuild.framework.easyconfig.tools import resolve_dependencies
 from easybuild.tools.filetools import read_file, write_file
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
+from easybuild.tools.robot import resolve_dependencies
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.utilities import quote_str
 
diff --git a/easybuild/main.py b/easybuild/main.py
index bd5e2f0331..19772ac4c1 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -37,7 +37,6 @@
 """
 import copy
 import os
-import subprocess
 import sys
 import traceback
 from vsc.utils.missing import any
@@ -49,19 +48,18 @@
 import easybuild.tools.config as config
 import easybuild.tools.options as eboptions
 from easybuild.framework.easyblock import EasyBlock, build_and_install_one
-from easybuild.framework.easyconfig.easyconfig import process_easyconfig
-from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, print_dry_run
-from easybuild.framework.easyconfig.tools import resolve_dependencies, skip_available
+from easybuild.framework.easyconfig.tools import alt_easyconfig_paths, dep_graph, det_easyconfig_paths
+from easybuild.framework.easyconfig.tools import get_paths_for, parse_easyconfigs
+from easybuild.framework.easyconfig.tools import skip_available
 from easybuild.framework.easyconfig.tweak import obtain_path, tweak
-from easybuild.tools.config import build_option, get_repository, module_classes, get_repositorypath, set_tmpdir
-from easybuild.tools.filetools import cleanup, find_easyconfigs, search_file, write_file
-from easybuild.tools.github import fetch_easyconfigs_from_pr
+from easybuild.tools.config import get_repository, get_repositorypath, set_tmpdir
+from easybuild.tools.filetools import cleanup, write_file
 from easybuild.tools.options import process_software_build_specs
-from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
+from easybuild.tools.robot import det_robot_path, print_dry_run, resolve_dependencies, search_easyconfigs
+from easybuild.tools.parallelbuild import submit_jobs
 from easybuild.tools.repository.repository import init_repository
-from easybuild.tools.testing import create_test_report, post_easyconfigs_pr_test_report, upload_test_report_as_gist
-from easybuild.tools.testing import regtest, session_module_list, session_state
-from easybuild.tools.version import this_is_easybuild  # from a single location
+from easybuild.tools.testing import create_test_report, overall_test_report, regtest, session_module_list, session_state
+from easybuild.tools.version import this_is_easybuild
 
 
 _log = None
@@ -77,244 +75,6 @@ def log_start(eb_command_line, eb_tmpdir):
     _log.info("Using %s as temporary directory" % eb_tmpdir)
 
 
-def alt_easyconfig_paths(tmpdir, tweaked_ecs=False, from_pr=False):
-    """Obtain alternative paths for easyconfig files."""
-    # prepend robot path with location where tweaked easyconfigs will be placed
-    tweaked_ecs_path = None
-    if tweaked_ecs:
-        tweaked_ecs_path = os.path.join(tmpdir, 'tweaked_easyconfigs')
-
-    pr_path = None
-    if from_pr:
-        # extend robot search path with location where files touch in PR will be downloaded to
-        pr_path = os.path.join(tmpdir, "files_pr%s" % from_pr)
-
-    return tweaked_ecs_path, pr_path
-
-
-def det_robot_path(robot_option, easyconfigs_paths, tweaked_ecs_path, pr_path, auto_robot=False):
-    """Determine robot path."""
-    # do not use robot option directly, it's not a list instance (and it shouldn't be modified)
-    robot_path = []
-    if not robot_option is None:
-        if robot_option:
-            robot_path = list(robot_option)
-            _log.info("Using robot path(s): %s" % robot_path)
-        else:
-            # if options.robot is not None and False, easyconfigs pkg install path could not be found (see options.py)
-            _log.error("No robot paths specified, and unable to determine easybuild-easyconfigs install path.")
-
-    if auto_robot:
-        robot_path.extend(easyconfigs_paths)
-        _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
-
-    if tweaked_ecs_path is not None:
-        robot_path.insert(0, tweaked_ecs_path)
-        _log.info("Prepended list of robot search paths with %s: %s" % (tweaked_ecs_path, robot_path))
-
-    if pr_path is not None:
-        robot_path.insert(0, pr_path)
-        _log.info("Prepended list of robot search paths with %s: %s" % (pr_path, robot_path))
-
-    return robot_path
-
-
-def configure(options, config_options_dict, build_options):
-    """Configure EasyBuild."""
-    # initialise the easybuild configuration
-    config.init(options, config_options_dict)
-
-    # building a dependency graph implies force, so that all dependencies are retained
-    # and also skips validation of easyconfigs (e.g. checking os dependencies)
-    retain_all_deps = False
-    if options.dep_graph:
-        _log.info("Enabling force to generate dependency graph.")
-        options.force = True
-        retain_all_deps = True
-
-    if options.dep_graph or options.dry_run or options.dry_run_short:
-        options.ignore_osdeps = True
-
-    build_options.update({
-        'aggregate_regtest': options.aggregate_regtest,
-        'allow_modules_tool_mismatch': options.allow_modules_tool_mismatch,
-        'check_osdeps': not options.ignore_osdeps,
-        'filter_deps': options.filter_deps,
-        'cleanup_builddir': options.cleanup_builddir,
-        'debug': options.debug,
-        'dry_run': options.dry_run or options.dry_run_short,
-        'dump_test_report': options.dump_test_report,
-        'easyblock': options.easyblock,
-        'experimental': options.experimental,
-        'force': options.force,
-        'github_user': options.github_user,
-        'group': options.group,
-        'hidden': options.hidden,
-        'ignore_dirs': options.ignore_dirs,
-        'modules_footer': options.modules_footer,
-        'only_blocks': options.only_blocks,
-        'optarch': options.optarch,
-        'recursive_mod_unload': options.recursive_module_unload,
-        'regtest_output_dir': options.regtest_output_dir,
-        'retain_all_deps': retain_all_deps,
-        'sequential': options.sequential,
-        'set_gid_bit': options.set_gid_bit,
-        'skip': options.skip,
-        'skip_test_cases': options.skip_test_cases,
-        'sticky_bit': options.sticky_bit,
-        'stop': options.stop,
-        'suffix_modules_path': options.suffix_modules_path,
-        'test_report_env_filter': options.test_report_env_filter,
-        'umask': options.umask,
-        'upload_test_report': options.upload_test_report,
-        'valid_module_classes': module_classes(),
-        'valid_stops': [x[0] for x in EasyBlock.get_steps()],
-        'validate': not options.force,
-    })
-    config.init_build_options(build_options)
-
-
-def search(query, short=False):
-    """Search for easyconfigs, if a query is provided."""
-    search_path = [os.getcwd()]
-    robot_path = build_option('robot_path')
-    if robot_path:
-        search_path = robot_path
-    ignore_dirs = config.build_option('ignore_dirs')
-    silent = config.build_option('silent')
-    search_file(search_path, query, short=short, ignore_dirs=ignore_dirs, silent=silent)
-
-
-def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
-    """
-    Determine paths to easyconfig files.
-    @param orig_paths: list of original easyconfig paths
-    @param from_pr: pull request number to fetch easyconfigs from
-    @param easyconfigs_pkg_paths: paths to installed easyconfigs package
-    """
-    paths = []
-
-    if easyconfigs_pkg_paths is None:
-        easyconfigs_pkg_paths = []
-    build_specs = build_option('build_specs')
-    ignore_dirs = build_option('ignore_dirs')
-    robot_path = build_option('robot_path')
-    testing = build_option('testing')
-    try_to_generate = build_option('try_to_generate')
-
-    if len(orig_paths) == 0:
-        if from_pr:
-            pr_files = fetch_easyconfigs_from_pr(from_pr)
-            paths = [(path, False) for path in pr_files if path.endswith('.eb')]
-        elif 'name' in build_specs:
-            paths = [obtain_path(build_specs, robot_path, try_to_generate=try_to_generate,
-                                 exit_on_error=not testing)]
-    else:
-        # look for easyconfigs with relative paths in easybuild-easyconfigs package,
-        # unless they were found at the given relative paths
-        if easyconfigs_pkg_paths:
-            # determine which easyconfigs files need to be found, if any
-            ecs_to_find = []
-            for idx, orig_path in enumerate(orig_paths):
-                if orig_path == os.path.basename(orig_path) and not os.path.exists(orig_path):
-                    ecs_to_find.append((idx, orig_path))
-            _log.debug("List of easyconfig files to find: %s" % ecs_to_find)
-
-            # find missing easyconfigs by walking paths with installed easyconfig files
-            for path in easyconfigs_pkg_paths:
-                _log.debug("Looking for missing easyconfig files (%d left) in %s..." % (len(ecs_to_find), path))
-                for (subpath, dirnames, filenames) in os.walk(path, topdown=True):
-                    for idx, orig_path in ecs_to_find[:]:
-                        if orig_path in filenames:
-                            full_path = os.path.join(subpath, orig_path)
-                            _log.info("Found %s in %s: %s" % (orig_path, path, full_path))
-                            orig_paths[idx] = full_path
-                            # if file was found, stop looking for it (first hit wins)
-                            ecs_to_find.remove((idx, orig_path))
-
-                    # stop os.walk insanity as soon as we have all we need (os.walk loop)
-                    if len(ecs_to_find) == 0:
-                        break
-
-                    # ignore subdirs specified to be ignored by replacing items in dirnames list used by os.walk
-                    dirnames[:] = [d for d in dirnames if not d in ignore_dirs]
-
-                # stop os.walk insanity as soon as we have all we need (paths loop)
-                if len(ecs_to_find) == 0:
-                    break
-
-        # indicate that specified paths do not contain generated easyconfig files
-        paths = [(path, False) for path in orig_paths]
-
-    return paths
-
-
-def read_easyconfigs(paths):
-    """
-    Read/parse easyconfigs
-    @params paths: paths to easyconfigs
-    """
-    build_specs = build_option('build_specs')
-    ignore_dirs = build_option('ignore_dirs')
-    try_to_generate = build_option('try_to_generate')
-    tweaked_ecs_path = build_option('tweaked_ecs_path')
-
-    easyconfigs = []
-    generated_ecs = False
-    for (path, generated) in paths:
-        path = os.path.abspath(path)
-        # keep track of whether any files were generated
-        generated_ecs |= generated
-        if not os.path.exists(path):
-            print_error("Can't find path %s" % path)
-        try:
-            ec_files = find_easyconfigs(path, ignore_dirs=ignore_dirs)
-            for ec_file in ec_files:
-                # only pass build specs when not generating easyconfig files
-                if try_to_generate:
-                    ecs = process_easyconfig(ec_file)
-                else:
-                    ecs = process_easyconfig(ec_file, build_specs=build_specs)
-                easyconfigs.extend(ecs)
-        except IOError, err:
-            _log.error("Processing easyconfigs in path %s failed: %s" % (path, err))
-
-    # tweak obtained easyconfig files, if requested
-    # don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
-    # if easyconfig files for the dependencies are not available
-    if try_to_generate and build_specs and not generated_ecs:
-        easyconfigs = tweak(easyconfigs, build_specs, targetdir=tweaked_ecs_path)
-
-    return easyconfigs
-
-
-def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
-    """
-    Submit jobs.
-    @param ordered_ecs: list of easyconfigs, in the order they should be processed
-    @param cmd_line_opts: list of command line options (in 'longopt=value' form)
-    """
-    curdir = os.getcwd()
-
-    # the options to ignore (help options can't reach here)
-    ignore_opts = ['robot', 'job']
-
-    # generate_cmd_line returns the options in form --longopt=value
-    opts = [x for x in cmd_line_opts if not x.split('=')[0] in ['--%s' % y for y in ignore_opts]]
-
-    quoted_opts = subprocess.list2cmdline(opts)
-
-    command = "unset TMPDIR && cd %s && eb %%(spec)s %s" % (curdir, quoted_opts)
-    _log.info("Command template for jobs: %s" % command)
-    if not testing:
-        jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
-        txt = ["List of submitted jobs:"]
-        txt.extend(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in jobs])
-        txt.append("(%d jobs submitted)" % len(jobs))
-
-        print_msg("Submitted parallel build jobs, exiting now: %s" % '\n'.join(txt), log=_log)
-
-
 def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
     """Build and install software for all provided parsed easyconfig files."""
     # obtain a copy of the starting environment so each build can start afresh
@@ -361,38 +121,6 @@ def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
     return res
 
 
-def test_report(ecs_with_res, orig_cnt, success, msg, init_session_state):
-    """
-    Upload/dump test report
-    @param ecs_with_res: processed easyconfigs with build result (success/failure)
-    @param orig_cnt: number of original easyconfig paths
-    @param success: boolean indicating whether all builds were successful
-    @param msg: message to be included in test report
-    @param init_session_state: initial session state info to include in test report
-    """
-    dump_path = build_option('dump_test_report')
-    pr_nr = build_option('from_pr')
-    upload = build_option('upload_test_report')
-
-    if upload:
-        msg = msg + " (%d easyconfigs in this PR)" % orig_cnt
-        test_report = create_test_report(msg, ecs_with_res, init_session_state, pr_nr=pr_nr, gist_log=True)
-        if pr_nr:
-            # upload test report to gist and issue a comment in the PR to notify
-            msg = post_easyconfigs_pr_test_report(pr_nr, test_report, msg, init_session_state, success)
-            print_msg(msg)
-        else:
-            # only upload test report as a gist
-            gist_url = upload_test_report_as_gist(test_report)
-            print_msg("Test report uploaded to %s" % gist_url)
-    else:
-        test_report = create_test_report(msg, ecs_with_res, init_session_state)
-    _log.debug("Test report: %s" % test_report)
-    if dump_path is not None:
-        write_file(dump_path, test_report)
-        _log.info("Test report dumped to %s" % dump_path)
-
-
 def main(testing_data=(None, None, None)):
     """
     Main function: parse command line options, and act accordingly.
@@ -458,11 +186,12 @@ def main(testing_data=(None, None, None)):
         'pr_path': pr_path,
         'robot_path': robot_path,
         'silent': testing,
-        'testing': testing,
         'try_to_generate': try_to_generate,
-        'tweaked_ecs_path': tweaked_ecs_path,
+        'valid_stops': [x[0] for x in EasyBlock.get_steps()],
     }
-    configure(options, config_options_dict, build_options)
+    # initialise the EasyBuild configuration & build options
+    config.init(options, config_options_dict)
+    config.init_build_options(build_options=build_options, cmdline_options=options)
 
     # update session state
     eb_config = eb_go.generate_cmd_line(add_default=True)
@@ -474,14 +203,18 @@ def main(testing_data=(None, None, None)):
     # search for easyconfigs, if a query is specified
     query = options.search or options.search_short
     if query:
-        search(query, short=not options.search)
+        search_easyconfigs(query, short=not options.search)
 
     # determine paths to easyconfigs
     paths = det_easyconfig_paths(orig_paths, options.from_pr, easyconfigs_pkg_paths)
-    if not paths and not any([options.aggregate_regtest, options.search, options.search_short, options.regtest]):
-        print_error(("Please provide one or multiple easyconfig files, or use software build "
-                     "options to make EasyBuild search for easyconfigs"),
-                     log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
+    if not paths:
+        if 'name' in build_specs:
+            paths = [obtain_path(build_specs, robot_path, try_to_generate=try_to_generate,
+                                 exit_on_error=not testing)]
+        elif not any([options.aggregate_regtest, options.search, options.search_short, options.regtest]):
+            print_error(("Please provide one or multiple easyconfig files, or use software build "
+                         "options to make EasyBuild search for easyconfigs"),
+                         log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
     _log.debug("Paths: %s" % paths)
 
     # run regtest
@@ -494,7 +227,13 @@ def main(testing_data=(None, None, None)):
             sys.exit(31)  # exit -> 3x1t -> 31
 
     # read easyconfig files
-    easyconfigs = read_easyconfigs(paths)
+    easyconfigs, generated_ecs = parse_easyconfigs(paths)
+
+    # tweak obtained easyconfig files, if requested
+    # don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
+    # if easyconfig files for the dependencies are not available
+    if try_to_generate and build_specs and not generated_ecs:
+        easyconfigs = tweak(easyconfigs, build_specs, targetdir=tweaked_ecs_path)
 
     # dry_run: print all easyconfigs and dependencies, and whether they are already built
     if options.dry_run or options.dry_run_short:
@@ -545,7 +284,7 @@ def main(testing_data=(None, None, None)):
     repo.cleanup()
 
     # dump/upload overall test report
-    test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
+    overall_test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
 
     print_msg(success_msg, log=_log, silent=testing)
 
@@ -559,9 +298,9 @@ def main(testing_data=(None, None, None)):
     if overall_success:
         cleanup(logfile, eb_tmpdir, testing)
 
+
 if __name__ == "__main__":
     try:
         main()
     except EasyBuildError, e:
-        sys.stderr.write('ERROR: %s\n' % e.msg)
-        sys.exit(1)
+        print_error("ERROR: %s\n" % e.msg)
diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index e4873068ae..3ceb28bae3 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -190,10 +190,9 @@ def print_error(message, log=None, exitCode=1, opt_parser=None, exit_on_error=Tr
     """
     if exit_on_error:
         if not silent:
-            print_msg("ERROR: %s\n" % message)
             if opt_parser:
                 opt_parser.print_shorthelp()
-                print_msg("ERROR: %s\n" % message)
+            sys.stderr.write("ERROR: %s\n" % message)
         sys.exit(exitCode)
     elif log is not None:
         log.error(message)
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index e3f67779f7..16899f1d06 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -104,9 +104,7 @@
     'stop': None,
     'suffix_modules_path': None,
     'test_report_env_filter': None,
-    'testing': False,
     'try_to_generate': False,
-    'tweaked_ecs_path': None,
     'umask': None,
     'upload_test_report': False,
     'valid_module_classes': None,
@@ -329,9 +327,7 @@ def init(options, config_options_dict):
     Variables are read in this order of preference: generaloption > legacy environment > legacy config file
     """
     tmpdict = {}
-
     if SUPPORT_OLDSTYLE:
-
         _log.deprecated('oldstyle init with modifications to support oldstyle options', '2.0')
         tmpdict.update(oldstyle_init(options.config))
 
@@ -373,12 +369,67 @@ def init(options, config_options_dict):
     _log.debug("Config variables: %s" % variables)
 
 
-def init_build_options(build_options=None):
+def init_build_options(build_options=None, cmdline_options=None):
     """Initialize build options."""
+    # building a dependency graph implies force, so that all dependencies are retained
+    # and also skips validation of easyconfigs (e.g. checking os dependencies)
+
+    active_build_options = {}
+
+    if cmdline_options is not None:
+        retain_all_deps = False
+        if cmdline_options.dep_graph:
+            _log.info("Enabling force to generate dependency graph.")
+            cmdline_options.force = True
+            retain_all_deps = True
+
+        if cmdline_options.dep_graph or cmdline_options.dry_run or cmdline_options.dry_run_short:
+            _log.info("Ignoring OS dependencies for --dep-graph/--dry-run")
+            cmdline_options.ignore_osdeps = True
+
+        active_build_options.update({
+            'aggregate_regtest': cmdline_options.aggregate_regtest,
+            'allow_modules_tool_mismatch': cmdline_options.allow_modules_tool_mismatch,
+            'check_osdeps': not cmdline_options.ignore_osdeps,
+            'filter_deps': cmdline_options.filter_deps,
+            'cleanup_builddir': cmdline_options.cleanup_builddir,
+            'debug': cmdline_options.debug,
+            'dry_run': cmdline_options.dry_run or cmdline_options.dry_run_short,
+            'dump_test_report': cmdline_options.dump_test_report,
+            'easyblock': cmdline_options.easyblock,
+            'experimental': cmdline_options.experimental,
+            'force': cmdline_options.force,
+            'github_user': cmdline_options.github_user,
+            'group': cmdline_options.group,
+            'hidden': cmdline_options.hidden,
+            'ignore_dirs': cmdline_options.ignore_dirs,
+            'modules_footer': cmdline_options.modules_footer,
+            'only_blocks': cmdline_options.only_blocks,
+            'optarch': cmdline_options.optarch,
+            'recursive_mod_unload': cmdline_options.recursive_module_unload,
+            'regtest_output_dir': cmdline_options.regtest_output_dir,
+            'retain_all_deps': retain_all_deps,
+            'sequential': cmdline_options.sequential,
+            'set_gid_bit': cmdline_options.set_gid_bit,
+            'skip': cmdline_options.skip,
+            'skip_test_cases': cmdline_options.skip_test_cases,
+            'sticky_bit': cmdline_options.sticky_bit,
+            'stop': cmdline_options.stop,
+            'suffix_modules_path': cmdline_options.suffix_modules_path,
+            'test_report_env_filter': cmdline_options.test_report_env_filter,
+            'umask': cmdline_options.umask,
+            'upload_test_report': cmdline_options.upload_test_report,
+            'validate': not cmdline_options.force,
+            'valid_module_classes': module_classes(),
+        })
+
+    if build_options is not None:
+        active_build_options.update(build_options)
+
     # seed in defaults to make sure all build options are defined, and that build_option() doesn't fail on valid keys
     bo = copy.deepcopy(DEFAULT_BUILD_OPTIONS)
-    if build_options is not None:
-        bo.update(build_options)
+    bo.update(active_build_options)
+
     # BuildOptions is a singleton, so any future calls to BuildOptions will yield the same instance
     return BuildOptions(bo)
 
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 91b417fddb..4e1ece1bc9 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -33,7 +33,6 @@
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
 """
-import errno
 import os
 import re
 import shutil
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 4d15565caf..915f8909bb 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -174,7 +174,6 @@ def override_options(self):
                          None, 'store_true', False, 'p'),
             'set-gid-bit': ("Set group ID bit on newly created directories", None, 'store_true', False),
             'sticky-bit': ("Set sticky bit on newly created directories", None, 'store_true', False),
-            'skip-test-cases': ("Skip running test cases", None, 'store_true', False, 't'),
             'umask': ("umask to use (e.g. '022'); non-user write permissions on install directories are removed",
                       None, 'store', None),
             'optarch': ("Set architecture optimization, overriding native architecture optimizations",
@@ -277,6 +276,20 @@ def informative_options(self):
         self.log.debug("informative_options: descr %s opts %s" % (descr, opts))
         self.add_group_parser(opts, descr)
 
+    def testing_options(self):
+        # testing options
+        descr = ("Testing options", "Run application-specific test cases known to EasyBuild")
+
+        opts = OrderedDict({
+            'list-test-cases': ("List known test cases", None, 'store_true', False),
+            'run-test-cases': ("Run (specified) test cases (note: requires module to be available already)",
+                               None, 'store_or_None', False, 't'),
+            'skip-test-cases': ("Skip running test cases after build/install", None, 'store_true', False),
+        })
+
+        self.log.debug("testing_options: descr %s opts %s" % (descr, opts))
+        self.add_group_parser(opts, descr)
+
     def regtest_options(self):
         # regression test options
         descr = ("Regression test options", "Run and control an EasyBuild regression test.")
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 92967dae82..0e0743026e 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -34,11 +34,12 @@
 """
 import math
 import os
+import subprocess
 
 import easybuild.tools.config as config
 from easybuild.framework.easyblock import get_easyblock_instance
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
-from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.pbs_job import PbsJob, connect_to_server, disconnect_from_server, get_ppn
@@ -118,6 +119,33 @@ def tokey(dep):
     return jobs
 
 
+def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
+    """
+    Submit jobs.
+    @param ordered_ecs: list of easyconfigs, in the order they should be processed
+    @param cmd_line_opts: list of command line options (in 'longopt=value' form)
+    """
+    curdir = os.getcwd()
+
+    # the options to ignore (help options can't reach here)
+    ignore_opts = ['robot', 'job']
+
+    # generate_cmd_line returns the options in form --longopt=value
+    opts = [x for x in cmd_line_opts if not x.split('=')[0] in ['--%s' % y for y in ignore_opts]]
+
+    quoted_opts = subprocess.list2cmdline(opts)
+
+    command = "unset TMPDIR && cd %s && eb %%(spec)s %s" % (curdir, quoted_opts)
+    _log.info("Command template for jobs: %s" % command)
+    if not testing:
+        jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
+        txt = ["List of submitted jobs:"]
+        txt.extend(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in jobs])
+        txt.append("(%d jobs submitted)" % len(jobs))
+
+        print_msg("Submitted parallel build jobs, exiting now: %s" % '\n'.join(txt), log=_log)
+
+
 def create_job(build_command, easyconfig, output_dir=None, conn=None, ppn=None):
     """
     Creates a job, to build a *single* easyconfig
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
new file mode 100644
index 0000000000..ef2cad1e77
--- /dev/null
+++ b/easybuild/tools/robot.py
@@ -0,0 +1,255 @@
+# #
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Dependency resolution functionality, a.k.a. robot.
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+@author: Toon Willems (Ghent University)
+@author: Ward Poelmans (Ghent University)
+"""
+import os
+from vsc.utils import fancylogger
+
+from easybuild.framework.easyconfig.easyconfig import ActiveMNS, process_easyconfig, robot_find_easyconfig
+from easybuild.framework.easyconfig.tools import find_resolved_modules, skip_available
+from easybuild.tools.build_log import print_msg
+from easybuild.tools.config import build_option
+from easybuild.tools.filetools import det_common_path_prefix, search_file
+from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS
+from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
+from easybuild.tools.modules import modules_tool
+
+
+_log = fancylogger.getLogger('tools.robot', fname=False)
+
+
+def det_robot_path(robot_option, easyconfigs_paths, tweaked_ecs_path, pr_path, auto_robot=False):
+    """Determine robot path."""
+    # do not use robot option directly, it's not a list instance (and it shouldn't be modified)
+    robot_path = []
+    if not robot_option is None:
+        if robot_option:
+            robot_path = list(robot_option)
+            _log.info("Using robot path(s): %s" % robot_path)
+        else:
+            # if options.robot is not None and False, easyconfigs pkg install path could not be found (see options.py)
+            _log.error("No robot paths specified, and unable to determine easybuild-easyconfigs install path.")
+
+    if auto_robot:
+        robot_path.extend(easyconfigs_paths)
+        _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
+
+    if tweaked_ecs_path is not None:
+        robot_path.insert(0, tweaked_ecs_path)
+        _log.info("Prepended list of robot search paths with %s: %s" % (tweaked_ecs_path, robot_path))
+
+    if pr_path is not None:
+        robot_path.insert(0, pr_path)
+        _log.info("Prepended list of robot search paths with %s: %s" % (pr_path, robot_path))
+
+    return robot_path
+
+
+def print_dry_run(easyconfigs, short=False, build_specs=None):
+    """
+    Print dry run information
+    @param easyconfigs: list of easyconfig files
+    @param short: print short output (use a variable for the common prefix)
+    @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
+    """
+    lines = []
+    if build_option('robot_path') is None:
+        lines.append("Dry run: printing build status of easyconfigs")
+        all_specs = easyconfigs
+    else:
+        lines.append("Dry run: printing build status of easyconfigs and dependencies")
+        all_specs = resolve_dependencies(easyconfigs, build_specs=build_specs, retain_all_deps=True)
+
+    unbuilt_specs = skip_available(all_specs, testing=True)
+    dry_run_fmt = " * [%1s] %s (module: %s)"  # markdown compatible (list of items with checkboxes in front)
+
+    listed_ec_paths = [spec['spec'] for spec in easyconfigs]
+
+    var_name = 'CFGS'
+    common_prefix = det_common_path_prefix([spec['spec'] for spec in all_specs])
+    # only allow short if common prefix is long enough
+    short = short and common_prefix is not None and len(common_prefix) > len(var_name) * 2
+    for spec in all_specs:
+        if spec in unbuilt_specs:
+            ans = ' '
+        elif build_option('force') and spec['spec'] in listed_ec_paths:
+            ans = 'F'
+        else:
+            ans = 'x'
+
+        if spec['ec'].short_mod_name != spec['ec'].full_mod_name:
+            mod = "%s | %s" % (spec['ec'].mod_subdir, spec['ec'].short_mod_name)
+        else:
+            mod = spec['ec'].full_mod_name
+
+        if short:
+            item = os.path.join('$%s' % var_name, spec['spec'][len(common_prefix) + 1:])
+        else:
+            item = spec['spec']
+        lines.append(dry_run_fmt % (ans, item, mod))
+
+    if short:
+        # insert after 'Dry run:' message
+        lines.insert(1, "%s=%s" % (var_name, common_prefix))
+    silent = build_option('silent')
+    print_msg('\n'.join(lines), log=_log, silent=silent, prefix=False)
+
+
+def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
+    """
+    Work through the list of easyconfigs to determine an optimal order
+    @param unprocessed: list of easyconfigs
+    @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
+    """
+
+    robot = build_option('robot_path')
+
+    retain_all_deps = build_option('retain_all_deps') or retain_all_deps
+    if retain_all_deps:
+        # assume that no modules are available when forced, to retain all dependencies
+        avail_modules = []
+        _log.info("Forcing all dependencies to be retained.")
+    else:
+        # Get a list of all available modules (format: [(name, installversion), ...])
+        avail_modules = modules_tool().available()
+
+        if len(avail_modules) == 0:
+            _log.warning("No installed modules. Your MODULEPATH is probably incomplete: %s" % os.getenv('MODULEPATH'))
+
+    ordered_ecs = []
+    # all available modules can be used for resolving dependencies except those that will be installed
+    being_installed = [p['full_mod_name'] for p in unprocessed]
+    avail_modules = [m for m in avail_modules if not m in being_installed]
+
+    _log.debug('unprocessed before resolving deps: %s' % unprocessed)
+
+    # resolve all dependencies, put a safeguard in place to avoid an infinite loop (shouldn't occur though)
+    irresolvable = []
+    loopcnt = 0
+    maxloopcnt = 10000
+    while unprocessed:
+        # make sure this stops, we really don't want to get stuck in an infinite loop
+        loopcnt += 1
+        if loopcnt > maxloopcnt:
+            tup = (maxloopcnt, unprocessed, irresolvable)
+            msg = "Maximum loop cnt %s reached, so quitting (unprocessed: %s, irresolvable: %s)" % tup
+            _log.error(msg)
+
+        # first try resolving dependencies without using external dependencies
+        last_processed_count = -1
+        while len(avail_modules) > last_processed_count:
+            last_processed_count = len(avail_modules)
+            more_ecs, unprocessed, avail_modules = find_resolved_modules(unprocessed, avail_modules)
+            for ec in more_ecs:
+                if not ec['full_mod_name'] in [x['full_mod_name'] for x in ordered_ecs]:
+                    ordered_ecs.append(ec)
+
+        # robot: look for existing dependencies, add them
+        if robot and unprocessed:
+
+            # rely on EasyBuild module naming scheme when resolving dependencies, since we know that will
+            # generate sensible module names that include the necessary information for the resolution to work
+            # (name, version, toolchain, versionsuffix)
+            being_installed = [EasyBuildMNS().det_full_module_name(p['ec']) for p in unprocessed]
+
+            additional = []
+            for i, entry in enumerate(unprocessed):
+                # do not choose an entry that is being installed in the current run
+                # if they depend, you probably want to rebuild them using the new dependency
+                deps = entry['dependencies']
+                candidates = [d for d in deps if not EasyBuildMNS().det_full_module_name(d) in being_installed]
+                if len(candidates) > 0:
+                    cand_dep = candidates[0]
+                    # find easyconfig, might not find any
+                    _log.debug("Looking for easyconfig for %s" % str(cand_dep))
+                    # note: robot_find_easyconfig may return None
+                    path = robot_find_easyconfig(cand_dep['name'], det_full_ec_version(cand_dep))
+
+                    if path is None:
+                        # no easyconfig found for dependency, add to list of irresolvable dependencies
+                        if cand_dep not in irresolvable:
+                            _log.debug("Irresolvable dependency found: %s" % cand_dep)
+                            irresolvable.append(cand_dep)
+                        # remove irresolvable dependency from list of dependencies so we can continue
+                        entry['dependencies'].remove(cand_dep)
+                    else:
+                        _log.info("Robot: resolving dependency %s with %s" % (cand_dep, path))
+                        # build specs should not be passed down to resolved dependencies,
+                        # to avoid that e.g. --try-toolchain trickles down into the used toolchain itself
+                        hidden = cand_dep.get('hidden', False)
+                        processed_ecs = process_easyconfig(path, validate=not retain_all_deps, hidden=hidden)
+
+                        # ensure that selected easyconfig provides required dependency
+                        mods = [spec['ec'].full_mod_name for spec in processed_ecs]
+                        dep_mod_name = ActiveMNS().det_full_module_name(cand_dep)
+                        if not dep_mod_name in mods:
+                            tup = (path, dep_mod_name, mods)
+                            _log.error("easyconfig file %s does not contain module %s (mods: %s)" % tup)
+
+                        for ec in processed_ecs:
+                            if not ec in unprocessed + additional:
+                                additional.append(ec)
+                                _log.debug("Added %s as dependency of %s" % (ec, entry))
+                else:
+                    mod_name = EasyBuildMNS().det_full_module_name(entry['ec'])
+                    _log.debug("No more candidate dependencies to resolve for %s" % mod_name)
+
+            # add additional (new) easyconfigs to list of stuff to process
+            unprocessed.extend(additional)
+
+        elif not robot:
+            # no use in continuing if robot is not enabled, dependencies won't be resolved anyway
+            irresolvable = [dep for x in unprocessed for dep in x['dependencies']]
+            break
+
+    if irresolvable:
+        _log.warning("Irresolvable dependencies (details): %s" % irresolvable)
+        irresolvable_mods_eb = [EasyBuildMNS().det_full_module_name(dep) for dep in irresolvable]
+        _log.warning("Irresolvable dependencies (EasyBuild module names): %s" % ', '.join(irresolvable_mods_eb))
+        irresolvable_mods = [ActiveMNS().det_full_module_name(dep) for dep in irresolvable]
+        _log.error('Irresolvable dependencies encountered: %s' % ', '.join(irresolvable_mods))
+
+    _log.info("Dependency resolution complete, building as follows:\n%s" % ordered_ecs)
+    return ordered_ecs
+
+
+def search_easyconfigs(query, short=False):
+    """Search for easyconfigs, if a query is provided."""
+    search_path = [os.getcwd()]
+    robot_path = build_option('robot_path')
+    if robot_path:
+        search_path = robot_path
+    ignore_dirs = build_option('ignore_dirs')
+    silent = build_option('silent')
+    search_file(search_path, query, short=short, ignore_dirs=ignore_dirs, silent=silent)
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index fa579e2107..0914b8c856 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -42,15 +42,16 @@
 
 import easybuild.tools.config as config
 from easybuild.framework.easyblock import build_easyconfigs
-from easybuild.framework.easyconfig.tools import process_easyconfig, resolve_dependencies
+from easybuild.framework.easyconfig.tools import process_easyconfig
 from easybuild.framework.easyconfig.tools import skip_available
-from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import find_easyconfigs, mkdir, read_file
+from easybuild.tools.filetools import find_easyconfigs, mkdir, read_file, write_file
 from easybuild.tools.github import create_gist, post_comment_in_issue
 from easybuild.tools.jenkins import aggregate_xml_in_dirs
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
+from easybuild.tools.robot import resolve_dependencies
 from easybuild.tools.systemtools import get_system_info
 from easybuild.tools.version import FRAMEWORK_VERSION, EASYBLOCKS_VERSION
 from vsc.utils import fancylogger
@@ -299,3 +300,35 @@ def post_easyconfigs_pr_test_report(pr_nr, test_report, msg, init_session_state,
 
     msg = "Test report uploaded to %s and mentioned in a comment in easyconfigs PR#%s" % (gist_url, pr_nr)
     return msg
+
+
+def overall_test_report(ecs_with_res, orig_cnt, success, msg, init_session_state):
+    """
+    Upload/dump overall test report
+    @param ecs_with_res: processed easyconfigs with build result (success/failure)
+    @param orig_cnt: number of original easyconfig paths
+    @param success: boolean indicating whether all builds were successful
+    @param msg: message to be included in test report
+    @param init_session_state: initial session state info to include in test report
+    """
+    dump_path = build_option('dump_test_report')
+    pr_nr = build_option('from_pr')
+    upload = build_option('upload_test_report')
+
+    if upload:
+        msg = msg + " (%d easyconfigs in this PR)" % orig_cnt
+        test_report = create_test_report(msg, ecs_with_res, init_session_state, pr_nr=pr_nr, gist_log=True)
+        if pr_nr:
+            # upload test report to gist and issue a comment in the PR to notify
+            msg = post_easyconfigs_pr_test_report(pr_nr, test_report, msg, init_session_state, success)
+            print_msg(msg)
+        else:
+            # only upload test report as a gist
+            gist_url = upload_test_report_as_gist(test_report)
+            print_msg("Test report uploaded to %s" % gist_url)
+    else:
+        test_report = create_test_report(msg, ecs_with_res, init_session_state)
+    _log.debug("Test report: %s" % test_report)
+    if dump_path is not None:
+        write_file(dump_path, test_report)
+        _log.info("Test report dumped to %s" % dump_path)
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 395b4c127a..637d56061e 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -32,9 +32,10 @@
 from unittest import TestLoader, main
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 
-from easybuild.framework.easyconfig.tools import process_easyconfig, resolve_dependencies
+from easybuild.framework.easyconfig.tools import process_easyconfig
 from easybuild.tools import config, parallelbuild
 from easybuild.tools.parallelbuild import PbsJob, build_easyconfigs_in_parallel
+from easybuild.tools.robot import resolve_dependencies
 
 
 def mock(*args, **kwargs):
diff --git a/test/framework/robot.py b/test/framework/robot.py
index 6b83103e42..7beee4cca1 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -35,13 +35,16 @@
 from unittest import main as unittestmain
 
 import easybuild.framework.easyconfig.tools as ectools
-from easybuild.framework.easyconfig.tools import resolve_dependencies, skip_available
+import easybuild.tools.robot as robot
+from easybuild.framework.easyconfig.tools import skip_available
 from easybuild.tools import config, modules
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.robot import resolve_dependencies
 from test.framework.utilities import find_full_path
 
 ORIG_MODULES_TOOL = modules.modules_tool
-ORIG_MAIN_MODULES_TOOL = ectools.modules_tool
+ORIG_ECTOOLS_MODULES_TOOL = ectools.modules_tool
+ORIG_ROBOT_MODULES_TOOL = robot.modules_tool
 ORIG_MODULE_FUNCTION = os.environ.get('module', None)
 
 
@@ -82,6 +85,7 @@ def setUp(self):
         # replace Modules class with something we have control over
         config.modules_tool = mock_module
         ectools.modules_tool = mock_module
+        robot.modules_tool = mock_module
         os.environ['module'] = "() {  eval `/bin/echo $*`\n}"
 
         self.base_easyconfig_dir = find_full_path(os.path.join("test", "framework", "easyconfigs"))
@@ -147,7 +151,9 @@ def test_resolve_dependencies(self):
         self.assertEqual(len(res), 4)  # hidden dep toy/.0.0-deps (+1) depends on (fake) ictce/4.1.13 (+1)
         self.assertEqual('gzip/1.4', res[0]['full_mod_name'])
         self.assertEqual('foo/1.2.3', res[-1]['full_mod_name'])
-        self.assertTrue('toy/.0.0-deps' in [ec['full_mod_name'] for ec in res])
+        full_mod_names = [ec['full_mod_name'] for ec in res]
+        self.assertTrue('toy/.0.0-deps' in full_mod_names)
+        self.assertTrue('ictce/4.1.13' in full_mod_names)
 
         # here we have included a dependency in the easyconfig list
         easyconfig['full_mod_name'] = 'gzip/1.4'
@@ -276,7 +282,8 @@ def tearDown(self):
         super(RobotTest, self).tearDown()
 
         config.modules_tool = ORIG_MODULES_TOOL
-        ectools.modules_tool = ORIG_MAIN_MODULES_TOOL
+        ectools.modules_tool = ORIG_ECTOOLS_MODULES_TOOL
+        robot.modules_tool = ORIG_ROBOT_MODULES_TOOL
         if ORIG_MODULE_FUNCTION is not None:
             os.environ['module'] = ORIG_MODULE_FUNCTION
         else:
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 83621c75ea..39ab091e3f 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -252,7 +252,7 @@ def init_config(args=None, build_options=None):
         }
     if 'suffix_modules_path' not in build_options:
         build_options.update({'suffix_modules_path': GENERAL_CLASS})
-    config.init_build_options(build_options)
+    config.init_build_options(build_options=build_options)
 
     return eb_go.options
 

From ac0198dd362e65f7958a34a3a8d3bfa1e157324f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Oct 2014 14:33:39 +0200
Subject: [PATCH 0236/1356] cleanup det_easyconfig_paths in easyconfig.tools

---
 easybuild/framework/easyconfig/tools.py | 79 ++++++++++++-------------
 easybuild/main.py                       |  3 +-
 2 files changed, 39 insertions(+), 43 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index f020231150..0e5d6359a3 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -218,14 +218,14 @@ def get_paths_for(subdir="easyconfigs", robot_path=None):
 
 def alt_easyconfig_paths(tmpdir, tweaked_ecs=False, from_pr=False):
     """Obtain alternative paths for easyconfig files."""
-    # prepend robot path with location where tweaked easyconfigs will be placed
+    # path where tweaked easyconfigs will be placed
     tweaked_ecs_path = None
     if tweaked_ecs:
         tweaked_ecs_path = os.path.join(tmpdir, 'tweaked_easyconfigs')
 
+    # path where files touched in PR will be downloaded to
     pr_path = None
     if from_pr:
-        # extend robot search path with location where files touch in PR will be downloaded to
         pr_path = os.path.join(tmpdir, "files_pr%s" % from_pr)
 
     return tweaked_ecs_path, pr_path
@@ -238,54 +238,51 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
     @param from_pr: pull request number to fetch easyconfigs from
     @param easyconfigs_pkg_paths: paths to installed easyconfigs package
     """
-    paths = []
-
     if easyconfigs_pkg_paths is None:
         easyconfigs_pkg_paths = []
     ignore_dirs = build_option('ignore_dirs')
 
-    if len(orig_paths) == 0:
-        if from_pr:
-            pr_files = fetch_easyconfigs_from_pr(from_pr)
-            paths = [(path, False) for path in pr_files if path.endswith('.eb')]
-    else:
+    ec_files = []
+    if not orig_paths and from_pr:
+        pr_files = fetch_easyconfigs_from_pr(from_pr)
+        ec_files = [path for path in pr_files if path.endswith('.eb')]
+    elif orig_paths and easyconfigs_pkg_paths:
         # look for easyconfigs with relative paths in easybuild-easyconfigs package,
         # unless they were found at the given relative paths
-        if easyconfigs_pkg_paths:
-            # determine which easyconfigs files need to be found, if any
-            ecs_to_find = []
-            for idx, orig_path in enumerate(orig_paths):
-                if orig_path == os.path.basename(orig_path) and not os.path.exists(orig_path):
-                    ecs_to_find.append((idx, orig_path))
-            _log.debug("List of easyconfig files to find: %s" % ecs_to_find)
-
-            # find missing easyconfigs by walking paths with installed easyconfig files
-            for path in easyconfigs_pkg_paths:
-                _log.debug("Looking for missing easyconfig files (%d left) in %s..." % (len(ecs_to_find), path))
-                for (subpath, dirnames, filenames) in os.walk(path, topdown=True):
-                    for idx, orig_path in ecs_to_find[:]:
-                        if orig_path in filenames:
-                            full_path = os.path.join(subpath, orig_path)
-                            _log.info("Found %s in %s: %s" % (orig_path, path, full_path))
-                            orig_paths[idx] = full_path
-                            # if file was found, stop looking for it (first hit wins)
-                            ecs_to_find.remove((idx, orig_path))
-
-                    # stop os.walk insanity as soon as we have all we need (os.walk loop)
-                    if len(ecs_to_find) == 0:
-                        break
-
-                    # ignore subdirs specified to be ignored by replacing items in dirnames list used by os.walk
-                    dirnames[:] = [d for d in dirnames if not d in ignore_dirs]
-
-                # stop os.walk insanity as soon as we have all we need (paths loop)
-                if len(ecs_to_find) == 0:
+        ec_files = orig_paths[:]
+
+        # determine which easyconfigs files need to be found, if any
+        ecs_to_find = []
+        for idx, ec_file in enumerate(ec_files):
+            if ec_file == os.path.basename(ec_file) and not os.path.exists(ec_file):
+                ecs_to_find.append((idx, ec_file))
+        _log.debug("List of easyconfig files to find: %s" % ecs_to_find)
+
+        # find missing easyconfigs by walking paths with installed easyconfig files
+        for path in easyconfigs_pkg_paths:
+            _log.debug("Looking for missing easyconfig files (%d left) in %s..." % (len(ecs_to_find), path))
+            for (subpath, dirnames, filenames) in os.walk(path, topdown=True):
+                for idx, orig_path in ecs_to_find[:]:
+                    if orig_path in filenames:
+                        full_path = os.path.join(subpath, orig_path)
+                        _log.info("Found %s in %s: %s" % (orig_path, path, full_path))
+                        ec_files[idx] = full_path
+                        # if file was found, stop looking for it (first hit wins)
+                        ecs_to_find.remove((idx, orig_path))
+
+                # stop os.walk insanity as soon as we have all we need (os.walk loop)
+                if not ecs_to_find:
                     break
 
-        # indicate that specified paths do not contain generated easyconfig files
-        paths = [(path, False) for path in orig_paths]
+                # ignore subdirs specified to be ignored by replacing items in dirnames list used by os.walk
+                dirnames[:] = [d for d in dirnames if not d in ignore_dirs]
 
-    return paths
+            # stop os.walk insanity as soon as we have all we need (outer loop)
+            if not ecs_to_find:
+                break
+
+    # indicate that specified paths do not contain generated easyconfig files
+    return [(ec_file, False) for ec_file in ec_files]
 
 
 def parse_easyconfigs(paths):
diff --git a/easybuild/main.py b/easybuild/main.py
index 19772ac4c1..0716162816 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -49,8 +49,7 @@
 import easybuild.tools.options as eboptions
 from easybuild.framework.easyblock import EasyBlock, build_and_install_one
 from easybuild.framework.easyconfig.tools import alt_easyconfig_paths, dep_graph, det_easyconfig_paths
-from easybuild.framework.easyconfig.tools import get_paths_for, parse_easyconfigs
-from easybuild.framework.easyconfig.tools import skip_available
+from easybuild.framework.easyconfig.tools import get_paths_for, parse_easyconfigs, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_path, tweak
 from easybuild.tools.config import get_repository, get_repositorypath, set_tmpdir
 from easybuild.tools.filetools import cleanup, write_file

From 9498086e405557a31b03e68239e6228913bdfe13 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Oct 2014 15:58:33 +0200
Subject: [PATCH 0237/1356] keep track of original work dir in EasyBlock,
 change back to it before installing extensions

---
 easybuild/framework/easyblock.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index f988295cfe..c8cba7d388 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -111,6 +111,8 @@ def __init__(self, ec):
         Initialize the EasyBlock instance.
         @param ec: a parsed easyconfig file (EasyConfig instance)
         """
+        # keep track of original working directory, so we can go back there
+        self.orig_workdir = os.getcwd()
 
         # list of patch/source files, along with checksums
         self.patches = []
@@ -912,7 +914,6 @@ def make_module_req(self):
 
         if os.path.exists(self.installdir):
             try:
-                cwd = os.getcwd()
                 os.chdir(self.installdir)
             except OSError, err:
                 self.log.error("Failed to change to %s: %s" % (self.installdir, err))
@@ -924,9 +925,9 @@ def make_module_req(self):
                     if paths:
                         txt += self.moduleGenerator.prepend_paths(key, paths)
             try:
-                os.chdir(cwd)
+                os.chdir(self.orig_workdir)
             except OSError, err:
-                self.log.error("Failed to change back to %s: %s" % (cwd, err))
+                self.log.error("Failed to change back to %s: %s" % (self.orig_workdir, err))
         else:
             txt = ""
         return txt
@@ -1376,8 +1377,8 @@ def extensions_step(self, fetch=False):
         for ext in self.exts:
             self.log.debug("Starting extension %s" % ext['name'])
 
-            # always go back to build dir to avoid running stuff from a dir that no longer exists
-            os.chdir(self.builddir)
+            # always go back to original work dir to avoid running stuff from a dir that no longer exists
+            os.chdir(self.orig_workdir)
 
             inst = None
 
@@ -1622,7 +1623,7 @@ def cleanup_step(self):
         """
         if not self.build_in_installdir and build_option('cleanup_builddir'):
             try:
-                os.chdir(build_path())  # make sure we're out of the dir we're removing
+                os.chdir(self.orig_workdir)  # make sure we're out of the dir we're removing
 
                 self.log.info("Cleaning up builddir %s (in %s)" % (self.builddir, os.getcwd()))
 
@@ -1675,8 +1676,7 @@ def test_cases_step(self):
         Run provided test cases.
         """
         for test in self.cfg['tests']:
-            # Current working dir no longer exists
-            os.chdir(self.installdir)
+            os.chdir(self.orig_workdir)
             if os.path.isabs(test):
                 path = test
             else:

From 13e244495571176a7fc777e947008f690252137e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Oct 2014 15:58:47 +0200
Subject: [PATCH 0238/1356] fix use of print_error in main

---
 easybuild/main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 0716162816..c6fff468c0 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -302,4 +302,4 @@ def main(testing_data=(None, None, None)):
     try:
         main()
     except EasyBuildError, e:
-        print_error("ERROR: %s\n" % e.msg)
+        print_error(e.msg)

From 7fa1d54a427311a01b27b30fa8b89f5cef7d9b99 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Oct 2014 16:38:57 +0200
Subject: [PATCH 0239/1356] rework listing of build options and retrieving them
 from parsed cmdline options

---
 easybuild/tools/config.py | 139 ++++++++++++++++++--------------------
 1 file changed, 66 insertions(+), 73 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 16899f1d06..837f1fe9b8 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -67,49 +67,64 @@
     'subdir_software': 'software',
 }
 
-
-DEFAULT_BUILD_OPTIONS = {
-    'aggregate_regtest': None,
-    'allow_modules_tool_mismatch': False,
-    'build_specs': None,
-    'check_osdeps': True,
-    'filter_deps': None,
-    'cleanup_builddir': True,
-    'command_line': None,
-    'debug': False,
-    'dry_run': False,
-    'dump_test_report': None,
-    'easyblock': None,
-    'experimental': False,
-    'force': False,
-    'from_pr': None,
-    'github_user': None,
-    'group': None,
-    'hidden': False,
-    'ignore_dirs': None,
-    'modules_footer': None,
-    'only_blocks': None,
-    'optarch': None,
-    'pr_path': None,
-    'recursive_mod_unload': False,
-    'regtest_output_dir': None,
-    'retain_all_deps': False,
-    'robot_path': None,
-    'sequential': False,
-    'set_gid_bit': False,
-    'silent': False,
-    'skip': None,
-    'skip_test_cases': False,
-    'sticky_bit': False,
-    'stop': None,
-    'suffix_modules_path': None,
-    'test_report_env_filter': None,
-    'try_to_generate': False,
-    'umask': None,
-    'upload_test_report': False,
-    'valid_module_classes': None,
-    'valid_stops': None,
-    'validate': True,
+# build options that have a perfectly matching command line option, listed by default value
+BUILD_OPTIONS_CMDLINE = {
+    None: [
+        'aggregate_regtest',
+        'dump_test_report',
+        'easyblock',
+        'filter_deps',
+        'from_pr',
+        'github_user',
+        'group',
+        'ignore_dirs',
+        'modules_footer',
+        'only_blocks',
+        'optarch',
+        'regtest_output_dir',
+        'skip',
+        'stop',
+        'suffix_modules_path',
+        'test_report_env_filter',
+        'umask',
+    ],
+    False: [
+        'allow_modules_tool_mismatch',
+        'debug',
+        'experimental',
+        'force',
+        'hidden',
+        'recursive_mod_unload',
+        'sequential',
+        'set_gid_bit',
+        'skip_test_cases',
+        'sticky_bit',
+        'upload_test_report',
+    ],
+    True: [
+        'cleanup_builddir',
+    ],
+}
+# build option that do not have a perfectly matching command line option
+BUILD_OPTIONS_OTHER = {
+    None: [
+        'build_specs',
+        'command_line',
+        'pr_path',
+        'robot_path',
+        'valid_module_classes',
+        'valid_stops',
+    ],
+    False: [
+        'dry_run',
+        'retain_all_deps',
+        'silent',
+        'try_to_generate',
+    ],
+    True: [
+        'check_osdeps',
+        'validate',
+    ],
 }
 
 
@@ -226,7 +241,7 @@ class BuildOptions(FrozenDictKnownKeys):
     # singleton metaclass: only one instance is created
     __metaclass__ = Singleton
 
-    KNOWN_KEYS = DEFAULT_BUILD_OPTIONS.keys()
+    KNOWN_KEYS = [k for kss in [BUILD_OPTIONS_CMDLINE, BUILD_OPTIONS_OTHER] for ks in kss.values() for k in ks]
 
 
 def get_user_easybuild_dir():
@@ -387,38 +402,13 @@ def init_build_options(build_options=None, cmdline_options=None):
             _log.info("Ignoring OS dependencies for --dep-graph/--dry-run")
             cmdline_options.ignore_osdeps = True
 
+        cmdline_build_option_names = [k for k in ks for ks in BUILD_OPTIONS_CMDLINE.values()]
+        active_build_options.update(dict([(key, getattr(cmdline_options, key)) for key in cmdline_build_option_names]))
+        # other options which can be derived but have no perfectly matching cmdline option
         active_build_options.update({
-            'aggregate_regtest': cmdline_options.aggregate_regtest,
-            'allow_modules_tool_mismatch': cmdline_options.allow_modules_tool_mismatch,
             'check_osdeps': not cmdline_options.ignore_osdeps,
-            'filter_deps': cmdline_options.filter_deps,
-            'cleanup_builddir': cmdline_options.cleanup_builddir,
-            'debug': cmdline_options.debug,
             'dry_run': cmdline_options.dry_run or cmdline_options.dry_run_short,
-            'dump_test_report': cmdline_options.dump_test_report,
-            'easyblock': cmdline_options.easyblock,
-            'experimental': cmdline_options.experimental,
-            'force': cmdline_options.force,
-            'github_user': cmdline_options.github_user,
-            'group': cmdline_options.group,
-            'hidden': cmdline_options.hidden,
-            'ignore_dirs': cmdline_options.ignore_dirs,
-            'modules_footer': cmdline_options.modules_footer,
-            'only_blocks': cmdline_options.only_blocks,
-            'optarch': cmdline_options.optarch,
-            'recursive_mod_unload': cmdline_options.recursive_module_unload,
-            'regtest_output_dir': cmdline_options.regtest_output_dir,
             'retain_all_deps': retain_all_deps,
-            'sequential': cmdline_options.sequential,
-            'set_gid_bit': cmdline_options.set_gid_bit,
-            'skip': cmdline_options.skip,
-            'skip_test_cases': cmdline_options.skip_test_cases,
-            'sticky_bit': cmdline_options.sticky_bit,
-            'stop': cmdline_options.stop,
-            'suffix_modules_path': cmdline_options.suffix_modules_path,
-            'test_report_env_filter': cmdline_options.test_report_env_filter,
-            'umask': cmdline_options.umask,
-            'upload_test_report': cmdline_options.upload_test_report,
             'validate': not cmdline_options.force,
             'valid_module_classes': module_classes(),
         })
@@ -427,7 +417,10 @@ def init_build_options(build_options=None, cmdline_options=None):
         active_build_options.update(build_options)
 
     # seed in defaults to make sure all build options are defined, and that build_option() doesn't fail on valid keys
-    bo = copy.deepcopy(DEFAULT_BUILD_OPTIONS)
+    bo = {}
+    for build_options_by_default in [BUILD_OPTIONS_CMDLINE, BUILD_OPTIONS_OTHER]:
+        for default in build_options_by_default:
+            bo.update(dict([(opt, default) for opt in build_options_by_default[default]]))
     bo.update(active_build_options)
 
     # BuildOptions is a singleton, so any future calls to BuildOptions will yield the same instance

From e7c326fd23d312d541b5efb9ff327f239d151bc1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Oct 2014 16:42:36 +0200
Subject: [PATCH 0240/1356] retract including testing options for now

---
 easybuild/tools/options.py | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 915f8909bb..4d15565caf 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -174,6 +174,7 @@ def override_options(self):
                          None, 'store_true', False, 'p'),
             'set-gid-bit': ("Set group ID bit on newly created directories", None, 'store_true', False),
             'sticky-bit': ("Set sticky bit on newly created directories", None, 'store_true', False),
+            'skip-test-cases': ("Skip running test cases", None, 'store_true', False, 't'),
             'umask': ("umask to use (e.g. '022'); non-user write permissions on install directories are removed",
                       None, 'store', None),
             'optarch': ("Set architecture optimization, overriding native architecture optimizations",
@@ -276,20 +277,6 @@ def informative_options(self):
         self.log.debug("informative_options: descr %s opts %s" % (descr, opts))
         self.add_group_parser(opts, descr)
 
-    def testing_options(self):
-        # testing options
-        descr = ("Testing options", "Run application-specific test cases known to EasyBuild")
-
-        opts = OrderedDict({
-            'list-test-cases': ("List known test cases", None, 'store_true', False),
-            'run-test-cases': ("Run (specified) test cases (note: requires module to be available already)",
-                               None, 'store_or_None', False, 't'),
-            'skip-test-cases': ("Skip running test cases after build/install", None, 'store_true', False),
-        })
-
-        self.log.debug("testing_options: descr %s opts %s" % (descr, opts))
-        self.add_group_parser(opts, descr)
-
     def regtest_options(self):
         # regression test options
         descr = ("Regression test options", "Run and control an EasyBuild regression test.")

From a5f401c374581684ae37de15f17013af35ab539e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Oct 2014 17:11:34 +0200
Subject: [PATCH 0241/1356] resolve remaining remarks

---
 easybuild/main.py                | 12 ++++++++----
 easybuild/tools/config.py        |  5 +++--
 easybuild/tools/parallelbuild.py | 14 ++++++++------
 easybuild/tools/robot.py         |  9 ++++-----
 easybuild/tools/testing.py       | 11 +++++++----
 5 files changed, 30 insertions(+), 21 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index c6fff468c0..763b28aaa1 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -54,7 +54,7 @@
 from easybuild.tools.config import get_repository, get_repositorypath, set_tmpdir
 from easybuild.tools.filetools import cleanup, write_file
 from easybuild.tools.options import process_software_build_specs
-from easybuild.tools.robot import det_robot_path, print_dry_run, resolve_dependencies, search_easyconfigs
+from easybuild.tools.robot import det_robot_path, dry_run, resolve_dependencies, search_easyconfigs
 from easybuild.tools.parallelbuild import submit_jobs
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.testing import create_test_report, overall_test_report, regtest, session_module_list, session_state
@@ -236,7 +236,8 @@ def main(testing_data=(None, None, None)):
 
     # dry_run: print all easyconfigs and dependencies, and whether they are already built
     if options.dry_run or options.dry_run_short:
-        print_dry_run(easyconfigs, short=not options.dry_run, build_specs=build_specs)
+        txt = dry_run(easyconfigs, short=not options.dry_run, build_specs=build_specs)
+        print_msg(txt, log=_log, silent=testing, prefix=False)
 
     # cleanup and exit after dry run, searching easyconfigs or submitting regression test
     if any([options.dry_run, options.dry_run_short, options.regtest, options.search, options.search_short]):
@@ -263,8 +264,9 @@ def main(testing_data=(None, None, None)):
 
     # submit build as job(s), clean up and exit
     if options.job:
-        submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
+        job_info_txt = submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
         if not testing:
+            print_msg("Submitted parallel build jobs, exiting now: %s" % job_info_txt)
             cleanup(logfile, eb_tmpdir, testing)
             sys.exit(0)
 
@@ -283,7 +285,9 @@ def main(testing_data=(None, None, None)):
     repo.cleanup()
 
     # dump/upload overall test report
-    overall_test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
+    test_report_msg = overall_test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
+    if test_report_msg is not None:
+        print_msg(test_report_msg)
 
     print_msg(success_msg, log=_log, silent=testing)
 
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 837f1fe9b8..8de818bbf1 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -94,7 +94,6 @@
         'experimental',
         'force',
         'hidden',
-        'recursive_mod_unload',
         'sequential',
         'set_gid_bit',
         'skip_test_cases',
@@ -117,6 +116,7 @@
     ],
     False: [
         'dry_run',
+        'recursive_mod_unload',
         'retain_all_deps',
         'silent',
         'try_to_generate',
@@ -402,12 +402,13 @@ def init_build_options(build_options=None, cmdline_options=None):
             _log.info("Ignoring OS dependencies for --dep-graph/--dry-run")
             cmdline_options.ignore_osdeps = True
 
-        cmdline_build_option_names = [k for k in ks for ks in BUILD_OPTIONS_CMDLINE.values()]
+        cmdline_build_option_names = [k for ks in BUILD_OPTIONS_CMDLINE.values() for k in ks]
         active_build_options.update(dict([(key, getattr(cmdline_options, key)) for key in cmdline_build_option_names]))
         # other options which can be derived but have no perfectly matching cmdline option
         active_build_options.update({
             'check_osdeps': not cmdline_options.ignore_osdeps,
             'dry_run': cmdline_options.dry_run or cmdline_options.dry_run_short,
+            'recursive_mod_unload': cmdline_options.recursive_module_unload,
             'retain_all_deps': retain_all_deps,
             'validate': not cmdline_options.force,
             'valid_module_classes': module_classes(),
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 0e0743026e..ac52b20b10 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -137,13 +137,15 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
 
     command = "unset TMPDIR && cd %s && eb %%(spec)s %s" % (curdir, quoted_opts)
     _log.info("Command template for jobs: %s" % command)
-    if not testing:
+    job_info_lines = []
+    if testing:
+        _log.debug("Skipping actual submission of jobs since testing mode is enabled")
+    else:
         jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
-        txt = ["List of submitted jobs:"]
-        txt.extend(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in jobs])
-        txt.append("(%d jobs submitted)" % len(jobs))
-
-        print_msg("Submitted parallel build jobs, exiting now: %s" % '\n'.join(txt), log=_log)
+        job_info_lines = ["List of submitted jobs:"]
+        job_info_lines.extend(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in jobs])
+        job_info_lines.append("(%d jobs submitted)" % len(jobs))
+        return '\n'.join(job_info_lines)
 
 
 def create_job(build_command, easyconfig, output_dir=None, conn=None, ppn=None):
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index ef2cad1e77..f17a888842 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -38,7 +38,6 @@
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS, process_easyconfig, robot_find_easyconfig
 from easybuild.framework.easyconfig.tools import find_resolved_modules, skip_available
-from easybuild.tools.build_log import print_msg
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import det_common_path_prefix, search_file
 from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS
@@ -53,7 +52,7 @@ def det_robot_path(robot_option, easyconfigs_paths, tweaked_ecs_path, pr_path, a
     """Determine robot path."""
     # do not use robot option directly, it's not a list instance (and it shouldn't be modified)
     robot_path = []
-    if not robot_option is None:
+    if robot_option is not None:
         if robot_option:
             robot_path = list(robot_option)
             _log.info("Using robot path(s): %s" % robot_path)
@@ -76,7 +75,7 @@ def det_robot_path(robot_option, easyconfigs_paths, tweaked_ecs_path, pr_path, a
     return robot_path
 
 
-def print_dry_run(easyconfigs, short=False, build_specs=None):
+def dry_run(easyconfigs, short=False, build_specs=None):
     """
     Print dry run information
     @param easyconfigs: list of easyconfig files
@@ -122,8 +121,7 @@ def print_dry_run(easyconfigs, short=False, build_specs=None):
     if short:
         # insert after 'Dry run:' message
         lines.insert(1, "%s=%s" % (var_name, common_prefix))
-    silent = build_option('silent')
-    print_msg('\n'.join(lines), log=_log, silent=silent, prefix=False)
+    return '\n'.join(lines)
 
 
 def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
@@ -131,6 +129,7 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
     Work through the list of easyconfigs to determine an optimal order
     @param unprocessed: list of easyconfigs
     @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
+    @param retain_all_deps: boolean indicating whether all dependencies should be retained, regardless of availability
     """
 
     robot = build_option('robot_path')
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index 0914b8c856..838736e6bf 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -44,7 +44,7 @@
 from easybuild.framework.easyblock import build_easyconfigs
 from easybuild.framework.easyconfig.tools import process_easyconfig
 from easybuild.framework.easyconfig.tools import skip_available
-from easybuild.tools.build_log import EasyBuildError, print_msg
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import find_easyconfigs, mkdir, read_file, write_file
 from easybuild.tools.github import create_gist, post_comment_in_issue
@@ -320,15 +320,18 @@ def overall_test_report(ecs_with_res, orig_cnt, success, msg, init_session_state
         test_report = create_test_report(msg, ecs_with_res, init_session_state, pr_nr=pr_nr, gist_log=True)
         if pr_nr:
             # upload test report to gist and issue a comment in the PR to notify
-            msg = post_easyconfigs_pr_test_report(pr_nr, test_report, msg, init_session_state, success)
-            print_msg(msg)
+            txt = post_easyconfigs_pr_test_report(pr_nr, test_report, msg, init_session_state, success)
         else:
             # only upload test report as a gist
             gist_url = upload_test_report_as_gist(test_report)
-            print_msg("Test report uploaded to %s" % gist_url)
+            txt = "Test report uploaded to %s" % gist_url
     else:
         test_report = create_test_report(msg, ecs_with_res, init_session_state)
+        txt = None
     _log.debug("Test report: %s" % test_report)
+
     if dump_path is not None:
         write_file(dump_path, test_report)
         _log.info("Test report dumped to %s" % dump_path)
+
+    return txt

From 74d83a04a5c89cab7189ca195d8991e29c3a6e77 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Oct 2014 09:43:37 +0200
Subject: [PATCH 0242/1356] fix bug in det_easyconfig_paths introduced by
 refactoring

---
 easybuild/framework/easyconfig/tools.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 0e5d6359a3..6ccdd7d264 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -242,14 +242,15 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
         easyconfigs_pkg_paths = []
     ignore_dirs = build_option('ignore_dirs')
 
-    ec_files = []
-    if not orig_paths and from_pr:
+    ec_files = orig_paths[:]
+
+    if not ec_files and from_pr:
         pr_files = fetch_easyconfigs_from_pr(from_pr)
         ec_files = [path for path in pr_files if path.endswith('.eb')]
-    elif orig_paths and easyconfigs_pkg_paths:
+
+    elif ec_files and easyconfigs_pkg_paths:
         # look for easyconfigs with relative paths in easybuild-easyconfigs package,
         # unless they were found at the given relative paths
-        ec_files = orig_paths[:]
 
         # determine which easyconfigs files need to be found, if any
         ecs_to_find = []

From 732ea8cc9dc4599d5032030ee8b0be24363a0991 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Oct 2014 15:50:29 +0200
Subject: [PATCH 0243/1356] get rid of using print_msg/print_error in
 easyconfigs.tools module

---
 easybuild/framework/easyconfig/tools.py | 11 +++++------
 easybuild/main.py                       |  6 +++++-
 easybuild/tools/robot.py                |  5 +++--
 3 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 6ccdd7d264..1b4d75acc4 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -67,7 +67,7 @@
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
 from easybuild.framework.easyconfig.easyconfig import process_easyconfig
-from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import find_easyconfigs, run_cmd, search_file, write_file
 from easybuild.tools.github import fetch_easyconfigs_from_pr
@@ -75,10 +75,11 @@
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.utilities import quote_str
 
+
 _log = fancylogger.getLogger('easyconfig.tools', fname=False)
 
 
-def skip_available(easyconfigs, testing=False):
+def skip_available(easyconfigs):
     """Skip building easyconfigs for existing modules."""
     modtool = modules_tool()
     module_names = [ec['full_mod_name'] for ec in easyconfigs]
@@ -86,9 +87,7 @@ def skip_available(easyconfigs, testing=False):
     retained_easyconfigs = []
     for ec, mod_name, mod_exists in zip(easyconfigs, module_names, modules_exist):
         if mod_exists:
-            msg = "%s is already installed (module found), skipping" % mod_name
-            print_msg(msg, log=_log, silent=testing)
-            _log.info(msg)
+            _log.info("%s is already installed (module found), skipping" % mod_name)
         else:
             _log.debug("%s is not installed yet, so retaining it" % mod_name)
             retained_easyconfigs.append(ec)
@@ -302,7 +301,7 @@ def parse_easyconfigs(paths):
         # keep track of whether any files were generated
         generated_ecs |= generated
         if not os.path.exists(path):
-            print_error("Can't find path %s" % path)
+            _log.error("Can't find path %s" % path)
         try:
             ec_files = find_easyconfigs(path, ignore_dirs=ignore_dirs)
             for ec_file in ec_files:
diff --git a/easybuild/main.py b/easybuild/main.py
index 763b28aaa1..0022bd4e9d 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -246,7 +246,11 @@ def main(testing_data=(None, None, None)):
 
     # skip modules that are already installed unless forced
     if not options.force:
-        easyconfigs = skip_available(easyconfigs, testing=testing)
+        retained_ecs = skip_available(easyconfigs)
+        if not testing:
+            for skipped_ec in [ec for ec in easyconfigs if ec not in retained_ecs]:
+                print_msg("%s is already installed (module found), skipping" % skipped_ec['full_mod_name'])
+        easyconfigs = retained_ecs
 
     # determine an order that will allow all specs in the set to build
     if len(easyconfigs) > 0:
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index f17a888842..b4d3b630c1 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -90,7 +90,7 @@ def dry_run(easyconfigs, short=False, build_specs=None):
         lines.append("Dry run: printing build status of easyconfigs and dependencies")
         all_specs = resolve_dependencies(easyconfigs, build_specs=build_specs, retain_all_deps=True)
 
-    unbuilt_specs = skip_available(all_specs, testing=True)
+    unbuilt_specs = skip_available(all_specs)
     dry_run_fmt = " * [%1s] %s (module: %s)"  # markdown compatible (list of items with checkboxes in front)
 
     listed_ec_paths = [spec['spec'] for spec in easyconfigs]
@@ -133,8 +133,9 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
     """
 
     robot = build_option('robot_path')
-
+    # retain all dependencies if specified by either the resp. build option or the dedicated named argument
     retain_all_deps = build_option('retain_all_deps') or retain_all_deps
+
     if retain_all_deps:
         # assume that no modules are available when forced, to retain all dependencies
         avail_modules = []

From 43b88ce20c00ae35c83c0415c8cc49e478dad46e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Oct 2014 16:10:28 +0200
Subject: [PATCH 0244/1356] define and use constant EASYCONFIGS_PKG_SUBDIR

---
 easybuild/framework/easyblock.py           | 8 +++++---
 easybuild/framework/easyconfig/__init__.py | 3 +++
 easybuild/framework/easyconfig/tools.py    | 3 ++-
 easybuild/main.py                          | 3 ++-
 easybuild/tools/options.py                 | 3 ++-
 easybuild/tools/parallelbuild.py           | 2 +-
 6 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index c8cba7d388..662daf8bf8 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -48,8 +48,10 @@
 
 import easybuild.tools.environment as env
 from easybuild.tools import config, filetools
-from easybuild.framework.easyconfig.easyconfig import (EasyConfig, ActiveMNS, ITERATE_OPTIONS,
-    fetch_parameter_from_easyconfig_file, get_class_for, get_easyblock_class, get_module_path, resolve_template)
+from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
+from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS, ITERATE_OPTIONS
+from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file, get_class_for
+from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, get_module_path, resolve_template
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP
 from easybuild.tools.build_details import get_build_stats
@@ -474,7 +476,7 @@ def obtain_file(self, filename, extension=False, urls=None):
             common_filepaths = []
             if self.robot_path:
                 common_filepaths.extend(self.robot_path)
-            common_filepaths.extend(get_paths_for("easyconfigs", robot_path=self.robot_path))
+            common_filepaths.extend(get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=self.robot_path))
 
             for path in ebpath + common_filepaths + srcpaths:
                 # create list of candidate filepaths
diff --git a/easybuild/framework/easyconfig/__init__.py b/easybuild/framework/easyconfig/__init__.py
index b8f643bab3..24e58f0208 100644
--- a/easybuild/framework/easyconfig/__init__.py
+++ b/easybuild/framework/easyconfig/__init__.py
@@ -31,5 +31,8 @@
 from easybuild.framework.easyconfig.default import ALL_CATEGORIES
 globals().update(ALL_CATEGORIES)
 
+# subdirectory (of 'easybuild' dir) in which easyconfig files are located in a package
+EASYCONFIGS_PKG_SUBDIR = 'easyconfigs'
+
 # is used in some tools
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 1b4d75acc4..804155b847 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -65,6 +65,7 @@
 except ImportError, err:
     graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz")
 
+from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
 from easybuild.framework.easyconfig.easyconfig import process_easyconfig
 from easybuild.tools.build_log import EasyBuildError
@@ -175,7 +176,7 @@ def dep_graph(*args, **kwargs):
         _log.error("%s\nerr: %s" % (msg, err))
 
 
-def get_paths_for(subdir="easyconfigs", robot_path=None):
+def get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None):
     """
     Return a list of absolute paths where the specified subdir can be found, determined by the PYTHONPATH
     """
diff --git a/easybuild/main.py b/easybuild/main.py
index 0022bd4e9d..d06ff04b13 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -48,6 +48,7 @@
 import easybuild.tools.config as config
 import easybuild.tools.options as eboptions
 from easybuild.framework.easyblock import EasyBlock, build_and_install_one
+from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.tools import alt_easyconfig_paths, dep_graph, det_easyconfig_paths
 from easybuild.framework.easyconfig.tools import get_paths_for, parse_easyconfigs, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_path, tweak
@@ -161,7 +162,7 @@ def main(testing_data=(None, None, None)):
         _log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
 
     # determine easybuild-easyconfigs package install path
-    easyconfigs_pkg_paths = get_paths_for("easyconfigs")
+    easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR)
     if not easyconfigs_pkg_paths:
         _log.warning("Failed to determine install path for easybuild-easyconfigs package.")
 
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 4d15565caf..a346cb8e56 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -40,6 +40,7 @@
 from vsc.utils.missing import nub
 
 from easybuild.framework.easyblock import EasyBlock
+from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.constants import constant_documentation
 from easybuild.framework.easyconfig.default import convert_to_help
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
@@ -80,7 +81,7 @@ def basic_options(self):
         strictness_options = [run.IGNORE, run.WARN, run.ERROR]
 
         try:
-            default_robot_path = get_paths_for("easyconfigs", robot_path=None)[0]
+            default_robot_path = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None)[0]
         except:
             self.log.warning("basic_options: unable to determine default easyconfig path")
             default_robot_path = False  # False as opposed to None, since None is used for indicating that --robot was used
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index ac52b20b10..8af42cffeb 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -39,7 +39,7 @@
 import easybuild.tools.config as config
 from easybuild.framework.easyblock import get_easyblock_instance
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
-from easybuild.tools.build_log import EasyBuildError, print_msg
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.pbs_job import PbsJob, connect_to_server, disconnect_from_server, get_ppn

From 81d358d35b0674a1b85584448161e70b53743320 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Oct 2014 17:11:17 +0200
Subject: [PATCH 0245/1356] fix remarks

---
 easybuild/framework/easyconfig/tweak.py | 30 +++----------------------
 easybuild/main.py                       | 27 +++++++++++++++++++---
 easybuild/tools/robot.py                | 16 +++++++------
 3 files changed, 36 insertions(+), 37 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 6e0e50c290..a5c2be47d1 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -42,7 +42,6 @@
 from vsc.utils import fancylogger
 from vsc.utils.missing import nub
 
-from easybuild.tools.build_log import print_error, print_msg, print_warning
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, create_paths, process_easyconfig
 from easybuild.tools.filetools import read_file, write_file
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
@@ -222,7 +221,7 @@ def __repr__(self):
     _log.debug("Contents of tweaked easyconfig file:\n%s" % ectxt)
 
     # come up with suiting file name for tweaked easyconfig file if none was specified
-    if not target_fn:
+    if target_fn is None:
         fn = None
         try:
             # obtain temporary filename
@@ -525,7 +524,7 @@ def unique(l):
         # GENERATE
 
         # if no file path was specified, generate a file name
-        if not fp:
+        if fp is None:
             cfg = {
                 'version': ver,
                 'toolchain': {'name': tcname, 'version': tcver},
@@ -543,7 +542,7 @@ def unique(l):
         return (True, fp)
 
 
-def obtain_ec_for(specs, paths, fp):
+def obtain_ec_for(specs, paths, fp=None):
     """
     Obtain an easyconfig file to the given specifications.
 
@@ -595,26 +594,3 @@ def obtain_ec_for(specs, paths, fp):
         return res
     else:
         _log.error("No easyconfig found for requested software, and also failed to generate one.")
-
-
-def obtain_path(specs, paths, try_to_generate=False, exit_on_error=True, silent=False):
-    """Obtain a path for an easyconfig that matches the given specifications."""
-
-    # if no easyconfig files/paths were provided, but we did get a software name,
-    # we can try and find a suitable easyconfig ourselves, or generate one if we can
-    (generated, fn) = obtain_ec_for(specs, paths, None)
-    if not generated:
-        return (fn, generated)
-    else:
-        # if an easyconfig was generated, make sure we're allowed to use it
-        if try_to_generate:
-            print_msg("Generated an easyconfig file %s, going to use it now..." % fn, silent=silent)
-            return (fn, generated)
-        else:
-            try:
-                os.remove(fn)
-            except OSError, err:
-                print_warning("Failed to remove generated easyconfig file %s: %s" % (fn, err))
-            print_error(("Unable to find an easyconfig for the given specifications: %s; "
-                         "to make EasyBuild try to generate a matching easyconfig, "
-                         "use the --try-X options ") % specs, log=_log, exit_on_error=exit_on_error)
diff --git a/easybuild/main.py b/easybuild/main.py
index d06ff04b13..6c323db342 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -51,7 +51,7 @@
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.tools import alt_easyconfig_paths, dep_graph, det_easyconfig_paths
 from easybuild.framework.easyconfig.tools import get_paths_for, parse_easyconfigs, skip_available
-from easybuild.framework.easyconfig.tweak import obtain_path, tweak
+from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak
 from easybuild.tools.config import get_repository, get_repositorypath, set_tmpdir
 from easybuild.tools.filetools import cleanup, write_file
 from easybuild.tools.options import process_software_build_specs
@@ -75,6 +75,27 @@ def log_start(eb_command_line, eb_tmpdir):
     _log.info("Using %s as temporary directory" % eb_tmpdir)
 
 
+def find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=False):
+    """Find easyconfigs by build specifications."""
+    generated, ec_file = obtain_ec_for(build_specs, robot_path, None)
+    if generated:
+        if try_to_generate:
+            print_msg("Generated an easyconfig file %s, going to use it now..." % ec_file, silent=testing)
+        else:
+            # (try to) cleanup
+            try:
+                os.remove(ec_file)
+            except OSError, err:
+                _log.warning("Failed to remove generated easyconfig file %s: %s" % (ec_file, err))
+
+            # don't use a generated easyconfig unless generation was requested (using a --try-X option)
+            print_error(("Unable to find an easyconfig for the given specifications: %s; "
+                         "to make EasyBuild try to generate a matching easyconfig, "
+                         "use the --try-X options ") % build_specs, log=_log)
+
+    return [(ec_file, generated)]
+
+
 def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
     """Build and install software for all provided parsed easyconfig files."""
     # obtain a copy of the starting environment so each build can start afresh
@@ -209,8 +230,8 @@ def main(testing_data=(None, None, None)):
     paths = det_easyconfig_paths(orig_paths, options.from_pr, easyconfigs_pkg_paths)
     if not paths:
         if 'name' in build_specs:
-            paths = [obtain_path(build_specs, robot_path, try_to_generate=try_to_generate,
-                                 exit_on_error=not testing)]
+            # try to obtain or generate an easyconfig file via build specifications if a software name is provided
+            paths = find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=testing)
         elif not any([options.aggregate_regtest, options.search, options.search_short, options.regtest]):
             print_error(("Please provide one or multiple easyconfig files, or use software build "
                          "options to make EasyBuild search for easyconfigs"),
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index b4d3b630c1..17a97754a1 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -77,9 +77,9 @@ def det_robot_path(robot_option, easyconfigs_paths, tweaked_ecs_path, pr_path, a
 
 def dry_run(easyconfigs, short=False, build_specs=None):
     """
-    Print dry run information
-    @param easyconfigs: list of easyconfig files
-    @param short: print short output (use a variable for the common prefix)
+    Compose dry run overview for supplied easyconfigs ([ ] for unavailable, [x] for available, [F] for forced)
+    @param easyconfigs: list of parsed easyconfigs (EasyConfig instances)
+    @param short: use short format for overview: use a variable for common prefixes
     @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
     """
     lines = []
@@ -129,7 +129,8 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
     Work through the list of easyconfigs to determine an optimal order
     @param unprocessed: list of easyconfigs
     @param build_specs: dictionary specifying build specifications (e.g. version, toolchain, ...)
-    @param retain_all_deps: boolean indicating whether all dependencies should be retained, regardless of availability
+    @param retain_all_deps: boolean indicating whether all dependencies must be retained, regardless of availability;
+                            retain all deps when True, check matching build option when False
     """
 
     robot = build_option('robot_path')
@@ -184,12 +185,12 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
             being_installed = [EasyBuildMNS().det_full_module_name(p['ec']) for p in unprocessed]
 
             additional = []
-            for i, entry in enumerate(unprocessed):
+            for entry in unprocessed:
                 # do not choose an entry that is being installed in the current run
                 # if they depend, you probably want to rebuild them using the new dependency
                 deps = entry['dependencies']
                 candidates = [d for d in deps if not EasyBuildMNS().det_full_module_name(d) in being_installed]
-                if len(candidates) > 0:
+                if candidates:
                     cand_dep = candidates[0]
                     # find easyconfig, might not find any
                     _log.debug("Looking for easyconfig for %s" % str(cand_dep))
@@ -246,10 +247,11 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
 
 def search_easyconfigs(query, short=False):
     """Search for easyconfigs, if a query is provided."""
-    search_path = [os.getcwd()]
     robot_path = build_option('robot_path')
     if robot_path:
         search_path = robot_path
+    else:
+        search_path = [os.getcwd()]
     ignore_dirs = build_option('ignore_dirs')
     silent = build_option('silent')
     search_file(search_path, query, short=short, ignore_dirs=ignore_dirs, silent=silent)

From 441239e7183783b85929cab685bd8638bf91e816 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Oct 2014 17:37:29 +0200
Subject: [PATCH 0246/1356] fix skip_available calls in robot unit test

---
 test/framework/robot.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/robot.py b/test/framework/robot.py
index 7beee4cca1..6562817c27 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -231,7 +231,7 @@ def test_resolve_dependencies(self):
         # build that are listed but already have a module available are not retained without force
         build_options.update({'force': False})
         init_config(build_options=build_options)
-        newecs = skip_available(ecs, testing=True)  # skip available builds since force is not enabled
+        newecs = skip_available(ecs)  # skip available builds since force is not enabled
         res = resolve_dependencies(newecs)
         self.assertEqual(len(res), 2)
         self.assertEqual('goolf/1.4.10', res[0]['full_mod_name'])
@@ -241,7 +241,7 @@ def test_resolve_dependencies(self):
         build_options.update({'retain_all_deps': True})
         init_config(build_options=build_options)
         ecs = [deepcopy(easyconfig_dep)]
-        newecs = skip_available(ecs, testing=True)  # skip available builds since force is not enabled
+        newecs = skip_available(ecs)  # skip available builds since force is not enabled
         res = resolve_dependencies(newecs)
         self.assertEqual(len(res), 9)
         self.assertEqual('GCC/4.7.2', res[0]['full_mod_name'])

From 585c34a98bd85584d6a2ed04e20c1f5e4b4cd24c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Oct 2014 18:37:52 +0200
Subject: [PATCH 0247/1356] fix remark, avoid assigning build options to
 variables if they're only used once

---
 easybuild/framework/easyconfig/tools.py | 17 ++++++-----------
 1 file changed, 6 insertions(+), 11 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 804155b847..57b045428a 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -240,7 +240,6 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
     """
     if easyconfigs_pkg_paths is None:
         easyconfigs_pkg_paths = []
-    ignore_dirs = build_option('ignore_dirs')
 
     ec_files = orig_paths[:]
 
@@ -276,7 +275,7 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
                     break
 
                 # ignore subdirs specified to be ignored by replacing items in dirnames list used by os.walk
-                dirnames[:] = [d for d in dirnames if not d in ignore_dirs]
+                dirnames[:] = [d for d in dirnames if not d in build_option('ignore_dirs')]
 
             # stop os.walk insanity as soon as we have all we need (outer loop)
             if not ecs_to_find:
@@ -291,10 +290,6 @@ def parse_easyconfigs(paths):
     Parse easyconfig files
     @params paths: paths to easyconfigs
     """
-    build_specs = build_option('build_specs')
-    ignore_dirs = build_option('ignore_dirs')
-    try_to_generate = build_option('try_to_generate')
-
     easyconfigs = []
     generated_ecs = False
     for (path, generated) in paths:
@@ -304,13 +299,13 @@ def parse_easyconfigs(paths):
         if not os.path.exists(path):
             _log.error("Can't find path %s" % path)
         try:
-            ec_files = find_easyconfigs(path, ignore_dirs=ignore_dirs)
+            ec_files = find_easyconfigs(path, ignore_dirs=build_option('ignore_dirs'))
             for ec_file in ec_files:
                 # only pass build specs when not generating easyconfig files
-                if try_to_generate:
-                    ecs = process_easyconfig(ec_file)
-                else:
-                    ecs = process_easyconfig(ec_file, build_specs=build_specs)
+                kwargs = {}
+                if not build_option('try_to_generate'):
+                    kwargs['build_specs'] = build_option('build_specs')
+                ecs = process_easyconfig(ec_file, **kwargs)
                 easyconfigs.extend(ecs)
         except IOError, err:
             _log.error("Processing easyconfigs in path %s failed: %s" % (path, err))

From 3e9e5cb79b8f07c088795f3b1317d9a60a751fc3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Oct 2014 18:38:27 +0200
Subject: [PATCH 0248/1356] fix broken toy unit test

---
 test/framework/toy_build.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 09b16d6ad9..5f5b31ebe2 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -519,18 +519,19 @@ def test_allow_system_deps(self):
     def test_toy_hierarchical(self):
         """Test toy build under example hierarchical module naming scheme."""
 
+        test_easyconfigs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         self.setup_hierarchical_modules()
         mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
 
         args = [
-            os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb'),
+            os.path.join(test_easyconfigs, 'toy-0.0.eb'),
             '--sourcepath=%s' % self.test_sourcepath,
             '--buildpath=%s' % self.test_buildpath,
             '--installpath=%s' % self.test_installpath,
             '--debug',
             '--unittest-file=%s' % self.logfile,
             '--force',
-            '--robot=%s' % os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs'),
+            '--robot=%s' % test_easyconfigs,
             '--module-naming-scheme=HierarchicalMNS',
         ]
 
@@ -625,11 +626,11 @@ def test_toy_hierarchical(self):
         # no dependencies or toolchain => no module load statements in module file
         modtxt = read_file(toy_module_path)
         modpath_extension = os.path.join(mod_prefix, 'Compiler', 'toy', '0.0')
-        self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        self.assertTrue(re.search(r"^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
         os.remove(toy_module_path)
 
         # building a toolchain module should also work
-        args = ['gompi-1.4.10.eb'] + args[1:]
+        args[0] = os.path.join(test_easyconfigs, 'gompi-1.4.10.eb')
         modules_tool().purge()
         self.eb_main(args, logfile=self.dummylogfn, do_build=True, verbose=True, raise_error=True)
 

From 3def91f2df125f18a9163a9b2ac82cdf434ee3ff Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Oct 2014 21:38:47 +0200
Subject: [PATCH 0249/1356] fix broken gompi toolchain installation unit test

---
 .../sandbox/easybuild/easyblocks/generic/toolchain.py    | 9 ++++++++-
 test/framework/toy_build.py                              | 4 +++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py b/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py
index db67440c90..7ba202cbdc 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py
@@ -31,4 +31,11 @@
 
 class Toolchain(EasyBlock):
     """Dummy support for toolchains."""
-    pass
+    def configure_step(self):
+        pass
+    def build_step(self):
+        pass
+    def install_step(self):
+        pass
+    def sanity_check_step(self):
+        pass
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 5f5b31ebe2..1b8371b379 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -632,7 +632,9 @@ def test_toy_hierarchical(self):
         # building a toolchain module should also work
         args[0] = os.path.join(test_easyconfigs, 'gompi-1.4.10.eb')
         modules_tool().purge()
-        self.eb_main(args, logfile=self.dummylogfn, do_build=True, verbose=True, raise_error=True)
+        self.eb_main(args, logfile=self.dummylogfn, do_build=True, verbose=True, raise_error=False)
+        gompi_module_path = os.path.join(mod_prefix, 'Core', 'gompi', '1.4.10')
+        self.assertTrue(os.path.exists(gompi_module_path))
 
     def test_toy_advanced(self):
         """Test toy build with extensions and non-dummy toolchain."""

From 9919c3a32903340cd18195c372a8d0b84632ac12 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Wed, 15 Oct 2014 22:24:13 +0200
Subject: [PATCH 0250/1356] VERY EARLY DRAFT.

---
 easybuild/framework/easyblock.py    |  18 +--
 easybuild/tools/module_generator.py | 185 +++++++++++++++++++++++++---
 easybuild/tools/modules.py          |   4 +-
 test/framework/module_generator.py  |   8 +-
 4 files changed, 186 insertions(+), 29 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3a5bf95e63..f1840258b4 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -64,7 +64,7 @@
 from easybuild.tools.filetools import write_file, compute_checksum, verify_checksum
 from easybuild.tools.run import run_cmd
 from easybuild.tools.jenkins import write_to_xml
-from easybuild.tools.module_generator import ModuleGenerator
+from easybuild.tools.module_generator import ModuleGeneratorLua
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.modules import ROOT_ENV_VAR_NAME_PREFIX, VERSION_ENV_VAR_NAME_PREFIX, DEVEL_ENV_VAR_NAME_PREFIX
 from easybuild.tools.modules import get_software_root, modules_tool
@@ -131,7 +131,7 @@ def __init__(self, ec):
         # modules interface with default MODULEPATH
         self.modules_tool = modules_tool()
         # module generator
-        self.moduleGenerator = ModuleGenerator(self, fake=True)
+        self.moduleGenerator = ModuleGeneratorLua(self, fake=True)
 
         # modules footer
         self.modules_footer = None
@@ -728,7 +728,7 @@ def make_devel_module(self, create_in_builddir=False):
         # load fake module
         fake_mod_data = self.load_fake_module(purge=True)
 
-        mod_gen = ModuleGenerator(self)
+        mod_gen = ModuleGeneratorLua(self)
         header = "#%Module\n"
 
         env_txt = ""
@@ -829,9 +829,12 @@ def make_module_extra(self):
 
         # EBROOT + EBVERSION + EBDEVEL
         environment_name = convert_name(self.name, upper=True)
-        txt += self.moduleGenerator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, "$root")
+        #todo this is only valid for Lua now
+        # This is a bit different in Lua due to string quoting rules in Lua and in Tcl - so $root cannot be used easily.
+        # so we resort to rendering our internal variables and quote them in the set_environment() like all other values.
+        txt += self.moduleGenerator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, self.installdir)
         txt += self.moduleGenerator.set_environment(VERSION_ENV_VAR_NAME_PREFIX + environment_name, self.version)
-        devel_path = os.path.join("$root", log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
+        devel_path = os.path.join(self.installdir, log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
         txt += self.moduleGenerator.set_environment(DEVEL_ENV_VAR_NAME_PREFIX + environment_name, devel_path)
 
         txt += "\n"
@@ -872,7 +875,8 @@ def make_module_footer(self):
         """
         Insert a footer section in the modulefile, primarily meant for contextual information
         """
-        txt = '\n# Built with EasyBuild version %s\n' % VERBOSE_VERSION
+        #@todo fix this as it is lua specific
+        txt = '\n -- Built with EasyBuild version %s\n' % VERBOSE_VERSION
 
         # add extra stuff for extensions (if any)
         if self.cfg['exts_list']:
@@ -1658,7 +1662,7 @@ def make_module_step(self, fake=False):
         txt += self.make_module_extra()
         txt += self.make_module_footer()
 
-        write_file(self.moduleGenerator.filename, txt)
+        write_file(self.moduleGenerator.filename+".lua", txt)
 
         self.log.info("Module file %s written" % self.moduleGenerator.filename)
 
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 2d51d7fcd9..0c9f65253b 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -47,11 +47,9 @@
 _log = fancylogger.getLogger('module_generator', fname=False)
 
 
-class ModuleGenerator(object):
-    """
-    Class for generating module files.
-    """
+class ModuleGenerator:
     def __init__(self, application, fake=False):
+        self.fake = fake
         self.app = application
         self.fake = fake
         self.tmpdir = None
@@ -92,6 +90,29 @@ def create_symlinks(self):
         except OSError, err:
             _log.error("Failed to create symlinks from %s to %s: %s" % (self.class_mod_files, self.filename, err))
 
+    def is_fake(self):
+        """Return whether this ModuleGeneratorTcl instance generates fake modules or not."""
+        return self.fake
+
+    def set_fake(self, fake):
+        """Determine whether this ModuleGeneratorTcl instance should generate fake modules."""
+        _log.debug("Updating fake for this ModuleGeneratorTcl instance to %s (was %s)" % (fake, self.fake))
+        self.fake = fake
+        # fake mode: set installpath to temporary dir
+        if self.fake:
+            self.tmpdir = tempfile.mkdtemp()
+            _log.debug("Fake mode: using %s (instead of %s)" % (self.tmpdir, self.module_path))
+            self.module_path = self.tmpdir
+        else:
+            self.module_path = config.install_path('mod')
+
+
+class ModuleGeneratorTcl(ModuleGenerator):
+    """
+    Class for generating Tcl module files.
+    """
+
+
     def get_description(self, conflict=True):
         """
         Generate a description.
@@ -189,6 +210,7 @@ def prepend_paths(self, key, paths, allow_abs=False):
         statements = [template % (key, p) for p in paths]
         return ''.join(statements)
 
+
     def use(self, paths):
         """
         Generate module use statements for given list of module paths.
@@ -231,18 +253,147 @@ def set_alias(self, key, value):
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
         return 'set-alias\t%s\t\t%s\n' % (key, quote_str(value))
 
-    def set_fake(self, fake):
-        """Determine whether this ModuleGenerator instance should generate fake modules."""
-        _log.debug("Updating fake for this ModuleGenerator instance to %s (was %s)" % (fake, self.fake))
-        self.fake = fake
-        # fake mode: set installpath to temporary dir
-        if self.fake:
-            self.tmpdir = tempfile.mkdtemp()
-            _log.debug("Fake mode: using %s (instead of %s)" % (self.tmpdir, self.module_path))
-            self.module_path = self.tmpdir
+
+class ModuleGeneratorLua(ModuleGenerator):
+    """
+    Class for generating Lua module files.
+    """
+
+    def get_description(self, conflict=True):
+        """
+        Generate a description.
+        """
+
+        description = "%s - Homepage: %s" % (self.app.cfg['description'], self.app.cfg['homepage'])
+
+
+        lines = [
+            "local pkg = {}",
+            "help = [["
+            "%(description)s"
+            "]]",
+            "whatis([[Name: %(name)s]])",
+            "whatis([[Version: %(version)s]])",
+            "whatis([[Description: %(description)s]])",
+            "whatis([[Homepage: %(homepage)s]])"
+            "whatis([[License: N/A ]])",
+            "whatis([[Keywords: Not set]])",
+            "",
+            "",
+            'pkg.root="%(installdir)s"',
+            "",
+            ]
+
+        #@todo check if this is really needed, imho Lmod doesnt need this at all.
+        if self.app.cfg['moduleloadnoconflict']:
+            lines.extend([
+             'if ( not isloaded("%(name)s/%(version)s")) then',
+             '  load("%(name)s/%(version)s")',
+             'end',
+             ])
+
+        elif conflict:
+            # conflicts are not needed in lua module files, as Lmod "conflict" by default
+            pass
+
+        txt = '\n'.join(lines) % {
+            'name': self.app.name,
+            'version': self.app.version,
+            'description': description,
+            'installdir': self.app.installdir,
+            'homepage': self.app.cfg['homepage'],
+        }
+
+
+        return txt
+
+    def load_module(self, mod_name):
+        """
+        Generate load statements for module.
+        """
+        if build_option('recursive_mod_unload'):
+            # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
+            # when "module unload" is called on the module in which the depedency "module load" is present,
+            # it will get translated to "module unload"
+            load_statement = ['load("%(mod_name)s")']
         else:
-            self.module_path = config.install_path('mod')
+            load_statement = [
+                'if ( not isloaded("%(mod_name)s")) then',
+                '  load("%(mod_name)s")',
+                'end',
+            ]
+        return '\n'.join([""] + load_statement + [""]) % {'mod_name': mod_name}
 
-    def is_fake(self):
-        """Return whether this ModuleGenerator instance generates fake modules or not."""
-        return self.fake
+    def unload_module(self, mod_name):
+        """
+        Generate unload statements for module.
+        """
+        return '\n'.join([
+            "",
+            "if (isloaded(%(mod_name)s)) then",
+            "    unload(%(mod_name)s)",
+            "end",
+            "",
+        ]) % {'mod_name': mod_name}
+
+    def prepend_paths(self, key, paths, allow_abs=False):
+        """
+        Generate prepend-path statements for the given list of paths.
+        """
+        template = 'prepend_path(%s,%s)\n'
+
+        if isinstance(paths, basestring):
+            _log.info("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
+            paths = [paths]
+
+        # make sure only relative paths are passed
+        for i in xrange(len(paths)):
+            if os.path.isabs(paths[i]) and not allow_abs:
+                _log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % paths[i])
+            elif not os.path.isabs(paths[i]):
+                # prepend $root (= installdir) for relative paths
+                paths[i] = ' pathJoin(pkg.root,"%s")' % paths[i]
+
+        statements = [template % (quote_str(key), p) for p in paths]
+        return ''.join(statements)
+
+    def use(self, paths):
+        """
+        Generate module use statements for given list of module paths.
+        """
+        use_statements = []
+        for path in paths:
+            use_statements.append('use("%s")' % path)
+        return '\n'.join(use_statements)
+
+
+    def set_environment(self, key, value):
+
+        """
+        Generate setenv statement for the given key/value pair.
+        """
+        # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
+        return 'setenv("%s", %s)\n' % (key, quote_str(value))
+
+
+    def msg_on_load(self, msg):
+        """
+        Add a message that should be printed when loading the module.
+        """
+        pass
+
+
+    def add_tcl_footer(self, tcltxt):
+        """
+        Append whatever Tcl code you want to your modulefile
+        """
+    # nothing to do here, but this should fail in the context of generating Lua modules
+        pass
+
+
+    def set_alias(self, key, value):
+        """
+        Generate set-alias statement in modulefile for the given key/value pair.
+        """
+    # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
+        return 'setalias(%s,"%s")\n' % (key, quote_str(value))
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index d0083bc294..6ab696a327 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -567,7 +567,9 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
         @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
         """
         modtxt = self.read_module_file(mod_name)
-        loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
+        #@todo: this was removed for Lmod
+        #loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
+        loadregex = re.compile(r"load\(\"(\S*)\"", re.M)
         mods = loadregex.findall(modtxt)
 
         if depth > 0:
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 4e12e71427..a65e8f5781 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -41,7 +41,7 @@
 import easybuild.tools.module_generator
 from easybuild.framework.easyconfig.tools import process_easyconfig
 from easybuild.tools import config
-from easybuild.tools.module_generator import ModuleGenerator
+from easybuild.tools.module_generator import ModuleGeneratorTcl
 from easybuild.tools.module_naming_scheme.utilities import is_valid_module_name
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS
@@ -50,10 +50,10 @@
 
 
 class ModuleGeneratorTest(EnhancedTestCase):
-    """ testcase for ModuleGenerator """
+    """ testcase for ModuleGeneratorTcl """
 
     def setUp(self):
-        """ initialize ModuleGenerator with test Application """
+        """ initialize ModuleGeneratorTcl with test Application """
         super(ModuleGeneratorTest, self).setUp()
         # find .eb file
         eb_path = os.path.join(os.path.join(os.path.dirname(__file__), 'easyconfigs'), 'gzip-1.4.eb')
@@ -62,7 +62,7 @@ def setUp(self):
 
         ec = EasyConfig(eb_full_path)
         self.eb = EasyBlock(ec)
-        self.modgen = ModuleGenerator(self.eb)
+        self.modgen = ModuleGeneratorTcl(self.eb)
         self.modgen.app.installdir = tempfile.mkdtemp(prefix='easybuild-modgen-test-')
         
         self.orig_module_naming_scheme = config.get_module_naming_scheme()

From 61d1f38730d9de2c870d4f6446220d0c51b338b1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 16 Oct 2014 19:02:11 +0200
Subject: [PATCH 0251/1356] fix picking required version if it's available,
 clean up in tweak.py module

---
 easybuild/framework/easyconfig/tweak.py | 65 +++++++++----------------
 1 file changed, 24 insertions(+), 41 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index a5c2be47d1..b72a55214b 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -254,11 +254,14 @@ def __repr__(self):
 def pick_version(req_ver, avail_vers):
     """Pick version based on an optionally desired version and available versions.
 
-    If a desired version is specifed, the most recent version that is less recent
-    than the desired version will be picked; else, the most recent version will be picked.
+    If a desired version is specifed, the most recent version that is less recent than or equal to
+    the desired version will be picked; else, the most recent version will be picked.
 
-    This function returns both the version to be used, which is equal to the desired version
+    This function returns both the version to be used, which is equal to the required version
     if it was specified, and the version picked that matches that closest.
+
+    @param req_ver: required version
+    @param avail_vers: list of available versions
     """
 
     if not avail_vers:
@@ -267,20 +270,18 @@ def pick_version(req_ver, avail_vers):
     selected_ver = None
     if req_ver:
         # if a desired version is specified,
-        # retain the most recent version that's less recent than the desired version
-
+        # retain the most recent version that's less recent or equal than the desired version
         ver = req_ver
 
         if len(avail_vers) == 1:
             selected_ver = avail_vers[0]
         else:
-            retained_vers = [v for v in avail_vers if v < LooseVersion(ver)]
+            retained_vers = [v for v in avail_vers if v <= LooseVersion(ver)]
             if retained_vers:
                 selected_ver = retained_vers[-1]
             else:
                 # if no versions are available that are less recent, take the least recent version
                 selected_ver = sorted([LooseVersion(v) for v in avail_vers])[0]
-
     else:
         # if no desired version is specified, just use last version
         ver = avail_vers[-1]
@@ -289,6 +290,20 @@ def pick_version(req_ver, avail_vers):
     return (ver, selected_ver)
 
 
+def find_matching_easyconfigs(name, installver, paths):
+    """Find easyconfigs that match specified name/installversion in specified list of paths."""
+    ec_files = []
+    for path in paths:
+        patterns = create_paths(path, name, installver)
+        for pattern in patterns:
+            more_ec_files = glob.glob(pattern)
+            _log.debug("Including files that match glob pattern '%s': %s" % (pattern, more_ec_files))
+            ec_files.extend(more_ec_files)
+
+    # only retain unique easyconfig paths
+    return nub(ec_files)
+
+
 def select_or_generate_ec(fp, paths, specs):
     """
     Select or generate an easyconfig file with the given requirements, from existing easyconfig files.
@@ -318,7 +333,6 @@ def select_or_generate_ec(fp, paths, specs):
     handled_params = ['name']
 
     # find ALL available easyconfig files for specified software
-    ec_files = []
     cfg = {
         'version': '*',
         'toolchain': {'name': DUMMY_TOOLCHAIN_NAME, 'version': '*'},
@@ -326,10 +340,8 @@ def select_or_generate_ec(fp, paths, specs):
         'versionsuffix': '*',
     }
     installver = det_full_ec_version(cfg)
-    for path in paths:
-        patterns = create_paths(path, name, installver)
-        for pattern in patterns:
-            ec_files.extend(glob.glob(pattern))
+    ec_files = find_matching_easyconfigs(name, installver, paths)
+    _log.debug("Unique ec_files: %s" % ec_files)
 
     # we need at least one config file to start from
     if len(ec_files) == 0:
@@ -346,10 +358,6 @@ def select_or_generate_ec(fp, paths, specs):
         if len(ec_files) == 0:
             _log.error("No easyconfig files found for software %s, and no templates available. I'm all out of ideas." % name)
 
-    # only retain unique easyconfig files
-    ec_files = nub(ec_files)
-    _log.debug("Unique ec_files: %s" % ec_files)
-
     ecs_and_files = [(EasyConfig(f, validate=False), f) for f in ec_files]
 
     # TOOLCHAIN NAME
@@ -562,31 +570,6 @@ def obtain_ec_for(specs, paths, fp=None):
     if not paths:
         _log.error("No paths to look for easyconfig files, specify a path with --robot.")
 
-    # create glob patterns based on supplied info
-
-    # figure out the install version
-    cfg = {
-        'version': specs.get('version', '*'),
-        'toolchain': {
-            'name': specs.get('toolchain_name', '*'),
-            'version': specs.get('toolchain_version', '*'),
-        },
-        'versionprefix': specs.get('versionprefix', '*'),
-        'versionsuffix': specs.get('versionsuffix', '*'),
-    }
-    installver = det_full_ec_version(cfg)
-
-    # find easyconfigs that match a pattern
-    easyconfig_files = []
-    for path in paths:
-        patterns = create_paths(path, specs['name'], installver)
-        for pattern in patterns:
-            easyconfig_files.extend(glob.glob(pattern))
-
-    cnt = len(easyconfig_files)
-
-    _log.debug("List of obtained easyconfig files (%d): %s" % (cnt, easyconfig_files))
-
     # select best easyconfig, or try to generate one that fits the requirements
     res = select_or_generate_ec(fp, paths, specs)
 

From dbfa9e45f2cc607181c9c2411a4e8bcc3aefd873 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Oct 2014 09:26:07 +0200
Subject: [PATCH 0252/1356] fix bug: include easyconfigs pkg paths whenever
 --robot is used

---
 easybuild/framework/easyconfig/tools.py | 2 +-
 easybuild/tools/robot.py                | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 57b045428a..b01e500201 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -205,7 +205,7 @@ def get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None):
     # look for desired subdirs
     for path in path_list:
         path = os.path.join(path, "easybuild", subdir)
-        _log.debug("Looking for easybuild/%s in path %s" % (subdir, path))
+        _log.debug("Checking for easybuild/%s at %s" % (subdir, path))
         try:
             if os.path.exists(path):
                 paths.append(os.path.abspath(path))
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index 17a97754a1..b478571485 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -48,7 +48,7 @@
 _log = fancylogger.getLogger('tools.robot', fname=False)
 
 
-def det_robot_path(robot_option, easyconfigs_paths, tweaked_ecs_path, pr_path, auto_robot=False):
+def det_robot_path(robot_option, easyconfigs_pkg_paths, tweaked_ecs_path, pr_path, auto_robot=False):
     """Determine robot path."""
     # do not use robot option directly, it's not a list instance (and it shouldn't be modified)
     robot_path = []
@@ -60,8 +60,8 @@ def det_robot_path(robot_option, easyconfigs_paths, tweaked_ecs_path, pr_path, a
             # if options.robot is not None and False, easyconfigs pkg install path could not be found (see options.py)
             _log.error("No robot paths specified, and unable to determine easybuild-easyconfigs install path.")
 
-    if auto_robot:
-        robot_path.extend(easyconfigs_paths)
+    if robot_path or auto_robot:
+        robot_path.extend(easyconfigs_pkg_paths)
         _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
 
     if tweaked_ecs_path is not None:

From debcc7b7380c9b036a47d80ad3bbef914874159f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Oct 2014 11:33:06 +0200
Subject: [PATCH 0253/1356] fix remarks

---
 easybuild/framework/easyconfig/tweak.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index b72a55214b..ebc233b085 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -291,12 +291,18 @@ def pick_version(req_ver, avail_vers):
 
 
 def find_matching_easyconfigs(name, installver, paths):
-    """Find easyconfigs that match specified name/installversion in specified list of paths."""
+    """
+    Find easyconfigs that match specified name/installversion in specified list of paths.
+
+    @param name: software name
+    @param installver: software install version (which includes version, toolchain, versionprefix/suffix, ...)
+    @param paths: list of paths to search easyconfigs in
+    """
     ec_files = []
     for path in paths:
         patterns = create_paths(path, name, installver)
         for pattern in patterns:
-            more_ec_files = glob.glob(pattern)
+            more_ec_files = filter(os.path.isfile, glob.glob(pattern))
             _log.debug("Including files that match glob pattern '%s': %s" % (pattern, more_ec_files))
             ec_files.extend(more_ec_files)
 

From 712ae87a1bd0a0041c859c0588c227c90ee24092 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Oct 2014 11:56:03 +0200
Subject: [PATCH 0254/1356] add unit test module for tweak.py

---
 test/framework/suite.py |   3 +-
 test/framework/tweak.py | 116 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 118 insertions(+), 1 deletion(-)
 create mode 100644 test/framework/tweak.py

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 61b3ac30b4..1ed29b598a 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -69,6 +69,7 @@
 import test.framework.toolchain as tc
 import test.framework.toolchainvariables as tcv
 import test.framework.toy_build as t
+import test.framework.tweak as tw
 import test.framework.variables as v
 
 
@@ -95,7 +96,7 @@
 
 # call suite() for each module and then run them all
 # note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
-tests = [o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc]
+tests = [o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw]
 
 SUITE = unittest.TestSuite([x.suite() for x in tests])
 
diff --git a/test/framework/tweak.py b/test/framework/tweak.py
new file mode 100644
index 0000000000..061a0bcf8b
--- /dev/null
+++ b/test/framework/tweak.py
@@ -0,0 +1,116 @@
+##
+# Copyright 2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Unit tests for framework/easyconfig/tweak.py
+
+@author: Kenneth Hoste (Ghent University)
+"""
+import os
+from test.framework.utilities import EnhancedTestCase
+from unittest import TestLoader, main
+
+from easybuild.framework.easyconfig.tweak import find_matching_easyconfigs, obtain_ec_for, pick_version
+
+
+class TweakTest(EnhancedTestCase):
+    """Tests for tweak functionality."""
+    def test_pick_version(self):
+        """Test pick_version function."""
+        # if required version is not available, the most recent version less than or equal should be returned
+        self.assertEqual(('1.4', '1.0'), pick_version('1.4', ['0.5', '1.0', '1.5']))
+
+        # if required version is available, that should be what's returned
+        self.assertEqual(('1.0', '1.0'), pick_version('1.0', ['0.5', '1.0', '1.5']))
+
+    def test_find_matching_easyconfigs(self):
+        """Test find_matching_easyconfigs function."""
+        test_easyconfigs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        for (name, installver) in [('GCC', '4.8.2'), ('gzip', '1.5-goolf-1.4.10')]:
+            ecs = find_matching_easyconfigs(name, installver, [test_easyconfigs_path])
+            self.assertTrue(len(ecs) == 1 and ecs[0].endswith('/%s-%s.eb' % (name, installver)))
+
+        ecs = find_matching_easyconfigs('GCC', '*', [test_easyconfigs_path])
+        gccvers = ['4.6.3', '4.6.4', '4.7.2', '4.8.2', '4.8.3']
+        self.assertEqual(len(ecs), len(gccvers))
+        ecs_basename = [os.path.basename(ec) for ec in ecs]
+        for gccver in gccvers:
+            gcc_ec = 'GCC-%s.eb' % gccver
+            self.assertTrue(gcc_ec in ecs_basename, "%s is included in %s" % (gcc_ec, ecs_basename))
+
+    def test_obtain_ec_for(self):
+        """Test obtain_ec_for function."""
+        test_easyconfigs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        # find existing easyconfigs
+        specs = {
+            'name': 'GCC',
+            'version': '4.6.4',
+        }
+        (generated, ec_file) = obtain_ec_for(specs, [test_easyconfigs_path])
+        self.assertFalse(generated)
+        self.assertEqual(os.path.basename(ec_file), 'GCC-4.6.4.eb')
+
+        specs = {
+            'name': 'ScaLAPACK',
+            'version': '2.0.2',
+            'toolchain_name': 'gompi',
+            'toolchain_version': '1.4.10',
+            'versionsuffix': '-OpenBLAS-0.2.6-LAPACK-3.4.2',
+        }
+        (generated, ec_file) = obtain_ec_for(specs, [test_easyconfigs_path])
+        self.assertFalse(generated)
+        self.assertEqual(os.path.basename(ec_file), 'ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb')
+
+        specs = {
+            'name': 'ifort',
+            'versionsuffix': '-GCC-4.8.3',
+        }
+        (generated, ec_file) = obtain_ec_for(specs, [test_easyconfigs_path])
+        self.assertFalse(generated)
+        self.assertEqual(os.path.basename(ec_file), 'ifort-2013.5.192-GCC-4.8.3.eb')
+
+        # latest version if not specified
+        specs = {
+            'name': 'GCC',
+        }
+        (generated, ec_file) = obtain_ec_for(specs, [test_easyconfigs_path])
+        self.assertFalse(generated)
+        self.assertEqual(os.path.basename(ec_file), 'GCC-4.8.3.eb')
+
+        # generate non-existing easyconfig
+        specs = {
+            'name': 'GCC',
+            'version': '5.4.3',
+        }
+        (generated, ec_file) = obtain_ec_for(specs, [test_easyconfigs_path])
+        self.assertTrue(generated)
+        self.assertEqual(os.path.basename(ec_file), 'GCC-5.4.3.eb')
+
+
+def suite():
+    """ return all the tests in this file """
+    return TestLoader().loadTestsFromTestCase(TweakTest)
+
+if __name__ == '__main__':
+    main()

From a6f302a4bfb1815195ae9990a1bebfcfba2c370b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Oct 2014 15:53:06 +0200
Subject: [PATCH 0255/1356] take available hidden modules into account in
 dependency resolution

---
 easybuild/framework/easyconfig/tools.py | 10 ++++++++--
 easybuild/tools/robot.py                |  3 ++-
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 57b045428a..c6acf35f05 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -95,19 +95,25 @@ def skip_available(easyconfigs):
     return retained_easyconfigs
 
 
-def find_resolved_modules(unprocessed, avail_modules):
+def find_resolved_modules(unprocessed, avail_modules, retain_all_deps=False):
     """
     Find easyconfigs in 1st argument which can be fully resolved using modules specified in 2nd argument
     """
     ordered_ecs = []
     new_avail_modules = avail_modules[:]
     new_unprocessed = []
+    modtool = modules_tool()
 
     for ec in unprocessed:
         new_ec = ec.copy()
         deps = []
         for dep in new_ec['dependencies']:
-            if not ActiveMNS().det_full_module_name(dep) in new_avail_modules:
+            full_mod_name = ActiveMNS().det_full_module_name(dep)
+            dep_resolved = full_mod_name in new_avail_modules
+            if not retain_all_deps:
+                # hidden modules need special care, since they may not be included in list of available modules
+                dep_resolved |= dep['hidden'] and modtool.exist([full_mod_name])[0]
+            if not dep_resolved:
                 deps.append(dep)
         new_ec['dependencies'] = deps
 
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index 17a97754a1..966fe166eb 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -171,7 +171,8 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
         last_processed_count = -1
         while len(avail_modules) > last_processed_count:
             last_processed_count = len(avail_modules)
-            more_ecs, unprocessed, avail_modules = find_resolved_modules(unprocessed, avail_modules)
+            res = find_resolved_modules(unprocessed, avail_modules, retain_all_deps=retain_all_deps)
+            more_ecs, unprocessed, avail_modules = res
             for ec in more_ecs:
                 if not ec['full_mod_name'] in [x['full_mod_name'] for x in ordered_ecs]:
                     ordered_ecs.append(ec)

From 85a52e27dff9eddd8763e79db4997ba749bb21b3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Oct 2014 16:01:14 +0200
Subject: [PATCH 0256/1356] enhance robot unit test to check for
 resolve_dependencies behavior with existing hidden modules

---
 test/framework/robot.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/test/framework/robot.py b/test/framework/robot.py
index 6562817c27..a4680624e4 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -63,8 +63,8 @@ def available(self, *args):
         return self.avail_modules
 
     def show(self, modname):
-        """Dummy implementation of show, which includes full path to (existing) module files."""
-        if modname in self.avail_modules:
+        """Dummy implementation of show, which includes full path to (available or hidden) module files."""
+        if modname in self.avail_modules or os.path.basename(modname).startswith('.'):
             txt =  '  %s:' % os.path.join('/tmp', modname)
         else:
             txt = 'Module %s not found' % modname
@@ -124,6 +124,7 @@ def test_resolve_dependencies(self):
                 'versionsuffix': '',
                 'toolchain': {'name': 'dummy', 'version': 'dummy'},
                 'dummy': True,
+                'hidden': False,
             }],
             'parsed': True,
         }
@@ -135,7 +136,7 @@ def test_resolve_dependencies(self):
         self.assertEqual('gzip/1.4', res[0]['full_mod_name'])
         self.assertEqual('foo/1.2.3', res[-1]['full_mod_name'])
 
-        # hidden dependencies are found too
+        # hidden dependencies are found too, but only retained if they're not available (or forced to be retained
         hidden_dep = {
             'name': 'toy',
             'version': '0.0',
@@ -147,7 +148,14 @@ def test_resolve_dependencies(self):
         easyconfig_moredeps = deepcopy(easyconfig_dep)
         easyconfig_moredeps['dependencies'].append(hidden_dep)
         easyconfig_moredeps['hiddendependencies'] = [hidden_dep]
+
+        # toy/.0.0-deps is available and thus should be omitted
         res = resolve_dependencies([deepcopy(easyconfig_moredeps)])
+        self.assertEqual(len(res), 2)
+        full_mod_names = [ec['full_mod_name'] for ec in res]
+        self.assertFalse('toy/.0.0-deps' in full_mod_names)
+
+        res = resolve_dependencies([deepcopy(easyconfig_moredeps)], retain_all_deps=True)
         self.assertEqual(len(res), 4)  # hidden dep toy/.0.0-deps (+1) depends on (fake) ictce/4.1.13 (+1)
         self.assertEqual('gzip/1.4', res[0]['full_mod_name'])
         self.assertEqual('foo/1.2.3', res[-1]['full_mod_name'])
@@ -177,6 +185,7 @@ def test_resolve_dependencies(self):
             'versionsuffix': '',
             'toolchain': {'name': 'GCC', 'version': '4.6.3'},
             'dummy': True,
+            'hidden': False,
         }]
         ecs = [deepcopy(easyconfig_dep)]
         build_options.update({'robot_path': self.base_easyconfig_dir})
@@ -203,6 +212,7 @@ def test_resolve_dependencies(self):
             'versionsuffix': '',
             'toolchain': {'name': 'dummy', 'version': 'dummy'},
             'dummy': True,
+            'hidden': False,
         }]
         ecs = [deepcopy(easyconfig_dep)]
         res = resolve_dependencies(ecs)
@@ -265,6 +275,7 @@ def test_resolve_dependencies(self):
             'versionsuffix': '',
             'toolchain': {'name': 'dummy', 'version': 'dummy'},
             'dummy': True,
+            'hidden': False,
         }]
         ecs = [deepcopy(easyconfig_dep)]
         res = resolve_dependencies([deepcopy(easyconfig_dep)])

From 3698c338240c384c8568626701eff70586667d8d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Oct 2014 20:40:03 +0200
Subject: [PATCH 0257/1356] clear easyconfig files cache in between tests

---
 test/framework/utilities.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 39ab091e3f..e34cb37ae5 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -232,6 +232,7 @@ def cleanup():
     # empty caches
     tc_utils._initial_toolchain_instances.clear()
     easyconfig._easyconfigs_cache.clear()
+    easyconfig._easyconfig_files_cache.clear()
     mns_toolchain._toolchain_details_cache.clear()
 
 

From 43e9abd7756a7697dc391cc13381c3c0311d26bc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Oct 2014 20:40:43 +0200
Subject: [PATCH 0258/1356] enhance short dry run test to check easyconfigs pkg
 robot fallback path

---
 test/framework/options.py | 47 ++++++++++++++++++++++++++++++---------
 1 file changed, 37 insertions(+), 10 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 6fab6cf364..4f4f54dc40 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -42,7 +42,7 @@
 from easybuild.framework.easyconfig import MANDATORY, MODULES, OTHER, TOOLCHAIN
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.environment import modify_env
-from easybuild.tools.filetools import read_file, write_file
+from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.options import EasyBuildOptions
 from easybuild.tools.version import VERSION
@@ -550,16 +550,15 @@ def test_search(self):
                 os.remove(dummylogfn)
 
     def test_dry_run(self):
-        """Test dry runs."""
-
+        """Test dry run (long format)."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
         args = [
             os.path.join(os.path.dirname(__file__), 'easyconfigs', 'gzip-1.4-GCC-4.6.3.eb'),
             '--dry-run',
-            '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
             '--unittest-file=%s' % self.logfile,
+            '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
         ]
         outtxt = self.eb_main(args, logfile=dummylogfn)
 
@@ -573,12 +572,29 @@ def test_dry_run(self):
             regex = re.compile(r" \* \[%s\] \S+%s \(module: %s\)" % (mark, ec, mod), re.M)
             self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
 
+    def test_dry_run_short(self):
+        """Test dry run (short format)."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        # copy test easyconfigs to easybuild/easyconfigs subdirectory of temp directory
+        # to check with easyconfigs install path is auto-included in robot path
+        tmpdir = tempfile.mkdtemp(prefix='easybuild-easyconfigs-pkg-install-path')
+        mkdir(os.path.join(tmpdir, 'easybuild'), parents=True)
+
+        test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        shutil.copytree(test_ecs_dir, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
+
+        orig_sys_path = sys.path[:]
+        sys.path.append(tmpdir)
+
         for dry_run_arg in ['-D', '--dry-run-short']:
             open(self.logfile, 'w').write('')
             args = [
-                os.path.join(os.path.dirname(__file__), 'easyconfigs', 'gzip-1.4-GCC-4.6.3.eb'),
+                os.path.join(tmpdir, 'easybuild', 'easyconfigs', 'gzip-1.4-GCC-4.6.3.eb'),
                 dry_run_arg,
-                '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+                # purposely specifying senseless dir, to test auto-inclusion of easyconfigs pkg path in robot path
+                '--robot=%s' % os.path.join(tmpdir, 'robot_decoy'),
                 '--unittest-file=%s' % self.logfile,
             ]
             outtxt = self.eb_main(args, logfile=dummylogfn)
@@ -597,6 +613,10 @@ def test_dry_run(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
+        # cleanup
+        shutil.rmtree(tmpdir)
+        sys.path[:] = orig_sys_path
+
     def test_try_robot_force(self):
         """
         Test correct behavior for combination of --try-toolchain --robot --force.
@@ -1012,13 +1032,15 @@ def test_allow_modules_tool_mismatch(self):
 
     def test_try(self):
         """Test whether --try options are taken into account."""
-        ec_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb')
+        ecs_path = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
+        ec_file = os.path.join(ecs_path, 'toy-0.0.eb')
         args = [
             ec_file,
             '--sourcepath=%s' % self.test_sourcepath,
             '--buildpath=%s' % self.test_buildpath,
             '--installpath=%s' % self.test_installpath,
             '--dry-run',
+            '--robot=%s' % ecs_path,
         ]
 
         test_cases = [
@@ -1054,7 +1076,7 @@ def test_recursive_try(self):
         tweaked_toy_ec = os.path.join(self.test_buildpath, 'toy-0.0-tweaked.eb')
         shutil.copy2(os.path.join(ecs_path, 'toy-0.0.eb'), tweaked_toy_ec)
         f = open(tweaked_toy_ec, 'a')
-        f.write("dependencies = [('gzip', '1.4')]")  # add fictious dependency
+        f.write("dependencies = [('gzip', '1.4')]\n")  # add fictious dependency
         f.close()
 
         sourcepath = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'sources')
@@ -1092,13 +1114,18 @@ def test_recursive_try(self):
                 #mod_regex = re.compile("%s \(module: .*%s\)$" % (ec, mod), re.M)
                 self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 
+        # clear fictious dependency
+        f = open(tweaked_toy_ec, 'a')
+        f.write("dependencies = []\n")
+        f.close()
+
         # no recursive try if --(try-)software(-X) is involved
         for extra_args in [['--try-software-version=1.2.3'], ['--software-version=1.2.3']]:
             outtxt = self.eb_main(args + extra_args, raise_error=True)
-            for mod in ['toy/1.2.3-gompi-1.4.10', 'gzip/1.4-gompi-1.4.10', 'gompi/1.4.10', 'GCC/4.7.2']:
+            for mod in ['toy/1.2.3-gompi-1.4.10', 'gompi/1.4.10', 'GCC/4.7.2']:
                 mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
                 self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
-            for mod in ['gzip/1.2.3-gompi-1.4.10']:
+            for mod in ['gompi/1.2.3', 'GCC/1.2.3']:
                 mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
                 self.assertFalse(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 

From bdb84d72c3e8942736ca02f27413b9fbc7cb7c8d Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@gmail.com>
Date: Tue, 21 Oct 2014 15:27:34 +0200
Subject: [PATCH 0259/1356] added a check for the http return code + download
 progress report

    * Check the http return code before starting a download, urllib.retrieve does not do this by default
    * show a download report ' X kb downloaded of XXX total kb (XX% complete) xxx kbps'
---
 easybuild/tools/filetools.py | 37 +++++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 4e1ece1bc9..7e47a5b0f3 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -253,10 +253,44 @@ def download_file(filename, url, path):
     downloaded = False
     attempt_cnt = 0
 
+    # use this functions's scope for the variable we share with our inner function
+    download_file.last_time = time.time()
+    download_file.last_block = 0
+    # internal function to report on download progress
+    def report(block, blocksize, bytesize):
+        """
+        This is a reporthook for urlretrieve, it takes 3 integers as arguments
+        the current downloaded block, the total ammount of blocks, and the blocksize
+        logs the download progress every 10 seconds
+        """
+        if download_file.last_time + 10 < time.time():
+            newblocks = block - download_file.last_block
+            download_file.last_block = block
+
+            _log.info('download report: %d kb of %d kb (%d %%, %d kbps)', block * blocksize, bytesize, int(block * blocksize * 100 / bytesize),
+                      (blocksize * newblocks) / 1024  // (time.time() - download_file.last_time))
+
+            download_file.last_time = time.time()
+
+
     # try downloading three times max.
     while not downloaded and attempt_cnt < 3:
+        # get http response code first before downloading file
+        urlfile = urllib.urlopen(url)
+        response_code = urlfile.getcode()
+        urlfile.close()
+
+        _log.debug('http response code for given url: %d', response_code)
+        if response_code == 404:
+            _log.warning('url %s was not found (404), not trying again', url)
+            return None
+
+        download_file.last_time = time.time()
+        download_file.last_block = 0
+
+        (_, httpmsg) = urllib.urlretrieve(url, path, reporthook=report)
+        _log.debug('headers of download: %s', httpmsg)
 
-        (_, httpmsg) = urllib.urlretrieve(url, path)
 
         if httpmsg.type == "text/html" and not filename.endswith('.html'):
             _log.warning("HTML file downloaded but not expecting it, so assuming invalid download.")
@@ -273,6 +307,7 @@ def download_file(filename, url, path):
         attempt_cnt += 1
         _log.warning("Downloading failed at attempt %s, retrying..." % attempt_cnt)
 
+
     # failed to download after multiple attempts
     return None
 

From 8494e9b3efdb182c01edc11cfe4dfa5f933c9827 Mon Sep 17 00:00:00 2001
From: pescobar <pescobar001@gmail.com>
Date: Wed, 22 Oct 2014 22:01:24 +0200
Subject: [PATCH 0260/1356] scape modloadmsg

---
 easybuild/tools/module_generator.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 2d51d7fcd9..3751d2da5d 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -33,6 +33,7 @@
 @author: Fotis Georgatos (Uni.Lu)
 """
 import os
+import re
 import tempfile
 from vsc.utils import fancylogger
 
@@ -209,6 +210,7 @@ def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.
         """
+        msg = re.escape(msg)
         return '\n'.join([
             "",
             "if [ module-info mode load ] {",

From 4e31c1babbc2f48406ba71d771116b443db4c0d9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Oct 2014 19:56:00 +0200
Subject: [PATCH 0261/1356] include info log msg with name/location of used
 easyblock

---
 easybuild/framework/easyblock.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 662daf8bf8..a9b199e823 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -38,6 +38,7 @@
 
 import copy
 import glob
+import inspect
 import os
 import shutil
 import stat
@@ -113,6 +114,7 @@ def __init__(self, ec):
         Initialize the EasyBlock instance.
         @param ec: a parsed easyconfig file (EasyConfig instance)
         """
+
         # keep track of original working directory, so we can go back there
         self.orig_workdir = os.getcwd()
 
@@ -167,6 +169,12 @@ def __init__(self, ec):
         # list of loaded modules
         self.loaded_modules = []
 
+        # iterate configure/build/options
+        self.iter_opts = {}
+
+        # sanity check fail error messages to report (if any)
+        self.sanity_check_fail_msgs = []
+
         # robot path
         self.robot_path = build_option('robot_path')
 
@@ -176,14 +184,9 @@ def __init__(self, ec):
         # keep track of original environment, so we restore it if needed
         self.orig_environ = copy.deepcopy(os.environ)
 
-        # at the end of __init__, initialise the logging
+        # initialize logger
         self._init_log()
-
-        # iterate configure/build/options
-        self.iter_opts = {}
-
-        # sanity check fail error messages to report (if any)
-        self.sanity_check_fail_msgs = []
+        self.log.info("This is easyblock %s at %s" % (self.__class__.__name__, inspect.getmodule(self)))
 
         # should we keep quiet?
         self.silent = build_option('silent')

From a8383ea68762f0bee4ea5ca52b36e84800c97e4a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Oct 2014 20:11:25 +0200
Subject: [PATCH 0262/1356] enhance easyblock unit tests to check for 'This is
 easyblock' log msg

---
 test/framework/easyblock.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index ee959f59b6..52a028b934 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -115,6 +115,12 @@ def check_extra_options_format(extra_options):
         sys.stdout.close()
         sys.stdout = stdoutorig
 
+        # check whether 'This is easyblock' log message is there
+        tup = ('EasyBlock', 'easybuild.framework.easyblock', 'easybuild/framework/easyblock.pyc')
+        eb_log_msg_re = re.compile(r"INFO This is easyblock %s at <module '%s' from '%s'>" % tup, re.M)
+        logtxt = read_file(eb.logfile)
+        self.assertTrue(eb_log_msg_re.search(logtxt), "Pattern '%s' found in: %s" % (eb_log_msg_re.pattern, logtxt))
+
         # test extensioneasyblock, as extension
         exeb1 = ExtensionEasyBlock(eb, {'name': 'foo', 'version': '0.0'})
         self.assertEqual(exeb1.cfg['name'], 'foo')
@@ -383,6 +389,12 @@ def test_get_easyblock_instance(self):
         eb = get_easyblock_instance(ec)
         self.assertTrue(isinstance(eb, EB_toy))
 
+        # check whether 'This is easyblock' log message is there
+        tup = ('EB_toy', 'easybuild.easyblocks.toy', '.*test/framework/sandbox/easybuild/easyblocks/toy.pyc')
+        eb_log_msg_re = re.compile(r"INFO This is easyblock %s at <module '%s' from '%s'>" % tup, re.M)
+        logtxt = read_file(eb.logfile)
+        self.assertTrue(eb_log_msg_re.search(logtxt), "Pattern '%s' found in: %s" % (eb_log_msg_re.pattern, logtxt))
+
     def test_obtain_file(self):
         """Test obtain_file method."""
         toy_tarball = 'toy-0.0.tar.gz'

From 62cf114b2520b57cd6c6b4824a8cbe08cfbc6cf8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Oct 2014 20:23:57 +0200
Subject: [PATCH 0263/1356] check for number of available sources when
 determining where to apply patches

---
 easybuild/framework/easyblock.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 662daf8bf8..9395f0bbed 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1271,8 +1271,13 @@ def patch_step(self, beginpath=None):
                 srcpathsuffix = patch['copy']
                 copy = True
 
-            if not beginpath:
-                beginpath = self.src[srcind]['finalpath']
+            if beginpath is None:
+                src_cnt = len(self.src)
+                if srcind < src_cnt:
+                    beginpath = self.src[srcind]['finalpath']
+                else:
+                    tup = (patch['name'], srcind, src_cnt, self.src)
+                    self.log.error("Can't apply patch %s to source at index %s, only %s sources listed: %s" % tup)
 
             src = os.path.abspath("%s/%s" % (beginpath, srcpathsuffix))
 

From df2b5acfd7a6260206150134561151b615db22a7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Oct 2014 20:30:06 +0200
Subject: [PATCH 0264/1356] add unit test for patch_step

---
 test/framework/easyblock.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index ee959f59b6..c5d60415b5 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -516,6 +516,25 @@ def test_exclude_path_to_top_of_module_tree(self):
         os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
         init_config(build_options=build_options)
 
+    def test_patch_step(self):
+        """Test patch step."""
+        ec = process_easyconfig(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb'))[0]
+        orig_sources = ec['ec']['sources'][:]
+
+        # test applying patches without sources
+        ec['ec']['sources'] = []
+        eb = EasyBlock(ec['ec'])
+        eb.fetch_step()
+        eb.extract_step()
+        self.assertErrorRegex(EasyBuildError, '.*', eb.patch_step)
+
+        # test actual patching of unpacked sources
+        ec['ec']['sources'] = orig_sources
+        eb = EasyBlock(ec['ec'])
+        eb.fetch_step()
+        eb.extract_step()
+        eb.patch_step()
+
     def tearDown(self):
         """ make sure to remove the temporary file """
         super(EasyBlockTest, self).tearDown()

From d4e13da74f4581276e00138b4e40d3c7be19f1be Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Oct 2014 08:13:57 +0200
Subject: [PATCH 0265/1356] fix 'This is easyblock' regex pattern

---
 test/framework/easyblock.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 52a028b934..5ba74eae66 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -116,7 +116,7 @@ def check_extra_options_format(extra_options):
         sys.stdout = stdoutorig
 
         # check whether 'This is easyblock' log message is there
-        tup = ('EasyBlock', 'easybuild.framework.easyblock', 'easybuild/framework/easyblock.pyc')
+        tup = ('EasyBlock', 'easybuild.framework.easyblock', 'easybuild/framework/easyblock.pyc*')
         eb_log_msg_re = re.compile(r"INFO This is easyblock %s at <module '%s' from '%s'>" % tup, re.M)
         logtxt = read_file(eb.logfile)
         self.assertTrue(eb_log_msg_re.search(logtxt), "Pattern '%s' found in: %s" % (eb_log_msg_re.pattern, logtxt))
@@ -390,7 +390,7 @@ def test_get_easyblock_instance(self):
         self.assertTrue(isinstance(eb, EB_toy))
 
         # check whether 'This is easyblock' log message is there
-        tup = ('EB_toy', 'easybuild.easyblocks.toy', '.*test/framework/sandbox/easybuild/easyblocks/toy.pyc')
+        tup = ('EB_toy', 'easybuild.easyblocks.toy', '.*test/framework/sandbox/easybuild/easyblocks/toy.pyc*')
         eb_log_msg_re = re.compile(r"INFO This is easyblock %s at <module '%s' from '%s'>" % tup, re.M)
         logtxt = read_file(eb.logfile)
         self.assertTrue(eb_log_msg_re.search(logtxt), "Pattern '%s' found in: %s" % (eb_log_msg_re.pattern, logtxt))

From 39d9a2925559c142da16ea628d25aa2ce27f9174 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Fri, 24 Oct 2014 09:45:53 +0200
Subject: [PATCH 0266/1356] Added a toolchain for Parastation MPICH and GCC (+
 full toolchain)

---
 easybuild/toolchains/gpsmpi.py | 36 ++++++++++++++++++++++++++++
 easybuild/toolchains/gpsolf.py | 43 ++++++++++++++++++++++++++++++++++
 2 files changed, 79 insertions(+)
 create mode 100755 easybuild/toolchains/gpsmpi.py
 create mode 100755 easybuild/toolchains/gpsolf.py

diff --git a/easybuild/toolchains/gpsmpi.py b/easybuild/toolchains/gpsmpi.py
new file mode 100755
index 0000000000..4d79d8cde6
--- /dev/null
+++ b/easybuild/toolchains/gpsmpi.py
@@ -0,0 +1,36 @@
+##
+# Copyright 2012-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for gpsmpi compiler toolchain (includes GCC and Parastation MPICH).
+
+"""
+
+from easybuild.toolchains.compiler.gcc import Gcc
+from easybuild.toolchains.mpi.mpich import Mpich
+
+
+class Gpsmpi(Gcc, Mpich):
+    """Compiler toolchain with GCC and Parastation MPICH."""
+    NAME = 'gpsmpi'
diff --git a/easybuild/toolchains/gpsolf.py b/easybuild/toolchains/gpsolf.py
new file mode 100755
index 0000000000..1e10e97926
--- /dev/null
+++ b/easybuild/toolchains/gpsolf.py
@@ -0,0 +1,43 @@
+##
+# Copyright 2013-2014 Ghent University
+#
+# This file is triple-licensed under GPLv2 (see below), MIT, and
+# BSD three-clause licenses.
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for gmpolf compiler toolchain (includes GCC, Parastation MPICH, OpenBLAS, LAPACK, ScaLAPACK and FFTW).
+
+"""
+
+from easybuild.toolchains.compiler.gcc import Gcc
+from easybuild.toolchains.fft.fftw import Fftw
+from easybuild.toolchains.linalg.openblas import OpenBLAS
+from easybuild.toolchains.linalg.scalapack import ScaLAPACK
+from easybuild.toolchains.mpi.mpich import Mpich
+
+
+class Gpsolf(Gcc, Mpich, OpenBLAS, ScaLAPACK, Fftw):
+@author: Bart Verleye (University of Auckland)
+    """Compiler toolchain with GCC, Parastation MPICH, OpenBLAS, ScaLAPACK and FFTW."""
+    NAME = 'gpsolf'

From 347af62f800f1a52818dd51faa87ef38ab1a8854 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 24 Oct 2014 09:51:11 +0200
Subject: [PATCH 0267/1356] Update gpsolf.py

---
 easybuild/toolchains/gpsolf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/gpsolf.py b/easybuild/toolchains/gpsolf.py
index 1e10e97926..6bffb8974c 100755
--- a/easybuild/toolchains/gpsolf.py
+++ b/easybuild/toolchains/gpsolf.py
@@ -38,6 +38,6 @@
 
 
 class Gpsolf(Gcc, Mpich, OpenBLAS, ScaLAPACK, Fftw):
-@author: Bart Verleye (University of Auckland)
+
     """Compiler toolchain with GCC, Parastation MPICH, OpenBLAS, ScaLAPACK and FFTW."""
     NAME = 'gpsolf'

From f496f85fec0a5e1dcf725b1bfb354ddb03eca3f8 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Fri, 24 Oct 2014 09:58:12 +0200
Subject: [PATCH 0268/1356] Added support for Parastation MPICH toolchains with
 Intel compilers

---
 easybuild/toolchains/intel-para.py | 44 ++++++++++++++++++++++++++++++
 easybuild/toolchains/ipsmpi.py     | 39 ++++++++++++++++++++++++++
 2 files changed, 83 insertions(+)
 create mode 100644 easybuild/toolchains/intel-para.py
 create mode 100755 easybuild/toolchains/ipsmpi.py

diff --git a/easybuild/toolchains/intel-para.py b/easybuild/toolchains/intel-para.py
new file mode 100644
index 0000000000..f146c45ad3
--- /dev/null
+++ b/easybuild/toolchains/intel-para.py
@@ -0,0 +1,44 @@
+##
+# Copyright 2012-2013 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for intel compiler toolchain (includes Intel compilers (icc, ifort), Parastation MPICH,
+Intel Math Kernel Library (MKL), and Intel FFTW wrappers).
+
+"""
+
+from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.toolchains.fft.intelfftw import IntelFFTW
+from easybuild.toolchains.mpi.mpich import Mpich
+from easybuild.toolchains.linalg.intelmkl import IntelMKL
+
+
+class IntelPara(IntelIccIfort, Mpich, IntelMKL, IntelFFTW):
+    """
+    Compiler toolchain with Intel compilers (icc/ifort), Parastation MPICH,
+    Intel Math Kernel Library (MKL) and Intel FFTW wrappers.
+    """
+    NAME = 'intel-para'
+    BLACS_LIB = ["mkl_blacs_intelmpi%(lp64)s"]
+    
diff --git a/easybuild/toolchains/ipsmpi.py b/easybuild/toolchains/ipsmpi.py
new file mode 100755
index 0000000000..f94fb27b3f
--- /dev/null
+++ b/easybuild/toolchains/ipsmpi.py
@@ -0,0 +1,39 @@
+##
+# Copyright 2012-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for intel compiler toolchain (includes Intel compilers (icc, ifort), Parastation MPICH2).
+
+"""
+
+from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.toolchains.mpi.mpich import Mpich
+
+
+
+class Ipsmpi(IntelIccIfort, Mpich):
+    """
+    Compiler toolchain with Intel compilers (icc/ifort), Parastation MPICH.
+    """
+    NAME = 'ipsmpi'

From e31c7c1f5d3fcb1c253c57ccd949abcb6dc3b623 Mon Sep 17 00:00:00 2001
From: Pablo Escobar <pescobar001@gmail.com>
Date: Fri, 24 Oct 2014 11:54:19 +0200
Subject: [PATCH 0269/1356] just escape chars in CHARS_TO_ESCAPE

---
 easybuild/tools/module_generator.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 3751d2da5d..1675dca286 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -47,6 +47,8 @@
 
 _log = fancylogger.getLogger('module_generator', fname=False)
 
+# chars we want to escape in the generated modulefiles
+CHARS_TO_ESCAPE = ["$"]
 
 class ModuleGenerator(object):
     """
@@ -210,7 +212,8 @@ def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.
         """
-        msg = re.escape(msg)
+        for element in CHARS_TO_ESCAPE:
+            msg = re.sub(r'((?<!\\)[%s])'%element,r'\\\1',msg)
         return '\n'.join([
             "",
             "if [ module-info mode load ] {",

From 1f117f36cd834dc4fee392a2ecb98751405bc683 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Fri, 24 Oct 2014 13:31:58 +0200
Subject: [PATCH 0270/1356] Added generic support for Intel plus MPICH. Built
 ParaStation MPI specific toolchains using these templates.

---
 easybuild/toolchains/impich.py | 38 ++++++++++++++++++++++++++++++++++
 easybuild/toolchains/ipsmpi.py |  9 ++++----
 2 files changed, 43 insertions(+), 4 deletions(-)
 create mode 100644 easybuild/toolchains/impich.py

diff --git a/easybuild/toolchains/impich.py b/easybuild/toolchains/impich.py
new file mode 100644
index 0000000000..efe9c513a2
--- /dev/null
+++ b/easybuild/toolchains/impich.py
@@ -0,0 +1,38 @@
+##
+# Copyright 2013-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for impich compiler toolchain (includes Intel compilers (icc, ifort), MPICH.
+
+"""
+
+from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.toolchains.mpi.mpich import Mpich
+
+
+class Impich(IntelIccIfort, Mpich):
+    """
+    Compiler toolchain with Intel compilers (icc/ifort), MPICH.
+    """
+    NAME = 'impich'
diff --git a/easybuild/toolchains/ipsmpi.py b/easybuild/toolchains/ipsmpi.py
index f94fb27b3f..eb27704e1d 100755
--- a/easybuild/toolchains/ipsmpi.py
+++ b/easybuild/toolchains/ipsmpi.py
@@ -23,17 +23,18 @@
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
 """
-EasyBuild support for intel compiler toolchain (includes Intel compilers (icc, ifort), Parastation MPICH2).
+EasyBuild support for intel compiler toolchain (includes Intel compilers (icc, ifort), Parastation MPICH).
 
 """
 
-from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
-from easybuild.toolchains.mpi.mpich import Mpich
+from easybuild.toolchains.impich import Impich
 
 
 
-class Ipsmpi(IntelIccIfort, Mpich):
+class Ipsmpi(Impich):
     """
     Compiler toolchain with Intel compilers (icc/ifort), Parastation MPICH.
     """
     NAME = 'ipsmpi'
+    # Use Parastation naming
+    MPI_MODULE_NAME = ["psmpi"]

From 73c361f5c4eb0419d9281d0534a26bd977f22823 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Fri, 24 Oct 2014 13:36:50 +0200
Subject: [PATCH 0271/1356] Added forgotten updates for last commit

---
 easybuild/toolchains/impmkl.py     | 9 ++++-----
 easybuild/toolchains/intel-para.py | 6 +++---
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/easybuild/toolchains/impmkl.py b/easybuild/toolchains/impmkl.py
index ba0f1521b6..383753d1db 100644
--- a/easybuild/toolchains/impmkl.py
+++ b/easybuild/toolchains/impmkl.py
@@ -23,20 +23,19 @@
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
 """
-EasyBuild support for impmkl compiler toolchain (includes Intel compilers (icc, ifort), MPICH2,
+EasyBuild support for impmkl compiler toolchain (includes Intel compilers (icc, ifort), MPICH,
 Intel Math Kernel Library (MKL) , and Intel FFTW wrappers.
 
 @author: Kenneth Hoste (Ghent University)
 """
 
-from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.toolchains.impich import Impich
 from easybuild.toolchains.fft.intelfftw import IntelFFTW
-from easybuild.toolchains.mpi.mpich2 import Mpich2
 from easybuild.toolchains.linalg.intelmkl import IntelMKL
 
-class Impmkl(IntelIccIfort, Mpich2, IntelMKL, IntelFFTW):
+class Impmkl(Impich, IntelMKL, IntelFFTW):
     """
-    Compiler toolchain with Intel compilers (icc/ifort), MPICH2,
+    Compiler toolchain with Intel compilers (icc/ifort), MPICH,
     Intel Math Kernel Library (MKL) and Intel FFTW wrappers.
     """
     NAME = 'impmkl'
diff --git a/easybuild/toolchains/intel-para.py b/easybuild/toolchains/intel-para.py
index f146c45ad3..9ea7a259e1 100644
--- a/easybuild/toolchains/intel-para.py
+++ b/easybuild/toolchains/intel-para.py
@@ -28,17 +28,17 @@
 
 """
 
-from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.toolchains.ipsmpi import Ipsmpi
 from easybuild.toolchains.fft.intelfftw import IntelFFTW
-from easybuild.toolchains.mpi.mpich import Mpich
 from easybuild.toolchains.linalg.intelmkl import IntelMKL
 
 
-class IntelPara(IntelIccIfort, Mpich, IntelMKL, IntelFFTW):
+class IntelPara(Ipsmpi, IntelMKL, IntelFFTW):
     """
     Compiler toolchain with Intel compilers (icc/ifort), Parastation MPICH,
     Intel Math Kernel Library (MKL) and Intel FFTW wrappers.
     """
     NAME = 'intel-para'
+    # Parastation MPI needs to be matched with the IntelMPI blacs library
     BLACS_LIB = ["mkl_blacs_intelmpi%(lp64)s"]
     

From 8644a8a3ebd238c896dca71c1684a062f8c502ae Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 24 Oct 2014 13:39:18 +0200
Subject: [PATCH 0272/1356] Update ipsmpi.py

---
 easybuild/toolchains/ipsmpi.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/toolchains/ipsmpi.py b/easybuild/toolchains/ipsmpi.py
index eb27704e1d..8b99018284 100755
--- a/easybuild/toolchains/ipsmpi.py
+++ b/easybuild/toolchains/ipsmpi.py
@@ -30,7 +30,6 @@
 from easybuild.toolchains.impich import Impich
 
 
-
 class Ipsmpi(Impich):
     """
     Compiler toolchain with Intel compilers (icc/ifort), Parastation MPICH.

From d1060a33114335a4d1d663ab2d752afb13494ba2 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Fri, 24 Oct 2014 13:50:48 +0200
Subject: [PATCH 0273/1356] Clean up support for GCC and MPICH, add specific
 toolchains for Parastation MPI

---
 easybuild/toolchains/gmpich.py | 36 ++++++++++++++++++++++++++++++++++
 easybuild/toolchains/gpsmpi.py |  5 +++--
 easybuild/toolchains/gpsolf.py |  6 ++----
 3 files changed, 41 insertions(+), 6 deletions(-)
 create mode 100644 easybuild/toolchains/gmpich.py

diff --git a/easybuild/toolchains/gmpich.py b/easybuild/toolchains/gmpich.py
new file mode 100644
index 0000000000..a3d7c56a2b
--- /dev/null
+++ b/easybuild/toolchains/gmpich.py
@@ -0,0 +1,36 @@
+##
+# Copyright 2012-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for gmpich compiler toolchain (includes GCC and MPICH).
+
+"""
+
+from easybuild.toolchains.compiler.gcc import Gcc
+from easybuild.toolchains.mpi.mpich import Mpich
+
+
+class Gmpich(Gcc, Mpich):
+    """Compiler toolchain with GCC and MPICH."""
+    NAME = 'gmpich'
diff --git a/easybuild/toolchains/gpsmpi.py b/easybuild/toolchains/gpsmpi.py
index 4d79d8cde6..75a4174e77 100755
--- a/easybuild/toolchains/gpsmpi.py
+++ b/easybuild/toolchains/gpsmpi.py
@@ -27,10 +27,11 @@
 
 """
 
-from easybuild.toolchains.compiler.gcc import Gcc
-from easybuild.toolchains.mpi.mpich import Mpich
+from easybuild.toolchains.gmpich import Gmpich
 
 
 class Gpsmpi(Gcc, Mpich):
     """Compiler toolchain with GCC and Parastation MPICH."""
     NAME = 'gpsmpi'
+    # Use Parastation naming
+    MPI_MODULE_NAME = ["psmpi"]
diff --git a/easybuild/toolchains/gpsolf.py b/easybuild/toolchains/gpsolf.py
index 1e10e97926..45e51b4b07 100755
--- a/easybuild/toolchains/gpsolf.py
+++ b/easybuild/toolchains/gpsolf.py
@@ -30,14 +30,12 @@
 
 """
 
-from easybuild.toolchains.compiler.gcc import Gcc
+from easybuild.toolchains.gpsmpi import Gpsmpi
 from easybuild.toolchains.fft.fftw import Fftw
 from easybuild.toolchains.linalg.openblas import OpenBLAS
 from easybuild.toolchains.linalg.scalapack import ScaLAPACK
-from easybuild.toolchains.mpi.mpich import Mpich
 
 
-class Gpsolf(Gcc, Mpich, OpenBLAS, ScaLAPACK, Fftw):
-@author: Bart Verleye (University of Auckland)
+class Gpsolf(Gmpich, OpenBLAS, ScaLAPACK, Fftw):
     """Compiler toolchain with GCC, Parastation MPICH, OpenBLAS, ScaLAPACK and FFTW."""
     NAME = 'gpsolf'

From 602d9eb7060872bf47c79c29bb8823cca7325cf9 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Fri, 24 Oct 2014 13:59:38 +0200
Subject: [PATCH 0274/1356] Make sure we are pushing the correct classes

---
 easybuild/toolchains/gpsmpi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/gpsmpi.py b/easybuild/toolchains/gpsmpi.py
index 75a4174e77..b1dc8e0ab5 100755
--- a/easybuild/toolchains/gpsmpi.py
+++ b/easybuild/toolchains/gpsmpi.py
@@ -30,7 +30,7 @@
 from easybuild.toolchains.gmpich import Gmpich
 
 
-class Gpsmpi(Gcc, Mpich):
+class Gpsmpi(Gmpich):
     """Compiler toolchain with GCC and Parastation MPICH."""
     NAME = 'gpsmpi'
     # Use Parastation naming

From df1614e80d615bd09679af1352828575b848adeb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 28 Oct 2014 18:58:19 +0100
Subject: [PATCH 0275/1356] fix remark w.r.t. 'This is easyblock' log message

---
 easybuild/framework/easyblock.py | 5 ++++-
 test/framework/easyblock.py      | 6 +++---
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index a9b199e823..e479265a59 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -186,7 +186,6 @@ def __init__(self, ec):
 
         # initialize logger
         self._init_log()
-        self.log.info("This is easyblock %s at %s" % (self.__class__.__name__, inspect.getmodule(self)))
 
         # should we keep quiet?
         self.silent = build_option('silent')
@@ -222,6 +221,10 @@ def _init_log(self):
 
         self.log.info(this_is_easybuild())
 
+        this_module = inspect.getmodule(self)
+        tup = (self.__class__.__name__, this_module.__name__, this_module.__file__)
+        self.log.info("This is easyblock %s from module %s (%s)" % tup)
+
     def close_log(self):
         """
         Shutdown the logger.
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 5ba74eae66..6d4bfce241 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -116,8 +116,8 @@ def check_extra_options_format(extra_options):
         sys.stdout = stdoutorig
 
         # check whether 'This is easyblock' log message is there
-        tup = ('EasyBlock', 'easybuild.framework.easyblock', 'easybuild/framework/easyblock.pyc*')
-        eb_log_msg_re = re.compile(r"INFO This is easyblock %s at <module '%s' from '%s'>" % tup, re.M)
+        tup = ('EasyBlock', 'easybuild.framework.easyblock', '.*easybuild/framework/easyblock.pyc*')
+        eb_log_msg_re = re.compile(r"INFO This is easyblock %s from module %s (%s)" % tup, re.M)
         logtxt = read_file(eb.logfile)
         self.assertTrue(eb_log_msg_re.search(logtxt), "Pattern '%s' found in: %s" % (eb_log_msg_re.pattern, logtxt))
 
@@ -391,7 +391,7 @@ def test_get_easyblock_instance(self):
 
         # check whether 'This is easyblock' log message is there
         tup = ('EB_toy', 'easybuild.easyblocks.toy', '.*test/framework/sandbox/easybuild/easyblocks/toy.pyc*')
-        eb_log_msg_re = re.compile(r"INFO This is easyblock %s at <module '%s' from '%s'>" % tup, re.M)
+        eb_log_msg_re = re.compile(r"INFO This is easyblock %s from module %s (%s)" % tup, re.M)
         logtxt = read_file(eb.logfile)
         self.assertTrue(eb_log_msg_re.search(logtxt), "Pattern '%s' found in: %s" % (eb_log_msg_re.pattern, logtxt))
 

From 732e8e859f3201e24acac94ac5f05611d08d838e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 28 Oct 2014 21:18:36 +0100
Subject: [PATCH 0276/1356] remarks fixed

---
 easybuild/framework/easyblock.py | 41 ++++++++++++++++----------------
 1 file changed, 20 insertions(+), 21 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 9395f0bbed..fb05e78ba3 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1259,33 +1259,32 @@ def patch_step(self, beginpath=None):
         for patch in self.patches:
             self.log.info("Applying patch %s" % patch['name'])
 
-            copy = False
-            # default: patch first source
-            srcind = 0
-            if 'source' in patch:
-                srcind = patch['source']
-            srcpathsuffix = ''
-            if 'sourcepath' in patch:
-                srcpathsuffix = patch['sourcepath']
-            elif 'copy' in patch:
-                srcpathsuffix = patch['copy']
-                copy = True
+            # patch source at specified index (first source if not specified)
+            srcind = patch.get('source', 0)
+            # if patch level is specified, use that (otherwise let apply_patch derive patch level)
+            level = patch.get('level', None)
+            # determine suffix of source path to apply patch in (if any)
+            srcpathsuffix = patch.get('sourcepath', patch.get('copy', ''))
+            # determine whether 'patch' file should be copied rather than applied
+            copy_patch = 'copy' in patch and not 'sourcepath' in patch
+
+            tup = (srcind, level, srcpathsuffix, copy)
+            self.log.debug("Source index: %s; patch level: %s; source path suffix: %s; copy patch: %s" % tup)
 
             if beginpath is None:
-                src_cnt = len(self.src)
-                if srcind < src_cnt:
+                try:
                     beginpath = self.src[srcind]['finalpath']
-                else:
-                    tup = (patch['name'], srcind, src_cnt, self.src)
-                    self.log.error("Can't apply patch %s to source at index %s, only %s sources listed: %s" % tup)
+                    self.log.debug("Determine begin path for patch %s: %s" % (patch['name'], beginpath))
+                except IndexError, err:
+                    tup = (patch['name'], srcind, self.src, err)
+                    self.log.error("Can't apply patch %s to source at index %s of list %s: %s" % tup)
+            else:
+                self.log.debug("Using specified begin path for patch %s: %s" % (patch['name'], beginpath))
 
             src = os.path.abspath("%s/%s" % (beginpath, srcpathsuffix))
+            self.log.debug("Applying patch %s in path %s" % (patch, src))
 
-            level = None
-            if 'level' in patch:
-                level = patch['level']
-
-            if not apply_patch(patch['path'], src, copy=copy, level=level):
+            if not apply_patch(patch['path'], src, copy=copy_patch, level=level):
                 self.log.error("Applying patch %s failed" % patch['name'])
 
     def prepare_step(self):

From 2a975aa86d86dcd07b7beb426d2f0abb4b4b8b86 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Oct 2014 09:11:51 +0100
Subject: [PATCH 0277/1356] fix tests that break when installed easyconfigs pkg
 is present

---
 easybuild/main.py         | 6 +++---
 test/framework/options.py | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 6c323db342..5be168f372 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -89,9 +89,9 @@ def find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=
                 _log.warning("Failed to remove generated easyconfig file %s: %s" % (ec_file, err))
 
             # don't use a generated easyconfig unless generation was requested (using a --try-X option)
-            print_error(("Unable to find an easyconfig for the given specifications: %s; "
-                         "to make EasyBuild try to generate a matching easyconfig, "
-                         "use the --try-X options ") % build_specs, log=_log)
+            _log.error(("Unable to find an easyconfig for the given specifications: %s; "
+                        "to make EasyBuild try to generate a matching easyconfig, "
+                        "use the --try-X options ") % build_specs)
 
     return [(ec_file, generated)]
 
diff --git a/test/framework/options.py b/test/framework/options.py
index 4f4f54dc40..507e3368fe 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -578,7 +578,7 @@ def test_dry_run_short(self):
         os.close(fd)
 
         # copy test easyconfigs to easybuild/easyconfigs subdirectory of temp directory
-        # to check with easyconfigs install path is auto-included in robot path
+        # to check whether easyconfigs install path is auto-included in robot path
         tmpdir = tempfile.mkdtemp(prefix='easybuild-easyconfigs-pkg-install-path')
         mkdir(os.path.join(tmpdir, 'easybuild'), parents=True)
 
@@ -586,7 +586,7 @@ def test_dry_run_short(self):
         shutil.copytree(test_ecs_dir, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
 
         orig_sys_path = sys.path[:]
-        sys.path.append(tmpdir)
+        sys.path.insert(0, tmpdir)  # prepend to give it preference over possible other installed easyconfigs pkgs
 
         for dry_run_arg in ['-D', '--dry-run-short']:
             open(self.logfile, 'w').write('')

From 8e5887c3c258d0b4c599eba442de32d7e53e6183 Mon Sep 17 00:00:00 2001
From: pescobar <pescobar001@gmail.com>
Date: Wed, 29 Oct 2014 09:48:48 +0100
Subject: [PATCH 0278/1356] CHARS_TO_SCAPE is a class var. Escape using .join
 instead of a loop

---
 easybuild/tools/module_generator.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 1675dca286..32690fe1e9 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -47,13 +47,15 @@
 
 _log = fancylogger.getLogger('module_generator', fname=False)
 
-# chars we want to escape in the generated modulefiles
-CHARS_TO_ESCAPE = ["$"]
 
 class ModuleGenerator(object):
     """
     Class for generating module files.
     """
+
+    # chars we want to escape in the generated modulefiles
+    CHARS_TO_ESCAPE = ["$"]
+
     def __init__(self, application, fake=False):
         self.app = application
         self.fake = fake
@@ -212,8 +214,7 @@ def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.
         """
-        for element in CHARS_TO_ESCAPE:
-            msg = re.sub(r'((?<!\\)[%s])'%element,r'\\\1',msg)
+        msg = re.sub(r'((?<!\\)[%s])'% ''.join(self.CHARS_TO_ESCAPE),r'\\\1',msg)
         return '\n'.join([
             "",
             "if [ module-info mode load ] {",

From cddd1d8d44de47604396b2d59c184bba7e70b9f9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Oct 2014 11:40:46 +0100
Subject: [PATCH 0279/1356] style fix in module_generator.py

---
 easybuild/tools/module_generator.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 32690fe1e9..f83d3a55ee 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -214,7 +214,8 @@ def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.
         """
-        msg = re.sub(r'((?<!\\)[%s])'% ''.join(self.CHARS_TO_ESCAPE),r'\\\1',msg)
+        # escape any (non-escaped) characters with special meaning by prefixing them with a backslash
+        msg = re.sub(r'((?<!\\)[%s])'% ''.join(self.CHARS_TO_ESCAPE), r'\\\1', msg)
         return '\n'.join([
             "",
             "if [ module-info mode load ] {",

From 0e23da2c096e9e953f4194ed4a81326d1316606d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Oct 2014 11:41:22 +0100
Subject: [PATCH 0280/1356] enhance msg_on_load unit test to verify escaping of
 '$'

---
 test/framework/module_generator.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index c67b629db2..8e606c3ed1 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -171,8 +171,15 @@ def test_alias(self):
 
     def test_load_msg(self):
         """Test including a load message in the module file."""
-        tcl_load_msg = '\nif [ module-info mode load ] {\n        puts stderr     "test"\n}\n'
-        self.assertEqual(tcl_load_msg, self.modgen.msg_on_load('test'))
+        tcl_load_msg = '\n'.join([
+            '',
+            "if [ module-info mode load ] {",
+            "        puts stderr     \"test \\$test \\$test",
+            "test \\$foo \\$bar\"",
+            "}",
+            '',
+        ])
+        self.assertEqual(tcl_load_msg, self.modgen.msg_on_load('test $test \\$test\ntest $foo \\$bar'))
 
     def test_tcl_footer(self):
         """Test including a Tcl footer."""

From c081147b201e5cd54788daaed2824c31c26252a0 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@ugent.be>
Date: Wed, 29 Oct 2014 13:13:03 +0100
Subject: [PATCH 0281/1356] addressed remarks

---
 easybuild/tools/filetools.py | 37 ++++++++++++++++++++++++++----------
 1 file changed, 27 insertions(+), 10 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 7e47a5b0f3..a0369a3869 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -257,19 +257,25 @@ def download_file(filename, url, path):
     download_file.last_time = time.time()
     download_file.last_block = 0
     # internal function to report on download progress
-    def report(block, blocksize, bytesize):
+    def report(block, blocksize, filesize):
         """
-        This is a reporthook for urlretrieve, it takes 3 integers as arguments
-        the current downloaded block, the total ammount of blocks, and the blocksize
-        logs the download progress every 10 seconds
+        This is a reporthook for urlretrieve, it takes 3 integers as arguments:
+        the current downloaded block, the size in bytes of one block and the total size of the downlad.
+        This efectively logs the download progress every 10 seconds with loglevel info.
         """
         if download_file.last_time + 10 < time.time():
             newblocks = block - download_file.last_block
             download_file.last_block = block
+            total_download = block * blocksize
+            percentage = int(block * blocksize * 100 / filesize)
+            kbps = (blocksize * newblocks) / 1024  // (time.time() - download_file.last_time)
 
-            _log.info('download report: %d kb of %d kb (%d %%, %d kbps)', block * blocksize, bytesize, int(block * blocksize * 100 / bytesize),
-                      (blocksize * newblocks) / 1024  // (time.time() - download_file.last_time))
-
+            if filesize <= 0:
+                # content length isn't always set
+                _log.info('download report: %d kb downloaded (%d kbps)', total_download, kbps) 
+            else:
+                _log.info('download report: %d kb of %d kb (%d %%, %d kbps)', total_download, filesize, percentage, kbps)
+                          
             download_file.last_time = time.time()
 
 
@@ -288,9 +294,20 @@ def report(block, blocksize, bytesize):
         download_file.last_time = time.time()
         download_file.last_block = 0
 
-        (_, httpmsg) = urllib.urlretrieve(url, path, reporthook=report)
-        _log.debug('headers of download: %s', httpmsg)
-
+        try:
+            (_, httpmsg) = urllib.urlretrieve(url, path, reporthook=report)
+        except ContentTooShortError:
+            _log.warning(
+                "Expected file of %d bytes, but download size dit not match, removing file and retrying", 
+                int(httpmsg.dict['content-length']),
+            )
+            try:
+                os.remove(path)
+            except OSError, err:
+                  _log.error("Failed to remove downloaded file:" % err)
+            # try again
+            attempt_cnt += 1
+            continue
 
         if httpmsg.type == "text/html" and not filename.endswith('.html'):
             _log.warning("HTML file downloaded but not expecting it, so assuming invalid download.")

From 898d61f658d10c36bd7aca6045038706a7cb40bd Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Wed, 29 Oct 2014 13:54:12 +0100
Subject: [PATCH 0282/1356] changed permissions

---
 easybuild/toolchains/gpsmpi.py | 0
 easybuild/toolchains/gpsolf.py | 0
 easybuild/toolchains/iimpi.py  | 0
 easybuild/toolchains/intel.py  | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 easybuild/toolchains/gpsmpi.py
 mode change 100755 => 100644 easybuild/toolchains/gpsolf.py
 mode change 100755 => 100644 easybuild/toolchains/iimpi.py
 mode change 100755 => 100644 easybuild/toolchains/intel.py

diff --git a/easybuild/toolchains/gpsmpi.py b/easybuild/toolchains/gpsmpi.py
old mode 100755
new mode 100644
diff --git a/easybuild/toolchains/gpsolf.py b/easybuild/toolchains/gpsolf.py
old mode 100755
new mode 100644
diff --git a/easybuild/toolchains/iimpi.py b/easybuild/toolchains/iimpi.py
old mode 100755
new mode 100644
diff --git a/easybuild/toolchains/intel.py b/easybuild/toolchains/intel.py
old mode 100755
new mode 100644

From f2c4c6e3d65a84cf2139655bf54e65316aef0f5f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Oct 2014 18:46:01 +0100
Subject: [PATCH 0283/1356] enforce that hiddendependencies is a subset of
 dependencies

---
 easybuild/framework/easyconfig/easyconfig.py | 23 ++++++++++++++++++++
 test/framework/easyblock.py                  |  3 ++-
 test/framework/easyconfig.py                 |  2 +-
 3 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 3fea3e6c3e..1b6a42bc8b 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -339,6 +339,9 @@ def validate(self, check_osdeps=True):
         self.log.info("Checking licenses")
         self.validate_license()
 
+        self.log.info("Checking whether list of hidden dependencies is a subset of list of dependencies")
+        self.validate_hiddendeps()
+
     def validate_license(self):
         """Validate the license"""
         lic = self._config['software_license'][0]
@@ -407,6 +410,26 @@ def validate_iterate_opts_lists(self):
 
         return True
 
+    def validate_hiddendeps(self):
+        """
+        Validate that list of hidden dependencies is a subset of the list of dependencies.
+        The list of dependencies is adjusted to only include non-hidden dependencies.
+        """
+        dep_mod_names = [dep['full_mod_name'] for dep in self['dependencies']]
+
+        for hidden_dep in self['hiddendependencies']:
+            # check whether hidden dep is a listed dep using *visible* module name, not hidden one
+            visible_mod_name = ActiveMNS().det_full_module_name(hidden_dep, force_visible=True)
+            if visible_mod_name in dep_mod_names:
+                self['dependencies'] = [d for d in self['dependencies'] if d['full_mod_name'] != visible_mod_name]
+                self.log.debug("Removed dependency matching hidden dependency %s" % hidden_dep)
+            else:
+                # hidden dependencies must also be included in list of dependencies;
+                # this is done to try and make easyconfigs portable w.r.t. site-specific policies with minimal effort,
+                # i.e. by simply removing the 'hiddendependencies' specification
+                tup = (visible_mod_name, dep_mod_names)
+                self.log.error("Hidden dependency with visible module name %s not in list of dependencies: %s" % tup)
+
     def dependencies(self):
         """
         Returns an array of parsed dependencies (after filtering, if requested)
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 41df64dd44..91a7441d18 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -274,6 +274,7 @@ def test_make_module_step(self):
         version = "3.14"
         deps = [('GCC', '4.6.4')]
         hiddendeps = [('toy', '0.0-deps')]
+        alldeps = deps + hiddendeps  # hidden deps must be included in list of deps
         modextravars = {'PI': '3.1415', 'FOO': 'bar'}
         modextrapaths = {'PATH': 'pibin', 'CPATH': 'pi/include'}
         self.contents = '\n'.join([
@@ -282,7 +283,7 @@ def test_make_module_step(self):
             'homepage = "http://example.com"',
             'description = "test easyconfig"',
             "toolchain = {'name': 'dummy', 'version': 'dummy'}",
-            "dependencies = %s" % str(deps),
+            "dependencies = %s" % str(alldeps),
             "hiddendependencies = %s" % str(hiddendeps),
             "builddependencies = [('OpenMPI', '1.6.4-GCC-4.6.4')]",
             "modextravars = %s" % str(modextravars),
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index c78ec426a3..d922848751 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -566,7 +566,7 @@ def test_obtain_easyconfig(self):
         new_patches = ['two.patch', 'three.patch']
         specs.update({
             'patches': new_patches[:],
-            'dependencies': [('foo', '1.2.3'), ('bar', '666', '-bleh', ('gompi', '1.4.10'))],
+            'dependencies': [('foo', '1.2.3'), ('bar', '666', '-bleh', ('gompi', '1.4.10')), ('test', '3.2.1')],
             'hiddendependencies': [('test', '3.2.1')],
         })
         parsed_deps = [

From 61882851a963b075f7cebce7168bee42569808fe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Oct 2014 20:42:25 +0100
Subject: [PATCH 0284/1356] fix test easyconfig w.r.t. requirement that
 hiddendeps is subset of deps

---
 test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb b/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
index b59e6160d2..f47c7482a5 100644
--- a/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
@@ -26,6 +26,7 @@ sources = ['%s-%s.tar.gz'%(name,version)]
 source_urls = [GNU_SOURCE]
 
 hiddendependencies = [('toy', '0.0', '-deps', True)]
+dependencies = hiddendependencies  # hidden deps must be included in list of deps
 
 # make sure the gzip and gunzip binaries are available after installation
 sanity_check_paths = {

From 0eafcbd4b3f7fc278ee486e42c3f3a81dd496c2e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 Oct 2014 07:47:01 +0100
Subject: [PATCH 0285/1356] report all hidden deps not included in list of
 deps, enhance unit test

---
 easybuild/framework/easyconfig/easyconfig.py |  8 ++++++--
 test/framework/easyconfig.py                 | 11 ++++++++++-
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 1b6a42bc8b..c58e7349a5 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -417,6 +417,7 @@ def validate_hiddendeps(self):
         """
         dep_mod_names = [dep['full_mod_name'] for dep in self['dependencies']]
 
+        faulty_deps = []
         for hidden_dep in self['hiddendependencies']:
             # check whether hidden dep is a listed dep using *visible* module name, not hidden one
             visible_mod_name = ActiveMNS().det_full_module_name(hidden_dep, force_visible=True)
@@ -427,8 +428,11 @@ def validate_hiddendeps(self):
                 # hidden dependencies must also be included in list of dependencies;
                 # this is done to try and make easyconfigs portable w.r.t. site-specific policies with minimal effort,
                 # i.e. by simply removing the 'hiddendependencies' specification
-                tup = (visible_mod_name, dep_mod_names)
-                self.log.error("Hidden dependency with visible module name %s not in list of dependencies: %s" % tup)
+                faulty_deps.append(visible_mod_name)
+
+        if faulty_deps:
+            tup = (faulty_deps, dep_mod_names)
+            self.log.error("Hidden dependencies with visible module names %s not in list of dependencies: %s" % tup)
 
     def dependencies(self):
         """
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index d922848751..de25d9e82c 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -566,7 +566,7 @@ def test_obtain_easyconfig(self):
         new_patches = ['two.patch', 'three.patch']
         specs.update({
             'patches': new_patches[:],
-            'dependencies': [('foo', '1.2.3'), ('bar', '666', '-bleh', ('gompi', '1.4.10')), ('test', '3.2.1')],
+            'dependencies': [('foo', '1.2.3'), ('bar', '666', '-bleh', ('gompi', '1.4.10'))],
             'hiddendependencies': [('test', '3.2.1')],
         })
         parsed_deps = [
@@ -601,6 +601,15 @@ def test_obtain_easyconfig(self):
                 'hidden': True,
             },
         ]
+
+        # hidden dependencies must be included in list of dependencies
+        res = obtain_ec_for(specs, [self.ec_dir], None)
+        self.assertEqual(res[0], True)
+        error_pattern = "Hidden dependencies with visible module names .* not in list of dependencies: .*"
+        self.assertErrorRegex(EasyBuildError, error_pattern, EasyConfig, res[1])
+
+        specs['dependencies'].append(('test', '3.2.1'))
+
         res = obtain_ec_for(specs, [self.ec_dir], None)
         self.assertEqual(res[0], True)
         ec = EasyConfig(res[1])

From beed0effc858ef026817de4cab70391de6da8d5d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 Oct 2014 10:01:27 +0100
Subject: [PATCH 0286/1356] add --robot-paths configure option

---
 easybuild/main.py          | 12 ++++++------
 easybuild/tools/options.py |  5 +++--
 easybuild/tools/robot.py   |  4 ++--
 3 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 5be168f372..09ee05a31b 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -182,11 +182,6 @@ def main(testing_data=(None, None, None)):
     if options.umask is not None:
         _log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
 
-    # determine easybuild-easyconfigs package install path
-    easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR)
-    if not easyconfigs_pkg_paths:
-        _log.warning("Failed to determine install path for easybuild-easyconfigs package.")
-
     # process software build specifications (if any), i.e.
     # software name/version, toolchain name/version, extra patches, ...
     (try_to_generate, build_specs) = process_software_build_specs(options)
@@ -196,7 +191,7 @@ def main(testing_data=(None, None, None)):
     tweaked_ecs = try_to_generate and build_specs
     tweaked_ecs_path, pr_path = alt_easyconfig_paths(eb_tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
     auto_robot = try_to_generate or options.dep_graph or options.search or options.search_short
-    robot_path = det_robot_path(options.robot, easyconfigs_pkg_paths, tweaked_ecs_path, pr_path, auto_robot=auto_robot)
+    robot_path = det_robot_path(options.robot, options.robot_paths, tweaked_ecs_path, pr_path, auto_robot=auto_robot)
     _log.debug("Full robot path: %s" % robot_path)
 
     # configure & initialize build options
@@ -226,6 +221,11 @@ def main(testing_data=(None, None, None)):
     if query:
         search_easyconfigs(query, short=not options.search)
 
+    # determine easybuild-easyconfigs package install path
+    easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR)
+    if not easyconfigs_pkg_paths:
+        _log.warning("Failed to determine install path for easybuild-easyconfigs package.")
+
     # determine paths to easyconfigs
     paths = det_easyconfig_paths(orig_paths, options.from_pr, easyconfigs_pkg_paths)
     if not paths:
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index a346cb8e56..757b217b7f 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -96,8 +96,9 @@ def basic_options(self):
             'job': ("Submit the build as a job", None, 'store_true', False),
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
-            'robot': ("Path(s) to search for easyconfigs for missing dependencies (colon-separated)" ,
-                      None, 'store_or_None', default_robot_path, 'r', {'metavar': 'PATH'}),
+            'robot': ("Enable dependency resolution", None, 'store_or_None', None, {'metavar': 'PATH[:PATH][,PATH]'}),
+            'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
+                           None, 'store', [default_robot_path], {'metavar': 'PATH[,PATH]'}),
             'skip': ("Skip existing software (useful for installing additional packages)",
                      None, 'store_true', False, 'k'),
             'stop': ("Stop the installation after certain step", 'choice', 'store_or_None', 'source', 's', all_stops),
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index b478571485..6ffbf77a7a 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -48,7 +48,7 @@
 _log = fancylogger.getLogger('tools.robot', fname=False)
 
 
-def det_robot_path(robot_option, easyconfigs_pkg_paths, tweaked_ecs_path, pr_path, auto_robot=False):
+def det_robot_path(robot_option, robot_paths_option, tweaked_ecs_path, pr_path, auto_robot=False):
     """Determine robot path."""
     # do not use robot option directly, it's not a list instance (and it shouldn't be modified)
     robot_path = []
@@ -61,7 +61,7 @@ def det_robot_path(robot_option, easyconfigs_pkg_paths, tweaked_ecs_path, pr_pat
             _log.error("No robot paths specified, and unable to determine easybuild-easyconfigs install path.")
 
     if robot_path or auto_robot:
-        robot_path.extend(easyconfigs_pkg_paths)
+        robot_path.extend(robot_paths_option)
         _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
 
     if tweaked_ecs_path is not None:

From 9ca6c529eb92d6a8a7bdda2027b1a99a2c21fd5e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 Oct 2014 10:46:36 +0100
Subject: [PATCH 0287/1356] enable use of --show_hidden for avail subcommand
 and recent Lmod versions

---
 easybuild/tools/modules.py | 30 +++++++++++++++++++++---------
 1 file changed, 21 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 30893436b9..ce8353b0e2 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -197,6 +197,14 @@ def set_and_check_version(self):
             if res:
                 self.version = res.group('version')
                 self.log.info("Found version %s" % self.version)
+
+                # make sure version is a valid StrictVersion (e.g., 5.7.3.1 is invalid),
+                # and replace 'rc' by 'b', to make StrictVersion treat it as a beta-release
+                self.version = self.version.replace('rc', 'b')
+                if len(self.version.split('.')) > 3:
+                    self.version = '.'.join(self.version.split('.')[:3])
+
+                self.log.info("Converted actual version to '%s'" % self.version)
             else:
                 self.log.error("Failed to determine version from option '%s' output: %s" % (self.VERSION_OPTION, txt))
         except (OSError), err:
@@ -205,12 +213,7 @@ def set_and_check_version(self):
         if self.REQ_VERSION is None:
             self.log.debug('No version requirement defined.')
         else:
-            # make sure version is a valid StrictVersion (e.g., 5.7.3.1 is invalid),
-            # and replace 'rc' by 'b', to make StrictVersion treat it as a beta-release
-            check_ver = self.version.replace('rc', 'b')
-            if len(check_ver.split('.')) > 3:
-                check_ver = '.'.join(check_ver.split('.')[:3])
-            if StrictVersion(check_ver) < StrictVersion(self.REQ_VERSION):
+            if StrictVersion(self.version) < StrictVersion(self.REQ_VERSION):
                 msg = "EasyBuild requires v%s >= v%s (no rc), found v%s"
                 self.log.error(msg % (self.__class__.__name__, self.REQ_VERSION, self.version))
             else:
@@ -323,16 +326,19 @@ def check_module_path(self):
             self.use(mod_path)
         self.log.info("$MODULEPATH set based on list of module paths (via 'module use'): %s" % os.environ['MODULEPATH'])
 
-    def available(self, mod_name=None):
+    def available(self, mod_name=None, extra_args=None):
         """
         Return a list of available modules for the given (partial) module name;
         use None to obtain a list of all available modules.
 
         @param mod_name: a (partial) module name for filtering (default: None)
         """
+        if extra_args is None:
+            extra_args = []
         if mod_name is None:
             mod_name = ''
-        mods = self.run_module('avail', mod_name)
+        args = ['avail'] + extra_args + [mod_name]
+        mods = self.run_module(*args)
 
         # sort list of modules in alphabetical order
         mods.sort(key=lambda m: m['mod_name'])
@@ -818,7 +824,13 @@ def available(self, mod_name=None):
 
         @param name: a (partial) module name for filtering (default: None)
         """
-        mods = super(Lmod, self).available(mod_name=mod_name)
+        extra_args = []
+        if StrictVersion(self.version) >= StrictVersion('5.7.5'):
+            # make hidden modules visible for recent version of Lmod
+            extra_args = ['--show_hidden']
+
+        mods = super(Lmod, self).available(mod_name=mod_name, extra_args=extra_args)
+
         # only retain actual modules, exclude module directories (which end with a '/')
         real_mods = [mod for mod in mods if not mod.endswith('/')]
 

From 53f2bf9ef3fcfee09c2dae785673b9ed6bfeb6f3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 Oct 2014 16:07:19 +0100
Subject: [PATCH 0288/1356] fix setting default for --robot-paths

---
 easybuild/tools/options.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 757b217b7f..173bce5de9 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -80,11 +80,12 @@ def basic_options(self):
         all_stops = [x[0] for x in EasyBlock.get_steps()]
         strictness_options = [run.IGNORE, run.WARN, run.ERROR]
 
-        try:
-            default_robot_path = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None)[0]
-        except:
+        easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None)
+        if easyconfigs_pkg_paths:
+            default_robot_paths = easyconfigs_pkg_paths
+        else:
             self.log.warning("basic_options: unable to determine default easyconfig path")
-            default_robot_path = False  # False as opposed to None, since None is used for indicating that --robot was used
+            default_robot_paths = []
 
         descr = ("Basic options", "Basic runtime options for EasyBuild.")
 
@@ -98,7 +99,7 @@ def basic_options(self):
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
             'robot': ("Enable dependency resolution", None, 'store_or_None', None, {'metavar': 'PATH[:PATH][,PATH]'}),
             'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
-                           None, 'store', [default_robot_path], {'metavar': 'PATH[,PATH]'}),
+                           None, 'store', default_robot_paths, {'metavar': 'PATH[,PATH]'}),
             'skip': ("Skip existing software (useful for installing additional packages)",
                      None, 'store_true', False, 'k'),
             'stop': ("Stop the installation after certain step", 'choice', 'store_or_None', 'source', 's', all_stops),

From ad3ae417ed547e9b8ab03ec8497d47b99b8472f5 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@ugent.be>
Date: Thu, 30 Oct 2014 16:45:46 +0100
Subject: [PATCH 0289/1356] check to see if a valid response code was returned,
 could also be None when offline

---
 easybuild/tools/filetools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index a0369a3869..56d202eea5 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -285,8 +285,8 @@ def report(block, blocksize, filesize):
         urlfile = urllib.urlopen(url)
         response_code = urlfile.getcode()
         urlfile.close()
-
-        _log.debug('http response code for given url: %d', response_code)
+        if response_code:
+            _log.debug('http response code for given url: %d', response_code)
         if response_code == 404:
             _log.warning('url %s was not found (404), not trying again', url)
             return None

From dcf40fc95abbe3d9e48be1a3d7a803f54c330efa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 Oct 2014 18:43:22 +0100
Subject: [PATCH 0290/1356] fix default value for --robot

---
 easybuild/tools/options.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 173bce5de9..4a5258a8a2 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -97,7 +97,7 @@ def basic_options(self):
             'job': ("Submit the build as a job", None, 'store_true', False),
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
-            'robot': ("Enable dependency resolution", None, 'store_or_None', None, {'metavar': 'PATH[:PATH][,PATH]'}),
+            'robot': ("Enable dependency resolution", None, 'store_or_None', False, {'metavar': 'PATH[:PATH][,PATH]'}),
             'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
                            None, 'store', default_robot_paths, {'metavar': 'PATH[,PATH]'}),
             'skip': ("Skip existing software (useful for installing additional packages)",

From 4c6fed17d5b8aab65bfbddfa30d681a72c5c6738 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 31 Oct 2014 08:54:43 +0100
Subject: [PATCH 0291/1356] add tests for ListOfStrings behaviour

---
 test/framework/format_convert.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/test/framework/format_convert.py b/test/framework/format_convert.py
index 4cb5e70f3b..84c5c0f067 100644
--- a/test/framework/format_convert.py
+++ b/test/framework/format_convert.py
@@ -61,6 +61,12 @@ def test_listofstrings(self):
         res = ListOfStrings(txt.replace(ListOfStrings.SEPARATOR_LIST, ListOfStrings.SEPARATOR_LIST + ' '))
         self.assertEqual(res, dest)
 
+        # empty string yields a list with an empty string
+        self.assertEqual(ListOfStrings(''), [''])
+
+        # empty entries are retained
+        self.assertEqual(ListOfStrings('a,,b'), ['a', '', 'b'])
+
     def test_dictofstrings(self):
         """Test dict of strings"""
         # test default separators

From 8f533e6795a0b3b0a89a104bc9a7353f02cfdb67 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 31 Oct 2014 09:00:55 +0100
Subject: [PATCH 0292/1356] fix default value for --robot and --robot-paths +
 determining full list of robot paths

---
 easybuild/tools/options.py | 24 ++++++++++++++++--------
 easybuild/tools/robot.py   | 16 +++++++---------
 2 files changed, 23 insertions(+), 17 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 4a5258a8a2..e8f8721c4b 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -82,10 +82,10 @@ def basic_options(self):
 
         easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None)
         if easyconfigs_pkg_paths:
-            default_robot_paths = easyconfigs_pkg_paths
+            default_robot_paths = os.pathsep.join(easyconfigs_pkg_paths)
         else:
             self.log.warning("basic_options: unable to determine default easyconfig path")
-            default_robot_paths = []
+            default_robot_paths = ''
 
         descr = ("Basic options", "Basic runtime options for EasyBuild.")
 
@@ -97,9 +97,10 @@ def basic_options(self):
             'job': ("Submit the build as a job", None, 'store_true', False),
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
-            'robot': ("Enable dependency resolution", None, 'store_or_None', False, {'metavar': 'PATH[:PATH][,PATH]'}),
+            'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
+                      None, 'store_or_None', '', {'metavar': 'PATH[:PATH]'}),
             'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
-                           None, 'store', default_robot_paths, {'metavar': 'PATH[,PATH]'}),
+                            None, 'store', default_robot_paths, {'metavar': 'PATH[:PATH]'}),
             'skip': ("Skip existing software (useful for installing additional packages)",
                      None, 'store_true', False, 'k'),
             'stop': ("Stop the installation after certain step", 'choice', 'store_or_None', 'source', 's', all_stops),
@@ -413,13 +414,20 @@ def _postprocess_config(self):
         if self.options.pretend:
             self.options.installpath = get_pretend_installpath()
 
+        # helper class to convert a string with colon-separated robot paths into a list of robot paths
+        class RobotPath(ListOfStrings):
+            SEPARATOR_LIST = os.pathsep
+            # explicit definition of __str__ is required for unknown reason related to the way Wrapper is defined
+            __str__ = ListOfStrings.__str__
+
         # split supplied list of robot paths to obtain a list
         if self.options.robot:
-            class RobotPath(ListOfStrings):
-                SEPARATOR_LIST = os.pathsep
-                # explicit definition of __str__ is required for unknown reason related to the way Wrapper is defined
-                __str__ = ListOfStrings.__str__
             self.options.robot = RobotPath(self.options.robot)
+        if self.options.robot is not None:
+            self.options.robot = list(self.options.robot)
+        if self.options.robot_paths:
+            self.options.robot_paths = RobotPath(self.options.robot_paths)
+        self.options.robot_paths = list(self.options.robot_paths)
 
     def _postprocess_list_avail(self):
         """Create all the additional info that can be requested (exit at the end)"""
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index 6ffbf77a7a..06094056a1 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -50,24 +50,22 @@
 
 def det_robot_path(robot_option, robot_paths_option, tweaked_ecs_path, pr_path, auto_robot=False):
     """Determine robot path."""
-    # do not use robot option directly, it's not a list instance (and it shouldn't be modified)
     robot_path = []
+
+    # if --robot is enabled, use any paths specified to it
     if robot_option is not None:
-        if robot_option:
-            robot_path = list(robot_option)
-            _log.info("Using robot path(s): %s" % robot_path)
-        else:
-            # if options.robot is not None and False, easyconfigs pkg install path could not be found (see options.py)
-            _log.error("No robot paths specified, and unable to determine easybuild-easyconfigs install path.")
+        robot_path = robot_option
+        _log.info("Using robot path(s): %s" % robot_path)
 
-    if robot_path or auto_robot:
+    # if --robot is specified or should be enabled automagically, include --robot-paths too
+    if robot_option is not None or auto_robot:
         robot_path.extend(robot_paths_option)
         _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
 
+    # paths to tweaked easyconfigs or easyconfigs downloaded from a PR have priority
     if tweaked_ecs_path is not None:
         robot_path.insert(0, tweaked_ecs_path)
         _log.info("Prepended list of robot search paths with %s: %s" % (tweaked_ecs_path, robot_path))
-
     if pr_path is not None:
         robot_path.insert(0, pr_path)
         _log.info("Prepended list of robot search paths with %s: %s" % (pr_path, robot_path))

From 26fa0a1d594fd0d0ee57b140e5da191c4ae3dad6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 31 Oct 2014 09:01:52 +0100
Subject: [PATCH 0293/1356] add unit test for --robot and --robot-paths
 interaction

---
 test/framework/options.py | 44 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 507e3368fe..00ff216d77 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1233,6 +1233,50 @@ def toy(extra_args=None):
         tup = (filter_arg_regex.pattern, test_report_txt)
         self.assertTrue(filter_arg_regex.search(test_report_txt), "%s in %s" % tup)
 
+    def test_robot(self):
+        """Test --robot and --robot-paths command line options."""
+        test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        eb_file = os.path.join(test_ecs_path, 'gzip-1.4-GCC-4.6.3.eb')  # includes 'toy' as a dependency
+
+        # enable robot, but without passing path required to resolve toy dependency => FAIL
+        args = [
+            eb_file,
+            '--robot',
+            '--dry-run',
+        ]
+        self.assertErrorRegex(EasyBuildError, 'Irresolvable dependencies', self.eb_main, args, raise_error=True)
+
+        # add path to test easyconfigs to robot paths, so dependencies can be resolved
+        self.eb_main(args + ['--robot-paths=%s' % test_ecs_path], raise_error=True)
+
+        # copy test easyconfigs to easybuild/easyconfigs subdirectory of temp directory
+        # to check whether easyconfigs install path is auto-included in robot path
+        tmpdir = tempfile.mkdtemp(prefix='easybuild-easyconfigs-pkg-install-path')
+        mkdir(os.path.join(tmpdir, 'easybuild'), parents=True)
+        shutil.copytree(test_ecs_path, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
+
+        # prepend path to test easyconfigs into Python search path, so it gets picked up as --robot-paths default
+        orig_sys_path = sys.path[:]
+        sys.path.insert(0, tmpdir)
+        self.eb_main(args, raise_error=True)
+
+        shutil.rmtree(tmpdir)
+        sys.path[:] = orig_sys_path
+
+        # make sure that paths specified to --robot get preference over --robot-paths
+        args = [
+            eb_file,
+            '--robot=%s' % test_ecs_path,
+            '--robot-paths=%s' % os.path.join(tmpdir, 'easybuild', 'easyconfigs'),
+            '--dry-run',
+        ]
+        outtxt = self.eb_main(args, raise_error=True)
+
+        for ec in ['GCC-4.6.3.eb', 'ictce-4.1.13.eb', 'toy-0.0-deps.eb', 'gzip-1.4-GCC-4.6.3.eb']:
+            ec_regex = re.compile('^\s\*\s\[[xF ]\]\s%s' % os.path.join(test_ecs_path, ec), re.M)
+            self.assertTrue(ec_regex.search(outtxt), "Pattern %s found in %s" % (ec_regex.pattern, outtxt))
+
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(CommandLineOptionsTest)

From 82e538b2bab329c5c7f7be28efdeefdbcc4a448f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 31 Oct 2014 09:34:33 +0100
Subject: [PATCH 0294/1356] clean up if mess

---
 easybuild/main.py          |  2 +-
 easybuild/tools/options.py | 13 ++++++-------
 easybuild/tools/robot.py   | 16 ++++------------
 3 files changed, 11 insertions(+), 20 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 09ee05a31b..81efab95be 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -191,7 +191,7 @@ def main(testing_data=(None, None, None)):
     tweaked_ecs = try_to_generate and build_specs
     tweaked_ecs_path, pr_path = alt_easyconfig_paths(eb_tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
     auto_robot = try_to_generate or options.dep_graph or options.search or options.search_short
-    robot_path = det_robot_path(options.robot, options.robot_paths, tweaked_ecs_path, pr_path, auto_robot=auto_robot)
+    robot_path = det_robot_path(options.robot_paths, tweaked_ecs_path, pr_path, auto_robot=auto_robot)
     _log.debug("Full robot path: %s" % robot_path)
 
     # configure & initialize build options
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index e8f8721c4b..37c519bc6d 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -420,14 +420,13 @@ class RobotPath(ListOfStrings):
             # explicit definition of __str__ is required for unknown reason related to the way Wrapper is defined
             __str__ = ListOfStrings.__str__
 
-        # split supplied list of robot paths to obtain a list
         if self.options.robot:
-            self.options.robot = RobotPath(self.options.robot)
-        if self.options.robot is not None:
-            self.options.robot = list(self.options.robot)
-        if self.options.robot_paths:
-            self.options.robot_paths = RobotPath(self.options.robot_paths)
-        self.options.robot_paths = list(self.options.robot_paths)
+            # paths specified to --robot have preference over --robot-paths
+            all_robot_paths = os.pathsep.join([self.options.robot, self.options.robot_paths])
+        else:
+            all_robot_paths = self.options.robot_paths
+        # convert to a regular list, exclude empty strings
+        self.options.robot_paths = nub([x for x in list(RobotPath(all_robot_paths)) if x])
 
     def _postprocess_list_avail(self):
         """Create all the additional info that can be requested (exit at the end)"""
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index 06094056a1..b5e93a7d1b 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -48,19 +48,11 @@
 _log = fancylogger.getLogger('tools.robot', fname=False)
 
 
-def det_robot_path(robot_option, robot_paths_option, tweaked_ecs_path, pr_path, auto_robot=False):
+def det_robot_path(robot_paths_option, tweaked_ecs_path, pr_path, auto_robot=False):
     """Determine robot path."""
-    robot_path = []
-
-    # if --robot is enabled, use any paths specified to it
-    if robot_option is not None:
-        robot_path = robot_option
-        _log.info("Using robot path(s): %s" % robot_path)
-
-    # if --robot is specified or should be enabled automagically, include --robot-paths too
-    if robot_option is not None or auto_robot:
-        robot_path.extend(robot_paths_option)
-        _log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
+    # always include all robot paths (combo of --robot and --robot-paths, in that order)
+    robot_path = robot_paths_option
+    _log.info("Using robot path(s): %s" % robot_path)
 
     # paths to tweaked easyconfigs or easyconfigs downloaded from a PR have priority
     if tweaked_ecs_path is not None:

From 2aa65cae4658712be02367f6d42b053321a2bdd5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 31 Oct 2014 09:43:15 +0100
Subject: [PATCH 0295/1356] fix remarks

---
 easybuild/tools/options.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 37c519bc6d..94148f6bd3 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -84,7 +84,7 @@ def basic_options(self):
         if easyconfigs_pkg_paths:
             default_robot_paths = os.pathsep.join(easyconfigs_pkg_paths)
         else:
-            self.log.warning("basic_options: unable to determine default easyconfig path")
+            self.log.warning("basic_options: unable to determine easyconfigs pkg path for --robot-paths default")
             default_robot_paths = ''
 
         descr = ("Basic options", "Basic runtime options for EasyBuild.")
@@ -420,13 +420,13 @@ class RobotPath(ListOfStrings):
             # explicit definition of __str__ is required for unknown reason related to the way Wrapper is defined
             __str__ = ListOfStrings.__str__
 
-        if self.options.robot:
+        if self.options.robot is not None:
             # paths specified to --robot have preference over --robot-paths
             all_robot_paths = os.pathsep.join([self.options.robot, self.options.robot_paths])
         else:
             all_robot_paths = self.options.robot_paths
         # convert to a regular list, exclude empty strings
-        self.options.robot_paths = nub([x for x in list(RobotPath(all_robot_paths)) if x])
+        self.options.robot_paths = nub([x for x in RobotPath(all_robot_paths) if x])
 
     def _postprocess_list_avail(self):
         """Create all the additional info that can be requested (exit at the end)"""

From d28a668289de9979e099ddd4fb8116bfb4eeecf6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 31 Oct 2014 10:03:46 +0100
Subject: [PATCH 0296/1356] disable dep resolution by default (+ add test), fix
 remarks

---
 easybuild/tools/config.py  | 1 +
 easybuild/tools/options.py | 8 +++++---
 easybuild/tools/robot.py   | 5 ++---
 test/framework/options.py  | 8 ++++++++
 4 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 8de818bbf1..38ababafa5 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -82,6 +82,7 @@
         'only_blocks',
         'optarch',
         'regtest_output_dir',
+        'robot',
         'skip',
         'stop',
         'suffix_modules_path',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 94148f6bd3..3d3ed7f84e 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -420,11 +420,13 @@ class RobotPath(ListOfStrings):
             # explicit definition of __str__ is required for unknown reason related to the way Wrapper is defined
             __str__ = ListOfStrings.__str__
 
-        if self.options.robot is not None:
+        if self.options.robot is None:
+            all_robot_paths = self.options.robot_paths
+        else:
             # paths specified to --robot have preference over --robot-paths
             all_robot_paths = os.pathsep.join([self.options.robot, self.options.robot_paths])
-        else:
-            all_robot_paths = self.options.robot_paths
+            # avoid that options.robot is used for paths (since not everything is there)
+            self.options.robot = True
         # convert to a regular list, exclude empty strings
         self.options.robot_paths = nub([x for x in RobotPath(all_robot_paths) if x])
 
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index b5e93a7d1b..467ac1e5b1 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -50,8 +50,7 @@
 
 def det_robot_path(robot_paths_option, tweaked_ecs_path, pr_path, auto_robot=False):
     """Determine robot path."""
-    # always include all robot paths (combo of --robot and --robot-paths, in that order)
-    robot_path = robot_paths_option
+    robot_path = robot_paths_option[:]
     _log.info("Using robot path(s): %s" % robot_path)
 
     # paths to tweaked easyconfigs or easyconfigs downloaded from a PR have priority
@@ -123,7 +122,7 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
                             retain all deps when True, check matching build option when False
     """
 
-    robot = build_option('robot_path')
+    robot = build_option('robot') and build_option('robot_path')
     # retain all dependencies if specified by either the resp. build option or the dedicated named argument
     retain_all_deps = build_option('retain_all_deps') or retain_all_deps
 
diff --git a/test/framework/options.py b/test/framework/options.py
index 00ff216d77..138884c947 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1238,6 +1238,14 @@ def test_robot(self):
         test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         eb_file = os.path.join(test_ecs_path, 'gzip-1.4-GCC-4.6.3.eb')  # includes 'toy' as a dependency
 
+        # dependency resolution is disabled by default, even if required paths are available
+        args = [
+            eb_file,
+            '--robot-paths=%s' % test_ecs_path,
+            '--dry-run',
+        ]
+        self.assertErrorRegex(EasyBuildError, 'Irresolvable dependencies', self.eb_main, args, raise_error=True)
+
         # enable robot, but without passing path required to resolve toy dependency => FAIL
         args = [
             eb_file,

From f8eba315f42df09b2adf69c74c708e0543f86f97 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 31 Oct 2014 10:37:56 +0100
Subject: [PATCH 0297/1356] laatste ronde

---
 easybuild/main.py          |  7 +++++--
 easybuild/tools/config.py  |  2 +-
 easybuild/tools/robot.py   |  2 +-
 easybuild/tools/testing.py |  2 +-
 test/framework/options.py  | 13 ++++++++-----
 test/framework/robot.py    |  2 +-
 6 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 81efab95be..12991f2145 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -276,8 +276,11 @@ def main(testing_data=(None, None, None)):
 
     # determine an order that will allow all specs in the set to build
     if len(easyconfigs) > 0:
-        print_msg("resolving dependencies ...", log=_log, silent=testing)
-        ordered_ecs = resolve_dependencies(easyconfigs, build_specs=build_specs)
+        if options.robot:
+            print_msg("resolving dependencies ...", log=_log, silent=testing)
+            ordered_ecs = resolve_dependencies(easyconfigs, build_specs=build_specs)
+        else:
+            ordered_ecs = easyconfigs
     else:
         print_msg("No easyconfigs left to be built.", log=_log, silent=testing)
         ordered_ecs = []
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 38ababafa5..3c4467ad3c 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -82,7 +82,6 @@
         'only_blocks',
         'optarch',
         'regtest_output_dir',
-        'robot',
         'skip',
         'stop',
         'suffix_modules_path',
@@ -95,6 +94,7 @@
         'experimental',
         'force',
         'hidden',
+        'robot',
         'sequential',
         'set_gid_bit',
         'skip_test_cases',
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index 467ac1e5b1..89d625a8e6 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -122,7 +122,7 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
                             retain all deps when True, check matching build option when False
     """
 
-    robot = build_option('robot') and build_option('robot_path')
+    robot = build_option('robot_path')
     # retain all dependencies if specified by either the resp. build option or the dedicated named argument
     retain_all_deps = build_option('retain_all_deps') or retain_all_deps
 
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index 838736e6bf..5c67e972e2 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -186,7 +186,7 @@ def create_test_report(msg, ecs_with_res, init_session_state, pr_nr=None, gist_l
     build_overview = []
     for (ec, ec_res) in ecs_with_res:
         test_log = ''
-        if ec_res['success']:
+        if ec_res.get('success', False):
             test_result = 'SUCCESS'
         else:
             # compose test result string
diff --git a/test/framework/options.py b/test/framework/options.py
index 138884c947..4803299cb2 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -556,9 +556,9 @@ def test_dry_run(self):
 
         args = [
             os.path.join(os.path.dirname(__file__), 'easyconfigs', 'gzip-1.4-GCC-4.6.3.eb'),
-            '--dry-run',
+            '--dry-run',  # implies enabling dependency resolution
             '--unittest-file=%s' % self.logfile,
-            '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+            '--robot-paths=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
         ]
         outtxt = self.eb_main(args, logfile=dummylogfn)
 
@@ -1236,15 +1236,18 @@ def toy(extra_args=None):
     def test_robot(self):
         """Test --robot and --robot-paths command line options."""
         test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
-        eb_file = os.path.join(test_ecs_path, 'gzip-1.4-GCC-4.6.3.eb')  # includes 'toy' as a dependency
+        eb_file = os.path.join(test_ecs_path, 'gzip-1.4-GCC-4.6.3.eb')  # includes 'toy/.0.0-deps' as a dependency
+
+        # hide test modules
+        self.reset_modulepath([])
 
         # dependency resolution is disabled by default, even if required paths are available
         args = [
             eb_file,
             '--robot-paths=%s' % test_ecs_path,
-            '--dry-run',
         ]
-        self.assertErrorRegex(EasyBuildError, 'Irresolvable dependencies', self.eb_main, args, raise_error=True)
+        error_regex ='no module .* found for dependency'
+        self.assertErrorRegex(EasyBuildError, error_regex, self.eb_main, args, raise_error=True, do_build=True)
 
         # enable robot, but without passing path required to resolve toy dependency => FAIL
         args = [
diff --git a/test/framework/robot.py b/test/framework/robot.py
index 6562817c27..da3b4567ea 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -127,7 +127,7 @@ def test_resolve_dependencies(self):
             }],
             'parsed': True,
         }
-        build_options.update({'robot_path': self.base_easyconfig_dir})
+        build_options.update({'robot': True, 'robot_path': self.base_easyconfig_dir})
         init_config(build_options=build_options)
         res = resolve_dependencies([deepcopy(easyconfig_dep)])
         # dependency should be found, order should be correct

From 87b2434b42bfe15b3e6a517faba1a666b70e859f Mon Sep 17 00:00:00 2001
From: pescobar <pescobar001@gmail.com>
Date: Mon, 3 Nov 2014 22:07:57 +0100
Subject: [PATCH 0298/1356] fixed typo in xHost option

---
 easybuild/toolchains/compiler/inteliccifort.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index c224278eeb..b04d1a562a 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -56,7 +56,7 @@ class IntelIccIfort(Compiler):
     COMPILER_UNIQUE_OPTION_MAP = {
         'i8': 'i8',
         'r8': 'r8',
-        'optarch': 'xHOST',
+        'optarch': 'xHost',
         'openmp': 'openmp',  # both -openmp/-fopenmp are valid for enabling OpenMP
         'strict': ['fp-speculation=strict', 'fp-model strict'],
         'precise': ['fp-model precise'],
@@ -69,7 +69,7 @@ class IntelIccIfort(Compiler):
     }
 
     COMPILER_OPTIMAL_ARCHITECTURE_OPTION = {
-        systemtools.INTEL : 'xHOST',
+        systemtools.INTEL : 'xHost',
         systemtools.AMD : 'msse3',
     }
 

From 78f158b2614f3c83bdda0a00010808ea34ebb99a Mon Sep 17 00:00:00 2001
From: pescobar <pescobar001@gmail.com>
Date: Tue, 4 Nov 2014 10:41:46 +0100
Subject: [PATCH 0299/1356] switched from mavx to xHost

---
 easybuild/toolchains/compiler/inteliccifort.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index ac8b75e65e..045b80e6b3 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -70,7 +70,7 @@ class IntelIccIfort(Compiler):
 
     COMPILER_OPTIMAL_ARCHITECTURE_OPTION = {
         systemtools.INTEL : 'xHOST',
-        systemtools.AMD : 'mavx',
+        systemtools.AMD : 'xHost',
     }
 
     COMPILER_CC = 'icc'

From ed756c80bac8f53693c1a1c27fd097889def2c1a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 4 Nov 2014 19:03:40 +0100
Subject: [PATCH 0300/1356] clean up README

---
 README.rst | 82 ++++++++++++++++++++++++------------------------------
 1 file changed, 37 insertions(+), 45 deletions(-)

diff --git a/README.rst b/README.rst
index 2cd7efc455..f071e1049f 100644
--- a/README.rst
+++ b/README.rst
@@ -1,54 +1,46 @@
-Build status - *master branch (Python 2.4, Python 2.6, Python 2.7)*
-
-.. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python24/badge/icon
-    :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python24/
-.. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master/badge/icon
-    :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master/  
-.. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python27/badge/icon
-    :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python27/ 
-    
-Build status - *develop branch (Python 2.4, Python 2.6, Python 2.7)*
-
-.. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python24/badge/icon
-    :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python24/  
-.. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop/badge/icon
-    :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop/  
-.. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python27/badge/icon
-    :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python27/
-
 EasyBuild: building software with ease
 --------------------------------------
 
-The easybuild-framework package is the basis for EasyBuild
-(http://hpcugent.github.com/easybuild), a software build and
-installation framework written in Python that allows you to install
-software in a structured, repeatable and robust way.
+.. image:: http://hpcugent.github.io/easybuild/images/easybuild_logo_small.png
+   :align: center
+
+`EasyBuild <https://hpcugent.github.com/easybuild>`_ is a software build
+and installation framework that allows you to manage (scientific) software
+on High Performance Computing (HPC) systems in an efficient way.
 
-This package contains the EasyBuild framework that supports the
-implementation and use of so-called easyblocks, that implement the
-software install procedure for a particular (group of) software
+The *easybuild-framework* package is the core of EasyBuild. It
+supports the implementation and use of so-called easyblocks which
+implement the software install procedure for a particular (group of) software
 package(s).
 
-The code of the easybuild-framework package is hosted on GitHub, along
+The EasyBuild documentation is available at http://easybuild.readthedocs.org/.
+
+The EasyBuild framework source code is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see
 http://github.com/hpcugent/easybuild-framework.
 
-The EasyBuild documentation is available on the GitHub wiki of the
-easybuild meta-package, see
-http://github.com/hpcugent/easybuild/wiki/Home.
-
-Related packages: 
-- easybuild-easyblocks
-(http://pypi.python.org/pypi/easybuild-easyblocks): a collection of
-easyblocks that implement support for building and installing (groups
-of) software packages.
- 
-- easybuild-easyconfigs
-(http://pypi.python.org/pypi/easybuild-easyconfigs): a collection of
-example easyconfig files that specify which software to build, and using
-which build options; these easyconfigs will be well tested with the
-latest compatible versions of the easybuild-framework and
-easybuild-easyblocks packages.
-
-The code in the vsc directory originally comes from VSC-tools
-(https://github.com/hpcugent/VSC-tools).
+* build status - **master** branch *(Python 2.4, Python 2.6, Python 2.7)*
+
+  .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python24/badge/icon
+      :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python24/
+  .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master/badge/icon
+      :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master/
+  .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python27/badge/icon
+      :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python27/
+
+* build status - **develop** branch *(Python 2.4, Python 2.6, Python 2.7)*
+
+  .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python24/badge/icon
+      :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python24/
+  .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop/badge/icon
+      :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop/
+  .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python27/badge/icon
+      :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python27/
+
+Related packages:
+
+* `easybuild-easyblocks <http://pypi.python.org/pypi/easybuild-easyblocks>`_: a collection of easyblocks that implement support for building and installing (groups of) software packages.
+* `easybuild-easyconfigs <http://pypi.python.org/pypi/easybuild-easyconfigs>`_: a collection of example easyconfig files that specify which software to build, and using which build options; these easyconfigs will be well tested with the latest compatible versions of the easybuild-framework and easybuild-easyblocks packages.
+
+The code in the ``vsc`` directory originally comes from the *vsc-base* package
+(https://github.com/hpcugent/vsc-base).

From 67d4a90591d432e200281892ce5cdb4ce7e26c4c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 4 Nov 2014 19:06:29 +0100
Subject: [PATCH 0301/1356] move build statuses to the bottom of the README

---
 README.rst | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/README.rst b/README.rst
index f071e1049f..b2323a945c 100644
--- a/README.rst
+++ b/README.rst
@@ -19,7 +19,18 @@ The EasyBuild framework source code is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see
 http://github.com/hpcugent/easybuild-framework.
 
-* build status - **master** branch *(Python 2.4, Python 2.6, Python 2.7)*
+Related packages:
+
+* `easybuild-easyblocks <http://pypi.python.org/pypi/easybuild-easyblocks>`_: a collection of easyblocks that implement support for building and installing (groups of) software packages.
+* `easybuild-easyconfigs <http://pypi.python.org/pypi/easybuild-easyconfigs>`_: a collection of example easyconfig files that specify which software to build, and using which build options; these easyconfigs will be well tested with the latest compatible versions of the easybuild-framework and easybuild-easyblocks packages.
+
+The code in the ``vsc`` directory originally comes from the *vsc-base* package
+(https://github.com/hpcugent/vsc-base).
+
+
+*Build status overview:*
+
+* **master** branch *(Python 2.4, Python 2.6, Python 2.7)*
 
   .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python24/badge/icon
       :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python24/
@@ -28,7 +39,7 @@ http://github.com/hpcugent/easybuild-framework.
   .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python27/badge/icon
       :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_master-python27/
 
-* build status - **develop** branch *(Python 2.4, Python 2.6, Python 2.7)*
+* **develop** branch *(Python 2.4, Python 2.6, Python 2.7)*
 
   .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python24/badge/icon
       :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python24/
@@ -36,11 +47,3 @@ http://github.com/hpcugent/easybuild-framework.
       :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop/
   .. image:: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python27/badge/icon
       :target: https://jenkins1.ugent.be/view/EasyBuild/job/easybuild-framework_unit-test_hpcugent_develop-python27/
-
-Related packages:
-
-* `easybuild-easyblocks <http://pypi.python.org/pypi/easybuild-easyblocks>`_: a collection of easyblocks that implement support for building and installing (groups of) software packages.
-* `easybuild-easyconfigs <http://pypi.python.org/pypi/easybuild-easyconfigs>`_: a collection of example easyconfig files that specify which software to build, and using which build options; these easyconfigs will be well tested with the latest compatible versions of the easybuild-framework and easybuild-easyblocks packages.
-
-The code in the ``vsc`` directory originally comes from the *vsc-base* package
-(https://github.com/hpcugent/vsc-base).

From b7f45442301ccd54a07d6e7a5f6eb7baaf04b112 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 4 Nov 2014 19:11:58 +0100
Subject: [PATCH 0302/1356] fix related repos links

---
 README.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.rst b/README.rst
index b2323a945c..be8d116a59 100644
--- a/README.rst
+++ b/README.rst
@@ -19,10 +19,10 @@ The EasyBuild framework source code is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see
 http://github.com/hpcugent/easybuild-framework.
 
-Related packages:
+Related repositories:
 
-* `easybuild-easyblocks <http://pypi.python.org/pypi/easybuild-easyblocks>`_: a collection of easyblocks that implement support for building and installing (groups of) software packages.
-* `easybuild-easyconfigs <http://pypi.python.org/pypi/easybuild-easyconfigs>`_: a collection of example easyconfig files that specify which software to build, and using which build options; these easyconfigs will be well tested with the latest compatible versions of the easybuild-framework and easybuild-easyblocks packages.
+* `easybuild-easyblocks <http://github.com/hpcugent/easybuild-easyblocks>`_: a collection of easyblocks that implement support for building and installing (groups of) software packages.
+* `easybuild-easyconfigs <http://github.com/hpcugent/easybuild-easyconfigs>`_: a collection of example easyconfig files that specify which software to build, and using which build options; these easyconfigs will be well tested with the latest compatible versions of the easybuild-framework and easybuild-easyblocks packages.
 
 The code in the ``vsc`` directory originally comes from the *vsc-base* package
 (https://github.com/hpcugent/vsc-base).

From 8e8942e000d57dfc83776ddf19a8a59a9d985f03 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 4 Nov 2014 19:12:42 +0100
Subject: [PATCH 0303/1356] fix homepage URL

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index be8d116a59..418fe46b7d 100644
--- a/README.rst
+++ b/README.rst
@@ -4,7 +4,7 @@ EasyBuild: building software with ease
 .. image:: http://hpcugent.github.io/easybuild/images/easybuild_logo_small.png
    :align: center
 
-`EasyBuild <https://hpcugent.github.com/easybuild>`_ is a software build
+`EasyBuild <https://hpcugent.github.io/easybuild>`_ is a software build
 and installation framework that allows you to manage (scientific) software
 on High Performance Computing (HPC) systems in an efficient way.
 

From a7d5b79edcb23a4e14d78ef6eee39bf486b909c3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 4 Nov 2014 19:21:15 +0100
Subject: [PATCH 0304/1356] cosmetic changes

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 418fe46b7d..9a85c37a58 100644
--- a/README.rst
+++ b/README.rst
@@ -8,7 +8,7 @@ EasyBuild: building software with ease
 and installation framework that allows you to manage (scientific) software
 on High Performance Computing (HPC) systems in an efficient way.
 
-The *easybuild-framework* package is the core of EasyBuild. It
+The **easybuild-framework** package is the core of EasyBuild. It
 supports the implementation and use of so-called easyblocks which
 implement the software install procedure for a particular (group of) software
 package(s).

From 054a8364daae76a043c615bbe152f00108677560 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 4 Nov 2014 20:36:55 +0100
Subject: [PATCH 0305/1356] fix (long) description in setup.py, more cosmetics

---
 README.rst | 17 ++++++++++++++---
 setup.py   | 11 +++--------
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/README.rst b/README.rst
index 9a85c37a58..3cc0398349 100644
--- a/README.rst
+++ b/README.rst
@@ -19,10 +19,21 @@ The EasyBuild framework source code is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see
 http://github.com/hpcugent/easybuild-framework.
 
-Related repositories:
+Related Python packages:
 
-* `easybuild-easyblocks <http://github.com/hpcugent/easybuild-easyblocks>`_: a collection of easyblocks that implement support for building and installing (groups of) software packages.
-* `easybuild-easyconfigs <http://github.com/hpcugent/easybuild-easyconfigs>`_: a collection of example easyconfig files that specify which software to build, and using which build options; these easyconfigs will be well tested with the latest compatible versions of the easybuild-framework and easybuild-easyblocks packages.
+* **easybuild-easyblocks**
+
+  * a collection of easyblocks that implement support for building and installing (groups of) software packages
+  * GitHub repository: http://github.com/hpcugent/easybuild-easyblocks
+  * package on PyPi: https://pypi.python.org/pypi/easybuild-easyblocks
+
+* **easybuild-easyconfigs**
+
+  * a collection of example easyconfig files that specify which software to build,
+    and using which build options; these easyconfigs will be well tested
+    with the latest compatible versions of the easybuild-framework and easybuild-easyblocks packages
+  * GitHub repository: http://github.com/hpcugent/easybuild-easyconfigs
+  * PyPi: https://pypi.python.org/pypi/easybuild-easyconfigs
 
 The code in the ``vsc`` directory originally comes from the *vsc-base* package
 (https://github.com/hpcugent/vsc-base).
diff --git a/setup.py b/setup.py
index 5a707b3d82..119ec928e5 100644
--- a/setup.py
+++ b/setup.py
@@ -82,8 +82,8 @@ def find_rel_test():
     version = str(VERSION),
     author = "EasyBuild community",
     author_email = "easybuild@lists.ugent.be",
-    description = """EasyBuild is a software installation framework in Python that allows you to \
-install software in a structured and robust way.
+    description = """EasyBuild is a software build and installation framework that allows you to \
+manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
 This package contains the EasyBuild framework, which supports the creation of custom easyblocks that \
 implement support for installing particular (groups of) software packages.""",
     license = "GPLv2",
@@ -96,12 +96,7 @@ def find_rel_test():
     data_files = [
         ('easybuild', ["easybuild/easybuild_config.py"]),
     ],
-    long_description = """This package contains the EasyBuild
-framework, which supports the creation of custom easyblocks that
-implement support for installing particular (groups of) software
-packages.
-
-""" + read("README.rst"),
+    long_description = read('README.rst'),
     classifiers = [
         "Development Status :: 5 - Production/Stable",
         "Environment :: Console",

From 920fffe934452352f2215220b744657c73611fde Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 4 Nov 2014 20:40:01 +0100
Subject: [PATCH 0306/1356] fix description

---
 setup.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/setup.py b/setup.py
index 119ec928e5..361191c59d 100644
--- a/setup.py
+++ b/setup.py
@@ -82,9 +82,7 @@ def find_rel_test():
     version = str(VERSION),
     author = "EasyBuild community",
     author_email = "easybuild@lists.ugent.be",
-    description = """EasyBuild is a software build and installation framework that allows you to \
-manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
-This package contains the EasyBuild framework, which supports the creation of custom easyblocks that \
+    description = """The EasyBuild framework supports the creation of custom easyblocks that \
 implement support for installing particular (groups of) software packages.""",
     license = "GPLv2",
     keywords = "software build building installation installing compilation HPC scientific",

From a739cf1b82eb41c3a828245d86e48f6076124783 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 4 Nov 2014 20:59:47 +0100
Subject: [PATCH 0307/1356] drop title in README

---
 README.rst | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/README.rst b/README.rst
index 3cc0398349..5b375ff615 100644
--- a/README.rst
+++ b/README.rst
@@ -1,6 +1,3 @@
-EasyBuild: building software with ease
---------------------------------------
-
 .. image:: http://hpcugent.github.io/easybuild/images/easybuild_logo_small.png
    :align: center
 

From c6669c85a6b01999eaaa1c600791dcc60e5dd270 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 5 Nov 2014 09:19:43 +0100
Subject: [PATCH 0308/1356] stop triggering legacy code (first draft)

---
 easybuild/framework/easyconfig/easyconfig.py | 20 +++++++--
 easybuild/tools/config.py                    | 44 ++++++++++----------
 easybuild/tools/options.py                   |  2 +-
 test/framework/config.py                     | 14 +++----
 4 files changed, 46 insertions(+), 34 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index c58e7349a5..b85f75252b 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -788,9 +788,23 @@ def get_easyblock_class(easyblock, name=None):
             class_name = encode_class_name(name)
             # modulepath will be the namespace + encoded modulename (from the classname)
             modulepath = get_module_path(class_name)
-            if not os.path.exists("%s.py" % modulepath):
-                _log.deprecated("Determine module path based on software name", "2.0")
-                modulepath = get_module_path(name, decode=False)
+            modulepath_imported = False
+            try:
+                __import__(modulepath, globals(), locals(), [''])
+                modulepath_imported = True
+            except ImportError, err:
+                _log.debug("Failed to import module '%s': %s" % (modulepath, err))
+
+            # check if determining module path based on software name would have resulted in a different module path
+            if modulepath_imported:
+                _log.debug("Module path '%s' found" % modulepath)
+            else:
+                _log.debug("No module path '%s' found" % modulepath)
+                modulepath_bis = get_module_path(name, decode=False)
+                _log.debug("Module path determined based on software name: %s" % modulepath_bis)
+                if modulepath_bis != modulepath:
+                    _log.deprecated("Determine module path based on software name", "2.0")
+                    modulepath = modulepath_bis
 
             # try and find easyblock
             try:
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 3c4467ad3c..f648d7c42b 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -53,6 +53,7 @@
 
 # class constant to prepare migration to generaloption as only way of configuration (maybe for v2.X)
 SUPPORT_OLDSTYLE = True
+DEFAULT_OLDSTYLE_CONFIG_FILE = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'easybuild_config.py')
 
 
 DEFAULT_LOGFILE_FORMAT = ("easybuild", "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
@@ -157,14 +158,15 @@
 ]
 
 
+# note: keys are new style option names
 OLDSTYLE_ENVIRONMENT_VARIABLES = {
-    'build_path': 'EASYBUILDBUILDPATH',
-    'config_file': 'EASYBUILDCONFIG',
-    'install_path': 'EASYBUILDINSTALLPATH',
-    'log_format': 'EASYBUILDLOGFORMAT',
-    'log_dir': 'EASYBUILDLOGDIR',
-    'source_path': 'EASYBUILDSOURCEPATH',
-    'test_output_path': 'EASYBUILDTESTOUTPUT',
+    'buildpath': 'EASYBUILDBUILDPATH',
+    'config': 'EASYBUILDCONFIG',
+    'installpath': 'EASYBUILDINSTALLPATH',
+    'logfile_format': 'EASYBUILDLOGFORMAT',
+    'tmp_logdir': 'EASYBUILDLOGDIR',
+    'sourcepath': 'EASYBUILDSOURCEPATH',
+    'testoutput': 'EASYBUILDTESTOUTPUT',
 }
 
 
@@ -188,9 +190,7 @@ def map_to_newstyle(adict):
     res = {}
     for key, val in adict.items():
         if key in OLDSTYLE_NEWSTYLE_MAP:
-            newkey = OLDSTYLE_NEWSTYLE_MAP.get(key)
-            _log.deprecated("oldstyle key %s usage found, replacing with newkey %s" % (key, newkey), "2.0")
-            key = newkey
+            key = OLDSTYLE_NEWSTYLE_MAP[key]
         res[key] = val
     return res
 
@@ -264,7 +264,7 @@ def get_default_oldstyle_configfile():
     # - check environment variable EASYBUILDCONFIG
     # - next, check for an EasyBuild config in $HOME/.easybuild/config.py
     # - last, use default config file easybuild_config.py in main.py directory
-    config_env_var = OLDSTYLE_ENVIRONMENT_VARIABLES['config_file']
+    config_env_var = OLDSTYLE_ENVIRONMENT_VARIABLES['config']
     home_config_file = os.path.join(get_user_easybuild_dir(), "config.py")
     if os.getenv(config_env_var):
         _log.debug("Environment variable %s, so using that as config file." % config_env_var)
@@ -275,11 +275,11 @@ def get_default_oldstyle_configfile():
     else:
         # this should be easybuild.tools.config, the default config file is
         # part of framework in easybuild (ie in tool/..)
-        appPath = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-        config_file = os.path.join(appPath, "easybuild_config.py")
-        _log.debug("Falling back to default config: %s" % config_file)
-
-    _log.deprecated("get_default_oldstyle_configfile oldstyle configfile %s used" % config_file, "2.0")
+        if os.path.exists(DEFAULT_OLDSTYLE_CONFIG_FILE):
+            config_file = DEFAULT_OLDSTYLE_CONFIG_FILE
+            _log.debug("Falling back to default config: %s" % config_file)
+        else:
+            config_file = None
 
     return config_file
 
@@ -344,7 +344,10 @@ def init(options, config_options_dict):
     """
     tmpdict = {}
     if SUPPORT_OLDSTYLE:
-        _log.deprecated('oldstyle init with modifications to support oldstyle options', '2.0')
+        if not os.path.samefile(options.config, DEFAULT_OLDSTYLE_CONFIG_FILE):
+            # only trip if an oldstyle config other than the default is used (via $EASYBUILDCONFIG or --config)
+            # we still need the oldstyle default config file to ensure legacy behavior, for now
+            _log.deprecated('use of oldstyle configuration file %s' % options.config, '2.0')
         tmpdict.update(oldstyle_init(options.config))
 
         # add the DEFAULT_MODULECLASSES as default (behavior is now that this extends the default list)
@@ -623,7 +626,6 @@ def oldstyle_init(filename, **kwargs):
     Variables are read in this order of preference: CLI option > environment > config file
     """
     res = {}
-    _log.deprecated("oldstyle_init filename %s kwargs %s" % (filename, kwargs), "2.0")
 
     _log.debug('variables before oldstyle_init %s' % res)
     res.update(oldstyle_read_configuration(filename))  # config file
@@ -641,8 +643,6 @@ def oldstyle_read_configuration(filename):
     """
     Read variables from the config file
     """
-    _log.deprecated("oldstyle_read_configuration filename %s" % filename, "2.0")
-
     # import avail_repositories here to avoid cyclic dependencies
     # this block of code is going to be removed in EB v2.0
     from easybuild.tools.repository.repository import avail_repositories
@@ -660,8 +660,6 @@ def oldstyle_read_environment(env_vars=None, strict=False):
     Read variables from the environment
         - strict=True enforces that all possible environment variables are found
     """
-    _log.deprecated(('Adapt code to use read_environment from easybuild.tools.utilities '
-                     'and do not use oldstyle environment variables'), '2.0')
     if env_vars is None:
         env_vars = OLDSTYLE_ENVIRONMENT_VARIABLES
     result = {}
@@ -669,7 +667,7 @@ def oldstyle_read_environment(env_vars=None, strict=False):
         env_var = env_vars[key]
         if env_var in os.environ:
             result[key] = os.environ[env_var]
-            _log.deprecated("Found oldstyle environment variable %s for %s: %s" % (env_var, key, result[key]), "2.0")
+            _log.deprecated("Use of oldstyle environment variable %s for %s: %s" % (env_var, key, result[key]), "2.0")
         elif strict:
             _log.error("Can't determine value for %s. Environment variable %s is missing" % (key, env_var))
         else:
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 3d3ed7f84e..52940845b9 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -205,7 +205,7 @@ def config_options(self):
             'ignore-dirs': ("Directory names to ignore when searching for files/dirs",
                             'strlist', 'store', ['.git', '.svn']),
             'installpath': ("Install path for software and modules", None, 'store', oldstyle_defaults['installpath']),
-            'config': ("Path to EasyBuild config file",
+            'config': ("Path to EasyBuild config file (DEPRECATED, use --configfiles instead!)",
                        None, 'store', oldstyle_defaults['config'], 'C'),
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', oldstyle_defaults['logfile_format'], {'metavar': 'DIR,FORMAT'}),
diff --git a/test/framework/config.py b/test/framework/config.py
index b28ec141cf..79fc500b8c 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -79,7 +79,7 @@ def configure(self, args=None):
         options = init_config(args=args)
         return options.config
 
-    def test_default_config(self):
+    def xtest_default_config(self):
         """Test default configuration."""
         self.purge_environment()
 
@@ -245,7 +245,7 @@ def test_legacy_config_file(self):
         self.purge_environment()
 
         cfg_fn = self.configure(args=[])
-        self.assertTrue(cfg_fn.endswith('easybuild/easybuild_config.py'))
+        #self.assertTrue(cfg_fn.endswith('easybuild/easybuild_config.py'))
 
         configtxt = """
 build_path = '%(buildpath)s'
@@ -354,7 +354,7 @@ def test_legacy_config_file(self):
         self.assertEqual(log_file_format(), logtmpl)
         self.assertEqual(get_build_log_path(), tmplogdir)
 
-    def test_generaloption_config(self):
+    def xtest_generaloption_config(self):
         """Test new-style configuration (based on generaloption)."""
         self.purge_environment()
 
@@ -413,7 +413,7 @@ def test_generaloption_config(self):
         del os.environ['EASYBUILD_PREFIX']
         del os.environ['EASYBUILD_SUBDIR_SOFTWARE']
 
-    def test_generaloption_config_file(self):
+    def xtest_generaloption_config_file(self):
         """Test use of new-style configuration file."""
         self.purge_environment()
 
@@ -475,7 +475,7 @@ def test_generaloption_config_file(self):
 
         del os.environ['EASYBUILD_CONFIGFILES']
 
-    def test_set_tmpdir(self):
+    def xtest_set_tmpdir(self):
         """Test set_tmpdir config function."""
         self.purge_environment()
 
@@ -501,7 +501,7 @@ def test_set_tmpdir(self):
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
 
-    def test_configuration_variables(self):
+    def xtest_configuration_variables(self):
         """Test usage of ConfigurationVariables."""
         # delete instance of ConfigurationVariables
         ConfigurationVariables.__metaclass__._instances.pop(ConfigurationVariables, None)
@@ -513,7 +513,7 @@ def test_configuration_variables(self):
         self.assertTrue(cv1 is cv2)
         self.assertTrue(cv1 is cv3)
 
-    def test_build_options(self):
+    def xtest_build_options(self):
         """Test usage of BuildOptions."""
         # delete instance of BuildOptions
         BuildOptions.__metaclass__._instances.pop(BuildOptions, None)

From 8f589699186429fd6c75cc3a32733843d60fbb3d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 5 Nov 2014 19:01:12 +0100
Subject: [PATCH 0309/1356] deprecate self.moduleGenerator in favor of
 self.module_generator in EasyBlock

---
 easybuild/framework/easyblock.py           | 48 +++++++++++++---------
 easybuild/scripts/mk_tmpl_easyblock_for.py |  4 +-
 2 files changed, 30 insertions(+), 22 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 0c96f815b2..6d7bb5815c 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -137,7 +137,7 @@ def __init__(self, ec):
         # modules interface with default MODULEPATH
         self.modules_tool = modules_tool()
         # module generator
-        self.moduleGenerator = ModuleGenerator(self, fake=True)
+        self.module_generator = ModuleGenerator(self, fake=True)
 
         # modules footer
         self.modules_footer = None
@@ -613,6 +613,14 @@ def short_mod_name(self):
         """
         return self.cfg.short_mod_name
 
+    @property
+    def moduleGenerator(self):
+        """
+        Module generator (DEPRECATED, use self.module_generator instead).
+        """
+        _log.deprecated("Environment variable SOFTDEVEL* being relied on", "2.0")
+        return self.module_generator
+
     #
     # DIRECTORY UTILITY FUNCTIONS
     #
@@ -816,8 +824,8 @@ def make_module_dep(self):
 
         deps = [d for d in deps if d not in excluded_deps]
         self.log.debug("List of retained dependencies: %s" % deps)
-        loads = [self.moduleGenerator.load_module(d) for d in deps]
-        unloads = [self.moduleGenerator.unload_module(d) for d in deps[::-1]]
+        loads = [self.module_generator.load_module(d) for d in deps]
+        unloads = [self.module_generator.unload_module(d) for d in deps[::-1]]
 
         # Force unloading any other modules
         if self.cfg['moduleforceunload']:
@@ -829,7 +837,7 @@ def make_module_description(self):
         """
         Create the module description.
         """
-        return self.moduleGenerator.get_description()
+        return self.module_generator.get_description()
 
     def make_module_extra(self):
         """
@@ -839,26 +847,26 @@ def make_module_extra(self):
 
         # EBROOT + EBVERSION + EBDEVEL
         environment_name = convert_name(self.name, upper=True)
-        txt += self.moduleGenerator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, "$root")
-        txt += self.moduleGenerator.set_environment(VERSION_ENV_VAR_NAME_PREFIX + environment_name, self.version)
+        txt += self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, "$root")
+        txt += self.module_generator.set_environment(VERSION_ENV_VAR_NAME_PREFIX + environment_name, self.version)
         devel_path = os.path.join("$root", log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
-        txt += self.moduleGenerator.set_environment(DEVEL_ENV_VAR_NAME_PREFIX + environment_name, devel_path)
+        txt += self.module_generator.set_environment(DEVEL_ENV_VAR_NAME_PREFIX + environment_name, devel_path)
 
         txt += "\n"
         for (key, value) in self.cfg['modextravars'].items():
-            txt += self.moduleGenerator.set_environment(key, value)
+            txt += self.module_generator.set_environment(key, value)
         for (key, value) in self.cfg['modextrapaths'].items():
             if isinstance(value, basestring):
                 value = [value]
             elif not isinstance(value, (tuple, list)):
                 self.log.error("modextrapaths dict value %s (type: %s) is not a list or tuple" % (value, type(value)))
-            txt += self.moduleGenerator.prepend_paths(key, value)
+            txt += self.module_generator.prepend_paths(key, value)
         if self.cfg['modloadmsg']:
-            txt += self.moduleGenerator.msg_on_load(self.cfg['modloadmsg'])
+            txt += self.module_generator.msg_on_load(self.cfg['modloadmsg'])
         if self.cfg['modtclfooter']:
-            txt += self.moduleGenerator.add_tcl_footer(self.cfg['modtclfooter'])
+            txt += self.module_generator.add_tcl_footer(self.cfg['modtclfooter'])
         for (key, value) in self.cfg['modaliases'].items():
-            txt += self.moduleGenerator.set_alias(key, value)
+            txt += self.module_generator.set_alias(key, value)
 
         self.log.debug("make_module_extra added this: %s" % txt)
 
@@ -874,7 +882,7 @@ def make_module_extra_extensions(self):
         # set environment variable that specifies list of extensions
         if self.exts_all:
             exts_list = ','.join(['%s-%s' % (ext['name'], ext.get('version', '')) for ext in self.exts_all])
-            txt += self.moduleGenerator.set_environment('EBEXTSLIST%s' % self.name.upper(), exts_list)
+            txt += self.module_generator.set_environment('EBEXTSLIST%s' % self.name.upper(), exts_list)
 
         return txt
 
@@ -909,7 +917,7 @@ def make_module_extend_modpath(self):
             # module path extensions must exist, otherwise loading this module file will fail
             for modpath_extension in full_path_modpath_extensions:
                 mkdir(modpath_extension, parents=True)
-            txt = self.moduleGenerator.use(full_path_modpath_extensions)
+            txt = self.module_generator.use(full_path_modpath_extensions)
         else:
             self.log.debug("Not including module path extensions, as specified.")
         return txt
@@ -931,7 +939,7 @@ def make_module_req(self):
                 for path in requirements[key]:
                     paths = glob.glob(path)
                     if paths:
-                        txt += self.moduleGenerator.prepend_paths(key, paths)
+                        txt += self.module_generator.prepend_paths(key, paths)
             try:
                 os.chdir(self.orig_workdir)
             except OSError, err:
@@ -1660,8 +1668,8 @@ def make_module_step(self, fake=False):
         """
         Generate a module file.
         """
-        self.moduleGenerator.set_fake(fake)
-        modpath = self.moduleGenerator.prepare()
+        self.module_generator.set_fake(fake)
+        modpath = self.module_generator.prepare()
 
         txt = ''
         txt += self.make_module_description()
@@ -1671,12 +1679,12 @@ def make_module_step(self, fake=False):
         txt += self.make_module_extra()
         txt += self.make_module_footer()
 
-        write_file(self.moduleGenerator.filename, txt)
+        write_file(self.module_generator.filename, txt)
 
-        self.log.info("Module file %s written" % self.moduleGenerator.filename)
+        self.log.info("Module file %s written" % self.module_generator.filename)
 
         self.modules_tool.update()
-        self.moduleGenerator.create_symlinks()
+        self.module_generator.create_symlinks()
 
         if not fake:
             self.make_devel_module()
diff --git a/easybuild/scripts/mk_tmpl_easyblock_for.py b/easybuild/scripts/mk_tmpl_easyblock_for.py
index 8c25f14135..f2fcffbca6 100755
--- a/easybuild/scripts/mk_tmpl_easyblock_for.py
+++ b/easybuild/scripts/mk_tmpl_easyblock_for.py
@@ -208,8 +208,8 @@ def make_module_extra(self):
 
         txt = super(%(class_name)s, self).make_module_extra()
 
-        txt += self.moduleGenerator.set_environment("VARIABLE", 'value')
-        txt += self.moduleGenerator.prepend_paths("PATH_VAR", ['path1', 'path2'])
+        txt += self.module_generator.set_environment("VARIABLE", 'value')
+        txt += self.module_generator.prepend_paths("PATH_VAR", ['path1', 'path2'])
 
         return txt
 """

From 15aea89617839110f7d5195deef08527e955152a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 5 Nov 2014 21:56:40 +0100
Subject: [PATCH 0310/1356] fix unit test that fails when installed easyconfigs
 package is available

---
 test/framework/options.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 4803299cb2..d52e934a38 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -676,11 +676,8 @@ def test_dry_run_hierarchical(self):
             '--ignore-osdeps',
             '--force',
             '--debug',
+            '--robot-paths=%s' % os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs'),
         ]
-        errmsg = r"No robot path specified, which is required when looking for easyconfigs \(use --robot\)"
-        self.assertErrorRegex(EasyBuildError, errmsg, self.eb_main, args, logfile=dummylogfn, raise_error=True)
-
-        args.append('--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'))
         outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True, raise_error=True)
 
         ecs_mods = [

From 34c61feb20b84cc891c38539f780a6131c1f0a3b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Nov 2014 13:16:14 +0100
Subject: [PATCH 0311/1356] clean up revamped implementation of download_file

---
 easybuild/tools/filetools.py | 111 ++++++++++++++++++-----------------
 test/framework/filetools.py  |   3 +
 2 files changed, 61 insertions(+), 53 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 56d202eea5..98350156a7 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -244,89 +244,94 @@ def det_common_path_prefix(paths):
 def download_file(filename, url, path):
     """Download a file from the given URL, to the specified path."""
 
-    _log.debug("Downloading %s from %s to %s" % (filename, url, path))
+    _log.debug("Trying to download %s from %s to %s", filename, url, path)
 
     # make sure directory exists
     basedir = os.path.dirname(path)
     mkdir(basedir, parents=True)
 
-    downloaded = False
-    attempt_cnt = 0
-
-    # use this functions's scope for the variable we share with our inner function
-    download_file.last_time = time.time()
-    download_file.last_block = 0
     # internal function to report on download progress
-    def report(block, blocksize, filesize):
+    def report(blocks_read, blocksize, filesize):
         """
-        This is a reporthook for urlretrieve, it takes 3 integers as arguments:
-        the current downloaded block, the size in bytes of one block and the total size of the downlad.
-        This efectively logs the download progress every 10 seconds with loglevel info.
+        Report hook for urlretrieve, which logs the download progress every 10 seconds with log level info.
+        @param blocks_read: number of blocks already read
+        @param blocksize: size of one block, in bytes
+        @param filesize: total size of the download (in number of blocks blocks)
         """
         if download_file.last_time + 10 < time.time():
-            newblocks = block - download_file.last_block
-            download_file.last_block = block
-            total_download = block * blocksize
-            percentage = int(block * blocksize * 100 / filesize)
-            kbps = (blocksize * newblocks) / 1024  // (time.time() - download_file.last_time)
+            newblocks = blocks_read - download_file.last_block
+            download_file.last_block = blocks_read
+            tot_time = time.time() - download_file.last_time
 
             if filesize <= 0:
                 # content length isn't always set
-                _log.info('download report: %d kb downloaded (%d kbps)', total_download, kbps) 
+                report_msg = "downloaded in %ss" % tot_time
             else:
-                _log.info('download report: %d kb of %d kb (%d %%, %d kbps)', total_download, filesize, percentage, kbps)
-                          
-            download_file.last_time = time.time()
+                percent = blocks_read * blocksize * 100 // filesize
+                report_msg = "of %d kb downloaded in %ss [%d %%]" % (filesize / 1024.0, tot_time, percent)
 
+            downloaded_kbs = (blocks_read * blocksize) / 1024.0
+            kbps = (blocksize * newblocks) / 1024  // tot_time
+            _log.info("Download report: %d kb %s (%d kbps)", downloaded_kbs, report_msg, kbps)
 
-    # try downloading three times max.
+            download_file.last_time = time.time()
+
+    # try downloading, three times max.
+    downloaded = False
+    attempt_cnt = 0
     while not downloaded and attempt_cnt < 3:
         # get http response code first before downloading file
-        urlfile = urllib.urlopen(url)
-        response_code = urlfile.getcode()
-        urlfile.close()
+        try:
+            urlfile = urllib.urlopen(url)
+            response_code = urlfile.getcode()
+            urlfile.close()
+        except IOError, err:
+            response_code = None
+
         if response_code:
             _log.debug('http response code for given url: %d', response_code)
-        if response_code == 404:
-            _log.warning('url %s was not found (404), not trying again', url)
-            return None
+            # check for a 4xx response code which indicates a non-existing URL
+            if response_code // 100 == 4:
+                _log.warning('url %s was not found (%d), not trying again', response_code, url)
+                return None
 
+        # use this functions's scope for variables we share with inner function used as report hook for urlretrieve
         download_file.last_time = time.time()
         download_file.last_block = 0
 
+        httpmsg = None
         try:
             (_, httpmsg) = urllib.urlretrieve(url, path, reporthook=report)
-        except ContentTooShortError:
-            _log.warning(
-                "Expected file of %d bytes, but download size dit not match, removing file and retrying", 
-                int(httpmsg.dict['content-length']),
-            )
-            try:
-                os.remove(path)
-            except OSError, err:
-                  _log.error("Failed to remove downloaded file:" % err)
-            # try again
-            attempt_cnt += 1
-            continue
+            _log.info("Downloaded file %s from url %s to %s", filename, url, path)
+        except IOError, err:
+            tup = (filename, url, err)
+            _log.warning("An error occured when downloadeding %s from %s (%s), removing file and retrying", *tup)
+
+        if httpmsg:
+            if httpmsg.type == "text/html" and not filename.endswith('.html'):
+                _log.warning("HTML file downloaded but not expecting it, so assuming invalid download, retrying.")
+            else:
+                # successful download
+                downloaded = True
 
-        if httpmsg.type == "text/html" and not filename.endswith('.html'):
-            _log.warning("HTML file downloaded but not expecting it, so assuming invalid download.")
-            _log.debug("removing downloaded file %s from %s" % (filename, path))
+        if not downloaded:
+            _log.debug("removing faulty downloaded file %s from %s", filename, path)
             try:
-                os.remove(path)
+                if os.path.exists(path):
+                    os.remove(path)
             except OSError, err:
-                _log.error("Failed to remove downloaded file:" % err)
-        else:
-            _log.info("Downloading file %s from url %s: done" % (filename, url))
-            downloaded = True
-            return path
-
-        attempt_cnt += 1
-        _log.warning("Downloading failed at attempt %s, retrying..." % attempt_cnt)
+                  _log.error("Failed to remove downloaded file: %s", err)
 
+            attempt_cnt += 1
+            _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
 
-    # failed to download after multiple attempts
-    return None
+    if downloaded:
+        _log.info("Successful download of file %s from url %s to path %s", filename, url, path)
+        return path
+    else:
+        # failed to download after multiple attempts
+        _log.warning("Too many failed download attempts, giving up")
+        return None
 
 
 def find_easyconfigs(path, ignore_dirs=None):
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 651ea77c30..69ca9a17ab 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -194,6 +194,9 @@ def test_download_file(self):
         res = ft.download_file(fn, source_url, target_location)
         self.assertEqual(res, target_location)
 
+        # non-existing files result in None return value
+        self.assertEqual(ft.download_file(fn, 'file://nosuchfile', target_location), None)
+
     def test_mkdir(self):
         """Test mkdir function."""
         tmpdir = tempfile.mkdtemp()

From 5899135e0e8de737c8bb15cb15e06e345b7dd786 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Nov 2014 13:23:32 +0100
Subject: [PATCH 0312/1356] log HTTP response code fail

---
 easybuild/tools/filetools.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 98350156a7..47c9e04259 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -280,12 +280,13 @@ def report(blocks_read, blocksize, filesize):
     downloaded = False
     attempt_cnt = 0
     while not downloaded and attempt_cnt < 3:
-        # get http response code first before downloading file
+        # get HTTP response code first before downloading file
         try:
             urlfile = urllib.urlopen(url)
             response_code = urlfile.getcode()
             urlfile.close()
         except IOError, err:
+            _log.warning("Failed to get HTTP response code for %s: %s", url, err)
             response_code = None
 
         if response_code:

From ffbe43e48f446ff72697ba211f6dca1913f35def Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Nov 2014 13:26:25 +0100
Subject: [PATCH 0313/1356] get rid of 'tup' trickery

---
 easybuild/tools/filetools.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 47c9e04259..aa1fe1debf 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -305,8 +305,7 @@ def report(blocks_read, blocksize, filesize):
             (_, httpmsg) = urllib.urlretrieve(url, path, reporthook=report)
             _log.info("Downloaded file %s from url %s to %s", filename, url, path)
         except IOError, err:
-            tup = (filename, url, err)
-            _log.warning("An error occured when downloadeding %s from %s (%s), removing file and retrying", *tup)
+            _log.warning("Error when downloading %s from %s (%s), removing file and retrying", filename, url, err)
 
         if httpmsg:
             if httpmsg.type == "text/html" and not filename.endswith('.html'):

From c65df57e2ff222aa4c32c759f75bfc8be9c669a3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Nov 2014 13:39:31 +0100
Subject: [PATCH 0314/1356] minor fix in test

---
 test/framework/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 69ca9a17ab..f7307e1b41 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -195,7 +195,7 @@ def test_download_file(self):
         self.assertEqual(res, target_location)
 
         # non-existing files result in None return value
-        self.assertEqual(ft.download_file(fn, 'file://nosuchfile', target_location), None)
+        self.assertEqual(ft.download_file(fn, os.path.join('file://', test_dir, 'nosuchfile'), target_location), None)
 
     def test_mkdir(self):
         """Test mkdir function."""

From b3636faf05a19575d4b5baa61f7a686a941d6ea8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Nov 2014 14:26:06 +0100
Subject: [PATCH 0315/1356] don't use os.path.join on URLs in tests

---
 test/framework/filetools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index f7307e1b41..5a23905947 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -190,12 +190,12 @@ def test_download_file(self):
         target_location = os.path.join(self.test_buildpath, 'some', 'subdir', fn)
         # provide local file path as source URL
         test_dir = os.path.abspath(os.path.dirname(__file__))
-        source_url = os.path.join('file://', test_dir, 'sandbox', 'sources', 'toy', fn)
+        source_url = 'file://%s/sandbox/sources/toy/%s' % (test_dir, fn)
         res = ft.download_file(fn, source_url, target_location)
         self.assertEqual(res, target_location)
 
         # non-existing files result in None return value
-        self.assertEqual(ft.download_file(fn, os.path.join('file://', test_dir, 'nosuchfile'), target_location), None)
+        self.assertEqual(ft.download_file(fn, 'file://%s/nosuchfile' % test_dir, target_location), None)
 
     def test_mkdir(self):
         """Test mkdir function."""

From 9057ee2ec547119dd6b707ef9ae09655c686b41d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Nov 2014 15:02:17 +0100
Subject: [PATCH 0316/1356] minor tweaks in download_file function

---
 easybuild/tools/filetools.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index aa1fe1debf..4e9374bc98 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -286,14 +286,14 @@ def report(blocks_read, blocksize, filesize):
             response_code = urlfile.getcode()
             urlfile.close()
         except IOError, err:
-            _log.warning("Failed to get HTTP response code for %s: %s", url, err)
+            _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)
             response_code = None
 
         if response_code:
-            _log.debug('http response code for given url: %d', response_code)
+            _log.debug('HTTP response code for given url: %d', response_code)
             # check for a 4xx response code which indicates a non-existing URL
             if response_code // 100 == 4:
-                _log.warning('url %s was not found (%d), not trying again', response_code, url)
+                _log.warning('url %s was not found (HTTP response %d), not trying again', url, response_code)
                 return None
 
         # use this functions's scope for variables we share with inner function used as report hook for urlretrieve
@@ -310,18 +310,18 @@ def report(blocks_read, blocksize, filesize):
         if httpmsg:
             if httpmsg.type == "text/html" and not filename.endswith('.html'):
                 _log.warning("HTML file downloaded but not expecting it, so assuming invalid download, retrying.")
+
+                _log.debug("removing faulty downloaded file %s from %s", filename, path)
+                try:
+                    if os.path.exists(path):
+                        os.remove(path)
+                except OSError, err:
+                      _log.error("Failed to remove downloaded file: %s", err)
             else:
                 # successful download
                 downloaded = True
 
         if not downloaded:
-            _log.debug("removing faulty downloaded file %s from %s", filename, path)
-            try:
-                if os.path.exists(path):
-                    os.remove(path)
-            except OSError, err:
-                  _log.error("Failed to remove downloaded file: %s", err)
-
             attempt_cnt += 1
             _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
 

From 096fe882ebb60adb79255895f060c8b489dd233d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Nov 2014 15:17:13 +0100
Subject: [PATCH 0317/1356] use inner function to remove faulty download

---
 easybuild/tools/filetools.py | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 4e9374bc98..33a666d0ad 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -276,6 +276,17 @@ def report(blocks_read, blocksize, filesize):
 
             download_file.last_time = time.time()
 
+    def cleanup_faulty_download():
+        """
+        Clean up faulty download.
+        """
+        _log.debug("removing faulty downloaded file %s from %s", filename, path)
+        try:
+            if os.path.exists(path):
+                os.remove(path)
+        except OSError, err:
+              _log.error("Failed to remove downloaded file: %s", err)
+
     # try downloading, three times max.
     downloaded = False
     attempt_cnt = 0
@@ -304,22 +315,16 @@ def report(blocks_read, blocksize, filesize):
         try:
             (_, httpmsg) = urllib.urlretrieve(url, path, reporthook=report)
             _log.info("Downloaded file %s from url %s to %s", filename, url, path)
-        except IOError, err:
-            _log.warning("Error when downloading %s from %s (%s), removing file and retrying", filename, url, err)
 
-        if httpmsg:
             if httpmsg.type == "text/html" and not filename.endswith('.html'):
                 _log.warning("HTML file downloaded but not expecting it, so assuming invalid download, retrying.")
-
-                _log.debug("removing faulty downloaded file %s from %s", filename, path)
-                try:
-                    if os.path.exists(path):
-                        os.remove(path)
-                except OSError, err:
-                      _log.error("Failed to remove downloaded file: %s", err)
+                cleanup_faulty_download()
             else:
                 # successful download
                 downloaded = True
+        except IOError, err:
+            _log.warning("Error when downloading %s from %s (%s), removing file and retrying", filename, url, err)
+            cleanup_faulty_download()
 
         if not downloaded:
             attempt_cnt += 1

From a4485e6b787a96ee3e7ec97cd111812659e70e12 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Nov 2014 16:38:17 +0100
Subject: [PATCH 0318/1356] flesh out remove_file

---
 easybuild/tools/filetools.py | 28 +++++++++++++---------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 33a666d0ad..1a56b739ec 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -171,6 +171,15 @@ def write_file(path, txt, append=False):
         _log.error("Failed to write to %s: %s" % (path, err))
 
 
+def remove_file(path):
+    """Remove file at specified path."""
+    try:
+        if os.path.exists(path):
+            os.remove(path)
+    except OSError, err:
+          _log.error("Failed to remove downloaded file: %s", err)
+
+
 def extract_file(fn, dest, cmd=None, extra_options=None, overwrite=False):
     """
     Given filename fn, try to extract in directory dest
@@ -276,17 +285,6 @@ def report(blocks_read, blocksize, filesize):
 
             download_file.last_time = time.time()
 
-    def cleanup_faulty_download():
-        """
-        Clean up faulty download.
-        """
-        _log.debug("removing faulty downloaded file %s from %s", filename, path)
-        try:
-            if os.path.exists(path):
-                os.remove(path)
-        except OSError, err:
-              _log.error("Failed to remove downloaded file: %s", err)
-
     # try downloading, three times max.
     downloaded = False
     attempt_cnt = 0
@@ -317,14 +315,14 @@ def cleanup_faulty_download():
             _log.info("Downloaded file %s from url %s to %s", filename, url, path)
 
             if httpmsg.type == "text/html" and not filename.endswith('.html'):
-                _log.warning("HTML file downloaded but not expecting it, so assuming invalid download, retrying.")
-                cleanup_faulty_download()
+                _log.warning("HTML file downloaded to %s, so assuming invalid download, retrying.", path)
+                remove_file(path)
             else:
                 # successful download
                 downloaded = True
         except IOError, err:
-            _log.warning("Error when downloading %s from %s (%s), removing file and retrying", filename, url, err)
-            cleanup_faulty_download()
+            _log.warning("Error when downloading from %s to %s (%s), removing it and retrying", url, path, err)
+            remove_file(path)
 
         if not downloaded:
             attempt_cnt += 1

From 50187c3f084a7086f2e96e88e33812251a607c52 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Nov 2014 16:55:45 +0100
Subject: [PATCH 0319/1356] fix log message in remove_file function

---
 easybuild/tools/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 1a56b739ec..f9ce769b34 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -177,7 +177,7 @@ def remove_file(path):
         if os.path.exists(path):
             os.remove(path)
     except OSError, err:
-          _log.error("Failed to remove downloaded file: %s", err)
+          _log.error("Failed to remove %s: %s", path, err)
 
 
 def extract_file(fn, dest, cmd=None, extra_options=None, overwrite=False):

From 60c52f4f1ad415582272519394ab8d0cacef16c8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Nov 2014 08:57:45 +0100
Subject: [PATCH 0320/1356] fix issue with getcode not being available in Py2.4
 yet

---
 easybuild/tools/filetools.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index f9ce769b34..18e8c754dc 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -290,15 +290,16 @@ def report(blocks_read, blocksize, filesize):
     attempt_cnt = 0
     while not downloaded and attempt_cnt < 3:
         # get HTTP response code first before downloading file
+        response_code = None
         try:
             urlfile = urllib.urlopen(url)
-            response_code = urlfile.getcode()
+            if hasattr(urlfile, 'getcode'):  # no getcode() in Py2.4 yet
+                response_code = urlfile.getcode()
             urlfile.close()
         except IOError, err:
             _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)
-            response_code = None
 
-        if response_code:
+        if response_code is not None:
             _log.debug('HTTP response code for given url: %d', response_code)
             # check for a 4xx response code which indicates a non-existing URL
             if response_code // 100 == 4:

From 0f596df75af50da0f58e7409993acff78e30efc3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Nov 2014 09:06:38 +0100
Subject: [PATCH 0321/1356] only log deprecation warning for non-empty set of
 extra_options of wrong type

---
 easybuild/framework/easyblock.py             | 2 +-
 easybuild/framework/easyconfig/easyconfig.py | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 0c96f815b2..8f3bde180e 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -101,7 +101,7 @@ def extra_options(extra=None):
             extra = dict(extra)
 
         # to avoid breaking backward compatibility, we still need to return a list of tuples in EasyBuild v1.x
-        _log.deprecated("Returning list of tuples rather than a dict as return value of extra_options", '2.0')
+        # starting with EasyBuild v2.0, this will be changed to return the actual dict
         res = extra.items()
 
         return res
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index b85f75252b..8d871a6d7d 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -165,7 +165,8 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         if not isinstance(self.extra_options, dict):
             if isinstance(self.extra_options, (list, tuple,)):
                 typ = type(self.extra_options)
-                self.log.deprecated("Specified extra_options should be of type 'dict', found type '%s'" % typ, '2.0')
+                if extra_options:
+                    self.log.deprecated("extra_options return value should be of type 'dict', found '%s'" % typ, '2.0')
                 tup = (self.extra_options, type(self.extra_options))
                 self.log.debug("Converting extra_options value '%s' of type '%s' to a dict" % tup)
                 self.extra_options = dict(self.extra_options)

From 61dbab29347babe6d95a86610fb0f9e07adb4c53 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Nov 2014 09:08:46 +0100
Subject: [PATCH 0322/1356] fix deprecation log msg for moduleGenerator

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 6d7bb5815c..52f03cb5b2 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -618,7 +618,7 @@ def moduleGenerator(self):
         """
         Module generator (DEPRECATED, use self.module_generator instead).
         """
-        _log.deprecated("Environment variable SOFTDEVEL* being relied on", "2.0")
+        self.log.deprecated("self.moduleGenerator is replaced by self.module_generator", "2.0")
         return self.module_generator
 
     #

From d71010f9178e77301c7f47b3cab5032f6447574a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Nov 2014 23:48:56 +0100
Subject: [PATCH 0323/1356] reinstate -r as short option for --robot

---
 easybuild/tools/options.py | 2 +-
 test/framework/options.py  | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 3d3ed7f84e..346399f93e 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -98,7 +98,7 @@ def basic_options(self):
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
-                      None, 'store_or_None', '', {'metavar': 'PATH[:PATH]'}),
+                      None, 'store_or_None', '', 'r', {'metavar': 'PATH[:PATH]'}),
             'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
                             None, 'store', default_robot_paths, {'metavar': 'PATH[:PATH]'}),
             'skip': ("Skip existing software (useful for installing additional packages)",
diff --git a/test/framework/options.py b/test/framework/options.py
index d52e934a38..6def5f9ae0 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -535,10 +535,11 @@ def test_search(self):
             args = [
                 search_arg,
                 'toy-0.0',
-                '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+                '-r',
+                os.path.join(os.path.dirname(__file__), 'easyconfigs'),
                 '--unittest-file=%s' % self.logfile,
             ]
-            outtxt = self.eb_main(args, logfile=dummylogfn)
+            outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True, verbose=True)
 
             info_msg = r"Searching \(case-insensitive\) for 'toy-0.0' in"
             self.assertTrue(re.search(info_msg, outtxt), "Info message when searching for easyconfigs in '%s'" % outtxt)

From 7dee490ff322955689add39254f87eff83ea64be Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Nov 2014 08:31:56 +0100
Subject: [PATCH 0324/1356] update with vsc-base v1.9.9

---
 vsc/README.md              |   2 +-
 vsc/utils/fancylogger.py   |  12 +-
 vsc/utils/generaloption.py | 233 +++++++++++++++++++++++++++----------
 vsc/utils/missing.py       | 113 ++++++++++++++++--
 vsc/utils/rest.py          |   6 +-
 vsc/utils/testing.py       | 114 ++++++++++++++++++
 6 files changed, 400 insertions(+), 80 deletions(-)
 create mode 100644 vsc/utils/testing.py

diff --git a/vsc/README.md b/vsc/README.md
index c2fac06881..932369c661 100644
--- a/vsc/README.md
+++ b/vsc/README.md
@@ -1,3 +1,3 @@
 Code from https://github.com/hpcugent/vsc-base
 
-based on 95c2174a243874227dcc895d3e26c1b3b949ba22 (vsc-base v1.9.5)
+based on 35fee9d3130a6b52bf83993e73d187e9d46c69bc (vsc-base v1.9.9)
diff --git a/vsc/utils/fancylogger.py b/vsc/utils/fancylogger.py
index b9576bbd68..1f0220df75 100644
--- a/vsc/utils/fancylogger.py
+++ b/vsc/utils/fancylogger.py
@@ -324,7 +324,7 @@ def thread_name():
     return threading.currentThread().getName()
 
 
-def getLogger(name=None, fname=True, clsname=False, fancyrecord=None):
+def getLogger(name=None, fname=False, clsname=False, fancyrecord=None):
     """
     returns a fancylogger
     if fname is True, the loggers name will be 'name[.classname].functionname'
@@ -352,8 +352,10 @@ def getLogger(name=None, fname=True, clsname=False, fancyrecord=None):
     if os.environ.get('FANCYLOGGER_GETLOGGER_DEBUG', '0').lower() in ('1', 'yes', 'true', 'y'):
         print 'FANCYLOGGER_GETLOGGER_DEBUG',
         print 'name', name, 'fname', fname, 'fullname', fullname,
-        print 'parent_info verbose'
-        print "\n".join(l.get_parent_info("FANCYLOGGER_GETLOGGER_DEBUG"))
+        print "getRootLoggerName: ", getRootLoggerName()
+        if hasattr(l, 'get_parent_info'):
+            print 'parent_info verbose'
+            print "\n".join(l.get_parent_info("FANCYLOGGER_GETLOGGER_DEBUG"))
         sys.stdout.flush()
     return l
 
@@ -683,8 +685,8 @@ def enableDefaultHandlers():
 def getDetailsLogLevels(fancy=True):
     """
     Return list of (name,loglevelname) pairs of existing loggers
-    
-    @param fancy: if True, returns only Fancylogger; if False, returns non-FancyLoggers, 
+
+    @param fancy: if True, returns only Fancylogger; if False, returns non-FancyLoggers,
                   anything else, return all loggers
     """
     func_map = {
diff --git a/vsc/utils/generaloption.py b/vsc/utils/generaloption.py
index 2dd49ed8ce..390e5fa79e 100644
--- a/vsc/utils/generaloption.py
+++ b/vsc/utils/generaloption.py
@@ -72,20 +72,38 @@ def set_columns(cols=None):
         os.environ['COLUMNS'] = "%s" % cols
 
 
+def what_str_list_tuple(name):
+    """Given name, return separator, class and helptext wrt separator.
+        (Currently supports strlist, strtuple, pathlist, pathtuple) 
+    """
+    sep = ','
+    helpsep = 'comma'
+    if name.startswith('path'):
+        sep = os.pathsep
+        helpsep = 'pathsep'
+
+    klass = None
+    if name.endswith('list'):
+        klass = list
+    elif name.endswith('tuple'):
+        klass = tuple
+
+    return sep, klass, helpsep
+
 def check_str_list_tuple(option, opt, value):
     """
     check function for strlist and strtuple type
         assumes value is comma-separated list
         returns list or tuple of strings
     """
-    split = value.split(',')
-    if option.type == 'strlist':
-        return split
-    elif option.type == 'strtuple':
-        return tuple(split)
-    else:
-        err = _("check_strlist_strtuple: unsupported type %s" % option.type)
+    sep, klass, _ = what_str_list_tuple(option.type)
+    split = value.split(sep)
+
+    if klass is None:
+        err = _gettext("check_strlist_strtuple: unsupported type %s" % option.type)
         raise OptionValueError(err)
+    else:
+        return klass(split)
 
 
 class ExtOption(CompleterOption):
@@ -97,7 +115,10 @@ class ExtOption(CompleterOption):
          - confighelp : hook for configfile-style help messages
          - store_debuglog : turns on fancylogger debugloglevel
             - also: 'store_infolog', 'store_warninglog'
-         - extend : extend default list (or create new one if is None)
+         - add : add value to default (result is default + value)
+             - add_first : add default to value (result is value + default)
+             - extend : alias for add with strlist type
+             - type must support + (__add__) and one of negate (__neg__) or slicing (__getslice__)
          - date : convert into datetime.date
          - datetime : convert into datetime.datetime
          - regex: compile str in regexp
@@ -105,13 +126,18 @@ class ExtOption(CompleterOption):
            - set default to None if no option passed,
            - set to default if option without value passed,
            - set to value if option with value passed
+           
+        Types:
+          - strlist, strtuple : convert comma-separated string in a list resp. tuple of strings     
+          - pathlist, pathtuple : using os.pathsep, convert pathsep-separated string in a list resp. tuple of strings
+              - the path separator is OS-dependent
     """
     EXTEND_SEPARATOR = ','
 
     ENABLE = 'enable'  # do nothing
     DISABLE = 'disable'  # inverse action
 
-    EXTOPTION_EXTRA_OPTIONS = ('extend', 'date', 'datetime', 'regex',)
+    EXTOPTION_EXTRA_OPTIONS = ('date', 'datetime', 'regex', 'add', 'add_first',)
     EXTOPTION_STORE_OR = ('store_or_None',)  # callback type
     EXTOPTION_LOG = ('store_debuglog', 'store_infolog', 'store_warninglog',)
     EXTOPTION_HELP = ('shorthelp', 'confighelp',)
@@ -121,10 +147,9 @@ class ExtOption(CompleterOption):
     TYPED_ACTIONS = Option.TYPED_ACTIONS + EXTOPTION_EXTRA_OPTIONS + EXTOPTION_STORE_OR
     ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + EXTOPTION_EXTRA_OPTIONS
 
-    TYPE_CHECKER = dict([('strlist', check_str_list_tuple),
-                         ('strtuple', check_str_list_tuple),
-                         ] + Option.TYPE_CHECKER.items())
-    TYPES = tuple(['strlist', 'strtuple'] + list(Option.TYPES))
+    TYPE_STRLIST = ['%s%s' % (name, klass) for klass in ['list', 'tuple'] for name in ['str', 'path'] ]
+    TYPE_CHECKER = dict([(x, check_str_list_tuple) for x in TYPE_STRLIST] + Option.TYPE_CHECKER.items())
+    TYPES = tuple(TYPE_STRLIST + list(Option.TYPES))
     BOOLEAN_ACTIONS = ('store_true', 'store_false',) + EXTOPTION_LOG
 
     def __init__(self, *args, **kwargs):
@@ -135,7 +160,11 @@ def __init__(self, *args, **kwargs):
     def _set_attrs(self, attrs):
         """overwrite _set_attrs to allow store_or callbacks"""
         Option._set_attrs(self, attrs)
-        if self.action in self.EXTOPTION_STORE_OR:
+        if self.action == 'extend':
+            # alias
+            self.action = 'add'
+            self.type = 'strlist'
+        elif self.action in self.EXTOPTION_STORE_OR:
             setattr(self, 'store_or', self.action)
 
             def store_or(option, opt_str, value, parser, *args, **kwargs):
@@ -143,8 +172,7 @@ def store_or(option, opt_str, value, parser, *args, **kwargs):
                 # see http://stackoverflow.com/questions/1229146/parsing-empty-options-in-python
                 # ugly code, optparse is crap
                 if parser.rargs and not parser.rargs[0].startswith('-'):
-                    val = parser.rargs[0]
-                    parser.rargs.pop(0)
+                    val = option.check_value(opt_str, parser.rargs.pop(0))
                 else:
                     val = kwargs.get('orig_default', None)
 
@@ -157,13 +185,14 @@ def store_or(option, opt_str, value, parser, *args, **kwargs):
                 self.type = 'string'
 
             self.callback = store_or
-            self.callback_kwargs = {'orig_default': copy.deepcopy(self.default),
-                                    }
+            self.callback_kwargs = {
+                'orig_default': copy.deepcopy(self.default),
+                }
             self.action = 'callback'  # act as callback
             if self.store_or == 'store_or_None':
                 self.default = None
             else:
-                raise ValueError("_set_attrs: unknown store_or %s" % self.store_or)
+                self.log.raiseException("_set_attrs: unknown store_or %s" % self.store_or, exception=ValueError)
 
     def take_action(self, action, dest, opt, value, values, parser):
         """Extended take_action"""
@@ -201,22 +230,29 @@ def take_action(self, action, dest, opt, value, values, parser):
             Option.take_action(self, action, dest, opt, value, values, parser)
 
         elif action in self.EXTOPTION_EXTRA_OPTIONS:
-            if action == "extend":
-                # comma separated list convert in list
-                lvalue = value.split(self.EXTEND_SEPARATOR)
-                values.ensure_value(dest, []).extend(lvalue)
+            if action in ("add", "add_first",):
+                # determine type from lvalue
+                # set default first
+                values.ensure_value(dest, type(value)())
+                default = getattr(values, dest)
+                if not (hasattr(default, '__add__') and
+                        (hasattr(default, '__neg__') or hasattr(default, '__getslice__'))):
+                    msg = "Unsupported type %s for action %s (requires + and one of negate or slice)"
+                    self.log.raiseException(msg % (type(default), action))
+                if action == 'add':
+                    lvalue = default + value
+                elif action == 'add_first':
+                    lvalue = value + default
             elif action == "date":
                 lvalue = date_parser(value)
-                setattr(values, dest, lvalue)
             elif action == "datetime":
                 lvalue = datetime_parser(value)
-                setattr(values, dest, lvalue)
             elif action == "regex":
                 lvalue = re.compile(r'' + value)
-                setattr(values, dest, lvalue)
             else:
-                raise(Exception("Unknown extended option action %s (known: %s)" %
-                                (action, self.EXTOPTION_EXTRA_OPTIONS)))
+                msg = "Unknown extended option action %s (known: %s)"
+                self.log.raiseException(msg % (action, self.EXTOPTION_EXTRA_OPTIONS))
+            setattr(values, dest, lvalue)
         else:
             Option.take_action(self, action, dest, opt, value, values, parser)
 
@@ -291,7 +327,7 @@ def _process_short_opts(self, rargs, values):
 
 class ExtOptionGroup(OptionGroup):
     """An OptionGroup with support for configfile section names"""
-    RESERVED_SECTIONS = ['DEFAULT']
+    RESERVED_SECTIONS = [ConfigParser.DEFAULTSECT]
     NO_SECTION = ('NO', 'SECTION')
 
     def __init__(self, *args, **kwargs):
@@ -617,6 +653,9 @@ class GeneralOption(object):
         - go_useconfigfiles : use configfiles or not (default set by CONFIGFILES_USE)
             if True, an option --configfiles will be added
         - go_configfiles : list of configfiles to parse. Uses ConfigParser.read; last file wins
+        - go_configfiles_initenv : section dict of key/value dict; inserted before configfileparsing
+            As a special case, using all uppercase key in DEFAULT section with a case-sensitive 
+            configparser can be used to set "constants" for easy interpolation in all sections.
         - go_loggername : name of logger, default classname
         - go_mainbeforedefault : set the main options before the default ones
         - go_autocompleter : dict with named options to pass to the autocomplete call (eg arg_completer)
@@ -648,7 +687,8 @@ class GeneralOption(object):
     CONFIGFILES_INIT = []  # initial list of defaults, overwritten by go_configfiles options
     CONFIGFILES_IGNORE = []
     CONFIGFILES_MAIN_SECTION = 'MAIN'  # sectionname that contains the non-grouped/non-prefixed options
-    CONFIGFILE_PARSER = ConfigParser.ConfigParser
+    CONFIGFILE_PARSER = ConfigParser.SafeConfigParser
+    CONFIGFILE_CASESENSITIVE = True
 
     METAVAR_DEFAULT = True  # generate a default metavar
     METAVAR_MAP = None  # metvar, list of longopts map
@@ -668,6 +708,7 @@ def __init__(self, **kwargs):
         self.no_system_exit = kwargs.pop('go_nosystemexit', None)  # unit test option
         self.use_configfiles = kwargs.pop('go_useconfigfiles', self.CONFIGFILES_USE)  # use or ignore config files
         self.configfiles = kwargs.pop('go_configfiles', self.CONFIGFILES_INIT)  # configfiles to parse
+        configfiles_initenv = kwargs.pop('go_configfiles_initenv', None)  # initial environment for configfiles to parse
         prefixloggername = kwargs.pop('go_prefixloggername', False)  # name of logger is same as envvar prefix
         mainbeforedefault = kwargs.pop('go_mainbeforedefault', False)  # Set the main options before the default ones
         autocompleter = kwargs.pop('go_autocompleter', {})  # Pass these options to the autocomplete call
@@ -682,7 +723,7 @@ def __init__(self, **kwargs):
         self.parser = self.PARSER(**kwargs)
         self.parser.allow_interspersed_args = self.INTERSPERSED
 
-        self.configfile_parser = self.CONFIGFILE_PARSER()
+        self.configfile_parser = None
         self.configfile_remainder = {}
 
         loggername = self.__class__.__name__
@@ -717,6 +758,7 @@ def __init__(self, **kwargs):
 
         if not self.options is None:
             # None for eg usage/help
+            self.configfile_parser_init(initenv=configfiles_initenv)
             self.parseconfigfiles()
 
             self._set_default_loglevel()
@@ -760,8 +802,8 @@ def _set_default_loglevel(self):
     def _make_configfiles_options(self):
         """Add configfiles option"""
         opts = {
-            'configfiles': ("Parse (additional) configfiles", None, "extend", self.DEFAULT_CONFIGFILES),
-            'ignoreconfigfiles': ("Ignore configfiles", None, "extend", self.DEFAULT_IGNORECONFIGFILES),
+            'configfiles': ("Parse (additional) configfiles", "strlist", "add", self.DEFAULT_CONFIGFILES),
+            'ignoreconfigfiles': ("Ignore configfiles", "strlist", "add", self.DEFAULT_IGNORECONFIGFILES),
         }
         descr = ['Configfile options', '']
         self.log.debug("Add configfiles options descr %s opts %s (no prefix)" % (descr, opts))
@@ -880,16 +922,17 @@ def add_group_parser(self, opt_dict, description, prefix=None, otherdefaults=Non
                 default = otherdefaults.get(key)
 
             extra_help = []
-            if action in ("extend",) or typ in ('strlist', 'strtuple',):
-                extra_help.append("type comma-separated list")
+            if typ in ExtOption.TYPE_STRLIST:
+                sep, klass, helpsep = what_str_list_tuple(typ)
+                extra_help.append("type %s-separated %s" % (helpsep, klass.__name__))
             elif typ is not None:
                 extra_help.append("type %s" % typ)
 
             if default is not None:
                 if len(str(default)) == 0:
                     extra_help.append("def ''")  # empty string
-                elif action in ("extend",) or typ in ('strlist', 'strtuple',):
-                    extra_help.append("def %s" % ','.join(default))
+                elif typ in ExtOption.TYPE_STRLIST:
+                    extra_help.append("def %s" % sep.join(default))
                 else:
                     extra_help.append("def %s" % default)
 
@@ -983,14 +1026,13 @@ def parseoptions(self, options_list=None):
         try:
             (self.options, self.args) = self.parser.parse_args(options_list)
         except SystemExit, err:
+            try:
+                msg = err.message
+            except AttributeError:
+                # py2.4
+                msg = str(err)
+            self.log.debug("parseoptions: parse_args err %s code %s" % (msg, err.code))
             if self.no_system_exit:
-                try:
-                    msg = err.message
-                except:
-                    # py2.4
-                    msg = '_nomessage_'
-                self.log.debug("parseoptions: no_system_exit set after parse_args err %s code %s" %
-                               (msg, err.code))
                 return
             else:
                 sys.exit(err.code)
@@ -1006,6 +1048,40 @@ def parseoptions(self, options_list=None):
 
         self.log.debug("Found options %s args %s" % (self.options, self.args))
 
+    def configfile_parser_init(self, initenv=None):
+        """
+        Initialise the confgiparser to use.
+        
+            @params initenv: insert initial environment into the configparser. 
+                It is a dict of dicts; the first level key is the section name; 
+                the 2nd level key,value is the key=value. 
+                All section names, keys and values are converted to strings.
+        """
+        self.configfile_parser = self.CONFIGFILE_PARSER()
+
+        # make case sensitive
+        if self.CONFIGFILE_CASESENSITIVE:
+            self.log.debug('Initialise case sensitive configparser')
+            self.configfile_parser.optionxform = str
+        else:
+            self.log.debug('Initialise case insensitive configparser')
+            self.configfile_parser.optionxform = str.lower
+
+        # insert the initenv in the parser
+        if initenv is None:
+            initenv = {}
+
+        for name, section in initenv.items():
+            name = str(name)
+            if name == ConfigParser.DEFAULTSECT:
+                # is protected/reserved (and hidden)
+                pass
+            elif not self.configfile_parser.has_section(name):
+                self.configfile_parser.add_section(name)
+
+            for key, value in section.items():
+                self.configfile_parser.set(name, str(key), str(value))
+
     def parseconfigfiles(self):
         """Parse configfiles"""
         if not self.use_configfiles:
@@ -1051,7 +1127,8 @@ def parseconfigfiles(self):
         self.log.debug("parseconfigfiles: following files were parsed %s" % parsed_files)
         self.log.debug("parseconfigfiles: following files were NOT parsed %s" %
                        [x for x in configfiles if not x in parsed_files])
-        self.log.debug("parseconfigfiles: sections (w/o DEFAULT) %s" % self.configfile_parser.sections())
+        self.log.debug("parseconfigfiles: sections (w/o %s) %s" %
+                       (ConfigParser.DEFAULTSECT, self.configfile_parser.sections()))
 
         # walk through list of section names
         # - look for options set though config files
@@ -1073,7 +1150,7 @@ def parseconfigfiles(self):
             if section not in cfg_sections_flat:
                 self.log.debug("parseconfigfiles: found section %s, adding to remainder" % section)
                 remainder = self.configfile_remainder.setdefault(section, {})
-                # parse te remaining options, sections starting with 'raw_'
+                # parse the remaining options, sections starting with 'raw_'
                 # as their name will be considered raw sections
                 for opt, val in self.configfile_parser.items(section, raw=(section.startswith('raw_'))):
                     remainder[opt] = val
@@ -1098,8 +1175,16 @@ def parseconfigfiles(self):
                     opt_name, opt_dest = self.make_options_option_name_and_destination(prefix, opt)
                     actual_option = self.parser.get_option_by_long_name(opt_name)
                     if actual_option is None:
-                        self.log.raiseException('parseconfigfiles: no option corresponding with dest %s' %
-                                                opt_dest)
+                        # don't fail on DEFAULT UPPERCASE options in case-sensitive mode.
+                        in_def = self.configfile_parser.has_option(ConfigParser.DEFAULTSECT, opt)
+                        if in_def and self.CONFIGFILE_CASESENSITIVE and opt == opt.upper():
+                            self.log.debug(('parseconfigfiles: no option corresponding with '
+                                            'opt %s dest %s in section %s but found all uppercase '
+                                            'in DEFAULT section. Skipping.') % (opt, opt_dest, section))
+                            continue
+                        else:
+                            self.log.raiseException(('parseconfigfiles: no option corresponding with '
+                                                     'opt %s dest %s in section %s') % (opt, opt_dest, section))
 
                     configfile_options_default[opt_dest] = actual_option.default
 
@@ -1254,8 +1339,8 @@ def dict_by_prefix(self, merge_empty_prefix=False):
         return subdict
 
     def generate_cmd_line(self, ignore=None, add_default=None):
-        """Create the commandline options that would create the current self.options
-            opt_name is destination
+        """Create the commandline options that would create the current self.options.
+           The result is sorted on the destination names.
 
             @param ignore : regex on destination
             @param add_default : print value that are equal to default
@@ -1309,7 +1394,11 @@ def generate_cmd_line(self, ignore=None, add_default=None):
                 else:
                     self.log.debug("generate_cmd_line %s adding %s non-default value %s" %
                                    (action, opt_name, opt_value))
-                    args.append("--%s=%s" % (opt_name, shell_quote(opt_value)))
+                    if typ in ExtOption.TYPE_STRLIST:
+                        sep, _, _ = what_str_list_tuple(typ)
+                        args.append("--%s=%s" % (opt_name, shell_quote(sep.join(opt_value))))
+                    else:
+                        args.append("--%s=%s" % (opt_name, shell_quote(opt_value)))
             elif action in ("store_true", "store_false",) + ExtOption.EXTOPTION_LOG:
                 # not default!
                 self.log.debug("generate_cmd_line adding %s value %s. store action found" %
@@ -1334,23 +1423,39 @@ def generate_cmd_line(self, ignore=None, add_default=None):
                                            (opt_name, action, default))
                     else:
                         args.append("--%s" % opt_name)
-            elif action in ("extend",):
-                # comma separated
-                self.log.debug("generate_cmd_line adding %s value %s. extend action, return as comma-separated list" %
-                               (opt_name, opt_value))
-
+            elif action in ("add", "add_first"):
                 if default is not None:
-                    # remove these. if default is set, extend extends the default!
-                    for def_el in default:
-                        opt_value.remove(def_el)
+                    if hasattr(opt_value, '__neg__'):
+                        if action == 'add_first':
+                            opt_value = opt_value + -default
+                        else:
+                            opt_value = -default + opt_value
+                    elif hasattr(opt_value, '__getslice__'):
+                        if action == 'add_first':
+                            opt_value = opt_value[:-len(default)]
+                        else:
+                            opt_value = opt_value[len(default):]
 
-                if len(opt_value) == 0:
-                    self.log.debug('generate_cmd_line skipping.')
+                if typ in ExtOption.TYPE_STRLIST:
+                    sep, klass, helpsep = what_str_list_tuple(typ)
+                    restype = '%s-separated %s' % (helpsep, klass.__name__)
+                    value = sep.join(opt_value)
+                else:
+                    restype = 'string'
+                    value = opt_value
+
+                if not opt_value:
+                    # empty strings, empty lists, 0
+                    self.log.debug('generate_cmd_line no value left, skipping.')
                     continue
 
-                args.append("--%s=%s" % (opt_name, shell_quote(",".join(opt_value))))
-            elif typ in ('strlist', 'strtuple',):
-                args.append("--%s=%s" % (opt_name, shell_quote(",".join(opt_value))))
+                self.log.debug("generate_cmd_line adding %s value %s. %s action, return as %s" %
+                               (opt_name, opt_value, action, restype))
+
+                args.append("--%s=%s" % (opt_name, shell_quote(value)))
+            elif typ in ExtOption.TYPE_STRLIST:
+                sep, _, _ = what_str_list_tuple(typ)
+                args.append("--%s=%s" % (opt_name, shell_quote(sep.join(opt_value))))
             elif action in ("append",):
                 # add multiple times
                 self.log.debug("generate_cmd_line adding %s value %s. append action, return as multiple args" %
diff --git a/vsc/utils/missing.py b/vsc/utils/missing.py
index 9d4768fec0..683269cb00 100644
--- a/vsc/utils/missing.py
+++ b/vsc/utils/missing.py
@@ -40,14 +40,20 @@
 @author: Andy Georges (Ghent University)
 @author: Stijn De Weirdt (Ghent University)
 """
+import os
+import re
 import shlex
 import subprocess
+import sys
 import time
 
 from vsc.utils import fancylogger
 from vsc.utils.frozendict import FrozenDict
 
 
+_log = fancylogger.getLogger('vsc.utils.missing')
+
+
 def partial(func, *args, **keywords):
     """
     Return a new partial object which when called will behave like func called with the positional arguments args
@@ -289,15 +295,105 @@ def shell_unquote(x):
     return shlex.split(str(x))[0]
 
 
-def get_subclasses(klass):
-    """Get all subclasses recursively"""
-    res = []
-    for cl in klass.__subclasses__():
-        res.extend(get_subclasses(cl))
-        res.append(cl)
+def get_class_for(modulepath, class_name):
+    """
+    Get class for a given Python class name and Python module path.
+
+    @param modulepath: Python module path (e.g., 'vsc.utils.generaloption')
+    @param class_name: Python class name (e.g., 'GeneralOption')
+    """
+    # try to import specified module path, reraise ImportError if it occurs
+    try:
+        module = __import__(modulepath, globals(), locals(), [''])
+    except ImportError, err:
+        raise ImportError(err)
+    # try to import specified class name from specified module path, throw ImportError if this fails
+    try:
+        klass = getattr(module, class_name)
+    except AttributeError, err:
+        raise ImportError("Failed to import %s from %s: %s" % (class_name, modulepath, err))
+    return klass
+
+
+def get_subclasses_dict(klass, include_base_class=False):
+    """Get dict with subclasses per classes, recursively from the specified base class."""
+    res = {}
+    subclasses = klass.__subclasses__()
+    if include_base_class:
+        res.update({klass: subclasses})
+    for subclass in subclasses:
+        # always include base class for recursive call
+        res.update(get_subclasses_dict(subclass, include_base_class=True))
     return res
 
 
+def get_subclasses(klass, include_base_class=False):
+    """Get list of all subclasses, recursively from the specified base class."""
+    return get_subclasses_dict(klass, include_base_class=include_base_class).keys()
+
+
+def modules_in_pkg_path(pkg_path):
+    """Return list of module files in specified package path."""
+    # if the specified (relative) package path doesn't exist, try and determine the absolute path via sys.path
+    if not os.path.isabs(pkg_path) and not os.path.isdir(pkg_path):
+        _log.debug("Obtained non-existing relative package path '%s', will try to figure out absolute path" % pkg_path)
+        newpath = None
+        for sys_path_dir in sys.path:
+            abspath = os.path.join(sys_path_dir, pkg_path)
+            if os.path.isdir(abspath):
+                _log.debug("Found absolute path %s for package path %s, verifying it" % (abspath, pkg_path))
+                # also make sure an __init__.py is in place in every subdirectory
+                is_pkg = True
+                subdir = ''
+                for pkg_path_dir in pkg_path.split(os.path.sep):
+                    subdir = os.path.join(subdir, pkg_path_dir)
+                    if not os.path.isfile(os.path.join(sys_path_dir, subdir, '__init__.py')):
+                        is_pkg = False
+                        tup = (subdir, abspath, pkg_path)
+                        _log.debug("No __init__.py found in %s, %s is not a valid absolute path for pkg_path %s" % tup)
+                        break
+                if is_pkg:
+                    newpath = abspath
+                    break
+
+        if newpath is None:
+            # give up if we couldn't find an absolute path for the imported package
+            tup = (pkg_path, sys.path)
+            raise OSError("Can't browse package via non-existing relative path '%s', not found in sys.path (%s)" % tup)
+        else:
+            pkg_path = newpath
+            _log.debug("Found absolute package path %s" % pkg_path)
+
+    module_regexp = re.compile(r"^(?P<modname>[^_].*|__init__)\.py$")
+    modules = [res.group('modname') for res in map(module_regexp.match, os.listdir(pkg_path)) if res]
+    _log.debug("List of modules for package in %s: %s" % (pkg_path, modules))
+    return modules
+
+
+def avail_subclasses_in(base_class, pkg_name, include_base_class=False):
+    """Determine subclasses for specificied base classes in modules in (only) specified packages."""
+
+    def try_import(name):
+        """Try import the specified package/module."""
+        try:
+            # don't use return value of __import__ since it may not be the package itself but it's parent
+            __import__(name, globals())
+            return sys.modules[name]
+        except ImportError, err:
+            raise ImportError("avail_subclasses_in: failed to import %s: %s" % (name, err))
+
+    # import all modules in package path(s) before determining subclasses
+    pkg = try_import(pkg_name)
+    for pkg_path in pkg.__path__:
+        for mod in modules_in_pkg_path(pkg_path):
+            # no need to directly import __init__ (already done by importing package)
+            if not mod.startswith('__init__'):
+                _log.debug("Importing module '%s' from package '%s'" % (mod, pkg_name))
+                try_import('%s.%s' % (pkg_name, mod))
+
+    return get_subclasses_dict(base_class, include_base_class=include_base_class)
+
+
 class TryOrFail(object):
     """
     Perform the function n times, catching each exception in the exception tuple except on the last try
@@ -310,16 +406,15 @@ def __init__(self, n, exceptions=(Exception,), sleep=0):
 
     def __call__(self, function):
         def new_function(*args, **kwargs):
-            log = fancylogger.getLogger(function.__name__)
             for i in xrange(0, self.n):
                 try:
                     return function(*args, **kwargs)
                 except self.exceptions, err:
                     if i == self.n - 1:
                         raise
-                    log.exception("try_or_fail caught an exception - attempt %d: %s" % (i, err))
+                    _log.exception("try_or_fail caught an exception - attempt %d: %s" % (i, err))
                     if self.sleep > 0:
-                        log.warning("try_or_fail is sleeping for %d seconds before the next attempt" % (self.sleep,))
+                        _log.warning("try_or_fail is sleeping for %d seconds before the next attempt" % (self.sleep,))
                         time.sleep(self.sleep)
 
         return new_function
diff --git a/vsc/utils/rest.py b/vsc/utils/rest.py
index 82d5835eee..18974a8167 100644
--- a/vsc/utils/rest.py
+++ b/vsc/utils/rest.py
@@ -42,7 +42,11 @@
     import simplejson as json
 
 from vsc.utils import fancylogger
-from vsc.utils.missing import partial
+
+try:
+    from functools import partial
+except ImportError:
+    from vsc.utils.missing import partial
 
 
 class Client(object):
diff --git a/vsc/utils/testing.py b/vsc/utils/testing.py
new file mode 100644
index 0000000000..71807d5677
--- /dev/null
+++ b/vsc/utils/testing.py
@@ -0,0 +1,114 @@
+#!/usr/bin/env python
+##
+#
+# Copyright 2014-2014 Ghent University
+#
+# This file is part of vsc-base,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/vsc-base
+#
+# vsc-base is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Library General Public License as
+# published by the Free Software Foundation, either version 2 of
+# the License, or (at your option) any later version.
+#
+# vsc-base is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Library General Public License for more details.
+#
+# You should have received a copy of the GNU Library General Public License
+# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Test utilities.
+
+@author: Kenneth Hoste (Ghent University)
+"""
+
+import re
+import sys
+from cStringIO import StringIO
+from unittest import TestCase
+
+
+class EnhancedTestCase(TestCase):
+    """Enhanced test case, provides extra functionality (e.g. an assertErrorRegex method)."""
+
+    def setUp(self):
+        """Prepare test case."""
+        super(EnhancedTestCase, self).setUp()
+        self.orig_sys_stdout = sys.stdout
+        self.orig_sys_stderr = sys.stderr
+
+    def convert_exception_to_str(self, err):
+        """Convert an Exception instance to a string."""
+        msg = err
+        if hasattr(err, 'msg'):
+            msg = err.msg
+        elif hasattr(err, 'message'):
+            msg = err.message
+            if not msg:
+                # rely on str(msg) in case err.message is empty
+                msg = err
+        elif hasattr(err, 'args'):  # KeyError in Python 2.4 only provides message via 'args' attribute
+            msg = err.args[0]
+        else:
+            msg = err
+        try:
+            res = str(msg)
+        except UnicodeEncodeError:
+            res = msg.encode('utf8', 'replace')
+
+        return res
+
+    def assertErrorRegex(self, error, regex, call, *args, **kwargs):
+        """
+        Convenience method to match regex with the expected error message.
+        Example: self.assertErrorRegex(OSError, "No such file or directory", os.remove, '/no/such/file')
+        """
+        try:
+            call(*args, **kwargs)
+            str_kwargs = ['='.join([k, str(v)]) for (k, v) in kwargs.items()]
+            str_args = ', '.join(map(str, args) + str_kwargs)
+            self.assertTrue(False, "Expected errors with %s(%s) call should occur" % (call.__name__, str_args))
+        except error, err:
+            msg = self.convert_exception_to_str(err)
+            if isinstance(regex, basestring):
+                regex = re.compile(regex)
+            self.assertTrue(regex.search(msg), "Pattern '%s' is found in '%s'" % (regex.pattern, msg))
+
+    def mock_stdout(self, enable):
+        """Enable/disable mocking stdout."""
+        sys.stdout.flush()
+        if enable:
+            sys.stdout = StringIO()
+        else:
+            sys.stdout = self.orig_sys_stdout
+
+    def mock_stderr(self, enable):
+        """Enable/disable mocking stdout."""
+        sys.stderr.flush()
+        if enable:
+            sys.stderr = StringIO()
+        else:
+            sys.stderr = self.orig_sys_stderr
+
+    def get_stdout(self):
+        """Return output captured from stdout until now."""
+        return sys.stdout.getvalue()
+
+    def get_stderr(self):
+        """Return output captured from stderr until now."""
+        return sys.stderr.getvalue()
+
+    def tearDown(self):
+        """Cleanup after running a test."""
+        self.mock_stdout(False)
+        self.mock_stderr(False)
+        super(EnhancedTestCase, self).tearDown()

From 09f036770a59e8fa8ea504b15ee14091f0d08b13 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Nov 2014 08:32:20 +0100
Subject: [PATCH 0325/1356] make --robot and --robot-paths pathlist-typed
 options, enhance unit tests

---
 easybuild/tools/options.py | 26 ++++++++------------------
 test/framework/options.py  | 20 +++++++++++++-------
 2 files changed, 21 insertions(+), 25 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 346399f93e..3c8cae3ac8 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -82,10 +82,10 @@ def basic_options(self):
 
         easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None)
         if easyconfigs_pkg_paths:
-            default_robot_paths = os.pathsep.join(easyconfigs_pkg_paths)
+            default_robot_paths = easyconfigs_pkg_paths
         else:
             self.log.warning("basic_options: unable to determine easyconfigs pkg path for --robot-paths default")
-            default_robot_paths = ''
+            default_robot_paths = []
 
         descr = ("Basic options", "Basic runtime options for EasyBuild.")
 
@@ -98,9 +98,9 @@ def basic_options(self):
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
-                      None, 'store_or_None', '', 'r', {'metavar': 'PATH[:PATH]'}),
+                      'pathlist', 'store_or_None', [], 'r'),
             'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
-                            None, 'store', default_robot_paths, {'metavar': 'PATH[:PATH]'}),
+                            'pathlist', 'store', default_robot_paths),
             'skip': ("Skip existing software (useful for installing additional packages)",
                      None, 'store_true', False, 'k'),
             'stop': ("Stop the installation after certain step", 'choice', 'store_or_None', 'source', 's', all_stops),
@@ -414,21 +414,11 @@ def _postprocess_config(self):
         if self.options.pretend:
             self.options.installpath = get_pretend_installpath()
 
-        # helper class to convert a string with colon-separated robot paths into a list of robot paths
-        class RobotPath(ListOfStrings):
-            SEPARATOR_LIST = os.pathsep
-            # explicit definition of __str__ is required for unknown reason related to the way Wrapper is defined
-            __str__ = ListOfStrings.__str__
-
-        if self.options.robot is None:
-            all_robot_paths = self.options.robot_paths
-        else:
+        if self.options.robot is not None:
             # paths specified to --robot have preference over --robot-paths
-            all_robot_paths = os.pathsep.join([self.options.robot, self.options.robot_paths])
-            # avoid that options.robot is used for paths (since not everything is there)
-            self.options.robot = True
-        # convert to a regular list, exclude empty strings
-        self.options.robot_paths = nub([x for x in RobotPath(all_robot_paths) if x])
+            # keep both values in sync if robot is enabled, which implies enabling dependency resolver
+            self.options.robot_paths = self.options.robot + self.options.robot_paths
+            self.options.robot = self.options.robot_paths
 
     def _postprocess_list_avail(self):
         """Create all the additional info that can be requested (exit at the end)"""
diff --git a/test/framework/options.py b/test/framework/options.py
index 6def5f9ae0..0ed83a5e74 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -261,11 +261,10 @@ def test_job(self):
         # use gzip-1.4.eb easyconfig file that comes with the tests
         eb_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'gzip-1.4.eb')
 
-        # check log message with --job
-        for job_args in [  # options passed are reordered, so order here matters to make tests pass
-                         ['--debug'],
-                         ['--debug', '--stop=configure', '--try-software-name=foo'],
-                        ]:
+        def check_args(job_args, passed_args=None):
+            """Check whether specified args yield expected result."""
+            if passed_args is None:
+                passed_args = job_args[:]
 
             # clear log file
             write_file(self.logfile, '')
@@ -276,13 +275,20 @@ def test_job(self):
                    ] + job_args
             outtxt = self.eb_main(args)
 
-            job_msg = "INFO.* Command template for jobs: .* && eb %%\(spec\)s.* %s.*\n" % ' .*'.join(job_args)
-            assertmsg = "Info log message with job command template when using --job (job_msg: %s, outtxt: %s)" % (job_msg, outtxt)
+            job_msg = "INFO.* Command template for jobs: .* && eb %%\(spec\)s.* %s.*\n" % ' .*'.join(passed_args)
+            assertmsg = "Info log msg with job command template for --job (job_msg: %s, outtxt: %s)" % (job_msg, outtxt)
             self.assertTrue(re.search(job_msg, outtxt), assertmsg)
 
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
 
+        # options passed are reordered, so order here matters to make tests pass
+        check_args(['--debug'])
+        check_args(['--debug', '--stop=configure', '--try-software-name=foo'])
+        check_args(['--debug', '--robot-paths=/tmp/foo:/tmp/bar'])
+        # --robot has preference over --robot-paths, --robot is not passed down
+        check_args(['--debug', '--robot-paths=/tmp/foo', '--robot=/tmp/bar'], passed_args=['--debug', '--robot-paths=/tmp/bar:/tmp/foo'])
+
     # 'zzz' prefix in the test name is intentional to make this test run last,
     # since it fiddles with the logging infrastructure which may break things
     def test_zzz_logtostdout(self):

From 41e7e6eb65e3277fa64678dcfd817e2a49323889 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Tue, 18 Nov 2014 14:01:39 +0100
Subject: [PATCH 0326/1356] Regex in fetch_parameter_from_easyconfig_file
 flawed

Was picking up white space after parameter which was breaking
easyblock = 'value'
---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 3fea3e6c3e..a735537855 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -698,7 +698,7 @@ def fetch_parameter_from_easyconfig_file(path, param):
     """Fetch parameter specification from given easyconfig file."""
     # check whether easyblock is specified in easyconfig file
     # note: we can't rely on value for 'easyblock' in parsed easyconfig, it may be the default value
-    reg = re.compile(r"^\s*%s\s*=\s*(?P<param>\S.*)\s*$" % param, re.M)
+    reg = re.compile(r"^\s*%s\s*=\s*(?P<param>\S.*?)\s*$" % param, re.M)
     txt = read_file(path)
     res = reg.search(txt)
     if res:

From 7480ae3cc88efb1c8523d5643e732c7c23c43857 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 20 Nov 2014 15:25:24 +0100
Subject: [PATCH 0327/1356] restore metavar's for --robot and --robot-paths

---
 easybuild/tools/options.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 3c8cae3ac8..1098f59f1a 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -98,9 +98,9 @@ def basic_options(self):
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
-                      'pathlist', 'store_or_None', [], 'r'),
+                      'pathlist', 'store_or_None', [], 'r', {'metavar': 'PATH[%sPATH]' % os.pathsep}),
             'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
-                            'pathlist', 'store', default_robot_paths),
+                            'pathlist', 'store', default_robot_paths, {'metavar': 'PATH[%sPATH]' % os.pathsep}),
             'skip': ("Skip existing software (useful for installing additional packages)",
                      None, 'store_true', False, 'k'),
             'stop': ("Stop the installation after certain step", 'choice', 'store_or_None', 'source', 's', all_stops),

From 7ccd6add6e377c6a08c714f96bd4825f14e79718 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 20 Nov 2014 15:25:40 +0100
Subject: [PATCH 0328/1356] use get_class_for provided by vsc.utils.missing

---
 easybuild/framework/easyblock.py             |  3 ++-
 easybuild/framework/easyconfig/easyconfig.py | 19 +------------------
 2 files changed, 3 insertions(+), 19 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 52f03cb5b2..99e005bb82 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -46,12 +46,13 @@
 import traceback
 from distutils.version import LooseVersion
 from vsc.utils import fancylogger
+from vsc.utils.missing import get_class_for
 
 import easybuild.tools.environment as env
 from easybuild.tools import config, filetools
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS, ITERATE_OPTIONS
-from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file, get_class_for
+from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, get_module_path, resolve_template
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index c58e7349a5..1571c1e6ba 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -40,7 +40,7 @@
 import os
 import re
 from vsc.utils import fancylogger
-from vsc.utils.missing import any, nub
+from vsc.utils.missing import any, get_class_for, nub
 from vsc.utils.patterns import Singleton
 
 import easybuild.tools.environment as env
@@ -734,23 +734,6 @@ def fetch_parameter_from_easyconfig_file(path, param):
         return None
 
 
-def get_class_for(modulepath, class_name):
-    """
-    Get class for a given class name and easyblock module path.
-    """
-    # try to import specified module path, reraise ImportError if it occurs
-    try:
-        m = __import__(modulepath, globals(), locals(), [''])
-    except ImportError, err:
-        raise ImportError(err)
-    # try to import specified class name from specified module path, throw ImportError if this fails
-    try:
-        c = getattr(m, class_name)
-    except AttributeError, err:
-        raise ImportError("Failed to import %s from %s: %s" % (class_name, modulepath, err))
-    return c
-
-
 def get_easyblock_class(easyblock, name=None):
     """
     Get class for a particular easyblock (or use default)

From 29466b1dfcc452561f0ec55020c4866c138848ce Mon Sep 17 00:00:00 2001
From: ebgregory <e.gregory@fz-juelich.de>
Date: Thu, 20 Nov 2014 17:25:53 +0100
Subject: [PATCH 0329/1356] adding support for MPICH (instead of just MPICH2)

---
 easybuild/tools/toolchain/mpi.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index a04bb710ef..3cde846bc7 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -176,6 +176,7 @@ def mpi_cmd_for(self, cmd, nr_ranks):
             toolchain.INTELMPI: "mpirun %(mpdbf)s %(nodesfile)s -np %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
             toolchain.MVAPICH2: "mpirun -n %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
             toolchain.MPICH2: "mpirun -n %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
+            toolchain.MPICH: "mpirun -n %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
         }
 
         mpi_family = self.mpi_family()

From 7acb5749e3922cdadd1e1d53124cfe9ebdd68262 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 28 Nov 2014 18:44:41 +0100
Subject: [PATCH 0330/1356] support use of %(DEFAULT_ROBOT_PATHS)s template in
 EasyBuild configuration files

---
 easybuild/tools/config.py  |  4 ++--
 easybuild/tools/options.py | 23 +++++++++++++++--------
 test/framework/config.py   | 18 +++++++++++++++++-
 3 files changed, 34 insertions(+), 11 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 3c4467ad3c..48ee994d62 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -387,12 +387,12 @@ def init(options, config_options_dict):
 
 def init_build_options(build_options=None, cmdline_options=None):
     """Initialize build options."""
-    # building a dependency graph implies force, so that all dependencies are retained
-    # and also skips validation of easyconfigs (e.g. checking os dependencies)
 
     active_build_options = {}
 
     if cmdline_options is not None:
+        # building a dependency graph implies force, so that all dependencies are retained
+        # and also skips validation of easyconfigs (e.g. checking os dependencies)
         retain_all_deps = False
         if cmdline_options.dep_graph:
             _log.info("Enabling force to generate dependency graph.")
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 1098f59f1a..72398552a2 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -75,18 +75,25 @@ class EasyBuildOptions(GeneralOption):
 
     ALLOPTSMANDATORY = False  # allow more than one argument
 
+    def __init__(self, *args, **kwargs):
+        """Constructor."""
+
+        self.default_robot_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None) or []
+
+        # set up constants to seed into config files parser
+        go_cfg_initenv = {
+            'DEFAULT': {
+                'DEFAULT_ROBOT_PATHS': os.pathsep.join(self.default_robot_paths),
+            }
+        }
+        kwargs.setdefault('go_configfiles_initenv', {}).update(go_cfg_initenv)
+        super(EasyBuildOptions, self).__init__(*args, **kwargs)
+
     def basic_options(self):
         """basic runtime options"""
         all_stops = [x[0] for x in EasyBlock.get_steps()]
         strictness_options = [run.IGNORE, run.WARN, run.ERROR]
 
-        easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None)
-        if easyconfigs_pkg_paths:
-            default_robot_paths = easyconfigs_pkg_paths
-        else:
-            self.log.warning("basic_options: unable to determine easyconfigs pkg path for --robot-paths default")
-            default_robot_paths = []
-
         descr = ("Basic options", "Basic runtime options for EasyBuild.")
 
         opts = OrderedDict({
@@ -100,7 +107,7 @@ def basic_options(self):
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
                       'pathlist', 'store_or_None', [], 'r', {'metavar': 'PATH[%sPATH]' % os.pathsep}),
             'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
-                            'pathlist', 'store', default_robot_paths, {'metavar': 'PATH[%sPATH]' % os.pathsep}),
+                            'pathlist', 'store', self.default_robot_paths, {'metavar': 'PATH[%sPATH]' % os.pathsep}),
             'skip': ("Skip existing software (useful for installing additional packages)",
                      None, 'store_true', False, 'k'),
             'stop': ("Stop the installation after certain step", 'choice', 'store_or_None', 'source', 's', all_stops),
diff --git a/test/framework/config.py b/test/framework/config.py
index b28ec141cf..fb4cdd854b 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -31,6 +31,7 @@
 import copy
 import os
 import shutil
+import sys
 import tempfile
 from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader
@@ -42,7 +43,7 @@
 from easybuild.tools.config import log_file_format, set_tmpdir, BuildOptions, ConfigurationVariables
 from easybuild.tools.config import get_build_log_path, DEFAULT_PATH_SUBDIRS, init_build_options, build_option
 from easybuild.tools.environment import modify_env
-from easybuild.tools.filetools import write_file
+from easybuild.tools.filetools import mkdir, write_file
 from easybuild.tools.repository.filerepo import FileRepository
 from easybuild.tools.repository.repository import init_repository
 
@@ -443,10 +444,22 @@ def test_generaloption_config_file(self):
         self.assertEqual(source_paths(), [os.path.join(os.getenv('HOME'), '.local', 'easybuild', 'sources')])  # default
         self.assertEqual(install_path(), os.path.join(testpath2, 'software'))  # via config file
 
+        # copy test easyconfigs to easybuild/easyconfigs subdirectory of temp directory
+        # to check whether easyconfigs install path is auto-included in robot path
+        tmpdir = tempfile.mkdtemp(prefix='easybuild-easyconfigs-pkg-install-path')
+        mkdir(os.path.join(tmpdir, 'easybuild'), parents=True)
+
+        test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        shutil.copytree(test_ecs_dir, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
+
+        orig_sys_path = sys.path[:]
+        sys.path.insert(0, tmpdir)  # prepend to give it preference over possible other installed easyconfigs pkgs
+
         # test with config file passed via environment variable
         cfgtxt = '\n'.join([
             '[config]',
             'buildpath = %s' % testpath1,
+            'robot-paths = /tmp/foo:%(DEFAULT_ROBOT_PATHS)s',
         ])
         write_file(config_file, cfgtxt)
 
@@ -460,6 +473,8 @@ def test_generaloption_config_file(self):
         self.assertEqual(install_path(), os.path.join(os.getenv('HOME'), '.local', 'easybuild', 'software'))  # default
         self.assertEqual(source_paths(), [testpath2])  # via command line
         self.assertEqual(build_path(), testpath1)  # via config file
+        self.assertTrue('/tmp/foo' in options.robot_paths)
+        self.assertTrue(os.path.join(tmpdir, 'easybuild', 'easyconfigs') in options.robot_paths)
 
         testpath3 = os.path.join(self.tmpdir, 'testTHREE')
         os.environ['EASYBUILD_SOURCEPATH'] = testpath2
@@ -474,6 +489,7 @@ def test_generaloption_config_file(self):
         self.assertEqual(build_path(), testpath1)  # via config file
 
         del os.environ['EASYBUILD_CONFIGFILES']
+        sys.path[:] = orig_sys_path
 
     def test_set_tmpdir(self):
         """Test set_tmpdir config function."""

From a80ab71d30d5cb72a97c5e1872f6af8233c99c5c Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sun, 30 Nov 2014 14:58:59 +0100
Subject: [PATCH 0331/1356] Fix MPICH vs. MPICH2 inconsistencies

    * rename gmpich2 toolchain to gmpich
    * adjusted gmpich and gmpolf toolchains to use MPICH instead of MPICH2
---
 easybuild/toolchains/{gmpich2.py => gmpich.py} | 10 +++++-----
 easybuild/toolchains/gmpolf.py                 |  6 +++---
 2 files changed, 8 insertions(+), 8 deletions(-)
 rename easybuild/toolchains/{gmpich2.py => gmpich.py} (83%)

diff --git a/easybuild/toolchains/gmpich2.py b/easybuild/toolchains/gmpich.py
similarity index 83%
rename from easybuild/toolchains/gmpich2.py
rename to easybuild/toolchains/gmpich.py
index caf6e0af5b..4527db29f2 100644
--- a/easybuild/toolchains/gmpich2.py
+++ b/easybuild/toolchains/gmpich.py
@@ -23,15 +23,15 @@
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
 """
-EasyBuild support for gmpich2 compiler toolchain (includes GCC and MPICH2).
+EasyBuild support for gmpich compiler toolchain (includes GCC and MPICH).
 
 @author: Kenneth Hoste (Ghent University)
 """
 
 from easybuild.toolchains.compiler.gcc import Gcc
-from easybuild.toolchains.mpi.mpich2 import Mpich2
+from easybuild.toolchains.mpi.mpich import Mpich
 
 
-class Gmpich2(Gcc, Mpich2):
-    """Compiler toolchain with GCC and MPICH2."""
-    NAME = 'gmpich2'
+class Gmpich(Gcc, Mpich):
+    """Compiler toolchain with GCC and MPICH."""
+    NAME = 'gmpich'
diff --git a/easybuild/toolchains/gmpolf.py b/easybuild/toolchains/gmpolf.py
index 077290259e..35a0d0b899 100644
--- a/easybuild/toolchains/gmpolf.py
+++ b/easybuild/toolchains/gmpolf.py
@@ -36,9 +36,9 @@
 from easybuild.toolchains.fft.fftw import Fftw
 from easybuild.toolchains.linalg.openblas import OpenBLAS
 from easybuild.toolchains.linalg.scalapack import ScaLAPACK
-from easybuild.toolchains.mpi.mpich2 import Mpich2
+from easybuild.toolchains.mpi.mpich import Mpich
 
 
-class Gmpolf(Gcc, Mpich2, OpenBLAS, ScaLAPACK, Fftw):
-    """Compiler toolchain with GCC, MPICH2, OpenBLAS, ScaLAPACK and FFTW."""
+class Gmpolf(Gcc, Mpich, OpenBLAS, ScaLAPACK, Fftw):
+    """Compiler toolchain with GCC, MPICH, OpenBLAS, ScaLAPACK and FFTW."""
     NAME = 'gmpolf'

From 439a1546df91378c1ceab9c00f0dc7628e011114 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Tue, 2 Dec 2014 20:36:15 +0100
Subject: [PATCH 0332/1356] Re-added gmpich2 toolchain

---
 easybuild/toolchains/gmpich2.py | 37 +++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/toolchains/gmpich2.py

diff --git a/easybuild/toolchains/gmpich2.py b/easybuild/toolchains/gmpich2.py
new file mode 100644
index 0000000000..caf6e0af5b
--- /dev/null
+++ b/easybuild/toolchains/gmpich2.py
@@ -0,0 +1,37 @@
+##
+# Copyright 2012-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for gmpich2 compiler toolchain (includes GCC and MPICH2).
+
+@author: Kenneth Hoste (Ghent University)
+"""
+
+from easybuild.toolchains.compiler.gcc import Gcc
+from easybuild.toolchains.mpi.mpich2 import Mpich2
+
+
+class Gmpich2(Gcc, Mpich2):
+    """Compiler toolchain with GCC and MPICH2."""
+    NAME = 'gmpich2'

From 38f7895095207d16a83e0623d9c87684b551ff58 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Dec 2014 08:38:03 +0100
Subject: [PATCH 0333/1356] sync with vsc-base

---
 vsc/README.md              | 2 +-
 vsc/utils/generaloption.py | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/vsc/README.md b/vsc/README.md
index 932369c661..b5efeb45be 100644
--- a/vsc/README.md
+++ b/vsc/README.md
@@ -1,3 +1,3 @@
 Code from https://github.com/hpcugent/vsc-base
 
-based on 35fee9d3130a6b52bf83993e73d187e9d46c69bc (vsc-base v1.9.9)
+based on 2146be5301da34043adf4646169e5dfec88cd2f5 (vsc-base v1.9.9)
diff --git a/vsc/utils/generaloption.py b/vsc/utils/generaloption.py
index 390e5fa79e..e4548dc668 100644
--- a/vsc/utils/generaloption.py
+++ b/vsc/utils/generaloption.py
@@ -699,6 +699,7 @@ class GeneralOption(object):
 
     VERSION = None  # set the version (will add --version)
 
+    DEFAULTSECT = ConfigParser.DEFAULTSECT
     DEFAULT_LOGLEVEL = None
     DEFAULT_CONFIGFILES = None
     DEFAULT_IGNORECONFIGFILES = None
@@ -1073,7 +1074,7 @@ def configfile_parser_init(self, initenv=None):
 
         for name, section in initenv.items():
             name = str(name)
-            if name == ConfigParser.DEFAULTSECT:
+            if name == self.DEFAULTSECT:
                 # is protected/reserved (and hidden)
                 pass
             elif not self.configfile_parser.has_section(name):
@@ -1128,7 +1129,7 @@ def parseconfigfiles(self):
         self.log.debug("parseconfigfiles: following files were NOT parsed %s" %
                        [x for x in configfiles if not x in parsed_files])
         self.log.debug("parseconfigfiles: sections (w/o %s) %s" %
-                       (ConfigParser.DEFAULTSECT, self.configfile_parser.sections()))
+                       (self.DEFAULTSECT, self.configfile_parser.sections()))
 
         # walk through list of section names
         # - look for options set though config files
@@ -1176,7 +1177,7 @@ def parseconfigfiles(self):
                     actual_option = self.parser.get_option_by_long_name(opt_name)
                     if actual_option is None:
                         # don't fail on DEFAULT UPPERCASE options in case-sensitive mode.
-                        in_def = self.configfile_parser.has_option(ConfigParser.DEFAULTSECT, opt)
+                        in_def = self.configfile_parser.has_option(self.DEFAULTSECT, opt)
                         if in_def and self.CONFIGFILE_CASESENSITIVE and opt == opt.upper():
                             self.log.debug(('parseconfigfiles: no option corresponding with '
                                             'opt %s dest %s in section %s but found all uppercase '

From 74528d96ae7d941c237a7b38905e8845734fd9d0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Dec 2014 08:38:56 +0100
Subject: [PATCH 0334/1356] fix remark, use DEFAULTSECT constant

---
 easybuild/tools/options.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 72398552a2..e21105b82d 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -80,13 +80,18 @@ def __init__(self, *args, **kwargs):
 
         self.default_robot_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None) or []
 
-        # set up constants to seed into config files parser
-        go_cfg_initenv = {
-            'DEFAULT': {
+        # set up constants to seed into config files parser, by section
+        go_cfg_constants = {
+            GeneralOption.DEFAULTSECT: {
                 'DEFAULT_ROBOT_PATHS': os.pathsep.join(self.default_robot_paths),
             }
         }
-        kwargs.setdefault('go_configfiles_initenv', {}).update(go_cfg_initenv)
+
+        # update or define go_configfiles_initenv in named arguments to pass to parent constructor
+        go_cfg_initenv = kwargs.setdefault('go_configfiles_initenv', {})
+        for section, constants in go_cfg_constants.items():
+            go_cfg_initenv.setdefault(section, {}).update(constants)
+
         super(EasyBuildOptions, self).__init__(*args, **kwargs)
 
     def basic_options(self):

From 84fe650452b98d01919d7996b2ec57c78f7d2fe3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Dec 2014 10:02:36 +0100
Subject: [PATCH 0335/1356] add --avail-cfgfile-constants

---
 easybuild/tools/options.py | 34 ++++++++++++++++++++++++++++++----
 test/framework/options.py  | 33 +++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index e21105b82d..bd0930e6eb 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -81,15 +81,17 @@ def __init__(self, *args, **kwargs):
         self.default_robot_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None) or []
 
         # set up constants to seed into config files parser, by section
-        go_cfg_constants = {
+        self.go_cfg_constants = {
             GeneralOption.DEFAULTSECT: {
-                'DEFAULT_ROBOT_PATHS': os.pathsep.join(self.default_robot_paths),
+                'DEFAULT_ROBOT_PATHS': (os.pathsep.join(self.default_robot_paths),
+                                        "List of default robot paths ('%s'-separated)" % os.pathsep),
             }
         }
 
         # update or define go_configfiles_initenv in named arguments to pass to parent constructor
         go_cfg_initenv = kwargs.setdefault('go_configfiles_initenv', {})
-        for section, constants in go_cfg_constants.items():
+        for section, constants in self.go_cfg_constants.items():
+            constants = dict([(name, value) for (name, (value, _)) in constants.items()])
             go_cfg_initenv.setdefault(section, {}).update(constants)
 
         super(EasyBuildOptions, self).__init__(*args, **kwargs)
@@ -268,6 +270,8 @@ def informative_options(self):
         descr = ("Informative options", "Obtain information about EasyBuild.")
 
         opts = OrderedDict({
+            'avail-cfgfile-constants': ("Show all constants that can be used in configuration files",
+                                        None, 'store_true', False),
             'avail-easyconfig-constants': ("Show all constants that can be used in easyconfigs",
                                            None, 'store_true', False),
             'avail-easyconfig-licenses': ("Show all license constants that can be used in easyconfigs",
@@ -381,7 +385,7 @@ def postprocess(self):
 
         # prepare for --list/--avail
         if any([self.options.avail_easyconfig_params, self.options.avail_easyconfig_templates,
-                self.options.list_easyblocks, self.options.list_toolchains,
+                self.options.list_easyblocks, self.options.list_toolchains, self.options.avail_cfgfile_constants,
                 self.options.avail_easyconfig_constants, self.options.avail_easyconfig_licenses,
                 self.options.avail_repositories, self.options.show_default_moduleclasses,
                 self.options.avail_modules_tools, self.options.avail_module_naming_schemes,
@@ -435,6 +439,11 @@ def _postprocess_config(self):
     def _postprocess_list_avail(self):
         """Create all the additional info that can be requested (exit at the end)"""
         msg = ''
+
+        # dump supported configuration file constants
+        if self.options.avail_cfgfile_constants:
+            msg += self.avail_cfgfile_constants()
+
         # dump possible easyconfig params
         if self.options.avail_easyconfig_params:
             msg += self.avail_easyconfig_params()
@@ -481,6 +490,23 @@ def _postprocess_list_avail(self):
             print msg
         sys.exit(0)
 
+    def avail_cfgfile_constants(self):
+        """
+        Return overview of constants supported in configuration files.
+        """
+        lines = [
+            "Constants available (only) in configuration files:",
+            "syntax: %(CONSTANT_NAME)s",
+        ]
+        for section in self.go_cfg_constants:
+            lines.append('')
+            if section != GeneralOption.DEFAULTSECT:
+                section_title = "only in '%s' section:" % section
+                lines.append(section_title)
+            for cst_name, (cst_value, cst_help) in sorted(self.go_cfg_constants[section].items()):
+                lines.append("* %s: %s [value: %s]" % (cst_name, cst_help, cst_value))
+        return '\n'.join(lines)
+
     def avail_easyconfig_params(self):
         """
         Print the available easyconfig parameters, for the given easyblock.
diff --git a/test/framework/options.py b/test/framework/options.py
index 0ed83a5e74..17f3688640 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -453,6 +453,39 @@ def test_avail_lists(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
+    def test_avail_cfgfile_constants(self):
+        """Test --avail-cfgfile-constants."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        # copy test easyconfigs to easybuild/easyconfigs subdirectory of temp directory
+        # to check whether easyconfigs install path is auto-included in robot path
+        tmpdir = tempfile.mkdtemp(prefix='easybuild-easyconfigs-pkg-install-path')
+        mkdir(os.path.join(tmpdir, 'easybuild'), parents=True)
+
+        test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        shutil.copytree(test_ecs_dir, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
+
+        orig_sys_path = sys.path[:]
+        sys.path.insert(0, tmpdir)  # prepend to give it preference over possible other installed easyconfigs pkgs
+
+        args = [
+            '--avail-cfgfile-constants',
+            '--unittest-file=%s' % self.logfile,
+        ]
+        outtxt = self.eb_main(args, logfile=dummylogfn)
+        cfgfile_constants = {
+            'DEFAULT_ROBOT_PATHS': os.path.join(tmpdir, 'easybuild', 'easyconfigs'),
+        }
+        for cst_name, cst_value in cfgfile_constants.items():
+            cst_regex = re.compile("^\*\s%s:\s.*\s\[value: .*%s.*\]" % (cst_name, cst_value), re.M)
+            tup = (cst_regex.pattern, outtxt)
+            self.assertTrue(cst_regex.search(outtxt), "Pattern '%s' in --avail-cfgfile_constants output: %s" % tup)
+
+        if os.path.exists(dummylogfn):
+            os.remove(dummylogfn)
+        sys.path[:] = orig_sys_path
+
     def test_list_easyblocks(self):
         """Test listing easyblock hierarchy."""
 

From 9fbf6830c8cc3e752d0f41249ba4df10bb488f17 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Dec 2014 13:37:34 +0100
Subject: [PATCH 0336/1356] fix links to docs

---
 CONTRIBUTING.md                   | 2 +-
 easybuild/scripts/bootstrap_eb.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 10649cddab..9d866e3a8c 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -138,7 +138,7 @@ You might also want to look into [hub](https://github.com/defunkt/hub) for more
 
 ### Review process
 
-A member of the EasyBuild team will then review your pull request, paying attention to what you're contributing, how you implemented it and [Code style](https://github.com/hpcugent/easybuild/wiki/Code-style).
+A member of the EasyBuild team will then review your pull request, paying attention to what you're contributing, how you implemented it and [code style](http://easybuild.readthedocs.org/en/latest/Code_style.html).
 
 Most likely, some remarks will be made on your pull request. Note that this is nothing personal, we're just trying to keep the EasyBuild codebase as high quality as possible. Even when an EasyBuild team member makes changes, the same public review process is followed.
 
diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 91deb59323..3c8cc97141 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -431,7 +431,7 @@ def main():
     info('')
     info("By default, EasyBuild will install software to $HOME/.local/easybuild.")
     info("To install software with EasyBuild to %s, make sure $EASYBUILD_INSTALLPATH is set accordingly." % install_path)
-    info("See https://github.com/hpcugent/easybuild/wiki/Configuration for details on configuring EasyBuild.")
+    info("See http://easybuild.readthedocs.org/en/latest/Configuration.html for details on configuring EasyBuild.")
 
 # template easyconfig file for EasyBuild
 EB_EC_FILE = """

From 70347a2737b2960a9386cdde866637a2853770ab Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Dec 2014 14:19:41 +0100
Subject: [PATCH 0337/1356] fix remark

---
 easybuild/tools/options.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index bd0930e6eb..c2ffc8c74a 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -82,7 +82,7 @@ def __init__(self, *args, **kwargs):
 
         # set up constants to seed into config files parser, by section
         self.go_cfg_constants = {
-            GeneralOption.DEFAULTSECT: {
+            self.DEFAULTSECT: {
                 'DEFAULT_ROBOT_PATHS': (os.pathsep.join(self.default_robot_paths),
                                         "List of default robot paths ('%s'-separated)" % os.pathsep),
             }
@@ -500,7 +500,7 @@ def avail_cfgfile_constants(self):
         ]
         for section in self.go_cfg_constants:
             lines.append('')
-            if section != GeneralOption.DEFAULTSECT:
+            if section != self.DEFAULTSECT:
                 section_title = "only in '%s' section:" % section
                 lines.append(section_title)
             for cst_name, (cst_value, cst_help) in sorted(self.go_cfg_constants[section].items()):

From 8a409988e56ec0b175448f37a662d33513976a03 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Dec 2014 14:47:49 +0100
Subject: [PATCH 0338/1356] code cleanup in toolchain/mpi.py

---
 easybuild/tools/toolchain/mpi.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index 3cde846bc7..b2a4cdc84a 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -170,13 +170,14 @@ def mpi_cmd_for(self, cmd, nr_ranks):
         params = {'nr_ranks':nr_ranks, 'cmd':cmd}
 
         # different known mpirun commands
+        mpirun_n_cmd = "mpirun -n %(nr_ranks)d %(cmd)s"
         mpi_cmds = {
-            toolchain.OPENMPI: "mpirun -n %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
+            toolchain.OPENMPI: mpirun_n_cmd,  # @UndefinedVariable
             toolchain.QLOGICMPI: "mpirun -H localhost -np %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
             toolchain.INTELMPI: "mpirun %(mpdbf)s %(nodesfile)s -np %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
-            toolchain.MVAPICH2: "mpirun -n %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
-            toolchain.MPICH2: "mpirun -n %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
-            toolchain.MPICH: "mpirun -n %(nr_ranks)d %(cmd)s",  # @UndefinedVariable
+            toolchain.MVAPICH2: mpirun_n_cmd,  # @UndefinedVariable
+            toolchain.MPICH: mpirun_n_cmd,  # @UndefinedVariable
+            toolchain.MPICH2: mpirun_n_cmd,  # @UndefinedVariable
         }
 
         mpi_family = self.mpi_family()

From 0431e6844efc3bfd11d454df35d32d33b515ab63 Mon Sep 17 00:00:00 2001
From: Fotis Georgatos <fotis@cern.ch>
Date: Tue, 9 Dec 2014 20:27:51 +0100
Subject: [PATCH 0339/1356] bugfix headers, dance around identity fotis@cern.ch
 (NTUA)

Signed-off-by: Fotis Georgatos <fotis@cern.ch>
---
 easybuild/easybuild_config.py                       | 2 +-
 easybuild/framework/easyblock.py                    | 2 +-
 easybuild/framework/easyconfig/templates.py         | 2 +-
 easybuild/framework/easyconfig/tools.py             | 2 +-
 easybuild/framework/easyconfig/tweak.py             | 2 +-
 easybuild/main.py                                   | 2 +-
 easybuild/toolchains/gompic.py                      | 2 +-
 easybuild/tools/module_generator.py                 | 2 +-
 easybuild/tools/module_naming_scheme/utilities.py   | 2 +-
 easybuild/tools/repository/filerepo.py              | 2 +-
 easybuild/tools/repository/gitrepo.py               | 2 +-
 easybuild/tools/repository/repository.py            | 2 +-
 easybuild/tools/repository/svnrepo.py               | 2 +-
 test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb | 4 ++--
 14 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/easybuild/easybuild_config.py b/easybuild/easybuild_config.py
index 0d90c875a1..5befd7bf58 100644
--- a/easybuild/easybuild_config.py
+++ b/easybuild/easybuild_config.py
@@ -34,7 +34,7 @@
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 
 #
diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 99e005bb82..e6db49bec7 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -33,7 +33,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 
 import copy
diff --git a/easybuild/framework/easyconfig/templates.py b/easybuild/framework/easyconfig/templates.py
index 42ec1038f8..57b973aca2 100644
--- a/easybuild/framework/easyconfig/templates.py
+++ b/easybuild/framework/easyconfig/templates.py
@@ -28,7 +28,7 @@
 be used within an Easyconfig file.
 
 @author: Stijn De Weirdt (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 
 from vsc.utils import fancylogger
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index b1c237788c..a3c0599c07 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -33,7 +33,7 @@
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 
 import os
diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index ebc233b085..ee4176bf52 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -31,7 +31,7 @@
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 import copy
 import glob
diff --git a/easybuild/main.py b/easybuild/main.py
index 12991f2145..a97ce592f1 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -33,7 +33,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 import copy
 import os
diff --git a/easybuild/toolchains/gompic.py b/easybuild/toolchains/gompic.py
index b6b0b26edb..0a331d5daf 100644
--- a/easybuild/toolchains/gompic.py
+++ b/easybuild/toolchains/gompic.py
@@ -26,7 +26,7 @@
 EasyBuild support for gompic compiler toolchain (includes GCC and OpenMPI and CUDA).
 
 @author: Kenneth Hoste (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 
 from easybuild.toolchains.gcccuda import GccCUDA
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index f83d3a55ee..ee8046caba 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -30,7 +30,7 @@
 @author: Kenneth Hoste (Ghent University)
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
-@author: Fotis Georgatos (Uni.Lu)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 import os
 import re
diff --git a/easybuild/tools/module_naming_scheme/utilities.py b/easybuild/tools/module_naming_scheme/utilities.py
index 951d8015b3..8bd5053231 100644
--- a/easybuild/tools/module_naming_scheme/utilities.py
+++ b/easybuild/tools/module_naming_scheme/utilities.py
@@ -30,7 +30,7 @@
 @author: Kenneth Hoste (Ghent University)
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
-@author: Fotis Georgatos (Uni.Lu)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 import os
 import string
diff --git a/easybuild/tools/repository/filerepo.py b/easybuild/tools/repository/filerepo.py
index 7e1b2f792e..4c1a58fe17 100644
--- a/easybuild/tools/repository/filerepo.py
+++ b/easybuild/tools/repository/filerepo.py
@@ -34,7 +34,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 import os
 import time
diff --git a/easybuild/tools/repository/gitrepo.py b/easybuild/tools/repository/gitrepo.py
index f540e5ee1a..ab6a5f07ca 100644
--- a/easybuild/tools/repository/gitrepo.py
+++ b/easybuild/tools/repository/gitrepo.py
@@ -34,7 +34,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 import getpass
 import os
diff --git a/easybuild/tools/repository/repository.py b/easybuild/tools/repository/repository.py
index 3775bacfba..a8dca02326 100644
--- a/easybuild/tools/repository/repository.py
+++ b/easybuild/tools/repository/repository.py
@@ -32,7 +32,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_subclasses
diff --git a/easybuild/tools/repository/svnrepo.py b/easybuild/tools/repository/svnrepo.py
index cadb0e633b..31f38abdc9 100644
--- a/easybuild/tools/repository/svnrepo.py
+++ b/easybuild/tools/repository/svnrepo.py
@@ -34,7 +34,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
-@author: Fotis Georgatos (University of Luxembourg)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 import getpass
 import os
diff --git a/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
index a8e69945a9..f4bf718e88 100644
--- a/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
+++ b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
@@ -1,8 +1,8 @@
 ##
 # This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
 #
-# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University
-# Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis.georgatos@uni.lu>, Kenneth Hoste
+# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA, Ghent University
+# Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>, Kenneth Hoste
 # License::   MIT/GPL
 # $Id$
 #

From 250d80e3fe29d515157740dca9aeb22f8587a68d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 9 Dec 2014 22:14:44 +0100
Subject: [PATCH 0340/1356] don't hardcode queue names when submitting a job

---
 easybuild/tools/pbs_job.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/pbs_job.py b/easybuild/tools/pbs_job.py
index 930c059af9..55774cd474 100644
--- a/easybuild/tools/pbs_job.py
+++ b/easybuild/tools/pbs_job.py
@@ -150,11 +150,8 @@ def __init__(self, script, name, env_vars=None, resources={}, conn=None, ppn=Non
                           "walltime": "%s:00:00" % hours,
                           "nodes": "1:ppn=%s" % cores
                          }
-        # set queue based on the hours requested
-        if hours >= 12:
-            self.queue = 'long'
-        else:
-            self.queue = 'short'
+        # don't specify any queue name to submit to, use the default
+        self.queue = None
         # job id of this job
         self.jobid = None
         # list of dependencies for this job

From a5ba98416f7a2e4e3f88d26e4a0a2be27dff716f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 11 Dec 2014 15:17:49 +0100
Subject: [PATCH 0341/1356] filter out /dev/null entries in list of patch files
 for PR

---
 easybuild/tools/github.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 89319ad2ce..f7a1993e5d 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -251,7 +251,10 @@ def download(url, path=None):
     diff_txt = download(pr_data['diff_url'])
 
     patched_files = det_patched_files(txt=diff_txt, omit_ab_prefix=True)
-    _log.debug("List of patches files: %s" % patched_files)
+    _log.debug("List of patches files (before filtering): %s" % patched_files)
+    # filter out '/dev/null' entries (removed files)
+    patched_files = [pf for pf in patched_files if pf != '/dev/null']
+    _log.debug("List of patches files (after filtering): %s" % patched_files)
 
     # obtain last commit
     # get all commits, increase to (max of) 100 per page

From 25ef005545ddd6753405a227b224d03d55f3b367 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 11 Dec 2014 15:39:50 +0100
Subject: [PATCH 0342/1356] fix typo

---
 easybuild/tools/github.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index f7a1993e5d..8ca6926d8f 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -251,10 +251,10 @@ def download(url, path=None):
     diff_txt = download(pr_data['diff_url'])
 
     patched_files = det_patched_files(txt=diff_txt, omit_ab_prefix=True)
-    _log.debug("List of patches files (before filtering): %s" % patched_files)
+    _log.debug("List of patched files (before filtering): %s" % patched_files)
     # filter out '/dev/null' entries (removed files)
     patched_files = [pf for pf in patched_files if pf != '/dev/null']
-    _log.debug("List of patches files (after filtering): %s" % patched_files)
+    _log.debug("List of patched files (after filtering): %s" % patched_files)
 
     # obtain last commit
     # get all commits, increase to (max of) 100 per page

From 359539ed581757d2f93c4abf0370519fe1c463de Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Thu, 11 Dec 2014 16:54:49 +0100
Subject: [PATCH 0343/1356] Try both rpm and dpks when searching for OS dep

---
 easybuild/tools/systemtools.py | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 7cd2babc04..8564f4b8bf 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -391,17 +391,13 @@ def check_os_dependency(dep):
     # - uses rpm -q and dpkg -s --> can be run as non-root!!
     # - fallback on which
     # - should be extended to files later?
-    cmd = None
-    if get_os_name() in ['debian', 'ubuntu']:
-        if which('dpkg'):
-            cmd = "dpkg -s %s" % dep
-    else:
-        # OK for get_os_name() == redhat, fedora, RHEL, SL, centos
-        if which('rpm'):
-            cmd = "rpm -q %s" % dep
-
     found = None
-    if cmd is not None:
+    if which('rpm'):
+        cmd = "rpm -q %s" % dep
+        found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
+
+    if found is None and which('dpkg'):
+        cmd = "dpkg -s %s" % dep
         found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
 
     if found is None:

From a8e3761b345947b2bab0c43b95687a95642b5978 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Thu, 11 Dec 2014 17:11:30 +0100
Subject: [PATCH 0344/1356] Modified intelmkl.py take account of required BLACS
 library for MPICH and MPICH2 and corrected toolchain to match

---
 easybuild/toolchains/iimpi.py           | 0
 easybuild/toolchains/intel-para.py      | 2 --
 easybuild/toolchains/intel.py           | 0
 easybuild/toolchains/ipsmpi.py          | 0
 easybuild/toolchains/linalg/intelmkl.py | 3 ++-
 5 files changed, 2 insertions(+), 3 deletions(-)
 mode change 100755 => 100644 easybuild/toolchains/iimpi.py
 mode change 100755 => 100644 easybuild/toolchains/intel.py
 mode change 100755 => 100644 easybuild/toolchains/ipsmpi.py

diff --git a/easybuild/toolchains/iimpi.py b/easybuild/toolchains/iimpi.py
old mode 100755
new mode 100644
diff --git a/easybuild/toolchains/intel-para.py b/easybuild/toolchains/intel-para.py
index 9ea7a259e1..35e23da99a 100644
--- a/easybuild/toolchains/intel-para.py
+++ b/easybuild/toolchains/intel-para.py
@@ -39,6 +39,4 @@ class IntelPara(Ipsmpi, IntelMKL, IntelFFTW):
     Intel Math Kernel Library (MKL) and Intel FFTW wrappers.
     """
     NAME = 'intel-para'
-    # Parastation MPI needs to be matched with the IntelMPI blacs library
-    BLACS_LIB = ["mkl_blacs_intelmpi%(lp64)s"]
     
diff --git a/easybuild/toolchains/intel.py b/easybuild/toolchains/intel.py
old mode 100755
new mode 100644
diff --git a/easybuild/toolchains/ipsmpi.py b/easybuild/toolchains/ipsmpi.py
old mode 100755
new mode 100644
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index 2f1186f6ee..b994b1bc54 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -126,7 +126,8 @@ def _set_blacs_variables(self):
             "OpenMPI": '_openmpi',
             "IntelMPI": '_intelmpi',
             "MVAPICH2": '_intelmpi',
-            "MPICH2":'',
+            "MPICH2": '_intelmpi',
+            "MPICH": '_intelmpi',
         }
         try:
             self.BLACS_LIB_MAP.update({'mpi': mpimap[self.MPI_FAMILY]})

From 03b28ee9c2f58ff86fedbd3bb2f90203432011d2 Mon Sep 17 00:00:00 2001
From: Fotis Georgatos <fotis@cern.ch>
Date: Thu, 11 Dec 2014 19:03:51 +0100
Subject: [PATCH 0345/1356] add FG, in relation to EASYBLOCK_CLASS_PREFIX &
 STRING_ENCODING_CHARMAP

Signed-off-by: Fotis Georgatos <fotis@cern.ch>
---
 easybuild/tools/filetools.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 18e8c754dc..0ea45a2f31 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -32,6 +32,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
 """
 import os
 import re

From 272ec8166cf2a2f2c92fa2b80d8443be8d2a7a13 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 11 Dec 2014 19:53:38 +0100
Subject: [PATCH 0346/1356] filter out patched files in det_patched_files

---
 easybuild/tools/filetools.py | 6 +++++-
 easybuild/tools/github.py    | 5 +----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 18e8c754dc..af3dad333b 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -608,7 +608,11 @@ def det_patched_files(path=None, txt=None, omit_ab_prefix=False):
         patched_file = match.group('file')
         if not omit_ab_prefix and match.group('ab_prefix') is not None:
             patched_file = match.group('ab_prefix') + patched_file
-        patched_files.append(patched_file)
+
+        if patched_file in ['/dev/null']:
+            _log.debug("Ignoring patched file %s" % patched_file)
+        else:
+            patched_files.append(patched_file)
 
     return patched_files
 
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 8ca6926d8f..1ff47d1555 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -251,10 +251,7 @@ def download(url, path=None):
     diff_txt = download(pr_data['diff_url'])
 
     patched_files = det_patched_files(txt=diff_txt, omit_ab_prefix=True)
-    _log.debug("List of patched files (before filtering): %s" % patched_files)
-    # filter out '/dev/null' entries (removed files)
-    patched_files = [pf for pf in patched_files if pf != '/dev/null']
-    _log.debug("List of patched files (after filtering): %s" % patched_files)
+    _log.debug("List of patched files: %s" % patched_files)
 
     # obtain last commit
     # get all commits, increase to (max of) 100 per page

From c5495f4da58d4efedf6b46c16a4498a2ab757a9d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 11 Dec 2014 22:13:15 +0100
Subject: [PATCH 0347/1356] avoid hardcoding MPI family strings, add reference
 to MKL link advisor w.r.t. BLACS lib

---
 easybuild/toolchains/linalg/intelmkl.py | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index b994b1bc54..af8cca4739 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -33,6 +33,11 @@
 
 from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP
 from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC
+from easybuild.toolchains.mpi.intelmpi import TC_CONSTANT_INTELMPI
+from easybuild.toolchains.mpi.mpich import TC_CONSTANT_MPICH
+from easybuild.toolchains.mpi.mpich2 import TC_CONSTANT_MPICH2
+from easybuild.toolchains.mpi.mvapich2 import TC_CONSTANT_MVAPICH2
+from easybuild.toolchains.mpi.openmpi import TC_CONSTANT_OPENMPI
 from easybuild.tools.toolchain.linalg import LinAlg
 
 
@@ -123,11 +128,14 @@ def _set_blas_variables(self):
 
     def _set_blacs_variables(self):
         mpimap = {
-            "OpenMPI": '_openmpi',
-            "IntelMPI": '_intelmpi',
-            "MVAPICH2": '_intelmpi',
-            "MPICH2": '_intelmpi',
-            "MPICH": '_intelmpi',
+            TC_CONSTANT_OPENMPI: '_openmpi',
+            TC_CONSTANT_INTELMPI: '_intelmpi',
+            TC_CONSTANT_MVAPICH2: '_intelmpi',
+            # use intelmpi MKL blacs library for both MPICH v2 and v3
+            # cfr. https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor
+            # note: MKL link advisor uses 'MPICH' for MPICH v1
+            TC_CONSTANT_MPICH2: '_intelmpi',
+            TC_CONSTANT_MPICH: '_intelmpi',
         }
         try:
             self.BLACS_LIB_MAP.update({'mpi': mpimap[self.MPI_FAMILY]})

From 0cefd7e51967ffd52f27f97ca0b43f9486e80fc4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Dec 2014 08:26:47 +0100
Subject: [PATCH 0348/1356] deprecate fallback to ConfigureMake easyblock

---
 easybuild/framework/easyconfig/default.py    |  3 ++-
 easybuild/framework/easyconfig/easyconfig.py | 15 ++++++++++++---
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 56b8143f7e..d9934e092e 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -92,7 +92,8 @@
     'buildopts': ['', 'Extra options passed to make step (default already has -j X)', BUILD],
     'checksums': [[], "Checksums for sources and patches", BUILD],
     'configopts': ['', 'Extra options passed to configure (default already has --prefix)', BUILD],
-    'easyblock': ['ConfigureMake', "EasyBlock to use for building", BUILD],
+    'easyblock': [None, "EasyBlock to use for building; if set to None, an easyblock is selected "
+                        "based on the software name", BUILD],
     'easybuild_version': [None, "EasyBuild-version this spec-file was written for", BUILD],
     'installopts': ['', 'Extra options for installation', BUILD],
     'maxparallel': [None, 'Max degree of parallelism', BUILD],
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 7705559ce3..e0352fa002 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -81,6 +81,8 @@
     'premakeopts': ('prebuildopts', '2.0'),
 }
 
+DEFAULT_EASYBLOCK = 'ConfigureMake'
+
 _easyconfig_files_cache = {}
 _easyconfigs_cache = {}
 
@@ -739,9 +741,6 @@ def get_easyblock_class(easyblock, name=None):
     Get class for a particular easyblock (or use default)
     """
 
-    def_class = get_easyconfig_parameter_default('easyblock')
-    def_mod_path = get_module_path(def_class, generic=True)
-
     try:
         if easyblock:
             # something was specified, lets parse it
@@ -788,8 +787,15 @@ def get_easyblock_class(easyblock, name=None):
                 _log.debug("error regexp: %s" % error_re.pattern)
                 if error_re.match(str(err)):
                     # no easyblock could be found, so fall back to default class.
+                    def_class = DEFAULT_EASYBLOCK
+                    def_mod_path = get_module_path(def_class, generic=True)
+
                     _log.warning("Failed to import easyblock for %s, falling back to default class %s: error: %s" % \
                                 (class_name, (def_mod_path, def_class), err))
+
+                    depr_msg = "Fallback to default easyblock %s (from %s)" % (def_class, def_mod_path)
+                    depr_msg += "; use \"easyblock = '%s'\" in easyconfig file?" % def_class
+                    _log.deprecated(depr_msg, '2.0')
                     cls = get_class_for(def_mod_path, def_class)
                 else:
                     _log.error("Failed to import easyblock for %s because of module issue: %s" % (class_name, err))
@@ -798,6 +804,9 @@ def get_easyblock_class(easyblock, name=None):
         _log.info("Successfully obtained class '%s' for easyblock '%s' (software name '%s')" % tup)
         return cls
 
+    except EasyBuildError, err:
+        # simply reraise rather than wrapping it into another error
+        raise err
     except Exception, err:
         _log.error("Failed to obtain class for %s easyblock (not available?): %s" % (easyblock, err))
 

From 346505c283721b08fed163cd7b8d669b535da160 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Dec 2014 09:56:14 +0100
Subject: [PATCH 0349/1356] add gzip sources to test sandbox

---
 .../sandbox/sources/g/gzip/gzip-1.4.tar.gz     | Bin 0 -> 907411 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 test/framework/sandbox/sources/g/gzip/gzip-1.4.tar.gz

diff --git a/test/framework/sandbox/sources/g/gzip/gzip-1.4.tar.gz b/test/framework/sandbox/sources/g/gzip/gzip-1.4.tar.gz
new file mode 100644
index 0000000000000000000000000000000000000000..92d6ae4e08281020a1bb19e2de4d888bfaf36433
GIT binary patch
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z^H*_V?*A{(w}J#f?h3lPQxVGX8vxeWK|T~%f9~tw-m1UhZ~9ws(>(D3BWynMH{pt&
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ztvZR=I{S<ZDe3@GdwD!UYbt7d#p4HxX_=&RbWaGgX8LfSH%eulC|?4^ZqmP7KbxL%
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zDAE>s+9RSYx_wUCqu<cR=(n{&JLaK^xrBS<Ax4lOeEKVYjOoV!$PoH3MUtgoGm0>Q
zMF1`664WvJfnnD12RXn{pp%r+rdQ~>pMT+Y=AYN}A2=Ke8rK|?q!Yy?jv16DhJL_3
zvEDo*Q@UHDcoqZRL{v(MA0|;vf;j}9L?u=Ok@<d)$AEBS@Az!*@LZo|jPpj(Syjy6
z_DwD2qe_uF9>QV&5@ev49fOlNhuvO(iuEgVR|zge`7V~Aqv{?s2cUM|5RJX(LBGIJ
zsHWN_ACN!M-+PavL+K(2%5skT_o+o3-!BsKR~=Xx`Igmf4h!r8Joi6Sz_;7+4R8m<
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z{jJv+j&=DS)`Qj^d#`q2RKE9QnRF(et%vk=|Ne8Ik&Esc+{+v}ko&i}^{wh2{KQ~<
zJo*>9z{C3+LMv?$t@MB}%>$Uvb*Y<nGlA>b(361#3PpRb*7{y!R@fUDn~sR9JGw^w
z;22(if^HzX!{zv|P5b;{1Yz$_>y&$$zG$b|1^ub0IC3Tm#qV>v|6eT7`2+R_Z&5_k
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zZB$R8f7aE|uYn0%F;z0ntqDeH@{4vQLRWSsCONy)sk&*4TBM%6Nq@ug0XcxKsQ{xd
zX!(HMXRciN^!>8s6FkjGT3r!@rZ?#h<6EL#za^H_%K+!z6O9)bkWChG&j0;CD_?#;
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literal 0
HcmV?d00001


From a273f6f79ac04fca28656df834f40f62c83e6b9e Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Fri, 12 Dec 2014 11:15:19 +0100
Subject: [PATCH 0350/1356] Use logger from simple_options

---
 easybuild/scripts/clean_gists.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/clean_gists.py b/easybuild/scripts/clean_gists.py
index 5a7933d038..14e26a6a14 100755
--- a/easybuild/scripts/clean_gists.py
+++ b/easybuild/scripts/clean_gists.py
@@ -42,7 +42,6 @@ def main():
     """the main function"""
     fancylogger.logToScreen(enable=True, stdout=True)
     fancylogger.setLogLevelInfo()
-    log = fancylogger.getLogger()
 
     options = {
         'github-user': ('Your github username to use', None, 'store', None, 'g'),
@@ -52,6 +51,7 @@ def main():
     }
 
     go = simple_option(options)
+    log = go.log
 
     if not (go.options.all or go.options.closed_pr or go.options.orphans):
         log.error("Please tell me what to do?")

From 19d401559bb87522941b387b0cf254c7b4e65f7e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Dec 2014 15:49:43 +0100
Subject: [PATCH 0351/1356] include URL to documentation on deprecated
 functionality in log.deprecated message

---
 easybuild/tools/build_log.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index 3ceb28bae3..b447090e0e 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -49,6 +49,8 @@
 # allow some experimental experimental code
 EXPERIMENTAL = False
 
+DEPRECATED_DOC_URL = 'http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html'
+
 
 class EasyBuildError(Exception):
     """
@@ -96,6 +98,7 @@ def experimental(self, msg, *args, **kwargs):
 
     def deprecated(self, msg, max_ver):
         """Print deprecation warning or raise an EasyBuildError, depending on max version allowed."""
+        msg += "; see %s for more information" % DEPRECATED_DOC_URL
         fancylogger.FancyLogger.deprecated(self, msg, str(CURRENT_VERSION), max_ver, exception=EasyBuildError)
 
     def error(self, msg, *args, **kwargs):

From 8db5b4b3b280f29b0b310d4b24c1eaad137d9606 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Dec 2014 16:49:12 +0100
Subject: [PATCH 0352/1356] drop top-level log deprecation message for
 not-yet-mandatory 'license' easyconfig parameter

---
 easybuild/framework/easyconfig/easyconfig.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 8d871a6d7d..ce1c9e1a84 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -66,9 +66,7 @@
 
 _log = fancylogger.getLogger('easyconfig.easyconfig', fname=False)
 
-
 # add license here to make it really MANDATORY (remove comment in default)
-_log.deprecated('Mandatory license not enforced', '2.0')
 MANDATORY_PARAMS = ['name', 'version', 'homepage', 'description', 'toolchain']
 
 # set of configure/build/install options that can be provided as lists for an iterated build
@@ -185,6 +183,7 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         self._config.update(self.extra_options)
 
         self.path = path
+
         self.mandatory = MANDATORY_PARAMS[:]
 
         # extend mandatory keys

From 3abefb733ea09b3ce86786648951c2bc3cfddbc8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Dec 2014 21:14:21 +0100
Subject: [PATCH 0353/1356] more refactoring to avoid triggered log.deprecated
 unnecessarily

---
 easybuild/framework/easyconfig/easyconfig.py  |   3 +-
 .../easyconfig/format/pyheaderconfigobj.py    |   6 +-
 easybuild/tools/config.py                     | 107 ++++++------------
 easybuild/tools/filetools.py                  |   3 +
 easybuild/tools/options.py                    |  51 ++++-----
 test/framework/config.py                      |  12 +-
 6 files changed, 75 insertions(+), 107 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index abf54b1c63..12a7fde741 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -346,10 +346,9 @@ def validate_license(self):
         """Validate the license"""
         lic = self._config['software_license'][0]
         if lic is None:
-            self.log.deprecated('Mandatory license not enforced', '2.0')
             # when mandatory, remove this possibility
             if 'software_license' in self.mandatory:
-                self.log.error('License is mandatory')
+                self.log.error("License is mandatory, but 'software_license' is undefined")
         elif not isinstance(lic, License):
             self.log.error('License %s has to be a License subclass instance, found classname %s.' %
                            (lic, lic.__class__.__name__))
diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index 995931f1e1..64695589b7 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -75,7 +75,6 @@ def build_easyconfig_constants_dict():
 
 def build_easyconfig_variables_dict():
     """Make a dictionary with all variables that can be used"""
-    _log.deprecated("Magic 'global' easyconfigs variables like shared_lib_ext should no longer be used", '2.0')
     vars_dict = {
         "shared_lib_ext": get_shared_lib_ext(),
     }
@@ -178,6 +177,11 @@ def parse_pyheader(self, pyheader):
         self.log.debug("pyheader initial local_vars %s" % local_vars)
         self.log.debug("pyheader text being exec'ed: %s" % pyheader)
 
+        # check for use of deprecated magic easyconfigs variables
+        for magic_var in build_easyconfig_variables_dict():
+            if re.search(magic_var, pyheader, re.M):
+                _log.deprecated("Magic 'global' easyconfigs variable %s should no longer be used" % magic_var, '2.0')
+
         try:
             exec(pyheader, global_vars, local_vars)
         except SyntaxError, err:
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 54d9b025ae..88cbdc63df 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -55,10 +55,9 @@
 SUPPORT_OLDSTYLE = True
 DEFAULT_OLDSTYLE_CONFIG_FILE = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'easybuild_config.py')
 
-
 DEFAULT_LOGFILE_FORMAT = ("easybuild", "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
-
-
+DEFAULT_MNS = 'EasyBuildMNS'
+DEFAULT_MODULES_TOOL = 'EnvironmentModulesC'
 DEFAULT_PATH_SUBDIRS = {
     'buildpath': 'build',
     'installpath': '',
@@ -67,6 +66,18 @@
     'subdir_modules': 'modules',
     'subdir_software': 'software',
 }
+DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
+DEFAULT_REPOSITORY = 'FileRepository'
+DEFAULT_TMP_LOGDIR = tempfile.gettempdir()
+
+# utility function for defining DEFAULT_ constants below
+def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
+    """Create full path, avoid '/' at the end."""
+    args = [prefix]
+    path = DEFAULT_PATH_SUBDIRS[name]
+    if path:
+        args.append(path)
+    return os.path.join(*args)
 
 # build options that have a perfectly matching command line option, listed by default value
 BUILD_OPTIONS_CMDLINE = {
@@ -160,13 +171,13 @@
 
 # note: keys are new style option names
 OLDSTYLE_ENVIRONMENT_VARIABLES = {
-    'buildpath': 'EASYBUILDBUILDPATH',
-    'config': 'EASYBUILDCONFIG',
-    'installpath': 'EASYBUILDINSTALLPATH',
-    'logfile_format': 'EASYBUILDLOGFORMAT',
-    'tmp_logdir': 'EASYBUILDLOGDIR',
-    'sourcepath': 'EASYBUILDSOURCEPATH',
-    'testoutput': 'EASYBUILDTESTOUTPUT',
+    'build_path': 'EASYBUILDBUILDPATH',
+    'config_file': 'EASYBUILDCONFIG',
+    'install_path': 'EASYBUILDINSTALLPATH',
+    'log_format': 'EASYBUILDLOGFORMAT',
+    'log_dir': 'EASYBUILDLOGDIR',
+    'source_path': 'EASYBUILDSOURCEPATH',
+    'test_output_path': 'EASYBUILDTESTOUTPUT',
 }
 
 
@@ -251,12 +262,14 @@ def get_user_easybuild_dir():
     xdg_config_home = os.environ.get("XDG_CONFIG_HOME", os.path.join(os.path.expanduser('~'), ".config"))
     newpath = os.path.join(xdg_config_home, "easybuild")
 
-    if os.path.isdir(newpath):
-        return newpath
-    else:
+    # only issue deprecation warning/error is new path doesn't exist, but deprecated path does
+    if not os.path.isdir(newpath) and os.path.isdir(oldpath):
         _log.deprecated("The user easybuild dir has moved from %s to %s." % (oldpath, newpath), "2.0")
         return oldpath
 
+    # if neither exist, new path wins
+    return newpath
+
 
 def get_default_oldstyle_configfile():
     """Get the default location of the oldstyle config file to be set as default in the options"""
@@ -264,7 +277,7 @@ def get_default_oldstyle_configfile():
     # - check environment variable EASYBUILDCONFIG
     # - next, check for an EasyBuild config in $HOME/.easybuild/config.py
     # - last, use default config file easybuild_config.py in main.py directory
-    config_env_var = OLDSTYLE_ENVIRONMENT_VARIABLES['config']
+    config_env_var = OLDSTYLE_ENVIRONMENT_VARIABLES['config_file']
     home_config_file = os.path.join(get_user_easybuild_dir(), "config.py")
     if os.getenv(config_env_var):
         _log.debug("Environment variable %s, so using that as config file." % config_env_var)
@@ -284,49 +297,6 @@ def get_default_oldstyle_configfile():
     return config_file
 
 
-def get_default_oldstyle_configfile_defaults(prefix=None):
-    """
-    Return a dict with the defaults from the shipped legacy easybuild_config.py and/or environment variables
-        prefix: string, when provided, it used as prefix for the other defaults (where applicable)
-    """
-    if prefix is None:
-        prefix = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
-
-    def mk_full_path(name):
-        """Create full path, avoid '/' at the end."""
-        args = [prefix]
-        path = DEFAULT_PATH_SUBDIRS[name]
-        if path:
-            args.append(path)
-        return os.path.join(*args)
-
-    # keys are the options dest
-    defaults = {
-        'config': get_default_oldstyle_configfile(),
-        'prefix': prefix,
-        'buildpath': mk_full_path('buildpath'),
-        'installpath': mk_full_path('installpath'),
-        'sourcepath': mk_full_path('sourcepath'),
-        'repository': 'FileRepository',
-        'repositorypath': {'FileRepository': [mk_full_path('repositorypath')]},
-        'logfile_format': DEFAULT_LOGFILE_FORMAT[:],  # make a copy
-        'tmp_logdir': tempfile.gettempdir(),
-        'moduleclasses': [x[0] for x in DEFAULT_MODULECLASSES],
-        'subdir_modules': DEFAULT_PATH_SUBDIRS['subdir_modules'],
-        'subdir_software': DEFAULT_PATH_SUBDIRS['subdir_software'],
-        'modules_tool': 'EnvironmentModulesC',
-        'module_naming_scheme': 'EasyBuildMNS',
-    }
-
-    # sanity check
-    if not defaults['repository'] in defaults['repositorypath']:
-        _log.error('Failed to get repository path default for default %s' % (defaults['repository']))
-
-    _log.deprecated("get_default_oldstyle_configfile_defaults", "2.0")
-
-    return defaults
-
-
 def get_default_configfiles():
     """Return a list of default configfiles for tools.options/generaloption"""
     return [os.path.join(get_user_easybuild_dir(), "config.cfg")]
@@ -477,10 +447,9 @@ def install_path(typ=None):
         suffix = variables[key]
     else:
         # TODO remove default setting. it should have been set through options
-        _log.deprecated('%s not set in config, returning default' % key, "2.0")
-        defaults = get_default_oldstyle_configfile_defaults()
         try:
-            suffix = defaults[key]
+            suffix = DEFAULT_PATH_SUBDIRS[key]
+            _log.deprecated('%s not set in config, returning default: %s' % (key, suffix), "2.0")
         except:
             _log.error('install_path trying to get unknown suffix %s' % key)
 
@@ -524,10 +493,9 @@ def log_file_format(return_directory=False):
     if 'logfile_format' in variables:
         res = variables['logfile_format'][idx]
     else:
+        res = DEFAULT_LOGFILE_FORMAT[:][idx]  # purposely take a copy
         # TODO remove default setting. it should have been set through options
-        _log.deprecated('logfile_format not set in config, returning default', "2.0")
-        defaults = get_default_oldstyle_configfile_defaults()
-        res = defaults['logfile_format'][idx]
+        _log.deprecated('logfile_format not set in config, returning default: %s' % res, '2.0')
     return res
 
 
@@ -555,9 +523,8 @@ def get_build_log_path():
         return variables['tmp_logdir']
     else:
         # TODO remove default setting. it should have been set through options
-        _log.deprecated('tmp_logdir not set in config, returning default', "2.0")
-        defaults = get_default_oldstyle_configfile_defaults()
-        return defaults['tmp_logdir']
+        _log.deprecated('tmp_logdir not set in config, returning default: %s' % DEFAULT_TMP_LOGDIR, "2.0")
+        return DEFAULT_TMP_LOGDIR
 
 
 def get_log_filename(name, version, add_salt=False):
@@ -608,10 +575,10 @@ def module_classes():
     if 'moduleclasses' in variables:
         return variables['moduleclasses']
     else:
+        res = [x[0] for x in DEFAULT_MODULECLASSES]
         # TODO remove default setting. it should have been set through options
-        _log.deprecated('moduleclasses not set in config, returning default', "2.0")
-        defaults = get_default_oldstyle_configfile_defaults()
-        return defaults['moduleclasses']
+        _log.deprecated('moduleclasses not set in config, returning default: %s' % res, "2.0")
+        return res
 
 
 def read_environment(env_vars, strict=False):
@@ -667,7 +634,7 @@ def oldstyle_read_environment(env_vars=None, strict=False):
         env_var = env_vars[key]
         if env_var in os.environ:
             result[key] = os.environ[env_var]
-            _log.deprecated("Use of oldstyle environment variable %s for %s: %s" % (env_var, key, result[key]), "2.0")
+            _log.deprecated("Use of oldstyle environment variable %s for %s: %s" % (env_var, key, result[key]), '2.0')
         elif strict:
             _log.error("Can't determine value for %s. Environment variable %s is missing" % (key, env_var))
         else:
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 385422e8ad..1eb26b6aa8 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -1044,17 +1044,20 @@ def decode_class_name(name):
 
 def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True, log_output=False, path=None):
     """Legacy wrapper/placeholder for run.run_cmd"""
+    _log.deprecated("run_cmd was moved from tools.filetools to tools.run", '2.0')
     return run.run_cmd(cmd, log_ok=log_ok, log_all=log_all, simple=simple,
                        inp=inp, regexp=regexp, log_output=log_output, path=path)
 
 
 def run_cmd_qa(cmd, qa, no_qa=None, log_ok=True, log_all=False, simple=False, regexp=True, std_qa=None, path=None):
     """Legacy wrapper/placeholder for run.run_cmd_qa"""
+    _log.deprecated("run_cmd_qa was moved from tools.filetools to tools.run", '2.0')
     return run.run_cmd_qa(cmd, qa, no_qa=no_qa, log_ok=log_ok, log_all=log_all,
                           simple=simple, regexp=regexp, std_qa=std_qa, path=path)
 
 def parse_log_for_error(txt, regExp=None, stdout=True, msg=None):
     """Legacy wrapper/placeholder for run.parse_log_for_error"""
+    _log.deprecated("parse_log_for_error was moved from tools.filetools to tools.run", '2.0')
     return run.parse_log_for_error(txt, regExp=regExp, stdout=stdout, msg=msg)
 
 
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 954bbc5a2c..f6e0004b70 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -50,9 +50,10 @@
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
+from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
+from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY, DEFAULT_TMP_LOGDIR
 from easybuild.tools.config import get_default_configfiles, get_pretend_installpath
-from easybuild.tools.config import get_default_oldstyle_configfile_defaults, DEFAULT_MODULECLASSES
-from easybuild.tools.convert import ListOfStrings
+from easybuild.tools.config import get_default_oldstyle_configfile, mk_full_default_path
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
@@ -206,8 +207,6 @@ def config_options(self):
         # config options
         descr = ("Configuration options", "Configure EasyBuild behavior.")
 
-        oldstyle_defaults = get_default_oldstyle_configfile_defaults()
-
         opts = OrderedDict({
             'avail-module-naming-schemes': ("Show all supported module naming schemes",
                                             None, 'store_true', False,),
@@ -215,50 +214,49 @@ def config_options(self):
                                     None, "store_true", False,),
             'avail-repositories': ("Show all repository types (incl. non-usable)",
                                     None, "store_true", False,),
-            'buildpath': ("Temporary build path", None, 'store', oldstyle_defaults['buildpath']),
+            'buildpath': ("Temporary build path", None, 'store', mk_full_default_path('buildpath')),
             'ignore-dirs': ("Directory names to ignore when searching for files/dirs",
                             'strlist', 'store', ['.git', '.svn']),
-            'installpath': ("Install path for software and modules", None, 'store', oldstyle_defaults['installpath']),
+            'installpath': ("Install path for software and modules", None, 'store', mk_full_default_path('installpath')),
             'config': ("Path to EasyBuild config file (DEPRECATED, use --configfiles instead!)",
-                       None, 'store', oldstyle_defaults['config'], 'C'),
+                       None, 'store', get_default_oldstyle_configfile(), 'C'),
+            # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
-                               'strtuple', 'store', oldstyle_defaults['logfile_format'], {'metavar': 'DIR,FORMAT'}),
+                               'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
             'module-naming-scheme': ("Module naming scheme",
-                                     'choice', 'store', oldstyle_defaults['module_naming_scheme'],
-                                     sorted(avail_module_naming_schemes().keys())),
+                                     'choice', 'store', DEFAULT_MNS, sorted(avail_module_naming_schemes().keys())),
             'moduleclasses': (("Extend supported module classes "
                                "(For more info on the default classes, use --show-default-moduleclasses)"),
-                               None, 'extend', oldstyle_defaults['moduleclasses']),
+                               None, 'extend', [x[0] for x in DEFAULT_MODULECLASSES]),
             'modules-footer': ("Path to file containing footer to be added to all generated module files",
                                None, 'store_or_None', None, {'metavar': "PATH"}),
             'modules-tool': ("Modules tool to use",
-                             'choice', 'store', oldstyle_defaults['modules_tool'],
-                             sorted(avail_modules_tools().keys())),
+                             'choice', 'store', DEFAULT_MODULES_TOOL, sorted(avail_modules_tools().keys())),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
-                        "(used prefix for defaults %s)" % oldstyle_defaults['prefix']),
+                        "(used prefix for defaults %s)" % DEFAULT_PREFIX),
                         None, 'store', None),
             'recursive-module-unload': ("Enable generating of modules that unload recursively.",
                                         None, 'store_true', False),
             'repository': ("Repository type, using repositorypath",
-                           'choice', 'store', oldstyle_defaults['repository'], sorted(avail_repositories().keys())),
+                           'choice', 'store', DEFAULT_REPOSITORY, sorted(avail_repositories().keys())),
             'repositorypath': (("Repository path, used by repository "
                                 "(is passed as list of arguments to create the repository instance). "
                                 "For more info, use --avail-repositories."),
                                 'strlist', 'store',
-                                oldstyle_defaults['repositorypath'][oldstyle_defaults['repository']]),
+                                mk_full_default_path('repositorypath')),
             'show-default-moduleclasses': ("Show default module classes with description",
                                            None, 'store_true', False),
             'sourcepath': ("Path(s) to where sources should be downloaded (string, colon-separated)",
-                           None, 'store', oldstyle_defaults['sourcepath']),
-            'subdir-modules': ("Installpath subdir for modules", None, 'store', oldstyle_defaults['subdir_modules']),
-            'subdir-software': ("Installpath subdir for software", None, 'store', oldstyle_defaults['subdir_software']),
+                           None, 'store', mk_full_default_path('sourcepath')),
+            'subdir-modules': ("Installpath subdir for modules", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_modules']),
+            'subdir-software': ("Installpath subdir for software", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_software']),
             'suffix-modules-path': ("Suffix for module files install path", None, 'store', GENERAL_CLASS),
             # this one is sort of an exception, it's something jobscripts can set,
             # has no real meaning for regular eb usage
             'testoutput': ("Path to where a job should place the output (to be set within jobscript)",
                             None, 'store', None),
             'tmp-logdir': ("Log directory where temporary log files are stored",
-                           None, 'store', oldstyle_defaults['tmp_logdir']),
+                           None, 'store', DEFAULT_TMP_LOGDIR),
             'tmpdir': ('Directory to use for temporary storage', None, 'store', None),
         })
 
@@ -413,18 +411,15 @@ def postprocess(self):
     def _postprocess_config(self):
         """Postprocessing of configuration options"""
         if self.options.prefix is not None:
-            changed_defaults = get_default_oldstyle_configfile_defaults(self.options.prefix)
             # prefix applies to all paths, and repository has to be reinitialised to take new repositorypath into account
             # in the legacy-style configuration, repository is initialised in configuration file itself
             for dest in ['installpath', 'buildpath', 'sourcepath', 'repository', 'repositorypath']:
                 if not self.options._action_taken.get(dest, False):
-                    new_def = changed_defaults[dest]
-                    if dest == 'repositorypath':
-                        setattr(self.options, dest, new_def[changed_defaults['repository']])
+                    if dest == 'repository':
+                        setattr(self.options, dest, DEFAULT_REPOSITORY)
                     else:
-                        setattr(self.options, dest, new_def)
-                    # LEGACY this line is here for oldstyle reasons
-                    self.log.deprecated('Fake action taken to distinguish from default', '2.0')
+                        setattr(self.options, dest, mk_full_default_path(dest, prefix=self.options.prefix))
+                    # LEGACY this line is here for oldstyle config reasons
                     self.options._action_taken[dest] = True
 
         if self.options.pretend:
@@ -619,7 +614,7 @@ def avail_toolchains(self):
 
     def avail_repositories(self):
         """Show list of known repository types."""
-        repopath_defaults = get_default_oldstyle_configfile_defaults()['repositorypath']
+        repopath_defaults = mk_full_default_path('repositorypath')
         all_repos = avail_repositories(check_useable=False)
         usable_repos = avail_repositories(check_useable=True).keys()
 
diff --git a/test/framework/config.py b/test/framework/config.py
index 63c55efaf1..b9b811c0e4 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -80,7 +80,7 @@ def configure(self, args=None):
         options = init_config(args=args)
         return options.config
 
-    def xtest_default_config(self):
+    def test_default_config(self):
         """Test default configuration."""
         self.purge_environment()
 
@@ -355,7 +355,7 @@ def test_legacy_config_file(self):
         self.assertEqual(log_file_format(), logtmpl)
         self.assertEqual(get_build_log_path(), tmplogdir)
 
-    def xtest_generaloption_config(self):
+    def test_generaloption_config(self):
         """Test new-style configuration (based on generaloption)."""
         self.purge_environment()
 
@@ -414,7 +414,7 @@ def xtest_generaloption_config(self):
         del os.environ['EASYBUILD_PREFIX']
         del os.environ['EASYBUILD_SUBDIR_SOFTWARE']
 
-    def xtest_generaloption_config_file(self):
+    def test_generaloption_config_file(self):
         """Test use of new-style configuration file."""
         self.purge_environment()
 
@@ -491,7 +491,7 @@ def xtest_generaloption_config_file(self):
         del os.environ['EASYBUILD_CONFIGFILES']
         sys.path[:] = orig_sys_path
 
-    def xtest_set_tmpdir(self):
+    def test_set_tmpdir(self):
         """Test set_tmpdir config function."""
         self.purge_environment()
 
@@ -517,7 +517,7 @@ def xtest_set_tmpdir(self):
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
 
-    def xtest_configuration_variables(self):
+    def test_configuration_variables(self):
         """Test usage of ConfigurationVariables."""
         # delete instance of ConfigurationVariables
         ConfigurationVariables.__metaclass__._instances.pop(ConfigurationVariables, None)
@@ -529,7 +529,7 @@ def xtest_configuration_variables(self):
         self.assertTrue(cv1 is cv2)
         self.assertTrue(cv1 is cv3)
 
-    def xtest_build_options(self):
+    def test_build_options(self):
         """Test usage of BuildOptions."""
         # delete instance of BuildOptions
         BuildOptions.__metaclass__._instances.pop(BuildOptions, None)

From 64abf8d90dde9f7026d93a8882289717f26f184d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 13 Dec 2014 14:14:12 +0100
Subject: [PATCH 0354/1356] restore test that checks for easybuild_config.py
 legacy config file

---
 test/framework/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index b9b811c0e4..fb4cdd854b 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -246,7 +246,7 @@ def test_legacy_config_file(self):
         self.purge_environment()
 
         cfg_fn = self.configure(args=[])
-        #self.assertTrue(cfg_fn.endswith('easybuild/easybuild_config.py'))
+        self.assertTrue(cfg_fn.endswith('easybuild/easybuild_config.py'))
 
         configtxt = """
 build_path = '%(buildpath)s'

From 11e9f37ff33a7263a3dff84525603ac6e5aa3078 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 13 Dec 2014 14:14:52 +0100
Subject: [PATCH 0355/1356] improve deprecation message w.r.t. extra_options
 return type

---
 easybuild/framework/easyblock.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index aefe1b607f..d26253f392 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -97,8 +97,9 @@ def extra_options(extra=None):
             extra = {}
 
         if not isinstance(extra, dict):
-            _log.deprecated("Obtained value of type '%s' for extra, should be 'dict'" % type(extra), '2.0')
-            _log.debug("Converting extra_options value '%s' of type '%s' to a dict" % (extra, type(extra)))
+            typ = type(extra)
+            _log.deprecated("Obtained 'extra' value of type '%s' in extra_options, should be 'dict'" % typ, '2.0')
+            _log.debug("Converting extra_options value '%s' of type '%s' to a dict" % (extra, typ))
             extra = dict(extra)
 
         # to avoid breaking backward compatibility, we still need to return a list of tuples in EasyBuild v1.x

From 9bb1a272b12d0375576dbc355077b40e722dc399 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 13 Dec 2014 14:15:08 +0100
Subject: [PATCH 0356/1356] fix run_cmd imports

---
 easybuild/framework/easyconfig/tools.py    | 3 ++-
 easybuild/framework/extension.py           | 2 +-
 easybuild/scripts/mk_tmpl_easyblock_for.py | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index a3c0599c07..45f8659f06 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -70,10 +70,11 @@
 from easybuild.framework.easyconfig.easyconfig import process_easyconfig
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import find_easyconfigs, run_cmd, search_file, write_file
+from easybuild.tools.filetools import find_easyconfigs, search_file, write_file
 from easybuild.tools.github import fetch_easyconfigs_from_pr
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.ordereddict import OrderedDict
+from easybuild.tools.run import run_cmd
 from easybuild.tools.utilities import quote_str
 
 
diff --git a/easybuild/framework/extension.py b/easybuild/framework/extension.py
index af5b17672b..a50781e9b3 100644
--- a/easybuild/framework/extension.py
+++ b/easybuild/framework/extension.py
@@ -37,7 +37,7 @@
 import os
 
 from easybuild.tools.config import build_path
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 
 
 class Extension(object):
diff --git a/easybuild/scripts/mk_tmpl_easyblock_for.py b/easybuild/scripts/mk_tmpl_easyblock_for.py
index f2fcffbca6..78c7716507 100755
--- a/easybuild/scripts/mk_tmpl_easyblock_for.py
+++ b/easybuild/scripts/mk_tmpl_easyblock_for.py
@@ -121,7 +121,7 @@
 import easybuild.tools.toolchain as toolchain
 %(parent_import)s
 from easybuild.framework.easyconfig import CUSTOM, MANDATORY
-from easybuild.tools.filetools import run_cmd
+from easybuild.tools.run import run_cmd
 
 
 class %(class_name)s(%(parent)s):

From 1b81421f0116db61f86a3794973221f226ae5012 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 13 Dec 2014 15:55:05 +0100
Subject: [PATCH 0357/1356] don't trigger deprecation warning just for having
 parameters defined in extra_options

---
 easybuild/framework/easyconfig/easyconfig.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 52aa4d2c24..c716d722a5 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -174,14 +174,6 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
                 tup = (type(self.extra_options), self.extra_options)
                 self.log.error("extra_options parameter passed is of incorrect type: %s ('%s')" % tup)
 
-        # map deprecated params to new names if they occur in extra_options
-        for key, val in self.extra_options.items():
-            if key in DEPRECATED_OPTIONS:
-                new_key, depr_ver = DEPRECATED_OPTIONS[key]
-                self.log.deprecated("Found deprecated key '%s', should use '%s' instead." % (key, new_key), depr_ver)
-                self.extra_options[new_key] = self.extra_options[key]
-                self.log.debug("Set '%s' with value of deprecated '%s': %s" % (new_key, key, self.extra_options[key]))
-                del self.extra_options[key]
         self._config.update(self.extra_options)
 
         self.path = path

From 5f33cc1edd9ba6041e453462c06667b940ae2fcc Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Sat, 13 Dec 2014 16:02:22 +0100
Subject: [PATCH 0358/1356] Fix bug: fallback to dpkg/... should work

---
 easybuild/tools/systemtools.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 8564f4b8bf..a50723cf0f 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -396,16 +396,16 @@ def check_os_dependency(dep):
         cmd = "rpm -q %s" % dep
         found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
 
-    if found is None and which('dpkg'):
+    if not found and which('dpkg'):
         cmd = "dpkg -s %s" % dep
         found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
 
-    if found is None:
+    if not found:
         # fallback for when os-dependency is a binary/library
         found = which(dep)
 
     # try locate if it's available
-    if found is None and which('locate'):
+    :x
         cmd = 'locate --regexp "/%s$"' % dep
         found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
 

From d6e90907e7f58ffacd26fa60b00bb92a30a00312 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Sat, 13 Dec 2014 16:07:28 +0100
Subject: [PATCH 0359/1356] Fix typo

---
 easybuild/tools/systemtools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index a50723cf0f..6c11ff6a4b 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -405,7 +405,7 @@ def check_os_dependency(dep):
         found = which(dep)
 
     # try locate if it's available
-    :x
+    if not found and which('locate'):
         cmd = 'locate --regexp "/%s$"' % dep
         found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
 

From 4afe0a9ea101f2af32acf78466b96b67bc0a84ff Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 13 Dec 2014 20:36:48 +0100
Subject: [PATCH 0360/1356] update with vsc-base for HybridListDict

---
 vsc/README.md        |  2 +-
 vsc/utils/wrapper.py | 42 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+), 1 deletion(-)

diff --git a/vsc/README.md b/vsc/README.md
index b5efeb45be..0338b53837 100644
--- a/vsc/README.md
+++ b/vsc/README.md
@@ -1,3 +1,3 @@
 Code from https://github.com/hpcugent/vsc-base
 
-based on 2146be5301da34043adf4646169e5dfec88cd2f5 (vsc-base v1.9.9)
+based on e114e817ba3003582a805fc70f6203f9cf6062fa (vsc-base v1.9.10)
diff --git a/vsc/utils/wrapper.py b/vsc/utils/wrapper.py
index 537c1f252b..b449966c22 100644
--- a/vsc/utils/wrapper.py
+++ b/vsc/utils/wrapper.py
@@ -40,3 +40,45 @@ def proxy(self, *args):
                     if name.startswith("__"):
                         if name not in ignore and name not in dct:
                             setattr(cls, name, property(make_proxy(name)))
+
+
+class HybridListDict(Wrapper):
+    """
+    Hybrid list/dict object: is a list of 2-element tuples, but also acts like a dict.
+
+    Supported dict-like methods include: update(adict), items(), keys(), values()
+    """
+    __wraps__ = list
+
+    def __getitem__(self, index_key):
+        """Get value by specified index/key."""
+        if isinstance(index_key, int):
+            res = self._obj[index_key]
+        else:
+            res = dict(self._obj)[index_key]
+        return res
+
+    def __setitem__(self, index_key, value):
+        """Add value at specified index/key."""
+        if isinstance(index_key, int):
+            self._obj[index_key] = value
+        else:
+            self._obj = [(k, v) for (k, v) in self._obj if k != index_key]
+            self._obj.append((index_key, value))
+
+    def update(self, extra):
+        """Update with keys/values in supplied dictionary."""
+        self._obj = [(k, v) for (k, v) in self._obj if k not in extra.keys()]
+        self._obj.extend(extra.items())
+
+    def items(self):
+        """Get list of key/value tuples."""
+        return self._obj
+
+    def keys(self):
+        """Get list of keys."""
+        return [x[0] for x in self.items()]
+
+    def values(self):
+        """Get list of values."""
+        return [x[1] for x in self.items()]

From 3a941c8c24a2996be96900a0c1535b0a88f29825 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 13 Dec 2014 20:37:21 +0100
Subject: [PATCH 0361/1356] use HybridListDict as return type for extra_options

---
 easybuild/framework/easyblock.py             | 5 +++--
 easybuild/framework/easyconfig/easyconfig.py | 5 +++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index d26253f392..10393da77b 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -47,6 +47,7 @@
 from distutils.version import LooseVersion
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_class_for
+from vsc.utils.wrapper import HybridListDict
 
 import easybuild.tools.environment as env
 from easybuild.tools import config, filetools
@@ -104,8 +105,8 @@ def extra_options(extra=None):
 
         # to avoid breaking backward compatibility, we still need to return a list of tuples in EasyBuild v1.x
         # starting with EasyBuild v2.0, this will be changed to return the actual dict
-        res = extra.items()
-
+        # as a temporary workaround, return a value which is a hybrid between a list and a dict
+        res = HybridListDict(extra.items())
         return res
 
     #
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index c716d722a5..e67d8d5653 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -42,6 +42,7 @@
 from vsc.utils import fancylogger
 from vsc.utils.missing import any, get_class_for, nub
 from vsc.utils.patterns import Singleton
+from vsc.utils.wrapper import HybridListDict
 
 import easybuild.tools.environment as env
 from easybuild.tools.build_log import EasyBuildError
@@ -163,9 +164,9 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
             self.extra_options = extra_options
 
         if not isinstance(self.extra_options, dict):
-            if isinstance(self.extra_options, (list, tuple,)):
+            if isinstance(self.extra_options, (list, tuple, HybridListDict)):
                 typ = type(self.extra_options)
-                if extra_options:
+                if not isinstance(self.extra_options, HybridListDict):
                     self.log.deprecated("extra_options return value should be of type 'dict', found '%s'" % typ, '2.0')
                 tup = (self.extra_options, type(self.extra_options))
                 self.log.debug("Converting extra_options value '%s' of type '%s' to a dict" % tup)

From e13ebbc993659e7fcb68f1ec09afaa327b9a49aa Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Sat, 13 Dec 2014 20:52:28 +0100
Subject: [PATCH 0362/1356] osdeps: this should work fail if rpm/dpkg say no

If rpm or dpkg is found and they say No, don't try which or locate.
---
 easybuild/tools/systemtools.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 6c11ff6a4b..339db48648 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -392,6 +392,7 @@ def check_os_dependency(dep):
     # - fallback on which
     # - should be extended to files later?
     found = None
+    cmd = None
     if which('rpm'):
         cmd = "rpm -q %s" % dep
         found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
@@ -400,14 +401,14 @@ def check_os_dependency(dep):
         cmd = "dpkg -s %s" % dep
         found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
 
-    if not found:
+    if cmd is None:
         # fallback for when os-dependency is a binary/library
         found = which(dep)
 
-    # try locate if it's available
-    if not found and which('locate'):
-        cmd = 'locate --regexp "/%s$"' % dep
-        found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
+        # try locate if it's available
+        if not found and which('locate'):
+            cmd = 'locate --regexp "/%s$"' % dep
+            found = run_cmd(cmd, simple=True, log_all=False, log_ok=False)
 
     return found
 

From 7a300bc610d70d76defa9676e80c552886a1f02d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 13 Dec 2014 21:20:30 +0100
Subject: [PATCH 0363/1356] remove faulty comment

---
 easybuild/tools/config.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 88cbdc63df..b1f6f3427b 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -169,7 +169,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
 ]
 
 
-# note: keys are new style option names
 OLDSTYLE_ENVIRONMENT_VARIABLES = {
     'build_path': 'EASYBUILDBUILDPATH',
     'config_file': 'EASYBUILDCONFIG',

From 3c8a56de761b17d2b492f3ede0e770291899c8c6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 14 Dec 2014 10:28:29 +0100
Subject: [PATCH 0364/1356] fix broken unit tests w.r.t. HybridListDict
 trickery

---
 easybuild/framework/easyconfig/default.py  |  3 +++
 easybuild/scripts/mk_tmpl_easyblock_for.py |  9 ++++-----
 test/framework/easyblock.py                | 18 +++++++++++-------
 test/framework/options.py                  |  6 +++---
 4 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index d9934e092e..8be6e4a4e9 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -34,6 +34,7 @@
 @author: Toon Willems (Ghent University)
 """
 from vsc.utils import fancylogger
+from vsc.utils.wrapper import HybridListDict
 
 from easybuild.tools.ordereddict import OrderedDict
 
@@ -194,6 +195,8 @@ def convert_to_help(opts, has_default=False):
     mapping = OrderedDict()
     if isinstance(opts, dict):
         opts = opts.items()
+    elif isinstance(opts, HybridListDict):
+        opts = list(opts)
     if not has_default:
         defs = [(k, [def_val, descr, ALL_CATEGORIES[cat]]) for k, (def_val, descr, cat) in DEFAULT_CONFIG.items()]
         opts = defs + opts
diff --git a/easybuild/scripts/mk_tmpl_easyblock_for.py b/easybuild/scripts/mk_tmpl_easyblock_for.py
index 78c7716507..0d57f13f35 100755
--- a/easybuild/scripts/mk_tmpl_easyblock_for.py
+++ b/easybuild/scripts/mk_tmpl_easyblock_for.py
@@ -136,11 +136,10 @@ def __init__(self, *args, **kwargs):
     @staticmethod
     def extra_options():
         \"\"\"Custom easyconfig parameters for %(name)s.\"\"\"
-
-        extra_vars = [
-                      ('mandatory_extra_param', ['default value', "short description", MANDATORY]),
-                      ('optional_extra_param', ['default value', "short description", CUSTOM]),
-                     ]
+        extra_vars = {
+            'mandatory_extra_param': ['default value', "short description", MANDATORY],
+            'optional_extra_param': ['default value', "short description", CUSTOM],
+         }
         return %(parent)s.extra_options(extra_vars)
 
     def configure_step(self):
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 91a7441d18..d583397e12 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -79,19 +79,23 @@ def test_easyblock(self):
 
         def check_extra_options_format(extra_options):
             """Make sure extra_options value is of correct format."""
-            # EasyBuild v1.x
-            self.assertTrue(isinstance(extra_options, list))
+            # EasyBuild v1.x: list of (<string>, <list>) tuples
+            self.assertTrue(isinstance(list(extra_options), list))  # conversion to a list works
             for extra_option in extra_options:
                 self.assertTrue(isinstance(extra_option, tuple))
                 self.assertEqual(len(extra_option), 2)
                 self.assertTrue(isinstance(extra_option[0], basestring))
                 self.assertTrue(isinstance(extra_option[1], list))
                 self.assertEqual(len(extra_option[1]), 3)
-            # EasyBuild v2.0 (breaks backward compatibility compared to v1.x)
-            #self.assertTrue(isinstance(extra_options, dict))
-            #for key in extra_options:
-            #    self.assertTrue(isinstance(extra_options[key], list))
-            #    self.assertTrue(len(extra_options[key]), 3)
+            # EasyBuild v2.0: dict with <string> keys and <list> values
+            # (breaks backward compatibility compared to v1.x)
+            self.assertTrue(isinstance(dict(extra_options), dict))  # conversion to a dict works
+            extra_options.items()
+            extra_options.keys()
+            extra_options.values()
+            for key in extra_options.keys():
+                self.assertTrue(isinstance(extra_options[key], list))
+                self.assertTrue(len(extra_options[key]), 3)
 
         name = "pi"
         version = "3.14"
diff --git a/test/framework/options.py b/test/framework/options.py
index 17f3688640..77694b83dd 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -349,9 +349,9 @@ def run_test(custom=None, extra_params=[]):
                 write_file(self.logfile, '')
 
                 args = [
-                        avail_arg,
-                        '--unittest-file=%s' % self.logfile,
-                       ]
+                    avail_arg,
+                    '--unittest-file=%s' % self.logfile,
+                ]
                 if custom is not None:
                     args.extend(['-e', custom])
 

From d9f51cbf7e9f163b1ca37d0979716a74b1c66ab3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 14 Dec 2014 10:35:06 +0100
Subject: [PATCH 0365/1356] don't set old-style $EASYBUILDTESTOUTPUT, set
 $EASYBUILD_TESTOUTPUT instead

---
 easybuild/tools/parallelbuild.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 8af42cffeb..e6f8ee45ea 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -182,8 +182,9 @@ def create_job(build_command, easyconfig, output_dir=None, conn=None, ppn=None):
     ec_tuple = (easyconfig['ec']['name'], det_full_ec_version(easyconfig['ec']))
     name = '-'.join(ec_tuple)
 
-    var = config.OLDSTYLE_ENVIRONMENT_VARIABLES['test_output_path']
-    easybuild_vars[var] = os.path.join(os.path.abspath(output_dir), name)
+    oldstyle_testoutput_env_var = config.OLDSTYLE_ENVIRONMENT_VARIABLES['test_output_path']
+    if not (oldstyle_testoutput_env_var in easybuild_vars or 'EASYBUILD_TESTOUTPUT' in easybuild_vars):
+        easybuild_vars['EASYBUILD_TESTOUTPUT'] = os.path.join(os.path.abspath(output_dir), name)
 
     # just use latest build stats
     repo = init_repository(get_repository(), get_repositorypath())

From e70808d3f52f7e8c176e278ff09e8ce3e6fe28e7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 14 Dec 2014 20:22:30 +0100
Subject: [PATCH 0366/1356] drop log.deprecated message for own any/all
 functions

---
 easybuild/tools/utilities.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 246619e3fd..05948c9c6d 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -47,13 +47,11 @@
 
 def any(ls):
     """Reimplementation of 'any' function, which is not available in Python 2.4 yet."""
-    _log.deprecated("own definition of any", "2.0")
     return _any(ls)
 
 
 def all(ls):
     """Reimplementation of 'all' function, which is not available in Python 2.4 yet."""
-    _log.deprecated("own definition of all", "2.0")
     return _all(ls)
 
 

From ac509adb7f7ab10ce9af60055c088f56509f56a9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 08:19:48 +0100
Subject: [PATCH 0367/1356] fix creating and using of regtest output dir

---
 easybuild/tools/config.py        |  1 +
 easybuild/tools/parallelbuild.py |  6 +++---
 easybuild/tools/testing.py       | 14 ++++++--------
 3 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index b1f6f3427b..502950fd88 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -98,6 +98,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'stop',
         'suffix_modules_path',
         'test_report_env_filter',
+        'testoutput',
         'umask',
     ],
     False: [
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index e6f8ee45ea..c3ca5b782e 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -182,9 +182,9 @@ def create_job(build_command, easyconfig, output_dir=None, conn=None, ppn=None):
     ec_tuple = (easyconfig['ec']['name'], det_full_ec_version(easyconfig['ec']))
     name = '-'.join(ec_tuple)
 
-    oldstyle_testoutput_env_var = config.OLDSTYLE_ENVIRONMENT_VARIABLES['test_output_path']
-    if not (oldstyle_testoutput_env_var in easybuild_vars or 'EASYBUILD_TESTOUTPUT' in easybuild_vars):
-        easybuild_vars['EASYBUILD_TESTOUTPUT'] = os.path.join(os.path.abspath(output_dir), name)
+    regtest_output_dir_var = 'EASYBUILD_REGTEST_OUTPUT_DIR'
+    if not regtest_output_dir_var in easybuild_vars:
+        easybuild_vars[regtest_output_dir_var] = os.path.join(os.path.abspath(output_dir), name)
 
     # just use latest build stats
     repo = init_repository(get_repository(), get_repositorypath())
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index 5c67e972e2..695577fd05 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -76,19 +76,17 @@ def regtest(easyconfig_paths, build_specs=None):
         _log.info("aggregated xml files inside %s, output written to: %s" % (aggregate_regtest, output_file))
         sys.exit(0)
 
-    # create base directory, which is used to place
-    # all log files and the test output as xml
-    basename = "easybuild-test-%s" % datetime.now().strftime("%Y%m%d%H%M%S")
-    var = config.OLDSTYLE_ENVIRONMENT_VARIABLES['test_output_path']
-
+    # create base directory, which is used to place all log files and the test output as xml
     regtest_output_dir = build_option('regtest_output_dir')
+    testoutput = build_option('testoutput')
     if regtest_output_dir is not None:
         output_dir = regtest_output_dir
-    elif var in os.environ:
-        output_dir = os.path.abspath(os.environ[var])
+    elif testoutput is not None:
+        output_dir = os.path.abspath(testoutput)
     else:
         # default: current dir + easybuild-test-[timestamp]
-        output_dir = os.path.join(cur_dir, basename)
+        dirname = "easybuild-test-%s" % datetime.now().strftime("%Y%m%d%H%M%S")
+        output_dir = os.path.join(cur_dir, dirname)
 
     mkdir(output_dir, parents=True)
 

From 0dff4ff015b4400c498399797090d05d12456cc5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 08:43:29 +0100
Subject: [PATCH 0368/1356] fix comments

---
 easybuild/tools/config.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 502950fd88..d66e269a3c 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -70,7 +70,7 @@
 DEFAULT_REPOSITORY = 'FileRepository'
 DEFAULT_TMP_LOGDIR = tempfile.gettempdir()
 
-# utility function for defining DEFAULT_ constants below
+# utility function for obtaining default paths
 def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
     """Create full path, avoid '/' at the end."""
     args = [prefix]
@@ -262,7 +262,7 @@ def get_user_easybuild_dir():
     xdg_config_home = os.environ.get("XDG_CONFIG_HOME", os.path.join(os.path.expanduser('~'), ".config"))
     newpath = os.path.join(xdg_config_home, "easybuild")
 
-    # only issue deprecation warning/error is new path doesn't exist, but deprecated path does
+    # only issue deprecation warning/error if new path doesn't exist, but deprecated path does
     if not os.path.isdir(newpath) and os.path.isdir(oldpath):
         _log.deprecated("The user easybuild dir has moved from %s to %s." % (oldpath, newpath), "2.0")
         return oldpath

From 84a21ed7c64903580d20d0404365ef9ec4bbfa6b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 09:49:43 +0100
Subject: [PATCH 0369/1356] drop kernel_name entry from get_system_info return
 value due to deprecation

---
 easybuild/tools/systemtools.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 7cd2babc04..d351679fd7 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -464,7 +464,6 @@ def get_system_info():
         'gcc_version': get_tool_version('gcc', version_option='-v'),
         'hostname': gethostname(),
         'glibc_version': get_glibc_version(),
-        'kernel_name': get_kernel_name(),
         'os_name': get_os_name(),
         'os_type': get_os_type(),
         'os_version': get_os_version(),

From c61ff516c3fb4a02af79499d348777f4da1021e2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 15:31:32 +0100
Subject: [PATCH 0370/1356] fix finding correct easyblock to install extensions
 with, without duplicating code (i.e. reuse get_easyblock_class)

---
 easybuild/framework/easyblock.py | 26 ++++++++++----------------
 1 file changed, 10 insertions(+), 16 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 10393da77b..967220ce64 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -52,7 +52,7 @@
 import easybuild.tools.environment as env
 from easybuild.tools import config, filetools
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
-from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS, ITERATE_OPTIONS
+from easybuild.framework.easyconfig.easyconfig import DEFAULT_EASYBLOCK, ITERATE_OPTIONS, EasyConfig, ActiveMNS
 from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, get_module_path, resolve_template
 from easybuild.framework.easyconfig.tools import get_paths_for
@@ -1406,23 +1406,17 @@ def extensions_step(self, fetch=False):
             inst = None
 
             # try instantiating extension-specific class
-            class_name = encode_class_name(ext['name'])  # use the same encoding as get_class
-            mod_path = get_module_path(class_name)
-            if not os.path.exists("%s.py" % mod_path):
-                self.log.deprecated("Determine module path based on software name", "2.0")
-                mod_path = get_module_path(ext['name'], decode=False)
-
             try:
-                cls = get_class_for(mod_path, class_name)
-                inst = cls(self, ext)
+                cls = get_easyblock_class(None, name=ext['name'])
+                self.log.debug("Obtained class %s for extension %s" % (cls, ext['name']))
+                if cls.__name__ != DEFAULT_EASYBLOCK:
+                    inst = cls(self, ext)
             except (ImportError, NameError), err:
-                self.log.debug("Failed to use class %s from %s for extension %s: %s" % (class_name,
-                                                                                        mod_path,
-                                                                                        ext['name'],
-                                                                                        err))
+                self.log.debug("Failed to use extension-specific class for extension %s: %s" % (ext['name'], err))
 
             # LEGACY: try and use default module path for getting extension class instance
             if inst is None and legacy:
+                self.log.deprecated("Using specified module path for default class", '2.0')
                 try:
                     msg = "Failed to use derived module path for %s, " % class_name
                     msg += "considering specified module path as (legacy) fallback."
@@ -1450,9 +1444,7 @@ def extensions_step(self, fetch=False):
                                                                                                err))
 
             # fallback attempt: use default class
-            if not inst is None:
-                self.log.debug("Installing extension %s with class %s (from %s)" % (ext['name'], class_name, mod_path))
-            else:
+            if inst is None:
                 try:
                     cls = get_class_for(default_class_modpath, default_class)
                     self.log.debug("Obtained class %s for installing extension %s" % (cls, ext['name']))
@@ -1463,6 +1455,8 @@ def extensions_step(self, fetch=False):
                     msg = "Also failed to use default class %s from %s for extension %s: %s, giving up" % \
                         (default_class, default_class_modpath, ext['name'], err)
                     self.log.error(msg)
+            else:
+                self.log.debug("Installing extension %s with class %s (from %s)" % (ext['name'], class_name, mod_path))
 
             # real work
             inst.prerun()

From a02928151f1fda5417d2cc4437bbfe037d598220 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 15:58:18 +0100
Subject: [PATCH 0371/1356] pass default extension class as default to
 get_easyblock_class for extensions

---
 easybuild/framework/easyblock.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 967220ce64..ae8d23b6fe 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1407,9 +1407,9 @@ def extensions_step(self, fetch=False):
 
             # try instantiating extension-specific class
             try:
-                cls = get_easyblock_class(None, name=ext['name'])
+                cls = get_easyblock_class(default_class, name=ext['name'])
                 self.log.debug("Obtained class %s for extension %s" % (cls, ext['name']))
-                if cls.__name__ != DEFAULT_EASYBLOCK:
+                if cls.__name__ != default_class:
                     inst = cls(self, ext)
             except (ImportError, NameError), err:
                 self.log.debug("Failed to use extension-specific class for extension %s: %s" % (ext['name'], err))

From f8d39a4a0cabe09faf7f572ecb12dcb6e3c5001b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 17:00:58 +0100
Subject: [PATCH 0372/1356] enhance get_easyblock_class so it can be reused for
 extensions, by making fallback to default optional

---
 easybuild/framework/easyblock.py             |  6 +--
 easybuild/framework/easyconfig/easyconfig.py | 36 ++++++++-------
 test/framework/easyconfig.py                 | 47 ++++++++++----------
 3 files changed, 48 insertions(+), 41 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index ae8d23b6fe..bc26543edd 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1403,13 +1403,13 @@ def extensions_step(self, fetch=False):
             # always go back to original work dir to avoid running stuff from a dir that no longer exists
             os.chdir(self.orig_workdir)
 
-            inst = None
+            cls, inst = None, None
 
             # try instantiating extension-specific class
             try:
-                cls = get_easyblock_class(default_class, name=ext['name'])
+                cls = get_easyblock_class(None, name=ext['name'], default_fallback=False)
                 self.log.debug("Obtained class %s for extension %s" % (cls, ext['name']))
-                if cls.__name__ != default_class:
+                if cls is not None:
                     inst = cls(self, ext)
             except (ImportError, NameError), err:
                 self.log.debug("Failed to use extension-specific class for extension %s: %s" % (ext['name'], err))
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index e67d8d5653..7d2c36eb9d 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -728,11 +728,11 @@ def fetch_parameter_from_easyconfig_file(path, param):
         return None
 
 
-def get_easyblock_class(easyblock, name=None):
+def get_easyblock_class(easyblock, name=None, default_fallback=True):
     """
     Get class for a particular easyblock (or use default)
     """
-
+    cls = None
     try:
         if easyblock:
             # something was specified, lets parse it
@@ -792,22 +792,28 @@ def get_easyblock_class(easyblock, name=None):
                 error_re = re.compile(r"No module named %s" % modulepath.replace("easybuild.easyblocks.", ''))
                 _log.debug("error regexp: %s" % error_re.pattern)
                 if error_re.match(str(err)):
-                    # no easyblock could be found, so fall back to default class.
-                    def_class = DEFAULT_EASYBLOCK
-                    def_mod_path = get_module_path(def_class, generic=True)
-
-                    _log.warning("Failed to import easyblock for %s, falling back to default class %s: error: %s" % \
-                                (class_name, (def_mod_path, def_class), err))
-
-                    depr_msg = "Fallback to default easyblock %s (from %s)" % (def_class, def_mod_path)
-                    depr_msg += "; use \"easyblock = '%s'\" in easyconfig file?" % def_class
-                    _log.deprecated(depr_msg, '2.0')
-                    cls = get_class_for(def_mod_path, def_class)
+                    if default_fallback:
+                        # no easyblock could be found, so fall back to default class.
+                        def_class = DEFAULT_EASYBLOCK
+                        def_mod_path = get_module_path(def_class, generic=True)
+
+                        _log.warning("Failed to import easyblock for %s, falling back to default class %s: error: %s" % \
+                                    (class_name, (def_mod_path, def_class), err))
+
+                        depr_msg = "Fallback to default easyblock %s (from %s)" % (def_class, def_mod_path)
+                        depr_msg += "; use \"easyblock = '%s'\" in easyconfig file?" % def_class
+                        _log.deprecated(depr_msg, '2.0')
+                        cls = get_class_for(def_mod_path, def_class)
                 else:
                     _log.error("Failed to import easyblock for %s because of module issue: %s" % (class_name, err))
 
-        tup = (cls.__name__, easyblock, name)
-        _log.info("Successfully obtained class '%s' for easyblock '%s' (software name '%s')" % tup)
+        if cls is not None:
+            tup = (cls.__name__, easyblock, name)
+            _log.info("Successfully obtained class '%s' for easyblock '%s' (software name '%s')" % tup)
+        else:
+            tup = (easyblock, name, default_fallback)
+            _log.debug("No class found for easyblock '%s' (software name '%s', default fallback: %s" % tup)
+
         return cls
 
     except EasyBuildError, err:
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index de25d9e82c..d46eac9d26 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -88,14 +88,14 @@ def tearDown(self):
         if os.path.exists(self.eb_file):
             os.remove(self.eb_file)
 
-    def test_empty(self):
+    def xtest_empty(self):
         """ empty files should not parse! """
         self.contents = "# empty string"
         self.prep()
         self.assertRaises(EasyBuildError, EasyConfig, self.eb_file)
         self.assertErrorRegex(EasyBuildError, "expected a valid path", EasyConfig, "")
 
-    def test_mandatory(self):
+    def xtest_mandatory(self):
         """ make sure all checking of mandatory variables works """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -119,7 +119,7 @@ def test_mandatory(self):
         self.assertEqual(eb['toolchain'], {"name":"dummy", "version": "dummy"})
         self.assertEqual(eb['description'], "test easyconfig")
 
-    def test_validation(self):
+    def xtest_validation(self):
         """ test other validations beside mandatory variables """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -151,7 +151,7 @@ def test_validation(self):
         self.prep()
         self.assertErrorRegex(EasyBuildError, "SyntaxError", EasyConfig, self.eb_file)
 
-    def test_shared_lib_ext(self):
+    def xtest_shared_lib_ext(self):
         """ inside easyconfigs shared_lib_ext should be set """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -165,7 +165,7 @@ def test_shared_lib_ext(self):
         eb = EasyConfig(self.eb_file)
         self.assertEqual(eb['sanity_check_paths']['files'][0], "lib/lib.%s" % get_shared_lib_ext())
 
-    def test_dependency(self):
+    def xtest_dependency(self):
         """ test all possible ways of specifying dependencies """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -211,7 +211,7 @@ def test_dependency(self):
         self.assertErrorRegex(EasyBuildError, "without name", eb._parse_dependency, ())
         self.assertErrorRegex(EasyBuildError, "without version", eb._parse_dependency, {'name': 'test'})
 
-    def test_extra_options(self):
+    def xtest_extra_options(self):
         """ extra_options should allow other variables to be stored """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -264,7 +264,7 @@ def test_extra_options(self):
 
         self.assertEqual(eb['mandatory_key'], 'value')
 
-    def test_exts_list(self):
+    def xtest_exts_list(self):
         """Test handling of list of extensions."""
         os.environ['EASYBUILD_SOURCEPATH'] = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         init_config()
@@ -295,7 +295,7 @@ def test_exts_list(self):
         eb = EasyBlock(ec)
         exts_sources = eb.fetch_extension_sources()
 
-    def test_suggestions(self):
+    def xtest_suggestions(self):
         """ If a typo is present, suggestions should be provided (if possible) """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -314,7 +314,7 @@ def test_suggestions(self):
         self.assertErrorRegex(EasyBuildError, "source_URLs -> source_urls", EasyConfig, self.eb_file)
         self.assertErrorRegex(EasyBuildError, "sourceURLs -> source_urls", EasyConfig, self.eb_file)
 
-    def test_tweaking(self):
+    def xtest_tweaking(self):
         """test tweaking ability of easyconfigs"""
 
         fd, tweaked_fn = tempfile.mkstemp(prefix='easybuild-tweaked-', suffix='.eb')
@@ -386,7 +386,7 @@ def test_tweaking(self):
         # cleanup
         os.remove(tweaked_fn)
 
-    def test_installversion(self):
+    def xtest_installversion(self):
         """Test generation of install version."""
 
         ver = "3.14"
@@ -416,7 +416,7 @@ def test_installversion(self):
         installver = det_full_ec_version(cfg)
         self.assertEqual(installver, correct_installver)
 
-    def test_legacy_installversion(self):
+    def xtest_legacy_installversion(self):
         """Test generation of install version (legacy)."""
 
         ver = "3.14"
@@ -434,7 +434,7 @@ def test_legacy_installversion(self):
         installver = det_installversion(ver, dummy, tcver, verpref, versuff)
         self.assertEqual(installver, correct_installver)
 
-    def test_obtain_easyconfig(self):
+    def xtest_obtain_easyconfig(self):
         """test obtaining an easyconfig file given certain specifications"""
 
         tcname = 'GCC'
@@ -670,7 +670,7 @@ def trim_path(path):
         # cleanup
         shutil.rmtree(self.ec_dir)
 
-    def test_templating(self):
+    def xtest_templating(self):
         """ test easyconfig templating """
         inp = {
            'name': 'PI',
@@ -707,7 +707,7 @@ def test_templating(self):
         eb['description'] = "test easyconfig % %% %s% %%% %(name)s %%(name)s %%%(name)s %%%%(name)s"
         self.assertEqual(eb['description'], "test easyconfig % %% %s% %%% PI %(name)s %PI %%(name)s")
 
-    def test_templating_doc(self):
+    def xtest_templating_doc(self):
         """test templating documentation"""
         doc = easyconfig.templates.template_documentation()
         # expected length: 1 per constant and 1 extra per constantgroup
@@ -720,7 +720,7 @@ def test_templating_doc(self):
                 ]
         self.assertEqual(len(doc.split('\n')), sum([len(temps)] + [len(x) for x in temps]))
 
-    def test_constant_doc(self):
+    def xtest_constant_doc(self):
         """test constant documentation"""
         doc = easyconfig.constants.constant_documentation()
         # expected length: 1 per constant and 1 extra per constantgroup
@@ -729,7 +729,7 @@ def test_constant_doc(self):
                 ]
         self.assertEqual(len(doc.split('\n')), sum([len(temps)] + [len(x) for x in temps]))
 
-    def test_build_options(self):
+    def xtest_build_options(self):
         """Test configure/build/install options, both strings and lists."""
         orig_contents = '\n'.join([
             'name = "pi"',
@@ -798,7 +798,7 @@ def test_build_options(self):
         self.prep()
         eb = EasyConfig(self.eb_file)
 
-    def test_buildininstalldir(self):
+    def xtest_buildininstalldir(self):
         """Test specifying build in install dir."""
         self.contents = '\n'.join([
             'name = "pi"',
@@ -818,7 +818,7 @@ def test_buildininstalldir(self):
         self.assertEqual(eb.builddir, eb.installdir)
         self.assertTrue(os.path.isdir(eb.builddir))
 
-    def test_format_equivalence_basic(self):
+    def xtest_format_equivalence_basic(self):
         """Test whether easyconfigs in different formats are equivalent."""
         # hard enable experimental
         orig_experimental = easybuild.tools.build_log.EXPERIMENTAL
@@ -850,7 +850,7 @@ def test_format_equivalence_basic(self):
         # restore
         easybuild.tools.build_log.EXPERIMENTAL = orig_experimental
 
-    def test_fetch_parameter_from_easyconfig_file(self):
+    def xtest_fetch_parameter_from_easyconfig_file(self):
         """Test fetch_easyblock_from_easyconfig_file function."""
         test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
         toy_ec_file = os.path.join(test_ecs_dir, 'toy-0.0.eb')
@@ -880,9 +880,10 @@ def test_get_easyblock_class(self):
             self.assertEqual(get_easyblock_class(easyblock), easyblock_class)
 
         self.assertEqual(get_easyblock_class(None, name='gzip'), ConfigureMake)
+        self.assertEqual(get_easyblock_class(None, name='gzip', default_fallback=False), None)
         self.assertEqual(get_easyblock_class(None, name='toy'), EB_toy)
 
-    def test_easyconfig_paths(self):
+    def xtest_easyconfig_paths(self):
         """Test create_paths function."""
         cand_paths = create_paths("/some/path", "Foo", "1.2.3")
         expected_paths = [
@@ -893,7 +894,7 @@ def test_easyconfig_paths(self):
         ]
         self.assertEqual(cand_paths, expected_paths)
 
-    def test_deprecated_options(self):
+    def xtest_deprecated_options(self):
         """Test whether deprecated options are handled correctly."""
         deprecated_options = [
             ('makeopts', 'buildopts', 'CC=foo'),
@@ -914,7 +915,7 @@ def test_deprecated_options(self):
             ec = EasyConfig(self.eb_file)
             self.assertEqual(ec[depr_opt], ec[new_opt])
 
-    def test_toolchain_inspection(self):
+    def xtest_toolchain_inspection(self):
         """Test whether available toolchain inspection functionality is working."""
         build_options = {
             'robot_path': os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs'),
@@ -935,7 +936,7 @@ def test_toolchain_inspection(self):
         self.assertEqual(det_toolchain_compilers(ec), None)
         self.assertEqual(det_toolchain_mpi(ec), None)
 
-    def test_filter_deps(self):
+    def xtest_filter_deps(self):
         """Test filtered dependencies."""
         test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
         ec_file = os.path.join(test_ecs_dir, 'goolf-1.4.10.eb')

From 45a4623dcc693f6f2560c0d4a663e49899a587e5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 17:27:05 +0100
Subject: [PATCH 0373/1356] restore class_name

---
 easybuild/framework/easyblock.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index bc26543edd..caf395dea4 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1404,6 +1404,7 @@ def extensions_step(self, fetch=False):
             os.chdir(self.orig_workdir)
 
             cls, inst = None, None
+            class_name = encode_class_name(ext['name'])
 
             # try instantiating extension-specific class
             try:

From 3e40297205f810ab495cbd39fbe36d1aaf9fdb56 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 17:44:00 +0100
Subject: [PATCH 0374/1356] restore mod_path

---
 easybuild/framework/easyblock.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index caf395dea4..4b8da3fc65 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1405,6 +1405,7 @@ def extensions_step(self, fetch=False):
 
             cls, inst = None, None
             class_name = encode_class_name(ext['name'])
+            mod_path = get_module_path(class_name)
 
             # try instantiating extension-specific class
             try:

From a247b8a27a6e7d7ca9b713c4f1738650b4eee7e2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 20:40:11 +0100
Subject: [PATCH 0375/1356] fix setting repositorypath when --prefix is set +
 unit test to check on it

---
 easybuild/tools/options.py | 4 +++-
 test/framework/config.py   | 2 ++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index f6e0004b70..a410d411f5 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -243,7 +243,7 @@ def config_options(self):
                                 "(is passed as list of arguments to create the repository instance). "
                                 "For more info, use --avail-repositories."),
                                 'strlist', 'store',
-                                mk_full_default_path('repositorypath')),
+                                [mk_full_default_path('repositorypath')]),
             'show-default-moduleclasses': ("Show default module classes with description",
                                            None, 'store_true', False),
             'sourcepath': ("Path(s) to where sources should be downloaded (string, colon-separated)",
@@ -417,6 +417,8 @@ def _postprocess_config(self):
                 if not self.options._action_taken.get(dest, False):
                     if dest == 'repository':
                         setattr(self.options, dest, DEFAULT_REPOSITORY)
+                    elif dest == 'repositorypath':
+                        setattr(self.options, dest, [mk_full_default_path(dest, prefix=self.options.prefix)])
                     else:
                         setattr(self.options, dest, mk_full_default_path(dest, prefix=self.options.prefix))
                     # LEGACY this line is here for oldstyle config reasons
diff --git a/test/framework/config.py b/test/framework/config.py
index fb4cdd854b..cf55b25ea1 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -367,6 +367,8 @@ def test_generaloption_config(self):
         options = init_config(args=[])
         self.assertEqual(build_path(), buildpath_env_var)
         self.assertEqual(install_path(), os.path.join(prefix, 'software'))
+        self.assertEqual(get_repositorypath(), [os.path.join(prefix, 'ebfiles_repo')])
+
         del os.environ['EASYBUILD_PREFIX']
         del os.environ['EASYBUILD_BUILDPATH']
 

From 9af552732386d2d199e3b613b6f91faddb8854d5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Dec 2014 20:58:27 +0100
Subject: [PATCH 0376/1356] don't fail on easyblock import attempt for
 extensions

---
 easybuild/framework/easyblock.py             | 4 +++-
 easybuild/framework/easyconfig/easyconfig.py | 7 +++++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 4b8da3fc65..bf6f681673 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1409,7 +1409,9 @@ def extensions_step(self, fetch=False):
 
             # try instantiating extension-specific class
             try:
-                cls = get_easyblock_class(None, name=ext['name'], default_fallback=False)
+                # don't fail when importing class fails, in case we run into an existing easyblock
+                # with a similar name (e.g., Perl Extension 'GO' vs 'Go' for which 'EB_Go' is available)
+                cls = get_easyblock_class(None, name=ext['name'], default_fallback=False, error_on_failed_import=True)
                 self.log.debug("Obtained class %s for extension %s" % (cls, ext['name']))
                 if cls is not None:
                     inst = cls(self, ext)
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 7d2c36eb9d..52b12ccf38 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -728,7 +728,7 @@ def fetch_parameter_from_easyconfig_file(path, param):
         return None
 
 
-def get_easyblock_class(easyblock, name=None, default_fallback=True):
+def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_failed_import=True):
     """
     Get class for a particular easyblock (or use default)
     """
@@ -805,7 +805,10 @@ def get_easyblock_class(easyblock, name=None, default_fallback=True):
                         _log.deprecated(depr_msg, '2.0')
                         cls = get_class_for(def_mod_path, def_class)
                 else:
-                    _log.error("Failed to import easyblock for %s because of module issue: %s" % (class_name, err))
+                    if error_on_failed_import:
+                        _log.error("Failed to import easyblock for %s because of module issue: %s" % (class_name, err))
+                    else:
+                        _log.debug("Failed to import easyblock for %s, but ignoring it: %s" % (class_name, err))
 
         if cls is not None:
             tup = (cls.__name__, easyblock, name)

From 3a85e8d07837d22faaa246162bd66822147143ed Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Dec 2014 09:22:53 +0100
Subject: [PATCH 0377/1356] fix error_on_failed_import on False for
 get_easyblock_class call for extensions

---
 easybuild/framework/easyblock.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index bf6f681673..a8457e82b0 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1409,9 +1409,9 @@ def extensions_step(self, fetch=False):
 
             # try instantiating extension-specific class
             try:
-                # don't fail when importing class fails, in case we run into an existing easyblock
+                # no error when importing class fails, in case we run into an existing easyblock
                 # with a similar name (e.g., Perl Extension 'GO' vs 'Go' for which 'EB_Go' is available)
-                cls = get_easyblock_class(None, name=ext['name'], default_fallback=False, error_on_failed_import=True)
+                cls = get_easyblock_class(None, name=ext['name'], default_fallback=False, error_on_failed_import=False)
                 self.log.debug("Obtained class %s for extension %s" % (cls, ext['name']))
                 if cls is not None:
                     inst = cls(self, ext)

From 5366ea35c3c9625039e875c25870edf0564f73a5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Dec 2014 09:50:16 +0100
Subject: [PATCH 0378/1356] Revert "update with vsc-base for HybridListDict"

This reverts commit 4afe0a9ea101f2af32acf78466b96b67bc0a84ff.
---
 vsc/README.md        |  2 +-
 vsc/utils/wrapper.py | 42 ------------------------------------------
 2 files changed, 1 insertion(+), 43 deletions(-)

diff --git a/vsc/README.md b/vsc/README.md
index 0338b53837..b5efeb45be 100644
--- a/vsc/README.md
+++ b/vsc/README.md
@@ -1,3 +1,3 @@
 Code from https://github.com/hpcugent/vsc-base
 
-based on e114e817ba3003582a805fc70f6203f9cf6062fa (vsc-base v1.9.10)
+based on 2146be5301da34043adf4646169e5dfec88cd2f5 (vsc-base v1.9.9)
diff --git a/vsc/utils/wrapper.py b/vsc/utils/wrapper.py
index b449966c22..537c1f252b 100644
--- a/vsc/utils/wrapper.py
+++ b/vsc/utils/wrapper.py
@@ -40,45 +40,3 @@ def proxy(self, *args):
                     if name.startswith("__"):
                         if name not in ignore and name not in dct:
                             setattr(cls, name, property(make_proxy(name)))
-
-
-class HybridListDict(Wrapper):
-    """
-    Hybrid list/dict object: is a list of 2-element tuples, but also acts like a dict.
-
-    Supported dict-like methods include: update(adict), items(), keys(), values()
-    """
-    __wraps__ = list
-
-    def __getitem__(self, index_key):
-        """Get value by specified index/key."""
-        if isinstance(index_key, int):
-            res = self._obj[index_key]
-        else:
-            res = dict(self._obj)[index_key]
-        return res
-
-    def __setitem__(self, index_key, value):
-        """Add value at specified index/key."""
-        if isinstance(index_key, int):
-            self._obj[index_key] = value
-        else:
-            self._obj = [(k, v) for (k, v) in self._obj if k != index_key]
-            self._obj.append((index_key, value))
-
-    def update(self, extra):
-        """Update with keys/values in supplied dictionary."""
-        self._obj = [(k, v) for (k, v) in self._obj if k not in extra.keys()]
-        self._obj.extend(extra.items())
-
-    def items(self):
-        """Get list of key/value tuples."""
-        return self._obj
-
-    def keys(self):
-        """Get list of keys."""
-        return [x[0] for x in self.items()]
-
-    def values(self):
-        """Get list of values."""
-        return [x[1] for x in self.items()]

From 194b59390c2ccc9d113111d39378a4ff1e4379c4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Dec 2014 09:55:29 +0100
Subject: [PATCH 0379/1356] implement ExtraOptionsDeprecatedReturnValue in
 tools.deprecated.eb_2_0 and use it

---
 easybuild/framework/easyblock.py             |  4 +-
 easybuild/framework/easyconfig/default.py    |  4 +-
 easybuild/framework/easyconfig/easyconfig.py |  6 +-
 easybuild/tools/deprecated/__init__.py       | 38 ++++++++++
 easybuild/tools/deprecated/eb_2_0.py         | 74 ++++++++++++++++++++
 5 files changed, 119 insertions(+), 7 deletions(-)
 create mode 100644 easybuild/tools/deprecated/__init__.py
 create mode 100644 easybuild/tools/deprecated/eb_2_0.py

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index a8457e82b0..4713be9aa3 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -47,7 +47,6 @@
 from distutils.version import LooseVersion
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_class_for
-from vsc.utils.wrapper import HybridListDict
 
 import easybuild.tools.environment as env
 from easybuild.tools import config, filetools
@@ -61,6 +60,7 @@
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
 from easybuild.tools.config import install_path, log_path, read_only_installdir, source_paths
+from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
 from easybuild.tools.environment import restore_env
 from easybuild.tools.filetools import DEFAULT_CHECKSUM
 from easybuild.tools.filetools import adjust_permissions, apply_patch, convert_name, download_file, encode_class_name
@@ -106,7 +106,7 @@ def extra_options(extra=None):
         # to avoid breaking backward compatibility, we still need to return a list of tuples in EasyBuild v1.x
         # starting with EasyBuild v2.0, this will be changed to return the actual dict
         # as a temporary workaround, return a value which is a hybrid between a list and a dict
-        res = HybridListDict(extra.items())
+        res = ExtraOptionsDeprecatedReturnValue(extra.items())
         return res
 
     #
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 8be6e4a4e9..acc99c33eb 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -34,8 +34,8 @@
 @author: Toon Willems (Ghent University)
 """
 from vsc.utils import fancylogger
-from vsc.utils.wrapper import HybridListDict
 
+from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
 from easybuild.tools.ordereddict import OrderedDict
 
 _log = fancylogger.getLogger('easyconfig.default', fname=False)
@@ -195,7 +195,7 @@ def convert_to_help(opts, has_default=False):
     mapping = OrderedDict()
     if isinstance(opts, dict):
         opts = opts.items()
-    elif isinstance(opts, HybridListDict):
+    elif isinstance(opts, ExtraOptionsDeprecatedReturnValue):
         opts = list(opts)
     if not has_default:
         defs = [(k, [def_val, descr, ALL_CATEGORIES[cat]]) for k, (def_val, descr, cat) in DEFAULT_CONFIG.items()]
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 52b12ccf38..103b792c1d 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -42,11 +42,11 @@
 from vsc.utils import fancylogger
 from vsc.utils.missing import any, get_class_for, nub
 from vsc.utils.patterns import Singleton
-from vsc.utils.wrapper import HybridListDict
 
 import easybuild.tools.environment as env
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_module_naming_scheme
+from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
 from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
@@ -164,9 +164,9 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
             self.extra_options = extra_options
 
         if not isinstance(self.extra_options, dict):
-            if isinstance(self.extra_options, (list, tuple, HybridListDict)):
+            if isinstance(self.extra_options, (list, tuple, ExtraOptionsDeprecatedReturnValue)):
                 typ = type(self.extra_options)
-                if not isinstance(self.extra_options, HybridListDict):
+                if not isinstance(self.extra_options, ExtraOptionsDeprecatedReturnValue):
                     self.log.deprecated("extra_options return value should be of type 'dict', found '%s'" % typ, '2.0')
                 tup = (self.extra_options, type(self.extra_options))
                 self.log.debug("Converting extra_options value '%s' of type '%s' to a dict" % tup)
diff --git a/easybuild/tools/deprecated/__init__.py b/easybuild/tools/deprecated/__init__.py
new file mode 100644
index 0000000000..8c26fd6795
--- /dev/null
+++ b/easybuild/tools/deprecated/__init__.py
@@ -0,0 +1,38 @@
+##
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+This declares the namespace for the tools.deprecated submodule of EasyBuild,
+which provides deprecated functionality.
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+"""
+from pkgutil import extend_path
+
+# we're not the only ones in this namespace
+__path__ = extend_path(__path__, __name__)  #@ReservedAssignment
diff --git a/easybuild/tools/deprecated/eb_2_0.py b/easybuild/tools/deprecated/eb_2_0.py
new file mode 100644
index 0000000000..55f43b4af4
--- /dev/null
+++ b/easybuild/tools/deprecated/eb_2_0.py
@@ -0,0 +1,74 @@
+# #
+# Copyright 2014-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Deprecated functionality for EasyBuild v1.x
+
+@author: Kenneth Hoste (Ghent University)
+"""
+from vsc.utils.wrapper import Wrapper
+
+
+class ExtraOptionsDeprecatedReturnValue(Wrapper):
+    """
+    Hybrid list/dict object: is a list (of 2-element tuples), but also acts like a dict.
+
+    Supported dict-like methods include: update(adict), items(), keys(), values()
+
+    Consistency of values being 2-element tuples is *not* checked!
+    """
+    __wraps__ = list
+
+    def __getitem__(self, index_key):
+        """Get value by specified index/key."""
+        if isinstance(index_key, int):
+            res = self._obj[index_key]
+        else:
+            res = dict(self._obj)[index_key]
+        return res
+
+    def __setitem__(self, index_key, value):
+        """Add value at specified index/key."""
+        if isinstance(index_key, int):
+            self._obj[index_key] = value
+        else:
+            self._obj = [(k, v) for (k, v) in self._obj if k != index_key]
+            self._obj.append((index_key, value))
+
+    def update(self, extra):
+        """Update with keys/values in supplied dictionary."""
+        self._obj = [(k, v) for (k, v) in self._obj if k not in extra.keys()]
+        self._obj.extend(extra.items())
+
+    def items(self):
+        """Get list of key/value tuples."""
+        return self._obj
+
+    def keys(self):
+        """Get list of keys."""
+        return [x[0] for x in self.items()]
+
+    def values(self):
+        """Get list of values."""
+        return [x[1] for x in self.items()]

From 77a68a103a356a8ff2693b158236f038e917adb3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Dec 2014 10:00:37 +0100
Subject: [PATCH 0380/1356] add tools.deprecated package to setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 361191c59d..783cce2062 100644
--- a/setup.py
+++ b/setup.py
@@ -71,7 +71,7 @@ def find_rel_test():
 easybuild_packages = [
     "easybuild", "easybuild.framework", "easybuild.framework.easyconfig", "easybuild.framework.easyconfig.format",
     "easybuild.toolchains", "easybuild.toolchains.compiler", "easybuild.toolchains.mpi",
-    "easybuild.toolchains.fft", "easybuild.toolchains.linalg", "easybuild.tools",
+    "easybuild.toolchains.fft", "easybuild.toolchains.linalg", "easybuild.tools", "easybuild.tools.deprecated",
     "easybuild.tools.toolchain", "easybuild.tools.module_naming_scheme", "easybuild.tools.repository",
     "test.framework", "test",
     "vsc", "vsc.utils",

From 10c31dec9d2a70384c1f2b9e43633cdca63eb0e8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Dec 2014 10:20:50 +0100
Subject: [PATCH 0381/1356] reinstate easyconfig unit tests

---
 test/framework/easyconfig.py | 46 ++++++++++++++++++------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index d46eac9d26..278d457db5 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -88,14 +88,14 @@ def tearDown(self):
         if os.path.exists(self.eb_file):
             os.remove(self.eb_file)
 
-    def xtest_empty(self):
+    def test_empty(self):
         """ empty files should not parse! """
         self.contents = "# empty string"
         self.prep()
         self.assertRaises(EasyBuildError, EasyConfig, self.eb_file)
         self.assertErrorRegex(EasyBuildError, "expected a valid path", EasyConfig, "")
 
-    def xtest_mandatory(self):
+    def test_mandatory(self):
         """ make sure all checking of mandatory variables works """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -119,7 +119,7 @@ def xtest_mandatory(self):
         self.assertEqual(eb['toolchain'], {"name":"dummy", "version": "dummy"})
         self.assertEqual(eb['description'], "test easyconfig")
 
-    def xtest_validation(self):
+    def test_validation(self):
         """ test other validations beside mandatory variables """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -151,7 +151,7 @@ def xtest_validation(self):
         self.prep()
         self.assertErrorRegex(EasyBuildError, "SyntaxError", EasyConfig, self.eb_file)
 
-    def xtest_shared_lib_ext(self):
+    def test_shared_lib_ext(self):
         """ inside easyconfigs shared_lib_ext should be set """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -165,7 +165,7 @@ def xtest_shared_lib_ext(self):
         eb = EasyConfig(self.eb_file)
         self.assertEqual(eb['sanity_check_paths']['files'][0], "lib/lib.%s" % get_shared_lib_ext())
 
-    def xtest_dependency(self):
+    def test_dependency(self):
         """ test all possible ways of specifying dependencies """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -211,7 +211,7 @@ def xtest_dependency(self):
         self.assertErrorRegex(EasyBuildError, "without name", eb._parse_dependency, ())
         self.assertErrorRegex(EasyBuildError, "without version", eb._parse_dependency, {'name': 'test'})
 
-    def xtest_extra_options(self):
+    def test_extra_options(self):
         """ extra_options should allow other variables to be stored """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -264,7 +264,7 @@ def xtest_extra_options(self):
 
         self.assertEqual(eb['mandatory_key'], 'value')
 
-    def xtest_exts_list(self):
+    def test_exts_list(self):
         """Test handling of list of extensions."""
         os.environ['EASYBUILD_SOURCEPATH'] = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         init_config()
@@ -295,7 +295,7 @@ def xtest_exts_list(self):
         eb = EasyBlock(ec)
         exts_sources = eb.fetch_extension_sources()
 
-    def xtest_suggestions(self):
+    def test_suggestions(self):
         """ If a typo is present, suggestions should be provided (if possible) """
         self.contents = '\n'.join([
             'name = "pi"',
@@ -314,7 +314,7 @@ def xtest_suggestions(self):
         self.assertErrorRegex(EasyBuildError, "source_URLs -> source_urls", EasyConfig, self.eb_file)
         self.assertErrorRegex(EasyBuildError, "sourceURLs -> source_urls", EasyConfig, self.eb_file)
 
-    def xtest_tweaking(self):
+    def test_tweaking(self):
         """test tweaking ability of easyconfigs"""
 
         fd, tweaked_fn = tempfile.mkstemp(prefix='easybuild-tweaked-', suffix='.eb')
@@ -386,7 +386,7 @@ def xtest_tweaking(self):
         # cleanup
         os.remove(tweaked_fn)
 
-    def xtest_installversion(self):
+    def test_installversion(self):
         """Test generation of install version."""
 
         ver = "3.14"
@@ -416,7 +416,7 @@ def xtest_installversion(self):
         installver = det_full_ec_version(cfg)
         self.assertEqual(installver, correct_installver)
 
-    def xtest_legacy_installversion(self):
+    def test_legacy_installversion(self):
         """Test generation of install version (legacy)."""
 
         ver = "3.14"
@@ -434,7 +434,7 @@ def xtest_legacy_installversion(self):
         installver = det_installversion(ver, dummy, tcver, verpref, versuff)
         self.assertEqual(installver, correct_installver)
 
-    def xtest_obtain_easyconfig(self):
+    def test_obtain_easyconfig(self):
         """test obtaining an easyconfig file given certain specifications"""
 
         tcname = 'GCC'
@@ -670,7 +670,7 @@ def trim_path(path):
         # cleanup
         shutil.rmtree(self.ec_dir)
 
-    def xtest_templating(self):
+    def test_templating(self):
         """ test easyconfig templating """
         inp = {
            'name': 'PI',
@@ -707,7 +707,7 @@ def xtest_templating(self):
         eb['description'] = "test easyconfig % %% %s% %%% %(name)s %%(name)s %%%(name)s %%%%(name)s"
         self.assertEqual(eb['description'], "test easyconfig % %% %s% %%% PI %(name)s %PI %%(name)s")
 
-    def xtest_templating_doc(self):
+    def test_templating_doc(self):
         """test templating documentation"""
         doc = easyconfig.templates.template_documentation()
         # expected length: 1 per constant and 1 extra per constantgroup
@@ -720,7 +720,7 @@ def xtest_templating_doc(self):
                 ]
         self.assertEqual(len(doc.split('\n')), sum([len(temps)] + [len(x) for x in temps]))
 
-    def xtest_constant_doc(self):
+    def test_constant_doc(self):
         """test constant documentation"""
         doc = easyconfig.constants.constant_documentation()
         # expected length: 1 per constant and 1 extra per constantgroup
@@ -729,7 +729,7 @@ def xtest_constant_doc(self):
                 ]
         self.assertEqual(len(doc.split('\n')), sum([len(temps)] + [len(x) for x in temps]))
 
-    def xtest_build_options(self):
+    def test_build_options(self):
         """Test configure/build/install options, both strings and lists."""
         orig_contents = '\n'.join([
             'name = "pi"',
@@ -798,7 +798,7 @@ def xtest_build_options(self):
         self.prep()
         eb = EasyConfig(self.eb_file)
 
-    def xtest_buildininstalldir(self):
+    def test_buildininstalldir(self):
         """Test specifying build in install dir."""
         self.contents = '\n'.join([
             'name = "pi"',
@@ -818,7 +818,7 @@ def xtest_buildininstalldir(self):
         self.assertEqual(eb.builddir, eb.installdir)
         self.assertTrue(os.path.isdir(eb.builddir))
 
-    def xtest_format_equivalence_basic(self):
+    def test_format_equivalence_basic(self):
         """Test whether easyconfigs in different formats are equivalent."""
         # hard enable experimental
         orig_experimental = easybuild.tools.build_log.EXPERIMENTAL
@@ -850,7 +850,7 @@ def xtest_format_equivalence_basic(self):
         # restore
         easybuild.tools.build_log.EXPERIMENTAL = orig_experimental
 
-    def xtest_fetch_parameter_from_easyconfig_file(self):
+    def test_fetch_parameter_from_easyconfig_file(self):
         """Test fetch_easyblock_from_easyconfig_file function."""
         test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
         toy_ec_file = os.path.join(test_ecs_dir, 'toy-0.0.eb')
@@ -883,7 +883,7 @@ def test_get_easyblock_class(self):
         self.assertEqual(get_easyblock_class(None, name='gzip', default_fallback=False), None)
         self.assertEqual(get_easyblock_class(None, name='toy'), EB_toy)
 
-    def xtest_easyconfig_paths(self):
+    def test_easyconfig_paths(self):
         """Test create_paths function."""
         cand_paths = create_paths("/some/path", "Foo", "1.2.3")
         expected_paths = [
@@ -894,7 +894,7 @@ def xtest_easyconfig_paths(self):
         ]
         self.assertEqual(cand_paths, expected_paths)
 
-    def xtest_deprecated_options(self):
+    def test_deprecated_options(self):
         """Test whether deprecated options are handled correctly."""
         deprecated_options = [
             ('makeopts', 'buildopts', 'CC=foo'),
@@ -915,7 +915,7 @@ def xtest_deprecated_options(self):
             ec = EasyConfig(self.eb_file)
             self.assertEqual(ec[depr_opt], ec[new_opt])
 
-    def xtest_toolchain_inspection(self):
+    def test_toolchain_inspection(self):
         """Test whether available toolchain inspection functionality is working."""
         build_options = {
             'robot_path': os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs'),
@@ -936,7 +936,7 @@ def xtest_toolchain_inspection(self):
         self.assertEqual(det_toolchain_compilers(ec), None)
         self.assertEqual(det_toolchain_mpi(ec), None)
 
-    def xtest_filter_deps(self):
+    def test_filter_deps(self):
         """Test filtered dependencies."""
         test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
         ec_file = os.path.join(test_ecs_dir, 'goolf-1.4.10.eb')

From b2e8c8ea6936ff0d78856c992c9279c7597444d1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Dec 2014 10:34:53 +0100
Subject: [PATCH 0382/1356] specify output dir for job output via --testoutput

---
 easybuild/tools/parallelbuild.py | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index c3ca5b782e..ac1d5e2f59 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -135,7 +135,7 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
 
     quoted_opts = subprocess.list2cmdline(opts)
 
-    command = "unset TMPDIR && cd %s && eb %%(spec)s %s" % (curdir, quoted_opts)
+    command = "unset TMPDIR && cd %s && eb %%(spec)s %s --testoutput=%%(output_dir)s" % (curdir, quoted_opts)
     _log.info("Command template for jobs: %s" % command)
     job_info_lines = []
     if testing:
@@ -153,7 +153,7 @@ def create_job(build_command, easyconfig, output_dir=None, conn=None, ppn=None):
     Creates a job, to build a *single* easyconfig
     @param build_command: format string for command, full path to an easyconfig file will be substituted in it
     @param easyconfig: easyconfig as processed by process_easyconfig
-    @param output_dir: optional output path; $EASYBUILDTESTOUTPUT will be set inside the job with this variable
+    @param output_dir: optional output path; --regtest-output-dir will be used inside the job with this variable
     @param conn: open connection to PBS server
     @param ppn: ppn setting to use (# 'processors' (cores) per node to use)
     returns the job
@@ -161,9 +161,6 @@ def create_job(build_command, easyconfig, output_dir=None, conn=None, ppn=None):
     if output_dir is None:
         output_dir = 'easybuild-build'
 
-    # create command based on build_command template
-    command = build_command % {'spec': easyconfig['spec']}
-
     # capture PYTHONPATH, MODULEPATH and all variables starting with EASYBUILD
     easybuild_vars = {}
     for name in os.environ:
@@ -182,9 +179,11 @@ def create_job(build_command, easyconfig, output_dir=None, conn=None, ppn=None):
     ec_tuple = (easyconfig['ec']['name'], det_full_ec_version(easyconfig['ec']))
     name = '-'.join(ec_tuple)
 
-    regtest_output_dir_var = 'EASYBUILD_REGTEST_OUTPUT_DIR'
-    if not regtest_output_dir_var in easybuild_vars:
-        easybuild_vars[regtest_output_dir_var] = os.path.join(os.path.abspath(output_dir), name)
+    # create command based on build_command template
+    command = build_command % {
+        'spec': easyconfig['spec'],
+        'output_dir': os.path.join(os.path.abspath(output_dir), name),
+    }
 
     # just use latest build stats
     repo = init_repository(get_repository(), get_repositorypath())

From bac1573091ed2b247537ab0d9282b3733247a6ec Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Dec 2014 10:55:36 +0100
Subject: [PATCH 0383/1356] extend get_easyblock_class tests

---
 test/framework/easyconfig.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 278d457db5..2e6de7ee1a 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -882,6 +882,8 @@ def test_get_easyblock_class(self):
         self.assertEqual(get_easyblock_class(None, name='gzip'), ConfigureMake)
         self.assertEqual(get_easyblock_class(None, name='gzip', default_fallback=False), None)
         self.assertEqual(get_easyblock_class(None, name='toy'), EB_toy)
+        self.assertErrorRegex(EasyBuildError, "Failed to import EB_TOY", get_easyblock_class, None, name='TOY')
+        self.assertEqual(get_easyblock_class(None, name='TOY', error_on_failed_import=False), None)
 
     def test_easyconfig_paths(self):
         """Test create_paths function."""

From 20ef28e8d9f1bcf3ca755841bf490cbc31e16925 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Dec 2014 11:28:34 +0100
Subject: [PATCH 0384/1356] also specify --testoutput for regtest jobs

---
 easybuild/tools/testing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index 695577fd05..8d283e0799 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -119,7 +119,7 @@ def regtest(easyconfig_paths, build_specs=None):
     else:
         resolved = resolve_dependencies(easyconfigs, build_specs=build_specs)
 
-        cmd = "eb %(spec)s --regtest --sequential -ld"
+        cmd = "eb %(spec)s --regtest --sequential -ld --testoutput=%%(output_dir)s"
         command = "unset TMPDIR && cd %s && %s; " % (cur_dir, cmd)
         # retry twice in case of failure, to avoid fluke errors
         command += "if [ $? -ne 0 ]; then %(cmd)s --force && %(cmd)s --force; fi" % {'cmd': cmd}

From a9cf70115a12888733ecc285f9af4372e4236d95 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Dec 2014 11:36:02 +0100
Subject: [PATCH 0385/1356] fix typo

---
 easybuild/tools/testing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index 8d283e0799..8bebbf3612 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -119,7 +119,7 @@ def regtest(easyconfig_paths, build_specs=None):
     else:
         resolved = resolve_dependencies(easyconfigs, build_specs=build_specs)
 
-        cmd = "eb %(spec)s --regtest --sequential -ld --testoutput=%%(output_dir)s"
+        cmd = "eb %(spec)s --regtest --sequential -ld --testoutput=%(output_dir)s"
         command = "unset TMPDIR && cd %s && %s; " % (cur_dir, cmd)
         # retry twice in case of failure, to avoid fluke errors
         command += "if [ $? -ne 0 ]; then %(cmd)s --force && %(cmd)s --force; fi" % {'cmd': cmd}

From 1511923d07616d9d3010787b434a84067c376868 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 17 Dec 2014 14:34:46 +0100
Subject: [PATCH 0386/1356] only issue deprecation warning for non-dict and
 non-ExtraOptionsDeprecatedReturnValue values in extra_options

---
 easybuild/framework/easyblock.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 4713be9aa3..84127c3dbc 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -99,7 +99,8 @@ def extra_options(extra=None):
 
         if not isinstance(extra, dict):
             typ = type(extra)
-            _log.deprecated("Obtained 'extra' value of type '%s' in extra_options, should be 'dict'" % typ, '2.0')
+            if not isinstance(extra, ExtraOptionsDeprecatedReturnValue):
+                _log.deprecated("Obtained 'extra' value of type '%s' in extra_options, should be 'dict'" % typ, '2.0')
             _log.debug("Converting extra_options value '%s' of type '%s' to a dict" % (extra, typ))
             extra = dict(extra)
 

From d61cc262018c463d417edb7de66c7af6eb633bb9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 17 Dec 2014 14:37:37 +0100
Subject: [PATCH 0387/1356] verbose warning on log.deprecated

---
 easybuild/tools/build_log.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index b447090e0e..52f35bd0d6 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -99,6 +99,7 @@ def experimental(self, msg, *args, **kwargs):
     def deprecated(self, msg, max_ver):
         """Print deprecation warning or raise an EasyBuildError, depending on max version allowed."""
         msg += "; see %s for more information" % DEPRECATED_DOC_URL
+        print_warning("Deprecated functionality, will no longer work in v%s: %s" % (max_ver, msg))
         fancylogger.FancyLogger.deprecated(self, msg, str(CURRENT_VERSION), max_ver, exception=EasyBuildError)
 
     def error(self, msg, *args, **kwargs):

From 86249343c2b2364c547a8ca8acbb6e9f7df53b49 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 17 Dec 2014 14:55:53 +0100
Subject: [PATCH 0388/1356] Revert "verbose warning on log.deprecated"

This reverts commit d61cc262018c463d417edb7de66c7af6eb633bb9.
---
 easybuild/tools/build_log.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index 52f35bd0d6..b447090e0e 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -99,7 +99,6 @@ def experimental(self, msg, *args, **kwargs):
     def deprecated(self, msg, max_ver):
         """Print deprecation warning or raise an EasyBuildError, depending on max version allowed."""
         msg += "; see %s for more information" % DEPRECATED_DOC_URL
-        print_warning("Deprecated functionality, will no longer work in v%s: %s" % (max_ver, msg))
         fancylogger.FancyLogger.deprecated(self, msg, str(CURRENT_VERSION), max_ver, exception=EasyBuildError)
 
     def error(self, msg, *args, **kwargs):

From 3cf79953b0028e85e616629afb412f2105c4049a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 08:42:47 +0100
Subject: [PATCH 0389/1356] bump version to 1.16.0 and update release notes

---
 RELEASE_NOTES              | 48 ++++++++++++++++++++++++++++++++++++++
 easybuild/tools/version.py |  2 +-
 2 files changed, 49 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index fe1835fc19..604a153609 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -1,6 +1,54 @@
 This file contains a description of the major changes to the easybuild-framework EasyBuild package.
 For more detailed information, please see the git log.
 
+These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
+
+v1.16.0 (December 18th 2014)
+----------------------------
+
+feature + bugfix release
+- deprecate automagic fallback to ConfigureMake easyblock (#1113)
+    - easyconfigs should specify easyblock = 'ConfigureMake' instead of relying on the fallback mechanism
+    - note: automagic fallback to ConfigureMake easyblock will be dropped in EasyBuild v2.0
+    - see also http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#configuremake-fallback
+- stop triggering deprecated functionality, to enable use of --deprecated=2.0 (#1107, #1115)
+    - see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#configuremake-fallback for more information
+- various other enhancements, including:
+    - add script to clean up gists created via --upload-test-report (#958)
+    - also use -xHost when using Intel compilers on AMD systems (as opposed to -msse3) (#960)
+    - add Python version check in eb command (#1046)
+    - take versionprefix into account in HierarchicalMNS module naming scheme (#1058)
+    - clean up and refactor main.py, move functionality to other modules (#1059, #1064, #1075, #1087)
+    - add check in download_file function for HTTP return code + show download progress report (#1066, #1090)
+    - include info log message with name and location of used easyblock (#1069)
+    - add toolchains definitions for gpsmpi, gpsolf, impich, intel-para, ipsmpi toolchains (#1072, #1073)
+        - support for Parastation MPI based toolchains
+    - enforce that hiddendependencies is a subset of dependencies (#1078)
+        - this is done to avoid that site-specific policies w.r.t. hidden modules slip into contributed easyconfigs
+    - enable use of --show_hidden for avail subcommand with recent Lmod versions (#1081)
+    - add --robot-paths configure option (#1080, #1093, #1095, #1114)
+    - support use of %(DEFAULT_ROBOT_PATHS)s template in EasyBuild configuration files (#1100)
+        - see also http://easybuild.readthedocs.org/en/latest/Using_the_EasyBuild_command_line.html#controlling-the-robot-search-path
+    - use -xHost rather than -xHOST, to match Intel documentation (#1084)
+    - update and cleanup README file (#1085)
+    - deprecate self.moduleGenerator in favor of self.module_generator in EasyBlock (#1088)
+    - also support MPICH MPI family in mpi_cmd_for function (#1098)
+    - update documentation references to point to http://easybuild.readthedocs.org (#1102)
+    - check for OS dependencies with both rpm and dpkg (if available) (#1111)
+- various bug fixes, including:
+    - fix picking required software version specified by --software-version and clean up tweak.py (#1062, #1063)
+    - escape $ characters in module load message specified via modloadmsg easyconfig parameter) (#1068)
+    - take available hidden modules into account in dependency resolution (#1065)
+    - fix hard crash when using patch files with an empty list of sources (#1070)
+    - fix Intel MKL BLACS library being used for MPICH/MPICH2-based toolchains (#1072)
+    - fix regular expression in fetch_parameter_from_easyconfig_file function (#1096)
+    - don’t hardcode queue names when submitting a job (#1106)
+    - fix affiliation/mail address for Fotis in headers (#1105)
+    - filter out /dev/null entries in patch file in det_patched_files function (#1108)
+    - fix gmpolf toolchain definition, to have gmpich as MPI components (instead of gmpich2) (#1101)
+        - ‘MPICH’ refers to MPICH v3.x, while MPICH2 refers to MPICH(2) v2.x (MPICH v1.x is ancient/obsolete)
+        - note: this requires to reinstall the gmpolf module, using the updated easyconfig from easybuild-easyconfigs#1217
+
 v1.15.2 (October 7th 2014)
 --------------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index f527eaecee..4ed5f0086d 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.16.0dev")
+VERSION = LooseVersion("1.16.0")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From b7c5c3fe2147a8c617ee572dddc2cb72f8f7479f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 09:23:35 +0100
Subject: [PATCH 0390/1356] bump version to 1.16.1dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 4ed5f0086d..e47bcb41ec 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.16.0")
+VERSION = LooseVersion("1.16.1dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From fe70342c3c934a92d302523fb31b2ce23f2a24f7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 09:24:13 +0100
Subject: [PATCH 0391/1356] bump version to 2.0.0dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index e47bcb41ec..1bd1419af5 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.16.1dev")
+VERSION = LooseVersion("2.0.0dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 82e4e7a5654f3767936de8a0a24c29bea83145d2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 10:37:31 +0100
Subject: [PATCH 0392/1356] only trip deprecation if extensions filter still
 relies on 'name'/'version' keys

---
 easybuild/framework/easyblock.py | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 84127c3dbc..2d77b4eccb 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1067,14 +1067,18 @@ def skip_extensions(self):
                 'src': ext.get('source'),
             }
 
-            deprecated_msg = "Providing 'name' and 'version' keys for extensions, should use 'ext_name', 'ext_version'"
-            self.log.deprecated(deprecated_msg, '2.0')
-            tmpldict.update({
-                'name': modname,
-                'version': ext.get('version'),
-            })
-
-            cmd = cmdtmpl % tmpldict
+            try:
+                cmd = cmdtmpl % tmpldict
+            except KeyError, err:
+                self.log.warning("Failed to complete filter command template '%s' with %s: %s" % (cmdtmpl, tmpldict, err))
+                deprecated_msg = "Providing 'name' and 'version' keys for extensions, should use 'ext_name', 'ext_version'"
+                self.log.deprecated(deprecated_msg, '2.0')
+                tmpldict.update({
+                    'name': modname,
+                    'version': ext.get('version'),
+                })
+                cmd = cmdtmpl % tmpldict
+
             if cmdinputtmpl:
                 stdin = cmdinputtmpl % tmpldict
                 (cmdstdouterr, ec) = run_cmd(cmd, log_all=False, log_ok=False, simple=False, inp=stdin, regexp=False)

From b6721086f2dc93185ce4878dc3e1e467d89edc2e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 10:40:39 +0100
Subject: [PATCH 0393/1356] add #1119 to release notes

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 604a153609..3f94327924 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -11,7 +11,7 @@ feature + bugfix release
     - easyconfigs should specify easyblock = 'ConfigureMake' instead of relying on the fallback mechanism
     - note: automagic fallback to ConfigureMake easyblock will be dropped in EasyBuild v2.0
     - see also http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#configuremake-fallback
-- stop triggering deprecated functionality, to enable use of --deprecated=2.0 (#1107, #1115)
+- stop triggering deprecated functionality, to enable use of --deprecated=2.0 (#1107, #1115, #1119)
     - see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#configuremake-fallback for more information
 - various other enhancements, including:
     - add script to clean up gists created via --upload-test-report (#958)

From 8064076bc8340eb958051ae13791cb46eee40cc8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 10:53:06 +0100
Subject: [PATCH 0394/1356] fix remark + long lines

---
 easybuild/framework/easyblock.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 2d77b4eccb..ba37110e6b 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1070,13 +1070,14 @@ def skip_extensions(self):
             try:
                 cmd = cmdtmpl % tmpldict
             except KeyError, err:
-                self.log.warning("Failed to complete filter command template '%s' with %s: %s" % (cmdtmpl, tmpldict, err))
-                deprecated_msg = "Providing 'name' and 'version' keys for extensions, should use 'ext_name', 'ext_version'"
+                self.log.warning("Failed to complete filter cmd templ '%s' using %s: %s" % (cmdtmpl, tmpldict, err))
+                deprecated_msg = "Providing 'name'/'version' keys for extensions, should use 'ext_name', 'ext_version'"
                 self.log.deprecated(deprecated_msg, '2.0')
                 tmpldict.update({
                     'name': modname,
                     'version': ext.get('version'),
                 })
+                self.log.debug("Retrying to complete filter cmd templ with added name/version keys: %s" % tmpldict)
                 cmd = cmdtmpl % tmpldict
 
             if cmdinputtmpl:

From 5a5fef138f9994f844e450ac2c4e200164b2bf6a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 11:16:46 +0100
Subject: [PATCH 0395/1356] sync with vsc-base 2.0.0

---
 vsc/README.md              | 2 +-
 vsc/utils/generaloption.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/vsc/README.md b/vsc/README.md
index b5efeb45be..165e0109fb 100644
--- a/vsc/README.md
+++ b/vsc/README.md
@@ -1,3 +1,3 @@
 Code from https://github.com/hpcugent/vsc-base
 
-based on 2146be5301da34043adf4646169e5dfec88cd2f5 (vsc-base v1.9.9)
+based on eb47bee435e5e24666b398d8dd41f82a40214b7a (vsc-base v2.0.0)
diff --git a/vsc/utils/generaloption.py b/vsc/utils/generaloption.py
index e4548dc668..af6d6397c0 100644
--- a/vsc/utils/generaloption.py
+++ b/vsc/utils/generaloption.py
@@ -1,6 +1,6 @@
 #
 #
-# Copyright 2011-2013 Ghent University
+# Copyright 2011-2014 Ghent University
 #
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -708,7 +708,7 @@ def __init__(self, **kwargs):
         go_args = kwargs.pop('go_args', None)
         self.no_system_exit = kwargs.pop('go_nosystemexit', None)  # unit test option
         self.use_configfiles = kwargs.pop('go_useconfigfiles', self.CONFIGFILES_USE)  # use or ignore config files
-        self.configfiles = kwargs.pop('go_configfiles', self.CONFIGFILES_INIT)  # configfiles to parse
+        self.configfiles = kwargs.pop('go_configfiles', self.CONFIGFILES_INIT[:])  # configfiles to parse
         configfiles_initenv = kwargs.pop('go_configfiles_initenv', None)  # initial environment for configfiles to parse
         prefixloggername = kwargs.pop('go_prefixloggername', False)  # name of logger is same as envvar prefix
         mainbeforedefault = kwargs.pop('go_mainbeforedefault', False)  # Set the main options before the default ones

From 876f21e69103fa7b08415bef4ede0b57afec1b32 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 11:17:16 +0100
Subject: [PATCH 0396/1356] clean up log file after running test

---
 test/framework/utilities.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index e34cb37ae5..e9c84d1e9e 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -131,9 +131,13 @@ def tearDown(self):
         # restore original Python search path
         sys.path = self.orig_sys_path
 
-        for path in [self.test_buildpath, self.test_installpath, self.test_prefix]:
+        # cleanup
+        for path in [self.logfile, self.test_buildpath, self.test_installpath, self.test_prefix]:
             try:
-                shutil.rmtree(path)
+                if os.path.isdir(path):
+                    shutil.rmtree(path)
+                else:
+                    os.remove(path)
             except OSError, err:
                 pass
 

From 10db9e0f30955e4fb43728878f1c3f833e1b5899 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 11:34:40 +0100
Subject: [PATCH 0397/1356] fix version to v1.16.0

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 1bd1419af5..4ed5f0086d 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("2.0.0dev")
+VERSION = LooseVersion("1.16.0")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 1f54e6ffb1db003bc93a67325dda14ea964cd439 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 12:13:21 +0100
Subject: [PATCH 0398/1356] bump version to 1.6.1dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 4ed5f0086d..e47bcb41ec 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.16.0")
+VERSION = LooseVersion("1.16.1dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 353565771b5025d7464458302c11cd071f7bd6cd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Dec 2014 12:13:43 +0100
Subject: [PATCH 0399/1356] bump version to 2.0.0dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index e47bcb41ec..1bd1419af5 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.16.1dev")
+VERSION = LooseVersion("2.0.0dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 49b80ff5c22ebec24c2846d7da24c9db2fca6048 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 09:22:58 +0100
Subject: [PATCH 0400/1356] don't include ConfigureMake-specific parameters in
 'eb -a' output, since fallback is deprecated

---
 easybuild/tools/options.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index a410d411f5..c0ab4c3577 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -508,10 +508,14 @@ def avail_easyconfig_params(self):
         """
         Print the available easyconfig parameters, for the given easyblock.
         """
-        app = get_easyblock_class(self.options.easyblock)
-        extra = app.extra_options()
+        extra = []
+        app = get_easyblock_class(self.options.easyblock, default_fallback=False)
+        if app is None:
+            extra = []
+        else:
+            extra = app.extra_options()
         mapping = convert_to_help(extra, has_default=False)
-        if len(extra) > 0:
+        if extra:
             ebb_msg = " (* indicates specific for the %s EasyBlock)" % app.__name__
             extra_names = [x[0] for x in extra]
         else:

From 4469dbe9dcf47ba2f665c81941b6bc76fb45d79a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 09:35:52 +0100
Subject: [PATCH 0401/1356] enhance unit tests for 'eb -a'

---
 test/framework/options.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 77694b83dd..9565b1d97c 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -382,6 +382,7 @@ def run_test(custom=None, extra_params=[]):
             if os.path.exists(dummylogfn):
                 os.remove(dummylogfn)
 
+        run_test()
         run_test(custom='EB_foo', extra_params=['foo_extra1', 'foo_extra2'])
         run_test(custom='bar', extra_params=['bar_extra1', 'bar_extra2'])
         run_test(custom='EB_foofoo', extra_params=['foofoo_extra1', 'foofoo_extra2'])

From 63734d4431550e813a630f3060f7e77fe77f1d1b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 09:44:10 +0100
Subject: [PATCH 0402/1356] style cleanup in avail_easyconfig_params

---
 easybuild/tools/options.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index c0ab4c3577..59a3503116 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -510,9 +510,7 @@ def avail_easyconfig_params(self):
         """
         extra = []
         app = get_easyblock_class(self.options.easyblock, default_fallback=False)
-        if app is None:
-            extra = []
-        else:
+        if app is not None:
             extra = app.extra_options()
         mapping = convert_to_help(extra, has_default=False)
         if extra:

From 763dce11ba002c8789c6e33e6438790678191a16 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 10:34:48 +0100
Subject: [PATCH 0403/1356] correctly check software_license value type

---
 easybuild/framework/easyconfig/easyconfig.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 103b792c1d..9a9936265b 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -99,13 +99,13 @@ def new_ec_method(self, key, *args, **kwargs):
         # make sure that value for software_license has correct type, convert if needed
         if key == 'software_license':
             # key 'license' will already be mapped to 'software_license' above
-            lic = self._config['software_license']
-            if not isinstance(lic, License):
+            lic = self._config['software_license'][0]
+            if lic is not None and not isinstance(lic, License):
                 self.log.deprecated('Type for software_license must to be instance of License (sub)class', '2.0')
                 lic_type = type(lic)
 
                 class LicenseLegacy(License, lic_type):
-                    """A special License class to deal with legacy license paramters"""
+                    """A special License class to deal with legacy license parameters"""
                     DESCRICPTION = ("Internal-only, legacy closed license class to deprecate license parameter."
                                     " (DO NOT USE).")
                     HIDDEN = False

From d9d867b450269e716b014e13e0c4bb5336226f1e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 11:23:05 +0100
Subject: [PATCH 0404/1356] stop triggering deprecated behavior in tests,
 unless intended

---
 test/framework/config.py                      |  18 ++-
 test/framework/easyblock.py                   |  15 +-
 test/framework/easyconfig.py                  | 145 ++++++++++++------
 .../easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb      |   1 +
 .../easyconfigs/FFTW-3.3.3-gompi-1.4.10.eb    |   2 +
 test/framework/easyconfigs/GCC-4.6.3.eb       |   2 +
 test/framework/easyconfigs/GCC-4.6.4.eb       |   2 +
 test/framework/easyconfigs/GCC-4.7.2.eb       |   2 +
 test/framework/easyconfigs/GCC-4.8.2.eb       |   2 +
 test/framework/easyconfigs/GCC-4.8.3.eb       |   3 +
 ...penBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb |   4 +-
 .../easyconfigs/OpenMPI-1.6.4-GCC-4.6.4.eb    |   4 +-
 .../easyconfigs/OpenMPI-1.6.4-GCC-4.7.2.eb    |   4 +-
 ...ompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb |   2 +
 .../easyconfigs/gzip-1.4-GCC-4.6.3.eb         |   1 +
 test/framework/easyconfigs/gzip-1.4.eb        |   1 +
 .../easyconfigs/gzip-1.5-goolf-1.4.10.eb      |   1 +
 .../easyconfigs/gzip-1.5-ictce-4.1.13.eb      |   1 +
 .../easyconfigs/hwloc-1.6.2-GCC-4.6.4.eb      |   2 +
 .../easyconfigs/hwloc-1.6.2-GCC-4.7.2.eb      |   2 +
 .../easyconfigs/icc-2013.5.192-GCC-4.8.3.eb   |   3 +
 .../framework/easyconfigs/ifort-2013.3.163.eb |   2 +
 .../easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb |   3 +
 .../imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb  |   3 +
 ...4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb |   3 +
 test/framework/easyconfigs/impi-4.1.3.049.eb  |   2 +
 test/framework/easyconfigs/v1.0/GCC-4.6.3.eb  |   2 +
 .../easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb    |   1 +
 test/framework/easyconfigs/v1.0/gzip-1.4.eb   |   1 +
 .../easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb |   1 +
 .../easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb |   1 +
 test/framework/easyconfigs/v2.0/GCC.eb        |   2 +
 .../easyconfigs/v2.0/doesnotexist.eb          |   1 +
 test/framework/easyconfigs/v2.0/gzip.eb       |   1 +
 test/framework/easyconfigs/v2.0/libpng.eb     |   1 +
 test/framework/filetools.py                   |  11 --
 test/framework/modules.py                     |   2 +
 test/framework/options.py                     |  79 ++++++----
 .../easybuild/easyblocks/generic/bar.py       |   9 +-
 .../easyblocks/generic/dummyextension.py      |  34 ++++
 .../sandbox/easybuild/easyblocks/toy.py       |   7 +-
 test/framework/systemtools.py                 |  18 ++-
 test/framework/utilities.py                   |   5 +
 43 files changed, 293 insertions(+), 113 deletions(-)
 create mode 100644 test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py

diff --git a/test/framework/config.py b/test/framework/config.py
index cf55b25ea1..5e433d1259 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -110,6 +110,10 @@ def test_default_config(self):
 
     def test_generaloption_overrides_legacy(self):
         """Test whether generaloption overrides legacy configuration."""
+        # lower 'current' version to avoid tripping over deprecation errors
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
+
         self.purge_environment()
         # if both legacy and generaloption style configuration is mixed, generaloption wins
         legacy_prefix = os.path.join(self.tmpdir, 'legacy')
@@ -140,6 +144,10 @@ def test_generaloption_overrides_legacy(self):
 
     def test_legacy_env_vars(self):
         """Test legacy environment variables."""
+        # lower 'current' version to avoid tripping over deprecation errors
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
+
         self.purge_environment()
 
         # build path
@@ -243,6 +251,10 @@ def test_legacy_env_vars(self):
 
     def test_legacy_config_file(self):
         """Test finding/using legacy configuration files."""
+        # lower 'current' version to avoid tripping over deprecation errors
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
+
         self.purge_environment()
 
         cfg_fn = self.configure(args=[])
@@ -381,7 +393,7 @@ def test_generaloption_config(self):
         write_file(config_file, '')
 
         args = [
-            '--config', config_file,  # force empty oldstyle config file
+            '--configfiles', config_file,  # force empty config file
             '--prefix', prefix,
             '--installpath', install,
             '--repositorypath', repopath,
@@ -394,14 +406,14 @@ def test_generaloption_config(self):
         self.assertEqual(install_path(typ='mod'), os.path.join(install, 'modules'))
 
         self.assertEqual(options.installpath, install)
-        self.assertEqual(options.config, config_file)
+        self.assertTrue(config_file in options.configfiles)
 
         # check mixed command line/env var configuration
         prefix = os.path.join(self.tmpdir, 'test3')
         install = os.path.join(self.tmpdir, 'test4', 'install')
         subdir_software = 'eb-soft'
         args = [
-            '--config', config_file,  # force empty oldstyle config file
+            '--configfiles', config_file,  # force empty config file
             '--installpath', install,
         ]
 
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index d583397e12..976c781c9a 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -100,6 +100,7 @@ def check_extra_options_format(extra_options):
         name = "pi"
         version = "3.14"
         self.contents =  '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "%s"' % name,
             'version = "%s"' % version,
             'homepage = "http://example.com"',
@@ -143,7 +144,7 @@ def check_extra_options_format(extra_options):
         class TestExtension(ExtensionEasyBlock):
             @staticmethod
             def extra_options():
-                return ExtensionEasyBlock.extra_options([('extra_param', [None, "help", CUSTOM])])
+                return ExtensionEasyBlock.extra_options({'extra_param': [None, "help", CUSTOM]})
         texeb = TestExtension(eb, {'name': 'bar'})
         self.assertEqual(texeb.cfg['name'], 'bar')
         extra_options = texeb.extra_options()
@@ -158,6 +159,7 @@ def extra_options():
     def test_fake_module_load(self):
         """Testcase for fake module load"""
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -177,6 +179,7 @@ def test_fake_module_load(self):
     def test_make_module_req(self):
         """Testcase for make_module_req"""
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -212,6 +215,7 @@ def test_make_module_req(self):
     def test_extensions_step(self):
         """Test the extensions_step"""
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -228,7 +232,7 @@ def test_extensions_step(self):
         self.assertErrorRegex(EasyBuildError, "No default extension class set", eb.extensions_step, fetch=True)
 
         # test if everything works fine if set
-        self.contents += "\nexts_defaultclass = ['easybuild.framework.extension', 'Extension']"
+        self.contents += "\nexts_defaultclass = 'DummyExtension'"
         self.writeEC()
         eb = EasyBlock(EasyConfig(self.eb_file))
         eb.builddir = config.build_path()
@@ -246,14 +250,15 @@ def test_extensions_step(self):
     def test_skip_extensions_step(self):
         """Test the skip_extensions_step"""
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
             'description = "test easyconfig"',
             'toolchain = {"name": "dummy", "version": "dummy"}',
             'exts_list = ["ext1", "ext2"]',
-            'exts_filter = ("if [ %(name)s == \'ext2\' ]; then exit 0; else exit 1; fi", "")',
-            'exts_defaultclass = ["easybuild.framework.extension", "Extension"]',
+            'exts_filter = ("if [ %(ext_name)s == \'ext2\' ]; then exit 0; else exit 1; fi", "")',
+            'exts_defaultclass = "DummyExtension"',
         ])
         # check if skip skips correct extensions
         self.writeEC()
@@ -282,6 +287,7 @@ def test_make_module_step(self):
         modextravars = {'PI': '3.1415', 'FOO': 'bar'}
         modextrapaths = {'PATH': 'pibin', 'CPATH': 'pi/include'}
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "%s"' % name,
             'version = "%s"' % version,
             'homepage = "http://example.com"',
@@ -333,6 +339,7 @@ def test_make_module_step(self):
     def test_gen_dirs(self):
         """Test methods that generate/set build/install directory names."""
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             "name = 'pi'",
             "version = '3.14'",
             "homepage = 'http://example.com'",
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 2e6de7ee1a..3a97e400b4 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -98,6 +98,7 @@ def test_empty(self):
     def test_mandatory(self):
         """ make sure all checking of mandatory variables works """
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
         ])
@@ -122,6 +123,7 @@ def test_mandatory(self):
     def test_validation(self):
         """ test other validations beside mandatory variables """
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -151,9 +153,13 @@ def test_validation(self):
         self.prep()
         self.assertErrorRegex(EasyBuildError, "SyntaxError", EasyConfig, self.eb_file)
 
-    def test_shared_lib_ext(self):
+    def test_deprecated_shared_lib_ext(self):
         """ inside easyconfigs shared_lib_ext should be set """
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
+
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -165,9 +171,25 @@ def test_shared_lib_ext(self):
         eb = EasyConfig(self.eb_file)
         self.assertEqual(eb['sanity_check_paths']['files'][0], "lib/lib.%s" % get_shared_lib_ext())
 
+    def test_SHLIB_EXT(self):
+        """ inside easyconfigs shared_lib_ext should be set """
+        self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
+            'name = "pi"',
+            'version = "3.14"',
+            'homepage = "http://example.com"',
+            'description = "test easyconfig"',
+            'toolchain = {"name":"dummy", "version": "dummy"}',
+            'sanity_check_paths = { "files": ["lib/lib.%s" % SHLIB_EXT] }',
+        ])
+        self.prep()
+        eb = EasyConfig(self.eb_file)
+        self.assertEqual(eb['sanity_check_paths']['files'][0], "lib/lib.%s" % get_shared_lib_ext())
+
     def test_dependency(self):
         """ test all possible ways of specifying dependencies """
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -214,6 +236,7 @@ def test_dependency(self):
     def test_extra_options(self):
         """ extra_options should allow other variables to be stored """
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -247,13 +270,8 @@ def test_extra_options(self):
         # test if extra toolchain options are being passed
         self.assertEqual(eb.toolchain.options['static'], True)
 
-        # test legacy behavior of passing a list of tuples rather than a dict
-        eb = EasyConfig(self.eb_file, extra_options=extra_vars.items())
-        self.assertEqual(eb['custom_key'], 'test')
-
-        extra_vars.update({'mandatory_key': ['default', 'another mandatory key', easyconfig.MANDATORY]})
-
         # test extra mandatory vars
+        extra_vars.update({'mandatory_key': ['default', 'another mandatory key', easyconfig.MANDATORY]})
         self.assertErrorRegex(EasyBuildError, r"mandatory variables? \S* not provided",
                               EasyConfig, self.eb_file, extra_vars)
 
@@ -264,11 +282,18 @@ def test_extra_options(self):
 
         self.assertEqual(eb['mandatory_key'], 'value')
 
+        # test legacy behavior of passing a list of tuples rather than a dict
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
+        eb = EasyConfig(self.eb_file, extra_options=extra_vars.items())
+        self.assertEqual(eb['custom_key'], 'test')
+
     def test_exts_list(self):
         """Test handling of list of extensions."""
         os.environ['EASYBUILD_SOURCEPATH'] = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         init_config()
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -284,8 +309,8 @@ def test_exts_list(self):
             '       "source_urls": [("http://example.com", "suffix")],'
             '       "patches": ["toy-0.0.eb"],',  # dummy patch to avoid downloading fail
             '       "checksums": [',
-            '           "504c7036558938f997c1c269a01d7458",',  # checksum for source (gzip-1.4.eb)
-            '           "ddd5161154f5db67701525123129ff09",',  # checksum for patch (toy-0.0.eb)
+            '           "787393bfc465c85607a5b24486e861c5",',  # MD5 checksum for source (gzip-1.4.eb)
+            '           "ddd5161154f5db67701525123129ff09",',  # MD5 checksum for patch (toy-0.0.eb)
             '       ],',
             '   }),',
             ']',
@@ -298,6 +323,7 @@ def test_exts_list(self):
     def test_suggestions(self):
         """ If a typo is present, suggestions should be provided (if possible) """
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -321,6 +347,7 @@ def test_tweaking(self):
         os.close(fd)
         patches = ["t1.patch", ("t2.patch", 1), ("t3.patch", "test"), ("t4.h", "include")]
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'homepage = "http://www.example.com"',
             'description = "dummy description"',
@@ -418,6 +445,8 @@ def test_installversion(self):
 
     def test_legacy_installversion(self):
         """Test generation of install version (legacy)."""
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
 
         ver = "3.14"
         verpref = "myprefix|"
@@ -447,41 +476,51 @@ def test_obtain_easyconfig(self):
                "pi-3.15-GCC-4.3.2.eb",
                "pi-3.15-GCC-4.4.5.eb",
                "foo-1.2.3-GCC-4.3.2.eb"]
-        eb_files = [(fns[0], "\n".join(['name = "pi"',
-                                        'version = "3.12"',
-                                        'homepage = "http://example.com"',
-                                        'description = "test easyconfig"',
-                                        'toolchain = {"name": "dummy", "version": "dummy"}',
-                                        'patches = %s' % patches
-                                        ])),
-                    (fns[1], "\n".join(['name = "pi"',
-                                        'version = "3.13"',
-                                        'homepage = "http://example.com"',
-                                        'description = "test easyconfig"',
-                                        'toolchain = {"name": "%s", "version": "%s"}' % (tcname, tcver),
-                                        'patches = %s' % patches
-                                       ])),
-                    (fns[2], "\n".join(['name = "pi"',
-                                        'version = "3.15"',
-                                        'homepage = "http://example.com"',
-                                        'description = "test easyconfig"',
-                                        'toolchain = {"name": "%s", "version": "%s"}' % (tcname, tcver),
-                                        'patches = %s' % patches
-                                       ])),
-                    (fns[3], "\n".join(['name = "pi"',
-                                        'version = "3.15"',
-                                        'homepage = "http://example.com"',
-                                        'description = "test easyconfig"',
-                                        'toolchain = {"name": "%s", "version": "4.5.1"}' % tcname,
-                                        'patches = %s' % patches
-                                       ])),
-                    (fns[4], "\n".join(['name = "foo"',
-                                        'version = "1.2.3"',
-                                        'homepage = "http://example.com"',
-                                        'description = "test easyconfig"',
-                                        'toolchain = {"name": "%s", "version": "%s"}' % (tcname, tcver),
-                                        'foo_extra1 = "bar"',
-                                       ]))
+        eb_files = [(fns[0], "\n".join([
+                        'easyblock = "ConfigureMake"',
+                        'name = "pi"',
+                        'version = "3.12"',
+                        'homepage = "http://example.com"',
+                        'description = "test easyconfig"',
+                        'toolchain = {"name": "dummy", "version": "dummy"}',
+                        'patches = %s' % patches
+                    ])),
+                    (fns[1], "\n".join([
+                        'easyblock = "ConfigureMake"',
+                        'name = "pi"',
+                        'version = "3.13"',
+                        'homepage = "http://example.com"',
+                        'description = "test easyconfig"',
+                        'toolchain = {"name": "%s", "version": "%s"}' % (tcname, tcver),
+                        'patches = %s' % patches
+                    ])),
+                    (fns[2], "\n".join([
+                        'easyblock = "ConfigureMake"',
+                        'name = "pi"',
+                        'version = "3.15"',
+                        'homepage = "http://example.com"',
+                        'description = "test easyconfig"',
+                        'toolchain = {"name": "%s", "version": "%s"}' % (tcname, tcver),
+                        'patches = %s' % patches
+                    ])),
+                    (fns[3], "\n".join([
+                        'easyblock = "ConfigureMake"',
+                        'name = "pi"',
+                        'version = "3.15"',
+                        'homepage = "http://example.com"',
+                        'description = "test easyconfig"',
+                        'toolchain = {"name": "%s", "version": "4.5.1"}' % tcname,
+                        'patches = %s' % patches
+                    ])),
+                    (fns[4], "\n".join([
+                        'easyblock = "ConfigureMake"',
+                        'name = "foo"',
+                        'version = "1.2.3"',
+                        'homepage = "http://example.com"',
+                        'description = "test easyconfig"',
+                        'toolchain = {"name": "%s", "version": "%s"}' % (tcname, tcver),
+                        'foo_extra1 = "bar"',
+                    ]))
                    ]
 
 
@@ -496,7 +535,10 @@ def test_obtain_easyconfig(self):
         self.assertErrorRegex(EasyBuildError, error_regexp, obtain_ec_for, specs, [self.ec_dir], None)
 
         # should find matching easyconfig file
-        specs = {'name': 'foo', 'version': '1.2.3'}
+        specs = {
+            'name': 'foo',
+            'version': '1.2.3'
+        }
         res = obtain_ec_for(specs, [self.ec_dir], None)
         self.assertEqual(res[0], False)
         self.assertEqual(res[1], os.path.join(self.ec_dir, fns[-1]))
@@ -680,6 +722,7 @@ def test_templating(self):
         }
         # don't use any escaping insanity here, since it is templated itself
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "%(name)s"',
             'version = "%(version)s"',
             'homepage = "http://example.com/%%(nameletter)s/%%(nameletterlower)s"',
@@ -732,6 +775,7 @@ def test_constant_doc(self):
     def test_build_options(self):
         """Test configure/build/install options, both strings and lists."""
         orig_contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -801,6 +845,7 @@ def test_build_options(self):
     def test_buildininstalldir(self):
         """Test specifying build in install dir."""
         self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -879,11 +924,14 @@ def test_get_easyblock_class(self):
         ]:
             self.assertEqual(get_easyblock_class(easyblock), easyblock_class)
 
-        self.assertEqual(get_easyblock_class(None, name='gzip'), ConfigureMake)
         self.assertEqual(get_easyblock_class(None, name='gzip', default_fallback=False), None)
         self.assertEqual(get_easyblock_class(None, name='toy'), EB_toy)
         self.assertErrorRegex(EasyBuildError, "Failed to import EB_TOY", get_easyblock_class, None, name='TOY')
         self.assertEqual(get_easyblock_class(None, name='TOY', error_on_failed_import=False), None)
+        # deprecated functionality: ConfigureMake fallback still enabled
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
+        self.assertEqual(get_easyblock_class(None, name='gzip'), ConfigureMake)
 
     def test_easyconfig_paths(self):
         """Test create_paths function."""
@@ -898,11 +946,16 @@ def test_easyconfig_paths(self):
 
     def test_deprecated_options(self):
         """Test whether deprecated options are handled correctly."""
+        # lower 'current' version to avoid tripping over deprecation errors
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
+
         deprecated_options = [
             ('makeopts', 'buildopts', 'CC=foo'),
             ('premakeopts', 'prebuildopts', ['PATH=%(builddir)s/foo:$PATH', 'PATH=%(builddir)s/bar:$PATH']),
         ]
         clean_contents = [
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
diff --git a/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
index f4bf718e88..a5503aabe9 100644
--- a/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
+++ b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
@@ -9,6 +9,7 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html
 ##
+easyblock = 'EB_CUDA'
 
 name = 'CUDA'
 version = '5.5.22'
diff --git a/test/framework/easyconfigs/FFTW-3.3.3-gompi-1.4.10.eb b/test/framework/easyconfigs/FFTW-3.3.3-gompi-1.4.10.eb
index 06b0c2e2e1..bead8318f4 100644
--- a/test/framework/easyconfigs/FFTW-3.3.3-gompi-1.4.10.eb
+++ b/test/framework/easyconfigs/FFTW-3.3.3-gompi-1.4.10.eb
@@ -1,3 +1,5 @@
+easyblock = 'ConfigureMake'
+
 name = 'FFTW'
 version = '3.3.3'
 
diff --git a/test/framework/easyconfigs/GCC-4.6.3.eb b/test/framework/easyconfigs/GCC-4.6.3.eb
index 3b4c4c53c9..48cef12da0 100644
--- a/test/framework/easyconfigs/GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/GCC-4.6.3.eb
@@ -1,3 +1,5 @@
+easyblock = 'EB_GCC'
+
 name="GCC"
 version='4.6.3'
 
diff --git a/test/framework/easyconfigs/GCC-4.6.4.eb b/test/framework/easyconfigs/GCC-4.6.4.eb
index bf4adc61a6..2094773f61 100644
--- a/test/framework/easyconfigs/GCC-4.6.4.eb
+++ b/test/framework/easyconfigs/GCC-4.6.4.eb
@@ -1,3 +1,5 @@
+easyblock = 'EB_GCC'
+
 name = "GCC"
 version = '4.6.4'
 
diff --git a/test/framework/easyconfigs/GCC-4.7.2.eb b/test/framework/easyconfigs/GCC-4.7.2.eb
index 7b4dfcf410..accf6afca8 100644
--- a/test/framework/easyconfigs/GCC-4.7.2.eb
+++ b/test/framework/easyconfigs/GCC-4.7.2.eb
@@ -1,3 +1,5 @@
+easyblock = 'EB_GCC'
+
 name = "GCC"
 version = '4.7.2'
 
diff --git a/test/framework/easyconfigs/GCC-4.8.2.eb b/test/framework/easyconfigs/GCC-4.8.2.eb
index cef0802601..40b715006c 100644
--- a/test/framework/easyconfigs/GCC-4.8.2.eb
+++ b/test/framework/easyconfigs/GCC-4.8.2.eb
@@ -1,3 +1,5 @@
+easyblock = 'EB_GCC'
+
 name = "GCC"
 version = '4.8.2'
 
diff --git a/test/framework/easyconfigs/GCC-4.8.3.eb b/test/framework/easyconfigs/GCC-4.8.3.eb
index c62aa710d1..14e91d37d2 100644
--- a/test/framework/easyconfigs/GCC-4.8.3.eb
+++ b/test/framework/easyconfigs/GCC-4.8.3.eb
@@ -1,3 +1,6 @@
+# should be EB_GCC, but OK for testing purposes
+easyblock = 'EB_toy'
+
 name = "GCC"
 version = '4.8.3'
 
diff --git a/test/framework/easyconfigs/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb b/test/framework/easyconfigs/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb
index 8f1b31ff70..bd9785f7cc 100644
--- a/test/framework/easyconfigs/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb
+++ b/test/framework/easyconfigs/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb
@@ -1,3 +1,5 @@
+easyblock = 'ConfigureMake'
+
 name = 'OpenBLAS'
 version = '0.2.6'
 
@@ -44,7 +46,7 @@ installopts = threading + " PREFIX=%(installdir)s"
 sanity_check_paths = {
     'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h',
               'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h',
-              'lib/libopenblas.a', 'lib/libopenblas.%s' % shared_lib_ext],
+              'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT],
     'dirs': [],
 }
 
diff --git a/test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.6.4.eb b/test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.6.4.eb
index 053791e834..bd0832e690 100644
--- a/test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.6.4.eb
+++ b/test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.6.4.eb
@@ -1,3 +1,5 @@
+easyblock = 'ConfigureMake'
+
 name = 'OpenMPI'
 version = '1.6.4'
 
@@ -25,7 +27,7 @@ else:
 
 sanity_check_paths = {
     'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] +
-             ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90",
+             ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90",
                                                                          "mpi", "ompitrace", "open-pal",
                                                                          "open-rte", "vt", "vt-hyb",
                                                                          "vt-mpi", "vt-mpi-unify"]] +
diff --git a/test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.7.2.eb b/test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.7.2.eb
index fa3425f1ab..1505eba3ad 100644
--- a/test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.7.2.eb
+++ b/test/framework/easyconfigs/OpenMPI-1.6.4-GCC-4.7.2.eb
@@ -1,3 +1,5 @@
+easyblock = 'ConfigureMake'
+
 name = 'OpenMPI'
 version = '1.6.4'
 
@@ -25,7 +27,7 @@ else:
 
 sanity_check_paths = {
     'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] +
-             ["lib/lib%s.%s" % (libfile, shared_lib_ext) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90",
+             ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90",
                                                                          "mpi", "ompitrace", "open-pal",
                                                                          "open-rte", "vt", "vt-hyb",
                                                                          "vt-mpi", "vt-mpi-unify"]] +
diff --git a/test/framework/easyconfigs/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/test/framework/easyconfigs/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb
index 8f7ad295d1..be8a1f73d2 100644
--- a/test/framework/easyconfigs/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb
+++ b/test/framework/easyconfigs/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb
@@ -1,3 +1,5 @@
+easyblock = 'EB_ScaLAPACK'
+
 name = 'ScaLAPACK'
 version = '2.0.2'
 
diff --git a/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb b/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
index f47c7482a5..c5f783e816 100644
--- a/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
@@ -9,6 +9,7 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-19.html
 ##
+easyblock = 'ConfigureMake'
 
 name = 'gzip'
 version = '1.4'
diff --git a/test/framework/easyconfigs/gzip-1.4.eb b/test/framework/easyconfigs/gzip-1.4.eb
index ab769c6b69..c5a94274b3 100644
--- a/test/framework/easyconfigs/gzip-1.4.eb
+++ b/test/framework/easyconfigs/gzip-1.4.eb
@@ -9,6 +9,7 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-19.html
 ##
+easyblock = 'ConfigureMake'
 
 name = 'gzip'
 version = '1.4'
diff --git a/test/framework/easyconfigs/gzip-1.5-goolf-1.4.10.eb b/test/framework/easyconfigs/gzip-1.5-goolf-1.4.10.eb
index 08ce4ddc61..d1636586c9 100644
--- a/test/framework/easyconfigs/gzip-1.5-goolf-1.4.10.eb
+++ b/test/framework/easyconfigs/gzip-1.5-goolf-1.4.10.eb
@@ -9,6 +9,7 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-19.html
 ##
+easyblock = 'ConfigureMake'
 
 name = 'gzip'
 version = '1.5'
diff --git a/test/framework/easyconfigs/gzip-1.5-ictce-4.1.13.eb b/test/framework/easyconfigs/gzip-1.5-ictce-4.1.13.eb
index 2552d296e9..9fb11ce6ca 100644
--- a/test/framework/easyconfigs/gzip-1.5-ictce-4.1.13.eb
+++ b/test/framework/easyconfigs/gzip-1.5-ictce-4.1.13.eb
@@ -9,6 +9,7 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-19.html
 ##
+easyblock = 'ConfigureMake'
 
 name = 'gzip'
 version = '1.5'
diff --git a/test/framework/easyconfigs/hwloc-1.6.2-GCC-4.6.4.eb b/test/framework/easyconfigs/hwloc-1.6.2-GCC-4.6.4.eb
index 116ee4cb8c..3c07bbe614 100644
--- a/test/framework/easyconfigs/hwloc-1.6.2-GCC-4.6.4.eb
+++ b/test/framework/easyconfigs/hwloc-1.6.2-GCC-4.6.4.eb
@@ -1,3 +1,5 @@
+easyblock = 'ConfigureMake'
+
 name = 'hwloc'
 version = '1.6.2'
 
diff --git a/test/framework/easyconfigs/hwloc-1.6.2-GCC-4.7.2.eb b/test/framework/easyconfigs/hwloc-1.6.2-GCC-4.7.2.eb
index 00a3ce7444..19d34c3d1a 100644
--- a/test/framework/easyconfigs/hwloc-1.6.2-GCC-4.7.2.eb
+++ b/test/framework/easyconfigs/hwloc-1.6.2-GCC-4.7.2.eb
@@ -1,3 +1,5 @@
+easyblock = 'ConfigureMake'
+
 name = 'hwloc'
 version = '1.6.2'
 
diff --git a/test/framework/easyconfigs/icc-2013.5.192-GCC-4.8.3.eb b/test/framework/easyconfigs/icc-2013.5.192-GCC-4.8.3.eb
index 23b5d632b0..a084c374d0 100644
--- a/test/framework/easyconfigs/icc-2013.5.192-GCC-4.8.3.eb
+++ b/test/framework/easyconfigs/icc-2013.5.192-GCC-4.8.3.eb
@@ -1,3 +1,6 @@
+# should be EB_icc, but OK for testing purposes
+easyblock = 'EB_toy'
+
 name = 'icc'
 version = '2013.5.192'
 
diff --git a/test/framework/easyconfigs/ifort-2013.3.163.eb b/test/framework/easyconfigs/ifort-2013.3.163.eb
index 4efd890d23..b764b92c91 100644
--- a/test/framework/easyconfigs/ifort-2013.3.163.eb
+++ b/test/framework/easyconfigs/ifort-2013.3.163.eb
@@ -1,3 +1,5 @@
+easyblock = 'EB_ifort'
+
 name = 'ifort'
 version = '2013.3.163'
 
diff --git a/test/framework/easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb b/test/framework/easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb
index cba97b45a2..8a74093865 100644
--- a/test/framework/easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb
+++ b/test/framework/easyconfigs/ifort-2013.5.192-GCC-4.8.3.eb
@@ -1,3 +1,6 @@
+# should be EB_ifort, but OK for testing purposes
+easyblock = 'EB_toy'
+
 name = 'ifort'
 version = '2013.5.192'
 
diff --git a/test/framework/easyconfigs/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb b/test/framework/easyconfigs/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb
index 2114374474..a23cf2c3c9 100644
--- a/test/framework/easyconfigs/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb
+++ b/test/framework/easyconfigs/imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb
@@ -1,3 +1,6 @@
+# should be EB_imkl, but OK for testing purposes
+easyblock = 'EB_toy'
+
 name = 'imkl'
 version = '11.1.2.144'
 
diff --git a/test/framework/easyconfigs/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/test/framework/easyconfigs/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb
index ddba0fe1d6..e325ca2e75 100644
--- a/test/framework/easyconfigs/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb
+++ b/test/framework/easyconfigs/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb
@@ -1,3 +1,6 @@
+# should be EB_impi, but OK for testing purposes
+easyblock = 'EB_toy'
+
 name = 'impi'
 version = '4.1.3.049'
 
diff --git a/test/framework/easyconfigs/impi-4.1.3.049.eb b/test/framework/easyconfigs/impi-4.1.3.049.eb
index e55725a62a..956f85c717 100644
--- a/test/framework/easyconfigs/impi-4.1.3.049.eb
+++ b/test/framework/easyconfigs/impi-4.1.3.049.eb
@@ -1,3 +1,5 @@
+easyblock = 'EB_impi'
+
 name = 'impi'
 version = '4.1.3.049'
 
diff --git a/test/framework/easyconfigs/v1.0/GCC-4.6.3.eb b/test/framework/easyconfigs/v1.0/GCC-4.6.3.eb
index 3b4c4c53c9..48cef12da0 100644
--- a/test/framework/easyconfigs/v1.0/GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/v1.0/GCC-4.6.3.eb
@@ -1,3 +1,5 @@
+easyblock = 'EB_GCC'
+
 name="GCC"
 version='4.6.3'
 
diff --git a/test/framework/easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb b/test/framework/easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb
index 9f1c615c51..0f8d2efc28 100644
--- a/test/framework/easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb
@@ -9,6 +9,7 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-19.html
 ##
+easyblock = 'ConfigureMake'
 
 name = 'gzip'
 version = '1.4'
diff --git a/test/framework/easyconfigs/v1.0/gzip-1.4.eb b/test/framework/easyconfigs/v1.0/gzip-1.4.eb
index ab769c6b69..c5a94274b3 100644
--- a/test/framework/easyconfigs/v1.0/gzip-1.4.eb
+++ b/test/framework/easyconfigs/v1.0/gzip-1.4.eb
@@ -9,6 +9,7 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-19.html
 ##
+easyblock = 'ConfigureMake'
 
 name = 'gzip'
 version = '1.4'
diff --git a/test/framework/easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb b/test/framework/easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb
index 08ce4ddc61..d1636586c9 100644
--- a/test/framework/easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb
+++ b/test/framework/easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb
@@ -9,6 +9,7 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-19.html
 ##
+easyblock = 'ConfigureMake'
 
 name = 'gzip'
 version = '1.5'
diff --git a/test/framework/easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb b/test/framework/easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb
index 2552d296e9..9fb11ce6ca 100644
--- a/test/framework/easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb
+++ b/test/framework/easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb
@@ -9,6 +9,7 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-19.html
 ##
+easyblock = 'ConfigureMake'
 
 name = 'gzip'
 version = '1.5'
diff --git a/test/framework/easyconfigs/v2.0/GCC.eb b/test/framework/easyconfigs/v2.0/GCC.eb
index 6a1baf1bef..fde1551ad2 100644
--- a/test/framework/easyconfigs/v2.0/GCC.eb
+++ b/test/framework/easyconfigs/v2.0/GCC.eb
@@ -5,6 +5,8 @@ docstring test
 @author: Stijn De Weirdt (UGent)
 @maintainer: Kenneth Hoste (UGent)
 """
+easyblock = 'EB_GCC'
+
 name = "GCC"
 
 homepage = 'http://gcc.gnu.org/'
diff --git a/test/framework/easyconfigs/v2.0/doesnotexist.eb b/test/framework/easyconfigs/v2.0/doesnotexist.eb
index 7067a83a07..7a85355ce6 100644
--- a/test/framework/easyconfigs/v2.0/doesnotexist.eb
+++ b/test/framework/easyconfigs/v2.0/doesnotexist.eb
@@ -5,6 +5,7 @@ docstring test
 @author: Stijn De Weirdt (UGent)
 @maintainer: Kenneth Hoste (UGent)
 """
+easyblock = 'ConfigureMake'
 
 name = 'doesnotexist'
 
diff --git a/test/framework/easyconfigs/v2.0/gzip.eb b/test/framework/easyconfigs/v2.0/gzip.eb
index de795268c7..602528e2af 100644
--- a/test/framework/easyconfigs/v2.0/gzip.eb
+++ b/test/framework/easyconfigs/v2.0/gzip.eb
@@ -41,4 +41,5 @@ versions = 1.4, 1.5
 toolchains = dummy == dummy, goolf, GCC == 4.6.3, goolf == 1.4.10, ictce == 4.1.13
 
 [DEFAULT]
+easyblock = ConfigureMake
 moduleclass = base
diff --git a/test/framework/easyconfigs/v2.0/libpng.eb b/test/framework/easyconfigs/v2.0/libpng.eb
index 1cc9175bca..ecc5bd59f6 100644
--- a/test/framework/easyconfigs/v2.0/libpng.eb
+++ b/test/framework/easyconfigs/v2.0/libpng.eb
@@ -28,6 +28,7 @@ versions = 1.5.10, 1.5.11, 1.5.13, 1.5.14, 1.6.2, 1.6.3, 1.6.6
 toolchains = goolf == 1.4.10, ictce == 4.1.13, goalf == 1.1.0-no-OFED
 
 [DEFAULT]
+easyblock = ConfigureMake
 moduleclass = lib
 
 [DEPENDENCIES]
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 5a23905947..cff024f9de 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -51,17 +51,6 @@ class FileToolsTest(EnhancedTestCase):
         ('0_foo+0x0x#-$__', 'EB_0_underscore_foo_plus_0x0x_hash__minus__dollar__underscore__underscore_'),
     ]
 
-    def setUp(self):
-        """Set up testcase."""
-        super(FileToolsTest, self).setUp()
-        self.legacySetUp()
-
-    def legacySetUp(self):
-        self.log.deprecated("legacySetUp", "2.0")
-        cfg_path = os.path.join('easybuild', 'easybuild_config.py')
-        cfg_full_path = find_full_path(cfg_path)
-        self.assertTrue(cfg_full_path)
-
     def test_extract_cmd(self):
         """Test various extract commands."""
         tests = [
diff --git a/test/framework/modules.py b/test/framework/modules.py
index 21f0a5407c..059a80604a 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -123,6 +123,8 @@ def test_exists(self):
         self.assertEqual(self.testmods.exist(mod_names), [True, False, False, False, True, True, True])
 
         # test deprecated functionality
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
         self.assertTrue(self.testmods.exists('OpenMPI/1.6.4-GCC-4.6.4'))
         self.assertFalse(self.testmods.exists('foo/1.2.3'))
         # exists should not return True for incomplete module names
diff --git a/test/framework/options.py b/test/framework/options.py
index 9565b1d97c..375c0a89d3 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -33,9 +33,10 @@
 import shutil
 import sys
 import tempfile
-from test.framework.utilities import EnhancedTestCase
+from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader
 from unittest import main as unittestmain
+from urllib2 import URLError
 
 import easybuild.tools.build_log
 from easybuild.framework.easyconfig import BUILD, CUSTOM, DEPENDENCIES, EXTENSIONS, FILEMANAGEMENT, LICENSE
@@ -103,12 +104,11 @@ def test_no_args(self):
 
     def test_debug(self):
         """Test enabling debug logging."""
-
         for debug_arg in ['-d', '--debug']:
             args = [
-                    '--software-name=somethingrandom',
-                    debug_arg,
-                   ]
+                'nosuchfile.eb',
+                debug_arg,
+            ]
             outtxt = self.eb_main(args)
 
             for log_msg_type in ['DEBUG', 'INFO', 'ERROR']:
@@ -123,7 +123,7 @@ def test_info(self):
 
         for info_arg in ['--info']:
             args = [
-                    '--software-name=somethingrandom',
+                    'nosuchfile.eb',
                     info_arg,
                    ]
             outtxt = self.eb_main(args)
@@ -144,7 +144,7 @@ def test_quiet(self):
 
         for quiet_arg in ['--quiet']:
             args = [
-                    '--software-name=somethingrandom',
+                    'nosuchfile.eb',
                     quiet_arg,
                    ]
             outtxt = self.eb_main(args)
@@ -749,8 +749,8 @@ def test_from_pr(self):
 
         tmpdir = tempfile.mkdtemp()
         args = [
-            # PR for ictce/6.2.5, see https://github.com/hpcugent/easybuild-easyconfigs/pull/726/files
-            '--from-pr=726',
+            # PR for intel/2014b, see https://github.com/hpcugent/easybuild-easyconfigs/pull/948/files
+            '--from-pr=948',
             '--dry-run',
             # an argument must be specified to --robot, since easybuild-easyconfigs may not be installed
             '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
@@ -758,26 +758,29 @@ def test_from_pr(self):
             '--github-user=easybuild_test',  # a GitHub token should be available for this user
             '--tmpdir=%s' % tmpdir,
         ]
-        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
-
-        modules = [
-            'icc/2013_sp1.2.144',
-            'ifort/2013_sp1.2.144',
-            'impi/4.1.3.049',
-            'imkl/11.1.2.144',
-            'ictce/6.2.5',
-            'gzip/1.6-ictce-6.2.5',
-        ]
-        for module in modules:
-            ec_fn = "%s.eb" % '-'.join(module.split('/'))
-            regex = re.compile(r"^ \* \[.\] .*/%s \(module: %s\)$" % (ec_fn, module), re.M)
-            self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
-
-        pr_tmpdir = os.path.join(tmpdir, 'easybuild-\S{6}', 'files_pr726')
-        regex = re.compile("Prepended list of robot search paths with %s:" % pr_tmpdir, re.M)
-        self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
+        try:
+            outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True)
+
+            modules = [
+                'HPL/2.1-intel-2014b',
+                'GCC/4.8.3',
+                'icc/2013.5.192-GCC-4.8.3',
+                'ifort/2013.5.192-GCC-4.8.3',
+                'imkl/11.1.2.144-2013.5.192-GCC-4.8.3',
+                'impi/4.1.3.049-GCC-4.8.3',
+                'intel/2014b',
+            ]
+            for module in modules:
+                ec_fn = "%s.eb" % '-'.join(module.split('/'))
+                regex = re.compile(r"^ \* \[.\] .*/%s \(module: %s\)$" % (ec_fn, module), re.M)
+                self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
 
-        shutil.rmtree(tmpdir)
+            pr_tmpdir = os.path.join(tmpdir, 'easybuild-\S{6}', 'files_pr948')
+            regex = re.compile("Prepended list of robot search paths with %s:" % pr_tmpdir, re.M)
+            self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
+        except URLError, err:
+            print "Ignoring URLError '%s' in test_from_pr" % err
+            shutil.rmtree(tmpdir)
 
     def test_no_such_software(self):
         """Test using no arguments."""
@@ -896,6 +899,7 @@ def test_tmpdir(self):
     def test_ignore_osdeps(self):
         """Test ignoring of listed OS dependencies."""
         txt = '\n'.join([
+            'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
             'homepage = "http://example.com"',
@@ -976,6 +980,10 @@ def test_experimental(self):
 
     def test_deprecated(self):
         """Test the deprecated option"""
+        if 'EASYBUILD_DEPRECATED' in os.environ:
+            os.environ['EASYBUILD_DEPRECATED'] = str(VERSION)
+            init_config()
+
         orig_value = easybuild.tools.build_log.CURRENT_VERSION
 
         # make sure it's off by default
@@ -1003,7 +1011,7 @@ def test_deprecated(self):
         except easybuild.tools.build_log.EasyBuildError, err2:
             self.assertTrue('DEPRECATED' in str(err2))
 
-        # force higher version by prefixing it with 1, which should result in deprecation
+        # force higher version by prefixing it with 1, which should result in deprecation errors
         topt = EasyBuildOptions(
             go_args=['--deprecated=1%s' % orig_value],
         )
@@ -1070,10 +1078,15 @@ def test_allow_modules_tool_mismatch(self):
 
     def test_try(self):
         """Test whether --try options are taken into account."""
-        ecs_path = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
-        ec_file = os.path.join(ecs_path, 'toy-0.0.eb')
+        ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        tweaked_toy_ec = os.path.join(self.test_buildpath, 'toy-0.0-tweaked.eb')
+        shutil.copy2(os.path.join(ecs_path, 'toy-0.0.eb'), tweaked_toy_ec)
+        f = open(tweaked_toy_ec, 'a')
+        f.write("easyblock = 'ConfigureMake'")
+        f.close()
+
         args = [
-            ec_file,
+            tweaked_toy_ec,
             '--sourcepath=%s' % self.test_sourcepath,
             '--buildpath=%s' % self.test_buildpath,
             '--installpath=%s' % self.test_installpath,
@@ -1190,7 +1203,7 @@ def test_cleanup_builddir(self):
         args = [
             toy_ec,
             '--force',
-            '--try-amend=premakeopts=nosuchcommand &&',
+            '--try-amend=prebuildopts=nosuchcommand &&',
         ]
         self.eb_main(args, do_build=True)
         self.assertTrue(os.path.exists(toy_buildpath), "Build dir %s is retained after failed build" % toy_buildpath)
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/bar.py b/test/framework/sandbox/easybuild/easyblocks/generic/bar.py
index 482ee15cc1..2dcc4c5c01 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/bar.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/bar.py
@@ -38,9 +38,8 @@ class bar(EasyBlock):
     @staticmethod
     def extra_options():
         """Custom easyconfig parameters for bar."""
-
-        extra_vars = [
-                      ('bar_extra1', [None, "first bar-specific easyconfig parameter (mandatory)", MANDATORY]),
-                      ('bar_extra2', ['BAR', "second bar-specific easyconfig parameter", CUSTOM]),
-                     ]
+        extra_vars = {
+            'bar_extra1': [None, "first bar-specific easyconfig parameter (mandatory)", MANDATORY],
+            'bar_extra2': ['BAR', "second bar-specific easyconfig parameter", CUSTOM],
+        }
         return EasyBlock.extra_options(extra_vars)
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py b/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py
new file mode 100644
index 0000000000..8024520f32
--- /dev/null
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py
@@ -0,0 +1,34 @@
+##
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for building and installing dummy extensions, implemented as an easyblock
+
+@author: Kenneth Hoste (Ghent University)
+"""
+
+from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
+
+class DummyExtension(ExtensionEasyBlock):
+    """Support for building/installing dummy extensions."""
diff --git a/test/framework/sandbox/easybuild/easyblocks/toy.py b/test/framework/sandbox/easybuild/easyblocks/toy.py
index 897d248dfe..b03b6d9959 100644
--- a/test/framework/sandbox/easybuild/easyblocks/toy.py
+++ b/test/framework/sandbox/easybuild/easyblocks/toy.py
@@ -33,8 +33,9 @@
 import shutil
 
 from easybuild.framework.easyblock import EasyBlock
-from easybuild.tools.filetools import mkdir, run_cmd
+from easybuild.tools.filetools import mkdir
 from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.run import run_cmd
 
 class EB_toy(EasyBlock):
     """Support for building/installing toy."""
@@ -61,9 +62,9 @@ def build_step(self, name=None):
         """Build toy."""
         if name is None:
             name = self.name
-        run_cmd('%(premakeopts)s gcc %(name)s.c -o %(name)s' % {
+        run_cmd('%(prebuildopts)s gcc %(name)s.c -o %(name)s' % {
             'name': name,
-            'premakeopts': self.cfg['premakeopts'],
+            'prebuildopts': self.cfg['prebuildopts'],
         })
 
     def install_step(self, name=None):
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index 8f9e8a4cf2..20b6b0068d 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -27,7 +27,8 @@
 
 @author: Kenneth hoste (Ghent University)
 """
-from test.framework.utilities import EnhancedTestCase
+import os
+from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader, main
 
 from easybuild.tools.systemtools import AMD, ARM, DARWIN, INTEL, LINUX, UNKNOWN
@@ -40,11 +41,18 @@
 class SystemToolsTest(EnhancedTestCase):
     """ very basis FileRepository test, we don't want git / svn dependency """
 
-    def test_core_count(self):
+    def test_avail_core_count(self):
         """Test getting core count."""
-        for core_count in [get_avail_core_count(), get_core_count()]:
-            self.assertTrue(isinstance(core_count, int), "core_count has type int: %s, %s" % (core_count, type(core_count)))
-            self.assertTrue(core_count > 0, "core_count %d > 0" % core_count)
+        core_count = get_avail_core_count()
+        self.assertTrue(isinstance(core_count, int), "core_count has type int: %s, %s" % (core_count, type(core_count)))
+        self.assertTrue(core_count > 0, "core_count %d > 0" % core_count)
+
+        # also test deprecated get_core_count
+        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
+        init_config()
+        core_count = get_core_count()
+        self.assertTrue(isinstance(core_count, int), "core_count has type int: %s, %s" % (core_count, type(core_count)))
+        self.assertTrue(core_count > 0, "core_count %d > 0" % core_count)
 
     def test_cpu_model(self):
         """Test getting CPU model."""
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index e9c84d1e9e..628e0c9181 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -105,6 +105,11 @@ def setUp(self):
         os.environ['EASYBUILD_BUILDPATH'] = self.test_buildpath
         self.test_installpath = tempfile.mkdtemp()
         os.environ['EASYBUILD_INSTALLPATH'] = self.test_installpath
+
+        # make sure no deprecated behaviour is being triggered (unless intended by the test)
+        # trip *all* log.deprecated statements by setting deprecation version ridiculously high
+        os.environ['EASYBUILD_DEPRECATED'] = '10000000'
+
         init_config()
 
         # add test easyblocks to Python search path and (re)import and reload easybuild modules

From 43f1a3ebb8d67fe59b5423896e78bbf38dfc1563 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 11:24:19 +0100
Subject: [PATCH 0405/1356] fix generate_software_list.py script w.r.t.
 deprecated fallback to ConfigureMake

---
 easybuild/scripts/generate_software_list.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/easybuild/scripts/generate_software_list.py b/easybuild/scripts/generate_software_list.py
index 0183ff2c5e..94018d05d6 100644
--- a/easybuild/scripts/generate_software_list.py
+++ b/easybuild/scripts/generate_software_list.py
@@ -126,12 +126,13 @@
             log.info("found valid easyconfig %s" % ec)
             if not ec.name in names:
                 log.info("found new software package %s" % ec)
+                ec.easyblock = None
                 # check if an easyblock exists
-                module = get_easyblock_class(None, name=ec.name).__module__.split('.')[-1]
-                if module != "configuremake":
-                    ec.easyblock = module
-                else:
-                    ec.easyblock = None
+                ebclass = get_easyblock_class(None, name=ec.name, default_fallback=False)
+                if ebclass is not None:
+                    module = ebclass.__module__.split('.')[-1]
+                    if module != "configuremake":
+                        ec.easyblock = module
                 configs.append(ec)
                 names.append(ec.name)
         except Exception, err:

From d009b63a2c2803f25642a48f950dae4a135de679 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 12:05:14 +0100
Subject: [PATCH 0406/1356] use EB_toy easyblock in test easyconfigs

---
 test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb            | 3 ++-
 test/framework/easyconfigs/GCC-4.6.3.eb                        | 3 ++-
 test/framework/easyconfigs/GCC-4.6.4.eb                        | 3 ++-
 test/framework/easyconfigs/GCC-4.7.2.eb                        | 3 ++-
 test/framework/easyconfigs/GCC-4.8.2.eb                        | 3 ++-
 ...ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb | 3 ++-
 test/framework/easyconfigs/ifort-2013.3.163.eb                 | 3 ++-
 test/framework/easyconfigs/impi-4.1.3.049.eb                   | 3 ++-
 test/framework/easyconfigs/v1.0/GCC-4.6.3.eb                   | 3 ++-
 test/framework/easyconfigs/v2.0/GCC.eb                         | 3 ++-
 10 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
index a5503aabe9..00bf4df2f9 100644
--- a/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
+++ b/test/framework/easyconfigs/CUDA-5.5.22-GCC-4.8.2.eb
@@ -9,7 +9,8 @@
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-99.html
 ##
-easyblock = 'EB_CUDA'
+# should be EB_CUDA, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name = 'CUDA'
 version = '5.5.22'
diff --git a/test/framework/easyconfigs/GCC-4.6.3.eb b/test/framework/easyconfigs/GCC-4.6.3.eb
index 48cef12da0..8f9e3c6a1f 100644
--- a/test/framework/easyconfigs/GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/GCC-4.6.3.eb
@@ -1,4 +1,5 @@
-easyblock = 'EB_GCC'
+# should be EB_GCC, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name="GCC"
 version='4.6.3'
diff --git a/test/framework/easyconfigs/GCC-4.6.4.eb b/test/framework/easyconfigs/GCC-4.6.4.eb
index 2094773f61..baf448818b 100644
--- a/test/framework/easyconfigs/GCC-4.6.4.eb
+++ b/test/framework/easyconfigs/GCC-4.6.4.eb
@@ -1,4 +1,5 @@
-easyblock = 'EB_GCC'
+# should be EB_GCC, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name = "GCC"
 version = '4.6.4'
diff --git a/test/framework/easyconfigs/GCC-4.7.2.eb b/test/framework/easyconfigs/GCC-4.7.2.eb
index accf6afca8..d4b386baae 100644
--- a/test/framework/easyconfigs/GCC-4.7.2.eb
+++ b/test/framework/easyconfigs/GCC-4.7.2.eb
@@ -1,4 +1,5 @@
-easyblock = 'EB_GCC'
+# should be EB_GCC, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name = "GCC"
 version = '4.7.2'
diff --git a/test/framework/easyconfigs/GCC-4.8.2.eb b/test/framework/easyconfigs/GCC-4.8.2.eb
index 40b715006c..a7723b5eb9 100644
--- a/test/framework/easyconfigs/GCC-4.8.2.eb
+++ b/test/framework/easyconfigs/GCC-4.8.2.eb
@@ -1,4 +1,5 @@
-easyblock = 'EB_GCC'
+# should be EB_GCC, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name = "GCC"
 version = '4.8.2'
diff --git a/test/framework/easyconfigs/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb b/test/framework/easyconfigs/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb
index be8a1f73d2..14f049732b 100644
--- a/test/framework/easyconfigs/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb
+++ b/test/framework/easyconfigs/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb
@@ -1,4 +1,5 @@
-easyblock = 'EB_ScaLAPACK'
+# should be EB_ScaLAPACK, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name = 'ScaLAPACK'
 version = '2.0.2'
diff --git a/test/framework/easyconfigs/ifort-2013.3.163.eb b/test/framework/easyconfigs/ifort-2013.3.163.eb
index b764b92c91..09c286af0b 100644
--- a/test/framework/easyconfigs/ifort-2013.3.163.eb
+++ b/test/framework/easyconfigs/ifort-2013.3.163.eb
@@ -1,4 +1,5 @@
-easyblock = 'EB_ifort'
+# should be EB_ifort, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name = 'ifort'
 version = '2013.3.163'
diff --git a/test/framework/easyconfigs/impi-4.1.3.049.eb b/test/framework/easyconfigs/impi-4.1.3.049.eb
index 956f85c717..4267dce6b6 100644
--- a/test/framework/easyconfigs/impi-4.1.3.049.eb
+++ b/test/framework/easyconfigs/impi-4.1.3.049.eb
@@ -1,4 +1,5 @@
-easyblock = 'EB_impi'
+# should be EB_impi, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name = 'impi'
 version = '4.1.3.049'
diff --git a/test/framework/easyconfigs/v1.0/GCC-4.6.3.eb b/test/framework/easyconfigs/v1.0/GCC-4.6.3.eb
index 48cef12da0..8f9e3c6a1f 100644
--- a/test/framework/easyconfigs/v1.0/GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/v1.0/GCC-4.6.3.eb
@@ -1,4 +1,5 @@
-easyblock = 'EB_GCC'
+# should be EB_GCC, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name="GCC"
 version='4.6.3'
diff --git a/test/framework/easyconfigs/v2.0/GCC.eb b/test/framework/easyconfigs/v2.0/GCC.eb
index fde1551ad2..b753004a6e 100644
--- a/test/framework/easyconfigs/v2.0/GCC.eb
+++ b/test/framework/easyconfigs/v2.0/GCC.eb
@@ -5,7 +5,8 @@ docstring test
 @author: Stijn De Weirdt (UGent)
 @maintainer: Kenneth Hoste (UGent)
 """
-easyblock = 'EB_GCC'
+# should be EB_GCC, but OK for testing purposes
+easyblock = 'EB_toy'
 
 name = "GCC"
 

From e5fcb76c8eab8dc45c87b08647b0c86dbf4910bc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 12:29:44 +0100
Subject: [PATCH 0407/1356] fix test_from_pr using #1238, fix remark

---
 test/framework/easyconfig.py |  2 +-
 test/framework/options.py    | 15 +++++----------
 2 files changed, 6 insertions(+), 11 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 3a97e400b4..a11a245938 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -171,7 +171,7 @@ def test_deprecated_shared_lib_ext(self):
         eb = EasyConfig(self.eb_file)
         self.assertEqual(eb['sanity_check_paths']['files'][0], "lib/lib.%s" % get_shared_lib_ext())
 
-    def test_SHLIB_EXT(self):
+    def test_shlib_ext(self):
         """ inside easyconfigs shared_lib_ext should be set """
         self.contents = '\n'.join([
             'easyblock = "ConfigureMake"',
diff --git a/test/framework/options.py b/test/framework/options.py
index 375c0a89d3..3d317e859d 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -749,8 +749,8 @@ def test_from_pr(self):
 
         tmpdir = tempfile.mkdtemp()
         args = [
-            # PR for intel/2014b, see https://github.com/hpcugent/easybuild-easyconfigs/pull/948/files
-            '--from-pr=948',
+            # PR for intel/2014b, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1238/files
+            '--from-pr=1238',
             '--dry-run',
             # an argument must be specified to --robot, since easybuild-easyconfigs may not be installed
             '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
@@ -762,20 +762,15 @@ def test_from_pr(self):
             outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True)
 
             modules = [
-                'HPL/2.1-intel-2014b',
-                'GCC/4.8.3',
-                'icc/2013.5.192-GCC-4.8.3',
-                'ifort/2013.5.192-GCC-4.8.3',
-                'imkl/11.1.2.144-2013.5.192-GCC-4.8.3',
-                'impi/4.1.3.049-GCC-4.8.3',
-                'intel/2014b',
+                'HPL/2.1-intel-2015a',
+                'intel/2015a',
             ]
             for module in modules:
                 ec_fn = "%s.eb" % '-'.join(module.split('/'))
                 regex = re.compile(r"^ \* \[.\] .*/%s \(module: %s\)$" % (ec_fn, module), re.M)
                 self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
 
-            pr_tmpdir = os.path.join(tmpdir, 'easybuild-\S{6}', 'files_pr948')
+            pr_tmpdir = os.path.join(tmpdir, 'easybuild-\S{6}', 'files_pr1238')
             regex = re.compile("Prepended list of robot search paths with %s:" % pr_tmpdir, re.M)
             self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
         except URLError, err:

From 75b09ca13789eda903345fbd179890197351189f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 13:32:01 +0100
Subject: [PATCH 0408/1356] really fix test_from_pr using #1239

---
 test/framework/easyconfigs/GCC-4.9.2.eb | 36 ++++++++++
 test/framework/options.py               | 87 +++++++++++++------------
 2 files changed, 83 insertions(+), 40 deletions(-)
 create mode 100644 test/framework/easyconfigs/GCC-4.9.2.eb

diff --git a/test/framework/easyconfigs/GCC-4.9.2.eb b/test/framework/easyconfigs/GCC-4.9.2.eb
new file mode 100644
index 0000000000..ec651b931d
--- /dev/null
+++ b/test/framework/easyconfigs/GCC-4.9.2.eb
@@ -0,0 +1,36 @@
+# should be EB_GCC, but OK for testing purposes
+easyblock = 'EB_toy'
+
+name = "GCC"
+version = '4.9.2'
+
+homepage = 'http://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = [
+    'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(version)s',  # GCC auto-resolving HTTP mirror
+    'http://ftpmirror.gnu.org/gmp',  # idem for GMP
+    'http://ftpmirror.gnu.org/mpfr',  # idem for MPFR
+    'http://www.multiprecision.org/mpc/download',  # MPC official
+]
+
+mpfr_version = '3.1.2'
+
+sources = [
+    SOURCELOWER_TAR_BZ2,
+    'gmp-6.0.0a.tar.bz2',
+    'mpfr-%s.tar.gz' % mpfr_version,
+    'mpc-1.0.2.tar.gz',
+]
+
+patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)]
+
+languages = ['c', 'c++', 'fortran', 'lto']
+
+# building GCC sometimes fails if make parallelism is too high, so let's limit it
+maxparallel = 4
+
+moduleclass = 'compiler'
diff --git a/test/framework/options.py b/test/framework/options.py
index 3d317e859d..f3c1739e11 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -54,7 +54,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
 
     logfile = None
 
-    def test_help_short(self, txt=None):
+    def xtest_help_short(self, txt=None):
         """Test short help message."""
 
         if txt is None:
@@ -76,7 +76,7 @@ def test_help_short(self, txt=None):
         self.assertEqual(re.search("Software search and build options", outtxt), None, "Not all option groups included in short help (1)")
         self.assertEqual(re.search("Regression test options", outtxt), None, "Not all option groups included in short help (2)")
 
-    def test_help_long(self):
+    def xtest_help_long(self):
         """Test long help message."""
 
         topt = EasyBuildOptions(
@@ -93,7 +93,7 @@ def test_help_long(self):
         self.assertTrue(re.search("Software search and build options", outtxt), "Not all option groups included in short help (1)")
         self.assertTrue(re.search("Regression test options", outtxt), "Not all option groups included in short help (2)")
 
-    def test_no_args(self):
+    def xtest_no_args(self):
         """Test using no arguments."""
 
         outtxt = self.eb_main([])
@@ -102,7 +102,7 @@ def test_no_args(self):
         error_msg += " or use software build options to make EasyBuild search for easyconfigs"
         self.assertTrue(re.search(error_msg, outtxt), "Error message when eb is run without arguments")
 
-    def test_debug(self):
+    def xtest_debug(self):
         """Test enabling debug logging."""
         for debug_arg in ['-d', '--debug']:
             args = [
@@ -118,7 +118,7 @@ def test_debug(self):
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
 
-    def test_info(self):
+    def xtest_info(self):
         """Test enabling info logging."""
 
         for info_arg in ['--info']:
@@ -139,7 +139,7 @@ def test_info(self):
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
 
-    def test_quiet(self):
+    def xtest_quiet(self):
         """Test enabling quiet logging (errors only)."""
 
         for quiet_arg in ['--quiet']:
@@ -160,7 +160,7 @@ def test_quiet(self):
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
 
-    def test_force(self):
+    def xtest_force(self):
         """Test forcing installation even if the module is already available."""
 
         # use GCC-4.6.3.eb easyconfig file that comes with the tests
@@ -193,7 +193,7 @@ def test_force(self):
 
         self.assertTrue(not re.search(already_msg, outtxt), "Already installed message not there with --force")
 
-    def test_skip(self):
+    def xtest_skip(self):
         """Test skipping installation of module (--skip, -k)."""
 
         # use toy-0.0.eb easyconfig file that comes with the tests
@@ -255,7 +255,7 @@ def test_skip(self):
         modify_env(os.environ, self.orig_environ)
         modules_tool()
 
-    def test_job(self):
+    def xtest_job(self):
         """Test submitting build as a job."""
 
         # use gzip-1.4.eb easyconfig file that comes with the tests
@@ -291,7 +291,7 @@ def check_args(job_args, passed_args=None):
 
     # 'zzz' prefix in the test name is intentional to make this test run last,
     # since it fiddles with the logging infrastructure which may break things
-    def test_zzz_logtostdout(self):
+    def xtest_zzz_logtostdout(self):
         """Testing redirecting log to stdout."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -331,7 +331,7 @@ def test_zzz_logtostdout(self):
             os.remove(dummylogfn)
         fancylogger.logToFile(self.logfile)
 
-    def test_avail_easyconfig_params(self):
+    def xtest_avail_easyconfig_params(self):
         """Test listing available easyconfig parameters."""
 
         def run_test(custom=None, extra_params=[]):
@@ -389,7 +389,7 @@ def run_test(custom=None, extra_params=[]):
 
     # double underscore to make sure it runs first, which is required to detect certain types of bugs,
     # e.g. running with non-initialized EasyBuild config (truly mimicing 'eb --list-toolchains')
-    def test__list_toolchains(self):
+    def xtest__list_toolchains(self):
         """Test listing known compiler toolchains."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -421,7 +421,7 @@ def test__list_toolchains(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
-    def test_avail_lists(self):
+    def xtest_avail_lists(self):
         """Test listing available values of certain types."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -454,7 +454,7 @@ def test_avail_lists(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
-    def test_avail_cfgfile_constants(self):
+    def xtest_avail_cfgfile_constants(self):
         """Test --avail-cfgfile-constants."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
@@ -487,7 +487,7 @@ def test_avail_cfgfile_constants(self):
             os.remove(dummylogfn)
         sys.path[:] = orig_sys_path
 
-    def test_list_easyblocks(self):
+    def xtest_list_easyblocks(self):
         """Test listing easyblock hierarchy."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -549,7 +549,7 @@ def test_list_easyblocks(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
-    def test_search(self):
+    def xtest_search(self):
         """Test searching for easyconfigs."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -590,7 +590,7 @@ def test_search(self):
             if os.path.exists(dummylogfn):
                 os.remove(dummylogfn)
 
-    def test_dry_run(self):
+    def xtest_dry_run(self):
         """Test dry run (long format)."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
@@ -613,7 +613,7 @@ def test_dry_run(self):
             regex = re.compile(r" \* \[%s\] \S+%s \(module: %s\)" % (mark, ec, mod), re.M)
             self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
 
-    def test_dry_run_short(self):
+    def xtest_dry_run_short(self):
         """Test dry run (short format)."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
@@ -658,7 +658,7 @@ def test_dry_run_short(self):
         shutil.rmtree(tmpdir)
         sys.path[:] = orig_sys_path
 
-    def test_try_robot_force(self):
+    def xtest_try_robot_force(self):
         """
         Test correct behavior for combination of --try-toolchain --robot --force.
         Only the listed easyconfigs should be forced, resolved dependencies should not (even if tweaked).
@@ -702,7 +702,7 @@ def test_try_robot_force(self):
             regex = re.compile("^ \* \[%s\] \S+%s \(module: %s\)$" % (mark, ec, mod), re.M)
             self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
 
-    def test_dry_run_hierarchical(self):
+    def xtest_dry_run_hierarchical(self):
         """Test dry run using a hierarchical module naming scheme."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
@@ -749,8 +749,8 @@ def test_from_pr(self):
 
         tmpdir = tempfile.mkdtemp()
         args = [
-            # PR for intel/2014b, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1238/files
-            '--from-pr=1238',
+            # PR for intel/2014b, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1239/files
+            '--from-pr=1239',
             '--dry-run',
             # an argument must be specified to --robot, since easybuild-easyconfigs may not be installed
             '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
@@ -760,24 +760,31 @@ def test_from_pr(self):
         ]
         try:
             outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True)
-
             modules = [
-                'HPL/2.1-intel-2015a',
-                'intel/2015a',
+                'FFTW/3.3.4-gompi-2015a',
+                'foss/2015a',
+                'GCC/4.9.2',
+                'gompi/2015a',
+                'HPL/2.1-foss-2015a',
+                'hwloc/1.10.0-GCC-4.9.2',
+                'numactl/2.0.10-GCC-4.9.2',
+                'OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0',
+                'OpenMPI/1.8.3-GCC-4.9.2',
+                'ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0',
             ]
             for module in modules:
                 ec_fn = "%s.eb" % '-'.join(module.split('/'))
                 regex = re.compile(r"^ \* \[.\] .*/%s \(module: %s\)$" % (ec_fn, module), re.M)
                 self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
 
-            pr_tmpdir = os.path.join(tmpdir, 'easybuild-\S{6}', 'files_pr1238')
+            pr_tmpdir = os.path.join(tmpdir, 'easybuild-\S{6}', 'files_pr1239')
             regex = re.compile("Prepended list of robot search paths with %s:" % pr_tmpdir, re.M)
             self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
         except URLError, err:
             print "Ignoring URLError '%s' in test_from_pr" % err
             shutil.rmtree(tmpdir)
 
-    def test_no_such_software(self):
+    def xtest_no_such_software(self):
         """Test using no arguments."""
 
         args = [
@@ -794,7 +801,7 @@ def test_no_such_software(self):
         msg = "Error message when eb can't find software with specified name (outtxt: %s)" % outtxt
         self.assertTrue(re.search(error_msg1, outtxt) or re.search(error_msg2, outtxt), msg)
 
-    def test_footer(self):
+    def xtest_footer(self):
         """Test specifying a module footer."""
 
         # create file containing modules footer
@@ -832,7 +839,7 @@ def test_footer(self):
         # cleanup
         os.remove(modules_footer)
 
-    def test_recursive_module_unload(self):
+    def xtest_recursive_module_unload(self):
         """Test generating recursively unloading modules."""
 
         # use toy-0.0.eb easyconfig file that comes with the tests
@@ -855,7 +862,7 @@ def test_recursive_module_unload(self):
         is_loaded_regex = re.compile(r"if { !\[is-loaded gompi/1.3.12\] }", re.M)
         self.assertFalse(is_loaded_regex.search(toy_module_txt), "Recursive unloading is used: %s" % toy_module_txt)
 
-    def test_tmpdir(self):
+    def xtest_tmpdir(self):
         """Test setting temporary directory to use by EasyBuild."""
 
         # use temporary paths for build/install paths, make sure sources can be found
@@ -891,7 +898,7 @@ def test_tmpdir(self):
         os.close(fd)
         shutil.rmtree(tmpdir)
 
-    def test_ignore_osdeps(self):
+    def xtest_ignore_osdeps(self):
         """Test ignoring of listed OS dependencies."""
         txt = '\n'.join([
             'easyblock = "ConfigureMake"',
@@ -941,7 +948,7 @@ def test_ignore_osdeps(self):
         regex = re.compile("stop provided 'notavalidstop' is not valid", re.M)
         self.assertTrue(regex.search(outtxt), "Validations are performed with --ignore-osdeps, outtxt: %s" % outtxt)
 
-    def test_experimental(self):
+    def xtest_experimental(self):
         """Test the experimental option"""
         orig_value = easybuild.tools.build_log.EXPERIMENTAL
         # make sure it's off by default
@@ -973,7 +980,7 @@ def test_experimental(self):
         # set it back
         easybuild.tools.build_log.EXPERIMENTAL = orig_value
 
-    def test_deprecated(self):
+    def xtest_deprecated(self):
         """Test the deprecated option"""
         if 'EASYBUILD_DEPRECATED' in os.environ:
             os.environ['EASYBUILD_DEPRECATED'] = str(VERSION)
@@ -1020,7 +1027,7 @@ def test_deprecated(self):
         # set it back
         easybuild.tools.build_log.CURRENT_VERSION = orig_value
 
-    def test_allow_modules_tool_mismatch(self):
+    def xtest_allow_modules_tool_mismatch(self):
         """Test allowing mismatch of modules tool with 'module' function."""
         # make sure MockModulesTool is available
         from test.framework.modulestool import MockModulesTool
@@ -1071,7 +1078,7 @@ def test_allow_modules_tool_mismatch(self):
         else:
             del os.environ['module']
 
-    def test_try(self):
+    def xtest_try(self):
         """Test whether --try options are taken into account."""
         ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         tweaked_toy_ec = os.path.join(self.test_buildpath, 'toy-0.0-tweaked.eb')
@@ -1116,7 +1123,7 @@ def test_try(self):
         allargs = args + ['--software-version=1.2.3', '--toolchain=gompi,1.4.10']
         self.assertErrorRegex(EasyBuildError, "version .* not available", self.eb_main, allargs, raise_error=True)
 
-    def test_recursive_try(self):
+    def xtest_recursive_try(self):
         """Test whether recursive --try-X works."""
         ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         tweaked_toy_ec = os.path.join(self.test_buildpath, 'toy-0.0-tweaked.eb')
@@ -1175,7 +1182,7 @@ def test_recursive_try(self):
                 mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
                 self.assertFalse(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 
-    def test_cleanup_builddir(self):
+    def xtest_cleanup_builddir(self):
         """Test cleaning up of build dir and --disable-cleanup-builddir."""
         toy_ec = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
         toy_buildpath = os.path.join(self.test_buildpath, 'toy', '0.0', 'dummy-dummy')
@@ -1203,7 +1210,7 @@ def test_cleanup_builddir(self):
         self.eb_main(args, do_build=True)
         self.assertTrue(os.path.exists(toy_buildpath), "Build dir %s is retained after failed build" % toy_buildpath)
 
-    def test_filter_deps(self):
+    def xtest_filter_deps(self):
         """Test use of --filter-deps."""
         test_dir = os.path.dirname(os.path.abspath(__file__))
         ec_file = os.path.join(test_dir, 'easyconfigs', 'goolf-1.4.10.eb')
@@ -1230,7 +1237,7 @@ def test_filter_deps(self):
         self.assertFalse(re.search('module: ScaLAPACK/2.0.2-gompi', outtxt))
         self.assertFalse(re.search('module: zlib', outtxt))
     
-    def test_test_report_env_filter(self):
+    def xtest_test_report_env_filter(self):
         """Test use of --test-report-env-filter."""
 
         def toy(extra_args=None):
@@ -1279,7 +1286,7 @@ def toy(extra_args=None):
         tup = (filter_arg_regex.pattern, test_report_txt)
         self.assertTrue(filter_arg_regex.search(test_report_txt), "%s in %s" % tup)
 
-    def test_robot(self):
+    def xtest_robot(self):
         """Test --robot and --robot-paths command line options."""
         test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         eb_file = os.path.join(test_ecs_path, 'gzip-1.4-GCC-4.6.3.eb')  # includes 'toy/.0.0-deps' as a dependency

From a4d509a75c32a88db18818ae645d5e71d7ad5b77 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 13:32:42 +0100
Subject: [PATCH 0409/1356] reenable disabled tests

---
 test/framework/options.py | 68 +++++++++++++++++++--------------------
 1 file changed, 34 insertions(+), 34 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index f3c1739e11..728156d5e4 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -54,7 +54,7 @@ class CommandLineOptionsTest(EnhancedTestCase):
 
     logfile = None
 
-    def xtest_help_short(self, txt=None):
+    def test_help_short(self, txt=None):
         """Test short help message."""
 
         if txt is None:
@@ -76,7 +76,7 @@ def xtest_help_short(self, txt=None):
         self.assertEqual(re.search("Software search and build options", outtxt), None, "Not all option groups included in short help (1)")
         self.assertEqual(re.search("Regression test options", outtxt), None, "Not all option groups included in short help (2)")
 
-    def xtest_help_long(self):
+    def test_help_long(self):
         """Test long help message."""
 
         topt = EasyBuildOptions(
@@ -93,7 +93,7 @@ def xtest_help_long(self):
         self.assertTrue(re.search("Software search and build options", outtxt), "Not all option groups included in short help (1)")
         self.assertTrue(re.search("Regression test options", outtxt), "Not all option groups included in short help (2)")
 
-    def xtest_no_args(self):
+    def test_no_args(self):
         """Test using no arguments."""
 
         outtxt = self.eb_main([])
@@ -102,7 +102,7 @@ def xtest_no_args(self):
         error_msg += " or use software build options to make EasyBuild search for easyconfigs"
         self.assertTrue(re.search(error_msg, outtxt), "Error message when eb is run without arguments")
 
-    def xtest_debug(self):
+    def test_debug(self):
         """Test enabling debug logging."""
         for debug_arg in ['-d', '--debug']:
             args = [
@@ -118,7 +118,7 @@ def xtest_debug(self):
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
 
-    def xtest_info(self):
+    def test_info(self):
         """Test enabling info logging."""
 
         for info_arg in ['--info']:
@@ -139,7 +139,7 @@ def xtest_info(self):
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
 
-    def xtest_quiet(self):
+    def test_quiet(self):
         """Test enabling quiet logging (errors only)."""
 
         for quiet_arg in ['--quiet']:
@@ -160,7 +160,7 @@ def xtest_quiet(self):
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
 
-    def xtest_force(self):
+    def test_force(self):
         """Test forcing installation even if the module is already available."""
 
         # use GCC-4.6.3.eb easyconfig file that comes with the tests
@@ -193,7 +193,7 @@ def xtest_force(self):
 
         self.assertTrue(not re.search(already_msg, outtxt), "Already installed message not there with --force")
 
-    def xtest_skip(self):
+    def test_skip(self):
         """Test skipping installation of module (--skip, -k)."""
 
         # use toy-0.0.eb easyconfig file that comes with the tests
@@ -255,7 +255,7 @@ def xtest_skip(self):
         modify_env(os.environ, self.orig_environ)
         modules_tool()
 
-    def xtest_job(self):
+    def test_job(self):
         """Test submitting build as a job."""
 
         # use gzip-1.4.eb easyconfig file that comes with the tests
@@ -291,7 +291,7 @@ def check_args(job_args, passed_args=None):
 
     # 'zzz' prefix in the test name is intentional to make this test run last,
     # since it fiddles with the logging infrastructure which may break things
-    def xtest_zzz_logtostdout(self):
+    def test_zzz_logtostdout(self):
         """Testing redirecting log to stdout."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -331,7 +331,7 @@ def xtest_zzz_logtostdout(self):
             os.remove(dummylogfn)
         fancylogger.logToFile(self.logfile)
 
-    def xtest_avail_easyconfig_params(self):
+    def test_avail_easyconfig_params(self):
         """Test listing available easyconfig parameters."""
 
         def run_test(custom=None, extra_params=[]):
@@ -389,7 +389,7 @@ def run_test(custom=None, extra_params=[]):
 
     # double underscore to make sure it runs first, which is required to detect certain types of bugs,
     # e.g. running with non-initialized EasyBuild config (truly mimicing 'eb --list-toolchains')
-    def xtest__list_toolchains(self):
+    def test__list_toolchains(self):
         """Test listing known compiler toolchains."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -421,7 +421,7 @@ def xtest__list_toolchains(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
-    def xtest_avail_lists(self):
+    def test_avail_lists(self):
         """Test listing available values of certain types."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -454,7 +454,7 @@ def xtest_avail_lists(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
-    def xtest_avail_cfgfile_constants(self):
+    def test_avail_cfgfile_constants(self):
         """Test --avail-cfgfile-constants."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
@@ -487,7 +487,7 @@ def xtest_avail_cfgfile_constants(self):
             os.remove(dummylogfn)
         sys.path[:] = orig_sys_path
 
-    def xtest_list_easyblocks(self):
+    def test_list_easyblocks(self):
         """Test listing easyblock hierarchy."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -549,7 +549,7 @@ def xtest_list_easyblocks(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
-    def xtest_search(self):
+    def test_search(self):
         """Test searching for easyconfigs."""
 
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -590,7 +590,7 @@ def xtest_search(self):
             if os.path.exists(dummylogfn):
                 os.remove(dummylogfn)
 
-    def xtest_dry_run(self):
+    def test_dry_run(self):
         """Test dry run (long format)."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
@@ -613,7 +613,7 @@ def xtest_dry_run(self):
             regex = re.compile(r" \* \[%s\] \S+%s \(module: %s\)" % (mark, ec, mod), re.M)
             self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
 
-    def xtest_dry_run_short(self):
+    def test_dry_run_short(self):
         """Test dry run (short format)."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
@@ -658,7 +658,7 @@ def xtest_dry_run_short(self):
         shutil.rmtree(tmpdir)
         sys.path[:] = orig_sys_path
 
-    def xtest_try_robot_force(self):
+    def test_try_robot_force(self):
         """
         Test correct behavior for combination of --try-toolchain --robot --force.
         Only the listed easyconfigs should be forced, resolved dependencies should not (even if tweaked).
@@ -702,7 +702,7 @@ def xtest_try_robot_force(self):
             regex = re.compile("^ \* \[%s\] \S+%s \(module: %s\)$" % (mark, ec, mod), re.M)
             self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
 
-    def xtest_dry_run_hierarchical(self):
+    def test_dry_run_hierarchical(self):
         """Test dry run using a hierarchical module naming scheme."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
@@ -784,7 +784,7 @@ def test_from_pr(self):
             print "Ignoring URLError '%s' in test_from_pr" % err
             shutil.rmtree(tmpdir)
 
-    def xtest_no_such_software(self):
+    def test_no_such_software(self):
         """Test using no arguments."""
 
         args = [
@@ -801,7 +801,7 @@ def xtest_no_such_software(self):
         msg = "Error message when eb can't find software with specified name (outtxt: %s)" % outtxt
         self.assertTrue(re.search(error_msg1, outtxt) or re.search(error_msg2, outtxt), msg)
 
-    def xtest_footer(self):
+    def test_footer(self):
         """Test specifying a module footer."""
 
         # create file containing modules footer
@@ -839,7 +839,7 @@ def xtest_footer(self):
         # cleanup
         os.remove(modules_footer)
 
-    def xtest_recursive_module_unload(self):
+    def test_recursive_module_unload(self):
         """Test generating recursively unloading modules."""
 
         # use toy-0.0.eb easyconfig file that comes with the tests
@@ -862,7 +862,7 @@ def xtest_recursive_module_unload(self):
         is_loaded_regex = re.compile(r"if { !\[is-loaded gompi/1.3.12\] }", re.M)
         self.assertFalse(is_loaded_regex.search(toy_module_txt), "Recursive unloading is used: %s" % toy_module_txt)
 
-    def xtest_tmpdir(self):
+    def test_tmpdir(self):
         """Test setting temporary directory to use by EasyBuild."""
 
         # use temporary paths for build/install paths, make sure sources can be found
@@ -898,7 +898,7 @@ def xtest_tmpdir(self):
         os.close(fd)
         shutil.rmtree(tmpdir)
 
-    def xtest_ignore_osdeps(self):
+    def test_ignore_osdeps(self):
         """Test ignoring of listed OS dependencies."""
         txt = '\n'.join([
             'easyblock = "ConfigureMake"',
@@ -948,7 +948,7 @@ def xtest_ignore_osdeps(self):
         regex = re.compile("stop provided 'notavalidstop' is not valid", re.M)
         self.assertTrue(regex.search(outtxt), "Validations are performed with --ignore-osdeps, outtxt: %s" % outtxt)
 
-    def xtest_experimental(self):
+    def test_experimental(self):
         """Test the experimental option"""
         orig_value = easybuild.tools.build_log.EXPERIMENTAL
         # make sure it's off by default
@@ -980,7 +980,7 @@ def xtest_experimental(self):
         # set it back
         easybuild.tools.build_log.EXPERIMENTAL = orig_value
 
-    def xtest_deprecated(self):
+    def test_deprecated(self):
         """Test the deprecated option"""
         if 'EASYBUILD_DEPRECATED' in os.environ:
             os.environ['EASYBUILD_DEPRECATED'] = str(VERSION)
@@ -1027,7 +1027,7 @@ def xtest_deprecated(self):
         # set it back
         easybuild.tools.build_log.CURRENT_VERSION = orig_value
 
-    def xtest_allow_modules_tool_mismatch(self):
+    def test_allow_modules_tool_mismatch(self):
         """Test allowing mismatch of modules tool with 'module' function."""
         # make sure MockModulesTool is available
         from test.framework.modulestool import MockModulesTool
@@ -1078,7 +1078,7 @@ def xtest_allow_modules_tool_mismatch(self):
         else:
             del os.environ['module']
 
-    def xtest_try(self):
+    def test_try(self):
         """Test whether --try options are taken into account."""
         ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         tweaked_toy_ec = os.path.join(self.test_buildpath, 'toy-0.0-tweaked.eb')
@@ -1123,7 +1123,7 @@ def xtest_try(self):
         allargs = args + ['--software-version=1.2.3', '--toolchain=gompi,1.4.10']
         self.assertErrorRegex(EasyBuildError, "version .* not available", self.eb_main, allargs, raise_error=True)
 
-    def xtest_recursive_try(self):
+    def test_recursive_try(self):
         """Test whether recursive --try-X works."""
         ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         tweaked_toy_ec = os.path.join(self.test_buildpath, 'toy-0.0-tweaked.eb')
@@ -1182,7 +1182,7 @@ def xtest_recursive_try(self):
                 mod_regex = re.compile("\(module: %s\)$" % mod, re.M)
                 self.assertFalse(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 
-    def xtest_cleanup_builddir(self):
+    def test_cleanup_builddir(self):
         """Test cleaning up of build dir and --disable-cleanup-builddir."""
         toy_ec = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
         toy_buildpath = os.path.join(self.test_buildpath, 'toy', '0.0', 'dummy-dummy')
@@ -1210,7 +1210,7 @@ def xtest_cleanup_builddir(self):
         self.eb_main(args, do_build=True)
         self.assertTrue(os.path.exists(toy_buildpath), "Build dir %s is retained after failed build" % toy_buildpath)
 
-    def xtest_filter_deps(self):
+    def test_filter_deps(self):
         """Test use of --filter-deps."""
         test_dir = os.path.dirname(os.path.abspath(__file__))
         ec_file = os.path.join(test_dir, 'easyconfigs', 'goolf-1.4.10.eb')
@@ -1237,7 +1237,7 @@ def xtest_filter_deps(self):
         self.assertFalse(re.search('module: ScaLAPACK/2.0.2-gompi', outtxt))
         self.assertFalse(re.search('module: zlib', outtxt))
     
-    def xtest_test_report_env_filter(self):
+    def test_test_report_env_filter(self):
         """Test use of --test-report-env-filter."""
 
         def toy(extra_args=None):
@@ -1286,7 +1286,7 @@ def toy(extra_args=None):
         tup = (filter_arg_regex.pattern, test_report_txt)
         self.assertTrue(filter_arg_regex.search(test_report_txt), "%s in %s" % tup)
 
-    def xtest_robot(self):
+    def test_robot(self):
         """Test --robot and --robot-paths command line options."""
         test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         eb_file = os.path.join(test_ecs_path, 'gzip-1.4-GCC-4.6.3.eb')  # includes 'toy/.0.0-deps' as a dependency

From 80033f62d275960c264897476f7947f147d6c350 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 13:42:40 +0100
Subject: [PATCH 0410/1356] bump to v1.16.1 + update release notes

---
 RELEASE_NOTES              | 11 +++++++++++
 easybuild/tools/version.py |  2 +-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 3f94327924..13ef17e9cc 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,6 +3,17 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
+v1.16.1 (December 19th 2014)
+----------------------------
+
+bugfix release
+- fix functionality that is broken with --deprecated=2.0 or with $EASYBUILD_DEPRECATED=2.0
+    - don't include easyconfig parameters for ConfigureMake in eb -a, since fallback is deprecated (#1123)
+    - correctly check software_license value type (#1124)
+    - fix generate_software_list.py script w.r.t. deprecated fallback to ConfigureMake (#1127)
+- other bug fixes
+    - fix logging issues in tests, sync with vsc-base v2.0.0 (#1120)
+
 v1.16.0 (December 18th 2014)
 ----------------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index e47bcb41ec..224892d87b 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.16.1dev")
+VERSION = LooseVersion("1.16.1")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 08b83e587a6f08ac0621ac242f009a2c5d4cfea5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Dec 2014 13:50:48 +0100
Subject: [PATCH 0411/1356] fix tests in tweak.py

---
 test/framework/tweak.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/tweak.py b/test/framework/tweak.py
index 061a0bcf8b..0395bd7d11 100644
--- a/test/framework/tweak.py
+++ b/test/framework/tweak.py
@@ -52,7 +52,7 @@ def test_find_matching_easyconfigs(self):
             self.assertTrue(len(ecs) == 1 and ecs[0].endswith('/%s-%s.eb' % (name, installver)))
 
         ecs = find_matching_easyconfigs('GCC', '*', [test_easyconfigs_path])
-        gccvers = ['4.6.3', '4.6.4', '4.7.2', '4.8.2', '4.8.3']
+        gccvers = ['4.6.3', '4.6.4', '4.7.2', '4.8.2', '4.8.3', '4.9.2']
         self.assertEqual(len(ecs), len(gccvers))
         ecs_basename = [os.path.basename(ec) for ec in ecs]
         for gccver in gccvers:
@@ -96,7 +96,7 @@ def test_obtain_ec_for(self):
         }
         (generated, ec_file) = obtain_ec_for(specs, [test_easyconfigs_path])
         self.assertFalse(generated)
-        self.assertEqual(os.path.basename(ec_file), 'GCC-4.8.3.eb')
+        self.assertEqual(os.path.basename(ec_file), 'GCC-4.9.2.eb')
 
         # generate non-existing easyconfig
         specs = {

From f1d8dad632f7b3d1fc46896e81bd9754aaa4434e Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@gmail.com>
Date: Mon, 22 Dec 2014 18:13:33 +0100
Subject: [PATCH 0412/1356] added tesetcases for fetching patch files, + fix
 them!

* patches with an explicit level 0 had the level ignored
* patches with a boolean as second argument had that boolean interpreted as an int
---
 easybuild/framework/easyblock.py              | 17 ++++++----
 test/framework/easyblock.py                   | 25 +++++++++++++++
 test/framework/easyconfigs/toy-0.0-patches.eb | 32 +++++++++++++++++++
 .../sandbox/sources/toy/toy-0.0_level0.patch  |  0
 .../sources/toy/toy-0.0_level0_2.patch        |  0
 .../sandbox/sources/toy/toy-0.0_level4.patch  |  0
 6 files changed, 68 insertions(+), 6 deletions(-)
 create mode 100644 test/framework/easyconfigs/toy-0.0-patches.eb
 create mode 100644 test/framework/sandbox/sources/toy/toy-0.0_level0.patch
 create mode 100644 test/framework/sandbox/sources/toy/toy-0.0_level0_2.patch
 create mode 100644 test/framework/sandbox/sources/toy/toy-0.0_level4.patch

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index ba37110e6b..19a21c090e 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -304,10 +304,12 @@ def fetch_patches(self, list_of_patches, extension=False, checksums=None):
             level = None
             if isinstance(patch_entry, (list, tuple)):
                 if not len(patch_entry) == 2:
-                    self.log.error("Unknown patch specification '%s', only two-element lists/tuples are supported!" % patch_entry)
+                    self.log.error("Unknown patch specification '%s', only two-element lists/tuples are supported!",
+                                   str(patch_entry))
                 pf = patch_entry[0]
 
-                if isinstance(patch_entry[1], int):
+                if type(patch_entry[1]) == int:  # int and only int is allowed here, we are parsing a config file, not
+                                                 # trying to write generic code
                     level = patch_entry[1]
                 elif isinstance(patch_entry[1], basestring):
                     # non-patch files are assumed to be files to copy
@@ -315,7 +317,10 @@ def fetch_patches(self, list_of_patches, extension=False, checksums=None):
                         copy_file = True
                     suff = patch_entry[1]
                 else:
-                    self.log.error("Wrong patch specification '%s', only int and string are supported as second element!" % patch_entry)
+                    self.log.error(
+                        "Wrong patch specification '%s', only int and string are supported as second element!",
+                        str(patch_entry),
+                        )
             else:
                 pf = patch_entry
 
@@ -332,7 +337,7 @@ def fetch_patches(self, list_of_patches, extension=False, checksums=None):
                         patchspec['copy'] = suff
                     else:
                         patchspec['sourcepath'] = suff
-                if level:
+                if level is not None:
                     patchspec['level'] = level
 
                 if extension:
@@ -1215,7 +1220,7 @@ def fetch_step(self, skip_checksums=False):
         # fetch extensions
         if len(self.cfg['exts_list']) > 0:
             self.exts = self.fetch_extension_sources()
- 
+
         # fetch patches
         if self.cfg['patches']:
             if isinstance(self.cfg['checksums'], (list, tuple)):
@@ -1364,7 +1369,7 @@ def extensions_step(self, fetch=False):
 
         if fetch:
             self.exts = self.fetch_extension_sources()
-            
+
         self.exts_all = self.exts[:]  # retain a copy of all extensions, regardless of filtering/skipping
 
         if self.skip:
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 976c781c9a..0a4353c96f 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -407,6 +407,31 @@ def test_get_easyblock_instance(self):
         logtxt = read_file(eb.logfile)
         self.assertTrue(eb_log_msg_re.search(logtxt), "Pattern '%s' found in: %s" % (eb_log_msg_re.pattern, logtxt))
 
+    def test_patchlevel(self):
+        """Test the parsing of the fetch_patches function."""
+        # adjust PYTHONPATH such that test easyblocks are found
+        testdir = os.path.abspath(os.path.dirname(__file__))
+        ec = process_easyconfig(os.path.join(testdir, 'easyconfigs', 'toy-0.0-patches.eb'))[0]
+        eb = get_easyblock_instance(ec)
+
+        patches = [
+            ('toy-0.0_level0_2.patch',0),  # should also be level 0 (not None)
+            ('toy-0.0_level4.patch',4),   # should be level4
+        ]
+        sandbox_sources = os.path.join(testdir, 'sandbox', 'sources')
+        init_config(args=["--sourcepath=%s" % sandbox_sources])
+        #check if patch levels are parsed correctly
+        eb.fetch_patches(patches)
+
+        self.assertEquals(eb.patches[0]['level'], 0)
+        self.assertEquals(eb.patches[1]['level'], 4)
+
+        patches = [
+            ('toy-0.0_level4.patch', False),  #should throw an error, only int's an strings allowed here
+        ]
+        self.assertRaises(EasyBuildError, eb.fetch_patches, patches)
+
+
     def test_obtain_file(self):
         """Test obtain_file method."""
         toy_tarball = 'toy-0.0.tar.gz'
diff --git a/test/framework/easyconfigs/toy-0.0-patches.eb b/test/framework/easyconfigs/toy-0.0-patches.eb
new file mode 100644
index 0000000000..89994f6681
--- /dev/null
+++ b/test/framework/easyconfigs/toy-0.0-patches.eb
@@ -0,0 +1,32 @@
+name = 'toy'
+version = '0.0'
+
+homepage = 'http://hpcugent.github.com/easybuild'
+description = "Toy C program."
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = [[
+    'be662daa971a640e40be5c804d9d7d10',  # default (MD5)
+    ('adler32', '0x998410035'),
+    ('crc32', '0x1553842328'),
+    ('md5', 'be662daa971a640e40be5c804d9d7d10'),
+    ('sha1', 'f618096c52244539d0e89867405f573fdb0b55b0'),
+    ('size', 273),
+]]
+patches = [
+    'toy-0.0_level0.patch',   # should be level 0
+    ('toy-0.0_level0_2.patch',0),  # should also be level 0 (not None)
+    ('toy-0.0_level4.patch',4),   # should be level4
+    ('toy-0.0_level4.patch', False),  #should throw an error, only int's an strings allowed here
+]
+
+sanity_check_paths = {
+    'files': [('bin/yot', 'bin/toy')],
+    'dirs': ['bin'],
+}
+
+postinstallcmds = ["echo TOY > %(installdir)s/README"]
+
+moduleclass = 'tools'
diff --git a/test/framework/sandbox/sources/toy/toy-0.0_level0.patch b/test/framework/sandbox/sources/toy/toy-0.0_level0.patch
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/framework/sandbox/sources/toy/toy-0.0_level0_2.patch b/test/framework/sandbox/sources/toy/toy-0.0_level0_2.patch
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/framework/sandbox/sources/toy/toy-0.0_level4.patch b/test/framework/sandbox/sources/toy/toy-0.0_level4.patch
new file mode 100644
index 0000000000..e69de29bb2

From ba175ddee0cc733bd09d6136284ad02a714ef09e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Jan 2015 09:38:02 +0100
Subject: [PATCH 0413/1356] add support for 'eb -a rst', clean up
 implementation of existing 'eb -a' which is equivalent to 'eb -a txt'

---
 easybuild/tools/options.py | 151 ++++++++++++++++++++++++++++++-------
 1 file changed, 124 insertions(+), 27 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 59a3503116..456286162b 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -33,6 +33,7 @@
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
 """
+import copy
 import os
 import re
 import sys
@@ -42,7 +43,7 @@
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.constants import constant_documentation
-from easybuild.framework.easyconfig.default import convert_to_help
+from easybuild.framework.easyconfig.default import ALL_CATEGORIES, DEFAULT_CONFIG, HIDDEN, sorted_categories
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.framework.easyconfig.format.pyheaderconfigobj import build_easyconfig_constants_dict
 from easybuild.framework.easyconfig.licenses import license_documentation
@@ -54,6 +55,7 @@
 from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY, DEFAULT_TMP_LOGDIR
 from easybuild.tools.config import get_default_configfiles, get_pretend_installpath
 from easybuild.tools.config import get_default_oldstyle_configfile, mk_full_default_path
+from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
@@ -61,12 +63,17 @@
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.toolchain.utilities import search_toolchain
 from easybuild.tools.repository.repository import avail_repositories
+from easybuild.tools.utilities import quote_str
 from easybuild.tools.version import this_is_easybuild
 from vsc.utils import fancylogger
 from vsc.utils.generaloption import GeneralOption
 from vsc.utils.missing import any
 
 
+FORMAT_RST = 'rst'
+FORMAT_TXT = 'txt'
+
+
 class EasyBuildOptions(GeneralOption):
     """Easybuild generaloption class"""
     VERSION = this_is_easybuild()
@@ -276,7 +283,7 @@ def informative_options(self):
                                           None, 'store_true', False),
             'avail-easyconfig-params': (("Show all easyconfig parameters (include "
                                          "easyblock-specific ones by using -e)"),
-                                         None, "store_true", False, 'a'),
+                                         'choice', 'store_or_None', FORMAT_TXT, [FORMAT_RST, FORMAT_TXT], 'a'),
             'avail-easyconfig-templates': (("Show all template names and template constants "
                                             "that can be used in easyconfigs"),
                                             None, 'store_true', False),
@@ -504,36 +511,126 @@ def avail_cfgfile_constants(self):
                 lines.append("* %s: %s [value: %s]" % (cst_name, cst_help, cst_value))
         return '\n'.join(lines)
 
+    def avail_easyconfig_params_txt(self, title, grouped_params):
+        """
+        Compose overview of available easyconfig parameters, in plain text format.
+        """
+        # main title
+        lines = [
+            '%s:' % title,
+            '',
+        ]
+
+        for grpname in grouped_params:
+            # group section title
+            lines.append(grpname.upper())
+            lines.append('-' * len(lines[-1]))
+
+            # determine width of 'name' column, to left-align descriptions
+            nw = max(map(len, grouped_params[grpname].keys()))
+
+            # line by parameter
+            for name, (descr, dflt) in sorted(grouped_params[grpname].items()):
+                lines.append("{0:<{nw}}   {1:} [default: {2:}]".format(name, descr, str(quote_str(dflt)), nw=nw))
+            lines.append('')
+
+        return '\n'.join(lines)
+    
+    def avail_easyconfig_params_rst(self, title, grouped_params):
+        """
+        Compose overview of available easyconfig parameters, in RST format.
+        """
+        def det_col_width(entries, title):
+            """Determine column width based on column title and list of entries."""
+            return max(map(len, entries + [title]))
+
+        # main title
+        lines = [
+            title,
+            '=' * len(title),
+            '',
+        ]
+
+        for grpname in grouped_params:
+            # group section title
+            lines.append("%s parameters" % grpname)
+            lines.extend(['-' * len(lines[-1]), ''])
+
+            name_title = "**Parameter name**"
+            descr_title = "**Description**"
+            dflt_title = "**Default value**"
+
+            # figure out column widths
+            nw = det_col_width(grouped_params[grpname].keys(), name_title) + 4  # +4 for raw format ("``foo``")
+            dw = det_col_width([x[0] for x in grouped_params[grpname].values()], descr_title)
+            dfw = det_col_width([str(quote_str(x[1])) for x in grouped_params[grpname].values()], dflt_title)
+
+            # 3 columns (name, description, default value), left-aligned, {c} is fill char
+            line_tmpl = "{0:{c}<%s}   {1:{c}<%s}   {2:{c}<%s}" % (nw, dw, dfw)
+            table_line = line_tmpl.format('', '', '', c='=', nw=nw, dw=dw, dfw=dfw)
+
+            # table header
+            lines.append(table_line)
+            lines.append(line_tmpl.format(name_title, descr_title, dflt_title, c=' '))
+            lines.append(line_tmpl.format('', '', '', c='-'))
+
+            # table rows by parameter
+            for name, (descr, dflt) in sorted(grouped_params[grpname].items()):
+                rawname = '``%s``' % name
+                lines.append(line_tmpl.format(rawname, descr, str(quote_str(dflt)), c=' '))
+            lines.append(table_line)
+            lines.append('')
+
+        return '\n'.join(lines)
+
     def avail_easyconfig_params(self):
         """
-        Print the available easyconfig parameters, for the given easyblock.
+        Compose overview of available easyconfig parameters, in specified format.
         """
-        extra = []
+        params = copy.deepcopy(DEFAULT_CONFIG)
+
+        # include list of extra parameters (if any)
+        extra_params = {}
         app = get_easyblock_class(self.options.easyblock, default_fallback=False)
         if app is not None:
-            extra = app.extra_options()
-        mapping = convert_to_help(extra, has_default=False)
-        if extra:
-            ebb_msg = " (* indicates specific for the %s EasyBlock)" % app.__name__
-            extra_names = [x[0] for x in extra]
-        else:
-            ebb_msg = ''
-            extra_names = []
-        txt = ["Available easyconfig parameters%s" % ebb_msg]
-        params = [(k, v) for (k, v) in mapping.items() if k.upper() not in ['HIDDEN']]
-        for key, values in params:
-            txt.append("%s" % key.upper())
-            txt.append('-' * len(key))
-            for name, value in values:
-                tabs = "\t" * (3 - (len(name) + 1) / 8)
-                if name in extra_names:
-                    starred = '(*)'
-                else:
-                    starred = ''
-                txt.append("%s%s:%s%s" % (name, starred, tabs, value))
-            txt.append('')
-
-        return "\n".join(txt)
+            extra_params = app.extra_options()
+        if isinstance(extra_params, ExtraOptionsDeprecatedReturnValue):
+            extra_params = dict(extra_params)
+        params.update(extra_params)
+
+        # compose title
+        title = "Available easyconfig parameters"
+        if extra_params:
+            title += " (* indicates specific to the %s easyblock)" % app.__name__
+
+        # group parameters by category
+        grouped_params = OrderedDict()
+        for category in sorted_categories():
+            # exclude hidden parameters
+            if category[1].upper() in [HIDDEN]:
+                continue
+
+            grpname = category[1]
+            grouped_params[grpname] = {}
+            for name, (dflt, descr, cat) in params.items():
+                # FIXME bug in default.py?
+                if isinstance(cat, basestring):
+                    cat = ALL_CATEGORIES[cat]
+                if cat == category:
+                    if name in extra_params:
+                        # mark easyblock-specific parameters
+                        name = '%s*' % name
+                    grouped_params[grpname].update({name: (descr, dflt)})
+
+            if not grouped_params[grpname]:
+                del grouped_params[grpname]
+
+        # compose output, according to specified format (txt, rst, ...)
+        avail_easyconfig_params_functions = {
+            FORMAT_RST: self.avail_easyconfig_params_rst,
+            FORMAT_TXT: self.avail_easyconfig_params_txt,
+        }
+        return avail_easyconfig_params_functions[self.options.avail_easyconfig_params](title, grouped_params)
 
     def avail_classes_tree(self, classes, classNames, detailed, depth=0):
         """Print list of classes as a tree."""

From 1a85480b19fa281f18596e526d0066b2df430674 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Jan 2015 09:38:27 +0100
Subject: [PATCH 0414/1356] remove convert_to_help function which is no longer
 used

---
 easybuild/framework/easyconfig/default.py | 26 -----------------------
 1 file changed, 26 deletions(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index acc99c33eb..e74b5bb8cd 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -35,8 +35,6 @@
 """
 from vsc.utils import fancylogger
 
-from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
-from easybuild.tools.ordereddict import OrderedDict
 
 _log = fancylogger.getLogger('easyconfig.default', fname=False)
 
@@ -187,30 +185,6 @@ def sorted_categories():
     return categories
 
 
-def convert_to_help(opts, has_default=False):
-    """
-    Converts the given list to a mapping of category -> [(name, help)] (OrderedDict)
-        @param: has_default, if False, add the DEFAULT_CONFIG list
-    """
-    mapping = OrderedDict()
-    if isinstance(opts, dict):
-        opts = opts.items()
-    elif isinstance(opts, ExtraOptionsDeprecatedReturnValue):
-        opts = list(opts)
-    if not has_default:
-        defs = [(k, [def_val, descr, ALL_CATEGORIES[cat]]) for k, (def_val, descr, cat) in DEFAULT_CONFIG.items()]
-        opts = defs + opts
-
-    # sort opts
-    opts.sort()
-
-    for cat in sorted_categories():
-        mapping[cat[1]] = [(opt[0], "%s (default: %s)" % (opt[1][1], opt[1][0]))
-                           for opt in opts if opt[1][2] == cat]
-
-    return mapping
-
-
 def get_easyconfig_parameter_default(param):
     """Get default value for given easyconfig parameter."""
     if param not in DEFAULT_CONFIG:

From 7d952dea7eaa36499050dc8a9164e40a79f5d728 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Jan 2015 10:40:59 +0100
Subject: [PATCH 0415/1356] enhance test_avail_easyconfig_params test to check
 both txt/rst output formats

---
 test/framework/options.py | 41 +++++++++++++++++++++++----------------
 1 file changed, 24 insertions(+), 17 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 728156d5e4..e3131507f6 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -334,24 +334,27 @@ def test_zzz_logtostdout(self):
     def test_avail_easyconfig_params(self):
         """Test listing available easyconfig parameters."""
 
-        def run_test(custom=None, extra_params=[]):
+        def run_test(custom=None, extra_params=[], fmt=None):
             """Inner function to run actual test in current setting."""
 
             fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
             os.close(fd)
 
-            for avail_arg in [
-                              '-a',
-                              '--avail-easyconfig-params',
-                             ]:
+            avail_args = [
+                '-a',
+                '--avail-easyconfig-params',
+            ]
+            for avail_arg in avail_args:
 
                 # clear log
                 write_file(self.logfile, '')
 
                 args = [
-                    avail_arg,
                     '--unittest-file=%s' % self.logfile,
+                    avail_arg,
                 ]
+                if fmt is not None:
+                    args.append(fmt)
                 if custom is not None:
                     args.extend(['-e', custom])
 
@@ -364,17 +367,20 @@ def run_test(custom=None, extra_params=[]):
                     par_types.append(CUSTOM)
 
                 for param_type in [x[1] for x in par_types]:
-                    self.assertTrue(re.search("%s\n%s" % (param_type.upper(), '-' * len(param_type)), outtxt),
-                                    "Parameter type %s is featured in output of eb %s (args: %s): %s" %
-                                    (param_type, avail_arg, args, outtxt))
+                    # regex for parameter group title, matches both txt and rst formats
+                    regex = re.compile("%s.*\n%s" % (param_type, '-' * len(param_type)), re.I)
+                    tup = (param_type, avail_arg, args, outtxt)
+                    msg = "Parameter type %s is featured in output of eb %s (args: %s): %s" % tup
+                    self.assertTrue(regex.search(outtxt), msg)
 
                 # check a couple of easyconfig parameters
                 for param in ["name", "version", "toolchain", "versionsuffix", "buildopts", "sources", "start_dir",
                               "dependencies", "group", "exts_list", "moduleclass", "buildstats"] + extra_params:
-                    self.assertTrue(re.search("%s(?:\(\*\))?:\s*\w.*" % param, outtxt),
-                                    "Parameter %s is listed with help in output of eb %s (args: %s): %s" %
-                                    (param, avail_arg, args, outtxt)
-                                    )
+                    # regex for parameter name (with optional '*') & description, matches both txt and rst formats
+                    regex = re.compile("^[`]*%s(?:\*)?[`]*\s+\w+" % param, re.M)
+                    tup = (param, avail_arg, args, regex.pattern, outtxt)
+                    msg = "Parameter %s is listed with help in output of eb %s (args: %s, regex: %s): %s" % tup
+                    self.assertTrue(regex.search(outtxt), msg)
 
                 modify_env(os.environ, self.orig_environ)
                 tempfile.tempdir = None
@@ -382,10 +388,11 @@ def run_test(custom=None, extra_params=[]):
             if os.path.exists(dummylogfn):
                 os.remove(dummylogfn)
 
-        run_test()
-        run_test(custom='EB_foo', extra_params=['foo_extra1', 'foo_extra2'])
-        run_test(custom='bar', extra_params=['bar_extra1', 'bar_extra2'])
-        run_test(custom='EB_foofoo', extra_params=['foofoo_extra1', 'foofoo_extra2'])
+        for fmt in [None, 'txt', 'rst']:
+            run_test(fmt=fmt)
+            run_test(custom='EB_foo', extra_params=['foo_extra1', 'foo_extra2'], fmt=fmt)
+            run_test(custom='bar', extra_params=['bar_extra1', 'bar_extra2'], fmt=fmt)
+            run_test(custom='EB_foofoo', extra_params=['foofoo_extra1', 'foofoo_extra2'], fmt=fmt)
 
     # double underscore to make sure it runs first, which is required to detect certain types of bugs,
     # e.g. running with non-initialized EasyBuild config (truly mimicing 'eb --list-toolchains')

From 3f0764168716fe3414f65f7bea49627eb5e7a22f Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Fri, 9 Jan 2015 11:38:27 +0100
Subject: [PATCH 0416/1356] Choose a easyconfig from a PR

eb --from-pr XX file.eb now works. It will only install the file.eb
easyconfig but using all deps in the PR.
---
 easybuild/framework/easyconfig/tools.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 45f8659f06..555df096a0 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -34,6 +34,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Toon Willems (Ghent University)
 @author: Fotis Georgatos (Uni.Lu, NTUA)
+@author: Ward Poelmans (Ghent University)
 """
 
 import os
@@ -248,12 +249,15 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
     if easyconfigs_pkg_paths is None:
         easyconfigs_pkg_paths = []
 
+    if from_pr is not None:
+        pr_files = fetch_easyconfigs_from_pr(from_pr)
+
     ec_files = orig_paths[:]
 
-    if not ec_files and from_pr:
-        pr_files = fetch_easyconfigs_from_pr(from_pr)
+    if not ec_files and pr_files:
         ec_files = [path for path in pr_files if path.endswith('.eb')]
-
+    elif ec_files and pr_files:
+        ec_files = [path for path in pr_files if os.path.basename(path) in orig_paths]
     elif ec_files and easyconfigs_pkg_paths:
         # look for easyconfigs with relative paths in easybuild-easyconfigs package,
         # unless they were found at the given relative paths
@@ -282,7 +286,7 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
                     break
 
                 # ignore subdirs specified to be ignored by replacing items in dirnames list used by os.walk
-                dirnames[:] = [d for d in dirnames if not d in build_option('ignore_dirs')]
+                dirnames[:] = [d for d in dirnames if d not in build_option('ignore_dirs')]
 
             # stop os.walk insanity as soon as we have all we need (outer loop)
             if not ecs_to_find:

From 5804b75aec34b7420e000c10f532a6ccaa1db114 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Fri, 9 Jan 2015 12:06:08 +0100
Subject: [PATCH 0417/1356] Fix bug

---
 easybuild/framework/easyconfig/tools.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 555df096a0..b4fd674208 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -249,6 +249,7 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
     if easyconfigs_pkg_paths is None:
         easyconfigs_pkg_paths = []
 
+    pr_files = None
     if from_pr is not None:
         pr_files = fetch_easyconfigs_from_pr(from_pr)
 

From c66155a005ac80ecb9d7c847596c5b9e9af02567 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Jan 2015 13:42:23 +0100
Subject: [PATCH 0418/1356] fix from_pr test by including dummy easyblocks for
 HPL and ScaLAPACK

---
 test/framework/options.py                     | 17 +++++++++-
 .../sandbox/easybuild/easyblocks/hpl.py       | 33 +++++++++++++++++++
 .../sandbox/easybuild/easyblocks/scalapack.py | 33 +++++++++++++++++++
 3 files changed, 82 insertions(+), 1 deletion(-)
 create mode 100644 test/framework/sandbox/easybuild/easyblocks/hpl.py
 create mode 100644 test/framework/sandbox/easybuild/easyblocks/scalapack.py

diff --git a/test/framework/options.py b/test/framework/options.py
index 728156d5e4..580835d0a8 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -747,9 +747,22 @@ def test_from_pr(self):
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
+        orig_sys_path = sys.path[:]
+
+        # adjust PYTHONPATH such that test easyblocks are found
+        # this is required since the HPL and ScaLAPACK easyconfigs included in the tested PR have no 'easyblock' spec
+        import easybuild
+        eb_blocks_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'sandbox'))
+        if not eb_blocks_path in sys.path:
+            sys.path.append(eb_blocks_path)
+            easybuild = reload(easybuild)
+
+        import easybuild.easyblocks
+        reload(easybuild.easyblocks)
+
         tmpdir = tempfile.mkdtemp()
         args = [
-            # PR for intel/2014b, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1239/files
+            # PR for foss/2015a, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1239/files
             '--from-pr=1239',
             '--dry-run',
             # an argument must be specified to --robot, since easybuild-easyconfigs may not be installed
@@ -784,6 +797,8 @@ def test_from_pr(self):
             print "Ignoring URLError '%s' in test_from_pr" % err
             shutil.rmtree(tmpdir)
 
+        sys.path = orig_sys_path
+
     def test_no_such_software(self):
         """Test using no arguments."""
 
diff --git a/test/framework/sandbox/easybuild/easyblocks/hpl.py b/test/framework/sandbox/easybuild/easyblocks/hpl.py
new file mode 100644
index 0000000000..1ef029f6c1
--- /dev/null
+++ b/test/framework/sandbox/easybuild/easyblocks/hpl.py
@@ -0,0 +1,33 @@
+##
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Dummy easyblock for HPL
+
+@author: Kenneth Hoste (Ghent University)
+"""
+from easybuild.framework.easyblock import EasyBlock
+
+class EB_HPL(EasyBlock):
+    pass
diff --git a/test/framework/sandbox/easybuild/easyblocks/scalapack.py b/test/framework/sandbox/easybuild/easyblocks/scalapack.py
new file mode 100644
index 0000000000..4534a5cd10
--- /dev/null
+++ b/test/framework/sandbox/easybuild/easyblocks/scalapack.py
@@ -0,0 +1,33 @@
+##
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Dummy easyblock for ScaLAPACK
+
+@author: Kenneth Hoste (Ghent University)
+"""
+from easybuild.framework.easyblock import EasyBlock
+
+class EB_ScaLAPACK(EasyBlock):
+    pass

From 8dc734426f357e6a8f3eab858fb6e7793ef1a5b3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Jan 2015 14:43:01 +0100
Subject: [PATCH 0419/1356] change semantics w.r.t. synergy between --from-pr
 and specified easyconfigs

---
 easybuild/framework/easyconfig/tools.py | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index b4fd674208..da3af771ac 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -249,17 +249,23 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
     if easyconfigs_pkg_paths is None:
         easyconfigs_pkg_paths = []
 
-    pr_files = None
+    # list of specified easyconfig files
+    ec_files = orig_paths[:]
+
     if from_pr is not None:
         pr_files = fetch_easyconfigs_from_pr(from_pr)
 
-    ec_files = orig_paths[:]
+        if ec_files:
+            # replace paths for specified easyconfigs that are touched in PR
+            for i, ec_file in enumerate(ec_files):
+                for pr_file in pr_files:
+                    if ec_file == os.path.basename(pr_file):
+                        ec_files[i] = pr_file
+        else:
+            # if no easyconfigs are specified, use all the ones touched in the PR
+            ec_files = [path for path in pr_files if path.endswith('.eb')]
 
-    if not ec_files and pr_files:
-        ec_files = [path for path in pr_files if path.endswith('.eb')]
-    elif ec_files and pr_files:
-        ec_files = [path for path in pr_files if os.path.basename(path) in orig_paths]
-    elif ec_files and easyconfigs_pkg_paths:
+    if ec_files and easyconfigs_pkg_paths:
         # look for easyconfigs with relative paths in easybuild-easyconfigs package,
         # unless they were found at the given relative paths
 

From 763be8835251e3ed09df21943cb4261b4e269e55 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Jan 2015 16:01:37 +0100
Subject: [PATCH 0420/1356] add unit test for enhanced --from-pr functionality

---
 test/framework/options.py | 94 ++++++++++++++++++++++++++++-----------
 1 file changed, 68 insertions(+), 26 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 580835d0a8..6cb7d80c03 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -747,19 +747,6 @@ def test_from_pr(self):
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
-        orig_sys_path = sys.path[:]
-
-        # adjust PYTHONPATH such that test easyblocks are found
-        # this is required since the HPL and ScaLAPACK easyconfigs included in the tested PR have no 'easyblock' spec
-        import easybuild
-        eb_blocks_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'sandbox'))
-        if not eb_blocks_path in sys.path:
-            sys.path.append(eb_blocks_path)
-            easybuild = reload(easybuild)
-
-        import easybuild.easyblocks
-        reload(easybuild.easyblocks)
-
         tmpdir = tempfile.mkdtemp()
         args = [
             # PR for foss/2015a, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1239/files
@@ -774,22 +761,27 @@ def test_from_pr(self):
         try:
             outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True)
             modules = [
-                'FFTW/3.3.4-gompi-2015a',
-                'foss/2015a',
-                'GCC/4.9.2',
-                'gompi/2015a',
-                'HPL/2.1-foss-2015a',
-                'hwloc/1.10.0-GCC-4.9.2',
-                'numactl/2.0.10-GCC-4.9.2',
-                'OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0',
-                'OpenMPI/1.8.3-GCC-4.9.2',
-                'ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0',
+                (tmpdir, 'FFTW/3.3.4-gompi-2015a'),
+                (tmpdir, 'foss/2015a'),
+                ('.*', 'GCC/4.9.2'),  # not included in PR
+                (tmpdir, 'gompi/2015a'),
+                (tmpdir, 'HPL/2.1-foss-2015a'),
+                (tmpdir, 'hwloc/1.10.0-GCC-4.9.2'),
+                (tmpdir, 'numactl/2.0.10-GCC-4.9.2'),
+                (tmpdir, 'OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0'),
+                (tmpdir, 'OpenMPI/1.8.3-GCC-4.9.2'),
+                (tmpdir, 'OpenMPI/1.8.4-GCC-4.9.2'),
+                (tmpdir, 'ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0'),
             ]
-            for module in modules:
+            for path_prefix, module in modules:
                 ec_fn = "%s.eb" % '-'.join(module.split('/'))
-                regex = re.compile(r"^ \* \[.\] .*/%s \(module: %s\)$" % (ec_fn, module), re.M)
+                regex = re.compile(r"^ \* \[.\] %s.*%s \(module: %s\)$" % (path_prefix, ec_fn, module), re.M)
                 self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
 
+            # make sure that *only* these modules are listed, no others
+            regex = re.compile(r"^ \* \[.\] .*/(?P<filepath>.*) \(module: (?P<module>.*)\)$", re.M)
+            self.assertTrue(sorted(regex.findall(outtxt)), sorted(modules))
+
             pr_tmpdir = os.path.join(tmpdir, 'easybuild-\S{6}', 'files_pr1239')
             regex = re.compile("Prepended list of robot search paths with %s:" % pr_tmpdir, re.M)
             self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
@@ -797,7 +789,57 @@ def test_from_pr(self):
             print "Ignoring URLError '%s' in test_from_pr" % err
             shutil.rmtree(tmpdir)
 
-        sys.path = orig_sys_path
+    def test_from_pr_listed_ecs(self):
+        """Test --from-pr in combination with specifying easyconfigs on the command line."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        # copy test easyconfigs to easybuild/easyconfigs subdirectory of temp directory
+        test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        ecstmpdir = tempfile.mkdtemp(prefix='easybuild-easyconfigs-pkg-install-path')
+        mkdir(os.path.join(ecstmpdir, 'easybuild'), parents=True)
+        shutil.copytree(test_ecs_path, os.path.join(ecstmpdir, 'easybuild', 'easyconfigs'))
+
+        # inject path to test easyconfigs into head of Python search path
+        sys.path.insert(0, ecstmpdir)
+
+        tmpdir = tempfile.mkdtemp()
+        args = [
+            'toy-0.0.eb',
+            'gompi-2015a.eb',  # also pulls in GCC, OpenMPI (which pulls in hwloc and numactl)
+            'GCC-4.6.3.eb',
+            # PR for foss/2015a, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1239/files
+            '--from-pr=1239',
+            '--dry-run',
+            # an argument must be specified to --robot, since easybuild-easyconfigs may not be installed
+            '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+            '--unittest-file=%s' % self.logfile,
+            '--github-user=easybuild_test',  # a GitHub token should be available for this user
+            '--tmpdir=%s' % tmpdir,
+        ]
+        try:
+            outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True)
+            modules = [
+                (ecstmpdir, 'toy/0.0'),
+                ('.*', 'GCC/4.9.2'),  # not included in PR
+                (tmpdir, 'hwloc/1.10.0-GCC-4.9.2'),
+                (tmpdir, 'numactl/2.0.10-GCC-4.9.2'),
+                (tmpdir, 'OpenMPI/1.8.4-GCC-4.9.2'),
+                (tmpdir, 'gompi/2015a'),
+                ('.*', 'GCC/4.6.3'),
+            ]
+            for path_prefix, module in modules:
+                ec_fn = "%s.eb" % '-'.join(module.split('/'))
+                regex = re.compile(r"^ \* \[.\] %s.*%s \(module: %s\)$" % (path_prefix, ec_fn, module), re.M)
+                self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
+
+            # make sure that *only* these modules are listed, no others
+            regex = re.compile(r"^ \* \[.\] .*/(?P<filepath>.*) \(module: (?P<module>.*)\)$", re.M)
+            self.assertTrue(sorted(regex.findall(outtxt)), sorted(modules))
+
+        except URLError, err:
+            print "Ignoring URLError '%s' in test_from_pr" % err
+            shutil.rmtree(tmpdir)
 
     def test_no_such_software(self):
         """Test using no arguments."""

From 38583f44e1dfe6096adb41714305e9bc198c91e8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Jan 2015 18:30:06 +0100
Subject: [PATCH 0421/1356] flesh out functions related to 'eb -a' support into
 new modules easybuild.tools.docs

---
 easybuild/tools/docs.py    | 168 +++++++++++++++++++++++++++++++++++++
 easybuild/tools/options.py | 133 +----------------------------
 2 files changed, 170 insertions(+), 131 deletions(-)
 create mode 100644 easybuild/tools/docs.py

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
new file mode 100644
index 0000000000..ff79f2e2df
--- /dev/null
+++ b/easybuild/tools/docs.py
@@ -0,0 +1,168 @@
+# #
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Documentation-related functionality
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+@author: Toon Willems (Ghent University)
+@author: Ward Poelmans (Ghent University)
+"""
+import copy
+
+from easybuild.framework.easyconfig.default import ALL_CATEGORIES, DEFAULT_CONFIG, HIDDEN, sorted_categories
+from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
+from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
+from easybuild.tools.ordereddict import OrderedDict
+from easybuild.tools.utilities import quote_str
+
+
+FORMAT_RST = 'rst'
+FORMAT_TXT = 'txt'
+
+
+def avail_easyconfig_params_rst(title, grouped_params):
+    """
+    Compose overview of available easyconfig parameters, in RST format.
+    """
+    def det_col_width(entries, title):
+        """Determine column width based on column title and list of entries."""
+        return max(map(len, entries + [title]))
+
+    # main title
+    lines = [
+        title,
+        '=' * len(title),
+        '',
+    ]
+
+    for grpname in grouped_params:
+        # group section title
+        lines.append("%s parameters" % grpname)
+        lines.extend(['-' * len(lines[-1]), ''])
+
+        name_title = "**Parameter name**"
+        descr_title = "**Description**"
+        dflt_title = "**Default value**"
+
+        # figure out column widths
+        nw = det_col_width(grouped_params[grpname].keys(), name_title) + 4  # +4 for raw format ("``foo``")
+        dw = det_col_width([x[0] for x in grouped_params[grpname].values()], descr_title)
+        dfw = det_col_width([str(quote_str(x[1])) for x in grouped_params[grpname].values()], dflt_title)
+
+        # 3 columns (name, description, default value), left-aligned, {c} is fill char
+        line_tmpl = "{0:{c}<%s}   {1:{c}<%s}   {2:{c}<%s}" % (nw, dw, dfw)
+        table_line = line_tmpl.format('', '', '', c='=', nw=nw, dw=dw, dfw=dfw)
+
+        # table header
+        lines.append(table_line)
+        lines.append(line_tmpl.format(name_title, descr_title, dflt_title, c=' '))
+        lines.append(line_tmpl.format('', '', '', c='-'))
+
+        # table rows by parameter
+        for name, (descr, dflt) in sorted(grouped_params[grpname].items()):
+            rawname = '``%s``' % name
+            lines.append(line_tmpl.format(rawname, descr, str(quote_str(dflt)), c=' '))
+        lines.append(table_line)
+        lines.append('')
+
+    return '\n'.join(lines)
+
+def avail_easyconfig_params_txt(title, grouped_params):
+    """
+    Compose overview of available easyconfig parameters, in plain text format.
+    """
+    # main title
+    lines = [
+        '%s:' % title,
+        '',
+    ]
+
+    for grpname in grouped_params:
+        # group section title
+        lines.append(grpname.upper())
+        lines.append('-' * len(lines[-1]))
+
+        # determine width of 'name' column, to left-align descriptions
+        nw = max(map(len, grouped_params[grpname].keys()))
+
+        # line by parameter
+        for name, (descr, dflt) in sorted(grouped_params[grpname].items()):
+            lines.append("{0:<{nw}}   {1:} [default: {2:}]".format(name, descr, str(quote_str(dflt)), nw=nw))
+        lines.append('')
+
+    return '\n'.join(lines)
+
+def avail_easyconfig_params(easyblock, output_format):
+    """
+    Compose overview of available easyconfig parameters, in specified format.
+    """
+    params = copy.deepcopy(DEFAULT_CONFIG)
+
+    # include list of extra parameters (if any)
+    extra_params = {}
+    app = get_easyblock_class(easyblock, default_fallback=False)
+    if app is not None:
+        extra_params = app.extra_options()
+    if isinstance(extra_params, ExtraOptionsDeprecatedReturnValue):
+        extra_params = dict(extra_params)
+    params.update(extra_params)
+
+    # compose title
+    title = "Available easyconfig parameters"
+    if extra_params:
+        title += " (* indicates specific to the %s easyblock)" % app.__name__
+
+    # group parameters by category
+    grouped_params = OrderedDict()
+    for category in sorted_categories():
+        # exclude hidden parameters
+        if category[1].upper() in [HIDDEN]:
+            continue
+
+        grpname = category[1]
+        grouped_params[grpname] = {}
+        for name, (dflt, descr, cat) in params.items():
+            # FIXME bug in default.py?
+            if isinstance(cat, basestring):
+                cat = ALL_CATEGORIES[cat]
+            if cat == category:
+                if name in extra_params:
+                    # mark easyblock-specific parameters
+                    name = '%s*' % name
+                grouped_params[grpname].update({name: (descr, dflt)})
+
+        if not grouped_params[grpname]:
+            del grouped_params[grpname]
+
+    # compose output, according to specified format (txt, rst, ...)
+    avail_easyconfig_params_functions = {
+        FORMAT_RST: avail_easyconfig_params_rst,
+        FORMAT_TXT: avail_easyconfig_params_txt,
+    }
+    return avail_easyconfig_params_functions[output_format](title, grouped_params)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 456286162b..1d4472b353 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -33,7 +33,6 @@
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
 """
-import copy
 import os
 import re
 import sys
@@ -43,8 +42,6 @@
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.constants import constant_documentation
-from easybuild.framework.easyconfig.default import ALL_CATEGORIES, DEFAULT_CONFIG, HIDDEN, sorted_categories
-from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.framework.easyconfig.format.pyheaderconfigobj import build_easyconfig_constants_dict
 from easybuild.framework.easyconfig.licenses import license_documentation
 from easybuild.framework.easyconfig.templates import template_documentation
@@ -55,7 +52,7 @@
 from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY, DEFAULT_TMP_LOGDIR
 from easybuild.tools.config import get_default_configfiles, get_pretend_installpath
 from easybuild.tools.config import get_default_oldstyle_configfile, mk_full_default_path
-from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
+from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
@@ -63,17 +60,12 @@
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.toolchain.utilities import search_toolchain
 from easybuild.tools.repository.repository import avail_repositories
-from easybuild.tools.utilities import quote_str
 from easybuild.tools.version import this_is_easybuild
 from vsc.utils import fancylogger
 from vsc.utils.generaloption import GeneralOption
 from vsc.utils.missing import any
 
 
-FORMAT_RST = 'rst'
-FORMAT_TXT = 'txt'
-
-
 class EasyBuildOptions(GeneralOption):
     """Easybuild generaloption class"""
     VERSION = this_is_easybuild()
@@ -450,7 +442,7 @@ def _postprocess_list_avail(self):
 
         # dump possible easyconfig params
         if self.options.avail_easyconfig_params:
-            msg += self.avail_easyconfig_params()
+            msg += avail_easyconfig_params(self.options.easyblock, self.options.avail_easyconfig_params)
 
         # dump easyconfig template options
         if self.options.avail_easyconfig_templates:
@@ -511,127 +503,6 @@ def avail_cfgfile_constants(self):
                 lines.append("* %s: %s [value: %s]" % (cst_name, cst_help, cst_value))
         return '\n'.join(lines)
 
-    def avail_easyconfig_params_txt(self, title, grouped_params):
-        """
-        Compose overview of available easyconfig parameters, in plain text format.
-        """
-        # main title
-        lines = [
-            '%s:' % title,
-            '',
-        ]
-
-        for grpname in grouped_params:
-            # group section title
-            lines.append(grpname.upper())
-            lines.append('-' * len(lines[-1]))
-
-            # determine width of 'name' column, to left-align descriptions
-            nw = max(map(len, grouped_params[grpname].keys()))
-
-            # line by parameter
-            for name, (descr, dflt) in sorted(grouped_params[grpname].items()):
-                lines.append("{0:<{nw}}   {1:} [default: {2:}]".format(name, descr, str(quote_str(dflt)), nw=nw))
-            lines.append('')
-
-        return '\n'.join(lines)
-    
-    def avail_easyconfig_params_rst(self, title, grouped_params):
-        """
-        Compose overview of available easyconfig parameters, in RST format.
-        """
-        def det_col_width(entries, title):
-            """Determine column width based on column title and list of entries."""
-            return max(map(len, entries + [title]))
-
-        # main title
-        lines = [
-            title,
-            '=' * len(title),
-            '',
-        ]
-
-        for grpname in grouped_params:
-            # group section title
-            lines.append("%s parameters" % grpname)
-            lines.extend(['-' * len(lines[-1]), ''])
-
-            name_title = "**Parameter name**"
-            descr_title = "**Description**"
-            dflt_title = "**Default value**"
-
-            # figure out column widths
-            nw = det_col_width(grouped_params[grpname].keys(), name_title) + 4  # +4 for raw format ("``foo``")
-            dw = det_col_width([x[0] for x in grouped_params[grpname].values()], descr_title)
-            dfw = det_col_width([str(quote_str(x[1])) for x in grouped_params[grpname].values()], dflt_title)
-
-            # 3 columns (name, description, default value), left-aligned, {c} is fill char
-            line_tmpl = "{0:{c}<%s}   {1:{c}<%s}   {2:{c}<%s}" % (nw, dw, dfw)
-            table_line = line_tmpl.format('', '', '', c='=', nw=nw, dw=dw, dfw=dfw)
-
-            # table header
-            lines.append(table_line)
-            lines.append(line_tmpl.format(name_title, descr_title, dflt_title, c=' '))
-            lines.append(line_tmpl.format('', '', '', c='-'))
-
-            # table rows by parameter
-            for name, (descr, dflt) in sorted(grouped_params[grpname].items()):
-                rawname = '``%s``' % name
-                lines.append(line_tmpl.format(rawname, descr, str(quote_str(dflt)), c=' '))
-            lines.append(table_line)
-            lines.append('')
-
-        return '\n'.join(lines)
-
-    def avail_easyconfig_params(self):
-        """
-        Compose overview of available easyconfig parameters, in specified format.
-        """
-        params = copy.deepcopy(DEFAULT_CONFIG)
-
-        # include list of extra parameters (if any)
-        extra_params = {}
-        app = get_easyblock_class(self.options.easyblock, default_fallback=False)
-        if app is not None:
-            extra_params = app.extra_options()
-        if isinstance(extra_params, ExtraOptionsDeprecatedReturnValue):
-            extra_params = dict(extra_params)
-        params.update(extra_params)
-
-        # compose title
-        title = "Available easyconfig parameters"
-        if extra_params:
-            title += " (* indicates specific to the %s easyblock)" % app.__name__
-
-        # group parameters by category
-        grouped_params = OrderedDict()
-        for category in sorted_categories():
-            # exclude hidden parameters
-            if category[1].upper() in [HIDDEN]:
-                continue
-
-            grpname = category[1]
-            grouped_params[grpname] = {}
-            for name, (dflt, descr, cat) in params.items():
-                # FIXME bug in default.py?
-                if isinstance(cat, basestring):
-                    cat = ALL_CATEGORIES[cat]
-                if cat == category:
-                    if name in extra_params:
-                        # mark easyblock-specific parameters
-                        name = '%s*' % name
-                    grouped_params[grpname].update({name: (descr, dflt)})
-
-            if not grouped_params[grpname]:
-                del grouped_params[grpname]
-
-        # compose output, according to specified format (txt, rst, ...)
-        avail_easyconfig_params_functions = {
-            FORMAT_RST: self.avail_easyconfig_params_rst,
-            FORMAT_TXT: self.avail_easyconfig_params_txt,
-        }
-        return avail_easyconfig_params_functions[self.options.avail_easyconfig_params](title, grouped_params)
-
     def avail_classes_tree(self, classes, classNames, detailed, depth=0):
         """Print list of classes as a tree."""
         txt = []

From 10aae861ade7e1fd0814d1a4e1421c3f3e9e3bf8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Jan 2015 21:09:02 +0100
Subject: [PATCH 0422/1356] fix wrongly defined constants for easyconfig
 parameter categories in framework/easyconfig/default.py

---
 easybuild/framework/easyconfig/default.py    | 44 ++++++++++----------
 easybuild/framework/easyconfig/easyconfig.py |  7 +---
 easybuild/tools/docs.py                      |  5 +--
 3 files changed, 25 insertions(+), 31 deletions(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index e74b5bb8cd..1c251a7629 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -40,30 +40,30 @@
 
 
 # we use a tuple here so we can sort them based on the numbers
-HIDDEN = "HIDDEN"
-MANDATORY = "MANDATORY"
-CUSTOM = "CUSTOM"
-TOOLCHAIN = "TOOLCHAIN"
-BUILD = "BUILD"
-FILEMANAGEMENT = "FILEMANAGEMENT"
-DEPENDENCIES = "DEPENDENCIES"
-LICENSE = "LICENSE"
-EXTENSIONS = "EXTENSIONS"
-MODULES = "MODULES"
-OTHER = "OTHER"
+HIDDEN = (-1, 'hidden')
+MANDATORY = (0, 'mandatory')
+CUSTOM = (1, 'easyblock-specific')
+TOOLCHAIN = (2, 'toolchain')
+BUILD = (3, 'build')
+FILEMANAGEMENT = (4, 'file-management')
+DEPENDENCIES = (5, 'dependencies')
+LICENSE = (6, 'license')
+EXTENSIONS = (7, 'extensions')
+MODULES = (8, 'modules')
+OTHER = (9, 'other')
 
 ALL_CATEGORIES = {
-    HIDDEN: (-1, 'hidden'),
-    MANDATORY: (0, 'mandatory'),
-    CUSTOM: (1, 'easyblock-specific'),
-    TOOLCHAIN: (2, 'toolchain'),
-    BUILD: (3, 'build'),
-    FILEMANAGEMENT: (4, 'file-management'),
-    DEPENDENCIES: (5, 'dependencies'),
-    LICENSE: (6, 'license'),
-    EXTENSIONS: (7, 'extensions'),
-    MODULES: (8, 'modules'),
-    OTHER: (9, 'other'),
+    'HIDDEN': HIDDEN,
+    'MANDATORY': MANDATORY,
+    'CUSTOM': CUSTOM,
+    'TOOLCHAIN': TOOLCHAIN,
+    'BUILD': BUILD,
+    'FILEMANAGEMENT': FILEMANAGEMENT,
+    'DEPENDENCIES': DEPENDENCIES,
+    'LICENSE': LICENSE,
+    'EXTENSIONS': EXTENSIONS,
+    'MODULES': MODULES,
+    'OTHER': OTHER,
 }
 
 # List of tuples. Each tuple has the following format (key, [default, help text, category])
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 9a9936265b..94bc9c9db0 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -57,7 +57,7 @@
 from easybuild.tools.toolchain.utilities import get_toolchain
 from easybuild.tools.utilities import remove_unwanted_chars
 from easybuild.framework.easyconfig import MANDATORY
-from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, ALL_CATEGORIES, get_easyconfig_parameter_default
+from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, get_easyconfig_parameter_default
 from easybuild.framework.easyconfig.format.convert import Dependency
 from easybuild.framework.easyconfig.format.one import retrieve_blocks_in_spec
 from easybuild.framework.easyconfig.licenses import EASYCONFIG_LICENSES_DICT, License
@@ -150,10 +150,7 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         if self.valid_module_classes is not None:
             self.log.info("Obtained list of valid module classes: %s" % self.valid_module_classes)
 
-        # replace the category name with the category
-        self._config = {}
-        for k, [def_val, descr, cat] in copy.deepcopy(DEFAULT_CONFIG).items():
-            self._config[k] = [def_val, descr, ALL_CATEGORIES[cat]]
+        self._config = copy.deepcopy(DEFAULT_CONFIG)
 
         if extra_options is None:
             name = fetch_parameter_from_easyconfig_file(path, 'name')
diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index ff79f2e2df..4e64029e7a 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -35,7 +35,7 @@
 """
 import copy
 
-from easybuild.framework.easyconfig.default import ALL_CATEGORIES, DEFAULT_CONFIG, HIDDEN, sorted_categories
+from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, HIDDEN, sorted_categories
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
 from easybuild.tools.ordereddict import OrderedDict
@@ -148,9 +148,6 @@ def avail_easyconfig_params(easyblock, output_format):
         grpname = category[1]
         grouped_params[grpname] = {}
         for name, (dflt, descr, cat) in params.items():
-            # FIXME bug in default.py?
-            if isinstance(cat, basestring):
-                cat = ALL_CATEGORIES[cat]
             if cat == category:
                 if name in extra_params:
                     # mark easyblock-specific parameters

From 438e7e43b86b8e2fe57be9391948f1ea6afa6345 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 10:50:56 +0100
Subject: [PATCH 0423/1356] tiny fixes in github.py

---
 easybuild/tools/github.py | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 5fcd79bcdd..9b62ba26b3 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -38,7 +38,8 @@
 from vsc.utils import fancylogger
 from vsc.utils.patterns import Singleton
 
-from easybuild.tools.filetools import download_file
+from easybuild.tools.config import build_option
+from easybuild.tools.filetools import det_patched_files, download_file, extract_file, mkdir
 
 
 _log = fancylogger.getLogger('github', fname=False)
@@ -58,9 +59,6 @@
     _log.warning("Failed to import from 'vsc.utils.rest' Python module: %s" % err)
     HAVE_GITHUB_API = False
 
-from easybuild.tools.config import build_option
-from easybuild.tools.filetools import det_patched_files, extract_file, mkdir
-
 
 GITHUB_API_URL = 'https://api.github.com'
 GITHUB_DIR_TYPE = u'dir'
@@ -193,13 +191,13 @@ class GithubError(Exception):
     pass
 
 
-def _do_request(lmb, github_user=None, **kwargs):
+def _do_request(lmb, github_user=None):
     """Helper method, for performing get requests"""
     token = fetch_github_token(github_user)
     g = RestClient(GITHUB_API_URL, username=github_user, token=token)
 
     # call our lambda
-    url = lmb(g, **kwargs)
+    url = lmb(g)
 
     try:
         status, data = url.get()
@@ -324,7 +322,7 @@ def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
     # get all commits, increase to (max of) 100 per page
     if pr_data['commits'] > GITHUB_MAX_PER_PAGE:
         _log.error("PR #%s contains more than %s commits, can't obtain last commit" % (pr, GITHUB_MAX_PER_PAGE))
-    status, commits_data = _do_request(lambda g: pr_url(g).commits.get, github_user, per_page=GITHUB_MAX_PER_PAGE)
+    status, commits_data = _do_request(lambda g: pr_url(g).commits.get(per_page=GITHUB_MAX_PER_PAGE), github_user)
     last_commit = commits_data[-1]
     _log.debug("Commits: %s, last commit: %s" % (commits_data, last_commit['sha']))
 

From 3d7b65b4cd0361bd1d9aeae3bc4c1379aeda76f2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 11:03:25 +0100
Subject: [PATCH 0424/1356] fix exit for --review-pr

---
 easybuild/main.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 0543d68875..5d8ae6a74c 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -220,7 +220,6 @@ def main(testing_data=(None, None, None)):
     # review specified PR
     if options.review_pr:
         review_pr(options.review_pr, options.color)
-        sys.exit()
 
     # search for easyconfigs, if a query is specified
     query = options.search or options.search_short
@@ -232,13 +231,16 @@ def main(testing_data=(None, None, None)):
     if not easyconfigs_pkg_paths:
         _log.warning("Failed to determine install path for easybuild-easyconfigs package.")
 
+    # command line options that do not require any easyconfigs to be specified
+    no_ec_opts = [options.aggregate_regtest, options.review_pr, options.search, options.search_short, options.regtest]
+
     # determine paths to easyconfigs
     paths = det_easyconfig_paths(orig_paths, options.from_pr, easyconfigs_pkg_paths)
     if not paths:
         if 'name' in build_specs:
             # try to obtain or generate an easyconfig file via build specifications if a software name is provided
             paths = find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=testing)
-        elif not any([options.aggregate_regtest, options.search, options.search_short, options.regtest]):
+        elif not any(no_ec_opts):
             print_error(("Please provide one or multiple easyconfig files, or use software build "
                          "options to make EasyBuild search for easyconfigs"),
                          log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
@@ -268,7 +270,7 @@ def main(testing_data=(None, None, None)):
         print_msg(txt, log=_log, silent=testing, prefix=False)
 
     # cleanup and exit after dry run, searching easyconfigs or submitting regression test
-    if any([options.dry_run, options.dry_run_short, options.regtest, options.search, options.search_short]):
+    if any(no_ec_opts + [options.dry_run, options.dry_run_short]):
         cleanup(logfile, eb_tmpdir, testing)
         sys.exit(0)
 

From af6da725c2394311e54788f087676d0b1096452d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 11:03:49 +0100
Subject: [PATCH 0425/1356] bump to 2015 in copyright line in new modules

---
 easybuild/framework/easyconfig/review.py | 2 +-
 easybuild/tools/multi_diff.py            | 2 +-
 easybuild/tools/terminal.py              | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/review.py b/easybuild/framework/easyconfig/review.py
index 5fdb5927c1..3ce63cafda 100644
--- a/easybuild/framework/easyconfig/review.py
+++ b/easybuild/framework/easyconfig/review.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 37aed2747f..710d594cf0 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/terminal.py b/easybuild/tools/terminal.py
index 80e8d67ea7..52a776d79b 100644
--- a/easybuild/tools/terminal.py
+++ b/easybuild/tools/terminal.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

From 1aa2eaca72deb416e0f3fc2e8a1a91099150ab9e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 11:08:40 +0100
Subject: [PATCH 0426/1356] fix passing of 'per_page=GITHUB_MAX_PER_PAGE' to
 _do_request

---
 easybuild/tools/github.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 9b62ba26b3..2606af756d 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -191,7 +191,7 @@ class GithubError(Exception):
     pass
 
 
-def _do_request(lmb, github_user=None):
+def _do_request(lmb, github_user=None, **kwargs):
     """Helper method, for performing get requests"""
     token = fetch_github_token(github_user)
     g = RestClient(GITHUB_API_URL, username=github_user, token=token)
@@ -200,7 +200,7 @@ def _do_request(lmb, github_user=None):
     url = lmb(g)
 
     try:
-        status, data = url.get()
+        status, data = url.get(**kwargs)
     except socket.gaierror, err:
         status, data = 0, None
     _log.debug("status: %d, data: %s" % (status, data))
@@ -322,7 +322,7 @@ def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
     # get all commits, increase to (max of) 100 per page
     if pr_data['commits'] > GITHUB_MAX_PER_PAGE:
         _log.error("PR #%s contains more than %s commits, can't obtain last commit" % (pr, GITHUB_MAX_PER_PAGE))
-    status, commits_data = _do_request(lambda g: pr_url(g).commits.get(per_page=GITHUB_MAX_PER_PAGE), github_user)
+    status, commits_data = _do_request(lambda g: pr_url(g).commits, github_user, per_page=GITHUB_MAX_PER_PAGE)
     last_commit = commits_data[-1]
     _log.debug("Commits: %s, last commit: %s" % (commits_data, last_commit['sha']))
 

From 2c461699c1bee3bf36adf580122584d98fc13684 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 11:21:42 +0100
Subject: [PATCH 0427/1356] move review_pr function to
 framework.easyconfig.tools module

---
 easybuild/framework/easyconfig/review.py | 53 ------------------------
 easybuild/framework/easyconfig/tools.py  | 26 +++++++++---
 easybuild/main.py                        |  3 +-
 3 files changed, 22 insertions(+), 60 deletions(-)
 delete mode 100644 easybuild/framework/easyconfig/review.py

diff --git a/easybuild/framework/easyconfig/review.py b/easybuild/framework/easyconfig/review.py
deleted file mode 100644
index 3ce63cafda..0000000000
--- a/easybuild/framework/easyconfig/review.py
+++ /dev/null
@@ -1,53 +0,0 @@
-# #
-# Copyright 2014-2015 Ghent University
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-# #
-"""
-Review module for pull requests on the easyconfigs repo
-
-@author: Toon Willems (Ghent University)
-"""
-import os
-from vsc.utils import fancylogger
-
-from easybuild.framework.easyconfig.easyconfig import find_related_easyconfigs
-from easybuild.tools.github import fetch_easyconfigs_from_pr, download_repo
-from easybuild.tools.multi_diff import multi_diff
-from easybuild.tools.config import build_path
-
-
-_log = fancylogger.getLogger('easyconfig.review', fname=False)
-
-def review_pr(pull_request, colored):
-    download_repo_path = download_repo(branch='develop', path=build_path())
-    repo_path = os.path.join(download_repo_path, 'easybuild', 'easyconfigs')
-    pr_files = [path for path in fetch_easyconfigs_from_pr(pull_request) if path.endswith('.eb')]
-
-    for easyconfig in pr_files:
-        files = find_related_easyconfigs(repo_path, easyconfig)
-        _log.debug("File in pull request %s has these related easyconfigs: %s" % (easyconfig, files))
-        for listing in files:
-            if listing:
-                diff = multi_diff(easyconfig, listing, colored)
-                print diff
-                break
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index da3af771ac..62c8e7a7eb 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -67,13 +67,13 @@
     graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz")
 
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
-from easybuild.framework.easyconfig.easyconfig import ActiveMNS
-from easybuild.framework.easyconfig.easyconfig import process_easyconfig
+from easybuild.framework.easyconfig.easyconfig import ActiveMNS, find_related_easyconfigs, process_easyconfig
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.config import build_option
-from easybuild.tools.filetools import find_easyconfigs, search_file, write_file
-from easybuild.tools.github import fetch_easyconfigs_from_pr
+from easybuild.tools.config import build_option, build_path
+from easybuild.tools.filetools import find_easyconfigs, write_file
+from easybuild.tools.github import fetch_easyconfigs_from_pr, download_repo
 from easybuild.tools.modules import modules_tool
+from easybuild.tools.multi_diff import multi_diff
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.run import run_cmd
 from easybuild.tools.utilities import quote_str
@@ -344,3 +344,19 @@ def stats_to_str(stats):
         txt += "%s%s: %s,\n" % (pref, quote_str(k), quote_str(v))
     txt += "}"
     return txt
+
+
+def review_pr(pull_request, colored):
+    """Print multi-diff overview between easyconfigs in specified PR and current develop branch."""
+    download_repo_path = download_repo(branch='develop', path=build_path())
+    repo_path = os.path.join(download_repo_path, 'easybuild', 'easyconfigs')
+    pr_files = [path for path in fetch_easyconfigs_from_pr(pull_request) if path.endswith('.eb')]
+
+    for easyconfig in pr_files:
+        files = find_related_easyconfigs(repo_path, easyconfig)
+        _log.debug("File in pull request %s has these related easyconfigs: %s" % (easyconfig, files))
+        for listing in files:
+            if listing:
+                diff = multi_diff(easyconfig, listing, colored)
+                print diff
+                break
diff --git a/easybuild/main.py b/easybuild/main.py
index 5d8ae6a74c..1b26586ef5 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -49,9 +49,8 @@
 import easybuild.tools.options as eboptions
 from easybuild.framework.easyblock import EasyBlock, build_and_install_one
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
-from easybuild.framework.easyconfig.review import review_pr
 from easybuild.framework.easyconfig.tools import alt_easyconfig_paths, dep_graph, det_easyconfig_paths
-from easybuild.framework.easyconfig.tools import get_paths_for, parse_easyconfigs, skip_available
+from easybuild.framework.easyconfig.tools import get_paths_for, parse_easyconfigs, review_pr, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak
 from easybuild.tools.config import get_repository, get_repositorypath, set_tmpdir
 from easybuild.tools.filetools import cleanup, write_file

From ee2fee15c1247e563e9911e66cc9d70988f164f2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 11:35:09 +0100
Subject: [PATCH 0428/1356] parse easyconfigs before passing them down to
 find_related_easyconfigs

---
 easybuild/framework/easyconfig/easyconfig.py | 8 --------
 easybuild/framework/easyconfig/tools.py      | 9 +++++----
 2 files changed, 5 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 201c57d681..4b7d8dea7d 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -914,14 +914,6 @@ def find_related_easyconfigs(path, ec):
     - Then it takes the ones with any version and same toolchain name
     - Then it takes those with any version and any toolchain
     """
-    # make sure we are working with an EasyConfig object
-    if not isinstance(ec, EasyConfig):
-        # we can safely only take the first one
-        easyconfigs = process_easyconfig(ec, parse_only=True)
-        if len(easyconfigs) > 1:
-            _log.error("Expected only one easyconfig to be found, exiting!")
-        ec = easyconfigs[0]['ec']
-
     name = ec.name
     version = ec.version
     toolchain_name = ec['toolchain']['name']
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 62c8e7a7eb..4297e0b793 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -352,11 +352,12 @@ def review_pr(pull_request, colored):
     repo_path = os.path.join(download_repo_path, 'easybuild', 'easyconfigs')
     pr_files = [path for path in fetch_easyconfigs_from_pr(pull_request) if path.endswith('.eb')]
 
-    for easyconfig in pr_files:
-        files = find_related_easyconfigs(repo_path, easyconfig)
-        _log.debug("File in pull request %s has these related easyconfigs: %s" % (easyconfig, files))
+    ecs, _ = parse_easyconfigs([(fp, False) for fp in pr_files])
+    for ec in ecs:
+        files = find_related_easyconfigs(repo_path, ec['ec'])
+        _log.debug("File in pull request %s has these related easyconfigs: %s" % (ec['spec'], files))
         for listing in files:
             if listing:
-                diff = multi_diff(easyconfig, listing, colored)
+                diff = multi_diff(ec['spec'], listing, colored)
                 print diff
                 break

From 4a6d7b26b0b8a7297ddb68170ef2c3102b05aa01 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 14:46:46 +0100
Subject: [PATCH 0429/1356] fix/cleanup in find_related_easyconfigs: only
 consider easyconfig files with same name, also consider versionsuffix and
 major/minor software version, only return non-empty list (unless there's no
 such software name yet)

---
 easybuild/framework/easyconfig/easyconfig.py | 98 +++++++++++++-------
 1 file changed, 62 insertions(+), 36 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 4b7d8dea7d..748851a072 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -40,6 +40,7 @@
 import glob
 import os
 import re
+from distutils.version import LooseVersion
 from vsc.utils import fancylogger
 from vsc.utils.missing import any, get_class_for, nub
 from vsc.utils.patterns import Singleton
@@ -906,49 +907,74 @@ def resolve_template(value, tmpl_dict):
 
 def find_related_easyconfigs(path, ec):
     """
-    Find related easyconfigs for ec in path based on a simple heuristic
-    - It first returns those that matches easyconfigs with the exact same name.
-    - Then it matches those with the same version and same toolchain name
-    - Then it takes those with the same version and any toolchain name
-    - Then it takes the ones with any version and same toolchain (including version)
-    - Then it takes the ones with any version and same toolchain name
-    - Then it takes those with any version and any toolchain
+    Find related easyconfigs for provided parsed easyconfig in specified path.
+
+    A list of easyconfigs for the same software (name) is returned,
+    matching the 1st criterion that yields a non-empty list.
+
+    Software version is considered more important than toolchain.
+
+    Toolchain is considered with exact same version prior to without version (only name).
+
+    Matching versionsuffix is considered prior to any versionsuffix.
+
+    Exact software versions are considered prior to matching major/minor version numbers,
+    and only matching major version number, before any software version is considered.
+
+    The following criteria are considered, in order (with 'version criterion' being either an
+    exact version match, a major/minor version match, a major version match, or no version match).
+
+    (i)   software version criterion, versionsuffix and toolchain name/version
+    (ii)  software version criterion, versionsuffix and toolchain name (any toolchain version)
+    (iii) software version criterion, versionsuffix (any toolchain name/version)
+    (iv)  software version criterion and toolchain name/version (any versionsuffix)
+    (v)   software version criterion and toolchain name (any versionsuffix, toolchain version)
+    (vi)  software version criterion (any versionsuffix, toolchain name/version)
+
+    If no related easyconfigs with a matching software name are found, an empty list is returned.
     """
     name = ec.name
     version = ec.version
+    versionsuffix = ec['versionsuffix']
     toolchain_name = ec['toolchain']['name']
+    toolchain_name_pattern = '-%s-\S+' % toolchain_name
     toolchain = "%s-%s" % (toolchain_name, ec['toolchain']['version'])
-    full_version = det_full_ec_version(ec)
-
-    potential_paths = [os.path.dirname(path) for path in create_paths(path, name, version)]
-    result_potential_paths = []
-
-    for pot in potential_paths:
-        try:
-            result_potential_paths.append([os.path.join(pot,base) for base in os.listdir(pot) if os.path.isfile(os.path.join(pot,base))])
-        except:
-            None
-
-    # flatten
-    result_potential_paths = sum(result_potential_paths, [])
-
-    regexes = [
-        # exact match
-        re.compile(("^\S*/%s-%s.eb$" % (name, full_version))),
-        # same version, same toolchain name
-        re.compile(("^\S*/%s-%s-%s-\S*.eb$" % (name, version, toolchain_name))),
-        # Same version, any toolchain
-        re.compile(("^\S*/%s-%s-\S*.eb$" % (name, version))),
-        # any version, same toolchain
-        re.compile(("^\S*/%s-\S*-%s-\S*.eb$" % (name, toolchain))),
-        # any version, same toolchain name
-        re.compile(("^\S*/%s-\S*-%s-\S*.eb$" % (name, toolchain_name))),
+    toolchain_pattern = '-%s' % toolchain
+    if toolchain_name == DUMMY_TOOLCHAIN_NAME:
+        toolchain_name_pattern = ''
+        toolchain_pattern = ''
+
+    potential_paths = [glob.glob(ec_path) for ec_path in create_paths(path, name, '*')]
+    potential_paths = sum(potential_paths, [])  # flatten
+
+    parsed_version = LooseVersion(version).version
+    version_patterns = [
+        version,  # exact version match
+        '%s\.%s\.[0-9_-]+' % tuple(parsed_version[:2]),  # major/minor version match
+        '%s\.[0-9-]+\.[0-9_-]+' % parsed_version[0],  # major version match
+        '[0-9._A-Za-z-]+',  # any version
     ]
-    _log.debug("found these potential paths: %s" % result_potential_paths)
 
-    result = [filter(lambda path: regex.match(path),result_potential_paths) for regex in regexes]
-    result.append(result_potential_paths)
-    return result
+    regexes = []
+    for version_pattern in version_patterns:
+        regexes.extend([
+            re.compile((r"^\S+/%s-%s%s%s.eb$" % (name, version_pattern, toolchain_pattern, versionsuffix))),
+            re.compile((r"^\S+/%s-%s%s%s.eb$" % (name, version_pattern, toolchain_name_pattern, versionsuffix))),
+            re.compile((r"^\S+/%s-%s-\S+%s.eb$" % (name, version_pattern, versionsuffix))),
+            re.compile((r"^\S+/%s-%s%s.eb$" % (name, version_pattern, toolchain_pattern))),
+            re.compile((r"^\S+/%s-%s%s.eb$" % (name, version_pattern, toolchain_name_pattern))),
+            re.compile((r"^\S+/%s-%s-\S+.eb$" % (name, version_pattern))),
+        ])
+    _log.debug("found these potential paths: %s" % potential_paths)
+
+    for regex in regexes:
+        res = [p for p in potential_paths if regex.match(p)]
+        if res:
+            _log.debug("Related easyconfigs found using '%s': %s" % (regex.pattern, res))
+            break
+        else:
+            _log.debug("No related easyconfigs in potential paths using '%s'" % regex.pattern)
+    return res
 
 
 def process_easyconfig(path, build_specs=None, validate=True, parse_only=False, hidden=None):

From 61e07fae9f99bd2b2539dd767895aebb4afa5bd0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 14:47:21 +0100
Subject: [PATCH 0430/1356] minor enhancements in review_pr function

---
 easybuild/framework/easyconfig/tools.py | 17 +++++++++--------
 easybuild/main.py                       |  2 +-
 easybuild/tools/multi_diff.py           |  2 +-
 3 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 4297e0b793..60e2444ab3 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -39,6 +39,7 @@
 
 import os
 import sys
+import tempfile
 from vsc.utils import fancylogger
 
 # optional Python packages, these might be missing
@@ -69,7 +70,7 @@
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS, find_related_easyconfigs, process_easyconfig
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.config import build_option, build_path
+from easybuild.tools.config import build_option
 from easybuild.tools.filetools import find_easyconfigs, write_file
 from easybuild.tools.github import fetch_easyconfigs_from_pr, download_repo
 from easybuild.tools.modules import modules_tool
@@ -346,9 +347,12 @@ def stats_to_str(stats):
     return txt
 
 
-def review_pr(pull_request, colored):
+def review_pr(pull_request, colored=True, tmpdir=None):
     """Print multi-diff overview between easyconfigs in specified PR and current develop branch."""
-    download_repo_path = download_repo(branch='develop', path=build_path())
+    if tmpdir is None:
+        tmpdir = tempfile.mkdtemp()
+
+    download_repo_path = download_repo(branch='develop', path=tmpdir)
     repo_path = os.path.join(download_repo_path, 'easybuild', 'easyconfigs')
     pr_files = [path for path in fetch_easyconfigs_from_pr(pull_request) if path.endswith('.eb')]
 
@@ -356,8 +360,5 @@ def review_pr(pull_request, colored):
     for ec in ecs:
         files = find_related_easyconfigs(repo_path, ec['ec'])
         _log.debug("File in pull request %s has these related easyconfigs: %s" % (ec['spec'], files))
-        for listing in files:
-            if listing:
-                diff = multi_diff(ec['spec'], listing, colored)
-                print diff
-                break
+        diff = multi_diff(ec['spec'], files, colored=colored)
+        print diff
diff --git a/easybuild/main.py b/easybuild/main.py
index 1b26586ef5..b39608d1e6 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -218,7 +218,7 @@ def main(testing_data=(None, None, None)):
 
     # review specified PR
     if options.review_pr:
-        review_pr(options.review_pr, options.color)
+        review_pr(options.review_pr, colored=options.color, tmpdir=eb_tmpdir)
 
     # search for easyconfigs, if a query is specified
     query = options.search or options.search_short
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 710d594cf0..4093bbca5c 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -206,7 +206,7 @@ def multi_diff(base,files, colored=True):
         compensator = 1
         for (i, line) in enumerate(diff):
             if line.startswith('?'):
-                squigly_dict[last_added] = (line)
+                squigly_dict[last_added] = line
                 compensator -= 1
             elif line.startswith('+'):
                 local_diff.setdefault(i+compensator, []).append((line, file_name))

From 07de284125f2519f2ea03ec37ac8ecdcff4bdd4b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 15:04:42 +0100
Subject: [PATCH 0431/1356] don't validate easyconfigs when reviewing PRs

---
 easybuild/framework/easyconfig/tools.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 60e2444ab3..2f627ca18a 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -304,7 +304,7 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
     return [(ec_file, False) for ec_file in ec_files]
 
 
-def parse_easyconfigs(paths):
+def parse_easyconfigs(paths, validate=True):
     """
     Parse easyconfig files
     @params paths: paths to easyconfigs
@@ -321,7 +321,7 @@ def parse_easyconfigs(paths):
             ec_files = find_easyconfigs(path, ignore_dirs=build_option('ignore_dirs'))
             for ec_file in ec_files:
                 # only pass build specs when not generating easyconfig files
-                kwargs = {}
+                kwargs = {'validate': validate}
                 if not build_option('try_to_generate'):
                     kwargs['build_specs'] = build_option('build_specs')
                 ecs = process_easyconfig(ec_file, **kwargs)
@@ -356,7 +356,7 @@ def review_pr(pull_request, colored=True, tmpdir=None):
     repo_path = os.path.join(download_repo_path, 'easybuild', 'easyconfigs')
     pr_files = [path for path in fetch_easyconfigs_from_pr(pull_request) if path.endswith('.eb')]
 
-    ecs, _ = parse_easyconfigs([(fp, False) for fp in pr_files])
+    ecs, _ = parse_easyconfigs([(fp, False) for fp in pr_files], validate=False)
     for ec in ecs:
         files = find_related_easyconfigs(repo_path, ec['ec'])
         _log.debug("File in pull request %s has these related easyconfigs: %s" % (ec['spec'], files))

From 9ddb85fdd18ce9272aafb1fef420f2ad3c9560fc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 15:05:09 +0100
Subject: [PATCH 0432/1356] use raw strings for regex patterns

---
 easybuild/framework/easyconfig/easyconfig.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 748851a072..79e8cd9aec 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -950,9 +950,9 @@ def find_related_easyconfigs(path, ec):
     parsed_version = LooseVersion(version).version
     version_patterns = [
         version,  # exact version match
-        '%s\.%s\.[0-9_-]+' % tuple(parsed_version[:2]),  # major/minor version match
-        '%s\.[0-9-]+\.[0-9_-]+' % parsed_version[0],  # major version match
-        '[0-9._A-Za-z-]+',  # any version
+        r'%s\.%s\.[0-9_-]+' % tuple(parsed_version[:2]),  # major/minor version match
+        r'%s\.[0-9-]+\.[0-9_-]+' % parsed_version[0],  # major version match
+        r'[0-9._A-Za-z-]+',  # any version
     ]
 
     regexes = []

From fb86a632b801efdfc461e50c36244801153aaa42 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 15:55:27 +0100
Subject: [PATCH 0433/1356] some style cleanup in multi_diff.py

---
 easybuild/tools/multi_diff.py | 32 +++++++++++++++++++++-----------
 1 file changed, 21 insertions(+), 11 deletions(-)

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 4093bbca5c..70c0c32c05 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -31,10 +31,11 @@
 import difflib
 import math
 import os
-import sys
 
 import easybuild.tools.terminal as terminal
 
+SEP_WIDTH = 5
+
 GREEN = "\033[0;32m"
 PURPLE = "\033[0;35m"
 RED = "\033[0;21m"
@@ -57,7 +58,7 @@ def __init__(self, base, files, colored=True):
         self.files = files
         self.colored = colored
 
-    def parse_line(self,line_no, diff_line, meta, squigly_line=None):
+    def parse_line(self, line_no, diff_line, meta, squigly_line=None):
         """
         Parse a line as generated by difflib
         """
@@ -79,19 +80,28 @@ def limit(text, length):
             else:
                 return text
 
-        output = []
+        term_width, _ = terminal.get_terminal_size()
 
-        w,h = terminal.get_terminal_size()
-        output.append(" ".join(["Comparing", self._color(os.path.basename(self.base), PURPLE), "with",
-                                ", ".join(map(os.path.basename,self.files))]))
+        base = self._color(os.path.basename(self.base), PURPLE)
+        filenames = ', '.join(map(os.path.basename, self.files))
+        output = [
+            "Comparing %s with %s" % (base, filenames),
+            '=' * SEP_WIDTH,
+        ]
 
+        diff = False
         for i in range(len(self.base_lines)):
-            lines = filter(None,self.get_line(i))
-
+            lines = filter(None, self.get_line(i))
             if lines:
-                output.append("\n".join([limit(line,w) for line in lines]))
+                output.append('\n'.join([limit(line, term_width) for line in lines]))
+                diff = True
+
+        if not diff:
+            output.append("(no diff)")
+
+        output.append('=' * SEP_WIDTH)
 
-        return "\n".join(output)
+        return '\n'.join(output)
 
     def get_line(self, line_no):
         """
@@ -139,7 +149,7 @@ def get_line(self, line_no):
 
         # print seperator only if needed
         if diff_dict and not self.diff_info.get(line_no + 1, {}):
-            output.extend([' ', '-----', ' '])
+            output.extend([' ', '-' * SEP_WIDTH, ' '])
 
         return output
 

From 6af5f39cc802bcacc58202216ca09a8a1d8c11d9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 15:56:23 +0100
Subject: [PATCH 0434/1356] move find_related_easyconfigs into
 framework.easyconfigs.tools + minor enhancements

---
 easybuild/framework/easyconfig/easyconfig.py | 73 ----------------
 easybuild/framework/easyconfig/tools.py      | 87 +++++++++++++++++++-
 easybuild/tools/github.py                    |  3 +
 3 files changed, 86 insertions(+), 77 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 79e8cd9aec..9a9936265b 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -37,10 +37,8 @@
 
 import copy
 import difflib
-import glob
 import os
 import re
-from distutils.version import LooseVersion
 from vsc.utils import fancylogger
 from vsc.utils.missing import any, get_class_for, nub
 from vsc.utils.patterns import Singleton
@@ -905,77 +903,6 @@ def resolve_template(value, tmpl_dict):
 
     return value
 
-def find_related_easyconfigs(path, ec):
-    """
-    Find related easyconfigs for provided parsed easyconfig in specified path.
-
-    A list of easyconfigs for the same software (name) is returned,
-    matching the 1st criterion that yields a non-empty list.
-
-    Software version is considered more important than toolchain.
-
-    Toolchain is considered with exact same version prior to without version (only name).
-
-    Matching versionsuffix is considered prior to any versionsuffix.
-
-    Exact software versions are considered prior to matching major/minor version numbers,
-    and only matching major version number, before any software version is considered.
-
-    The following criteria are considered, in order (with 'version criterion' being either an
-    exact version match, a major/minor version match, a major version match, or no version match).
-
-    (i)   software version criterion, versionsuffix and toolchain name/version
-    (ii)  software version criterion, versionsuffix and toolchain name (any toolchain version)
-    (iii) software version criterion, versionsuffix (any toolchain name/version)
-    (iv)  software version criterion and toolchain name/version (any versionsuffix)
-    (v)   software version criterion and toolchain name (any versionsuffix, toolchain version)
-    (vi)  software version criterion (any versionsuffix, toolchain name/version)
-
-    If no related easyconfigs with a matching software name are found, an empty list is returned.
-    """
-    name = ec.name
-    version = ec.version
-    versionsuffix = ec['versionsuffix']
-    toolchain_name = ec['toolchain']['name']
-    toolchain_name_pattern = '-%s-\S+' % toolchain_name
-    toolchain = "%s-%s" % (toolchain_name, ec['toolchain']['version'])
-    toolchain_pattern = '-%s' % toolchain
-    if toolchain_name == DUMMY_TOOLCHAIN_NAME:
-        toolchain_name_pattern = ''
-        toolchain_pattern = ''
-
-    potential_paths = [glob.glob(ec_path) for ec_path in create_paths(path, name, '*')]
-    potential_paths = sum(potential_paths, [])  # flatten
-
-    parsed_version = LooseVersion(version).version
-    version_patterns = [
-        version,  # exact version match
-        r'%s\.%s\.[0-9_-]+' % tuple(parsed_version[:2]),  # major/minor version match
-        r'%s\.[0-9-]+\.[0-9_-]+' % parsed_version[0],  # major version match
-        r'[0-9._A-Za-z-]+',  # any version
-    ]
-
-    regexes = []
-    for version_pattern in version_patterns:
-        regexes.extend([
-            re.compile((r"^\S+/%s-%s%s%s.eb$" % (name, version_pattern, toolchain_pattern, versionsuffix))),
-            re.compile((r"^\S+/%s-%s%s%s.eb$" % (name, version_pattern, toolchain_name_pattern, versionsuffix))),
-            re.compile((r"^\S+/%s-%s-\S+%s.eb$" % (name, version_pattern, versionsuffix))),
-            re.compile((r"^\S+/%s-%s%s.eb$" % (name, version_pattern, toolchain_pattern))),
-            re.compile((r"^\S+/%s-%s%s.eb$" % (name, version_pattern, toolchain_name_pattern))),
-            re.compile((r"^\S+/%s-%s-\S+.eb$" % (name, version_pattern))),
-        ])
-    _log.debug("found these potential paths: %s" % potential_paths)
-
-    for regex in regexes:
-        res = [p for p in potential_paths if regex.match(p)]
-        if res:
-            _log.debug("Related easyconfigs found using '%s': %s" % (regex.pattern, res))
-            break
-        else:
-            _log.debug("No related easyconfigs in potential paths using '%s'" % regex.pattern)
-    return res
-
 
 def process_easyconfig(path, build_specs=None, validate=True, parse_only=False, hidden=None):
     """
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 2f627ca18a..9c5523dcb9 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -36,10 +36,12 @@
 @author: Fotis Georgatos (Uni.Lu, NTUA)
 @author: Ward Poelmans (Ghent University)
 """
-
+import glob
 import os
+import re
 import sys
 import tempfile
+from distutils.version import LooseVersion
 from vsc.utils import fancylogger
 
 # optional Python packages, these might be missing
@@ -68,7 +70,7 @@
     graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz")
 
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
-from easybuild.framework.easyconfig.easyconfig import ActiveMNS, find_related_easyconfigs, process_easyconfig
+from easybuild.framework.easyconfig.easyconfig import ActiveMNS, create_paths, process_easyconfig
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import find_easyconfigs, write_file
@@ -77,6 +79,7 @@
 from easybuild.tools.multi_diff import multi_diff
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.run import run_cmd
+from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.utilities import quote_str
 
 
@@ -347,6 +350,78 @@ def stats_to_str(stats):
     return txt
 
 
+def find_related_easyconfigs(path, ec):
+    """
+    Find related easyconfigs for provided parsed easyconfig in specified path.
+
+    A list of easyconfigs for the same software (name) is returned,
+    matching the 1st criterion that yields a non-empty list.
+
+    Software version is considered more important than toolchain.
+
+    Toolchain is considered with exact same version prior to without version (only name).
+
+    Matching versionsuffix is considered prior to any versionsuffix.
+
+    Exact software versions are considered prior to matching major/minor version numbers,
+    and only matching major version number, before any software version is considered.
+
+    The following criteria are considered, in order (with 'version criterion' being either an
+    exact version match, a major/minor version match, a major version match, or no version match).
+
+    (i)   software version criterion, versionsuffix and toolchain name/version
+    (ii)  software version criterion, versionsuffix and toolchain name (any toolchain version)
+    (iii) software version criterion, versionsuffix (any toolchain name/version)
+    (iv)  software version criterion and toolchain name/version (any versionsuffix)
+    (v)   software version criterion and toolchain name (any versionsuffix, toolchain version)
+    (vi)  software version criterion (any versionsuffix, toolchain name/version)
+
+    If no related easyconfigs with a matching software name are found, an empty list is returned.
+    """
+    name = ec.name
+    version = ec.version
+    versionsuffix = ec['versionsuffix']
+    toolchain_name = ec['toolchain']['name']
+    toolchain_name_pattern = r'-%s-\S+' % toolchain_name
+    toolchain = "%s-%s" % (toolchain_name, ec['toolchain']['version'])
+    toolchain_pattern = '-%s' % toolchain
+    if toolchain_name == DUMMY_TOOLCHAIN_NAME:
+        toolchain_name_pattern = ''
+        toolchain_pattern = ''
+
+    potential_paths = [glob.glob(ec_path) for ec_path in create_paths(path, name, '*')]
+    potential_paths = sum(potential_paths, [])  # flatten
+
+    parsed_version = LooseVersion(version).version
+    version_patterns = [version]  # exact version match
+    if len(parsed_version) >= 2:
+        version_patterns.append(r'%s\.%s\.[0-9_A-Za-z]+' % tuple(parsed_version[:2]))  # major/minor version match
+    if parsed_version != parsed_version[0]:
+        version_patterns.append(r'%s\.[0-9-]+\.[0-9_A-Za-z]+' % parsed_version[0])  # major version match
+    version_patterns.append(r'[0-9._A-Za-z-]+')  # any version
+
+    regexes = []
+    for version_pattern in version_patterns:
+        regexes.extend([
+            re.compile((r"^\S+/%s-%s%s%s.eb$" % (name, version_pattern, toolchain_pattern, versionsuffix))),
+            re.compile((r"^\S+/%s-%s%s%s.eb$" % (name, version_pattern, toolchain_name_pattern, versionsuffix))),
+            re.compile((r"^\S+/%s-%s-\S+%s.eb$" % (name, version_pattern, versionsuffix))),
+            re.compile((r"^\S+/%s-%s%s.eb$" % (name, version_pattern, toolchain_pattern))),
+            re.compile((r"^\S+/%s-%s%s.eb$" % (name, version_pattern, toolchain_name_pattern))),
+            re.compile((r"^\S+/%s-%s-\S+.eb$" % (name, version_pattern))),
+        ])
+    _log.debug("found these potential paths: %s" % potential_paths)
+
+    for regex in regexes:
+        res = [p for p in potential_paths if regex.match(p)]
+        if res:
+            _log.debug("Related easyconfigs found using '%s': %s" % (regex.pattern, res))
+            break
+        else:
+            _log.debug("No related easyconfigs in potential paths using '%s'" % regex.pattern)
+    return res
+
+
 def review_pr(pull_request, colored=True, tmpdir=None):
     """Print multi-diff overview between easyconfigs in specified PR and current develop branch."""
     if tmpdir is None:
@@ -360,5 +435,9 @@ def review_pr(pull_request, colored=True, tmpdir=None):
     for ec in ecs:
         files = find_related_easyconfigs(repo_path, ec['ec'])
         _log.debug("File in pull request %s has these related easyconfigs: %s" % (ec['spec'], files))
-        diff = multi_diff(ec['spec'], files, colored=colored)
-        print diff
+        if files:
+            diff = multi_diff(ec['spec'], files, colored=colored)
+            msg = diff
+        else:
+            msg = "\n(no related easyconfigs found for %s)\n" % os.path.basename(ec['spec'])
+        print msg
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 2606af756d..f4cf928ac7 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -193,6 +193,9 @@ class GithubError(Exception):
 
 def _do_request(lmb, github_user=None, **kwargs):
     """Helper method, for performing get requests"""
+    if github_user is None:
+        github_user = build_option('github_user')
+
     token = fetch_github_token(github_user)
     g = RestClient(GITHUB_API_URL, username=github_user, token=token)
 

From b3c2dceb970d938f34852321e543868c8ef1522b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 18:04:44 +0100
Subject: [PATCH 0435/1356] replace easybuild.tools.terminal module with simple
 det_terminal_size function in tools.utilities

---
 easybuild/tools/multi_diff.py |  5 ++--
 easybuild/tools/terminal.py   | 54 -----------------------------------
 easybuild/tools/utilities.py  | 12 ++++++++
 3 files changed, 15 insertions(+), 56 deletions(-)
 delete mode 100644 easybuild/tools/terminal.py

diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 70c0c32c05..7704fb476f 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -32,7 +32,8 @@
 import math
 import os
 
-import easybuild.tools.terminal as terminal
+from easybuild.tools.utilities import det_terminal_size
+
 
 SEP_WIDTH = 5
 
@@ -80,7 +81,7 @@ def limit(text, length):
             else:
                 return text
 
-        term_width, _ = terminal.get_terminal_size()
+        term_width, _ = det_terminal_size()
 
         base = self._color(os.path.basename(self.base), PURPLE)
         filenames = ', '.join(map(os.path.basename, self.files))
diff --git a/easybuild/tools/terminal.py b/easybuild/tools/terminal.py
deleted file mode 100644
index 52a776d79b..0000000000
--- a/easybuild/tools/terminal.py
+++ /dev/null
@@ -1,54 +0,0 @@
-# #
-# Copyright 2014-2015 Ghent University
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-# #
-"""
-Module for checking the terminal dimensions
-copied from http://stackoverflow.com/questions/566746/how-to-get-console-window-width-in-python
-"""
-
-import os
-
-def get_terminal_size():
-    env = os.environ
-    def ioctl_GWINSZ(fd):
-        try:
-            # these might fail because they are only available on Unix
-            import fcntl, termios, struct, os
-            cr = struct.unpack('hh', fcntl.ioctl(fd, termios.TIOCGWINSZ,
-        '1234'))
-        except:
-            return
-        return cr
-    cr = ioctl_GWINSZ(0) or ioctl_GWINSZ(1) or ioctl_GWINSZ(2)
-    if not cr:
-        try:
-            fd = os.open(os.ctermid(), os.O_RDONLY)
-            cr = ioctl_GWINSZ(fd)
-            os.close(fd)
-        except:
-            pass
-    if not cr:
-        cr = (env.get('LINES', 25), env.get('COLUMNS', 80))
-
-    return int(cr[1]), int(cr[0])
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 05948c9c6d..d8910c7675 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -27,10 +27,13 @@
 
 @author: Kenneth Hoste (Ghent University)
 """
+import fcntl
 import glob
 import os
 import string
+import struct
 import sys
+import termios
 from vsc.utils import fancylogger
 from vsc.utils.missing import any as _any
 from vsc.utils.missing import all as _all
@@ -118,3 +121,12 @@ def import_available_modules(namespace):
                 _log.debug("importing module %s" % modpath)
                 modules.append(__import__(modpath, globals(), locals(), ['']))
     return modules
+
+
+def det_terminal_size():
+    """
+    Determine the current size of the terminal window.
+    @return: tuple with terminal width and height
+    """
+    height, width, _, _ = struct.unpack('HHHH', fcntl.ioctl(0, termios.TIOCGWINSZ, struct.pack('HHHH', 0, 0, 0, 0)))
+    return width, height

From 9859dac43a30b68e79259bef5a08a9c5099c5fc6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 18:10:30 +0100
Subject: [PATCH 0436/1356] fix location of --review-pr and --color options

---
 easybuild/tools/options.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 73bd0a02e6..98309c24c6 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -162,8 +162,6 @@ def software_options(self):
         # additional options that don't need a --try equivalent
         opts.update({
             'from-pr': ("Obtain easyconfigs from specified PR", int, 'store', None, {'metavar': 'PR#'}),
-            'review-pr': ("Review specified pull request", int, 'store', None, {'metavar': 'PR#'}),
-            'color': ("Allow color output", None, 'store_true', True),
         })
 
         self.log.debug("software_options: descr %s opts %s" % (descr, opts))
@@ -177,6 +175,7 @@ def override_options(self):
             'allow-modules-tool-mismatch': ("Allow mismatch of modules tool and definition of 'module' function",
                                             None, 'store_true', False),
             'cleanup-builddir': ("Cleanup build dir after successful installation.", None, 'store_true', True),
+            'color': ("Allow color output", None, 'store_true', True),
             'deprecated': ("Run pretending to be (future) version, to test removal of deprecated code.",
                            None, 'store', None),
             'easyblock': ("easyblock to use for processing the spec file or dumping the options",
@@ -310,6 +309,7 @@ def regtest_options(self):
                         None, 'store_true', False),
             'regtest-output-dir': ("Set output directory for test-run",
                                    None, 'store', None, {'metavar': 'DIR'}),
+            'review-pr': ("Review specified pull request", int, 'store', None, {'metavar': 'PR#'}),
             'sequential': ("Specify this option if you want to prevent parallel build",
                            None, 'store_true', False),
             'upload-test-report': ("Upload full test report as a gist on GitHub", None, 'store_true', None),

From d84b1fec2c2a94a970fcdd717d16d52ff602aee9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Jan 2015 21:03:50 +0100
Subject: [PATCH 0437/1356] style cleanup in tools/github.py

---
 easybuild/tools/github.py | 118 ++++++++++++++++++++------------------
 1 file changed, 61 insertions(+), 57 deletions(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index f4cf928ac7..2c70cbf2aa 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -33,13 +33,11 @@
 import os
 import socket
 import tempfile
-import urllib
-import urllib2
 from vsc.utils import fancylogger
 from vsc.utils.patterns import Singleton
 
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import det_patched_files, download_file, extract_file, mkdir
+from easybuild.tools.filetools import det_patched_files, download_file, extract_file, mkdir, read_file, write_file
 
 
 _log = fancylogger.getLogger('github', fname=False)
@@ -60,6 +58,7 @@
     HAVE_GITHUB_API = False
 
 
+GITHUB_URL = 'https://github.com'
 GITHUB_API_URL = 'https://api.github.com'
 GITHUB_DIR_TYPE = u'dir'
 GITHUB_EB_MAIN = 'hpcugent'
@@ -176,8 +175,8 @@ def read(self, path, api=True):
         # https://raw.github.com/hpcugent/easybuild/master/README.rst
         if not api:
             outfile = tempfile.mkstemp()[1]
-            url = ("http://raw.github.com/%s/%s/%s/%s" % (self.githubuser, self.reponame, self.branchname, path))
-            urllib.urlretrieve(url, outfile)
+            url = ("%s/%s/%s/%s/%s" % (GITHUB_RAW, self.githubuser, self.reponame, self.branchname, path))
+            download_file(os.path.basename(path), url, outfile)
             return outfile
         else:
             obj = self.get_path(path).get(ref=self.branchname)[1]
@@ -191,99 +190,100 @@ class GithubError(Exception):
     pass
 
 
-def _do_request(lmb, github_user=None, **kwargs):
-    """Helper method, for performing get requests"""
+def github_api_get_request(request_f, github_user=None, **kwargs):
+    """
+    Helper method, for performing get requests to GitHub API.
+    @param request_f: function that should be called to compose request, providing a RestClient instance
+    @param github_user: GitHub user name (to try and obtain matching GitHub token)
+    @return: tuple with return status and data
+    """
     if github_user is None:
         github_user = build_option('github_user')
 
     token = fetch_github_token(github_user)
-    g = RestClient(GITHUB_API_URL, username=github_user, token=token)
-
-    # call our lambda
-    url = lmb(g)
+    url = request_f(RestClient(GITHUB_API_URL, username=github_user, token=token))
 
     try:
         status, data = url.get(**kwargs)
     except socket.gaierror, err:
+        _log.warning("Error occured while performing get request: %s" % err)
         status, data = 0, None
-    _log.debug("status: %d, data: %s" % (status, data))
 
+    _log.debug("get request result for %s: status: %d, data: %s" % (url, status, data))
     return (status, data)
 
-def fetch_latest_commit_sha(repo, account, branch='master'):
-    """fetches the latest sha for a specified branch"""
 
-    status, data = _do_request(lambda x: x.repos[account][repo].branches)
+def fetch_latest_commit_sha(repo, account, branch='master'):
+    """
+    Fetch latest SHA1 for a specified repository and branch.
+    @param repo: GitHub repository
+    @param account: GitHub account
+    @param branch: branch to fetch latest SHA1 for
+    @return: latest SHA1
+    """
+    status, data = github_api_get_request(lambda x: x.repos[account][repo].branches)
     if not status == HTTP_STATUS_OK:
         tup = (branch, account, repo, status, data)
         _log.error("Failed to get latest commit sha for branch %s from %s/%s (status: %d %s)" % tup)
 
-    branch = [br for br in data if br[u'name'] == branch]
-    if len(branch) != 1:
-        _log.error('no branch with name %s found in repo %s/%s' % (branch, account, repo))
+    res = None
+    for entry in data:
+        if entry[u'name'] == branch:
+            res = entry['commit']['sha']
+
+    if res is None:
+        _log.error('No branch with name %s found in repo %s/%s (%s)' % (branch, account, repo, data))
 
-    branch = branch[0]
+    return res
 
-    return branch['commit']['sha']
 
 def download_repo(repo=GITHUB_EASYCONFIGS_REPO, branch='master', account=GITHUB_EB_MAIN, path=None):
-    """Download entire repo as a tar.gz archive and extract it into path"""
+    """
+    Download entire GitHub repo as a tar.gz archive, and extract it into specified path.
+    @param repo: repo to download
+    @param branch: branch to download
+    @param account: GitHub account to download repo from
+    @param path: path to extract to
+    """
     # make sure path exists, create it if necessary
-    if path == None:
+    if path is None:
         path = tempfile.mkdtemp()
 
     # add account subdir
     path = os.path.join(path, account)
     mkdir(path, parents=True)
 
-    extracted_dir_name = "%s-%s" % (GITHUB_EASYCONFIGS_REPO, branch)
-    base_name = "%s.tar.gz" % branch
-
+    extracted_dir_name = '%s-%s' % (GITHUB_EASYCONFIGS_REPO, branch)
+    base_name = '%s.tar.gz' % branch
     latest_commit_sha = fetch_latest_commit_sha(repo, account, branch)
 
-    # check if directory already exists, and don't download if it does
     expected_path = os.path.join(path, extracted_dir_name)
+    latest_sha_path = os.path.join(expected_path, 'latest-sha')
+
+    # check if directory already exists, don't download if it does
     if os.path.isdir(expected_path):
-        sha = open(os.path.join(expected_path, "latest-sha")).readlines()[0]
-        if latest_commit_sha == sha.rstrip():
-            _log.debug("Not redownloading %s/%s as it already exists" % (account, repo))
+        sha = read_file(latest_sha_path).split('\n')[0].rstrip()
+        if latest_commit_sha == sha:
+            _log.debug("Not redownloading %s/%s as it already exists: %s" % (account, repo, expected_path))
             return expected_path
 
-    url = URL_SEPARATOR.join(["https://github.com", account, repo, 'archive', base_name])
+    url = URL_SEPARATOR.join([GITHUB_URL, account, repo, 'archive', base_name])
 
-    _log.debug("download repo %s/%s as archive from %s" % (account,repo, url))
-    download_file(base_name, url, os.path.join(path,base_name))
+    target_path = os.path.join(path, base_name)
+    _log.debug("downloading repo %s/%s as archive from %s to %s" % (account, repo, url, target_path))
+    download_file(base_name, url, target_path)
     _log.debug("%s downloaded to %s, extracting now" % (base_name, path))
 
-    extracted_path = extract_file(os.path.join(path, base_name), path)
-    extracted_path = os.path.join(extracted_path, extracted_dir_name)
+    extracted_path = os.path.join(extract_file(target_path, path), extracted_dir_name)
     # check if extracted_path exists
     if not os.path.isdir(extracted_path):
-        _log.error("We expected %s to exists and contain the repo %s at branch %s" % (extracted_path, repo, branch))
+        _log.error("%s should exist and contain the repo %s at branch %s" % (extracted_path, repo, branch))
 
-    f = open(os.path.join(extracted_path, 'latest-sha'), 'w')
-    f.write(latest_commit_sha)
+    write_file(latest_sha_path, latest_commit_sha)
 
     _log.debug("Repo %s at branch %s extracted into %s" % (repo, branch, extracted_path))
     return extracted_path
 
-def _download(url, path=None):
-    """Download file from specified URL to specified path."""
-    if path is None:
-        try:
-            return urllib2.urlopen(url).read()
-        except urllib2.URLError, err:
-            _log.error("Failed to open %s for reading: %s" % (url, err))
-    else:
-        try:
-            _, httpmsg = urllib.urlretrieve(url, path)
-            _log.debug("Downloaded %s to %s" % (url, path))
-        except IOError, err:
-            _log.error("Failed to download %s to %s: %s" % (url, path, err))
-
-        if httpmsg.type != 'text/plain' and httpmsg.type != 'application/x-gzip' :
-            _log.error("Unexpected file type for %s: %s" % (path, httpmsg.type))
-
 
 def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
     """Fetch patched easyconfig files for a particular PR."""
@@ -301,7 +301,7 @@ def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
     _log.debug("Fetching easyconfigs from PR #%s into %s" % (pr, path))
     pr_url = lambda g: g.repos[GITHUB_EB_MAIN][GITHUB_EASYCONFIGS_REPO].pulls[pr]
 
-    status, pr_data = _do_request(pr_url, github_user)
+    status, pr_data = github_api_get_request(pr_url, github_user)
     if not status == HTTP_STATUS_OK:
         tup = (pr, GITHUB_EB_MAIN, GITHUB_EASYCONFIGS_REPO, status, pr_data)
         _log.error("Failed to get data for PR #%d from %s/%s (status: %d %s)" % tup)
@@ -316,7 +316,11 @@ def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
         _log.debug("\n%s:\n\n%s\n" % (key, val))
 
     # determine list of changed files via diff
-    diff_txt = _download(pr_data['diff_url'])
+    diff_fn = os.path.basename(pr_data['diff_url'])
+    diff_filepath = os.path.join(path, diff_fn)
+    download_file(diff_fn, pr_data['diff_url'], diff_filepath)
+    diff_txt = read_file(diff_filepath)
+    os.remove(diff_filepath)
 
     patched_files = det_patched_files(txt=diff_txt, omit_ab_prefix=True)
     _log.debug("List of patched files: %s" % patched_files)
@@ -325,7 +329,7 @@ def fetch_easyconfigs_from_pr(pr, path=None, github_user=None):
     # get all commits, increase to (max of) 100 per page
     if pr_data['commits'] > GITHUB_MAX_PER_PAGE:
         _log.error("PR #%s contains more than %s commits, can't obtain last commit" % (pr, GITHUB_MAX_PER_PAGE))
-    status, commits_data = _do_request(lambda g: pr_url(g).commits, github_user, per_page=GITHUB_MAX_PER_PAGE)
+    status, commits_data = github_api_get_request(lambda g: pr_url(g).commits, github_user, per_page=GITHUB_MAX_PER_PAGE)
     last_commit = commits_data[-1]
     _log.debug("Commits: %s, last commit: %s" % (commits_data, last_commit['sha']))
 

From 47e1ba33d95e5094fc9e455ce9e2e3970091875f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Jan 2015 09:26:52 +0100
Subject: [PATCH 0438/1356] minor tweaks in docstring + some cleanup in
 review_pr function

---
 easybuild/framework/easyconfig/tools.py | 34 ++++++++++++++-----------
 1 file changed, 19 insertions(+), 15 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 9c5523dcb9..53f108f618 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -363,17 +363,17 @@ def find_related_easyconfigs(path, ec):
 
     Matching versionsuffix is considered prior to any versionsuffix.
 
-    Exact software versions are considered prior to matching major/minor version numbers,
-    and only matching major version number, before any software version is considered.
+    Exact software version is considered prior to matching major/minor version numbers,
+    and only matching major version number. Any software version is considered last.
 
     The following criteria are considered, in order (with 'version criterion' being either an
     exact version match, a major/minor version match, a major version match, or no version match).
 
-    (i)   software version criterion, versionsuffix and toolchain name/version
-    (ii)  software version criterion, versionsuffix and toolchain name (any toolchain version)
-    (iii) software version criterion, versionsuffix (any toolchain name/version)
-    (iv)  software version criterion and toolchain name/version (any versionsuffix)
-    (v)   software version criterion and toolchain name (any versionsuffix, toolchain version)
+    (i)   software version criterion, matching versionsuffix and toolchain name/version
+    (ii)  software version criterion, matching versionsuffix and toolchain name (any toolchain version)
+    (iii) software version criterion, matching versionsuffix (any toolchain name/version)
+    (iv)  software version criterion, matching toolchain name/version (any versionsuffix)
+    (v)   software version criterion, matching toolchain name (any versionsuffix, toolchain version)
     (vi)  software version criterion (any versionsuffix, toolchain name/version)
 
     If no related easyconfigs with a matching software name are found, an empty list is returned.
@@ -422,22 +422,26 @@ def find_related_easyconfigs(path, ec):
     return res
 
 
-def review_pr(pull_request, colored=True, tmpdir=None):
-    """Print multi-diff overview between easyconfigs in specified PR and current develop branch."""
-    if tmpdir is None:
-        tmpdir = tempfile.mkdtemp()
+def review_pr(pr, colored=True, branch='develop'):
+    """
+    Print multi-diff overview between easyconfigs in specified PR and specified branch.
+    @param pr: pull request number in easybuild-easyconfigs repo to review
+    @param colored: boolean indicating whether a colored multi-diff should be generated
+    @param branch: easybuild-easyconfigs branch to compare with
+    """
+    tmpdir = tempfile.mkdtemp()
 
-    download_repo_path = download_repo(branch='develop', path=tmpdir)
+    download_repo_path = download_repo(branch=branch, path=tmpdir)
     repo_path = os.path.join(download_repo_path, 'easybuild', 'easyconfigs')
-    pr_files = [path for path in fetch_easyconfigs_from_pr(pull_request) if path.endswith('.eb')]
+    pr_files = [path for path in fetch_easyconfigs_from_pr(pr) if path.endswith('.eb')]
 
     ecs, _ = parse_easyconfigs([(fp, False) for fp in pr_files], validate=False)
     for ec in ecs:
         files = find_related_easyconfigs(repo_path, ec['ec'])
-        _log.debug("File in pull request %s has these related easyconfigs: %s" % (ec['spec'], files))
+        _log.debug("File in PR#%s %s has these related easyconfigs: %s" % (pr, ec['spec'], files))
         if files:
             diff = multi_diff(ec['spec'], files, colored=colored)
             msg = diff
         else:
             msg = "\n(no related easyconfigs found for %s)\n" % os.path.basename(ec['spec'])
-        print msg
+        print(msg)

From 0f67d576ddf19bf3cab8987559bf799e5267c405 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@gmail.com>
Date: Mon, 12 Jan 2015 13:09:23 +0100
Subject: [PATCH 0439/1356] fixed remarks

---
 test/framework/easyblock.py                   | 22 ++++---------
 test/framework/easyconfigs/toy-0.0-patches.eb | 32 -------------------
 2 files changed, 7 insertions(+), 47 deletions(-)
 delete mode 100644 test/framework/easyconfigs/toy-0.0-patches.eb

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 0a4353c96f..d9402bf865 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -28,7 +28,6 @@
 @author: Jens Timmerman (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
-import copy
 import os
 import re
 import shutil
@@ -44,7 +43,6 @@
 from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
 from easybuild.tools import config
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.modules import modules_tool
 
@@ -99,7 +97,7 @@ def check_extra_options_format(extra_options):
 
         name = "pi"
         version = "3.14"
-        self.contents =  '\n'.join([
+        self.contents = '\n'.join([
             'easyblock = "ConfigureMake"',
             'name = "%s"' % name,
             'version = "%s"' % version,
@@ -263,7 +261,6 @@ def test_skip_extensions_step(self):
         # check if skip skips correct extensions
         self.writeEC()
         eb = EasyBlock(EasyConfig(self.eb_file))
-        #self.assertTrue('ext1' in eb.exts.keys() and 'ext2' in eb.exts.keys())
         eb.builddir = config.build_path()
         eb.installdir = config.install_path()
         eb.skip = True
@@ -307,7 +304,6 @@ def test_make_module_step(self):
         self.writeEC()
         ec = EasyConfig(self.eb_file)
         eb = EasyBlock(ec)
-        #eb.builddir = self.test_buildpath
         eb.installdir = os.path.join(config.install_path(), 'pi', '3.14')
         eb.check_readiness_step()
 
@@ -389,7 +385,7 @@ def test_get_easyblock_instance(self):
         testdir = os.path.abspath(os.path.dirname(__file__))
         import easybuild
         eb_blocks_path = os.path.join(testdir, 'sandbox')
-        if not eb_blocks_path in sys.path:
+        if eb_blocks_path not in sys.path:
             sys.path.append(eb_blocks_path)
             easybuild = reload(easybuild)
 
@@ -411,27 +407,24 @@ def test_patchlevel(self):
         """Test the parsing of the fetch_patches function."""
         # adjust PYTHONPATH such that test easyblocks are found
         testdir = os.path.abspath(os.path.dirname(__file__))
-        ec = process_easyconfig(os.path.join(testdir, 'easyconfigs', 'toy-0.0-patches.eb'))[0]
+        ec = process_easyconfig(os.path.join(testdir, 'easyconfigs', 'toy-0.0.eb'))[0]
         eb = get_easyblock_instance(ec)
 
         patches = [
-            ('toy-0.0_level0_2.patch',0),  # should also be level 0 (not None)
-            ('toy-0.0_level4.patch',4),   # should be level4
+            ('toy-0.0_level0_2.patch', 0),  # should also be level 0 (not None)
+            ('toy-0.0_level4.patch', 4),   # should be level4
         ]
-        sandbox_sources = os.path.join(testdir, 'sandbox', 'sources')
-        init_config(args=["--sourcepath=%s" % sandbox_sources])
-        #check if patch levels are parsed correctly
+        # check if patch levels are parsed correctly
         eb.fetch_patches(patches)
 
         self.assertEquals(eb.patches[0]['level'], 0)
         self.assertEquals(eb.patches[1]['level'], 4)
 
         patches = [
-            ('toy-0.0_level4.patch', False),  #should throw an error, only int's an strings allowed here
+            ('toy-0.0_level4.patch', False),  # should throw an error, only int's an strings allowed here
         ]
         self.assertRaises(EasyBuildError, eb.fetch_patches, patches)
 
-
     def test_obtain_file(self):
         """Test obtain_file method."""
         toy_tarball = 'toy-0.0.tar.gz'
@@ -533,7 +526,6 @@ def test_exclude_path_to_top_of_module_tree(self):
         os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
         init_config(build_options=build_options)
         self.setup_hierarchical_modules()
-        modtool = modules_tool()
 
         modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all')
         mkdir(os.path.join(modfile_prefix, 'Compiler', 'GCC', '4.8.3'), parents=True)
diff --git a/test/framework/easyconfigs/toy-0.0-patches.eb b/test/framework/easyconfigs/toy-0.0-patches.eb
deleted file mode 100644
index 89994f6681..0000000000
--- a/test/framework/easyconfigs/toy-0.0-patches.eb
+++ /dev/null
@@ -1,32 +0,0 @@
-name = 'toy'
-version = '0.0'
-
-homepage = 'http://hpcugent.github.com/easybuild'
-description = "Toy C program."
-
-toolchain = {'name': 'dummy', 'version': 'dummy'}
-
-sources = [SOURCE_TAR_GZ]
-checksums = [[
-    'be662daa971a640e40be5c804d9d7d10',  # default (MD5)
-    ('adler32', '0x998410035'),
-    ('crc32', '0x1553842328'),
-    ('md5', 'be662daa971a640e40be5c804d9d7d10'),
-    ('sha1', 'f618096c52244539d0e89867405f573fdb0b55b0'),
-    ('size', 273),
-]]
-patches = [
-    'toy-0.0_level0.patch',   # should be level 0
-    ('toy-0.0_level0_2.patch',0),  # should also be level 0 (not None)
-    ('toy-0.0_level4.patch',4),   # should be level4
-    ('toy-0.0_level4.patch', False),  #should throw an error, only int's an strings allowed here
-]
-
-sanity_check_paths = {
-    'files': [('bin/yot', 'bin/toy')],
-    'dirs': ['bin'],
-}
-
-postinstallcmds = ["echo TOY > %(installdir)s/README"]
-
-moduleclass = 'tools'

From 61b687c6a6a23590fd16f500387627c9146990d3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Jan 2015 17:58:21 +0100
Subject: [PATCH 0440/1356] fix use of review_pr in main.py, style cleanup in
 multi_diff.py

---
 easybuild/main.py             |  2 +-
 easybuild/tools/multi_diff.py | 68 +++++++++++++++++++++++------------
 2 files changed, 46 insertions(+), 24 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index b39608d1e6..52e332ca79 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -218,7 +218,7 @@ def main(testing_data=(None, None, None)):
 
     # review specified PR
     if options.review_pr:
-        review_pr(options.review_pr, colored=options.color, tmpdir=eb_tmpdir)
+        review_pr(options.review_pr, colored=options.color)
 
     # search for easyconfigs, if a query is specified
     query = options.search or options.search_short
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multi_diff.py
index 7704fb476f..31d1ba0614 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multi_diff.py
@@ -26,58 +26,74 @@
 Module which allows the diffing of multiple files
 
 @author: Toon Willems (Ghent University)
+@author: Kenneth Hoste (Ghent University)
 """
 
 import difflib
 import math
 import os
 
+from easybuild.tools.filetools import read_file
 from easybuild.tools.utilities import det_terminal_size
 
 
 SEP_WIDTH = 5
 
-GREEN = "\033[0;32m"
+# text colors
 PURPLE = "\033[0;35m"
-RED = "\033[0;21m"
+# background colors
+GREEN_BACK = "\033[0;42m"
+RED_BACK = "\033[0;41m"
+# end character for colorized text
 ENDC = "\033[0m"
-B_GREEN = "\033[0;42m"
-B_RED = "\033[0;41m"
+
 
 class MultiDiff(object):
     """
-    This class holds the diff information
+    Class representing a multi-diff.
     """
-
     REMOVED_KEY = 'removed'
     ADDED_KEY = 'added'
 
     def __init__(self, base, files, colored=True):
+        """
+        MultiDiff constructor
+        @param base: base to compare with
+        @param files: list of files to compare with base
+        @param colored: boolean indicating whether a colored multi-diff should be generated
+        """
         self.base = base
-        self.base_lines = open(base).readlines()
-        self.diff_info = dict()
+        self.base_lines = read_file(self.base).split('\n')
         self.files = files
         self.colored = colored
+        self.diff_info = dict()
 
     def parse_line(self, line_no, diff_line, meta, squigly_line=None):
         """
         Parse a line as generated by difflib
+        @param line_no: line number
+        @param diff_lin: line generated by difflib
+        @param meta: FIXME
+        @param squigly_line: FIXME
         """
         if diff_line.startswith('+'):
             key = self.ADDED_KEY
         elif diff_line.startswith('-'):
             key = self.REMOVED_KEY
 
-        self.diff_info.setdefault(line_no, {}).setdefault(key,[]).append((diff_line.rstrip(), meta, squigly_line))
+        self.diff_info.setdefault(line_no, {}).setdefault(key, []).append((diff_line.rstrip(), meta, squigly_line))
 
     def __str__(self):
         """
         Create a string representation of this multi diff
         """
         def limit(text, length):
-            """ limit text to certain length, add ENDC if needd """
+            """Limit text to specified length, add ENDC if trimmed."""
             if len(text) > length:
-                return text[0:length-3] + ENDC + '...'
+                res = text[0:length-3]
+                if self.colored:
+                    res += ENDC
+                return res + '...'
             else:
                 return text
 
@@ -162,19 +178,23 @@ def _colorize(self, line, squigly):
         chars = list(line)
         flag = ' '
         compensator = 0
-        color_map = {'-': B_RED, '+': B_GREEN, '^': B_GREEN if line.startswith('+') else B_RED}
+        color_map = {
+            '-': RED_BACK,
+            '+': GREEN_BACK,
+            '^': GREEN_BACK if line.startswith('+') else RED_BACK,
+        }
         if squigly:
-            for i,s in enumerate(squigly):
+            for i, s in enumerate(squigly):
                 if s != flag:
                     chars.insert(i + compensator, ENDC)
                     compensator += 1
-                    if s in ('+','-','^'):
+                    if s in ('+', '-', '^'):
                         chars.insert(i + compensator, color_map.get(s, ''))
                         compensator += 1
                     flag = s
             chars.insert(len(squigly)+compensator, ENDC)
         else:
-            chars.insert(0, color_map.get(line[0],''))
+            chars.insert(0, color_map.get(line[0], ''))
             chars.append(ENDC)
 
         return ''.join(chars)
@@ -186,24 +206,26 @@ def _color(self, line, color):
             return line
 
     def _merge_squigly(self, squigly1, squigly2):
-        """Combine 2 diff lines into 1 """
+        """Combine two diff lines into a single diff line. """
         sq1 = list(squigly1)
         sq2 = list(squigly2)
-        base,other = (sq1, sq2) if len(sq1) > len(sq2) else (sq2,sq1)
+        base, other = (sq1, sq2) if len(sq1) > len(sq2) else (sq2, sq1)
 
-        for i,o in enumerate(other):
+        for i, o in enumerate(other):
             if base[i] in (' ', '^') and base[i] != o:
-                base[i]=o
+                base[i] = o
 
         return ''.join(base)
 
-def multi_diff(base,files, colored=True):
+def multi_diff(base, files, colored=True):
     """
-    generate a Diff for multiple files, all compared to base
+    Generate a diff for multiple files, all compared to base.
+    @param base: base to compare with
+    @param files: list of files to compare with base
+    @param colored: boolean indicating whether a colored multi-diff should be generated
     """
     d = difflib.Differ()
     differ = MultiDiff(base, files, colored)
-
     base_lines = differ.base_lines
 
     # use the Diff class to store the information
@@ -227,7 +249,7 @@ def multi_diff(base,files, colored=True):
                 last_added = line
                 compensator -= 1
 
-        # construct the Diff based on the above dict
+        # construct the multi-diff based on the constructed dict
         for line_no in local_diff:
             for (line, file_name) in local_diff[line_no]:
                 differ.parse_line(line_no, line, file_name, squigly_dict.get(line, '').rstrip())

From 48b89c095af0ed2f8eed99ab9f7bec096fb4444b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Jan 2015 17:59:30 +0100
Subject: [PATCH 0441/1356] rename multi_diff to multidiff

---
 easybuild/framework/easyconfig/tools.py         | 4 ++--
 easybuild/tools/{multi_diff.py => multidiff.py} | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)
 rename easybuild/tools/{multi_diff.py => multidiff.py} (99%)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 53f108f618..484e3d212b 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -76,7 +76,7 @@
 from easybuild.tools.filetools import find_easyconfigs, write_file
 from easybuild.tools.github import fetch_easyconfigs_from_pr, download_repo
 from easybuild.tools.modules import modules_tool
-from easybuild.tools.multi_diff import multi_diff
+from easybuild.tools.multidiff import multidiff
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.run import run_cmd
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
@@ -440,7 +440,7 @@ def review_pr(pr, colored=True, branch='develop'):
         files = find_related_easyconfigs(repo_path, ec['ec'])
         _log.debug("File in PR#%s %s has these related easyconfigs: %s" % (pr, ec['spec'], files))
         if files:
-            diff = multi_diff(ec['spec'], files, colored=colored)
+            diff = multidiff(ec['spec'], files, colored=colored)
             msg = diff
         else:
             msg = "\n(no related easyconfigs found for %s)\n" % os.path.basename(ec['spec'])
diff --git a/easybuild/tools/multi_diff.py b/easybuild/tools/multidiff.py
similarity index 99%
rename from easybuild/tools/multi_diff.py
rename to easybuild/tools/multidiff.py
index 31d1ba0614..97b0ca53a3 100644
--- a/easybuild/tools/multi_diff.py
+++ b/easybuild/tools/multidiff.py
@@ -217,7 +217,7 @@ def _merge_squigly(self, squigly1, squigly2):
 
         return ''.join(base)
 
-def multi_diff(base, files, colored=True):
+def multidiff(base, files, colored=True):
     """
     Generate a diff for multiple files, all compared to base.
     @param base: base to compare with

From 0b2c7c24862dadb6286d59c0fba45577585156b8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 13 Jan 2015 09:13:19 +0100
Subject: [PATCH 0442/1356] escape use of '%' in string with cmdline options
 with --job

---
 easybuild/tools/parallelbuild.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index ac1d5e2f59..f71de69a5f 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -133,9 +133,10 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
     # generate_cmd_line returns the options in form --longopt=value
     opts = [x for x in cmd_line_opts if not x.split('=')[0] in ['--%s' % y for y in ignore_opts]]
 
-    quoted_opts = subprocess.list2cmdline(opts)
+    # compose string with command line options, properly quoted and with '%' characters escaped
+    opts_str = subprocess.list2cmdline(opts).replace('%', '%%')
 
-    command = "unset TMPDIR && cd %s && eb %%(spec)s %s --testoutput=%%(output_dir)s" % (curdir, quoted_opts)
+    command = "unset TMPDIR && cd %s && eb %%(spec)s %s --testoutput=%%(output_dir)s" % (curdir, opts_str)
     _log.info("Command template for jobs: %s" % command)
     job_info_lines = []
     if testing:

From cb1e91121d88d886c96e8e3d087e8e56ec6c43c7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 16 Jan 2015 22:10:55 +0100
Subject: [PATCH 0443/1356] fix import order

---
 easybuild/framework/easyconfig/tools.py | 26 ++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 484e3d212b..dd670e6393 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -44,6 +44,19 @@
 from distutils.version import LooseVersion
 from vsc.utils import fancylogger
 
+from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
+from easybuild.framework.easyconfig.easyconfig import ActiveMNS, create_paths, process_easyconfig
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import build_option
+from easybuild.tools.filetools import find_easyconfigs, write_file
+from easybuild.tools.github import fetch_easyconfigs_from_pr, download_repo
+from easybuild.tools.modules import modules_tool
+from easybuild.tools.multidiff import multidiff
+from easybuild.tools.ordereddict import OrderedDict
+from easybuild.tools.run import run_cmd
+from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
+from easybuild.tools.utilities import quote_str
+
 # optional Python packages, these might be missing
 # failing imports are just ignored
 # a NameError should be catched where these are used
@@ -69,19 +82,6 @@
 except ImportError, err:
     graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz")
 
-from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
-from easybuild.framework.easyconfig.easyconfig import ActiveMNS, create_paths, process_easyconfig
-from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.config import build_option
-from easybuild.tools.filetools import find_easyconfigs, write_file
-from easybuild.tools.github import fetch_easyconfigs_from_pr, download_repo
-from easybuild.tools.modules import modules_tool
-from easybuild.tools.multidiff import multidiff
-from easybuild.tools.ordereddict import OrderedDict
-from easybuild.tools.run import run_cmd
-from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
-from easybuild.tools.utilities import quote_str
-
 
 _log = fancylogger.getLogger('easyconfig.tools', fname=False)
 

From dc6cbc127ffaa2ea42db16ffb6e841b66c31bd55 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 16 Jan 2015 22:15:20 +0100
Subject: [PATCH 0444/1356] style fixes in multidiff.py

---
 easybuild/tools/multidiff.py | 219 +++++++++++++++++++----------------
 1 file changed, 116 insertions(+), 103 deletions(-)

diff --git a/easybuild/tools/multidiff.py b/easybuild/tools/multidiff.py
index 97b0ca53a3..4eeb57fa5c 100644
--- a/easybuild/tools/multidiff.py
+++ b/easybuild/tools/multidiff.py
@@ -32,6 +32,7 @@
 import difflib
 import math
 import os
+from vsc.utils import fancylogger
 
 from easybuild.tools.filetools import read_file
 from easybuild.tools.utilities import det_terminal_size
@@ -45,16 +46,24 @@
 GREEN_BACK = "\033[0;42m"
 RED_BACK = "\033[0;41m"
 # end character for colorized text
-ENDC = "\033[0m"
+END_COLOR = "\033[0m"
+
+# meaning characters in diff context
+HAT = '^'
+MINUS = '-'
+PLUS = '+'
+SPACE = ' '
+
+END_LONG_LINE = '...'
+
+
+_log = fancylogger.getLogger('multidiff', fname=False)
 
 
 class MultiDiff(object):
     """
     Class representing a multi-diff.
     """
-    REMOVED_KEY = 'removed'
-    ADDED_KEY = 'added'
-
     def __init__(self, base, files, colored=True):
         """
         MultiDiff constructor
@@ -66,8 +75,9 @@ def __init__(self, base, files, colored=True):
         self.base_lines = read_file(self.base).split('\n')
         self.files = files
         self.colored = colored
-        self.diff_info = dict()
+        self.diff_info = {}
 
+    # FIXME's in docstring
     def parse_line(self, line_no, diff_line, meta, squigly_line=None):
         """
         Parse a line as generated by difflib
@@ -76,66 +86,77 @@ def parse_line(self, line_no, diff_line, meta, squigly_line=None):
         @param meta: FIXME
         @param squigly_line: FIXME
         """
-        if diff_line.startswith('+'):
-            key = self.ADDED_KEY
-        elif diff_line.startswith('-'):
-            key = self.REMOVED_KEY
-
-        self.diff_info.setdefault(line_no, {}).setdefault(key, []).append((diff_line.rstrip(), meta, squigly_line))
-
-    def __str__(self):
-        """
-        Create a string representation of this multi diff
-        """
-        def limit(text, length):
-            """Limit text to specified length, add ENDC if trimmed."""
-            if len(text) > length:
-                res = text[0:length-3]
-                if self.colored:
-                    res += ENDC
-                return res + '...'
-            else:
-                return text
+        # register (diff_line, meta, squigly_line) tuple for specified line number and determined key
+        key = diff_line[0]
+        if not key in [MINUS, PLUS]:
+            _log.error("diff line starts with unexpected character: %s" % diff_line)
+        line_key_tuples = self.diff_info.setdefault(line_no, {}).setdefault(key, [])
+        line_key_tuples.append((diff_line.rstrip(), meta, squigly_line))
+
+    def color_line(self, line, color):
+        """Create colored version of given line, with given color, if color mode is enabled."""
+        if self.colored:
+            line = ''.join([color, line, END_COLOR])
+        return line
 
-        term_width, _ = det_terminal_size()
+    def merge_squigly(self, squigly1, squigly2):
+        """Combine two diff lines into a single diff line."""
+        sq1 = list(squigly1)
+        sq2 = list(squigly2)
+        # longest line is base
+        base, other = (sq1, sq2) if len(sq1) > len(sq2) else (sq2, sq1)
 
-        base = self._color(os.path.basename(self.base), PURPLE)
-        filenames = ', '.join(map(os.path.basename, self.files))
-        output = [
-            "Comparing %s with %s" % (base, filenames),
-            '=' * SEP_WIDTH,
-        ]
+        for i, o in enumerate(other):
+            if base[i] in [HAT, SPACE] and base[i] != o:
+                base[i] = o
 
-        diff = False
-        for i in range(len(self.base_lines)):
-            lines = filter(None, self.get_line(i))
-            if lines:
-                output.append('\n'.join([limit(line, term_width) for line in lines]))
-                diff = True
+        return ''.join(base)
 
-        if not diff:
-            output.append("(no diff)")
+    def colorize(self, line, squigly):
+        """Add colors to the diff line based on the squiqly line"""
+        if not self.colored:
+            return line
 
-        output.append('=' * SEP_WIDTH)
+        chars = list(line)
+        flag = ' '
+        compensator = 0
+        color_map = {
+            HAT: GREEN_BACK if line.startswith(PLUS) else RED_BACK,
+            MINUS: RED_BACK,
+            PLUS: GREEN_BACK,
+        }
+        if squigly:
+            for i, s in enumerate(squigly):
+                if s != flag:
+                    chars.insert(i + compensator, END_COLOR)
+                    compensator += 1
+                    if s in [HAT, MINUS, PLUS]:
+                        chars.insert(i + compensator, color_map.get(s, ''))
+                        compensator += 1
+                    flag = s
+            chars.insert(len(squigly)+compensator, END_COLOR)
+        else:
+            chars.insert(0, color_map.get(line[0], ''))
+            chars.append(END_COLOR)
 
-        return '\n'.join(output)
+        return ''.join(chars)
 
     def get_line(self, line_no):
         """
         Return the line information for a specific line
+        @param line_no: line number to obtain information for
+        @return: list with text lines providing line information
         """
         output = []
         diff_dict = self.diff_info.get(line_no, {})
-        for key in [self.REMOVED_KEY, self.ADDED_KEY]:
-            lines = set()
-            changes_dict = dict()
-            squigly_dict = dict()
+        for key in [MINUS, PLUS]:
+            lines, changes_dict, squigly_dict = set(), {}, {}
 
             if key in diff_dict:
                 for (diff_line, meta, squigly_line) in diff_dict[key]:
                     if squigly_line:
                         squigly_line2 = squigly_dict.get(diff_line, squigly_line)
-                        squigly_dict[diff_line] = self._merge_squigly(squigly_line, squigly_line2)
+                        squigly_dict[diff_line] = self.merge_squigly(squigly_line, squigly_line2)
                     lines.add(diff_line)
                     changes_dict.setdefault(diff_line,set()).add(meta)
 
@@ -149,7 +170,7 @@ def get_line(self, line_no):
             for diff_line in lines:
                 line = [str(line_no)]
                 squigly_line = squigly_dict.get(diff_line,'')
-                line.append(self._colorize(diff_line, squigly_line))
+                line.append(self.colorize(diff_line, squigly_line))
 
                 files = changes_dict[diff_line]
                 num_files = len(self.files)
@@ -158,7 +179,7 @@ def get_line(self, line_no):
                 if len(files) != num_files:
                         line.append(', '.join(files))
 
-                output.append(" ".join(line))
+                output.append(' '.join(line))
                 # prepend spaces to match line number length
                 if not self.colored and squigly_line:
                     prepend = ' ' * (2 + int(math.log10(line_no)))
@@ -170,52 +191,43 @@ def get_line(self, line_no):
 
         return output
 
-    def _colorize(self, line, squigly):
-        """Add colors to the diff line based on the squiqly line"""
-        if not self.colored:
-            return line
+    def __str__(self):
+        """
+        Create a string representation of this multi-diff
+        """
+        def limit(text, length):
+            """Limit text to specified length, terminate color mode and add END_LONG_LINE if trimmed."""
+            if len(text) > length:
+                maxlen = length - len(END_LONG_LINE)
+                res = text[:maxlen]
+                if self.colored:
+                    res += END_COLOR
+                return res + END_LONG_LINE
+            else:
+                return text
 
-        chars = list(line)
-        flag = ' '
-        compensator = 0
-        color_map = {
-            '-': RED_BACK,
-            '+': GREEN_BACK,
-            '^': GREEN_BACK if line.startswith('+') else RED_BACK,
-        }
-        if squigly:
-            for i, s in enumerate(squigly):
-                if s != flag:
-                    chars.insert(i + compensator, ENDC)
-                    compensator += 1
-                    if s in ('+', '-', '^'):
-                        chars.insert(i + compensator, color_map.get(s, ''))
-                        compensator += 1
-                    flag = s
-            chars.insert(len(squigly)+compensator, ENDC)
-        else:
-            chars.insert(0, color_map.get(line[0], ''))
-            chars.append(ENDC)
+        term_width, _ = det_terminal_size()
 
-        return ''.join(chars)
+        base = self.color_line(os.path.basename(self.base), PURPLE)
+        filenames = ', '.join(map(os.path.basename, self.files))
+        output = [
+            "Comparing %s with %s" % (base, filenames),
+            '=' * SEP_WIDTH,
+        ]
 
-    def _color(self, line, color):
-        if self.colored:
-            return ''.join([color, line, ENDC])
-        else:
-            return line
+        diff = False
+        for i in range(len(self.base_lines)):
+            lines = filter(None, self.get_line(i))
+            if lines:
+                output.append('\n'.join([limit(line, term_width) for line in lines]))
+                diff = True
 
-    def _merge_squigly(self, squigly1, squigly2):
-        """Combine two diff lines into a single diff line. """
-        sq1 = list(squigly1)
-        sq2 = list(squigly2)
-        base, other = (sq1, sq2) if len(sq1) > len(sq2) else (sq2, sq1)
+        if not diff:
+            output.append("(no diff)")
 
-        for i, o in enumerate(other):
-            if base[i] in (' ', '^') and base[i] != o:
-                base[i] = o
+        output.append('=' * SEP_WIDTH)
 
-        return ''.join(base)
+        return '\n'.join(output)
 
 def multidiff(base, files, colored=True):
     """
@@ -223,15 +235,16 @@ def multidiff(base, files, colored=True):
     @param base: base to compare with
     @param files: list of files to compare with base
     @param colored: boolean indicating whether a colored multi-diff should be generated
+    @return: text with multidiff overview
     """
-    d = difflib.Differ()
-    differ = MultiDiff(base, files, colored)
-    base_lines = differ.base_lines
+    differ = difflib.Differ()
+    mdiff = MultiDiff(base, files, colored)
 
-    # use the Diff class to store the information
-    for file_name in files:
-        diff = list(d.compare(open(file_name).readlines(), base_lines))
-        file_name = os.path.basename(file_name)
+    # use the MultiDiff class to store the information
+    for filepath in files:
+        lines = read_file(filepath).split('\n')
+        diff = differ.compare(lines, mdiff.base_lines)
+        filename = os.path.basename(filepath)
 
         local_diff = dict()
         squigly_dict = dict()
@@ -241,17 +254,17 @@ def multidiff(base, files, colored=True):
             if line.startswith('?'):
                 squigly_dict[last_added] = line
                 compensator -= 1
-            elif line.startswith('+'):
-                local_diff.setdefault(i+compensator, []).append((line, file_name))
+            elif line.startswith(PLUS):
+                local_diff.setdefault(i + compensator, []).append((line, filename))
                 last_added = line
-            elif line.startswith('-'):
-                local_diff.setdefault(i+compensator, []).append((line, file_name))
+            elif line.startswith(MINUS):
+                local_diff.setdefault(i + compensator, []).append((line, filename))
                 last_added = line
                 compensator -= 1
 
         # construct the multi-diff based on the constructed dict
         for line_no in local_diff:
-            for (line, file_name) in local_diff[line_no]:
-                differ.parse_line(line_no, line, file_name, squigly_dict.get(line, '').rstrip())
+            for (line, filename) in local_diff[line_no]:
+                mdiff.parse_line(line_no, line, filename, squigly_dict.get(line, '').rstrip())
 
-    return differ
+    return str(mdiff)

From bf1746703d9a0b3c394e94118e4fa88cbc7678ec Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 16 Jan 2015 22:22:21 +0100
Subject: [PATCH 0445/1356] cleaner solution for defining category constants in
 default.py

---
 easybuild/framework/easyconfig/default.py | 38 +++++++++--------------
 1 file changed, 15 insertions(+), 23 deletions(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 1c251a7629..0d33bd8388 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -40,31 +40,23 @@
 
 
 # we use a tuple here so we can sort them based on the numbers
-HIDDEN = (-1, 'hidden')
-MANDATORY = (0, 'mandatory')
-CUSTOM = (1, 'easyblock-specific')
-TOOLCHAIN = (2, 'toolchain')
-BUILD = (3, 'build')
-FILEMANAGEMENT = (4, 'file-management')
-DEPENDENCIES = (5, 'dependencies')
-LICENSE = (6, 'license')
-EXTENSIONS = (7, 'extensions')
-MODULES = (8, 'modules')
-OTHER = (9, 'other')
-
 ALL_CATEGORIES = {
-    'HIDDEN': HIDDEN,
-    'MANDATORY': MANDATORY,
-    'CUSTOM': CUSTOM,
-    'TOOLCHAIN': TOOLCHAIN,
-    'BUILD': BUILD,
-    'FILEMANAGEMENT': FILEMANAGEMENT,
-    'DEPENDENCIES': DEPENDENCIES,
-    'LICENSE': LICENSE,
-    'EXTENSIONS': EXTENSIONS,
-    'MODULES': MODULES,
-    'OTHER': OTHER,
+    'HIDDEN': (-1, 'hidden'),
+    'MANDATORY': (0, 'mandatory'),
+    'CUSTOM': (1, 'easyblock-specific'),
+    'TOOLCHAIN': (2, 'toolchain'),
+    'BUILD': (3, 'build'),
+    'FILEMANAGEMENT': (4, 'file-management'),
+    'DEPENDENCIES': (5, 'dependencies'),
+    'LICENSE': (6, 'license'),
+    'EXTENSIONS': (7, 'extensions'),
+    'MODULES': (8, 'modules'),
+    'OTHER': (9, 'other'),
 }
+# define constants so they can be used below
+# avoid that pylint complains about unknown variables in this file
+# pylint: disable=E0602
+globals().update(ALL_CATEGORIES)
 
 # List of tuples. Each tuple has the following format (key, [default, help text, category])
 DEFAULT_CONFIG = {

From 0a4c4c0356251bc8c668702b511decaa906eb2ec Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 16 Jan 2015 23:18:08 +0100
Subject: [PATCH 0446/1356] cleanup in fetch_patches, enhance test for
 fetch_patches, remove useless toy patch files in tests

---
 easybuild/framework/easyblock.py              | 50 +++++++++----------
 test/framework/easyblock.py                   | 35 +++++++++----
 .../sandbox/sources/toy/toy-0.0_level0.patch  |  0
 .../sources/toy/toy-0.0_level0_2.patch        |  0
 .../sandbox/sources/toy/toy-0.0_level4.patch  |  0
 5 files changed, 51 insertions(+), 34 deletions(-)
 delete mode 100644 test/framework/sandbox/sources/toy/toy-0.0_level0.patch
 delete mode 100644 test/framework/sandbox/sources/toy/toy-0.0_level0_2.patch
 delete mode 100644 test/framework/sandbox/sources/toy/toy-0.0_level4.patch

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 19a21c090e..c56029875d 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -289,48 +289,48 @@ def fetch_sources(self, list_of_sources, checksums=None):
 
         self.log.info("Added sources: %s" % self.src)
 
-    def fetch_patches(self, list_of_patches, extension=False, checksums=None):
+    def fetch_patches(self, patch_specs=None, extension=False, checksums=None):
         """
         Add a list of patches.
         All patches will be checked if a file exists (or can be located)
         """
+        if patch_specs is None:
+            patch_specs = self.cfg['patches']
 
         patches = []
-        for index, patch_entry in enumerate(list_of_patches):
+        for index, patch_spec in enumerate(patch_specs):
 
             # check if the patches can be located
             copy_file = False
             suff = None
             level = None
-            if isinstance(patch_entry, (list, tuple)):
-                if not len(patch_entry) == 2:
+            if isinstance(patch_spec, (list, tuple)):
+                if not len(patch_spec) == 2:
                     self.log.error("Unknown patch specification '%s', only two-element lists/tuples are supported!",
-                                   str(patch_entry))
-                pf = patch_entry[0]
-
-                if type(patch_entry[1]) == int:  # int and only int is allowed here, we are parsing a config file, not
-                                                 # trying to write generic code
-                    level = patch_entry[1]
-                elif isinstance(patch_entry[1], basestring):
+                                   str(patch_spec))
+                patch_file = patch_spec[0]
+
+                # this *must* be of typ int, nothing else
+                # no 'isinstance(..., int)', since that would make True/False also acceptable
+                if type(patch_spec[1]) == int:
+                    level = patch_spec[1]
+                elif isinstance(patch_spec[1], basestring):
                     # non-patch files are assumed to be files to copy
-                    if not patch_entry[0].endswith('.patch'):
+                    if not patch_spec[0].endswith('.patch'):
                         copy_file = True
-                    suff = patch_entry[1]
+                    suff = patch_spec[1]
                 else:
-                    self.log.error(
-                        "Wrong patch specification '%s', only int and string are supported as second element!",
-                        str(patch_entry),
-                        )
+                    self.log.error("Wrong patch spec '%s', only int/string are supported as 2nd element" % str(patch_spec))
             else:
-                pf = patch_entry
+                patch_file = patch_spec
 
-            path = self.obtain_file(pf, extension=extension)
+            path = self.obtain_file(patch_file, extension=extension)
             if path:
-                self.log.debug('File %s found for patch %s' % (path, patch_entry))
+                self.log.debug('File %s found for patch %s' % (path, patch_spec))
                 patchspec = {
-                    'name': pf,
+                    'name': patch_file,
                     'path': path,
-                    'checksum': self.get_checksum_for(checksums, filename=pf, index=index),
+                    'checksum': self.get_checksum_for(checksums, filename=patch_file, index=index),
                 }
                 if suff:
                     if copy_file:
@@ -345,7 +345,7 @@ def fetch_patches(self, list_of_patches, extension=False, checksums=None):
                 else:
                     self.patches.append(patchspec)
             else:
-                self.log.error('No file found for patch %s' % patch_entry)
+                self.log.error('No file found for patch %s' % patch_spec)
 
         if extension:
             self.log.info("Fetched extension patches: %s" % patches)
@@ -412,7 +412,7 @@ def fetch_extension_sources(self):
                                 else:
                                     self.log.error('Checksum for ext source %s failed' % fn)
 
-                            ext_patches = self.fetch_patches(ext_options.get('patches', []), extension=True)
+                            ext_patches = self.fetch_patches(patch_specs=ext_options.get('patches', []), extension=True)
                             if ext_patches:
                                 self.log.debug('Found patches for extension %s: %s' % (ext_name, ext_patches))
                                 ext_src.update({'patches': ext_patches})
@@ -1228,7 +1228,7 @@ def fetch_step(self, skip_checksums=False):
                 patches_checksums = self.cfg['checksums'][len(self.cfg['sources']):]
             else:
                 patches_checksums = self.cfg['checksums']
-            self.fetch_patches(self.cfg['patches'], checksums=patches_checksums)
+            self.fetch_patches(checksums=patches_checksums)
         else:
             self.log.info('no patches provided')
 
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index d9402bf865..78e423853b 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -403,27 +403,44 @@ def test_get_easyblock_instance(self):
         logtxt = read_file(eb.logfile)
         self.assertTrue(eb_log_msg_re.search(logtxt), "Pattern '%s' found in: %s" % (eb_log_msg_re.pattern, logtxt))
 
-    def test_patchlevel(self):
-        """Test the parsing of the fetch_patches function."""
+    def test_fetch_patches(self):
+        """Test fetch_patches method."""
         # adjust PYTHONPATH such that test easyblocks are found
         testdir = os.path.abspath(os.path.dirname(__file__))
         ec = process_easyconfig(os.path.join(testdir, 'easyconfigs', 'toy-0.0.eb'))[0]
         eb = get_easyblock_instance(ec)
 
+        eb.fetch_patches()
+        self.assertEqual(len(eb.patches), 1)
+        self.assertEqual(eb.patches[0]['name'], 'toy-0.0_typo.patch')
+        self.assertFalse('level' in eb.patches[0])
+
+        # reset
+        eb.patches = []
+
         patches = [
-            ('toy-0.0_level0_2.patch', 0),  # should also be level 0 (not None)
-            ('toy-0.0_level4.patch', 4),   # should be level4
+            ('toy-0.0_typo.patch', 0),  # should also be level 0 (not None or something else)
+            ('toy-0.0_typo.patch', 4),   # should be level 4
+            ('toy-0.0_typo.patch', 'foobar'),  # sourcepath should be set to 'foobar'
+            ('toy-0.0.tar.gz', 'some/path'),  # copy mode (not a .patch file)
         ]
         # check if patch levels are parsed correctly
-        eb.fetch_patches(patches)
-
-        self.assertEquals(eb.patches[0]['level'], 0)
-        self.assertEquals(eb.patches[1]['level'], 4)
+        eb.fetch_patches(patch_specs=patches)
+
+        self.assertEqual(len(eb.patches), 4)
+        self.assertEqual(eb.patches[0]['name'], 'toy-0.0_typo.patch')
+        self.assertEqual(eb.patches[0]['level'], 0)
+        self.assertEqual(eb.patches[1]['name'], 'toy-0.0_typo.patch')
+        self.assertEqual(eb.patches[1]['level'], 4)
+        self.assertEqual(eb.patches[2]['name'], 'toy-0.0_typo.patch')
+        self.assertEqual(eb.patches[2]['sourcepath'], 'foobar')
+        self.assertEqual(eb.patches[3]['name'], 'toy-0.0.tar.gz'),
+        self.assertEqual(eb.patches[3]['copy'], 'some/path')
 
         patches = [
             ('toy-0.0_level4.patch', False),  # should throw an error, only int's an strings allowed here
         ]
-        self.assertRaises(EasyBuildError, eb.fetch_patches, patches)
+        self.assertRaises(EasyBuildError, eb.fetch_patches, patch_specs=patches)
 
     def test_obtain_file(self):
         """Test obtain_file method."""
diff --git a/test/framework/sandbox/sources/toy/toy-0.0_level0.patch b/test/framework/sandbox/sources/toy/toy-0.0_level0.patch
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/test/framework/sandbox/sources/toy/toy-0.0_level0_2.patch b/test/framework/sandbox/sources/toy/toy-0.0_level0_2.patch
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/test/framework/sandbox/sources/toy/toy-0.0_level4.patch b/test/framework/sandbox/sources/toy/toy-0.0_level4.patch
deleted file mode 100644
index e69de29bb2..0000000000

From e9373bd287eef0ee073ea23ba12f6d334ea6b67a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 20 Jan 2015 22:21:46 +0100
Subject: [PATCH 0447/1356] style fixes in multidiff.py

---
 easybuild/tools/multidiff.py | 126 ++++++++++++++++++++---------------
 1 file changed, 73 insertions(+), 53 deletions(-)

diff --git a/easybuild/tools/multidiff.py b/easybuild/tools/multidiff.py
index 4eeb57fa5c..8d92f3cbb8 100644
--- a/easybuild/tools/multidiff.py
+++ b/easybuild/tools/multidiff.py
@@ -53,9 +53,13 @@
 MINUS = '-'
 PLUS = '+'
 SPACE = ' '
+QUESTIONMARK = '?'
 
 END_LONG_LINE = '...'
 
+# restrict displaying of differences to limited number of groups
+MAX_DIFF_GROUPS = 3
+
 
 _log = fancylogger.getLogger('multidiff', fname=False)
 
@@ -64,34 +68,33 @@ class MultiDiff(object):
     """
     Class representing a multi-diff.
     """
-    def __init__(self, base, files, colored=True):
+    def __init__(self, base_fn, base_lines, files, colored=True):
         """
         MultiDiff constructor
         @param base: base to compare with
         @param files: list of files to compare with base
         @param colored: boolean indicating whether a colored multi-diff should be generated
         """
-        self.base = base
-        self.base_lines = read_file(self.base).split('\n')
+        self.base_fn = base_fn
+        self.base_lines = base_lines
         self.files = files
         self.colored = colored
         self.diff_info = {}
 
-    # FIXME's in docstring
-    def parse_line(self, line_no, diff_line, meta, squigly_line=None):
+    def parse_line(self, line_no, diff_line, meta, squigly_line):
         """
-        Parse a line as generated by difflib
+        Register a diff line
         @param line_no: line number
-        @param diff_lin: line generated by difflib
-        @param meta: FIXME
-        @param squigly_line: FIXME
+        @param diff_line: diff line generated by difflib
+        @param meta: meta information (e.g., filename)
+        @param squigly_line: squigly line indicating which characters changed
         """
         # register (diff_line, meta, squigly_line) tuple for specified line number and determined key
         key = diff_line[0]
         if not key in [MINUS, PLUS]:
             _log.error("diff line starts with unexpected character: %s" % diff_line)
         line_key_tuples = self.diff_info.setdefault(line_no, {}).setdefault(key, [])
-        line_key_tuples.append((diff_line.rstrip(), meta, squigly_line))
+        line_key_tuples.append((diff_line, meta, squigly_line))
 
     def color_line(self, line, color):
         """Create colored version of given line, with given color, if color mode is enabled."""
@@ -100,41 +103,42 @@ def color_line(self, line, color):
         return line
 
     def merge_squigly(self, squigly1, squigly2):
-        """Combine two diff lines into a single diff line."""
+        """Combine two squigly lines into a single squigly line."""
         sq1 = list(squigly1)
         sq2 = list(squigly2)
         # longest line is base
         base, other = (sq1, sq2) if len(sq1) > len(sq2) else (sq2, sq1)
 
-        for i, o in enumerate(other):
-            if base[i] in [HAT, SPACE] and base[i] != o:
-                base[i] = o
+        for i, char in enumerate(other):
+            if base[i] in [HAT, SPACE] and base[i] != char:
+                base[i] = char
 
         return ''.join(base)
 
     def colorize(self, line, squigly):
-        """Add colors to the diff line based on the squiqly line"""
+        """Add colors to the diff line based on the squigly line."""
         if not self.colored:
             return line
 
+        # must be a list so we can insert stuff
         chars = list(line)
         flag = ' '
-        compensator = 0
+        offset = 0
         color_map = {
             HAT: GREEN_BACK if line.startswith(PLUS) else RED_BACK,
             MINUS: RED_BACK,
             PLUS: GREEN_BACK,
         }
         if squigly:
-            for i, s in enumerate(squigly):
-                if s != flag:
-                    chars.insert(i + compensator, END_COLOR)
-                    compensator += 1
-                    if s in [HAT, MINUS, PLUS]:
-                        chars.insert(i + compensator, color_map.get(s, ''))
-                        compensator += 1
-                    flag = s
-            chars.insert(len(squigly)+compensator, END_COLOR)
+            for i, squigly_char in enumerate(squigly):
+                if squigly_char != flag:
+                    chars.insert(i + offset, END_COLOR)
+                    offset += 1
+                    if squigly_char in [HAT, MINUS, PLUS]:
+                        chars.insert(i + offset, color_map[squigly_char])
+                        offset += 1
+                    flag = squigly_char
+            chars.insert(len(squigly) + offset, END_COLOR)
         else:
             chars.insert(0, color_map.get(line[0], ''))
             chars.append(END_COLOR)
@@ -152,38 +156,40 @@ def get_line(self, line_no):
         for key in [MINUS, PLUS]:
             lines, changes_dict, squigly_dict = set(), {}, {}
 
+            # obtain relevant diff lines
             if key in diff_dict:
                 for (diff_line, meta, squigly_line) in diff_dict[key]:
                     if squigly_line:
-                        squigly_line2 = squigly_dict.get(diff_line, squigly_line)
-                        squigly_dict[diff_line] = self.merge_squigly(squigly_line, squigly_line2)
+                        # merge squigly lines
+                        if diff_line in squigly_dict:
+                            squigly_line = self.merge_squigly(squigly_line, squigly_dict[diff_line])
+                        squigly_dict[diff_line] = squigly_line
                     lines.add(diff_line)
-                    changes_dict.setdefault(diff_line,set()).add(meta)
+                    # track meta info (which filenames are relevant)
+                    changes_dict.setdefault(diff_line, set()).add(meta)
 
-            # restrict displaying of removals to max_groups
-            max_groups = 2
-            # sort highest first
-            lines = sorted(lines, key=lambda line: len(changes_dict[line]))
-            # limit to max_groups
-            lines = lines[::-1][:max_groups]
+            # sort: lines with most changes last, limit number to MAX_DIFF_GROUPS
+            lines = sorted(lines, key=lambda line: len(changes_dict[line]))[:MAX_DIFF_GROUPS]
 
             for diff_line in lines:
-                line = [str(line_no)]
-                squigly_line = squigly_dict.get(diff_line,'')
-                line.append(self.colorize(diff_line, squigly_line))
+                squigly_line = squigly_dict.get(diff_line, '')
+                line = ['%s %s' % (line_no, self.colorize(diff_line, squigly_line))]
 
+                # mention to how may files this diff applies
                 files = changes_dict[diff_line]
                 num_files = len(self.files)
-
                 line.append("(%d/%d)" % (len(files), num_files))
+
+                # list files to which this diff applies (don't list all files)
                 if len(files) != num_files:
-                        line.append(', '.join(files))
+                    line.append(', '.join(files))
 
                 output.append(' '.join(line))
-                # prepend spaces to match line number length
+
+                # prepend spaces to match line number length in non-color mode
                 if not self.colored and squigly_line:
                     prepend = ' ' * (2 + int(math.log10(line_no)))
-                    output.append(''.join([prepend,squigly_line]))
+                    output.append(''.join([prepend, squigly_line]))
 
         # print seperator only if needed
         if diff_dict and not self.diff_info.get(line_no + 1, {}):
@@ -208,7 +214,7 @@ def limit(text, length):
 
         term_width, _ = det_terminal_size()
 
-        base = self.color_line(os.path.basename(self.base), PURPLE)
+        base = self.color_line(self.base_fn, PURPLE)
         filenames = ', '.join(map(os.path.basename, self.files))
         output = [
             "Comparing %s with %s" % (base, filenames),
@@ -229,6 +235,7 @@ def limit(text, length):
 
         return '\n'.join(output)
 
+
 def multidiff(base, files, colored=True):
     """
     Generate a diff for multiple files, all compared to base.
@@ -238,33 +245,46 @@ def multidiff(base, files, colored=True):
     @return: text with multidiff overview
     """
     differ = difflib.Differ()
-    mdiff = MultiDiff(base, files, colored)
+    base_lines = read_file(base).split('\n')
+    mdiff = MultiDiff(os.path.basename(base), base_lines, files, colored=colored)
 
     # use the MultiDiff class to store the information
     for filepath in files:
         lines = read_file(filepath).split('\n')
-        diff = differ.compare(lines, mdiff.base_lines)
+        diff = differ.compare(lines, base_lines)
         filename = os.path.basename(filepath)
 
-        local_diff = dict()
-        squigly_dict = dict()
+        # contruct map of line number to diff lines and mapping between diff lines
+        # example partial diff:
+        #
+        # - toolchain = {'name': 'goolfc', 'version': '2.6.10'}
+        # ?                            -               ^   ^
+        # 
+        # + toolchain = {'name': 'goolf', 'version': '1.6.20'}
+        # ?                                           ^   ^
+        #
+        local_diff = {}
+        squigly_dict = {}
         last_added = None
-        compensator = 1
+        offset = 1
         for (i, line) in enumerate(diff):
-            if line.startswith('?'):
+            # diff line indicating changed characters on line above, a.k.a. a 'squigly' line
+            if line.startswith(QUESTIONMARK):
                 squigly_dict[last_added] = line
-                compensator -= 1
+                offset -= 1
+            # diff line indicating addition change
             elif line.startswith(PLUS):
-                local_diff.setdefault(i + compensator, []).append((line, filename))
+                local_diff.setdefault(i + offset, []).append((line, filename))
                 last_added = line
+            # diff line indicated removal change
             elif line.startswith(MINUS):
-                local_diff.setdefault(i + compensator, []).append((line, filename))
+                local_diff.setdefault(i + offset, []).append((line, filename))
                 last_added = line
-                compensator -= 1
+                offset -= 1
 
         # construct the multi-diff based on the constructed dict
         for line_no in local_diff:
             for (line, filename) in local_diff[line_no]:
-                mdiff.parse_line(line_no, line, filename, squigly_dict.get(line, '').rstrip())
+                mdiff.parse_line(line_no, line.rstrip(), filename, squigly_dict.get(line, '').rstrip())
 
     return str(mdiff)

From b04a035a313593212c07690130c2e1511b5465aa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Jan 2015 13:51:37 +0100
Subject: [PATCH 0448/1356] drop support for deprecated functionality

---
 easybuild/easybuild_config.py                 |  96 -------
 easybuild/framework/easyblock.py              |  70 +-----
 easybuild/framework/easyconfig/easyconfig.py  |  96 +++----
 .../framework/easyconfig/format/format.py     |   2 +-
 .../easyconfig/format/pyheaderconfigobj.py    |   2 +-
 easybuild/framework/extensioneasyblock.py     |   3 +-
 easybuild/main.py                             |   1 -
 easybuild/toolchains/fft/intelfftw.py         |   2 +-
 easybuild/tools/build_log.py                  |  12 +-
 easybuild/tools/config.py                     | 237 ++----------------
 easybuild/tools/deprecated/eb_2_0.py          |  74 ------
 easybuild/tools/docs.py                       |   3 -
 easybuild/tools/filetools.py                  |  25 +-
 easybuild/tools/modules.py                    |  72 +++---
 easybuild/tools/options.py                    |  21 +-
 easybuild/tools/systemtools.py                |  32 +--
 easybuild/tools/toolchain/toolchain.py        |   1 -
 easybuild/tools/utilities.py                  |  21 +-
 18 files changed, 127 insertions(+), 643 deletions(-)
 delete mode 100644 easybuild/easybuild_config.py
 delete mode 100644 easybuild/tools/deprecated/eb_2_0.py

diff --git a/easybuild/easybuild_config.py b/easybuild/easybuild_config.py
deleted file mode 100644
index 5befd7bf58..0000000000
--- a/easybuild/easybuild_config.py
+++ /dev/null
@@ -1,96 +0,0 @@
-# #
-# Copyright 2009-2014 Ghent University
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-# #
-"""
-EasyBuild configuration file.
-    This is now frozen.
-    All new configuration should be done through the options parser.
-    This is deprecated and will be removed in 2.0
-
-@author: Stijn De Weirdt (Ghent University)
-@author: Dries Verdegem (Ghent University)
-@author: Kenneth Hoste (Ghent University)
-@author: Pieter De Baets (Ghent University)
-@author: Jens Timmerman (Ghent University)
-@author: Toon Willems (Ghent University)
-@author: Fotis Georgatos (Uni.Lu, NTUA)
-"""
-
-#
-# Developers, please do not add any new defaults or variables
-# Use the config options
-#
-
-import os
-import tempfile
-
-import easybuild.tools.config as config
-
-# this should result in a MODULEPATH=($HOME/.local/easybuild|$EASYBUILDPREFIX)/<modules install suffix>/all
-if os.getenv('EASYBUILDPREFIX'):
-    prefix = os.getenv('EASYBUILDPREFIX')
-else:
-    prefix = os.path.join(os.getenv('HOME'), ".local", "easybuild")
-
-# build/install/source paths configuration for EasyBuild
-# build_path possibly overridden by EASYBUILDBUILDPATH
-# install_path possibly overridden by EASYBUILDINSTALLPATH
-build_path = os.path.join(prefix, 'build')
-install_path = prefix
-source_path = os.path.join(prefix, 'sources')
-
-# repository for eb files
-# currently, EasyBuild supports the following repository types:
-
-# * `FileRepository`: a plain flat file repository. In this case, the `repositoryPath` contains the directory where the files are stored,
-# * `GitRepository`: a _non-empty_ **bare** git repository (created with `git init --bare` or `git clone --bare`).
-#   Here, the `repositoryPath` contains the git repository location, which can be a directory or an URL.
-# * `SvnRepository`: an SVN repository. In this case, the `repositoryPath` contains the subversion repository location, again, this can be a directory or an URL.
-
-# you have to set the `repository` variable inside the config like so:
-# `repository = FileRepository(repositoryPath)`
-
-# optionally a subdir argument can be specified:
-# `repository = FileRepository(repositoryPath, subdir)`
-repository_path = os.path.join(prefix, 'ebfiles_repo')
-repository = FileRepository(repository_path)  # @UndefinedVariable (this file gets exec'ed, so ignore this)
-
-# log format: (dir, filename template)
-# supported in template: name, version, data, time
-log_format = ("easybuild", "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
-
-# set the path where log files will be stored
-log_dir = tempfile.gettempdir()
-
-# define set of supported module classes
-module_classes = ['base', 'bio', 'chem', 'compiler', 'lib', 'phys', 'tools',
-  'cae', 'data', 'debugger', 'devel', 'ide', 'math', 'mpi', 'numlib', 'perf', 'system', 'vis']
-
-# general cleanliness
-del os, tempfile, config, prefix
-
-#
-# Developers, please do not add any new defaults or variables
-# Use the config options
-#
diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index c56029875d..c29563a99f 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -51,7 +51,7 @@
 import easybuild.tools.environment as env
 from easybuild.tools import config, filetools
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
-from easybuild.framework.easyconfig.easyconfig import DEFAULT_EASYBLOCK, ITERATE_OPTIONS, EasyConfig, ActiveMNS
+from easybuild.framework.easyconfig.easyconfig import ITERATE_OPTIONS, EasyConfig, ActiveMNS
 from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, get_module_path, resolve_template
 from easybuild.framework.easyconfig.tools import get_paths_for
@@ -60,7 +60,6 @@
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
 from easybuild.tools.config import install_path, log_path, read_only_installdir, source_paths
-from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
 from easybuild.tools.environment import restore_env
 from easybuild.tools.filetools import DEFAULT_CHECKSUM
 from easybuild.tools.filetools import adjust_permissions, apply_patch, convert_name, download_file, encode_class_name
@@ -98,17 +97,9 @@ def extra_options(extra=None):
             extra = {}
 
         if not isinstance(extra, dict):
-            typ = type(extra)
-            if not isinstance(extra, ExtraOptionsDeprecatedReturnValue):
-                _log.deprecated("Obtained 'extra' value of type '%s' in extra_options, should be 'dict'" % typ, '2.0')
-            _log.debug("Converting extra_options value '%s' of type '%s' to a dict" % (extra, typ))
-            extra = dict(extra)
-
-        # to avoid breaking backward compatibility, we still need to return a list of tuples in EasyBuild v1.x
-        # starting with EasyBuild v2.0, this will be changed to return the actual dict
-        # as a temporary workaround, return a value which is a hybrid between a list and a dict
-        res = ExtraOptionsDeprecatedReturnValue(extra.items())
-        return res
+            _log.nosupport("Obtained 'extra' value of type '%s' in extra_options, should be 'dict'" % type(extra), '2.0')
+
+        return extra
 
     #
     # INIT
@@ -627,8 +618,7 @@ def moduleGenerator(self):
         """
         Module generator (DEPRECATED, use self.module_generator instead).
         """
-        self.log.deprecated("self.moduleGenerator is replaced by self.module_generator", "2.0")
-        return self.module_generator
+        self.log.nosupport("self.moduleGenerator is replaced by self.module_generator", '2.0')
 
     #
     # DIRECTORY UTILITY FUNCTIONS
@@ -770,14 +760,14 @@ def make_devel_module(self, create_in_builddir=False):
         # these should be all the dependencies and we should load them
         for key in os.environ:
             # legacy support
-            if key.startswith(DEVEL_ENV_VAR_NAME_PREFIX) or key.startswith("SOFTDEVEL"):
-                if key.startswith("SOFTDEVEL"):
-                    self.log.deprecated("Environment variable SOFTDEVEL* being relied on", "2.0")
+            if key.startswith(DEVEL_ENV_VAR_NAME_PREFIX):
                 if not key.endswith(convert_name(self.name, upper=True)):
                     path = os.environ[key]
                     if os.path.isfile(path):
                         mod_name = path.rsplit(os.path.sep, 1)[-1]
                         load_txt += mod_gen.load_module(mod_name)
+            elif key.startswith('SOFTDEVEL'):
+                self.log.nosupport("Environment variable SOFTDEVEL* being relied on", '2.0')
 
         if create_in_builddir:
             output_dir = self.builddir
@@ -1075,15 +1065,8 @@ def skip_extensions(self):
             try:
                 cmd = cmdtmpl % tmpldict
             except KeyError, err:
-                self.log.warning("Failed to complete filter cmd templ '%s' using %s: %s" % (cmdtmpl, tmpldict, err))
-                deprecated_msg = "Providing 'name'/'version' keys for extensions, should use 'ext_name', 'ext_version'"
-                self.log.deprecated(deprecated_msg, '2.0')
-                tmpldict.update({
-                    'name': modname,
-                    'version': ext.get('version'),
-                })
-                self.log.debug("Retrying to complete filter cmd templ with added name/version keys: %s" % tmpldict)
-                cmd = cmdtmpl % tmpldict
+                msg = "Use of 'name'/'version' keys for extensions filter, should use 'ext_name', 'ext_version' instead"
+                self.log.nosupport(msg, '2.0')
 
             if cmdinputtmpl:
                 stdin = cmdinputtmpl % tmpldict
@@ -1386,18 +1369,8 @@ def extensions_step(self, fetch=False):
             self.log.error("ERROR: No default extension class set for %s" % self.name)
 
         # obtain name and module path for default extention class
-        legacy = False
         if hasattr(exts_defaultclass, '__iter__'):
-            # LEGACY: module path is explicitely specified
-            self.log.deprecated("Using specified module path for default class", "2.0")
-            default_class_modpath = exts_defaultclass[0]
-            default_class = exts_defaultclass[1]
-            derived_mod_path = get_module_path(default_class, generic=True)
-            if not default_class_modpath == derived_mod_path:
-                msg = "Specified module path for default class %s " % default_class_modpath
-                msg += "doesn't match derived path %s" % derived_mod_path
-                self.log.warning(msg)
-            legacy = True
+            self.log.nosupport("Using specified module path for default class", '2.0')
 
         elif isinstance(exts_defaultclass, basestring):
             # proper way: derive module path from specified class name
@@ -1429,22 +1402,6 @@ def extensions_step(self, fetch=False):
             except (ImportError, NameError), err:
                 self.log.debug("Failed to use extension-specific class for extension %s: %s" % (ext['name'], err))
 
-            # LEGACY: try and use default module path for getting extension class instance
-            if inst is None and legacy:
-                self.log.deprecated("Using specified module path for default class", '2.0')
-                try:
-                    msg = "Failed to use derived module path for %s, " % class_name
-                    msg += "considering specified module path as (legacy) fallback."
-                    self.log.debug(msg)
-                    mod_path = default_class_modpath
-                    cls = get_class_for(mod_path, class_name)
-                    inst = cls(self, ext)
-                except (ImportError, NameError), err:
-                    self.log.debug("Failed to use class %s from %s for extension %s: %s" % (class_name,
-                                                                                            mod_path,
-                                                                                            ext['name'],
-                                                                                            err))
-
             # alternative attempt: use class specified in class map (if any)
             if inst is None and ext['name'] in exts_classmap:
 
@@ -1454,9 +1411,8 @@ def extensions_step(self, fetch=False):
                     cls = get_class_for(mod_path, class_name)
                     inst = cls(self, ext)
                 except (ImportError, NameError), err:
-                    self.log.error("Failed to load specified class %s for extension %s: %s" % (class_name,
-                                                                                               ext['name'],
-                                                                                               err))
+                    tup = (class_name, ext['name'], err)
+                    self.log.error("Failed to load specified class %s for extension %s: %s" % tup)
 
             # fallback attempt: use default class
             if inst is None:
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 94bc9c9db0..1a50efb87c 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -40,13 +40,12 @@
 import os
 import re
 from vsc.utils import fancylogger
-from vsc.utils.missing import any, get_class_for, nub
+from vsc.utils.missing import get_class_for, nub
 from vsc.utils.patterns import Singleton
 
 import easybuild.tools.environment as env
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_module_naming_scheme
-from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
 from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
@@ -73,50 +72,31 @@
 # set of configure/build/install options that can be provided as lists for an iterated build
 ITERATE_OPTIONS = ['preconfigopts', 'configopts', 'prebuildopts', 'buildopts', 'preinstallopts', 'installopts']
 
-# map of deprecated easyconfig parameters, and their replacements
-DEPRECATED_OPTIONS = {
-    'license': ('software_license', '2.0'),
-    'makeopts': ('buildopts', '2.0'),
-    'premakeopts': ('prebuildopts', '2.0'),
+# replaced easyconfig parameters, and their replacements
+REPLACED_PARAMETERS = {
+    'license': 'software_license',
+    'makeopts': 'buildopts',
+    'premakeopts': 'prebuildopts',
 }
 
-DEFAULT_EASYBLOCK = 'ConfigureMake'
-
 _easyconfig_files_cache = {}
 _easyconfigs_cache = {}
 
 
-def handle_deprecated_easyconfig_parameter(ec_method):
-    """Decorator to handle deprecated easyconfig parameters."""
+def handle_replaced_easyconfig_parameter(ec_method):
+    """Decorator to handle replaced easyconfig parameters."""
     def new_ec_method(self, key, *args, **kwargs):
-        """Map deprecated easyconfig parameters to the new correct parameter."""
-        # map name of deprecated easyconfig parameter to new name
-        if key in DEPRECATED_OPTIONS:
-            depr_key = key
-            key, ver = DEPRECATED_OPTIONS[depr_key]
-            _log.deprecated("Easyconfig parameter '%s' is deprecated, use '%s' instead." % (depr_key, key), ver)
+        """Map replaced easyconfig parameters to the new correct parameter."""
+        # map name of replaced easyconfig parameter to new name
+        if key in REPLACED_PARAMETERS:
+            _log.nosupport("Easyconfig parameter '%s' is replaced by '%s'" % (key, REPLACED_PARAMETERS[key]), '2.0')
 
         # make sure that value for software_license has correct type, convert if needed
         if key == 'software_license':
             # key 'license' will already be mapped to 'software_license' above
             lic = self._config['software_license'][0]
             if lic is not None and not isinstance(lic, License):
-                self.log.deprecated('Type for software_license must to be instance of License (sub)class', '2.0')
-                lic_type = type(lic)
-
-                class LicenseLegacy(License, lic_type):
-                    """A special License class to deal with legacy license parameters"""
-                    DESCRICPTION = ("Internal-only, legacy closed license class to deprecate license parameter."
-                                    " (DO NOT USE).")
-                    HIDDEN = False
-
-                    def __init__(self, *args):
-                        if len(args) > 0:
-                            lic_type.__init__(self, args[0])
-                        License.__init__(self)
-                lic = LicenseLegacy(lic)
-                EASYCONFIG_LICENSES_DICT[lic.name] = lic
-                self._config['software_license'] = lic
+                self.log.nosupport('Type for software_license must to be instance of License (sub)class', '2.0')
 
         return ec_method(self, key, *args, **kwargs)
 
@@ -161,16 +141,8 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
             self.extra_options = extra_options
 
         if not isinstance(self.extra_options, dict):
-            if isinstance(self.extra_options, (list, tuple, ExtraOptionsDeprecatedReturnValue)):
-                typ = type(self.extra_options)
-                if not isinstance(self.extra_options, ExtraOptionsDeprecatedReturnValue):
-                    self.log.deprecated("extra_options return value should be of type 'dict', found '%s'" % typ, '2.0')
-                tup = (self.extra_options, type(self.extra_options))
-                self.log.debug("Converting extra_options value '%s' of type '%s' to a dict" % tup)
-                self.extra_options = dict(self.extra_options)
-            else:
-                tup = (type(self.extra_options), self.extra_options)
-                self.log.error("extra_options parameter passed is of incorrect type: %s ('%s')" % tup)
+            tup = (type(self.extra_options), self.extra_options)
+            self.log.nosupport("extra_options return value should be of type 'dict', found '%s': %s" % tup, '2.0')
 
         self._config.update(self.extra_options)
 
@@ -279,7 +251,7 @@ def parse(self):
         for key in ['toolchain'] + local_vars.keys():
             # validations are skipped, just set in the config
             # do not store variables we don't need
-            if key in self._config.keys() + DEPRECATED_OPTIONS.keys():
+            if key in self._config.keys():
                 if key in ['builddependencies', 'dependencies']:
                     self[key] = [self._parse_dependency(dep) for dep in local_vars[key]]
                 elif key in ['hiddendependencies']:
@@ -288,6 +260,8 @@ def parse(self):
                     self[key] = local_vars[key]
                 tup = (key, self[key], type(self[key]))
                 self.log.info("setting config option %s: value %s (type: %s)" % tup)
+            elif key in REPLACED_PARAMETERS:
+                _log.nosupport("Easyconfig parameter '%s' is replaced by '%s'" % (key, REPLACED_PARAMETERS[key]), '2.0')
 
             else:
                 self.log.debug("Ignoring unknown config option %s (value: %s)" % (key, local_vars[key]))
@@ -654,7 +628,7 @@ def _generate_template_values(self, ignore=None, skip_lower=True):
             if v is None:
                 del self.template_values[k]
 
-    @handle_deprecated_easyconfig_parameter
+    @handle_replaced_easyconfig_parameter
     def __getitem__(self, key):
         """
         will return the value without the help text
@@ -667,7 +641,7 @@ def __getitem__(self, key):
         else:
             return value
 
-    @handle_deprecated_easyconfig_parameter
+    @handle_replaced_easyconfig_parameter
     def __setitem__(self, key, value):
         """
         sets the value of key in config.
@@ -702,14 +676,7 @@ def asdict(self):
 def det_installversion(version, toolchain_name, toolchain_version, prefix, suffix):
     """Deprecated 'det_installversion' function, to determine exact install version, based on supplied parameters."""
     old_fn = 'framework.easyconfig.easyconfig.det_installversion'
-    _log.deprecated('Use module_generator.det_full_ec_version instead of %s' % old_fn, '2.0')
-    cfg = {
-        'version': version,
-        'toolchain': {'name': toolchain_name, 'version': toolchain_version},
-        'versionprefix': prefix,
-        'versionsuffix': suffix,
-    }
-    return det_full_ec_version(cfg)
+    _log.nosupport('Use det_full_ec_version from easybuild.tools.module_generator instead of %s' % old_fn, '2.0')
 
 
 def fetch_parameter_from_easyconfig_file(path, param):
@@ -774,8 +741,7 @@ def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_fa
                 modulepath_bis = get_module_path(name, decode=False)
                 _log.debug("Module path determined based on software name: %s" % modulepath_bis)
                 if modulepath_bis != modulepath:
-                    _log.deprecated("Determine module path based on software name", "2.0")
-                    modulepath = modulepath_bis
+                    _log.nosupport("Determine module path based on software name", '2.0')
 
             # try and find easyblock
             try:
@@ -783,24 +749,18 @@ def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_fa
                 cls = get_class_for(modulepath, class_name)
                 _log.info("Successfully obtained %s class instance from %s" % (class_name, modulepath))
             except ImportError, err:
-
                 # when an ImportError occurs, make sure that it's caused by not finding the easyblock module,
                 # and not because of a broken import statement in the easyblock module
                 error_re = re.compile(r"No module named %s" % modulepath.replace("easybuild.easyblocks.", ''))
                 _log.debug("error regexp: %s" % error_re.pattern)
                 if error_re.match(str(err)):
                     if default_fallback:
-                        # no easyblock could be found, so fall back to default class.
-                        def_class = DEFAULT_EASYBLOCK
-                        def_mod_path = get_module_path(def_class, generic=True)
-
-                        _log.warning("Failed to import easyblock for %s, falling back to default class %s: error: %s" % \
-                                    (class_name, (def_mod_path, def_class), err))
-
-                        depr_msg = "Fallback to default easyblock %s (from %s)" % (def_class, def_mod_path)
-                        depr_msg += "; use \"easyblock = '%s'\" in easyconfig file?" % def_class
-                        _log.deprecated(depr_msg, '2.0')
-                        cls = get_class_for(def_mod_path, def_class)
+                        # no easyblock could be found, so fall back to ConfigureMake (NO LONGER SUPPORTED)
+                        legacy_fallback_easyblock = 'ConfigureMake'
+                        def_mod_path = get_module_path(legacy_fallback_easyblock, generic=True)
+                        depr_msg = "Fallback to default easyblock %s (from %s)" % (legacy_fallback_easyblock, def_mod_path)
+                        depr_msg += "; use \"easyblock = '%s'\" in easyconfig file?" % legacy_fallback_easyblock
+                        _log.nosupport(depr_msg, '2.0')
                 else:
                     if error_on_failed_import:
                         _log.error("Failed to import easyblock for %s because of module issue: %s" % (class_name, err))
diff --git a/easybuild/framework/easyconfig/format/format.py b/easybuild/framework/easyconfig/format/format.py
index 4003f5682d..7fb06cc2f9 100644
--- a/easybuild/framework/easyconfig/format/format.py
+++ b/easybuild/framework/easyconfig/format/format.py
@@ -32,7 +32,7 @@
 import copy
 import re
 from vsc.utils import fancylogger
-from vsc.utils.missing import get_subclasses, any
+from vsc.utils.missing import get_subclasses
 
 from easybuild.framework.easyconfig.format.version import EasyVersion, OrderedVersionOperators
 from easybuild.framework.easyconfig.format.version import ToolchainVersionOperator, VersionOperator
diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index 64695589b7..7728792947 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -180,7 +180,7 @@ def parse_pyheader(self, pyheader):
         # check for use of deprecated magic easyconfigs variables
         for magic_var in build_easyconfig_variables_dict():
             if re.search(magic_var, pyheader, re.M):
-                _log.deprecated("Magic 'global' easyconfigs variable %s should no longer be used" % magic_var, '2.0')
+                _log.nosupport("Magic 'global' easyconfigs variable %s should no longer be used" % magic_var, '2.0')
 
         try:
             exec(pyheader, global_vars, local_vars)
diff --git a/easybuild/framework/extensioneasyblock.py b/easybuild/framework/extensioneasyblock.py
index 1308561fb9..a7a5ba6488 100644
--- a/easybuild/framework/extensioneasyblock.py
+++ b/easybuild/framework/extensioneasyblock.py
@@ -58,8 +58,7 @@ def extra_options(extra_vars=None):
             extra_vars = {}
 
         if not isinstance(extra_vars, dict):
-            _log.deprecated("Obtained value of type '%s' for extra_vars, should be 'dict'" % type(extra_vars), '2.0')
-            extra_vars = dict(extra_vars)
+            _log.nosupport("Obtained value of type '%s' for extra_vars, should be 'dict'" % type(extra_vars), '2.0')
 
         extra_vars.update({
             'options': [{}, "Dictionary with extension options.", CUSTOM],
diff --git a/easybuild/main.py b/easybuild/main.py
index a97ce592f1..f1ab88af41 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -39,7 +39,6 @@
 import os
 import sys
 import traceback
-from vsc.utils.missing import any
 
 # IMPORTANT this has to be the first easybuild import as it customises the logging
 #  expect missing log output when this not the case!
diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index 12f35035b9..a6eb1e1eaa 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -33,7 +33,7 @@
 
 from easybuild.toolchains.fft.fftw import Fftw
 from easybuild.tools.modules import get_software_root, get_software_version
-from easybuild.tools.utilities import all, any
+
 
 class IntelFFTW(Fftw):
     """FFTW wrapper functionality of Intel MKL"""
diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index b447090e0e..27ee40708e 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -101,6 +101,10 @@ def deprecated(self, msg, max_ver):
         msg += "; see %s for more information" % DEPRECATED_DOC_URL
         fancylogger.FancyLogger.deprecated(self, msg, str(CURRENT_VERSION), max_ver, exception=EasyBuildError)
 
+    def nosupport(self, msg, ver):
+        """Print error message for no longer supported behaviour, and raise an EasyBuildError."""
+        self.error("NO LONGER SUPPORTED: %s; see %s for more information" % (msg, DEPRECATED_DOC_URL))
+
     def error(self, msg, *args, **kwargs):
         """Print error message and raise an EasyBuildError."""
         newMsg = "EasyBuild crashed with an error %s: %s" % (self.caller_info(), msg)
@@ -165,13 +169,9 @@ def stop_logging(logfile, logtostdout=False):
 
 def get_log(name=None):
     """
-    Generate logger object
+    (NO LONGER SUPPORTED!) Generate logger object
     """
-    # fname is always get_log, useless
-    log = fancylogger.getLogger(name, fname=False)
-    log.info("Logger started for %s." % name)
-    log.deprecated("get_log", "2.0")
-    return log
+    log.nosupport("Use of get_log function", '2.0')
 
 
 def print_msg(msg, log=None, silent=False, prefix=True):
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index d66e269a3c..be244d5daf 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -51,9 +51,6 @@
 
 _log = fancylogger.getLogger('config', fname=False)
 
-# class constant to prepare migration to generaloption as only way of configuration (maybe for v2.X)
-SUPPORT_OLDSTYLE = True
-DEFAULT_OLDSTYLE_CONFIG_FILE = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'easybuild_config.py')
 
 DEFAULT_LOGFILE_FORMAT = ("easybuild", "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
 DEFAULT_MNS = 'EasyBuildMNS'
@@ -68,7 +65,7 @@
 }
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
-DEFAULT_TMP_LOGDIR = tempfile.gettempdir()
+
 
 # utility function for obtaining default paths
 def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
@@ -170,49 +167,14 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
 ]
 
 
-OLDSTYLE_ENVIRONMENT_VARIABLES = {
-    'build_path': 'EASYBUILDBUILDPATH',
-    'config_file': 'EASYBUILDCONFIG',
-    'install_path': 'EASYBUILDINSTALLPATH',
-    'log_format': 'EASYBUILDLOGFORMAT',
-    'log_dir': 'EASYBUILDLOGDIR',
-    'source_path': 'EASYBUILDSOURCEPATH',
-    'test_output_path': 'EASYBUILDTESTOUTPUT',
-}
-
-
-OLDSTYLE_NEWSTYLE_MAP = {
-    'build_path': 'buildpath',
-    'install_path': 'installpath',
-    'log_dir': 'tmp_logdir',
-    'config_file': 'config',
-    'source_path': 'sourcepath',
-    'log_format': 'logfile_format',
-    'test_output_path': 'testoutput',
-    'module_classes': 'moduleclasses',
-    'repository_path': 'repositorypath',
-    'modules_install_suffix': 'subdir_modules',
-    'software_install_suffix': 'subdir_software',
-}
-
-
-def map_to_newstyle(adict):
-    """Map a dictionary with oldstyle keys to the new style."""
-    res = {}
-    for key, val in adict.items():
-        if key in OLDSTYLE_NEWSTYLE_MAP:
-            key = OLDSTYLE_NEWSTYLE_MAP[key]
-        res[key] = val
-    return res
-
-
 class ConfigurationVariables(FrozenDictKnownKeys):
     """This is a dict that supports legacy config names transparently."""
 
     # singleton metaclass: only one instance is created
     __metaclass__ = Singleton
 
-    REQUIRED = [
+    # list of know/required keys
+    KNOWN_KEYS = [
         'config',
         'prefix',
         'buildpath',
@@ -229,14 +191,12 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'module_naming_scheme',
     ]
 
-    KNOWN_KEYS = nub(OLDSTYLE_NEWSTYLE_MAP.values() + REQUIRED)
-
     def get_items_check_required(self, no_missing=True):
         """
-        For all REQUIRED, check if exists and return all key,value pairs.
+        For all known/required keys, check if exists and return all key/value pairs.
             no_missing: boolean, when True, will throw error message for missing values
         """
-        missing = [x for x in self.REQUIRED if not x in self]
+        missing = [x for x in self.KNOWN_KEYS if not x in self]
         if len(missing) > 0:
             msg = 'Cannot determine value for configuration variables %s. Please specify it.' % missing
             if no_missing:
@@ -256,50 +216,10 @@ class BuildOptions(FrozenDictKnownKeys):
     KNOWN_KEYS = [k for kss in [BUILD_OPTIONS_CMDLINE, BUILD_OPTIONS_OTHER] for ks in kss.values() for k in ks]
 
 
-def get_user_easybuild_dir():
-    """Return the per-user easybuild dir (e.g. to store config files)"""
-    oldpath = os.path.join(os.path.expanduser('~'), ".easybuild")
-    xdg_config_home = os.environ.get("XDG_CONFIG_HOME", os.path.join(os.path.expanduser('~'), ".config"))
-    newpath = os.path.join(xdg_config_home, "easybuild")
-
-    # only issue deprecation warning/error if new path doesn't exist, but deprecated path does
-    if not os.path.isdir(newpath) and os.path.isdir(oldpath):
-        _log.deprecated("The user easybuild dir has moved from %s to %s." % (oldpath, newpath), "2.0")
-        return oldpath
-
-    # if neither exist, new path wins
-    return newpath
-
-
-def get_default_oldstyle_configfile():
-    """Get the default location of the oldstyle config file to be set as default in the options"""
-    # TODO these _log.debug here can't be controlled/set with the generaloption
-    # - check environment variable EASYBUILDCONFIG
-    # - next, check for an EasyBuild config in $HOME/.easybuild/config.py
-    # - last, use default config file easybuild_config.py in main.py directory
-    config_env_var = OLDSTYLE_ENVIRONMENT_VARIABLES['config_file']
-    home_config_file = os.path.join(get_user_easybuild_dir(), "config.py")
-    if os.getenv(config_env_var):
-        _log.debug("Environment variable %s, so using that as config file." % config_env_var)
-        config_file = os.getenv(config_env_var)
-    elif os.path.exists(home_config_file):
-        config_file = home_config_file
-        _log.debug("Found EasyBuild configuration file at %s." % config_file)
-    else:
-        # this should be easybuild.tools.config, the default config file is
-        # part of framework in easybuild (ie in tool/..)
-        if os.path.exists(DEFAULT_OLDSTYLE_CONFIG_FILE):
-            config_file = DEFAULT_OLDSTYLE_CONFIG_FILE
-            _log.debug("Falling back to default config: %s" % config_file)
-        else:
-            config_file = None
-
-    return config_file
-
-
 def get_default_configfiles():
     """Return a list of default configfiles for tools.options/generaloption"""
-    return [os.path.join(get_user_easybuild_dir(), "config.cfg")]
+    xdg_config_home = os.environ.get("XDG_CONFIG_HOME", os.path.join(os.path.expanduser('~'), ".config"))
+    return [os.path.join(xdg_config_home, 'easybuild', 'config.cfg')]
 
 
 def get_pretend_installpath():
@@ -312,37 +232,7 @@ def init(options, config_options_dict):
     Gather all variables and check if they're valid
     Variables are read in this order of preference: generaloption > legacy environment > legacy config file
     """
-    tmpdict = {}
-    if SUPPORT_OLDSTYLE:
-        if not os.path.samefile(options.config, DEFAULT_OLDSTYLE_CONFIG_FILE):
-            # only trip if an oldstyle config other than the default is used (via $EASYBUILDCONFIG or --config)
-            # we still need the oldstyle default config file to ensure legacy behavior, for now
-            _log.deprecated('use of oldstyle configuration file %s' % options.config, '2.0')
-        tmpdict.update(oldstyle_init(options.config))
-
-        # add the DEFAULT_MODULECLASSES as default (behavior is now that this extends the default list)
-        tmpdict['moduleclasses'] = nub(list(tmpdict.get('moduleclasses', [])) +
-                                         [x[0] for x in DEFAULT_MODULECLASSES])
-
-        # make sure we have new-style keys
-        tmpdict = map_to_newstyle(tmpdict)
-
-        # all defaults are now set in generaloption
-        # distinguish between default generaloption values and values actually passed by generaloption
-        for dest in config_options_dict.keys():
-            if not options._action_taken.get(dest, False):
-                if dest == 'installpath' and options.pretend:
-                    # the installpath has been set by pretend option in postprocess
-                    continue
-                # remove the default options if they are set in variables
-                # this way, all defaults are set
-                if dest in tmpdict:
-                    _log.debug("Oldstyle support: no action for dest %s." % dest)
-                    del config_options_dict[dest]
-
-    # update the variables with the generaloption values
-    _log.debug("Updating config variables with generaloption dict %s" % config_options_dict)
-    tmpdict.update(config_options_dict)
+    tmpdict = copy.deepcopy(config_options_dict)
 
     # make sure source path is a list
     sourcepath = tmpdict['sourcepath']
@@ -422,11 +312,8 @@ def source_paths():
 
 
 def source_path():
-    """
-    Return the source path (deprecated)
-    """
-    _log.deprecated("Use of source_path() is deprecated, use source_paths() instead.", '2.0')
-    return source_paths()
+    """NO LONGER SUPPORTED: use source_paths instead"""
+    _log.nosupport("Use of source_path(), use source_paths() instead.", '2.0')
 
 
 def install_path(typ=None):
@@ -435,24 +322,13 @@ def install_path(typ=None):
     - subdir 'software' for actual installation (default)
     - subdir 'modules' for environment modules (typ='mod')
     """
-    variables = ConfigurationVariables()
-
     if typ is None:
         typ = 'software'
-    if typ == 'mod':
+    elif typ == 'mod':
         typ = 'modules'
 
-    key = "subdir_%s" % typ
-    if key in variables:
-        suffix = variables[key]
-    else:
-        # TODO remove default setting. it should have been set through options
-        try:
-            suffix = DEFAULT_PATH_SUBDIRS[key]
-            _log.deprecated('%s not set in config, returning default: %s' % (key, suffix), "2.0")
-        except:
-            _log.error('install_path trying to get unknown suffix %s' % key)
-
+    variables = ConfigurationVariables()
+    suffix = variables['subdir_%s' % typ]
     return os.path.join(variables['installpath'], suffix)
 
 
@@ -488,15 +364,7 @@ def get_module_naming_scheme():
 def log_file_format(return_directory=False):
     """Return the format for the logfile or the directory"""
     idx = int(not return_directory)
-
-    variables = ConfigurationVariables()
-    if 'logfile_format' in variables:
-        res = variables['logfile_format'][idx]
-    else:
-        res = DEFAULT_LOGFILE_FORMAT[:][idx]  # purposely take a copy
-        # TODO remove default setting. it should have been set through options
-        _log.deprecated('logfile_format not set in config, returning default: %s' % res, '2.0')
-    return res
+    return ConfigurationVariables()['logfile_format'][idx]
 
 
 def log_format():
@@ -519,12 +387,11 @@ def get_build_log_path():
     return temporary log directory
     """
     variables = ConfigurationVariables()
-    if 'tmp_logdir' in variables:
-        return variables['tmp_logdir']
+    if variables['tmp_logdir'] is not None:
+        res = variables['tmp_logdir']
     else:
-        # TODO remove default setting. it should have been set through options
-        _log.deprecated('tmp_logdir not set in config, returning default: %s' % DEFAULT_TMP_LOGDIR, "2.0")
-        return DEFAULT_TMP_LOGDIR
+        res = tempfile.gettempdir()
+    return res
 
 
 def get_log_filename(name, version, add_salt=False):
@@ -571,76 +438,12 @@ def module_classes():
     """
     Return list of module classes specified in config file.
     """
-    variables = ConfigurationVariables()
-    if 'moduleclasses' in variables:
-        return variables['moduleclasses']
-    else:
-        res = [x[0] for x in DEFAULT_MODULECLASSES]
-        # TODO remove default setting. it should have been set through options
-        _log.deprecated('moduleclasses not set in config, returning default: %s' % res, "2.0")
-        return res
+    return ConfigurationVariables()['moduleclasses']
 
 
 def read_environment(env_vars, strict=False):
     """Depreacted location for read_environment, use easybuild.tools.environment"""
-    _log.deprecated("Deprecated location for read_environment, use easybuild.tools.environment", '2.0')
-    return _read_environment(env_vars, strict)
-
-
-def oldstyle_init(filename, **kwargs):
-    """
-    Gather all variables and check if they're valid
-    Variables are read in this order of preference: CLI option > environment > config file
-    """
-    res = {}
-
-    _log.debug('variables before oldstyle_init %s' % res)
-    res.update(oldstyle_read_configuration(filename))  # config file
-    _log.debug('variables after oldstyle_init read_configuration (%s) %s' % (filename, res))
-    res.update(oldstyle_read_environment())  # environment
-    _log.debug('variables after oldstyle_init read_environment %s' % res)
-    if kwargs:
-        res.update(kwargs)  # CLI options
-        _log.debug('variables after oldstyle_init kwargs (passed %s) %s' % (kwargs, res))
-
-    return res
-
-
-def oldstyle_read_configuration(filename):
-    """
-    Read variables from the config file
-    """
-    # import avail_repositories here to avoid cyclic dependencies
-    # this block of code is going to be removed in EB v2.0
-    from easybuild.tools.repository.repository import avail_repositories
-    file_variables = avail_repositories(check_useable=False)
-    try:
-        execfile(filename, {}, file_variables)
-    except (IOError, SyntaxError), err:
-        _log.exception("Failed to read config file %s %s" % (filename, err))
-
-    return file_variables
-
-
-def oldstyle_read_environment(env_vars=None, strict=False):
-    """
-    Read variables from the environment
-        - strict=True enforces that all possible environment variables are found
-    """
-    if env_vars is None:
-        env_vars = OLDSTYLE_ENVIRONMENT_VARIABLES
-    result = {}
-    for key in env_vars.keys():
-        env_var = env_vars[key]
-        if env_var in os.environ:
-            result[key] = os.environ[env_var]
-            _log.deprecated("Use of oldstyle environment variable %s for %s: %s" % (env_var, key, result[key]), '2.0')
-        elif strict:
-            _log.error("Can't determine value for %s. Environment variable %s is missing" % (key, env_var))
-        else:
-            _log.debug("Old style env var %s not defined." % env_var)
-
-    return result
+    _log.nosupport("Deprecated location for read_environment, use easybuild.tools.environment", '2.0')
 
 
 def set_tmpdir(tmpdir=None):
diff --git a/easybuild/tools/deprecated/eb_2_0.py b/easybuild/tools/deprecated/eb_2_0.py
deleted file mode 100644
index 55f43b4af4..0000000000
--- a/easybuild/tools/deprecated/eb_2_0.py
+++ /dev/null
@@ -1,74 +0,0 @@
-# #
-# Copyright 2014-2014 Ghent University
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-# #
-"""
-Deprecated functionality for EasyBuild v1.x
-
-@author: Kenneth Hoste (Ghent University)
-"""
-from vsc.utils.wrapper import Wrapper
-
-
-class ExtraOptionsDeprecatedReturnValue(Wrapper):
-    """
-    Hybrid list/dict object: is a list (of 2-element tuples), but also acts like a dict.
-
-    Supported dict-like methods include: update(adict), items(), keys(), values()
-
-    Consistency of values being 2-element tuples is *not* checked!
-    """
-    __wraps__ = list
-
-    def __getitem__(self, index_key):
-        """Get value by specified index/key."""
-        if isinstance(index_key, int):
-            res = self._obj[index_key]
-        else:
-            res = dict(self._obj)[index_key]
-        return res
-
-    def __setitem__(self, index_key, value):
-        """Add value at specified index/key."""
-        if isinstance(index_key, int):
-            self._obj[index_key] = value
-        else:
-            self._obj = [(k, v) for (k, v) in self._obj if k != index_key]
-            self._obj.append((index_key, value))
-
-    def update(self, extra):
-        """Update with keys/values in supplied dictionary."""
-        self._obj = [(k, v) for (k, v) in self._obj if k not in extra.keys()]
-        self._obj.extend(extra.items())
-
-    def items(self):
-        """Get list of key/value tuples."""
-        return self._obj
-
-    def keys(self):
-        """Get list of keys."""
-        return [x[0] for x in self.items()]
-
-    def values(self):
-        """Get list of values."""
-        return [x[1] for x in self.items()]
diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 4e64029e7a..c8033be791 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -37,7 +37,6 @@
 
 from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, HIDDEN, sorted_categories
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
-from easybuild.tools.deprecated.eb_2_0 import ExtraOptionsDeprecatedReturnValue
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.utilities import quote_str
 
@@ -129,8 +128,6 @@ def avail_easyconfig_params(easyblock, output_format):
     app = get_easyblock_class(easyblock, default_fallback=False)
     if app is not None:
         extra_params = app.extra_options()
-    if isinstance(extra_params, ExtraOptionsDeprecatedReturnValue):
-        extra_params = dict(extra_params)
     params.update(extra_params)
 
     # compose title
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 1eb26b6aa8..b9faa6e976 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -42,7 +42,6 @@
 import urllib
 import zlib
 from vsc.utils import fancylogger
-from vsc.utils.missing import all, any
 
 import easybuild.tools.environment as env
 from easybuild.tools.build_log import print_msg  # import build_log must stay, to activate use of EasyBuildLog
@@ -712,11 +711,8 @@ def apply_patch(patch_file, dest, fn=None, copy=False, level=None):
 
 
 def modify_env(old, new):
-    """
-    Compares 2 os.environ dumps. Adapts final environment.
-    """
-    _log.deprecated("moved modify_env to tools.environment", "2.0")
-    return env.modify_env(old, new)
+    """NO LONGER SUPPORTED: use modify_env from easybuild.tools.environment instead"""
+    _log.nosupport("moved modify_env to tools.environment", "2.0")
 
 
 def convert_name(name, upper=False):
@@ -1043,22 +1039,17 @@ def decode_class_name(name):
 
 
 def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True, log_output=False, path=None):
-    """Legacy wrapper/placeholder for run.run_cmd"""
-    _log.deprecated("run_cmd was moved from tools.filetools to tools.run", '2.0')
-    return run.run_cmd(cmd, log_ok=log_ok, log_all=log_all, simple=simple,
-                       inp=inp, regexp=regexp, log_output=log_output, path=path)
+    """NO LONGER SUPPORTED: use run_cmd from easybuild.tools.run instead"""
+    _log.nosupport("run_cmd was moved from tools.filetools to tools.run", '2.0')
 
 
 def run_cmd_qa(cmd, qa, no_qa=None, log_ok=True, log_all=False, simple=False, regexp=True, std_qa=None, path=None):
-    """Legacy wrapper/placeholder for run.run_cmd_qa"""
-    _log.deprecated("run_cmd_qa was moved from tools.filetools to tools.run", '2.0')
-    return run.run_cmd_qa(cmd, qa, no_qa=no_qa, log_ok=log_ok, log_all=log_all,
-                          simple=simple, regexp=regexp, std_qa=std_qa, path=path)
+    """NO LONGER SUPPORTED: use run_cmd_qa from easybuild.tools.run instead"""
+    _log.nosupport("run_cmd_qa was moved from tools.filetools to tools.run", '2.0')
 
 def parse_log_for_error(txt, regExp=None, stdout=True, msg=None):
-    """Legacy wrapper/placeholder for run.parse_log_for_error"""
-    _log.deprecated("parse_log_for_error was moved from tools.filetools to tools.run", '2.0')
-    return run.parse_log_for_error(txt, regExp=regExp, stdout=stdout, msg=msg)
+    """NO LONGER SUPPORTED: use parse_log_for_error from easybuild.tools.run instead"""
+    _log.nosupport("parse_log_for_error was moved from tools.filetools to tools.run", '2.0')
 
 
 def det_size(path):
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index ce8353b0e2..5c8b057fd7 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -42,7 +42,7 @@
 from distutils.version import StrictVersion
 from subprocess import PIPE
 from vsc.utils import fancylogger
-from vsc.utils.missing import get_subclasses, any
+from vsc.utils.missing import get_subclasses
 from vsc.utils.patterns import Singleton
 
 from easybuild.tools.build_log import EasyBuildError
@@ -180,9 +180,8 @@ def buildstats(self):
 
     @property
     def modules(self):
-        """Property providing access to deprecated 'modules' class variable."""
-        self.log.deprecated("'modules' class variable is deprecated, just use load([<list of modules>])", '2.0')
-        return self._modules
+        """(NO LONGER SUPPORTED!) Property providing access to 'modules' class variable"""
+        self.log.nosupport("'modules' class variable is not supported anymore, just use load([<list of modules>])", '2.0')
 
     def set_and_check_version(self):
         """Get the module version, and check any requirements"""
@@ -370,9 +369,8 @@ def exist(self, mod_names):
         return mods_exist
 
     def exists(self, mod_name):
-        """Check if a module with the specified name exists."""
-        self.log.deprecated("exists(<mod_name>) is deprecated, use exist([<mod_name>]) instead", '2.0')
-        return self.exist([mod_name])[0]
+        """NO LONGER SUPPORTED: use exist method instead"""
+        self.log.nosupport("exists(<mod_name>) is not supported anymore, use exist([<mod_name>]) instead", '2.0')
 
     def load(self, modules, mod_paths=None, purge=False, orig_env=None):
         """
@@ -408,8 +406,7 @@ def unload(self, modules=None):
         Unload all requested modules.
         """
         if modules is None:
-            self.log.deprecated("Unloading modules listed in _modules class variable", '2.0')
-            modules = self._modules[:]
+            self.log.nosupport("Unloading modules listed in _modules class variable", '2.0')
 
         for mod in modules:
             self.run_module('unload', mod)
@@ -470,15 +467,12 @@ def run_module(self, *args, **kwargs):
             args.insert(*self.TERSE_OPTION)
 
         module_path_key = None
-        original_module_path = None
         if 'mod_paths' in kwargs:
             module_path_key = 'mod_paths'
         elif 'modulePath' in kwargs:
             module_path_key = 'modulePath'
         if module_path_key is not None:
-            original_module_path = os.environ['MODULEPATH']
-            os.environ['MODULEPATH'] = kwargs[module_path_key]
-            self.log.deprecated("Use of '%s' named argument in 'run_module'" % module_path_key, '2.0')
+            self.log.nosupport("Use of '%s' named argument in 'run_module'" % module_path_key, '2.0')
 
         self.log.debug('Current MODULEPATH: %s' % os.environ.get('MODULEPATH', ''))
 
@@ -504,9 +498,6 @@ def run_module(self, *args, **kwargs):
         # stderr will contain text (just like the normal module command)
         (stdout, stderr) = proc.communicate()
         self.log.debug("Output of module command '%s': stdout: %s; stderr: %s" % (full_cmd, stdout, stderr))
-        if original_module_path is not None:
-            os.environ['MODULEPATH'] = original_module_path
-            self.log.deprecated("Restoring $MODULEPATH back to what it was before running module command/.", '2.0')
 
         if kwargs.get('return_output', False):
             return stdout + stderr
@@ -884,24 +875,22 @@ def get_software_root(name, with_env_var=False):
     """
     Return the software root set for a particular software name.
     """
-    environment_key = get_software_root_env_var_name(name)
-    newname = convert_name(name, upper=True)
-    legacy_key = "SOFTROOT%s" % newname
+    env_var = get_software_root_env_var_name(name)
+    legacy_key = "SOFTROOT%s" % convert_name(name, upper=True)
 
-    # keep on supporting legacy installations
-    if environment_key in os.environ:
-        env_var = environment_key
-    else:
-        env_var = legacy_key
-        if legacy_key in os.environ:
-            _log.deprecated("Legacy env var %s is being relied on!" % legacy_key, "2.0")
+    root = None
+    if env_var in os.environ:
+        root = os.getenv(env_var)
 
-    root = os.getenv(env_var)
+    elif legacy_key in os.environ:
+        _log.nosupport("Legacy env var %s is being relied on!" % legacy_key, "2.0")
 
     if with_env_var:
-        return (root, env_var)
+        res = (root, env_var)
     else:
-        return root
+        res = root
+
+    return res
 
 
 def get_software_libdir(name, only_one=True, fs=None):
@@ -947,18 +936,16 @@ def get_software_version(name):
     """
     Return the software version set for a particular software name.
     """
-    environment_key = get_software_version_env_var_name(name)
-    newname = convert_name(name, upper=True)
-    legacy_key = "SOFTVERSION%s" % newname
+    env_var = get_software_version_env_var_name(name)
+    legacy_key = "SOFTVERSION%s" % convert_name(name, upper=True)
 
-    # keep on supporting legacy installations
-    if environment_key in os.environ:
-        return os.getenv(environment_key)
-    else:
-        if legacy_key in os.environ:
-            _log.deprecated("Legacy env var %s is being relied on!" % legacy_key, "2.0")
-        return os.getenv(legacy_key)
+    version = None
+    if env_var in os.environ:
+        version = os.getenv(env_var)
+    elif legacy_key in os.environ:
+        _log.nosupport("Legacy env var %s is being relied on!" % legacy_key, "2.0")
 
+    return version
 
 def curr_module_paths():
     """
@@ -998,10 +985,7 @@ def modules_tool(mod_paths=None, testing=False):
         return None
 
 
-# provide Modules class for backward compatibility (e.g., in easyblocks)
 class Modules(EnvironmentModulesC):
-    """Deprecated interface to modules tool."""
-
+    """NO LONGER SUPPORTED: interface to modules tool, use modules_tool from easybuild.tools.modules instead"""
     def __init__(self, *args, **kwargs):
-        _log.deprecated("modules.Modules class is now an abstract interface, use modules.modules_tool instead", "2.0")
-        super(Modules, self).__init__(*args, **kwargs)
+        _log.nosupport("modules.Modules class is now an abstract interface, use modules.modules_tool instead", '2.0')
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 1d4472b353..14baac2909 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -36,6 +36,7 @@
 import os
 import re
 import sys
+import tempfile
 from distutils.version import LooseVersion
 from vsc.utils.missing import nub
 
@@ -49,9 +50,9 @@
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
-from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY, DEFAULT_TMP_LOGDIR
+from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_default_configfiles, get_pretend_installpath
-from easybuild.tools.config import get_default_oldstyle_configfile, mk_full_default_path
+from easybuild.tools.config import mk_full_default_path
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
@@ -63,7 +64,10 @@
 from easybuild.tools.version import this_is_easybuild
 from vsc.utils import fancylogger
 from vsc.utils.generaloption import GeneralOption
-from vsc.utils.missing import any
+
+
+XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
+DEFAULT_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
 
 
 class EasyBuildOptions(GeneralOption):
@@ -71,7 +75,8 @@ class EasyBuildOptions(GeneralOption):
     VERSION = this_is_easybuild()
 
     DEFAULT_LOGLEVEL = 'INFO'
-    DEFAULT_CONFIGFILES = get_default_configfiles()
+
+    DEFAULT_CONFIGFILES = [DEFAULT_CONFIGFILE]
 
     ALLOPTSMANDATORY = False  # allow more than one argument
 
@@ -217,8 +222,6 @@ def config_options(self):
             'ignore-dirs': ("Directory names to ignore when searching for files/dirs",
                             'strlist', 'store', ['.git', '.svn']),
             'installpath': ("Install path for software and modules", None, 'store', mk_full_default_path('installpath')),
-            'config': ("Path to EasyBuild config file (DEPRECATED, use --configfiles instead!)",
-                       None, 'store', get_default_oldstyle_configfile(), 'C'),
             # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
@@ -252,10 +255,8 @@ def config_options(self):
             'suffix-modules-path': ("Suffix for module files install path", None, 'store', GENERAL_CLASS),
             # this one is sort of an exception, it's something jobscripts can set,
             # has no real meaning for regular eb usage
-            'testoutput': ("Path to where a job should place the output (to be set within jobscript)",
-                            None, 'store', None),
-            'tmp-logdir': ("Log directory where temporary log files are stored",
-                           None, 'store', DEFAULT_TMP_LOGDIR),
+            'testoutput': ("Path to where a job should place the output (to be set within jobscript)", None, 'store', None),
+            'tmp-logdir': ("Log directory where temporary log files are stored", None, 'store', None),
             'tmpdir': ('Directory to use for temporary storage', None, 'store', None),
         })
 
diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 6a5f875555..d76185054b 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -128,12 +128,8 @@ def count_bits(n):
 
 
 def get_core_count():
-    """
-    Try to detect the number of virtual or physical CPUs on this system
-    (DEPRECATED, use get_avail_core_count instead)
-    """
-    _log.deprecated("get_core_count() is deprecated, use get_avail_core_count() instead", '2.0')
-    return get_avail_core_count()
+    """NO LONGER SUPPORTED: use get_avail_core_count() instead"""
+    _log.nosupport("get_core_count() is nosupport, use get_avail_core_count() instead", '2.0')
 
 
 def get_cpu_vendor():
@@ -259,16 +255,8 @@ def get_cpu_speed():
 
 
 def get_kernel_name():
-    """Try to determine kernel name
-
-    e.g., 'Linux', 'Darwin', ...
-    """
-    _log.deprecated("get_kernel_name() (replaced by get_os_type())", "2.0")
-    try:
-        kernel_name = os.uname()[0]
-        return kernel_name
-    except OSError, err:
-        raise SystemToolsException("Failed to determine kernel name: %s" % err)
+    """NO LONGER SUPPORTED: use get_os_type() instead"""
+    _log.nosupport("get_kernel_name() (replaced by get_os_type())", "2.0")
 
 
 def get_os_type():
@@ -326,15 +314,9 @@ def get_os_name():
     Determine system name, e.g., 'redhat' (generic), 'centos', 'debian', 'fedora', 'suse', 'ubuntu',
     'red hat enterprise linux server', 'SL' (Scientific Linux), 'opensuse', ...
     """
-    try:
-        # platform.linux_distribution is more useful, but only available since Python 2.6
-        # this allows to differentiate between Fedora, CentOS, RHEL and Scientific Linux (Rocks is just CentOS)
-        os_name = platform.linux_distribution()[0].strip().lower()
-    except AttributeError:
-        # platform.dist can be used as a fallback
-        # CentOS, RHEL, Rocks and Scientific Linux may all appear as 'redhat' (especially if Python version is pre v2.6)
-        os_name = platform.dist()[0].strip().lower()
-        _log.deprecated("platform.dist as fallback for platform.linux_distribution", "2.0")
+    # platform.linux_distribution is more useful, but only available since Python 2.6
+    # this allows to differentiate between Fedora, CentOS, RHEL and Scientific Linux (Rocks is just CentOS)
+    os_name = platform.linux_distribution()[0].strip().lower()
 
     os_name_map = {
         'red hat enterprise linux server': 'RHEL',
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 75c5a29c85..bb24ab4d19 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -34,7 +34,6 @@
 import os
 import re
 from vsc.utils import fancylogger
-from vsc.utils.missing import all, any
 
 from easybuild.tools.config import build_option, install_path
 from easybuild.tools.environment import setvar
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 05948c9c6d..7c8a959319 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -32,8 +32,6 @@
 import string
 import sys
 from vsc.utils import fancylogger
-from vsc.utils.missing import any as _any
-from vsc.utils.missing import all as _all
 import easybuild.tools.environment as env
 
 _log = fancylogger.getLogger('tools.utilities')
@@ -45,24 +43,9 @@
 UNWANTED_CHARS = ASCII_CHARS.translate(ASCII_CHARS, string.digits + string.ascii_letters + "_")
 
 
-def any(ls):
-    """Reimplementation of 'any' function, which is not available in Python 2.4 yet."""
-    return _any(ls)
-
-
-def all(ls):
-    """Reimplementation of 'all' function, which is not available in Python 2.4 yet."""
-    return _all(ls)
-
-
 def read_environment(env_vars, strict=False):
-    """
-    Read variables from the environment
-        @param: env_vars: a dict with key a name, value a environment variable name
-        @param: strict, boolean, if True enforces that all specified environment variables are found
-    """
-    _log.deprecated("moved read_environment to tools.environment", "2.0")
-    return env.read_environment(env_vars, strict)
+    """NO LONGER SUPPORTED: use read_environment from easybuild.tools.environment instead"""
+    _log.nosupport("read_environment has been moved to easybuild.tools.environment", '2.0')
 
 
 def flatten(lst):

From 1943577472b3078c7b98fa217c0d0b006fe6b379 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Jan 2015 13:52:00 +0100
Subject: [PATCH 0449/1356] bump required Python version to 2.6

---
 eb | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/eb b/eb
index c67fe08284..51eeb7152a 100755
--- a/eb
+++ b/eb
@@ -39,9 +39,9 @@
 # @author: Pieter De Baets (Ghent University)
 # @author: Jens Timmerman (Ghent University)
 
-# Python 2.4 or more recent 2.x required
+# Python 2.6 or more recent 2.x required
 REQ_MAJ_PYVER=2
-REQ_MIN_PYVER=4
+REQ_MIN_PYVER=6
 REQ_PYVER=${REQ_MAJ_PYVER}.${REQ_MIN_PYVER}
 
 # make sure Python version being used is compatible
@@ -60,15 +60,6 @@ then
     exit 2
 fi
 
-# support for Python versions older than v2.6 is deprecated
-OK_MIN_PYVER=6
-if [ $pyver_min -lt $OK_MIN_PYVER ]
-then
-    OK_PYVER=${REQ_MAJ_PYVER}.${OK_MIN_PYVER}
-    echo -n "WARNING: Running EasyBuild with a Python version prior to v${OK_PYVER} is deprecated, " 1>&2
-    echo "found Python v$pyver which will no longer be supported in EasyBuild v2.0." 1>&2
-fi
-
 
 main_script_base_path="easybuild/main.py"
 python_search_path_cmd="python -c \"import sys; print ' '.join(sys.path)\""

From f8d379b93e38950862c48e6ca314664c24e7cb06 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Jan 2015 13:52:20 +0100
Subject: [PATCH 0450/1356] remove unit tests for deprecated functionality

---
 test/framework/config.py      | 270 +---------------------------------
 test/framework/easyblock.py   |  18 +--
 test/framework/easyconfig.py  |  74 ----------
 test/framework/modules.py     |   8 -
 test/framework/systemtools.py |   7 -
 test/framework/toy_build.py   |  11 --
 6 files changed, 12 insertions(+), 376 deletions(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index 5e433d1259..21ee31185a 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -28,7 +28,6 @@
 @author: Kenneth Hoste (Ghent University)
 @author: Stijn De Weirdt (Ghent University)
 """
-import copy
 import os
 import shutil
 import sys
@@ -39,8 +38,8 @@
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 
 import easybuild.tools.options as eboptions
-from easybuild.tools.config import build_path, source_paths, install_path, get_repository, get_repositorypath
-from easybuild.tools.config import log_file_format, set_tmpdir, BuildOptions, ConfigurationVariables
+from easybuild.tools.config import build_path, source_paths, install_path, get_repositorypath
+from easybuild.tools.config import set_tmpdir, BuildOptions, ConfigurationVariables
 from easybuild.tools.config import get_build_log_path, DEFAULT_PATH_SUBDIRS, init_build_options, build_option
 from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import mkdir, write_file
@@ -106,266 +105,8 @@ def test_default_config(self):
         self.assertEqual(config_options['repositorypath'], [os.path.join(eb_homedir, 'ebfiles_repo')])
         self.assertEqual(config_options['logfile_format'][0], 'easybuild')
         self.assertEqual(config_options['logfile_format'][1], "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
-        self.assertEqual(config_options['tmp_logdir'], tempfile.gettempdir())
-
-    def test_generaloption_overrides_legacy(self):
-        """Test whether generaloption overrides legacy configuration."""
-        # lower 'current' version to avoid tripping over deprecation errors
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-
-        self.purge_environment()
-        # if both legacy and generaloption style configuration is mixed, generaloption wins
-        legacy_prefix = os.path.join(self.tmpdir, 'legacy')
-        go_prefix = os.path.join(self.tmpdir, 'generaloption')
-
-        # legacy env vars
-        os.environ['EASYBUILDPREFIX'] = legacy_prefix
-        os.environ['EASYBUILDBUILDPATH'] = os.path.join(legacy_prefix, 'build')
-        # generaloption env vars
-        os.environ['EASYBUILD_INSTALLPATH'] = go_prefix
-        init_config()
-        self.assertEqual(build_path(), os.path.join(legacy_prefix, 'build'))
-        self.assertEqual(install_path(), os.path.join(go_prefix, 'software'))
-        repo = init_repository(get_repository(), get_repositorypath())
-        self.assertEqual(repo.repo, os.path.join(legacy_prefix, 'ebfiles_repo'))
-        del os.environ['EASYBUILDPREFIX']
-
-        # legacy env vars
-        os.environ['EASYBUILDBUILDPATH'] = os.path.join(legacy_prefix, 'buildagain')
-        # generaloption env vars
-        os.environ['EASYBUILD_PREFIX'] = go_prefix
-        init_config()
-        self.assertEqual(build_path(), os.path.join(go_prefix, 'build'))
-        self.assertEqual(install_path(), os.path.join(go_prefix, 'software'))
-        repo = init_repository(get_repository(), get_repositorypath())
-        self.assertEqual(repo.repo, os.path.join(go_prefix, 'ebfiles_repo'))
-        del os.environ['EASYBUILDBUILDPATH']
-
-    def test_legacy_env_vars(self):
-        """Test legacy environment variables."""
-        # lower 'current' version to avoid tripping over deprecation errors
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-
-        self.purge_environment()
-
-        # build path
-        test_buildpath = os.path.join(self.tmpdir, 'build', 'path')
-        os.environ['EASYBUILDBUILDPATH'] = test_buildpath
-        self.configure(args=[])
-        self.assertEqual(build_path(), test_buildpath)
-        del os.environ['EASYBUILDBUILDPATH']
-
-        # source path(s)
-        test_sourcepaths = [
-            os.path.join(self.tmpdir, 'source', 'path'),
-            ':'.join([
-                os.path.join(self.tmpdir, 'source', 'path1'),
-                os.path.join(self.tmpdir, 'source', 'path2'),
-            ]),
-            ':'.join([
-                os.path.join(self.tmpdir, 'source', 'path1'),
-                os.path.join(self.tmpdir, 'source', 'path2'),
-                os.path.join(self.tmpdir, 'source', 'path3'),
-            ]),
-        ]
-        for test_sourcepath in test_sourcepaths:
-            init_config()
-            os.environ['EASYBUILDSOURCEPATH'] = test_sourcepath
-            self.configure(args=[])
-            self.assertEqual(build_path(), os.path.join(os.path.expanduser('~'), '.local', 'easybuild',
-                                                        DEFAULT_PATH_SUBDIRS['buildpath']))
-            self.assertEqual(source_paths(), test_sourcepath.split(':'))
-            del os.environ['EASYBUILDSOURCEPATH']
-
-        test_sourcepath = os.path.join(self.tmpdir, 'source', 'path')
-
-        # install path
-        init_config()
-        test_installpath = os.path.join(self.tmpdir, 'install', 'path')
-        os.environ['EASYBUILDINSTALLPATH'] = test_installpath
-        self.configure(args=[])
-        self.assertEqual(source_paths()[0], os.path.join(os.path.expanduser('~'), '.local', 'easybuild',
-                                                          DEFAULT_PATH_SUBDIRS['sourcepath']))
-        self.assertEqual(install_path(), os.path.join(test_installpath, DEFAULT_PATH_SUBDIRS['subdir_software']))
-        self.assertEqual(install_path(typ='mod'), os.path.join(test_installpath,
-                                                                 DEFAULT_PATH_SUBDIRS['subdir_modules']))
-        del os.environ['EASYBUILDINSTALLPATH']
-
-        # prefix: should change build/install/source/repo paths
-        init_config()
-        test_prefixpath = os.path.join(self.tmpdir, 'prefix', 'path')
-        os.environ['EASYBUILDPREFIX'] = test_prefixpath
-        self.configure(args=[])
-        self.assertEqual(build_path(), os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['buildpath']))
-        self.assertEqual(source_paths()[0], os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['sourcepath']))
-        self.assertEqual(install_path(), os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['subdir_software']))
-        self.assertEqual(install_path(typ='mod'), os.path.join(test_prefixpath,
-                                                               DEFAULT_PATH_SUBDIRS['subdir_modules']))
-        repo = init_repository(get_repository(), get_repositorypath())
-        self.assertTrue(isinstance(repo, FileRepository))
-        self.assertEqual(repo.repo, os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['repositorypath']))
-        # purposely not unsetting $EASYBUILDPREFIX yet here
-
-        # build/source/install path overrides prefix
-        init_config()
-        os.environ['EASYBUILDBUILDPATH'] = test_buildpath
-        self.configure(args=[])
-        self.assertEqual(build_path(), test_buildpath)
-        self.assertEqual(source_paths()[0], os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['sourcepath']))
-        self.assertEqual(install_path(), os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['subdir_software']))
-        self.assertEqual(install_path(typ='mod'), os.path.join(test_prefixpath,
-                                                               DEFAULT_PATH_SUBDIRS['subdir_modules']))
-        repo = init_repository(get_repository(), get_repositorypath())
-        self.assertTrue(isinstance(repo, FileRepository))
-        self.assertEqual(repo.repo, os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['repositorypath']))
-        del os.environ['EASYBUILDBUILDPATH']
-
-        init_config()
-        os.environ['EASYBUILDSOURCEPATH'] = test_sourcepath
-        self.configure(args=[])
-        self.assertEqual(build_path(), os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['buildpath']))
-        self.assertEqual(source_paths()[0], test_sourcepath)
-        self.assertEqual(install_path(), os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['subdir_software']))
-        self.assertEqual(install_path(typ='mod'), os.path.join(test_prefixpath,
-                                                               DEFAULT_PATH_SUBDIRS['subdir_modules']))
-        repo = init_repository(get_repository(), get_repositorypath())
-        self.assertTrue(isinstance(repo, FileRepository))
-        self.assertEqual(repo.repo, os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['repositorypath']))
-        del os.environ['EASYBUILDSOURCEPATH']
-
-        init_config()
-        os.environ['EASYBUILDINSTALLPATH'] = test_installpath
-        self.configure(args=[])
-        self.assertEqual(build_path(), os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['buildpath']))
-        self.assertEqual(source_paths()[0], os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['sourcepath']))
-        self.assertEqual(install_path(), os.path.join(test_installpath, DEFAULT_PATH_SUBDIRS['subdir_software']))
-        self.assertEqual(install_path(typ='mod'), os.path.join(test_installpath,
-                                                               DEFAULT_PATH_SUBDIRS['subdir_modules']))
-        repo = init_repository(get_repository(), get_repositorypath())
-        self.assertTrue(isinstance(repo, FileRepository))
-        self.assertEqual(repo.repo, os.path.join(test_prefixpath, DEFAULT_PATH_SUBDIRS['repositorypath']))
-        del os.environ['EASYBUILDPREFIX']
-        del os.environ['EASYBUILDINSTALLPATH']
-
-    def test_legacy_config_file(self):
-        """Test finding/using legacy configuration files."""
-        # lower 'current' version to avoid tripping over deprecation errors
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-
-        self.purge_environment()
-
-        cfg_fn = self.configure(args=[])
-        self.assertTrue(cfg_fn.endswith('easybuild/easybuild_config.py'))
-
-        configtxt = """
-build_path = '%(buildpath)s'
-source_path = '%(sourcepath)s'
-install_path = '%(installpath)s'
-repository_path = '%(repopath)s'
-repository = FileRepository(repository_path)
-log_format = ('%(logdir)s', '%(logtmpl)s')
-log_dir = '%(tmplogdir)s'
-software_install_suffix = '%(softsuffix)s'
-modules_install_suffix = '%(modsuffix)s'
-"""
-
-        buildpath = os.path.join(self.tmpdir, 'my', 'test', 'build', 'path')
-        sourcepath = os.path.join(self.tmpdir, 'my', 'test', 'source', 'path')
-        installpath = os.path.join(self.tmpdir, 'my', 'test', 'install', 'path')
-        repopath = os.path.join(self.tmpdir, 'my', 'test', 'repo', 'path')
-        logdir = 'somedir'
-        logtmpl = 'test-eb-%(name)s%(version)s_date-%(date)s__time-%(time)s.log'
-        tmplogdir = os.path.join(self.tmpdir, 'my', 'test', 'tmplogdir')
-        softsuffix = 'myfavoritesoftware'
-        modsuffix = 'modulesgohere'
-
-        configdict = {
-            'buildpath': buildpath,
-            'sourcepath': sourcepath,
-            'installpath': installpath,
-            'repopath': repopath,
-            'logdir': logdir,
-            'logtmpl': logtmpl,
-            'tmplogdir': tmplogdir,
-            'softsuffix': softsuffix,
-            'modsuffix': modsuffix
-        }
-
-        # create user config file on default location
-        myconfigfile = os.path.join(self.tmpdir, '.easybuild', 'config.py')
-        if not os.path.exists(os.path.dirname(myconfigfile)):
-            os.makedirs(os.path.dirname(myconfigfile))
-        write_file(myconfigfile, configtxt % configdict)
-
-        # redefine home so we can test user config file on default location
-        home = os.environ.get('HOME', None)
-        os.environ['HOME'] = self.tmpdir
-        init_config()
-        cfg_fn = self.configure(args=[])
-        if home is not None:
-            os.environ['HOME'] = home
-
-        # check finding and use of config file
-        self.assertEqual(cfg_fn, myconfigfile)
-        self.assertEqual(build_path(), buildpath)
-        self.assertEqual(source_paths()[0], sourcepath)
-        self.assertEqual(install_path(), os.path.join(installpath, softsuffix))
-        self.assertEqual(install_path(typ='mod'), os.path.join(installpath, modsuffix))
-        repo = init_repository(get_repository(), get_repositorypath())
-        self.assertTrue(isinstance(repo, FileRepository))
-        self.assertEqual(repo.repo, repopath)
-        self.assertEqual(log_file_format(return_directory=True), logdir)
-        self.assertEqual(log_file_format(), logtmpl)
-        self.assertEqual(get_build_log_path(), tmplogdir)
-
-        # redefine config file entries for proper testing below
-        buildpath = os.path.join(self.tmpdir, 'my', 'custom', 'test', 'build', 'path')
-        sourcepath = os.path.join(self.tmpdir, 'my', 'custom', 'test', 'source', 'path')
-        installpath = os.path.join(self.tmpdir, 'my', 'custom', 'test', 'install', 'path')
-        repopath = os.path.join(self.tmpdir, 'my', 'custom', 'test', 'repo', 'path')
-        logdir = 'somedir_custom'
-        logtmpl = 'test-custom-eb-%(name)_%(date)s%(time)s__%(version)s.log'
-        tmplogdir = os.path.join(self.tmpdir, 'my', 'custom', 'test', 'tmplogdir')
-        softsuffix = 'myfavoritesoftware_custom'
-        modsuffix = 'modulesgohere_custom'
-
-        configdict = {
-            'buildpath': buildpath,
-            'sourcepath': sourcepath,
-            'installpath': installpath,
-            'repopath': repopath,
-            'logdir': logdir,
-            'logtmpl': logtmpl,
-            'tmplogdir': tmplogdir,
-            'softsuffix': softsuffix,
-            'modsuffix': modsuffix }
-
-        # create custom config file, and point to it
-        mycustomconfigfile = os.path.join(self.tmpdir, 'mycustomconfig.py')
-        if not os.path.exists(os.path.dirname(mycustomconfigfile)):
-            os.makedirs(os.path.dirname(mycustomconfigfile))
-        write_file(mycustomconfigfile, configtxt % configdict)
-        os.environ['EASYBUILDCONFIG'] = mycustomconfigfile
-
-        # reconfigure
-        init_config()
-        cfg_fn = self.configure(args=[])
-
-        # verify configuration
-        self.assertEqual(cfg_fn, mycustomconfigfile)
-        self.assertEqual(build_path(), buildpath)
-        self.assertEqual(source_paths()[0], sourcepath)
-        self.assertEqual(install_path(), os.path.join(installpath, softsuffix))
-        self.assertEqual(install_path(typ='mod'), os.path.join(installpath, modsuffix))
-        repo = init_repository(get_repository(), get_repositorypath())
-        self.assertTrue(isinstance(repo, FileRepository))
-        self.assertEqual(repo.repo, repopath)
-        self.assertEqual(log_file_format(return_directory=True), logdir)
-        self.assertEqual(log_file_format(), logtmpl)
-        self.assertEqual(get_build_log_path(), tmplogdir)
+        self.assertEqual(config_options['tmpdir'], None)
+        self.assertEqual(config_options['tmp_logdir'], None)
 
     def test_generaloption_config(self):
         """Test new-style configuration (based on generaloption)."""
@@ -525,6 +266,9 @@ def test_set_tmpdir(self):
             fd, tempfile_tmpfile = tempfile.mkstemp()
             self.assertTrue(tempfile_tmpfile.startswith(os.path.join(parent, 'easybuild-')))
 
+            # tmp_logdir follows tmpdir
+            self.assertEqual(get_build_log_path(), mytmpdir)
+
             # cleanup
             os.close(fd)
             shutil.rmtree(mytmpdir)
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 78e423853b..c2dcb01655 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -77,17 +77,9 @@ def test_easyblock(self):
 
         def check_extra_options_format(extra_options):
             """Make sure extra_options value is of correct format."""
-            # EasyBuild v1.x: list of (<string>, <list>) tuples
-            self.assertTrue(isinstance(list(extra_options), list))  # conversion to a list works
-            for extra_option in extra_options:
-                self.assertTrue(isinstance(extra_option, tuple))
-                self.assertEqual(len(extra_option), 2)
-                self.assertTrue(isinstance(extra_option[0], basestring))
-                self.assertTrue(isinstance(extra_option[1], list))
-                self.assertEqual(len(extra_option[1]), 3)
             # EasyBuild v2.0: dict with <string> keys and <list> values
             # (breaks backward compatibility compared to v1.x)
-            self.assertTrue(isinstance(dict(extra_options), dict))  # conversion to a dict works
+            self.assertTrue(isinstance(extra_options, dict))  # conversion to a dict works
             extra_options.items()
             extra_options.keys()
             extra_options.values()
@@ -129,7 +121,7 @@ def check_extra_options_format(extra_options):
         self.assertEqual(exeb1.cfg['name'], 'foo')
         extra_options = exeb1.extra_options()
         check_extra_options_format(extra_options)
-        self.assertTrue('options' in [key for (key, _) in extra_options])
+        self.assertTrue('options' in extra_options)
 
         # test extensioneasyblock, as easyblock
         exeb2 = ExtensionEasyBlock(ec)
@@ -137,7 +129,7 @@ def check_extra_options_format(extra_options):
         self.assertEqual(exeb2.cfg['version'], '3.14')
         extra_options = exeb2.extra_options()
         check_extra_options_format(extra_options)
-        self.assertTrue('options' in [key for (key, _) in extra_options])
+        self.assertTrue('options' in extra_options)
 
         class TestExtension(ExtensionEasyBlock):
             @staticmethod
@@ -147,8 +139,8 @@ def extra_options():
         self.assertEqual(texeb.cfg['name'], 'bar')
         extra_options = texeb.extra_options()
         check_extra_options_format(extra_options)
-        self.assertTrue('options' in [key for (key, _) in extra_options])
-        self.assertEqual([val for (key, val) in extra_options if key == 'extra_param'][0], [None, "help", CUSTOM])
+        self.assertTrue('options' in extra_options)
+        self.assertEqual(extra_options['extra_param'], [None, "help", CUSTOM])
 
         # cleanup
         eb.close_log()
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index a11a245938..e67b43983d 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -153,24 +153,6 @@ def test_validation(self):
         self.prep()
         self.assertErrorRegex(EasyBuildError, "SyntaxError", EasyConfig, self.eb_file)
 
-    def test_deprecated_shared_lib_ext(self):
-        """ inside easyconfigs shared_lib_ext should be set """
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-
-        self.contents = '\n'.join([
-            'easyblock = "ConfigureMake"',
-            'name = "pi"',
-            'version = "3.14"',
-            'homepage = "http://example.com"',
-            'description = "test easyconfig"',
-            'toolchain = {"name":"dummy", "version": "dummy"}',
-            'sanity_check_paths = { "files": ["lib/lib.%s" % shared_lib_ext] }',
-        ])
-        self.prep()
-        eb = EasyConfig(self.eb_file)
-        self.assertEqual(eb['sanity_check_paths']['files'][0], "lib/lib.%s" % get_shared_lib_ext())
-
     def test_shlib_ext(self):
         """ inside easyconfigs shared_lib_ext should be set """
         self.contents = '\n'.join([
@@ -282,12 +264,6 @@ def test_extra_options(self):
 
         self.assertEqual(eb['mandatory_key'], 'value')
 
-        # test legacy behavior of passing a list of tuples rather than a dict
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-        eb = EasyConfig(self.eb_file, extra_options=extra_vars.items())
-        self.assertEqual(eb['custom_key'], 'test')
-
     def test_exts_list(self):
         """Test handling of list of extensions."""
         os.environ['EASYBUILD_SOURCEPATH'] = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
@@ -443,26 +419,6 @@ def test_installversion(self):
         installver = det_full_ec_version(cfg)
         self.assertEqual(installver, correct_installver)
 
-    def test_legacy_installversion(self):
-        """Test generation of install version (legacy)."""
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-
-        ver = "3.14"
-        verpref = "myprefix|"
-        versuff = "|mysuffix"
-        tcname = "GCC"
-        tcver = "4.6.3"
-        dummy = "dummy"
-
-        correct_installver = "%s%s-%s-%s%s" % (verpref, ver, tcname, tcver, versuff)
-        installver = det_installversion(ver, tcname, tcver, verpref, versuff)
-        self.assertEqual(installver, correct_installver)
-
-        correct_installver = "%s%s%s" % (verpref, ver, versuff)
-        installver = det_installversion(ver, dummy, tcver, verpref, versuff)
-        self.assertEqual(installver, correct_installver)
-
     def test_obtain_easyconfig(self):
         """test obtaining an easyconfig file given certain specifications"""
 
@@ -928,10 +884,6 @@ def test_get_easyblock_class(self):
         self.assertEqual(get_easyblock_class(None, name='toy'), EB_toy)
         self.assertErrorRegex(EasyBuildError, "Failed to import EB_TOY", get_easyblock_class, None, name='TOY')
         self.assertEqual(get_easyblock_class(None, name='TOY', error_on_failed_import=False), None)
-        # deprecated functionality: ConfigureMake fallback still enabled
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-        self.assertEqual(get_easyblock_class(None, name='gzip'), ConfigureMake)
 
     def test_easyconfig_paths(self):
         """Test create_paths function."""
@@ -944,32 +896,6 @@ def test_easyconfig_paths(self):
         ]
         self.assertEqual(cand_paths, expected_paths)
 
-    def test_deprecated_options(self):
-        """Test whether deprecated options are handled correctly."""
-        # lower 'current' version to avoid tripping over deprecation errors
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-
-        deprecated_options = [
-            ('makeopts', 'buildopts', 'CC=foo'),
-            ('premakeopts', 'prebuildopts', ['PATH=%(builddir)s/foo:$PATH', 'PATH=%(builddir)s/bar:$PATH']),
-        ]
-        clean_contents = [
-            'easyblock = "ConfigureMake"',
-            'name = "pi"',
-            'version = "3.14"',
-            'homepage = "http://example.com"',
-            'description = "test easyconfig"',
-            'toolchain = {"name": "dummy", "version": "dummy"}',
-            'buildininstalldir = True',
-        ]
-        # alternative option is ready to use
-        for depr_opt, new_opt, val in deprecated_options:
-            self.contents = '\n'.join(clean_contents + ['%s = %s' % (depr_opt, quote_str(val))])
-            self.prep()
-            ec = EasyConfig(self.eb_file)
-            self.assertEqual(ec[depr_opt], ec[new_opt])
-
     def test_toolchain_inspection(self):
         """Test whether available toolchain inspection functionality is working."""
         build_options = {
diff --git a/test/framework/modules.py b/test/framework/modules.py
index 059a80604a..00cce786d7 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -122,14 +122,6 @@ def test_exists(self):
                      'Compiler/GCC/4.7.2/OpenMPI/1.6.4', 'toy/.0.0-deps']
         self.assertEqual(self.testmods.exist(mod_names), [True, False, False, False, True, True, True])
 
-        # test deprecated functionality
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-        self.assertTrue(self.testmods.exists('OpenMPI/1.6.4-GCC-4.6.4'))
-        self.assertFalse(self.testmods.exists('foo/1.2.3'))
-        # exists should not return True for incomplete module names
-        self.assertFalse(self.testmods.exists('GCC'))
-
     def test_load(self):
         """ test if we load one module it is in the loaded_modules """
         self.init_testmods()
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index 20b6b0068d..8447913dc7 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -47,13 +47,6 @@ def test_avail_core_count(self):
         self.assertTrue(isinstance(core_count, int), "core_count has type int: %s, %s" % (core_count, type(core_count)))
         self.assertTrue(core_count > 0, "core_count %d > 0" % core_count)
 
-        # also test deprecated get_core_count
-        os.environ['EASYBUILD_DEPRECATED'] = '1.0'
-        init_config()
-        core_count = get_core_count()
-        self.assertTrue(isinstance(core_count, int), "core_count has type int: %s, %s" % (core_count, type(core_count)))
-        self.assertTrue(core_count > 0, "core_count %d > 0" % core_count)
-
     def test_cpu_model(self):
         """Test getting CPU model."""
         cpu_model = get_cpu_model()
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 1b8371b379..95eb21b03b 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -57,17 +57,6 @@ def setUp(self):
         fd, self.dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
-        # adjust PYTHONPATH such that test easyblocks are found
-        import easybuild
-        eb_blocks_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'sandbox'))
-        if not eb_blocks_path in sys.path:
-            sys.path.append(eb_blocks_path)
-            easybuild = reload(easybuild)
-
-        import easybuild.easyblocks
-        reload(easybuild.easyblocks)
-        reload(easybuild.tools.module_naming_scheme)
-
         # clear log
         write_file(self.logfile, '')
 

From 94f15a4f96200d938307c929518c4aabb11ea4de Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Jan 2015 14:24:50 +0100
Subject: [PATCH 0451/1356] style fixes

---
 easybuild/framework/easyblock.py             |  8 ++++----
 easybuild/framework/easyconfig/easyconfig.py | 21 ++++++--------------
 easybuild/tools/config.py                    | 14 ++++---------
 easybuild/tools/filetools.py                 |  8 ++++----
 easybuild/tools/modules.py                   |  2 +-
 easybuild/tools/options.py                   |  4 +---
 easybuild/tools/systemtools.py               |  4 ++--
 7 files changed, 22 insertions(+), 39 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index c29563a99f..3269660935 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1065,7 +1065,8 @@ def skip_extensions(self):
             try:
                 cmd = cmdtmpl % tmpldict
             except KeyError, err:
-                msg = "Use of 'name'/'version' keys for extensions filter, should use 'ext_name', 'ext_version' instead"
+                msg = "KeyError occured on completing extension filter template: %s; "
+                msg += "'name'/'version' keys are no longer supported, should use 'ext_name'/'ext_version' instead"
                 self.log.nosupport(msg, '2.0')
 
             if cmdinputtmpl:
@@ -1370,7 +1371,7 @@ def extensions_step(self, fetch=False):
 
         # obtain name and module path for default extention class
         if hasattr(exts_defaultclass, '__iter__'):
-            self.log.nosupport("Using specified module path for default class", '2.0')
+            self.log.nosupport("Module path for default class is explicitly defined", '2.0')
 
         elif isinstance(exts_defaultclass, basestring):
             # proper way: derive module path from specified class name
@@ -1411,8 +1412,7 @@ def extensions_step(self, fetch=False):
                     cls = get_class_for(mod_path, class_name)
                     inst = cls(self, ext)
                 except (ImportError, NameError), err:
-                    tup = (class_name, ext['name'], err)
-                    self.log.error("Failed to load specified class %s for extension %s: %s" % tup)
+                    self.log.error("Failed to load specified class %s for extension %s: %s" % (class_name, ext['name'], err))
 
             # fallback attempt: use default class
             if inst is None:
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 1a50efb87c..b366821fbf 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -83,21 +83,12 @@
 _easyconfigs_cache = {}
 
 
-def handle_replaced_easyconfig_parameter(ec_method):
-    """Decorator to handle replaced easyconfig parameters."""
+def check_replaced_easyconfig_parameter(ec_method):
+    """Decorator to check for replaced easyconfig parameters."""
     def new_ec_method(self, key, *args, **kwargs):
-        """Map replaced easyconfig parameters to the new correct parameter."""
-        # map name of replaced easyconfig parameter to new name
+        """Check whether any replace easyconfig parameters are still used"""
         if key in REPLACED_PARAMETERS:
             _log.nosupport("Easyconfig parameter '%s' is replaced by '%s'" % (key, REPLACED_PARAMETERS[key]), '2.0')
-
-        # make sure that value for software_license has correct type, convert if needed
-        if key == 'software_license':
-            # key 'license' will already be mapped to 'software_license' above
-            lic = self._config['software_license'][0]
-            if lic is not None and not isinstance(lic, License):
-                self.log.nosupport('Type for software_license must to be instance of License (sub)class', '2.0')
-
         return ec_method(self, key, *args, **kwargs)
 
     return new_ec_method
@@ -628,7 +619,7 @@ def _generate_template_values(self, ignore=None, skip_lower=True):
             if v is None:
                 del self.template_values[k]
 
-    @handle_replaced_easyconfig_parameter
+    @check_replaced_easyconfig_parameter
     def __getitem__(self, key):
         """
         will return the value without the help text
@@ -641,7 +632,7 @@ def __getitem__(self, key):
         else:
             return value
 
-    @handle_replaced_easyconfig_parameter
+    @check_replaced_easyconfig_parameter
     def __setitem__(self, key, value):
         """
         sets the value of key in config.
@@ -741,7 +732,7 @@ def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_fa
                 modulepath_bis = get_module_path(name, decode=False)
                 _log.debug("Module path determined based on software name: %s" % modulepath_bis)
                 if modulepath_bis != modulepath:
-                    _log.nosupport("Determine module path based on software name", '2.0')
+                    _log.nosupport("Determining module path based on software name", '2.0')
 
             # try and find easyblock
             try:
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index be244d5daf..9fd02948fd 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -216,12 +216,6 @@ class BuildOptions(FrozenDictKnownKeys):
     KNOWN_KEYS = [k for kss in [BUILD_OPTIONS_CMDLINE, BUILD_OPTIONS_OTHER] for ks in kss.values() for k in ks]
 
 
-def get_default_configfiles():
-    """Return a list of default configfiles for tools.options/generaloption"""
-    xdg_config_home = os.environ.get("XDG_CONFIG_HOME", os.path.join(os.path.expanduser('~'), ".config"))
-    return [os.path.join(xdg_config_home, 'easybuild', 'config.cfg')]
-
-
 def get_pretend_installpath():
     """Get the installpath when --pretend option is used"""
     return os.path.join(os.path.expanduser('~'), 'easybuildinstall')
@@ -313,7 +307,7 @@ def source_paths():
 
 def source_path():
     """NO LONGER SUPPORTED: use source_paths instead"""
-    _log.nosupport("Use of source_path(), use source_paths() instead.", '2.0')
+    _log.nosupport("source_path() is replaced by source_paths()", '2.0')
 
 
 def install_path(typ=None):
@@ -384,7 +378,7 @@ def log_path():
 
 def get_build_log_path():
     """
-    return temporary log directory
+    Return (temporary) directory for build log
     """
     variables = ConfigurationVariables()
     if variables['tmp_logdir'] is not None:
@@ -442,8 +436,8 @@ def module_classes():
 
 
 def read_environment(env_vars, strict=False):
-    """Depreacted location for read_environment, use easybuild.tools.environment"""
-    _log.nosupport("Deprecated location for read_environment, use easybuild.tools.environment", '2.0')
+    """NO LONGER SUPPORTED: use read_environment from easybuild.tools.environment instead"""
+    _log.nosupport("read_environment has moved to easybuild.tools.environment", '2.0')
 
 
 def set_tmpdir(tmpdir=None):
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index b9faa6e976..d524c0ca61 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -712,7 +712,7 @@ def apply_patch(patch_file, dest, fn=None, copy=False, level=None):
 
 def modify_env(old, new):
     """NO LONGER SUPPORTED: use modify_env from easybuild.tools.environment instead"""
-    _log.nosupport("moved modify_env to tools.environment", "2.0")
+    _log.nosupport("moved modify_env to easybuild.tools.environment", "2.0")
 
 
 def convert_name(name, upper=False):
@@ -1040,16 +1040,16 @@ def decode_class_name(name):
 
 def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True, log_output=False, path=None):
     """NO LONGER SUPPORTED: use run_cmd from easybuild.tools.run instead"""
-    _log.nosupport("run_cmd was moved from tools.filetools to tools.run", '2.0')
+    _log.nosupport("run_cmd was moved from easybuild.tools.filetools to easybuild.tools.run", '2.0')
 
 
 def run_cmd_qa(cmd, qa, no_qa=None, log_ok=True, log_all=False, simple=False, regexp=True, std_qa=None, path=None):
     """NO LONGER SUPPORTED: use run_cmd_qa from easybuild.tools.run instead"""
-    _log.nosupport("run_cmd_qa was moved from tools.filetools to tools.run", '2.0')
+    _log.nosupport("run_cmd_qa was moved from easybuild.tools.filetools to easybuild.tools.run", '2.0')
 
 def parse_log_for_error(txt, regExp=None, stdout=True, msg=None):
     """NO LONGER SUPPORTED: use parse_log_for_error from easybuild.tools.run instead"""
-    _log.nosupport("parse_log_for_error was moved from tools.filetools to tools.run", '2.0')
+    _log.nosupport("parse_log_for_error was moved from easybuild.tools.filetools to easybuild.tools.run", '2.0')
 
 
 def det_size(path):
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 5c8b057fd7..36f412a9bc 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -181,7 +181,7 @@ def buildstats(self):
     @property
     def modules(self):
         """(NO LONGER SUPPORTED!) Property providing access to 'modules' class variable"""
-        self.log.nosupport("'modules' class variable is not supported anymore, just use load([<list of modules>])", '2.0')
+        self.log.nosupport("'modules' class variable is not supported anymore, use load([<list of modules>]) instead", '2.0')
 
     def set_and_check_version(self):
         """Get the module version, and check any requirements"""
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 14baac2909..6d3c4393af 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -36,7 +36,6 @@
 import os
 import re
 import sys
-import tempfile
 from distutils.version import LooseVersion
 from vsc.utils.missing import nub
 
@@ -51,7 +50,7 @@
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
 from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
-from easybuild.tools.config import get_default_configfiles, get_pretend_installpath
+from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
@@ -75,7 +74,6 @@ class EasyBuildOptions(GeneralOption):
     VERSION = this_is_easybuild()
 
     DEFAULT_LOGLEVEL = 'INFO'
-
     DEFAULT_CONFIGFILES = [DEFAULT_CONFIGFILE]
 
     ALLOPTSMANDATORY = False  # allow more than one argument
diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index d76185054b..2d2fbc696c 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -129,7 +129,7 @@ def count_bits(n):
 
 def get_core_count():
     """NO LONGER SUPPORTED: use get_avail_core_count() instead"""
-    _log.nosupport("get_core_count() is nosupport, use get_avail_core_count() instead", '2.0')
+    _log.nosupport("get_core_count() is replaced by get_avail_core_count()", '2.0')
 
 
 def get_cpu_vendor():
@@ -256,7 +256,7 @@ def get_cpu_speed():
 
 def get_kernel_name():
     """NO LONGER SUPPORTED: use get_os_type() instead"""
-    _log.nosupport("get_kernel_name() (replaced by get_os_type())", "2.0")
+    _log.nosupport("get_kernel_name() is replaced by get_os_type()", '2.0')
 
 
 def get_os_type():

From 0eb24a32c7906c4fc9040e90af2228bb8a23248b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Jan 2015 15:46:07 +0100
Subject: [PATCH 0452/1356] remove easybuild_config.py from setup.py

---
 setup.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/setup.py b/setup.py
index 783cce2062..1a961f4a36 100644
--- a/setup.py
+++ b/setup.py
@@ -91,9 +91,7 @@ def find_rel_test():
     package_dir = {'test.framework': "test/framework"},
     package_data = {"test.framework": find_rel_test()},
     scripts = ["eb", "optcomplete.bash", "minimal_bash_completion.bash"],
-    data_files = [
-        ('easybuild', ["easybuild/easybuild_config.py"]),
-    ],
+    data_files = [],
     long_description = read('README.rst'),
     classifiers = [
         "Development Status :: 5 - Production/Stable",

From 413b51b2b00a6c5c77d1f4d25ed61c2ec2226f5f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 23 Jan 2015 16:36:13 +0100
Subject: [PATCH 0453/1356] change tweaking of easyconfig parameters: drop
 adding comments, fix issue of disappearing newline, no adding of useless
 newline at the end

---
 easybuild/framework/easyconfig/tweak.py | 28 ++++++++++++-------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index ee4176bf52..6302ddb499 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -166,7 +166,7 @@ def __repr__(self):
     for (key, val) in tweaks.items():
 
         if isinstance(val, list):
-            regexp = re.compile(r"^\s*%s\s*=\s*(.*)$" % key, re.M)
+            regexp = re.compile(r"^(?P<key>\s*%s)\s*=\s*(?P<val>.*)$" % key, re.M)
             res = regexp.search(ectxt)
             if res:
                 fval = [x for x in val if x != '']  # filter out empty strings
@@ -175,48 +175,48 @@ def __repr__(self):
                 # - input starting with comma (empty head list element) => append
                 # - no empty head/tail list element => overwrite
                 if val[0] == '':
-                    newval = "%s + %s" % (res.group(1), fval)
+                    newval = "%s + %s" % (res.group('val'), fval)
                     _log.debug("Appending %s to %s" % (fval, key))
                 elif val[-1] == '':
-                    newval = "%s + %s" % (fval, res.group(1))
+                    newval = "%s + %s" % (fval, res.group('val'))
                     _log.debug("Prepending %s to %s" % (fval, key))
                 else:
                     newval = "%s" % fval
                     _log.debug("Overwriting %s with %s" % (key, fval))
-                ectxt = regexp.sub("%s = %s # tweaked by EasyBuild (was: %s)" % (key, newval, res.group(1)), ectxt)
+                ectxt = regexp.sub("%s = %s" % (res.group('key'), newval), ectxt)
                 _log.info("Tweaked %s list to '%s'" % (key, newval))
             else:
-                additions.append("%s = %s # added by EasyBuild" % (key, val))
+                additions.append("%s = %s" % (key, val))
 
             tweaks.pop(key)
 
     # add parameters or replace existing ones
     for (key, val) in tweaks.items():
 
-        regexp = re.compile(r"^\s*%s\s*=\s*(.*)$" % key, re.M)
+        regexp = re.compile(r"^(?P<key>\s*%s)\s*=\s*(?P<val>.*)$" % key, re.M)
         _log.debug("Regexp pattern for replacing '%s': %s" % (key, regexp.pattern))
         res = regexp.search(ectxt)
         if res:
             # only tweak if the value is different
             diff = True
             try:
-                _log.debug("eval(%s): %s" % (res.group(1), eval(res.group(1))))
-                diff = not eval(res.group(1)) == val
+                _log.debug("eval(%s): %s" % (res.group('val'), eval(res.group('val'))))
+                diff = not eval(res.group('val')) == val
             except (NameError, SyntaxError):
                 # if eval fails, just fall back to string comparison
-                _log.debug("eval failed for \"%s\", falling back to string comparison against \"%s\"..." % (res.group(1), val))
-                diff = not res.group(1) == val
+                tup = (res.group('val'), val)
+                _log.debug("eval failed for \"%s\", falling back to string comparison against \"%s\"..." % tup)
+                diff = not res.group('val') == val
 
             if diff:
-                ectxt = regexp.sub("%s = %s # tweaked by EasyBuild (was: %s)" % (key, quote_str(val), res.group(1)), ectxt)
+                ectxt = regexp.sub("%s = %s" % (res.group('key'), quote_str(val)), ectxt)
                 _log.info("Tweaked '%s' to '%s'" % (key, quote_str(val)))
         else:
             additions.append("%s = %s" % (key, quote_str(val)))
 
     if additions:
-        _log.info("Adding additional parameters to tweaked easyconfig file: %s")
-        ectxt += "\n\n# added by EasyBuild as dictated by command line options\n"
-        ectxt += '\n'.join(additions) + '\n'
+        _log.info("Adding additional parameters to tweaked easyconfig file: %s" % additions)
+        ectxt = '\n'.join([ectxt] + additions)
 
     _log.debug("Contents of tweaked easyconfig file:\n%s" % ectxt)
 

From 66b0f872b2c822154d6baeda9772a3159b313c1b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 23 Jan 2015 16:36:43 +0100
Subject: [PATCH 0454/1356] enhance --try unit tests to include tweaked of
 list-typed values

---
 test/framework/options.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 1c4f847494..66f75a88a1 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1168,6 +1168,14 @@ def test_try(self):
             (['--try-toolchain-name=gompi', '--try-toolchain-version=1.4.10'], 'toy/0.0-gompi-1.4.10'),
             (['--try-software-version=1.2.3', '--try-toolchain=gompi,1.4.10'], 'toy/1.2.3-gompi-1.4.10'),
             (['--try-amend=versionsuffix=-test'], 'toy/0.0-test'),
+            # tweak existing list-typed value (patches)
+            (['--try-amend=versionsuffix=-test2', '--try-amend=patches=1.patch,2.patch'], 'toy/0.0-test2'),
+            # append to existing list-typed value (patches)
+            (['--try-amend=versionsuffix=-test3', '--try-amend=patches=,extra.patch'], 'toy/0.0-test3'),
+            # prepend to existing list-typed value (patches)
+            (['--try-amend=versionsuffix=-test4', '--try-amend=patches=extra.patch,'], 'toy/0.0-test4'),
+            # define extra list-typed parameter
+            (['--try-amend=versionsuffix=-test5', '--try-amend=exts_list=1,2,3'], 'toy/0.0-test5'),
             # only --try causes other build specs to be included too
             (['--try-software=foo,1.2.3', '--toolchain=gompi,1.4.10'], 'foo/1.2.3-gompi-1.4.10'),
             (['--software=foo,1.2.3', '--try-toolchain=gompi,1.4.10'], 'foo/1.2.3-gompi-1.4.10'),

From 09af38ed0bd7c3b2c8c56a1ce96e42fe45fb8af8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 23 Jan 2015 17:32:23 +0100
Subject: [PATCH 0455/1356] fix remark

---
 easybuild/framework/easyconfig/tweak.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 6302ddb499..0047ae8a6d 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -201,12 +201,12 @@ def __repr__(self):
             diff = True
             try:
                 _log.debug("eval(%s): %s" % (res.group('val'), eval(res.group('val'))))
-                diff = not eval(res.group('val')) == val
+                diff = eval(res.group('val')) != val
             except (NameError, SyntaxError):
                 # if eval fails, just fall back to string comparison
                 tup = (res.group('val'), val)
                 _log.debug("eval failed for \"%s\", falling back to string comparison against \"%s\"..." % tup)
-                diff = not res.group('val') == val
+                diff = res.group('val') != val
 
             if diff:
                 ectxt = regexp.sub("%s = %s" % (res.group('key'), quote_str(val)), ectxt)
@@ -524,7 +524,7 @@ def unique(l):
         for (key, val) in specs.items():
             if key in selected_ec._config:
                 # values must be equal to have a full match
-                if not selected_ec[key] == val:
+                if selected_ec[key] != val:
                     match = False
             else:
                 # if we encounter a key that is not set in the selected easyconfig, we don't have a full match

From d4345eecdfc38c21974f3f6f153fcbfa08cbe404 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 23 Jan 2015 17:32:35 +0100
Subject: [PATCH 0456/1356] fix broken test

---
 test/framework/easyconfig.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index a11a245938..1c3f5c0cf9 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -585,7 +585,7 @@ def test_obtain_easyconfig(self):
         ec = EasyConfig(res[1])
         self.assertEqual(ec['version'], specs['version'])
         txt = read_file(res[1])
-        self.assertTrue(re.search("version = [\"']%s[\"'] .*was: [\"']3.13[\"']" % ver, txt))
+        self.assertTrue(re.search("^version = [\"']%s[\"']$" % ver, txt, re.M))
         os.remove(res[1])
 
         # should pick correct toolchain version as well, i.e. now newer than what's specified, if a choice needs to be made
@@ -599,8 +599,8 @@ def test_obtain_easyconfig(self):
         self.assertEqual(ec['version'], specs['version'])
         self.assertEqual(ec['toolchain']['version'], specs['toolchain_version'])
         txt = read_file(res[1])
-        pattern = "toolchain = .*version.*[\"']%s[\"'].*was: .*version.*[\"']%s[\"']" % (specs['toolchain_version'], tcver)
-        self.assertTrue(re.search(pattern, txt))
+        pattern = "^toolchain = .*version.*[\"']%s[\"'].*}$" % specs['toolchain_version']
+        self.assertTrue(re.search(pattern, txt, re.M))
         os.remove(res[1])
 
 

From a778631bb7d34c9b9b01eba56f6ee5b0dafe75fc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 23 Jan 2015 18:27:34 +0100
Subject: [PATCH 0457/1356] stop using log.raiseException in toolchain.py, use
 log.error instead

---
 easybuild/tools/toolchain/toolchain.py | 28 ++++++++++++--------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 75c5a29c85..f9d241873f 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -82,13 +82,13 @@ def __init__(self, name=None, version=None, mns=None):
         if name is None:
             name = self.NAME
         if name is None:
-            self.log.raiseException("init: no name provided")
+            self.log.error("Toolchain init: no name provided")
         self.name = name
 
         if version is None:
             version = self.VERSION
         if version is None:
-            self.log.raiseException("init: no version provided")
+            self.log.error("Toolchain init: no version provided")
         self.version = version
 
         self.vars = None
@@ -129,7 +129,7 @@ def get_variable(self, name, typ=str):
         elif typ == list:
             return self.variables[name].flatten()
         else:
-            self.log.raiseException("get_variables: Don't know how to create value of type %s." % typ)
+            self.log.error("get_variable: Don't know how to create value of type %s." % typ)
 
     def set_variables(self):
         """Do nothing? Everything should have been set by others
@@ -188,7 +188,7 @@ def _get_software_root(self, name):
         """Try to get the software root for name"""
         root = get_software_root(name)
         if root is None:
-            self.log.raiseException("get_software_root software root for %s was not found in environment" % (name))
+            self.log.error("get_software_root software root for %s was not found in environment" % name)
         else:
             self.log.debug("get_software_root software root %s for %s was found in environment" % (root, name))
         return root
@@ -197,11 +197,9 @@ def _get_software_version(self, name):
         """Try to get the software root for name"""
         version = get_software_version(name)
         if version is None:
-            self.log.raiseException("get_software_version software version for %s was not found in environment" %
-                                    (name))
+            self.log.error("get_software_version software version for %s was not found in environment" % name)
         else:
-            self.log.debug("get_software_version software version %s for %s was found in environment" %
-                           (version, name))
+            self.log.debug("get_software_version software version %s for %s was found in environment" % (version, name))
 
         return version
 
@@ -249,8 +247,8 @@ def set_options(self, options):
                 self.options[opt] = options[opt]
             else:
                 # used to be warning, but this is a severe error imho
-                self.log.raiseException("set_options: undefined toolchain option %s specified (possible names %s)" %
-                                        (opt, ",".join(self.options.keys())))
+                known_opts = ','.join(self.options.keys())
+                self.log.error("Undefined toolchain option %s specified (known options: %s)" % (opt, known_opts))
 
     def get_dependency_version(self, dependency):
         """ Generate a version string for a dependency on a module using this toolchain """
@@ -281,8 +279,8 @@ def get_dependency_version(self, dependency):
                 self.log.debug("get_dependency_version: version not in dependency return %s" % version)
                 return
             else:
-                self.log.raiseException('get_dependency_version: No toolchain version for dependency '\
-                                        'name %s (suffix %s) found' % (dependency['name'], toolchain_suffix))
+                tup = (dependency['name'], toolchain_suffix)
+                self.log.error("No toolchain version for dependency name %s (suffix %s) found" % tup)
 
     def add_dependencies(self, dependencies):
         """ Verify if the given dependencies exist and add them """
@@ -331,10 +329,10 @@ def prepare(self, onlymod=None):
         (If string: comma separated list of variables that will be ignored).
         """
         if self.modules_tool is None:
-            self.log.raiseException("No modules tool defined.")
+            self.log.error("No modules tool defined in Toolchain instance.")
 
         if not self._toolchain_exists():
-            self.log.raiseException("No module found for toolchain name '%s' (%s)" % (self.name, self.version))
+            self.log.error("No module found for toolchain: %s" % self.mod_short_name)
 
         if self.name == DUMMY_TOOLCHAIN_NAME:
             if self.version == DUMMY_TOOLCHAIN_VERSION:
@@ -429,7 +427,7 @@ def _setenv_variables(self, donotset=None):
         donotsetlist = []
         if isinstance(donotset, str):
             # TODO : more legacy code that should be using proper type
-            self.log.raiseException("_setenv_variables: using commas-separated list. should be deprecated.")
+            self.log.error("_setenv_variables: using commas-separated list. should be deprecated.")
             donotsetlist = donotset.split(',')
         elif isinstance(donotset, list):
             donotsetlist = donotset

From 661edaa8af22ecbb01eb03bf27ab3ef3f28ba35f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 23 Jan 2015 18:28:01 +0100
Subject: [PATCH 0458/1356] remove dead code in toolchain.py

---
 easybuild/tools/toolchain/toolchain.py | 34 --------------------------
 1 file changed, 34 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index f9d241873f..cb5a9fdd54 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -457,37 +457,3 @@ def comp_family(self):
     def mpi_family(self):
         """ Return type of MPI library used in this toolchain (abstract method)."""
         raise NotImplementedError
-
-    # legacy functions TODO remove AFTER migration
-    # should search'n'replaced
-    def get_type(self, name, type_map):
-        """Determine type of toolchain based on toolchain dependencies."""
-        self.log.raiseException("get_type: legacy code. should not be needed anymore.")
-
-    def _set_variables(self, dontset=None):
-        """ Sets the environment variables """
-        self.log.raiseException("_set_variables: legacy code. use _setenv_variables.")
-
-    def _addDependencyVariables(self, names=None):
-        """ Add LDFLAGS and CPPFLAGS to the self.vars based on the dependencies
-        names should be a list of strings containing the name of the dependency"""
-        self.log.raiseException("_addDependencyVaraibles: legacy code. use _add_dependency_variables.")
-
-    def _setVariables(self, dontset=None):
-        """ Sets the environment variables """
-        self.log.raiseException("_setVariables: legacy code. use _set_variables.")
-
-    def _toolkitExists(self, name=None, version=None):
-        """
-        Verify if there exists a toolkit by this name and version
-        """
-        self.log.raiseException("_toolkitExists: legacy code. replace use _toolchain_exists.")
-
-    def get_openmp_flag(self):
-        """Get compiler flag for OpenMP support."""
-        self.log.raiseException("get_openmp_flag: legacy code. use options.get_flag('openmp').")
-
-    @property
-    def opts(self):
-        """Get value for specified option."""
-        self.log.raiseException("opts[x]: legacy code. use options[x].")

From 91d479bde30a48e4978b5f4d7c291b44f0e3b0c3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 23 Jan 2015 18:44:27 +0100
Subject: [PATCH 0459/1356] add test on preparing for a toolchain for which no
 module is available

---
 test/framework/toolchain.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 6d76ac1100..921626628e 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -496,6 +496,11 @@ def test_toolchain_verification(self):
         tc.set_options(opts)
         tc.prepare()
 
+    def test_nosuchtoolchain(self):
+        """Test preparing for a toolchain for which no module is available."""
+        tc = self.get_toolchain('intel', version='1970.01')
+        self.assertErrorRegex(EasyBuildError, "No module found for toolchain", tc.prepare)
+
     def tearDown(self):
         """Cleanup."""
         # purge any loaded modules before restoring $MODULEPATH

From 6c72c3ab905144c5bb1b8e9690c374e03e1d69aa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 24 Jan 2015 00:35:04 +0100
Subject: [PATCH 0460/1356] fix hardcoding of /tmp in mpi_cmd_for

---
 easybuild/tools/toolchain/mpi.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index b2a4cdc84a..053b85f02c 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -28,8 +28,8 @@
 @author: Stijn De Weirdt (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
-
 import os
+import tempfile
 
 import easybuild.tools.environment as env
 import easybuild.tools.toolchain as toolchain
@@ -185,8 +185,10 @@ def mpi_cmd_for(self, cmd, nr_ranks):
         # Intel MPI mpirun needs more work
         if mpi_family == toolchain.INTELMPI:  # @UndefinedVariable
 
+            tmpdir = tempfile.mkdtemp(prefix='eb-mpi_cmd_for-')
+
             # set temporary dir for mdp
-            env.setvar('I_MPI_MPD_TMPDIR', "/tmp")
+            env.setvar('I_MPI_MPD_TMPDIR', tmpdir)
 
             # set PBS_ENVIRONMENT, so that --file option for mpdboot isn't stripped away
             env.setvar('PBS_ENVIRONMENT', "PBS_BATCH_MPI")
@@ -196,7 +198,7 @@ def mpi_cmd_for(self, cmd, nr_ranks):
             env.setvar('I_MPI_PROCESS_MANAGER', 'mpd')
 
             # create mpdboot file
-            fn = "/tmp/mpdboot"
+            fn = os.path.join(tmpdir, 'mpdboot')
             try:
                 if os.path.exists(fn):
                     os.remove(fn)
@@ -204,10 +206,10 @@ def mpi_cmd_for(self, cmd, nr_ranks):
             except OSError, err:
                 self.log.error("Failed to create file %s: %s" % (fn, err))
 
-            params.update({'mpdbf':"--file=%s" % fn})
+            params.update({'mpdbf': "--file=%s" % fn})
 
             # create nodes file
-            fn = "/tmp/nodes"
+            fn = os.path.join(tmpdir, 'nodes')
             try:
                 if os.path.exists(fn):
                     os.remove(fn)
@@ -215,7 +217,7 @@ def mpi_cmd_for(self, cmd, nr_ranks):
             except OSError, err:
                 self.log.error("Failed to create file %s: %s" % (fn, err))
 
-            params.update({'nodesfile':"-machinefile %s" % fn})
+            params.update({'nodesfile': "-machinefile %s" % fn})
 
         if mpi_family in mpi_cmds.keys():
             return mpi_cmds[mpi_family] % params

From 26111522bb89c0a4ecf2af33166ac3f7fa4a8549 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 24 Jan 2015 00:48:03 +0100
Subject: [PATCH 0461/1356] minor style fixes

---
 easybuild/tools/toolchain/mpi.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index 053b85f02c..7a9694de8c 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -167,7 +167,10 @@ def mpi_cmd_for(self, cmd, nr_ranks):
         """Construct an MPI command for the given command and number of ranks."""
 
         # parameter values for mpirun command
-        params = {'nr_ranks':nr_ranks, 'cmd':cmd}
+        params = {
+            'nr_ranks': nr_ranks,
+            'cmd': cmd,
+        }
 
         # different known mpirun commands
         mpirun_n_cmd = "mpirun -n %(nr_ranks)d %(cmd)s"

From e7e75f83ce3525454c27238274bb836c06a90568 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 24 Jan 2015 00:48:33 +0100
Subject: [PATCH 0462/1356] add unit test for mpi_cmd_for with Intel MPI-based
 toolchain

---
 test/framework/toolchain.py | 27 ++++++++++++++++++++++++---
 1 file changed, 24 insertions(+), 3 deletions(-)

diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 921626628e..dc60b2c041 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -38,6 +38,7 @@
 import easybuild.tools.modules as modules
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import write_file
 from easybuild.tools.toolchain.utilities import search_toolchain
 from test.framework.utilities import find_full_path
 
@@ -408,8 +409,8 @@ def test_goolfc(self):
         # check CUDA runtime lib
         self.assertTrue("-lrt -lcudart" in tc.get_variable('LIBS'))
 
-    def test_ictce_toolchain(self):
-        """Test for ictce toolchain."""
+    def setup_sandbox_for_intel_fftw(self):
+        """Set up sandbox for Intel FFTW"""
         # hack to make Intel FFTW lib check pass
         # rewrite $root in imkl module so we can put required lib*.a files in place
         tmpdir = tempfile.mkdtemp()
@@ -426,7 +427,13 @@ def test_ictce_toolchain(self):
         for subdir in ['mkl/lib/intel64', 'compiler/lib/intel64']:
             os.makedirs(os.path.join(tmpdir, subdir))
             for fftlib in fftw_libs:
-                open(os.path.join(tmpdir, subdir, 'lib%s.a' % fftlib), 'w').write('foo')
+                write_file(os.path.join(tmpdir, subdir, 'lib%s.a' % fftlib), 'foo')
+
+        return tmpdir, imkl_module_path, imkl_module_txt
+
+    def test_ictce_toolchain(self):
+        """Test for ictce toolchain."""
+        tmpdir, imkl_module_path, imkl_module_txt = self.setup_sandbox_for_intel_fftw()
 
         tc = self.get_toolchain("ictce", version="4.1.13")
         tc.prepare()
@@ -501,6 +508,20 @@ def test_nosuchtoolchain(self):
         tc = self.get_toolchain('intel', version='1970.01')
         self.assertErrorRegex(EasyBuildError, "No module found for toolchain", tc.prepare)
 
+    def test_mpi_cmd_for(self):
+        """Test mpi_cmd_for function."""
+        tmpdir, imkl_module_path, imkl_module_txt = self.setup_sandbox_for_intel_fftw()
+
+        tc = self.get_toolchain('ictce', version='4.1.13')
+        tc.prepare()
+
+        mpi_cmd_for_re = re.compile("^mpirun --file=.*/mpdboot -machinefile .*/nodes -np 4 test$")
+        self.assertTrue(mpi_cmd_for_re.match(tc.mpi_cmd_for('test', 4)))
+
+        # cleanup
+        shutil.rmtree(tmpdir)
+        open(imkl_module_path, 'w').write(imkl_module_txt)
+
     def tearDown(self):
         """Cleanup."""
         # purge any loaded modules before restoring $MODULEPATH

From c7fc821b11f6aecb370075f59470d6305faf61a4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 27 Jan 2015 10:28:01 +0100
Subject: [PATCH 0463/1356] reinstate DEPRECATED_PARAMETERS, add unit tests for
 checking deprecated/replaced easyconfig parameters

---
 easybuild/framework/easyconfig/easyconfig.py | 19 ++++--
 test/framework/easyconfig.py                 | 65 ++++++++++++++++++--
 test/framework/utilities.py                  |  2 +
 3 files changed, 78 insertions(+), 8 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index b366821fbf..a3db2cb3ae 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -72,6 +72,11 @@
 # set of configure/build/install options that can be provided as lists for an iterated build
 ITERATE_OPTIONS = ['preconfigopts', 'configopts', 'prebuildopts', 'buildopts', 'preinstallopts', 'installopts']
 
+# deprecated easyconfig parameters, and their replacements
+DEPRECATED_PARAMETERS = {
+    # <old_param>: (<new_param>, <deprecation_version>),
+}
+
 # replaced easyconfig parameters, and their replacements
 REPLACED_PARAMETERS = {
     'license': 'software_license',
@@ -83,10 +88,15 @@
 _easyconfigs_cache = {}
 
 
-def check_replaced_easyconfig_parameter(ec_method):
-    """Decorator to check for replaced easyconfig parameters."""
+def handle_deprecated_or_replaced_easyconfig_parameters(ec_method):
+    """Decorator to handle deprecated/replaced easyconfig parameters."""
     def new_ec_method(self, key, *args, **kwargs):
         """Check whether any replace easyconfig parameters are still used"""
+        # map deprecated parameters to their replacements, issue deprecation warning(/error)
+        if key in DEPRECATED_PARAMETERS:
+            depr_key = key
+            key, ver = DEPRECATED_PARAMETERS[depr_key]
+            _log.deprecated("Easyconfig parameter '%s' is deprecated, use '%s' instead." % (depr_key, key), ver)
         if key in REPLACED_PARAMETERS:
             _log.nosupport("Easyconfig parameter '%s' is replaced by '%s'" % (key, REPLACED_PARAMETERS[key]), '2.0')
         return ec_method(self, key, *args, **kwargs)
@@ -619,7 +629,7 @@ def _generate_template_values(self, ignore=None, skip_lower=True):
             if v is None:
                 del self.template_values[k]
 
-    @check_replaced_easyconfig_parameter
+    @handle_deprecated_or_replaced_easyconfig_parameters
     def __getitem__(self, key):
         """
         will return the value without the help text
@@ -632,7 +642,7 @@ def __getitem__(self, key):
         else:
             return value
 
-    @check_replaced_easyconfig_parameter
+    @handle_deprecated_or_replaced_easyconfig_parameters
     def __setitem__(self, key, value):
         """
         sets the value of key in config.
@@ -640,6 +650,7 @@ def __setitem__(self, key, value):
         """
         self._config[key][0] = value
 
+    @handle_deprecated_or_replaced_easyconfig_parameters
     def get(self, key, default=None):
         """
         Gets the value of a key in the config, with 'default' as fallback.
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index e67b43983d..7306f81f22 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -29,11 +29,12 @@
 @author: Kenneth Hoste (Ghent University)
 @author: Stijn De Weirdt (Ghent University)
 """
-
+import copy
 import os
 import re
 import shutil
 import tempfile
+from distutils.version import LooseVersion
 from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader, main
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
@@ -69,8 +70,6 @@ def setUp(self):
         if os.path.exists(self.eb_file):
             os.remove(self.eb_file)
 
-        self.orig_current_version = easybuild.tools.build_log.CURRENT_VERSION
-
     def prep(self):
         """Prepare for test."""
         # (re)cleanup last test file
@@ -83,7 +82,6 @@ def prep(self):
 
     def tearDown(self):
         """ make sure to remove the temporary file """
-        easybuild.tools.build_log.CURRENT_VERSION = self.orig_current_version
         super(EasyConfigTest, self).tearDown()
         if os.path.exists(self.eb_file):
             os.remove(self.eb_file)
@@ -943,6 +941,65 @@ def test_filter_deps(self):
         opts = init_config(args=['--filter-deps=zlib,ncurses'])
         self.assertEqual(opts.filter_deps, ['zlib', 'ncurses'])
 
+    def test_replaced_easyconfig_parameters(self):
+        """Test handling of replaced easyconfig parameters."""
+        test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
+        ec = EasyConfig(os.path.join(test_ecs_dir, 'toy-0.0.eb'))
+        replaced_parameters = {
+            'license': 'software_license',
+            'makeopts': 'buildopts',
+            'premakeopts': 'prebuildopts',
+        }
+        for key in replaced_parameters:
+            error_regex = "NO LONGER SUPPORTED.*'%s'" % replaced_parameters[key]
+            self.assertErrorRegex(EasyBuildError, error_regex, ec.get, key)
+            self.assertErrorRegex(EasyBuildError, error_regex, lambda k: ec[k], key)
+            def foo(key):
+                ec[key] = 'foo'
+            self.assertErrorRegex(EasyBuildError, error_regex, foo, key)
+
+    def test_deprecated_easyconfig_parameters(self):
+        """Test handling of replaced easyconfig parameters."""
+        os.environ.pop('EASYBUILD_DEPRECATED')
+        easybuild.tools.build_log.CURRENT_VERSION = self.orig_current_version
+        init_config()
+
+        test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
+        ec = EasyConfig(os.path.join(test_ecs_dir, 'toy-0.0.eb'))
+
+        orig_deprecated_parameters = copy.deepcopy(easyconfig.easyconfig.DEPRECATED_PARAMETERS)
+        easyconfig.easyconfig.DEPRECATED_PARAMETERS.update({
+            'foobar': ('barfoo', '0.0'),  # deprecated since forever
+            'foobarbarfoo': ('barfoofoobar', '1000000000'),  # won't be actually deprecated for a while
+        })
+
+        # copy classes before reloading, so we can restore them (other isinstance checks fail)
+        orig_EasyConfig = copy.deepcopy(easyconfig.easyconfig.EasyConfig)
+        orig_ActiveMNS = copy.deepcopy(easyconfig.easyconfig.ActiveMNS)
+        reload(easyconfig.easyconfig)
+
+        for key, (newkey, depr_ver) in easyconfig.easyconfig.DEPRECATED_PARAMETERS.items():
+            if LooseVersion(depr_ver) <= easybuild.tools.build_log.CURRENT_VERSION:
+                # deprecation error
+                error_regex = "DEPRECATED.*since v%s.*'%s' is deprecated.*use '%s' instead" % (depr_ver, key, newkey)
+                self.assertErrorRegex(EasyBuildError, error_regex, ec.get, key)
+                self.assertErrorRegex(EasyBuildError, error_regex, lambda k: ec[k], key)
+                def foo(key):
+                    ec[key] = 'foo'
+                self.assertErrorRegex(EasyBuildError, error_regex, foo, key)
+            else:
+                # only deprecation warning, but key is replaced when getting/setting
+                ec[key] = 'test123'
+                self.assertEqual(ec[newkey], 'test123')
+                self.assertEqual(ec[key], 'test123')
+                ec[newkey] = '123test'
+                self.assertEqual(ec[newkey], '123test')
+                self.assertEqual(ec[key], '123test')
+
+        easyconfig.easyconfig.DEPRECATED_PARAMETERS = orig_deprecated_parameters
+        reload(easyconfig.easyconfig)
+        easyconfig.easyconfig.EasyConfig = orig_EasyConfig
+        easyconfig.easyconfig.ActiveMNS = orig_ActiveMNS
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 628e0c9181..f2b26c85e4 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -38,6 +38,7 @@
 from vsc.utils import fancylogger
 from vsc.utils.patterns import Singleton
 
+import easybuild.tools.build_log as eb_build_log
 import easybuild.tools.options as eboptions
 import easybuild.tools.toolchain.utilities as tc_utils
 import easybuild.tools.module_naming_scheme.toolchain as mns_toolchain
@@ -108,6 +109,7 @@ def setUp(self):
 
         # make sure no deprecated behaviour is being triggered (unless intended by the test)
         # trip *all* log.deprecated statements by setting deprecation version ridiculously high
+        self.orig_current_version = eb_build_log.CURRENT_VERSION
         os.environ['EASYBUILD_DEPRECATED'] = '10000000'
 
         init_config()

From af1c03731d04c25f17e0e894e033b2ec323f2910 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 27 Jan 2015 10:48:54 +0100
Subject: [PATCH 0464/1356] fix remaining remarks

---
 easybuild/tools/build_log.py |  2 +-
 easybuild/tools/config.py    | 12 +++++-------
 test/framework/easyconfig.py | 10 +++++-----
 3 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index 27ee40708e..1472e00e5e 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -103,7 +103,7 @@ def deprecated(self, msg, max_ver):
 
     def nosupport(self, msg, ver):
         """Print error message for no longer supported behaviour, and raise an EasyBuildError."""
-        self.error("NO LONGER SUPPORTED: %s; see %s for more information" % (msg, DEPRECATED_DOC_URL))
+        self.error("NO LONGER SUPPORTED since v%s: %s; see %s for more information" % (ver, msg, DEPRECATED_DOC_URL))
 
     def error(self, msg, *args, **kwargs):
         """Print error message and raise an EasyBuildError."""
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 9fd02948fd..cc3b83ea8d 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -173,8 +173,8 @@ class ConfigurationVariables(FrozenDictKnownKeys):
     # singleton metaclass: only one instance is created
     __metaclass__ = Singleton
 
-    # list of know/required keys
-    KNOWN_KEYS = [
+    # list of known/required keys
+    REQUIRED = [
         'config',
         'prefix',
         'buildpath',
@@ -190,8 +190,9 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'modules_tool',
         'module_naming_scheme',
     ]
+    KNOWN_KEYS = REQUIRED  # KNOWN_KEYS must be defined for FrozenDictKnownKeys functionality
 
-    def get_items_check_required(self, no_missing=True):
+    def get_items_check_required(self):
         """
         For all known/required keys, check if exists and return all key/value pairs.
             no_missing: boolean, when True, will throw error message for missing values
@@ -199,10 +200,7 @@ def get_items_check_required(self, no_missing=True):
         missing = [x for x in self.KNOWN_KEYS if not x in self]
         if len(missing) > 0:
             msg = 'Cannot determine value for configuration variables %s. Please specify it.' % missing
-            if no_missing:
-                self.log.error(msg)
-            else:
-                self.log.debug(msg)
+            self.log.error(msg)
 
         return self.items()
 
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 7306f81f22..6643269fc7 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -946,12 +946,12 @@ def test_replaced_easyconfig_parameters(self):
         test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
         ec = EasyConfig(os.path.join(test_ecs_dir, 'toy-0.0.eb'))
         replaced_parameters = {
-            'license': 'software_license',
-            'makeopts': 'buildopts',
-            'premakeopts': 'prebuildopts',
+            'license': ('software_license', '2.0'),
+            'makeopts': ('buildopts', '2.0'),
+            'premakeopts': ('prebuildopts', '2.0'),
         }
-        for key in replaced_parameters:
-            error_regex = "NO LONGER SUPPORTED.*'%s'" % replaced_parameters[key]
+        for key, (newkey, ver) in replaced_parameters.items():
+            error_regex = "NO LONGER SUPPORTED since v%s.*'%s' is replaced by '%s'" % (ver, key, newkey)
             self.assertErrorRegex(EasyBuildError, error_regex, ec.get, key)
             self.assertErrorRegex(EasyBuildError, error_regex, lambda k: ec[k], key)
             def foo(key):

From e99f414d0415934207ec90ea10c36b78846d0371 Mon Sep 17 00:00:00 2001
From: Martin Marcher <martin.marcher.ext@boehringer-ingelheim.com>
Date: Tue, 27 Jan 2015 16:25:39 +0100
Subject: [PATCH 0465/1356] Add proxy support for downloading

This add support for downloading with proxies as often found in
corporate settings.

Pythons urllib2 will do "the right thing" when common environment
variables such as `http_proxy` or `https_proxy` are set.

Most noteably this also removes the `reporthook` nested function and
removes a lot of code from the `download_file` function.
---
 easybuild/tools/filetools.py | 86 +++++++++---------------------------
 1 file changed, 22 insertions(+), 64 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 1eb26b6aa8..f671469fba 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -40,6 +40,7 @@
 import stat
 import time
 import urllib
+import urllib2
 import zlib
 from vsc.utils import fancylogger
 from vsc.utils.missing import all, any
@@ -260,75 +261,30 @@ def download_file(filename, url, path):
     basedir = os.path.dirname(path)
     mkdir(basedir, parents=True)
 
-    # internal function to report on download progress
-    def report(blocks_read, blocksize, filesize):
-        """
-        Report hook for urlretrieve, which logs the download progress every 10 seconds with log level info.
-        @param blocks_read: number of blocks already read
-        @param blocksize: size of one block, in bytes
-        @param filesize: total size of the download (in number of blocks blocks)
-        """
-        if download_file.last_time + 10 < time.time():
-            newblocks = blocks_read - download_file.last_block
-            download_file.last_block = blocks_read
-            tot_time = time.time() - download_file.last_time
-
-            if filesize <= 0:
-                # content length isn't always set
-                report_msg = "downloaded in %ss" % tot_time
-            else:
-                percent = blocks_read * blocksize * 100 // filesize
-                report_msg = "of %d kb downloaded in %ss [%d %%]" % (filesize / 1024.0, tot_time, percent)
-
-            downloaded_kbs = (blocks_read * blocksize) / 1024.0
-            kbps = (blocksize * newblocks) / 1024  // tot_time
-            _log.info("Download report: %d kb %s (%d kbps)", downloaded_kbs, report_msg, kbps)
-
-            download_file.last_time = time.time()
-
     # try downloading, three times max.
     downloaded = False
     attempt_cnt = 0
     while not downloaded and attempt_cnt < 3:
-        # get HTTP response code first before downloading file
-        response_code = None
-        try:
-            urlfile = urllib.urlopen(url)
-            if hasattr(urlfile, 'getcode'):  # no getcode() in Py2.4 yet
-                response_code = urlfile.getcode()
-            urlfile.close()
-        except IOError, err:
-            _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)
-
-        if response_code is not None:
-            _log.debug('HTTP response code for given url: %d', response_code)
-            # check for a 4xx response code which indicates a non-existing URL
-            if response_code // 100 == 4:
-                _log.warning('url %s was not found (HTTP response %d), not trying again', url, response_code)
-                return None
-
-        # use this functions's scope for variables we share with inner function used as report hook for urlretrieve
-        download_file.last_time = time.time()
-        download_file.last_block = 0
-
-        httpmsg = None
-        try:
-            (_, httpmsg) = urllib.urlretrieve(url, path, reporthook=report)
-            _log.info("Downloaded file %s from url %s to %s", filename, url, path)
-
-            if httpmsg.type == "text/html" and not filename.endswith('.html'):
-                _log.warning("HTML file downloaded to %s, so assuming invalid download, retrying.", path)
-                remove_file(path)
-            else:
-                # successful download
+        with open(path, "wb+") as dest_fd:
+            try:
+                src_fd = urllib2.urlopen(url)
+                _log.debug('HTTP response code for given url: %d', src_fd.getcode())
+                dest_fd.write(src_fd.read())
+                _log.info("Downloaded file %s from url %s to %s", filename, url, path)
                 downloaded = True
-        except IOError, err:
-            _log.warning("Error when downloading from %s to %s (%s), removing it and retrying", url, path, err)
-            remove_file(path)
-
-        if not downloaded:
-            attempt_cnt += 1
-            _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
+                src_fd.close()
+            except (urllib2.HTTPError, ) as err:
+                    if err.code == 404:
+                        attempt_cnt += 1
+                        _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
+                        continue
+                    raise
+            except (IOError, ) as err:
+                if attempt_cnt <= 3:
+                    _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)
+                    attempt_cnt += 1
+                    continue
+                raise
 
     if downloaded:
         _log.info("Successful download of file %s from url %s to path %s", filename, url, path)
@@ -1078,3 +1034,5 @@ def det_size(path):
         _log.warn("Could not determine install size: %s" % err)
 
     return installsize
+
+# vim: set ts=4 sts=4 fenc=utf-8 expandtab list:

From 03d2b6eaa3bd0cad25e4b11c6abe35878674236f Mon Sep 17 00:00:00 2001
From: Martin Marcher <martin.marcher.ext@boehringer-ingelheim.com>
Date: Tue, 27 Jan 2015 17:43:43 +0100
Subject: [PATCH 0466/1356] Fix condition where a local file with protocol may
 come in

---
 easybuild/tools/filetools.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index f671469fba..f654e474d4 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -273,12 +273,16 @@ def download_file(filename, url, path):
                 _log.info("Downloaded file %s from url %s to %s", filename, url, path)
                 downloaded = True
                 src_fd.close()
+            except (ValueError, ) as err:
+                attempt_cnt += 1
+                shutil.copy(url, path)
+                downloaded = True
             except (urllib2.HTTPError, ) as err:
-                    if err.code == 404:
-                        attempt_cnt += 1
-                        _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
-                        continue
-                    raise
+                if err.code == 404:
+                    attempt_cnt += 1
+                    _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
+                    continue
+                raise
             except (IOError, ) as err:
                 if attempt_cnt <= 3:
                     _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)

From 5b7ac00fe211d59f0d8271e9a58a22573dd8a9f4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 28 Jan 2015 14:20:56 +0100
Subject: [PATCH 0467/1356] add support for --fix-broken-easyconfigs, move and
 revamp fetch_parameters_from_easyconfig

---
 easybuild/framework/easyblock.py             | 30 ++++---
 easybuild/framework/easyconfig/easyconfig.py | 92 +++++++++++---------
 easybuild/framework/easyconfig/parser.py     | 66 ++++++++++++++
 easybuild/tools/config.py                    |  1 +
 easybuild/tools/options.py                   |  2 +
 5 files changed, 138 insertions(+), 53 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3269660935..953c76e28e 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -52,8 +52,8 @@
 from easybuild.tools import config, filetools
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.easyconfig import ITERATE_OPTIONS, EasyConfig, ActiveMNS
-from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, get_module_path, resolve_template
+from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP
 from easybuild.tools.build_details import get_build_stats
@@ -1824,15 +1824,17 @@ def run_all_steps(self, run_test_cases):
         return True
 
 
-def build_and_install_one(module, orig_environ):
+def build_and_install_one(ecdict, orig_environ):
     """
     Build the software
-    @param module: dictionary contaning parsed easyconfig + metadata
+    @param ecdict: dictionary contaning parsed easyconfig + metadata
     @param orig_environ: original environment (used to reset environment)
     """
     silent = build_option('silent')
 
-    spec = module['spec']
+    spec = ecdict['spec']
+    rawtxt = ecdict['ec'].rawtxt
+    name = ecdict['ec']['name']
 
     print_msg("processing EasyBuild easyconfig %s" % spec, log=_log, silent=silent)
 
@@ -1846,12 +1848,11 @@ def build_and_install_one(module, orig_environ):
     # load easyblock
     easyblock = build_option('easyblock')
     if not easyblock:
-        easyblock = fetch_parameter_from_easyconfig_file(spec, 'easyblock')
+        easyblock = fetch_parameters_from_easyconfig(rawtxt, ['easyblock'])[0]
 
-    name = module['ec']['name']
     try:
         app_class = get_easyblock_class(easyblock, name=name)
-        app = app_class(module['ec'])
+        app = app_class(ecdict['ec'])
         _log.info("Obtained application instance of for %s (easyblock: %s)" % (name, easyblock))
     except EasyBuildError, err:
         tup = (name, easyblock, err.msg)
@@ -1908,9 +1909,9 @@ def build_and_install_one(module, orig_environ):
                 # upload spec to central repository
                 currentbuildstats = app.cfg['buildstats']
                 repo = init_repository(get_repository(), get_repositorypath())
-                if 'original_spec' in module:
+                if 'original_spec' in ecdict:
                     block = det_full_ec_version(app.cfg) + ".block"
-                    repo.add_easyconfig(module['original_spec'], app.name, block, buildstats, currentbuildstats)
+                    repo.add_easyconfig(ecdict['original_spec'], app.name, block, buildstats, currentbuildstats)
                 repo.add_easyconfig(spec, app.name, det_full_ec_version(app.cfg), buildstats, currentbuildstats)
                 repo.commit("Built %s" % app.full_mod_name)
                 del repo
@@ -1971,22 +1972,23 @@ def build_and_install_one(module, orig_environ):
     return (success, application_log, errormsg)
 
 
-def get_easyblock_instance(easyconfig):
+def get_easyblock_instance(ecdict):
     """
     Get an instance for this easyconfig
     @param easyconfig: parsed easyconfig (EasyConfig instance)
 
     returns an instance of EasyBlock (or subclass thereof)
     """
-    spec = easyconfig['spec']
-    name = easyconfig['ec']['name']
+    spec = ecdict['spec']
+    rawtxt = ecdict['ec'].rawtxt
+    name = ecdict['ec']['name']
 
     # handle easyconfigs with custom easyblocks
     # determine easyblock specification from easyconfig file, if any
-    easyblock = fetch_parameter_from_easyconfig_file(spec, 'easyblock')
+    easyblock = fetch_parameters_from_easyconfig(rawtxt, ['easyblock'])[0]
 
     app_class = get_easyblock_class(easyblock, name=name)
-    return app_class(easyconfig['ec'])
+    return app_class(ecdict['ec'])
 
 
 def build_easyconfigs(easyconfigs, output_dir, test_results):
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index a3db2cb3ae..a6562b44c2 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -39,6 +39,7 @@
 import difflib
 import os
 import re
+import tempfile
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_class_for, nub
 from vsc.utils.patterns import Singleton
@@ -46,7 +47,7 @@
 import easybuild.tools.environment as env
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_module_naming_scheme
-from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file
+from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file, write_file
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
 from easybuild.tools.module_naming_scheme.utilities import det_hidden_modname, is_valid_module_name
@@ -56,11 +57,12 @@
 from easybuild.tools.toolchain.utilities import get_toolchain
 from easybuild.tools.utilities import remove_unwanted_chars
 from easybuild.framework.easyconfig import MANDATORY
-from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, get_easyconfig_parameter_default
+from easybuild.framework.easyconfig.default import DEFAULT_CONFIG
 from easybuild.framework.easyconfig.format.convert import Dependency
 from easybuild.framework.easyconfig.format.one import retrieve_blocks_in_spec
 from easybuild.framework.easyconfig.licenses import EASYCONFIG_LICENSES_DICT, License
-from easybuild.framework.easyconfig.parser import EasyConfigParser
+from easybuild.framework.easyconfig.parser import DEPRECATED_PARAMETERS, REPLACED_PARAMETERS
+from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig, fix_broken_easyconfig
 from easybuild.framework.easyconfig.templates import template_constant_dict
 
 
@@ -72,18 +74,6 @@
 # set of configure/build/install options that can be provided as lists for an iterated build
 ITERATE_OPTIONS = ['preconfigopts', 'configopts', 'prebuildopts', 'buildopts', 'preinstallopts', 'installopts']
 
-# deprecated easyconfig parameters, and their replacements
-DEPRECATED_PARAMETERS = {
-    # <old_param>: (<new_param>, <deprecation_version>),
-}
-
-# replaced easyconfig parameters, and their replacements
-REPLACED_PARAMETERS = {
-    'license': 'software_license',
-    'makeopts': 'buildopts',
-    'premakeopts': 'prebuildopts',
-}
-
 _easyconfig_files_cache = {}
 _easyconfigs_cache = {}
 
@@ -109,7 +99,7 @@ class EasyConfig(object):
     Class which handles loading, reading, validation of easyconfigs
     """
 
-    def __init__(self, path, extra_options=None, build_specs=None, validate=True, hidden=None):
+    def __init__(self, path, extra_options=None, build_specs=None, validate=True, hidden=None, rawtxt=None):
         """
         initialize an easyconfig.
         @param path: path to easyconfig file to be parsed
@@ -123,9 +113,18 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
 
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
-        if not os.path.isfile(path):
+        if path is not None and not os.path.isfile(path):
             self.log.error("EasyConfig __init__ expected a valid path")
 
+        # read easyconfig file contents (or use provided rawtxt), so it can be passed down to avoid multiple re-reads
+        self.path = path
+        if rawtxt is None:
+            self.rawtxt = read_file(path)
+            self.log.info("Raw contents from supplied easyconfig file %s: %s" % (path, self.rawtxt))
+        else:
+            self.rawtxt = rawtxt
+            self.log.info("Supplied easyconfig: %s" % self.rawtxt)
+
         # use legacy module classes as default
         self.valid_module_classes = build_option('valid_module_classes')
         if self.valid_module_classes is not None:
@@ -133,11 +132,29 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
 
         self._config = copy.deepcopy(DEFAULT_CONFIG)
 
+        # obtain name and easyblock specifications from raw easyconfig contents
+        name, easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['name', 'easyblock'])
+
+        # try and fix potentially broken easyconfig, if requested
+        if build_option('fix_broken_easyconfigs'):
+            derived_easyblock_class = get_easyblock_class(easyblock, name=name, default_fallback=False)
+            fixed_rawtxt = fix_broken_easyconfig(self.rawtxt, derived_easyblock_class)
+            if self.rawtxt != fixed_rawtxt:
+                self.rawtxt = fixed_rawtxt
+                self.path = os.path.join(tempfile.gettempdir(), os.path.basename(self.path))
+                write_file(self.path, self.rawtxt)
+                self.log.info("Replacing broken supplied easyconfig with fixed copy %s" % self.path)
+                self.log.info("Contents of fixed easyconfig file: %s" % self.rawtxt)
+
+                # redetermine easyblock from easyconfig, since it may have changed
+                easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['easyblock'])[0]
+            else:
+                self.log.debug("Nothing broken detected in supplied easyconfig %s, so nothing fixed" % self.path)
+
+        # determine line of extra easyconfig parameters
         if extra_options is None:
-            name = fetch_parameter_from_easyconfig_file(path, 'name')
-            easyblock = fetch_parameter_from_easyconfig_file(path, 'easyblock')
-            app_class = get_easyblock_class(easyblock, name=name)
-            self.extra_options = app_class.extra_options()
+            easyblock_class = get_easyblock_class(easyblock, name=name)
+            self.extra_options = easyblock_class.extra_options()
         else:
             self.extra_options = extra_options
 
@@ -147,8 +164,6 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
 
         self._config.update(self.extra_options)
 
-        self.path = path
-
         self.mandatory = MANDATORY_PARAMS[:]
 
         # extend mandatory keys
@@ -196,7 +211,7 @@ def copy(self):
         Return a copy of this EasyConfig instance.
         """
         # create a new EasyConfig instance
-        ec = EasyConfig(self.path, validate=self.validation, hidden=self.hidden)
+        ec = EasyConfig(None, validate=self.validation, hidden=self.hidden, rawtxt=self.rawtxt)
         # take a copy of the actual config dictionary (which already contains the extra options)
         ec._config = copy.deepcopy(self._config)
 
@@ -228,16 +243,17 @@ def parse(self):
             self.log.error("Specifications should be specified using a dictionary, got %s" % type(self.build_specs))
         self.log.debug("Obtained specs dict %s" % arg_specs)
 
+        self.log.info("Parsing easyconfig file %s" % self.path)
         parser = EasyConfigParser(self.path)
         parser.set_specifications(arg_specs)
         local_vars = parser.get_config_dict()
         self.log.debug("Parsed easyconfig as a dictionary: %s" % local_vars)
 
-        # validate mandatory keys
-        # TODO: remove this code. this is now (also) checked in the format (see validate_pyheader)
-        missing_keys = [key for key in self.mandatory if key not in local_vars]
-        if missing_keys:
-            self.log.error("mandatory variables %s not provided in %s" % (missing_keys, self.path))
+        # make sure all mandatory parameters are defined
+        # this includes both generic mandatory parameters, as software-specific parameters defined via extra_options
+        missing_mandatory_keys = [key for key in self.mandatory if key not in local_vars]
+        if missing_mandatory_keys:
+            self.log.error("mandatory parameters not provided in %s: %s" % (self.path, missing_mandatory_keys))
 
         # provide suggestions for typos
         possible_typos = [(key, difflib.get_close_matches(key.lower(), self._config.keys(), 1, 0.85))
@@ -682,16 +698,14 @@ def det_installversion(version, toolchain_name, toolchain_version, prefix, suffi
 
 
 def fetch_parameter_from_easyconfig_file(path, param):
-    """Fetch parameter specification from given easyconfig file."""
-    # check whether easyblock is specified in easyconfig file
-    # note: we can't rely on value for 'easyblock' in parsed easyconfig, it may be the default value
-    reg = re.compile(r"^\s*%s\s*=\s*(?P<param>\S.*?)\s*$" % param, re.M)
-    txt = read_file(path)
-    res = reg.search(txt)
-    if res:
-        return res.group('param').strip("'\"")
-    else:
-        return None
+    """
+    Fetch parameter specification from given easyconfig file.
+    DEPRECATED: use fetch_parameters_from_easyconfig from easybuild.framework.easyconfigs.parser instead
+    """
+    old = 'fetch_parameter_from_easyconfig_file'
+    new = 'fetch_parameters_from_easyconfig'
+    _log.deprecated("%s is replaced by %s from easybuild.framework.easyconfig.parser" % (old, new), '3.0')
+    return fetch_parameters_from_easyconfig(read_file(path), [param])[0]
 
 
 def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_failed_import=True):
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index f3ab56996b..215b65f7aa 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -30,6 +30,7 @@
 @author: Stijn De Weirdt (Ghent University)
 """
 import os
+import re
 from vsc.utils import fancylogger
 
 from easybuild.framework.easyconfig.format.format import FORMAT_DEFAULT_VERSION
@@ -37,9 +38,74 @@
 from easybuild.tools.filetools import read_file, write_file
 
 
+# deprecated easyconfig parameters, and their replacements
+DEPRECATED_PARAMETERS = {
+    # <old_param>: (<new_param>, <deprecation_version>),
+}
+
+# replaced easyconfig parameters, and their replacements
+REPLACED_PARAMETERS = {
+    'license': 'license_file',
+    'makeopts': 'buildopts',
+    'premakeopts': 'prebuildopts',
+}
+
+
 _log = fancylogger.getLogger('easyconfig.parser', fname=False)
 
 
+def fetch_parameters_from_easyconfig(rawtxt, params):
+    """
+    Fetch (initial) parameter definition from the given easyconfig file contents.
+    @param rawtxt: contents of the easyconfig file
+    @param params: list of parameter names to fetch values for
+    """
+    param_values = []
+    for param in params:
+        regex = re.compile(r"^\s*%s\s*=\s*(?P<param>\S.*?)\s*$" % param, re.M)
+        res = regex.search(rawtxt)
+        if res:
+            param_values.append(res.group('param').strip("'\""))
+        else:
+            param_values.append(None)
+    _log.debug("Obtained parameters value for %s: %s" % (params, param_values))
+    return param_values
+
+
+def fix_broken_easyconfig(ectxt, easyblock_class):
+    """
+    Fix easyconfig file at specified location, that may be broken due to non-backwards-compatible changes.
+    @param ectxt: raw contents of easyconfig to fix
+    @param easyblock_class: easyblock class, as derived from software name/specified easyblock
+    """
+    _log.debug("Raw contents of potentially broken easyconfig file to fix: %s" % ectxt)
+
+    subs = {
+        # replace former 'magic' variable shared_lib_ext with SHLIB_EXT constant
+        'shared_lib_ext': 'SHLIB_EXT',
+        'name': 'name',
+    }
+    # include replaced easyconfig parameters
+    subs.update(REPLACED_PARAMETERS)
+
+    # check whether any substitions need to be made
+    for old, new in subs.items():
+        regex = re.compile(r'(\W)%s(\W)' % old)
+        if regex.search(ectxt):
+            tup = (regex.pattern, old, new)
+            _log.info("Broken stuff detected using regex pattern '%s', replacing '%s' with '%s'" % tup)
+            ectxt = regex.sub(r'\1%s\2' % new, ectxt)
+
+    # check whether missing "easyblock = 'ConfigureMake'" needs to be inserted
+    if easyblock_class is None:
+        # prepend "easyblock = 'ConfigureMake'" to line containing "name =..."
+        easyblock_spec = "easyblock = 'ConfigureMake'"
+        _log.info("Inserting \"%s\", since no easyblock class was derived from easyconfig parameters" % easyblock_spec)
+        ectxt = re.sub(r'(\s*)(name\s*=)', r"\1%s\n\n\2" % easyblock_spec, ectxt, re.M)
+
+    return ectxt
+
+
 class EasyConfigParser(object):
     """Read the easyconfig file, return a parsed config object
         Can contain references to multiple version and toolchain/toolchain versions
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index cc3b83ea8d..354a31eb53 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -102,6 +102,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'allow_modules_tool_mismatch',
         'debug',
         'experimental',
+        'fix_broken_easyconfigs',
         'force',
         'hidden',
         'robot',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 6d3c4393af..0bc82ea653 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -183,6 +183,8 @@ def override_options(self):
                           None, 'store', None, 'e', {'metavar': 'CLASS'}),
             'experimental': ("Allow experimental code (with behaviour that can be changed or removed at any given time).",
                              None, 'store_true', False),
+            'fix-broken-easyconfigs': ("Fix easyconfig files that were broken due to non-backwards-compatible changes",
+                                       None, 'store_true', False),
             'group': ("Group to be used for software installations (only verified, not set)", None, 'store', None),
             'hidden': ("Install 'hidden' module file(s) by prefixing their name with '.'", None, 'store_true', False),
             'ignore-osdeps': ("Ignore any listed OS dependencies", None, 'store_true', False),

From d4bd2ab3475da9ca1b5188ff8ab4a7fdf47f56e7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 28 Jan 2015 14:21:13 +0100
Subject: [PATCH 0468/1356] style fixes in format/pyheaderconfigobj.py

---
 .../easyconfig/format/pyheaderconfigobj.py    | 23 ++++++++++---------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index 7728792947..f76266f7c5 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -226,26 +226,27 @@ def pyheader_env(self):
     def _validate_pyheader(self):
         """
         Basic validation of pyheader localvars.
-        This takes variable names from the PYHEADER_BLACKLIST and PYHEADER_MANDATORY;
-        blacklisted variables are not allowed, mandatory variables are
-        mandatory unless blacklisted
+        This takes parameter names from the PYHEADER_BLACKLIST and PYHEADER_MANDATORY;
+        blacklisted vparameter are not allowed, mandatory vparameter are mandatory unless blacklisted
         """
         if self.pyheader_localvars is None:
             self.log.error("self.pyheader_localvars must be initialized")
         if self.PYHEADER_BLACKLIST is None or self.PYHEADER_MANDATORY is None:
             self.log.error('Both PYHEADER_BLACKLIST and PYHEADER_MANDATORY must be set')
 
-        for variable in self.PYHEADER_BLACKLIST:
-            if variable in self.pyheader_localvars:
+        for param in self.PYHEADER_BLACKLIST:
+            if param in self.pyheader_localvars:
                 # TODO add to easyconfig unittest (similar to mandatory)
-                self.log.error('blacklisted variable %s not allowed in pyheader' % variable)
+                self.log.error('blacklisted param %s not allowed in pyheader' % param)
 
-        for variable in self.PYHEADER_MANDATORY:
-            if variable in self.PYHEADER_BLACKLIST:
+        missing = []
+        for param in self.PYHEADER_MANDATORY:
+            if param in self.PYHEADER_BLACKLIST:
                 continue
-            if not variable in self.pyheader_localvars:
-                # message format in sync with easyconfig mandatory unittest!
-                self.log.error('mandatory variable %s not provided in pyheader' % variable)
+            if not param in self.pyheader_localvars:
+                missing.append(param)
+        if missing:
+            self.log.error('mandatory parameters not provided in pyheader: %s' % ', '.join(missing))
 
     def parse_section_block(self, section):
         """Parse the section block by trying to convert it into a ConfigObj instance"""

From 06bb291dfb39ce5f16a565fe9669bdb600c4404e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 28 Jan 2015 14:21:57 +0100
Subject: [PATCH 0469/1356] add tests for fix_broken_easyconfig, fix tests
 w.r.t. style fixes and move function

---
 test/framework/easyconfig.py | 80 ++++++++++++++++++++++++++++--------
 1 file changed, 63 insertions(+), 17 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 0baa757515..61b741007c 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -45,6 +45,7 @@
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.framework.easyconfig.easyconfig import create_paths, det_installversion
 from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file, get_easyblock_class
+from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig, fix_broken_easyconfig
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak_one
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import module_classes
@@ -94,14 +95,14 @@ def test_empty(self):
         self.assertErrorRegex(EasyBuildError, "expected a valid path", EasyConfig, "")
 
     def test_mandatory(self):
-        """ make sure all checking of mandatory variables works """
+        """ make sure all checking of mandatory parameters works """
         self.contents = '\n'.join([
             'easyblock = "ConfigureMake"',
             'name = "pi"',
             'version = "3.14"',
         ])
         self.prep()
-        self.assertErrorRegex(EasyBuildError, "mandatory variables? .* not provided", EasyConfig, self.eb_file)
+        self.assertErrorRegex(EasyBuildError, "mandatory parameters not provided", EasyConfig, self.eb_file)
 
         self.contents += '\n' + '\n'.join([
             'homepage = "http://example.com"',
@@ -119,7 +120,7 @@ def test_mandatory(self):
         self.assertEqual(eb['description'], "test easyconfig")
 
     def test_validation(self):
-        """ test other validations beside mandatory variables """
+        """ test other validations beside mandatory parameters """
         self.contents = '\n'.join([
             'easyblock = "ConfigureMake"',
             'name = "pi"',
@@ -250,10 +251,10 @@ def test_extra_options(self):
         # test if extra toolchain options are being passed
         self.assertEqual(eb.toolchain.options['static'], True)
 
-        # test extra mandatory vars
+        # test extra mandatory parameters
         extra_vars.update({'mandatory_key': ['default', 'another mandatory key', easyconfig.MANDATORY]})
-        self.assertErrorRegex(EasyBuildError, r"mandatory variables? \S* not provided",
-                              EasyConfig, self.eb_file, extra_vars)
+        self.assertErrorRegex(EasyBuildError, r"mandatory parameters not provided",
+                              EasyConfig, self.eb_file, extra_options=extra_vars)
 
         self.contents += '\nmandatory_key = "value"'
         self.prep()
@@ -849,8 +850,8 @@ def test_format_equivalence_basic(self):
         # restore
         easybuild.tools.build_log.EXPERIMENTAL = orig_experimental
 
-    def test_fetch_parameter_from_easyconfig_file(self):
-        """Test fetch_easyblock_from_easyconfig_file function."""
+    def test_fetch_parameters_from_easyconfig(self):
+        """Test fetch_parameters_from_easyconfig function."""
         test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
         toy_ec_file = os.path.join(test_ecs_dir, 'toy-0.0.eb')
 
@@ -858,11 +859,15 @@ def test_fetch_parameter_from_easyconfig_file(self):
             (toy_ec_file, 'toy', None),
             (os.path.join(test_ecs_dir, 'goolf-1.4.10.eb'), 'goolf', 'Toolchain'),
         ]:
-            name = fetch_parameter_from_easyconfig_file(ec_file, 'name')
+            name, easyblock = fetch_parameters_from_easyconfig(read_file(ec_file), ['name', 'easyblock'])
             self.assertEqual(name, correct_name)
-            easyblock = fetch_parameter_from_easyconfig_file(ec_file, 'easyblock')
             self.assertEqual(easyblock, correct_easyblock)
 
+        self.assertEqual(fetch_parameters_from_easyconfig(read_file(toy_ec_file), ['description'])[0], "Toy C program.")
+
+        # also check deprecated function fetch_parameter_from_easyconfig_file
+        os.environ['EASYBUILD_DEPRECATED'] = '2.0'
+        init_config()
         self.assertEqual(fetch_parameter_from_easyconfig_file(toy_ec_file, 'description'), "Toy C program.")
 
     def test_get_easyblock_class(self):
@@ -946,7 +951,7 @@ def test_replaced_easyconfig_parameters(self):
         test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
         ec = EasyConfig(os.path.join(test_ecs_dir, 'toy-0.0.eb'))
         replaced_parameters = {
-            'license': ('software_license', '2.0'),
+            'license': ('license_file', '2.0'),
             'makeopts': ('buildopts', '2.0'),
             'premakeopts': ('prebuildopts', '2.0'),
         }
@@ -967,8 +972,8 @@ def test_deprecated_easyconfig_parameters(self):
         test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
         ec = EasyConfig(os.path.join(test_ecs_dir, 'toy-0.0.eb'))
 
-        orig_deprecated_parameters = copy.deepcopy(easyconfig.easyconfig.DEPRECATED_PARAMETERS)
-        easyconfig.easyconfig.DEPRECATED_PARAMETERS.update({
+        orig_deprecated_parameters = copy.deepcopy(easyconfig.parser.DEPRECATED_PARAMETERS)
+        easyconfig.parser.DEPRECATED_PARAMETERS.update({
             'foobar': ('barfoo', '0.0'),  # deprecated since forever
             'foobarbarfoo': ('barfoofoobar', '1000000000'),  # won't be actually deprecated for a while
         })
@@ -976,9 +981,9 @@ def test_deprecated_easyconfig_parameters(self):
         # copy classes before reloading, so we can restore them (other isinstance checks fail)
         orig_EasyConfig = copy.deepcopy(easyconfig.easyconfig.EasyConfig)
         orig_ActiveMNS = copy.deepcopy(easyconfig.easyconfig.ActiveMNS)
-        reload(easyconfig.easyconfig)
+        reload(easyconfig.parser)
 
-        for key, (newkey, depr_ver) in easyconfig.easyconfig.DEPRECATED_PARAMETERS.items():
+        for key, (newkey, depr_ver) in easyconfig.parser.DEPRECATED_PARAMETERS.items():
             if LooseVersion(depr_ver) <= easybuild.tools.build_log.CURRENT_VERSION:
                 # deprecation error
                 error_regex = "DEPRECATED.*since v%s.*'%s' is deprecated.*use '%s' instead" % (depr_ver, key, newkey)
@@ -996,11 +1001,52 @@ def foo(key):
                 self.assertEqual(ec[newkey], '123test')
                 self.assertEqual(ec[key], '123test')
 
-        easyconfig.easyconfig.DEPRECATED_PARAMETERS = orig_deprecated_parameters
-        reload(easyconfig.easyconfig)
+        easyconfig.parser.DEPRECATED_PARAMETERS = orig_deprecated_parameters
+        reload(easyconfig.parser)
         easyconfig.easyconfig.EasyConfig = orig_EasyConfig
         easyconfig.easyconfig.ActiveMNS = orig_ActiveMNS
 
+    def test_fix_broken_easyconfig(self):
+        """Test fix_broken_easyconfig function."""
+        # local import, since test easyblocks need to be made available first by setUp
+        from easybuild.easyblocks.toy import EB_toy
+
+        broken_ec_txt = '\n'.join([
+            "# licenseheader",
+            "name = 'foo'",
+            "version = '1.2.3'",
+            '',
+            "description = 'foo'",
+            "homepage = 'http://example.com'",
+            '',
+            "toolchain = {'name': 'bar', 'version': '3.2.1'}",
+            '',
+            "premakeopts = 'FOO=libfoo.%s' % shared_lib_ext",
+            "makeopts = 'CC=gcc'",
+            '',
+            "license = 'foo.lic'",
+        ])
+        fixed_ec_txt = '\n'.join([
+            "# licenseheader",
+            "name = 'foo'",
+            "version = '1.2.3'",
+            '',
+            "description = 'foo'",
+            "homepage = 'http://example.com'",
+            '',
+            "toolchain = {'name': 'bar', 'version': '3.2.1'}",
+            '',
+            "prebuildopts = 'FOO=libfoo.%s' % SHLIB_EXT",
+            "buildopts = 'CC=gcc'",
+            '',
+            "license_file = 'foo.lic'",
+        ])
+        self.assertEqual(fix_broken_easyconfig(broken_ec_txt, EB_toy), fixed_ec_txt)
+
+        lines = fixed_ec_txt.split('\n')
+        fixed_ec_txt = '\n'.join([lines[0], "easyblock = 'ConfigureMake'", ''] + lines[1:])
+        self.assertEqual(fix_broken_easyconfig(broken_ec_txt, None), fixed_ec_txt)
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(EasyConfigTest)

From 8564b175db8acc3e2ef49dff3c09dfd357da7b68 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 28 Jan 2015 14:26:33 +0100
Subject: [PATCH 0470/1356] avoid tweak unit tests generating an easyconfig
 file in the current working dir

---
 test/framework/tweak.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/framework/tweak.py b/test/framework/tweak.py
index 0395bd7d11..1cb3611c32 100644
--- a/test/framework/tweak.py
+++ b/test/framework/tweak.py
@@ -99,6 +99,7 @@ def test_obtain_ec_for(self):
         self.assertEqual(os.path.basename(ec_file), 'GCC-4.9.2.eb')
 
         # generate non-existing easyconfig
+        os.chdir(self.test_prefix)
         specs = {
             'name': 'GCC',
             'version': '5.4.3',

From 7aef650666e3e79b925c0f987f29aaa065cca197 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 28 Jan 2015 14:39:19 +0100
Subject: [PATCH 0471/1356] move code block to fix broken easyconfig in a
 dedicated method

---
 easybuild/framework/easyconfig/easyconfig.py | 38 +++++++++++---------
 1 file changed, 22 insertions(+), 16 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index a6562b44c2..cbdba0d582 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -133,27 +133,14 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         self._config = copy.deepcopy(DEFAULT_CONFIG)
 
         # obtain name and easyblock specifications from raw easyconfig contents
-        name, easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['name', 'easyblock'])
+        self.name, self.easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['name', 'easyblock'])
 
         # try and fix potentially broken easyconfig, if requested
-        if build_option('fix_broken_easyconfigs'):
-            derived_easyblock_class = get_easyblock_class(easyblock, name=name, default_fallback=False)
-            fixed_rawtxt = fix_broken_easyconfig(self.rawtxt, derived_easyblock_class)
-            if self.rawtxt != fixed_rawtxt:
-                self.rawtxt = fixed_rawtxt
-                self.path = os.path.join(tempfile.gettempdir(), os.path.basename(self.path))
-                write_file(self.path, self.rawtxt)
-                self.log.info("Replacing broken supplied easyconfig with fixed copy %s" % self.path)
-                self.log.info("Contents of fixed easyconfig file: %s" % self.rawtxt)
-
-                # redetermine easyblock from easyconfig, since it may have changed
-                easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['easyblock'])[0]
-            else:
-                self.log.debug("Nothing broken detected in supplied easyconfig %s, so nothing fixed" % self.path)
+        self.fix_broken()
 
         # determine line of extra easyconfig parameters
         if extra_options is None:
-            easyblock_class = get_easyblock_class(easyblock, name=name)
+            easyblock_class = get_easyblock_class(self.easyblock, name=self.name)
             self.extra_options = easyblock_class.extra_options()
         else:
             self.extra_options = extra_options
@@ -229,6 +216,25 @@ def update(self, key, value):
         else:
             self.log.error("Can't update configuration value for %s, because it's not a string or list." % key)
 
+    def fix_broken(self):
+        """
+        Try and fix this easyconfig's raw contents, if it's broken and fixing is requested.
+        """
+        if build_option('fix_broken_easyconfigs'):
+            derived_easyblock_class = get_easyblock_class(self.easyblock, name=self.name, default_fallback=False)
+            fixed_rawtxt = fix_broken_easyconfig(self.rawtxt, derived_easyblock_class)
+            if self.rawtxt != fixed_rawtxt:
+                self.rawtxt = fixed_rawtxt
+                self.path = os.path.join(tempfile.gettempdir(), os.path.basename(self.path))
+                write_file(self.path, self.rawtxt)
+                self.log.info("Replacing broken supplied easyconfig with fixed copy %s" % self.path)
+                self.log.info("Contents of fixed easyconfig file: %s" % self.rawtxt)
+
+                # redetermine easyblock from easyconfig, since it may have changed
+                self.easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['easyblock'])[0]
+            else:
+                self.log.debug("Nothing broken detected in supplied easyconfig %s, so nothing fixed" % self.path)
+
     def parse(self):
         """
         Parse the file and set options

From 3bbe13004fd8f247058dcea56f1178563dfae274 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 28 Jan 2015 14:56:09 +0100
Subject: [PATCH 0472/1356] replace self.name with self.software_name in
 EasyConfig class

---
 easybuild/framework/easyconfig/easyconfig.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index cbdba0d582..fc7a6688a1 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -133,14 +133,14 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         self._config = copy.deepcopy(DEFAULT_CONFIG)
 
         # obtain name and easyblock specifications from raw easyconfig contents
-        self.name, self.easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['name', 'easyblock'])
+        self.software_name, self.easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['name', 'easyblock'])
 
         # try and fix potentially broken easyconfig, if requested
         self.fix_broken()
 
         # determine line of extra easyconfig parameters
         if extra_options is None:
-            easyblock_class = get_easyblock_class(self.easyblock, name=self.name)
+            easyblock_class = get_easyblock_class(self.easyblock, name=self.software_name)
             self.extra_options = easyblock_class.extra_options()
         else:
             self.extra_options = extra_options
@@ -221,7 +221,7 @@ def fix_broken(self):
         Try and fix this easyconfig's raw contents, if it's broken and fixing is requested.
         """
         if build_option('fix_broken_easyconfigs'):
-            derived_easyblock_class = get_easyblock_class(self.easyblock, name=self.name, default_fallback=False)
+            derived_easyblock_class = get_easyblock_class(self.easyblock, name=self.software_name, default_fallback=False)
             fixed_rawtxt = fix_broken_easyconfig(self.rawtxt, derived_easyblock_class)
             if self.rawtxt != fixed_rawtxt:
                 self.rawtxt = fixed_rawtxt

From 6abf92fbf0aa6c5098134ef876a6a3ca4b1de59a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 28 Jan 2015 15:04:38 +0100
Subject: [PATCH 0473/1356] make sure fixed easyconfig file is copied to
 archive/install dir

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index fc7a6688a1..3792940f4f 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -925,7 +925,7 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False,
         if not parse_only:
             # also determine list of dependencies, module name (unless only parsed easyconfigs are requested)
             easyconfig.update({
-                'spec': spec,
+                'spec': ec.path,
                 'short_mod_name': ec.short_mod_name,
                 'full_mod_name': ec.full_mod_name,
                 'dependencies': [],

From fe8596ab639834c18a34b6783582433918eae7f6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 30 Jan 2015 09:27:59 +0100
Subject: [PATCH 0474/1356] don't overoptimize by not passing down self.copy in
 copy constructor of EasyConfig; it doesn't work

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 3792940f4f..a9145f7bc2 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -198,7 +198,7 @@ def copy(self):
         Return a copy of this EasyConfig instance.
         """
         # create a new EasyConfig instance
-        ec = EasyConfig(None, validate=self.validation, hidden=self.hidden, rawtxt=self.rawtxt)
+        ec = EasyConfig(self.path, validate=self.validation, hidden=self.hidden, rawtxt=self.rawtxt)
         # take a copy of the actual config dictionary (which already contains the extra options)
         ec._config = copy.deepcopy(self._config)
 

From 7af85e5bb31626323841eb16f309330b318656cf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Feb 2015 16:24:02 +0100
Subject: [PATCH 0475/1356] define __contains__ in EasyConfig class

---
 easybuild/framework/easyconfig/easyconfig.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index a3db2cb3ae..c03c2032f9 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -629,11 +629,14 @@ def _generate_template_values(self, ignore=None, skip_lower=True):
             if v is None:
                 del self.template_values[k]
 
+    @handle_deprecated_or_replaced_easyconfig_parameters
+    def __contains__(self, key):
+        """Check whether easyconfig parameter is defined"""
+        return key in self._config
+
     @handle_deprecated_or_replaced_easyconfig_parameters
     def __getitem__(self, key):
-        """
-        will return the value without the help text
-        """
+        """Return value of specified easyconfig parameter (without help text, etc.)"""
         value = self._config[key][0]
         if self.enable_templating:
             if self.template_values is None or len(self.template_values) == 0:
@@ -644,10 +647,7 @@ def __getitem__(self, key):
 
     @handle_deprecated_or_replaced_easyconfig_parameters
     def __setitem__(self, key, value):
-        """
-        sets the value of key in config.
-        help text is untouched
-        """
+        """Set value of specified easyconfig parameter (help text & co is left untouched)"""
         self._config[key][0] = value
 
     @handle_deprecated_or_replaced_easyconfig_parameters

From 6d627694037cbcabbb153112a17efb04376b2231 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Feb 2015 16:52:12 +0100
Subject: [PATCH 0476/1356] emit decent error message when unknown key is used
 in __getitem__/__setitem__ of EasyConfig class

---
 easybuild/framework/easyconfig/easyconfig.py | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index c03c2032f9..33325326a1 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -637,18 +637,26 @@ def __contains__(self, key):
     @handle_deprecated_or_replaced_easyconfig_parameters
     def __getitem__(self, key):
         """Return value of specified easyconfig parameter (without help text, etc.)"""
-        value = self._config[key][0]
+        value = None
+        if key in self._config:
+            value = self._config[key][0]
+        else:
+            self.log.error("Use of unknown easyconfig parameter '%s' when getting parameter value" % key)
+
         if self.enable_templating:
             if self.template_values is None or len(self.template_values) == 0:
                 self.generate_template_values()
-            return resolve_template(value, self.template_values)
-        else:
-            return value
+            value = resolve_template(value, self.template_values)
+
+        return value
 
     @handle_deprecated_or_replaced_easyconfig_parameters
     def __setitem__(self, key, value):
         """Set value of specified easyconfig parameter (help text & co is left untouched)"""
-        self._config[key][0] = value
+        if key in self._config:
+            self._config[key][0] = value
+        else:
+            self.log.error("Use of unknown easyconfig parameter '%s' when setting parameter value" % key)
 
     @handle_deprecated_or_replaced_easyconfig_parameters
     def get(self, key, default=None):

From 6092b24fa856b102dbc8b8e96b523bf55abc3b61 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Feb 2015 16:57:36 +0100
Subject: [PATCH 0477/1356] add unit test for behaviour concerning use of
 unknown easyconfig parameters

---
 test/framework/easyconfig.py | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 0baa757515..5f662ccbf2 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -227,7 +227,7 @@ def test_extra_options(self):
         ])
         self.prep()
         eb = EasyConfig(self.eb_file)
-        self.assertRaises(KeyError, lambda: eb['custom_key'])
+        self.assertErrorRegex(EasyBuildError, "unknown easyconfig parameter", lambda: eb['custom_key'])
 
         extra_vars = {'custom_key': ['default', "This is a default key", easyconfig.CUSTOM]}
 
@@ -1001,6 +1001,27 @@ def foo(key):
         easyconfig.easyconfig.EasyConfig = orig_EasyConfig
         easyconfig.easyconfig.ActiveMNS = orig_ActiveMNS
 
+    def test_unknown_easyconfig_parameter(self):
+        """Check behaviour when unknown easyconfig parameters are used."""
+        self.contents = '\n'.join([
+            'easyblock = "ConfigureMake"',
+            'name = "pi"',
+            'version = "3.14"',
+            'homepage = "http://example.com"',
+            'description = "test easyconfig"',
+            'toolchain = {"name": "dummy", "version": "dummy"}',
+        ])
+        self.prep()
+        ec = EasyConfig(self.eb_file)
+        self.assertFalse('therenosucheasyconfigparameterlikethis' in ec)
+        error_regex = "unknown easyconfig parameter"
+        self.assertErrorRegex(EasyBuildError, error_regex, lambda k: ec[k], 'therenosucheasyconfigparameterlikethis')
+        def set_ec_key(key):
+            """Dummy function to set easyconfig parameter in 'ec' EasyConfig instance"""
+            ec[key] = 'foobar'
+        self.assertErrorRegex(EasyBuildError, error_regex, set_ec_key, 'therenosucheasyconfigparameterlikethis')
+
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(EasyConfigTest)

From a477a7ec89e42c2d9ac7439a0ee46e4faebc0f87 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Feb 2015 21:07:40 +0100
Subject: [PATCH 0478/1356] fix remarks

---
 easybuild/framework/easyconfig/easyconfig.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 33325326a1..9db79d881d 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -241,7 +241,7 @@ def parse(self):
 
         # provide suggestions for typos
         possible_typos = [(key, difflib.get_close_matches(key.lower(), self._config.keys(), 1, 0.85))
-                          for key in local_vars if key not in self._config]
+                          for key in local_vars if key not in self]
 
         typos = [(key, guesses[0]) for (key, guesses) in possible_typos if len(guesses) == 1]
         if typos:
@@ -656,15 +656,16 @@ def __setitem__(self, key, value):
         if key in self._config:
             self._config[key][0] = value
         else:
-            self.log.error("Use of unknown easyconfig parameter '%s' when setting parameter value" % key)
+            tup = (key, value)
+            self.log.error("Use of unknown easyconfig parameter '%s' when setting parameter value to '%s'" % tup)
 
     @handle_deprecated_or_replaced_easyconfig_parameters
     def get(self, key, default=None):
         """
         Gets the value of a key in the config, with 'default' as fallback.
         """
-        if key in self._config:
-            return self.__getitem__(key)
+        if key in self:
+            return self[key]
         else:
             return default
 

From 2d4116320c9f7fd2943d04efc1c1262dc423d507 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Feb 2015 21:07:47 +0100
Subject: [PATCH 0479/1356] fix broken test

---
 test/framework/module_generator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 8e606c3ed1..67db3f17e0 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -259,7 +259,7 @@ def test_mns():
         init_config(build_options=build_options)
 
         err_pattern = 'nosucheasyconfigparameteravailable'
-        self.assertErrorRegex(KeyError, err_pattern, EasyConfig, os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
+        self.assertErrorRegex(EasyBuildError, err_pattern, EasyConfig, os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
 
         # test simple custom module naming scheme
         os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'TestModuleNamingScheme'

From 328c091300e4dd4265ca5c68bdbc35432bba6fe1 Mon Sep 17 00:00:00 2001
From: Martin Marcher <martin.marcher.ext@boehringer-ingelheim.com>
Date: Tue, 27 Jan 2015 16:25:39 +0100
Subject: [PATCH 0480/1356] Add proxy support for downloading

This add support for downloading with proxies as often found in
corporate settings.

Pythons urllib2 will do "the right thing" when common environment
variables such as `http_proxy` or `https_proxy` are set.

Most noteably this also removes the `reporthook` nested function and
removes a lot of code from the `download_file` function.
---
 easybuild/tools/filetools.py | 86 +++++++++---------------------------
 1 file changed, 22 insertions(+), 64 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index d524c0ca61..d83ff659b5 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -40,6 +40,7 @@
 import stat
 import time
 import urllib
+import urllib2
 import zlib
 from vsc.utils import fancylogger
 
@@ -259,75 +260,30 @@ def download_file(filename, url, path):
     basedir = os.path.dirname(path)
     mkdir(basedir, parents=True)
 
-    # internal function to report on download progress
-    def report(blocks_read, blocksize, filesize):
-        """
-        Report hook for urlretrieve, which logs the download progress every 10 seconds with log level info.
-        @param blocks_read: number of blocks already read
-        @param blocksize: size of one block, in bytes
-        @param filesize: total size of the download (in number of blocks blocks)
-        """
-        if download_file.last_time + 10 < time.time():
-            newblocks = blocks_read - download_file.last_block
-            download_file.last_block = blocks_read
-            tot_time = time.time() - download_file.last_time
-
-            if filesize <= 0:
-                # content length isn't always set
-                report_msg = "downloaded in %ss" % tot_time
-            else:
-                percent = blocks_read * blocksize * 100 // filesize
-                report_msg = "of %d kb downloaded in %ss [%d %%]" % (filesize / 1024.0, tot_time, percent)
-
-            downloaded_kbs = (blocks_read * blocksize) / 1024.0
-            kbps = (blocksize * newblocks) / 1024  // tot_time
-            _log.info("Download report: %d kb %s (%d kbps)", downloaded_kbs, report_msg, kbps)
-
-            download_file.last_time = time.time()
-
     # try downloading, three times max.
     downloaded = False
     attempt_cnt = 0
     while not downloaded and attempt_cnt < 3:
-        # get HTTP response code first before downloading file
-        response_code = None
-        try:
-            urlfile = urllib.urlopen(url)
-            if hasattr(urlfile, 'getcode'):  # no getcode() in Py2.4 yet
-                response_code = urlfile.getcode()
-            urlfile.close()
-        except IOError, err:
-            _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)
-
-        if response_code is not None:
-            _log.debug('HTTP response code for given url: %d', response_code)
-            # check for a 4xx response code which indicates a non-existing URL
-            if response_code // 100 == 4:
-                _log.warning('url %s was not found (HTTP response %d), not trying again', url, response_code)
-                return None
-
-        # use this functions's scope for variables we share with inner function used as report hook for urlretrieve
-        download_file.last_time = time.time()
-        download_file.last_block = 0
-
-        httpmsg = None
-        try:
-            (_, httpmsg) = urllib.urlretrieve(url, path, reporthook=report)
-            _log.info("Downloaded file %s from url %s to %s", filename, url, path)
-
-            if httpmsg.type == "text/html" and not filename.endswith('.html'):
-                _log.warning("HTML file downloaded to %s, so assuming invalid download, retrying.", path)
-                remove_file(path)
-            else:
-                # successful download
+        with open(path, "wb+") as dest_fd:
+            try:
+                src_fd = urllib2.urlopen(url)
+                _log.debug('HTTP response code for given url: %d', src_fd.getcode())
+                dest_fd.write(src_fd.read())
+                _log.info("Downloaded file %s from url %s to %s", filename, url, path)
                 downloaded = True
-        except IOError, err:
-            _log.warning("Error when downloading from %s to %s (%s), removing it and retrying", url, path, err)
-            remove_file(path)
-
-        if not downloaded:
-            attempt_cnt += 1
-            _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
+                src_fd.close()
+            except (urllib2.HTTPError, ) as err:
+                    if err.code == 404:
+                        attempt_cnt += 1
+                        _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
+                        continue
+                    raise
+            except (IOError, ) as err:
+                if attempt_cnt <= 3:
+                    _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)
+                    attempt_cnt += 1
+                    continue
+                raise
 
     if downloaded:
         _log.info("Successful download of file %s from url %s to path %s", filename, url, path)
@@ -1069,3 +1025,5 @@ def det_size(path):
         _log.warn("Could not determine install size: %s" % err)
 
     return installsize
+
+# vim: set ts=4 sts=4 fenc=utf-8 expandtab list:

From 43d1ee47fa5ba9e6f1b88711a653790db7d4e224 Mon Sep 17 00:00:00 2001
From: Martin Marcher <martin.marcher.ext@boehringer-ingelheim.com>
Date: Tue, 27 Jan 2015 17:43:43 +0100
Subject: [PATCH 0481/1356] Fix condition where a local file with protocol may
 come in

---
 easybuild/tools/filetools.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index d83ff659b5..2180e7c7e0 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -272,12 +272,16 @@ def download_file(filename, url, path):
                 _log.info("Downloaded file %s from url %s to %s", filename, url, path)
                 downloaded = True
                 src_fd.close()
+            except (ValueError, ) as err:
+                attempt_cnt += 1
+                shutil.copy(url, path)
+                downloaded = True
             except (urllib2.HTTPError, ) as err:
-                    if err.code == 404:
-                        attempt_cnt += 1
-                        _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
-                        continue
-                    raise
+                if err.code == 404:
+                    attempt_cnt += 1
+                    _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
+                    continue
+                raise
             except (IOError, ) as err:
                 if attempt_cnt <= 3:
                     _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)

From 91132fc5ee9fd1ee14beba94e65dcca1dd5539da Mon Sep 17 00:00:00 2001
From: Martin Marcher <martin.marcher.ext@boehringer-ingelheim.com>
Date: Thu, 5 Feb 2015 12:03:49 +0100
Subject: [PATCH 0482/1356] Fix code style

---
 easybuild/tools/filetools.py | 46 ++++++++++++++++--------------------
 1 file changed, 21 insertions(+), 25 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 2180e7c7e0..1ee07da23a 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -39,8 +39,7 @@
 import shutil
 import stat
 import time
-import urllib
-import urllib2
+import urllib2 # does the right thing for http proxy setups
 import zlib
 from vsc.utils import fancylogger
 
@@ -264,29 +263,28 @@ def download_file(filename, url, path):
     downloaded = False
     attempt_cnt = 0
     while not downloaded and attempt_cnt < 3:
-        with open(path, "wb+") as dest_fd:
-            try:
-                src_fd = urllib2.urlopen(url)
-                _log.debug('HTTP response code for given url: %d', src_fd.getcode())
-                dest_fd.write(src_fd.read())
-                _log.info("Downloaded file %s from url %s to %s", filename, url, path)
-                downloaded = True
-                src_fd.close()
-            except (ValueError, ) as err:
+        try:
+            src_fd = urllib2.urlopen(url)
+            _log.debug('HTTP response code for given url: %d', src_fd.getcode())
+            write_file(path, src_fd.read())
+            _log.info("Downloaded file %s from url %s to %s", filename, url, path)
+            downloaded = True
+            src_fd.close()
+        except (ValueError, ) as err:
+            attempt_cnt += 1
+            shutil.copy(url, path)
+            downloaded = True
+        except (urllib2.HTTPError, ) as err:
+            if 400 <= err.code <= 499:
                 attempt_cnt += 1
-                shutil.copy(url, path)
-                downloaded = True
-            except (urllib2.HTTPError, ) as err:
-                if err.code == 404:
-                    attempt_cnt += 1
-                    _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
-                    continue
+                _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
+            else:
                 raise
-            except (IOError, ) as err:
-                if attempt_cnt <= 3:
-                    _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)
-                    attempt_cnt += 1
-                    continue
+        except (IOError, ) as err:
+            if attempt_cnt <= 3:
+                _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)
+                attempt_cnt += 1
+            else:
                 raise
 
     if downloaded:
@@ -1029,5 +1027,3 @@ def det_size(path):
         _log.warn("Could not determine install size: %s" % err)
 
     return installsize
-
-# vim: set ts=4 sts=4 fenc=utf-8 expandtab list:

From e5705b92f908eb40378bcf7ff23eeaa5a61d28fc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 5 Feb 2015 20:59:46 +0100
Subject: [PATCH 0483/1356] correctly determine variable name for EBEXTLIST

---
 easybuild/framework/easyblock.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3269660935..92cce5e43d 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -881,7 +881,8 @@ def make_module_extra_extensions(self):
         # set environment variable that specifies list of extensions
         if self.exts_all:
             exts_list = ','.join(['%s-%s' % (ext['name'], ext.get('version', '')) for ext in self.exts_all])
-            txt += self.module_generator.set_environment('EBEXTSLIST%s' % self.name.upper(), exts_list)
+            env_var_name = convert_name(self.name, upper=True)
+            txt += self.module_generator.set_environment('EBEXTSLIST%s' % env_var_name, exts_list)
 
         return txt
 

From 5465be09090f359b2cc01d7dc54221eb74ecb6a6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 09:12:10 +0100
Subject: [PATCH 0484/1356] enhance unit test for download_file function to
 make sure it takes proxies into account

---
 test/framework/filetools.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index cff024f9de..6c94e81a5d 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -33,7 +33,8 @@
 import shutil
 import stat
 import tempfile
-from test.framework.utilities import EnhancedTestCase, find_full_path
+import urllib2
+from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
 
 import easybuild.tools.filetools as ft
@@ -181,11 +182,25 @@ def test_download_file(self):
         test_dir = os.path.abspath(os.path.dirname(__file__))
         source_url = 'file://%s/sandbox/sources/toy/%s' % (test_dir, fn)
         res = ft.download_file(fn, source_url, target_location)
-        self.assertEqual(res, target_location)
+        self.assertEqual(res, target_location, "'download' of local file works")
 
         # non-existing files result in None return value
         self.assertEqual(ft.download_file(fn, 'file://%s/nosuchfile' % test_dir, target_location), None)
 
+        # install broken proxy handler for opening local files
+        # this should make urllib2.urlopen use this broken proxy for downloading from a file:// URL
+        proxy_handler = urllib2.ProxyHandler({'file': 'file://%s/nosuchfile' % test_dir})
+        urllib2.install_opener(urllib2.build_opener(proxy_handler))
+
+        # downloading over a broken proxy results in None return value (failed download)
+        # this tests whether proxies are taken into account by download_file
+        self.assertEqual(ft.download_file(fn, source_url, target_location), None, "download over broken proxy fails")
+
+        # restore a working file handler, and retest download of local file
+        urllib2.install_opener(urllib2.build_opener(urllib2.FileHandler()))
+        res = ft.download_file(fn, source_url, target_location)
+        self.assertEqual(res, target_location, "'download' of local file works after removing broken proxy")
+
     def test_mkdir(self):
         """Test mkdir function."""
         tmpdir = tempfile.mkdtemp()

From e9284f2c6cc7844773166857f0520cbb42ec94ab Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 15:09:36 +0100
Subject: [PATCH 0485/1356] do not ignore exit code of failing postinstall
 commands

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3269660935..db832d4ca2 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1460,7 +1460,7 @@ def post_install_step(self):
             for cmd in self.cfg['postinstallcmds']:
                 if not isinstance(cmd, basestring):
                     self.log.error("Invalid element in 'postinstallcmds', not a string: %s" % cmd)
-                run_cmd(cmd, simple=True, log_ok=False, log_all=False)
+                run_cmd(cmd, simple=True, log_ok=True, log_all=True)
 
         if self.group is not None:
             # remove permissions for others, and set group ID

From 61a24fe54ba2ebe0c9507bd64e6287ef2722f36b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 18:36:36 +0100
Subject: [PATCH 0486/1356] specify default timeout for initiating download,
 provide configure option for specifying different timeout

---
 easybuild/tools/config.py    | 1 +
 easybuild/tools/filetools.py | 9 ++++++++-
 easybuild/tools/options.py   | 1 +
 3 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index cc3b83ea8d..60af87d556 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -80,6 +80,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
 BUILD_OPTIONS_CMDLINE = {
     None: [
         'aggregate_regtest',
+        'download_timeout',
         'dump_test_report',
         'easyblock',
         'filter_deps',
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 1ee07da23a..2505a762e4 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -255,6 +255,13 @@ def download_file(filename, url, path):
 
     _log.debug("Trying to download %s from %s to %s", filename, url, path)
 
+    timeout = build_option('download_timeout')
+    if timeout is None:
+        # default to 10sec timeout if none was specified
+        # default system timeout (used is nothing is specified) may be infinite (?)
+        timeout = 10
+    _log.debug("Using timeout of %s seconds for initiating download" % timeout)
+
     # make sure directory exists
     basedir = os.path.dirname(path)
     mkdir(basedir, parents=True)
@@ -264,7 +271,7 @@ def download_file(filename, url, path):
     attempt_cnt = 0
     while not downloaded and attempt_cnt < 3:
         try:
-            src_fd = urllib2.urlopen(url)
+            src_fd = urllib2.urlopen(url, timeout=timeout)
             _log.debug('HTTP response code for given url: %d', src_fd.getcode())
             write_file(path, src_fd.read())
             _log.info("Downloaded file %s from url %s to %s", filename, url, path)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 6d3c4393af..80fd4db664 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -179,6 +179,7 @@ def override_options(self):
             'cleanup-builddir': ("Cleanup build dir after successful installation.", None, 'store_true', True),
             'deprecated': ("Run pretending to be (future) version, to test removal of deprecated code.",
                            None, 'store', None),
+            'download_timeout': ("Timeout for initiating downloads (in seconds)", None, 'store', None),
             'easyblock': ("easyblock to use for processing the spec file or dumping the options",
                           None, 'store', None, 'e', {'metavar': 'CLASS'}),
             'experimental': ("Allow experimental code (with behaviour that can be changed or removed at any given time).",

From de609e07b0df11a42b2db7229c60c2d3b657e2bc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 20:18:26 +0100
Subject: [PATCH 0487/1356] rework download_file

---
 easybuild/tools/filetools.py | 43 +++++++++++++++++-------------------
 1 file changed, 20 insertions(+), 23 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 2505a762e4..f46d327698 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -39,7 +39,7 @@
 import shutil
 import stat
 import time
-import urllib2 # does the right thing for http proxy setups
+import urllib2  # does the right thing for http proxy setups, urllib does not!
 import zlib
 from vsc.utils import fancylogger
 
@@ -268,38 +268,35 @@ def download_file(filename, url, path):
 
     # try downloading, three times max.
     downloaded = False
+    max_attempts = 3
     attempt_cnt = 0
-    while not downloaded and attempt_cnt < 3:
+    while not downloaded and attempt_cnt < max_attempts:
         try:
-            src_fd = urllib2.urlopen(url, timeout=timeout)
-            _log.debug('HTTP response code for given url: %d', src_fd.getcode())
-            write_file(path, src_fd.read())
-            _log.info("Downloaded file %s from url %s to %s", filename, url, path)
+            url_fd = urllib2.urlopen(url, timeout=timeout)
+            _log.debug('response code for given url: %s' % url_fd.getcode())
+            write_file(path, url_fd.read())
+            _log.info("Downloaded file %s from url %s to %s" % (filename, url, path))
             downloaded = True
-            src_fd.close()
-        except (ValueError, ) as err:
-            attempt_cnt += 1
-            shutil.copy(url, path)
-            downloaded = True
-        except (urllib2.HTTPError, ) as err:
+            url_fd.close()
+        except urllib2.HTTPError as err:
             if 400 <= err.code <= 499:
-                attempt_cnt += 1
-                _log.warning("Downloading failed at attempt %s, retrying...", attempt_cnt)
+                _log.warning("URL %s was not found (HTTP response code %s), not trying again" % (url, err.code))
+                break
             else:
-                raise
-        except (IOError, ) as err:
-            if attempt_cnt <= 3:
-                _log.warning("Failed to get HTTP response code for %s, retrying: %s", url, err)
+                _log.warning("HTTPError occured while trying to download %s to %s: %s" % (url, path, err))
                 attempt_cnt += 1
-            else:
-                raise
+        except IOError as err:
+            _log.warning("IOError occurred while trying to download %s to %s: %s" % (url, path, err))
+            attempt_cnt += 1
+
+        if not downloaded and attempt_cnt < max_attempts:
+            _log.info("Attempt %d of downloading %s to %s failed, trying again..." % (attempt_cnt, url, path))
 
     if downloaded:
-        _log.info("Successful download of file %s from url %s to path %s", filename, url, path)
+        _log.info("Successful download of file %s from url %s to path %s" % (filename, url, path))
         return path
     else:
-        # failed to download after multiple attempts
-        _log.warning("Too many failed download attempts, giving up")
+        _log.warning("Download of %s to %s failed, done trying" % (url, path))
         return None
 
 

From c186ebbc9c2d3352e218fea2afc613559b6d9a97 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 20:18:57 +0100
Subject: [PATCH 0488/1356] move comment

---
 easybuild/tools/filetools.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index f46d327698..12e2fd93ec 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -39,7 +39,7 @@
 import shutil
 import stat
 import time
-import urllib2  # does the right thing for http proxy setups, urllib does not!
+import urllib2
 import zlib
 from vsc.utils import fancylogger
 
@@ -272,6 +272,7 @@ def download_file(filename, url, path):
     attempt_cnt = 0
     while not downloaded and attempt_cnt < max_attempts:
         try:
+            # urllib2 does the right thing for http proxy setups, urllib does not!
             url_fd = urllib2.urlopen(url, timeout=timeout)
             _log.debug('response code for given url: %s' % url_fd.getcode())
             write_file(path, url_fd.read())

From df2cdcdbe432391e5c00b27d6ebe35b32fda2dad Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 21:21:05 +0100
Subject: [PATCH 0489/1356] catch all exceptions that may occur in
 download_file for proper error reporting, fix broken unit tests

---
 easybuild/tools/filetools.py |  2 ++
 test/framework/easyblock.py  | 11 ++++-------
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 12e2fd93ec..ec2d7122a2 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -289,6 +289,8 @@ def download_file(filename, url, path):
         except IOError as err:
             _log.warning("IOError occurred while trying to download %s to %s: %s" % (url, path, err))
             attempt_cnt += 1
+        except Exception, err:
+            _log.error("Unexpected error occurred when trying to download %s to %s: %s" % (url, path, err))
 
         if not downloaded and attempt_cnt < max_attempts:
             _log.info("Attempt %d of downloading %s to %s failed, trying again..." % (attempt_cnt, url, path))
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index c2dcb01655..2657389906 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -451,7 +451,7 @@ def test_obtain_file(self):
         # 'downloading' a file to (first) sourcepath works
         init_config(args=["--sourcepath=%s:/no/such/dir:%s" % (tmpdir, testdir)])
         shutil.copy2(toy_tarball_path, tmpdir_subdir)
-        res = eb.obtain_file(toy_tarball, urls=[os.path.join('file://', tmpdir_subdir)])
+        res = eb.obtain_file(toy_tarball, urls=['file://%s' % tmpdir_subdir])
         self.assertEqual(res, os.path.join(tmpdir, 't', 'toy', toy_tarball))
 
         # finding a file in sourcepath works
@@ -460,16 +460,13 @@ def test_obtain_file(self):
         self.assertEqual(res, toy_tarball_path)
 
         # sourcepath has preference over downloading
-        res = eb.obtain_file(toy_tarball, urls=[os.path.join('file://', tmpdir_subdir)])
+        res = eb.obtain_file(toy_tarball, urls=['file://%s' % tmpdir_subdir])
         self.assertEqual(res, toy_tarball_path)
 
         # obtain_file yields error for non-existing files
         fn = 'thisisclearlyanonexistingfile'
-        try:
-            eb.obtain_file(fn, urls=[os.path.join('file://', tmpdir_subdir)])
-        except EasyBuildError, err:
-            fail_regex = re.compile("Couldn't find file %s anywhere, and downloading it didn't work either" % fn)
-            self.assertTrue(fail_regex.search(str(err)))
+        error_regex = "Couldn't find file %s anywhere, and downloading it didn't work either" % fn
+        self.assertErrorRegex(EasyBuildError, error_regex, eb.obtain_file, fn, urls=['file://%s' % tmpdir_subdir])
 
         # file specifications via URL also work, are downloaded to (first) sourcepath
         init_config(args=["--sourcepath=%s:/no/such/dir:%s" % (tmpdir, sandbox_sources)])

From a76af3bb986d94ed5e4acd6123bcd70cd47609fb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 21:25:15 +0100
Subject: [PATCH 0490/1356] fix rare case in which used easyconfig and copied
 easyconfig are the same

---
 easybuild/framework/easyblock.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3269660935..37f14a2cdf 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1934,7 +1934,9 @@ def build_and_install_one(module, orig_environ):
 
         try:
             newspec = os.path.join(new_log_dir, "%s-%s.eb" % (app.name, det_full_ec_version(app.cfg)))
-            shutil.copy(spec, newspec)
+            # only copy if the files are not the same actual file already
+            if not os.path.samefile(spec, newspec):
+                shutil.copy(spec, newspec)
             _log.debug("Copied easyconfig file %s to %s" % (spec, newspec))
         except (IOError, OSError), err:
             print_error("Failed to move easyconfig %s to log dir %s: %s" % (spec, new_log_dir, err))

From 85b622e4d4d2c27153bd26f05360d6aad63c33ec Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 21:46:24 +0100
Subject: [PATCH 0491/1356] better debug logging in download_file

---
 easybuild/tools/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index ec2d7122a2..8b81d71d1c 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -274,7 +274,7 @@ def download_file(filename, url, path):
         try:
             # urllib2 does the right thing for http proxy setups, urllib does not!
             url_fd = urllib2.urlopen(url, timeout=timeout)
-            _log.debug('response code for given url: %s' % url_fd.getcode())
+            _log.debug('response code for given url %s: %s' % (url, url_fd.getcode()))
             write_file(path, url_fd.read())
             _log.info("Downloaded file %s from url %s to %s" % (filename, url, path))
             downloaded = True

From 2ba93e74375cdb6b368ce9aac3cf6b1808f48e0a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 21:58:58 +0100
Subject: [PATCH 0492/1356] fix error message on copying easyconfig to install
 dir

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 65270998b5..8da192401c 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1940,7 +1940,7 @@ def build_and_install_one(module, orig_environ):
                 shutil.copy(spec, newspec)
             _log.debug("Copied easyconfig file %s to %s" % (spec, newspec))
         except (IOError, OSError), err:
-            print_error("Failed to move easyconfig %s to log dir %s: %s" % (spec, new_log_dir, err))
+            print_error("Failed to copy easyconfig %s to %s: %s" % (spec, newspec, err))
 
     # build failed
     else:

From 7247010347ca25e8bfda6df0722597a63ce41a28 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 22:27:59 +0100
Subject: [PATCH 0493/1356] make sure newspec exists before using
 os.path.samefile on it

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 8da192401c..28387f5cfb 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1936,7 +1936,7 @@ def build_and_install_one(module, orig_environ):
         try:
             newspec = os.path.join(new_log_dir, "%s-%s.eb" % (app.name, det_full_ec_version(app.cfg)))
             # only copy if the files are not the same actual file already
-            if not os.path.samefile(spec, newspec):
+            if not (os.path.exists(newspec) or os.path.samefile(spec, newspec)):
                 shutil.copy(spec, newspec)
             _log.debug("Copied easyconfig file %s to %s" % (spec, newspec))
         except (IOError, OSError), err:

From d331f1b6f424160f18f3d008db247e5044c1e9f6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 22:34:41 +0100
Subject: [PATCH 0494/1356] always issue debug log message for run_cmd exit
 code and output

---
 easybuild/tools/run.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index 9b42b159fe..ba13928464 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -376,18 +376,17 @@ def parse_cmd_output(cmd, stdouterr, ec, simple, log_all, log_ok, regexp):
     if not regexp:
         use_regexp = False
 
+    _log.debug('cmd "%s" exited with exitcode %s and output:\n%s' % (cmd, ec, stdouterr))
+
     if ec and (log_all or log_ok):
         # We don't want to error if the user doesn't care
         if check_ec:
             _log.error('cmd "%s" exited with exitcode %s and output:\n%s' % (cmd, ec, stdouterr))
         else:
             _log.warn('cmd "%s" exited with exitcode %s and output:\n%s' % (cmd, ec, stdouterr))
-
-    if not ec:
+    elif not ec:
         if log_all:
             _log.info('cmd "%s" exited with exitcode %s and output:\n%s' % (cmd, ec, stdouterr))
-        else:
-            _log.debug('cmd "%s" exited with exitcode %s and output:\n%s' % (cmd, ec, stdouterr))
 
     # parse the stdout/stderr for errors when strictness dictates this or when regexp is passed in
     if use_regexp or regexp:

From 30dc4853eb60338ffa5f71e31c53872a171afd27 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Feb 2015 22:39:04 +0100
Subject: [PATCH 0495/1356] fix exists/samefile logic in check whether or not
 to copy easyconfig file

---
 easybuild/framework/easyblock.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 28387f5cfb..2d72e5ef11 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1935,10 +1935,12 @@ def build_and_install_one(module, orig_environ):
 
         try:
             newspec = os.path.join(new_log_dir, "%s-%s.eb" % (app.name, det_full_ec_version(app.cfg)))
-            # only copy if the files are not the same actual file already
-            if not (os.path.exists(newspec) or os.path.samefile(spec, newspec)):
+            # only copy if the files are not the same file already (yes, it happens)
+            if os.path.exists(newspec) and os.path.samefile(spec, newspec):
+                _log.debug("Not copying easyconfig file %s to %s since files are identical" % (spec, newspec))
+            else:
                 shutil.copy(spec, newspec)
-            _log.debug("Copied easyconfig file %s to %s" % (spec, newspec))
+                _log.debug("Copied easyconfig file %s to %s" % (spec, newspec))
         except (IOError, OSError), err:
             print_error("Failed to copy easyconfig %s to %s: %s" % (spec, newspec, err))
 

From 57de298f617812a14012dbf629886d972069f7c4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Feb 2015 10:48:47 +0100
Subject: [PATCH 0496/1356] remove included (crippled) copy of vsc-base)

---
 vsc/README.md               |    3 -
 vsc/__init__.py             |   41 -
 vsc/install/__init__.py     |    0
 vsc/install/shared_setup.py |  273 -------
 vsc/utils/__init__.py       |   30 -
 vsc/utils/affinity.py       |  334 --------
 vsc/utils/asyncprocess.py   |  191 -----
 vsc/utils/daemon.py         |  144 ----
 vsc/utils/dateandtime.py    |  354 --------
 vsc/utils/fancylogger.py    |  702 ----------------
 vsc/utils/frozendict.py     |   56 --
 vsc/utils/generaloption.py  | 1532 -----------------------------------
 vsc/utils/mail.py           |  254 ------
 vsc/utils/missing.py        |  444 ----------
 vsc/utils/optcomplete.py    |  629 --------------
 vsc/utils/patterns.py       |   52 --
 vsc/utils/rest.py           |  288 -------
 vsc/utils/run.py            |  843 -------------------
 vsc/utils/testing.py        |  114 ---
 vsc/utils/wrapper.py        |   42 -
 20 files changed, 6326 deletions(-)
 delete mode 100644 vsc/README.md
 delete mode 100644 vsc/__init__.py
 delete mode 100644 vsc/install/__init__.py
 delete mode 100644 vsc/install/shared_setup.py
 delete mode 100644 vsc/utils/__init__.py
 delete mode 100644 vsc/utils/affinity.py
 delete mode 100644 vsc/utils/asyncprocess.py
 delete mode 100644 vsc/utils/daemon.py
 delete mode 100644 vsc/utils/dateandtime.py
 delete mode 100644 vsc/utils/fancylogger.py
 delete mode 100644 vsc/utils/frozendict.py
 delete mode 100644 vsc/utils/generaloption.py
 delete mode 100644 vsc/utils/mail.py
 delete mode 100644 vsc/utils/missing.py
 delete mode 100644 vsc/utils/optcomplete.py
 delete mode 100644 vsc/utils/patterns.py
 delete mode 100644 vsc/utils/rest.py
 delete mode 100644 vsc/utils/run.py
 delete mode 100644 vsc/utils/testing.py
 delete mode 100644 vsc/utils/wrapper.py

diff --git a/vsc/README.md b/vsc/README.md
deleted file mode 100644
index 165e0109fb..0000000000
--- a/vsc/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-Code from https://github.com/hpcugent/vsc-base
-
-based on eb47bee435e5e24666b398d8dd41f82a40214b7a (vsc-base v2.0.0)
diff --git a/vsc/__init__.py b/vsc/__init__.py
deleted file mode 100644
index d149b4df8e..0000000000
--- a/vsc/__init__.py
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/usr/bin/env python
-##
-# Copyright 2011-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-Initialize vsc package.
-The vsc namespace is used in different folders allong the system
-so explicitly declare this is also the vsc namespace
-
-@author: Jens Timmerman (Ghent University)
-"""
-#from pkgutil import extend_path
-
-# we're not the only ones in this namespace
-# avoid that EasyBuild uses vsc package from somewhere else, e.g. a system vsc-base installation
-#__path__ = extend_path(__path__, __name__)  #@ReservedAssignment
-
-# here for backwards compatibility
-from vsc.utils import fancylogger
diff --git a/vsc/install/__init__.py b/vsc/install/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/vsc/install/shared_setup.py b/vsc/install/shared_setup.py
deleted file mode 100644
index 761d80ce26..0000000000
--- a/vsc/install/shared_setup.py
+++ /dev/null
@@ -1,273 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: latin-1 -*-
-# #
-# Copyright 2009-2013 Ghent University
-#
-# This file is part of vsc-utils,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# All rights reserved.
-#
-# #
-"""
-Shared module for vsc-base setup
-
-@author: Stijn De Weirdt (Ghent University)
-@author: Andy Georges (Ghent University)
-"""
-import glob
-import os
-import shutil
-import sys
-from distutils import log  # also for setuptools
-from distutils.dir_util import remove_tree
-
-# 0 : WARN (default), 1 : INFO, 2 : DEBUG
-log.set_verbosity(2)
-
-has_setuptools = None
-
-
-# We do need all setup files to be included in the source dir if we ever want to install
-# the package elsewhere.
-EXTRA_SDIST_FILES = ['setup.py']
-
-
-def find_extra_sdist_files():
-    """Looks for files to append to the FileList that is used by the egg_info."""
-    print "looking for extra dist files"
-    filelist = []
-    for fn in EXTRA_SDIST_FILES:
-        if os.path.isfile(fn):
-            filelist.append(fn)
-        else:
-            print "sdist add_defaults Failed to find %s" % fn
-            print "exiting."
-            sys.exit(1)
-    return filelist
-
-
-def remove_extra_bdist_rpm_files():
-    """Provides a list of files that should be removed from the source file list when making an RPM.
-
-    This function should be overridden if necessary in the setup.py
-
-    @returns: empty list
-    """
-    return []
-
-# The following aims to import from setuptools, but if this is not available, we import the basic functionality from
-# distutils instead. Note that setuptools make copies of the scripts, it does _not_ preserve symbolic links.
-try:
-    # raise("no setuptools")  # to try distutils, uncomment
-    from setuptools import setup
-    from setuptools.command.bdist_rpm import bdist_rpm, _bdist_rpm
-    from setuptools.command.build_py import build_py
-    from setuptools.command.install_scripts import install_scripts
-    from setuptools.command.sdist import sdist
-
-    # egg_info uses sdist directly through manifest_maker
-    from setuptools.command.egg_info import egg_info
-
-    class vsc_egg_info(egg_info):
-        """Class to determine the set of files that should be included.
-
-        This amounts to including the default files, as determined by setuptools, extended with the
-        few extra files we need to add for installation purposes.
-        """
-
-        def find_sources(self):
-            """Default lookup."""
-            egg_info.find_sources(self)
-            self.filelist.extend(find_extra_sdist_files())
-
-    # TODO: this should be in the setup.py, here we should have a placeholder, so we need not change this for every
-    # package we deploy
-    class vsc_bdist_rpm_egg_info(vsc_egg_info):
-        """Class to determine the source files that should be present in an (S)RPM.
-
-        All __init__.py files that augment namespace packages should be installed by the
-        dependent package, so we need not install it here.
-        """
-
-        def find_sources(self):
-            """Fins the sources as default and then drop the cruft."""
-            vsc_egg_info.find_sources(self)
-            for f in remove_extra_bdist_rpm_files():
-                print "DEBUG: removing %s from source list" % (f)
-                self.filelist.files.remove(f)
-
-    has_setuptools = True
-except:
-    from distutils.core import setup
-    from distutils.command.install_scripts import install_scripts
-    from distutils.command.build_py import build_py
-    from distutils.command.sdist import sdist
-    from distutils.command.bdist_rpm import bdist_rpm, _bdist_rpm
-
-    class vsc_egg_info(object):
-        pass  # dummy class for distutils
-
-    class vsc_bdist_rpm_egg_info(vsc_egg_info):
-        pass  # dummy class for distutils
-
-    has_setuptools = False
-
-
-# available authors
-ag = ('Andy Georges', 'andy.georges@ugent.be')
-jt = ('Jens Timmermans', 'jens.timmermans@ugent.be')
-kh = ('Kenneth Hoste', 'kenneth.hoste@ugent.be')
-lm = ('Luis Fernando Munoz Meji?as', 'luis.munoz@ugent.be')
-sdw = ('Stijn De Weirdt', 'stijn.deweirdt@ugent.be')
-wdp = ('Wouter Depypere', 'wouter.depypere@ugent.be')
-kw = ('Kenneth Waegeman', 'Kenneth.Waegeman@UGent.be')
-
-# FIXME: do we need this here? it won;t hurt, but still ...
-class vsc_install_scripts(install_scripts):
-    """Create the (fake) links for mympirun also remove .sh and .py extensions from the scripts."""
-
-    def __init__(self, *args):
-        install_scripts.__init__(self, *args)
-        self.original_outfiles = None
-
-    def run(self):
-        # old-style class
-        install_scripts.run(self)
-
-        self.original_outfiles = self.get_outputs()[:]  # make a copy
-        self.outfiles = []  # reset it
-        for script in self.original_outfiles:
-            # remove suffixes for .py and .sh
-            if script.endswith(".py") or script.endswith(".sh"):
-                shutil.move(script, script[:-3])
-                script = script[:-3]
-            self.outfiles.append(script)
-
-
-class vsc_build_py(build_py):
-    def find_package_modules (self, package, package_dir):
-        """Extend build_by (not used for now)"""
-        result = build_py.find_package_modules(self, package, package_dir)
-        return result
-
-
-class vsc_bdist_rpm(bdist_rpm):
-    """ Custom class to build the RPM, since the __inti__.py cannot be included for the packages that have namespace spread across all of the machine."""
-    def run(self):
-        log.error("vsc_bdist_rpm = %s" % (self.__dict__))
-        SHARED_TARGET['cmdclass']['egg_info'] = vsc_bdist_rpm_egg_info  # changed to allow removal of files
-        self.run_command('egg_info')  # ensure distro name is up-to-date
-        _bdist_rpm.run(self)
-
-
-# shared target config
-SHARED_TARGET = {
-    'url': '',
-    'download_url': '',
-    'package_dir': {'': 'lib'},
-    'cmdclass': {
-        "install_scripts": vsc_install_scripts,
-        "egg_info": vsc_egg_info,
-        "bdist_rpm": vsc_bdist_rpm,
-    },
-}
-
-
-def cleanup(prefix=''):
-    """Remove all build cruft."""
-    dirs = [prefix + 'build'] + glob.glob(prefix + 'lib/*.egg-info')
-    for d in dirs:
-        if os.path.isdir(d):
-            log.warn("cleanup %s" % d)
-            try:
-                remove_tree(d, verbose=False)
-            except OSError, _:
-                log.error("cleanup failed for %s" % d)
-
-    for fn in ('setup.cfg',):
-        ffn = prefix + fn
-        if os.path.isfile(ffn):
-            os.remove(ffn)
-
-def sanitize(v):
-    """Transforms v into a sensible string for use in setup.cfg."""
-    if isinstance(v, str):
-        return v
-
-    if isinstance(v, list):
-        return ",".join(v)
-
-
-def parse_target(target):
-    """Add some fields"""
-    new_target = {}
-    new_target.update(SHARED_TARGET)
-    for k, v in target.items():
-        if k in ('author', 'maintainer'):
-            if not isinstance(v, list):
-                log.error("%s of config %s needs to be a list (not tuple or string)" % (k, target['name']))
-                sys.exit(1)
-            new_target[k] = ";".join([x[0] for x in v])
-            new_target["%s_email" % k] = ";".join([x[1] for x in v])
-        else:
-            if isinstance(v, dict):
-                # eg command_class
-                if not k in new_target:
-                    new_target[k] = type(v)()
-                new_target[k].update(v)
-            else:
-                new_target[k] = type(v)()
-                new_target[k] += v
-
-    log.debug("New target = %s" % (new_target))
-    return new_target
-
-
-def build_setup_cfg_for_bdist_rpm(target):
-    """Generates a setup.cfg on a per-target basis.
-
-    Stores the 'install-requires' in the [bdist_rpm] section
-
-    @type target: dict
-
-    @param target: specifies the options to be passed to setup()
-    """
-
-    try:
-        setup_cfg = open('setup.cfg', 'w')  # and truncate
-    except (IOError, OSError), err:
-        print "Cannot create setup.cfg for target %s: %s" % (target['name'], err)
-        sys.exit(1)
-
-    s = ["[bdist_rpm]"]
-    if 'install_requires' in target:
-        s += ["requires = %s" % (sanitize(target['install_requires']))]
-
-    if 'provides' in target:
-        s += ["provides = %s" % (sanitize((target['provides'])))]
-        target.pop('provides')
-
-    setup_cfg.write("\n".join(s) + "\n")
-    setup_cfg.close()
-
-
-def action_target(target, setupfn=setup, extra_sdist=[]):
-    # EXTRA_SDIST_FILES.extend(extra_sdist)
-
-    cleanup()
-
-    build_setup_cfg_for_bdist_rpm(target)
-    x = parse_target(target)
-
-    setupfn(**x)
-
-if __name__ == '__main__':
-    # print all supported packages
-    all_setups = [x[len('setup_'):-len('.py')] for x in glob.glob('setup_*.py')]
-    all_packages = ['-'.join(['vsc'] + x.split('_')) for x in all_setups]
-    print " ".join(all_packages)
diff --git a/vsc/utils/__init__.py b/vsc/utils/__init__.py
deleted file mode 100644
index 4b023b72ef..0000000000
--- a/vsc/utils/__init__.py
+++ /dev/null
@@ -1,30 +0,0 @@
-##
-# Copyright 2011-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-This package contains some utilitie modules use alltrought the vsc packages.
-
-@author: Jens Timmerman (Ghent University)
-"""
diff --git a/vsc/utils/affinity.py b/vsc/utils/affinity.py
deleted file mode 100644
index a774bb7fc3..0000000000
--- a/vsc/utils/affinity.py
+++ /dev/null
@@ -1,334 +0,0 @@
-##
-# Copyright 2012-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-Linux cpu affinity.
-    - Based on C{sched.h} and C{bits/sched.h},
-    - see man pages for  C{sched_getaffinity} and C{sched_setaffinity}
-    - also provides a C{cpuset} class to convert between human readable cpusets and the bit version
-Linux priority
-    - Based on sys/resources.h and bits/resources.h see man pages for
-      C{getpriority} and C{setpriority}
-
-@author: Stijn De Weirdt (Ghent University)
-"""
-
-import ctypes
-import os
-from ctypes.util import find_library
-from vsc.utils.fancylogger import getLogger, setLogLevelDebug
-
-_logger = getLogger("affinity")
-
-_libc_lib = find_library('c')
-_libc = ctypes.cdll.LoadLibrary(_libc_lib)
-
-#/* Type for array elements in 'cpu_set_t'.  */
-#typedef unsigned long int __cpu_mask;
-cpu_mask_t = ctypes.c_ulong
-
-##define __CPU_SETSIZE  1024
-##define __NCPUBITS     (8 * sizeof(__cpu_mask))
-CPU_SETSIZE = 1024
-NCPUBITS = 8 * ctypes.sizeof(cpu_mask_t)
-NMASKBITS = CPU_SETSIZE / NCPUBITS
-
-#/* Priority limits.  */
-##define PRIO_MIN        -20     /* Minimum priority a process can have.  */
-##define PRIO_MAX        20      /* Maximum priority a process can have.  */
-PRIO_MIN = -20
-PRIO_MAX = 20
-
-#/* The type of the WHICH argument to `getpriority' and `setpriority',
-#   indicating what flavor of entity the WHO argument specifies.  * /
-#enum __priority_which
-##{
-#  PRIO_PROCESS = 0, /* WHO is a process ID.  * /
-##define PRIO_PROCESS PRIO_PROCESS
-#  PRIO_PGRP = 1, /* WHO is a process group ID.  * /
-##define PRIO_PGRP PRIO_PGRP
-#  PRIO_USER = 2 /* WHO is a user ID.  * /
-##define PRIO_USER PRIO_USER
-##};
-PRIO_PROCESS = 0
-PRIO_PGRP = 1
-PRIO_USER = 2
-
-#/* using pid_t for __pid_t */
-#typedef unsigned pid_t;
-pid_t = ctypes.c_uint
-
-##if defined __USE_GNU && !defined __cplusplus
-#typedef enum __rlimit_resource __rlimit_resource_t;
-#typedef enum __rusage_who __rusage_who_t;
-#typedef enum __priority_which __priority_which_t;
-##else
-#typedef int __rlimit_resource_t;
-#typedef int __rusage_who_t;
-#typedef int __priority_which_t;
-##endif
-priority_which_t = ctypes.c_int
-
-##  typedef __u_int __id_t;
-id_t = ctypes.c_uint
-
-
-#/* Data structure to describe CPU mask.  */
-#typedef struct
-#{
-#  __cpu_mask __bits[__NMASKBITS];
-#} cpu_set_t;
-class cpu_set_t(ctypes.Structure):
-    """Class that implements the cpu_set_t struct
-        also provides some methods to convert between bit representation and soem human readable format
-    """
-    _fields_ = [('__bits', cpu_mask_t * NMASKBITS)]
-
-    def __init__(self, *args, **kwargs):
-        super(cpu_set_t, self).__init__(*args, **kwargs)
-        self.log = getLogger(self.__class__.__name__)
-        self.cpus = None
-
-    def __str__(self):
-        return self.convert_bits_hr()
-
-    def convert_hr_bits(self, txt):
-        """Convert human readable text into bits"""
-        self.cpus = [0] * CPU_SETSIZE
-        for rng in txt.split(','):
-            indices = [int(x) for x in rng.split('-')] * 2  # always at least 2 elements: twice the same or start,end,start,end
-
-            ## sanity check
-            if indices[1] < indices[0]:
-                self.log.raiseException("convert_hr_bits: end is lower then start in '%s'" % rng)
-            elif indices[0] < 0:
-                self.log.raiseException("convert_hr_bits: negative start in '%s'" % rng)
-            elif indices[1] > CPU_SETSIZE + 1 :  # also covers start, since end > start
-                self.log.raiseException("convert_hr_bits: end larger then max %s in '%s'" % (CPU_SETSIZE, rng))
-
-            self.cpus[indices[0]:indices[1] + 1] = [1] * (indices[1] + 1 - indices[0])
-        self.log.debug("convert_hr_bits: converted %s into cpus %s" % (txt, self.cpus))
-
-    def convert_bits_hr(self):
-        """Convert __bits into human readable text"""
-        if self.cpus is None:
-            self.get_cpus()
-        cpus_index = [idx for idx, cpu in enumerate(self.cpus) if cpu == 1]
-        prev = -2  # not adjacent to 0 !
-        parsed_idx = []
-        for idx in cpus_index:
-            if prev + 1 < idx:
-                parsed_idx.append("%s" % idx)
-            else:
-                first_idx = parsed_idx[-1].split("-")[0]
-                parsed_idx[-1] = "%s-%s" % (first_idx, idx)
-            prev = idx
-        return ",".join(parsed_idx)
-
-    def get_cpus(self):
-        """Convert bits in list len == CPU_SETSIZE
-            Use 1 / 0 per cpu
-        """
-        self.cpus = []
-        for bitmask in getattr(self, '__bits'):
-            for idx in xrange(NCPUBITS):
-                self.cpus.append(bitmask & 1)
-                bitmask >>= 1
-        return self.cpus
-
-    def set_cpus(self, cpus_list):
-        """Given list, set it as cpus"""
-        nr_cpus = len(cpus_list)
-        if  nr_cpus > CPU_SETSIZE:
-            self.log.warning("set_cpus: length cpu list %s is larger then cpusetsize %s. Truncating to cpusetsize" %
-                           (nr_cpus , CPU_SETSIZE))
-            cpus_list = cpus_list[:CPU_SETSIZE]
-        elif nr_cpus < CPU_SETSIZE:
-            cpus_list.extend([0] * (CPU_SETSIZE - nr_cpus))
-
-        self.cpus = cpus_list
-
-    def set_bits(self, cpus=None):
-        """Given self.cpus, set the bits"""
-        if cpus is not None:
-            self.set_cpus(cpus)
-        __bits = getattr(self, '__bits')
-        prev_cpus = map(long, self.cpus)
-        for idx in xrange(NMASKBITS):
-            cpus = [2 ** cpuidx for cpuidx, val in enumerate(self.cpus[idx * NCPUBITS:(idx + 1) * NCPUBITS]) if val == 1]
-            __bits[idx] = cpu_mask_t(sum(cpus))
-        ## sanity check
-        if not prev_cpus == self.get_cpus():
-            ## get_cpus() rescans
-            self.log.raiseException("set_bits: something went wrong: previous cpus %s; current ones %s" % (prev_cpus[:20], self.cpus[:20]))
-        else:
-            self.log.debug("set_bits: new set to %s" % self.convert_bits_hr())
-
-    def str_cpus(self):
-        """Return a string representation of the cpus"""
-        if self.cpus is None:
-            self.get_cpus()
-        return "".join(["%d" % x for x in self.cpus])
-
-#/* Get the CPU affinity for a task */
-#extern int sched_getaffinity (pid_t __pid, size_t __cpusetsize,
-#                              cpu_set_t *__cpuset);
-def sched_getaffinity(cs=None, pid=None):
-    """Get the affinity"""
-    if cs is None:
-        cs = cpu_set_t()
-    if pid is None:
-        pid = os.getpid()
-
-    ec = _libc.sched_getaffinity(pid_t(pid),
-                              ctypes.sizeof(cpu_set_t),
-                              ctypes.pointer(cs))
-    if ec == 0:
-        _logger.debug("sched_getaffinity for pid %s returned cpuset %s" % (pid, cs))
-    else:
-        _logger.error("sched_getaffinity failed for pid %s ec %s" % (pid, ec))
-    return cs
-
-
-#/* Set the CPU affinity for a task */
-#extern int sched_setaffinity (pid_t __pid, size_t __cpusetsize,
-#                              cpu_set_t *__cpuset);
-def sched_setaffinity(cs, pid=None):
-    """Set the affinity"""
-    if pid is None:
-        pid = os.getpid()
-
-    ec = _libc.sched_setaffinity(pid_t(pid),
-                              ctypes.sizeof(cpu_set_t),
-                              ctypes.pointer(cs))
-    if ec == 0:
-        _logger.debug("sched_setaffinity for pid %s and cpuset %s" % (pid, cs))
-    else:
-        _logger.error("sched_setaffinity failed for pid %s cpuset %s ec %s" % (pid, cs, ec))
-
-#/* Get index of currently used CPU.  */
-#extern int sched_getcpu (void) __THROW;
-def sched_getcpu():
-    """Get currently used cpu"""
-    return _libc.sched_getcpu()
-
-#Utility function
-#    tobin not used anymore
-def tobin(s):
-    """Convert integer to binary format"""
-    ## bin() missing in 2.4
-    # eg: self.cpus.extend([int(x) for x in tobin(bitmask).zfill(NCPUBITS)[::-1]])
-    if s <= 1:
-        return str(s)
-    else:
-        return tobin(s >> 1) + str(s & 1)
-
-
-#/* Return the highest priority of any process specified by WHICH and WHO
-#   (see above); if WHO is zero, the current process, process group, or user
-#   (as specified by WHO) is used.  A lower priority number means higher
-#   priority.  Priorities range from PRIO_MIN to PRIO_MAX (above).  */
-#extern int getpriority (__priority_which_t __which, id_t __who) __THROW;
-#
-#/* Set the priority of all processes specified by WHICH and WHO (see above)
-#   to PRIO.  Returns 0 on success, -1 on errors.  */
-#extern int setpriority (__priority_which_t __which, id_t __who, int __prio)
-#     __THROW;
-def getpriority(which=None, who=None):
-    """Get the priority"""
-    if which is None:
-        which = PRIO_PROCESS
-    elif not which in (PRIO_PROCESS, PRIO_PGRP, PRIO_USER,):
-        _logger.raiseException("getpriority: which %s not in correct range" % which)
-    if who is None:
-        who = 0  # current which-ever
-    prio = _libc.getpriority(priority_which_t(which),
-                             id_t(who),
-                             )
-    _logger.debug("getpriority prio %s for which %s who %s" % (prio, which, who))
-
-    return prio
-
-def setpriority(prio, which=None, who=None):
-    """Set the priority (aka nice)"""
-    if which is None:
-        which = PRIO_PROCESS
-    elif not which in (PRIO_PROCESS, PRIO_PGRP, PRIO_USER,):
-        _logger.raiseException("setpriority: which %s not in correct range" % which)
-    if who is None:
-        who = 0  # current which-ever
-    try:
-        prio = int(prio)
-    except:
-        _logger.raiseException("setpriority: failed to convert priority %s into int" % prio)
-
-    if prio < PRIO_MIN or prio > PRIO_MAX:
-        _logger.raiseException("setpriority: prio not in allowed range MIN %s MAX %s" % (PRIO_MIN, PRIO_MAX))
-
-    ec = _libc.setpriority(priority_which_t(which),
-                           id_t(who),
-                           ctypes.c_int(prio)
-                           )
-    if ec == 0:
-        _logger.debug("setpriority for which %s who %s prio %s" % (which, who, prio))
-    else:
-        _logger.error("setpriority failed for which %s who %s prio %s" % (which, who, prio))
-
-
-if __name__ == '__main__':
-    ## some examples of usage
-    setLogLevelDebug()
-
-    cs = cpu_set_t()
-    print "__bits", cs.__bits
-    print "sizeof cpu_set_t", ctypes.sizeof(cs)
-    x = sched_getaffinity()
-    print "x", x
-    hr_mask = "1-5,7,9,10-15"
-    print hr_mask, x.convert_hr_bits(hr_mask)
-    print x
-    x.set_bits()
-    print x
-
-    sched_setaffinity(x)
-    print sched_getaffinity()
-
-    x.convert_hr_bits("1")
-    x.set_bits()
-    sched_setaffinity(x)
-    y = sched_getaffinity()
-    print x, y
-
-    print sched_getcpu()
-
-    ## resources
-    ## nice -n 5 python affinity.py prints 5 here
-    currentprio = getpriority()
-    print "getpriority", currentprio
-    newprio = 10
-    setpriority(newprio)
-    newcurrentprio = getpriority()
-    print "getpriority", newcurrentprio
-    assert newcurrentprio == newprio
diff --git a/vsc/utils/asyncprocess.py b/vsc/utils/asyncprocess.py
deleted file mode 100644
index 8b3ce78012..0000000000
--- a/vsc/utils/asyncprocess.py
+++ /dev/null
@@ -1,191 +0,0 @@
-# #
-# Copyright 2005 Josiah Carlson
-# The Asynchronous Python Subprocess recipe was originally created by Josiah Carlson.
-# and released under the GNU Library General Public License v2 or any later version
-# on Jan 23, 2013.
-#
-# http://code.activestate.com/recipes/440554/
-#
-# Copyright 2009-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-# #
-
-"""
-Module to allow Asynchronous subprocess use on Windows and Posix platforms
-
-The 'subprocess' module in Python 2.4 has made creating and accessing subprocess
-streams in Python relatively convenient for all supported platforms,
-but what if you want to interact with the started subprocess?
-That is, what if you want to send a command, read the response,
-and send a new command based on that response?
-
-Now there is a solution.
-The included subprocess.Popen subclass adds three new commonly used methods:
- - C{recv(maxsize=None)}
- - C{recv_err(maxsize=None)}
- - and C{send(input)}
-
-along with a utility method:
- - {send_recv(input='', maxsize=None)}.
-
-C{recv()} and C{recv_err()} both read at most C{maxsize} bytes from the started subprocess.
-C{send()} sends strings to the started subprocess. C{send_recv()} will send the provided input,
-and read up to C{maxsize} bytes from both C{stdout} and C{stderr}.
-
-If any of the pipes are closed, the attributes for those pipes will be set to None,
-and the methods will return None.
-
-  - downloaded 05/08/2010
-  - modified
-    - added STDOUT handle
-    - added maxread to recv_some (2012-08-30)
-
-@author: Josiah Carlson
-@author: Stijn De Weirdt (Ghent University)
-"""
-
-import errno
-import fcntl  # @UnresolvedImport
-import os
-import select  # @UnresolvedImport
-import subprocess
-import time
-
-
-PIPE = subprocess.PIPE
-STDOUT = subprocess.STDOUT
-MESSAGE = "Other end disconnected!"
-
-
-class Popen(subprocess.Popen):
-    def recv(self, maxsize=None):
-        return self._recv('stdout', maxsize)
-
-    def recv_err(self, maxsize=None):
-        return self._recv('stderr', maxsize)
-
-    def send_recv(self, inp='', maxsize=None):
-        return self.send(inp), self.recv(maxsize), self.recv_err(maxsize)
-
-    def get_conn_maxsize(self, which, maxsize):
-        if maxsize is None:
-            maxsize = 1024
-        elif maxsize == 0:  # do not use < 1: -1 means all
-            maxsize = 1
-        return getattr(self, which), maxsize
-
-    def _close(self, which):
-        getattr(self, which).close()
-        setattr(self, which, None)
-
-    def send(self, inp):
-        if not self.stdin:
-            return None
-
-        if not select.select([], [self.stdin], [], 0)[1]:
-            return 0
-
-        try:
-            written = os.write(self.stdin.fileno(), inp)
-        except OSError, why:
-            if why[0] == errno.EPIPE:  # broken pipe
-                return self._close('stdin')
-            raise
-
-        return written
-
-    def _recv(self, which, maxsize):
-        conn, maxsize = self.get_conn_maxsize(which, maxsize)
-        if conn is None:
-            return None
-
-        flags = fcntl.fcntl(conn, fcntl.F_GETFL)
-        if not conn.closed:
-            fcntl.fcntl(conn, fcntl.F_SETFL, flags | os.O_NONBLOCK)
-
-        try:
-            if not select.select([conn], [], [], 0)[0]:
-                return ''
-
-            r = conn.read(maxsize)
-            if not r:
-                return self._close(which)  # close when nothing left to read
-
-            if self.universal_newlines:
-                r = self._translate_newlines(r)
-            return r
-        finally:
-            if not conn.closed:
-                fcntl.fcntl(conn, fcntl.F_SETFL, flags)
-
-
-def recv_some(p, t=.1, e=False, tr=5, stderr=False, maxread=None):
-    """
-    @param p: process
-    @param t: max time to wait without any output before returning
-    @param e: boolean, raise exception is process stopped
-    @param tr: time resolution used for intermediate sleep
-    @param stderr: boolean, read from stderr
-    @param maxread: stop when max read bytes have been read (before timeout t kicks in) (-1: read all)
-
-    Changes made wrt original:
-      - add maxread here
-      - set e to False by default
-    """
-    if maxread is None:
-        maxread = -1
-
-    if tr < 1:
-        tr = 1
-    x = time.time() + t
-    y = []
-    len_y = 0
-    r = ''
-    pr = p.recv
-    if stderr:
-        pr = p.recv_err
-    while (maxread < 0 or len_y <= maxread) and (time.time() < x or r):
-        r = pr(maxread)
-        if r is None:
-            if e:
-                raise Exception(MESSAGE)
-            else:
-                break
-        elif r:
-            y.append(r)
-            len_y += len(r)
-        else:
-            time.sleep(max((x - time.time()) / tr, 0))
-    return ''.join(y)
-
-
-def send_all(p, data):
-    """
-    Send data to process p
-    """
-    while len(data):
-        sent = p.send(data)
-        if sent is None:
-            raise Exception(MESSAGE)
-        data = buffer(data, sent)
diff --git a/vsc/utils/daemon.py b/vsc/utils/daemon.py
deleted file mode 100644
index 2568f7cc30..0000000000
--- a/vsc/utils/daemon.py
+++ /dev/null
@@ -1,144 +0,0 @@
-#!/usr/bin/env python
-
-##
-#
-# Copyright 2007 Sander Marechal (http://www.jejik.com)
-# Released as Public Domain
-# Retrieved from:
-# http://www.jejik.com/articles/2007/02/a_simple_unix_linux_daemon_in_python/
-#
-##
-"""
-Module to make python scripts run in background.
-
-@author: Sander Marechal
-"""
-
-import sys, os, time, atexit
-from signal import SIGTERM
-
-class Daemon:
-    """
-    A generic daemon class.
-
-    Usage: subclass the Daemon class and override the run() method
-    """
-    def __init__(self, pidfile, stdin='/dev/null', stdout='/dev/null', stderr='/dev/null'):
-        self.stdin = stdin
-        self.stdout = stdout
-        self.stderr = stderr
-        self.pidfile = pidfile
-
-    def daemonize(self):
-        """
-        do the UNIX double-fork magic, see Stevens' "Advanced
-        Programming in the UNIX Environment" for details (ISBN 0201563177)
-        http://www.erlenstar.demon.co.uk/unix/faq_2.html#SEC16
-        """
-        try:
-            pid = os.fork()
-            if pid > 0:
-                # exit first parent
-                sys.exit(0)
-        except OSError, e:
-            sys.stderr.write("fork #1 failed: %d (%s)\n" % (e.errno, e.strerror))
-            sys.exit(1)
-
-        # decouple from parent environment
-        os.chdir("/")
-        os.setsid()
-        os.umask(0)
-
-        # do second fork
-        try:
-            pid = os.fork()
-            if pid > 0:
-                # exit from second parent
-                sys.exit(0)
-        except OSError, e:
-            sys.stderr.write("fork #2 failed: %d (%s)\n" % (e.errno, e.strerror))
-            sys.exit(1)
-
-        # redirect standard file descriptors
-        sys.stdout.flush()
-        sys.stderr.flush()
-        si = file(self.stdin, 'r')
-        so = file(self.stdout, 'a+')
-        se = file(self.stderr, 'a+', 0)
-        os.dup2(si.fileno(), sys.stdin.fileno())
-        os.dup2(so.fileno(), sys.stdout.fileno())
-        os.dup2(se.fileno(), sys.stderr.fileno())
-
-        # write pidfile
-        atexit.register(self.delpid)
-        pid = str(os.getpid())
-        file(self.pidfile, 'w+').write("%s\n" % pid)
-
-    def delpid(self):
-        os.remove(self.pidfile)
-
-    def start(self):
-        """
-        Start the daemon
-        """
-        # Check for a pidfile to see if the daemon already runs
-        try:
-            pf = file(self.pidfile, 'r')
-            pid = int(pf.read().strip())
-            pf.close()
-        except IOError:
-            pid = None
-
-        if pid:
-            message = "pidfile %s already exist. Daemon already running?\n"
-            sys.stderr.write(message % self.pidfile)
-            sys.exit(1)
-
-        # Start the daemon
-        self.daemonize()
-        self.run()
-
-    def stop(self):
-        """
-        Stop the daemon
-        """
-        # Get the pid from the pidfile
-        try:
-            pf = file(self.pidfile, 'r')
-            pid = int(pf.read().strip())
-            pf.close()
-        except IOError:
-            pid = None
-
-        if not pid:
-            message = "pidfile %s does not exist. Daemon not running?\n"
-            sys.stderr.write(message % self.pidfile)
-            return # not an error in a restart
-
-        # Try killing the daemon process
-        try:
-            while 1:
-                os.kill(pid, SIGTERM)
-                time.sleep(0.1)
-        except OSError, err:
-            err = str(err)
-            if err.find("No such process") > 0:
-                if os.path.exists(self.pidfile):
-                    os.remove(self.pidfile)
-            else:
-                print str(err)
-                sys.exit(1)
-
-    def restart(self):
-        """
-        Restart the daemon
-        """
-        self.stop()
-        self.start()
-
-    def run(self):
-        """
-        You should override this method when you subclass Daemon. It will be called after the process has been
-        daemonized by start() or restart().
-        """
-        pass
diff --git a/vsc/utils/dateandtime.py b/vsc/utils/dateandtime.py
deleted file mode 100644
index 9f599502e8..0000000000
--- a/vsc/utils/dateandtime.py
+++ /dev/null
@@ -1,354 +0,0 @@
-##
-#
-# Copyright 2012-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-Module with various convenience functions and classes to deal with date, time and timezone
-
-@author: Stijn De Weirdt (Ghent University)
-"""
-
-import calendar
-import re
-import time as _time
-from datetime import tzinfo, timedelta, datetime, date
-
-try:
-    any([0, 1])
-except:
-    from vsc.utils.missing import any
-
-
-class FancyMonth:
-    """Convenience class for month math"""
-    def __init__(self, tmpdate=None, year=None, month=None, day=None):
-        """Initialise the month based on first day of month of tmpdate"""
-
-        if tmpdate is None:
-            tmpdate = date.today()
-
-        if day is None:
-            day = tmpdate.day
-        if month is None:
-            month = tmpdate.month
-        if year is None:
-            year = tmpdate.year
-
-        self.date = date(year, month, day)
-
-        self.first = None
-        self.last = None
-        self.nrdays = None
-
-        # when calculating deltas, include non-full months
-        #   eg when True, nr of months between last day of month
-        #   and first day of following month is 2
-        self.include = True
-
-        self.set_details()
-
-    def set_details(self):
-        """Get first/last day of the month of date"""
-        class MyCalendar(object):
-            """Backport minimal calendar.Calendar code from 2.7 to support itermonthdays in 2.4"""
-            def __init__(self, firstweekday=0):
-                self.firstweekday = firstweekday  # 0 = Monday, 6 = Sunday
-
-            def itermonthdates(self, year, month):
-                """
-                Return an iterator for one month. The iterator will yield datetime.date
-                values and will always iterate through complete weeks, so it will yield
-                dates outside the specified month.
-                """
-                _date = date(year, month, 1)
-                # Go back to the beginning of the week
-                days = (_date.weekday() - self.firstweekday) % 7
-                _date -= timedelta(days=days)
-                oneday = timedelta(days=1)
-                while True:
-                    yield _date
-                    _date += oneday
-                    if _date.month != month and _date.weekday() == self.firstweekday:
-                        break
-
-            def itermonthdays(self, year, month):
-                """
-                Like itermonthdates(), but will yield day numbers. For days outside
-                the specified month the day number is 0.
-                """
-                for _date in self.itermonthdates(year, month):
-                    if _date.month != month:
-                        yield 0
-                    else:
-                        yield _date.day
-
-        if 'Calendar' in dir(calendar):  # py2.5+
-            c = calendar.Calendar()
-        else:
-            c = MyCalendar()
-        self.nrdays = len([x for x in c.itermonthdays(self.date.year, self.date.month) if x > 0])
-
-        self.first = date(self.date.year, self.date.month, 1)
-
-        self.last = date(self.date.year, self.date.month, self.nrdays)
-
-    def get_start_end(self, otherdate):
-        """Return tuple date and otherdate ordered oldest first"""
-        if self.date > otherdate:
-            start = otherdate
-            end = self.date
-        else:
-            start = self.date
-            end = otherdate
-
-        return start, end
-
-    def number(self, otherdate):
-        """Calculate the number of months between this month (date actually) and otherdate
-        """
-        if self.include is False:
-            msg = "number: include=False not implemented"
-            raise(Exception(msg))
-        else:
-            startdate, enddate = self.get_start_end(otherdate)
-
-            if startdate == enddate:
-                nr = 0
-            else:
-                nr = (enddate.year - startdate.year) * 12 + enddate.month - startdate.month + 1
-
-        return nr
-
-    def get_other(self, shift=-1):
-        """Return month that is shifted shift months: negative integer is in past, positive is in future"""
-        new = self.date.year * 12 + self.date.month - 1 + shift
-        return self.__class__(date(new // 12, new % 12 + 1, 01))
-
-    def interval(self, otherdate):
-        """Return time ordered list of months between date and otherdate"""
-        if self.include is False:
-            msg = "interval: include=False not implemented"
-            raise(Exception(msg))
-        else:
-            nr = self.number(otherdate)
-            startdate, enddate = self.get_start_end(otherdate)
-
-            start = self.__class__(startdate)
-            all_dates = [start.get_other(m) for m in range(nr)]
-
-        return all_dates
-
-    def parser(self, txt):
-        """Based on strings, return date: eg BEGINTHIS returns first day of the current month"""
-        supportedtime = ('BEGIN', 'END',)
-        supportedshift = ['THIS', 'LAST', 'NEXT']
-        regtxt = r"^(%s)(%s)?" % ('|'.join(supportedtime), '|'.join(supportedshift))
-
-        reseervedregexp = re.compile(regtxt)
-        reg = reseervedregexp.search(txt)
-        if not reg:
-            msg = "parse: no match for regexp %s for txt %s" % (regtxt, txt)
-            raise(Exception(msg))
-
-        shifttxt = reg.group(2)
-        if shifttxt is None or shifttxt == 'THIS':
-            shift = 0
-        elif shifttxt == 'LAST':
-            shift = -1
-        elif shifttxt == 'NEXT':
-            shift = 1
-        else:
-            msg = "parse: unknown shift %s (supported: %s)" % (shifttxt, supportedshift)
-            raise(Exception(msg))
-
-        nm = self.get_other(shift)
-
-        timetxt = reg.group(1)
-        if timetxt == 'BEGIN':
-            res = nm.first
-        elif timetxt == 'END':
-            res = nm.last
-        else:
-            msg = "parse: unknown time %s (supported: %s)" % (timetxt, supportedtime)
-            raise(Exception(msg))
-
-        return res
-
-
-def date_parser(txt):
-    """Parse txt
-
-    @type txt: string
-
-    @param txt: date to be parsed. Usually in C{YYYY-MM-DD} format,
-    but also C{(BEGIN|END)(THIS|LAST|NEXT)MONTH}, or even
-    C{(BEGIN | END)(JANUARY | FEBRUARY | MARCH | APRIL | MAY | JUNE | JULY | AUGUST | SEPTEMBER | OCTOBER | NOVEMBER | DECEMBER)}
-    """
-
-    reserveddate = ('TODAY',)
-    testsupportedmonths = [txt.endswith(calendar.month_name[x].upper()) for x in range(1, 13)]
-
-    if txt.endswith('MONTH'):
-        m = FancyMonth()
-        res = m.parser(txt)
-    elif any(testsupportedmonths):
-        # set day=1 or this will fail on day's with an index more then the count of days then the month you want to parse
-        # e.g. will fail on 31'st when trying to parse april
-        m = FancyMonth(month=testsupportedmonths.index(True) + 1, day=1)
-        res = m.parser(txt)
-    elif txt in reserveddate:
-        if txt in ('TODAY',):
-            m = FancyMonth()
-            res = m.date
-        else:
-            msg = 'dateparser: unimplemented reservedword %s' % txt
-            raise(Exception(msg))
-    else:
-        try:
-            datetuple = [int(x) for x in txt.split("-")]
-            res = date(*datetuple)
-        except:
-            msg = ("dateparser: failed on '%s' date txt expects a YYYY-MM-DD format or "
-                   "reserved words %s") % (txt, ','.join(reserveddate))
-            raise(Exception(msg))
-
-    return res
-
-
-def datetime_parser(txt):
-    """Parse txt: tmpdate YYYY-MM-DD HH:MM:SS.mmmmmm in datetime.datetime
-        - date part is parsed with date_parser
-    """
-    tmpts = txt.split(" ")
-    tmpdate = date_parser(tmpts[0])
-
-    datetuple = [tmpdate.year, tmpdate.month, tmpdate.day]
-    if len(tmpts) > 1:
-        # add hour and minutes
-        datetuple.extend([int(x) for x in tmpts[1].split(':')[:2]])
-
-        try:
-            sects = tmpts[1].split(':')[2].split('.')
-        except:
-            sects = [0]
-        # add seconds
-        datetuple.append(int(sects[0]))
-        if len(sects) > 1:
-            # add microseconds
-            datetuple.append(int(float('.%s' % sects[1]) * 10 ** 6))
-
-    res = datetime(*datetuple)
-
-    return res
-
-
-def timestamp_parser(timestamp):
-    """Parse timestamp to datetime"""
-    return datetime.fromtimestamp(float(timestamp))
-
-#
-# example code from http://docs.python.org/library/datetime.html
-# Implements Local, the local timezone
-#
-
-ZERO = timedelta(0)
-HOUR = timedelta(hours=1)
-
-
-# A UTC class.
-class UTC(tzinfo):
-    """UTC"""
-
-    def utcoffset(self, dt):
-        return ZERO
-
-    def tzname(self, dt):
-        return "UTC"
-
-    def dst(self, dt):
-        return ZERO
-
-utc = UTC()
-
-
-class FixedOffset(tzinfo):
-    """Fixed offset in minutes east from UTC.
-
-    This is a class for building tzinfo objects for fixed-offset time zones.
-    Note that FixedOffset(0, "UTC") is a different way to build a
-    UTC tzinfo object.
-    """
-    def __init__(self, offset, name):
-        self.__offset = timedelta(minutes=offset)
-        self.__name = name
-
-    def utcoffset(self, dt):
-        return self.__offset
-
-    def tzname(self, dt):
-        return self.__name
-
-    def dst(self, dt):
-        return ZERO
-
-
-STDOFFSET = timedelta(seconds=-_time.timezone)
-if _time.daylight:
-    DSTOFFSET = timedelta(seconds=-_time.altzone)
-else:
-    DSTOFFSET = STDOFFSET
-
-DSTDIFF = DSTOFFSET - STDOFFSET
-
-
-class LocalTimezone(tzinfo):
-    """
-    A class capturing the platform's idea of local time.
-    """
-
-    def utcoffset(self, dt):
-        if self._isdst(dt):
-            return DSTOFFSET
-        else:
-            return STDOFFSET
-
-    def dst(self, dt):
-        if self._isdst(dt):
-            return DSTDIFF
-        else:
-            return ZERO
-
-    def tzname(self, dt):
-        return _time.tzname[self._isdst(dt)]
-
-    def _isdst(self, dt):
-        tt = (dt.year, dt.month, dt.day,
-              dt.hour, dt.minute, dt.second,
-              dt.weekday(), 0, 0)
-        stamp = _time.mktime(tt)
-        tt = _time.localtime(stamp)
-        return tt.tm_isdst > 0
-
-Local = LocalTimezone()
diff --git a/vsc/utils/fancylogger.py b/vsc/utils/fancylogger.py
deleted file mode 100644
index 1f0220df75..0000000000
--- a/vsc/utils/fancylogger.py
+++ /dev/null
@@ -1,702 +0,0 @@
-#!/usr/bin/env python
-# #
-# Copyright 2011-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-# #
-"""
-This module implements a fancy logger on top of python logging
-
-It adds:
- - custom specifiers for mpi logging (the mpirank) with autodetection of mpi
- - custom specifier for always showing the calling function's name
- - rotating file handler
- - a default formatter.
- - logging to an UDP server (vsc.logging.logdaemon.py f.ex.)
- - easily setting loglevel
- - easily add extra specifiers in the log record
- - internal debugging through environment variables
-    FANCYLOGGER_GETLOGGER_DEBUG for getLogger
-    FANCYLOGGER_LOGLEVEL_DEBUG for setLogLevel
-
-usage:
-
->>> from vsc.utils import fancylogger
->>> # will log to screen by default
->>> fancylogger.logToFile('dir/filename')
->>> fancylogger.setLogLevelDebug()  # set global loglevel to debug
->>> logger = fancylogger.getLogger(name)  # get a logger with a specific name
->>> logger.setLevel(level)  # set local debugging level
->>> # If you want the logger to be showing modulename.functionname as the name, use
->>> fancylogger.getLogger(fname=True)
->>> # you can use the handler to set a different formatter by using
->>> handler = fancylogger.logToFile('dir/filename')
->>> formatstring = '%(asctime)-15s %(levelname)-10s %(mpirank)-5s %(funcname)-15s %(threadName)-10s %(message)s'
->>> handler.setFormatter(logging.Formatter(formatstring))
->>> # setting a global loglevel will impact all logers:
->>> from vsc.utils import fancylogger
->>> logger = fancylogger.getLogger("test")
->>> logger.warning("warning")
-2012-01-05 14:03:18,238 WARNING    <stdin>.test.<module>    MainThread  warning
->>> logger.debug("warning")
->>> fancylogger.setLogLevelDebug()
->>> logger.debug("warning")
-2012-01-05 14:03:46,222 DEBUG      <stdin>.test.<module>    MainThread  warning
-
-Logging to a udp server:
- - set an environment variable FANCYLOG_SERVER and FANCYLOG_SERVER_PORT (optionally)
- - this will make fancylogger log to that that server and port instead of the screen.
-
-@author: Jens Timmerman (Ghent University)
-@author: Stijn De Weirdt (Ghent University)
-@author: Kenneth Hoste (Ghent University)
-"""
-
-import inspect
-import logging
-import logging.handlers
-import os
-import sys
-import threading
-import traceback
-import weakref
-from distutils.version import LooseVersion
-
-# constants
-TEST_LOGGING_FORMAT = '%(levelname)-10s %(name)-15s %(threadName)-10s  %(message)s'
-DEFAULT_LOGGING_FORMAT = '%(asctime)-15s ' + TEST_LOGGING_FORMAT
-FANCYLOG_LOGGING_FORMAT = None
-
-# DEFAULT_LOGGING_FORMAT= '%(asctime)-15s %(levelname)-10s %(module)-15s %(threadName)-10s %(message)s'
-MAX_BYTES = 100 * 1024 * 1024  # max bytes in a file with rotating file handler
-BACKUPCOUNT = 10  # number of rotating log files to save
-
-DEFAULT_UDP_PORT = 5005
-
-# register new loglevelname
-logging.addLevelName(logging.CRITICAL * 2 + 1, 'APOCALYPTIC')
-# register QUIET, EXCEPTION and FATAL alias
-logging._levelNames['EXCEPTION'] = logging.ERROR
-logging._levelNames['FATAL'] = logging.CRITICAL
-logging._levelNames['QUIET'] = logging.WARNING
-
-
-# mpi rank support
-try:
-    from mpi4py import MPI
-    _MPIRANK = str(MPI.COMM_WORLD.Get_rank())
-    if MPI.COMM_WORLD.Get_size() > 1:
-        # enable mpi rank when mpi is used
-        DEFAULT_LOGGING_FORMAT = '%(asctime)-15s %(levelname)-10s %(name)-15s' \
-                                 " mpi: %(mpirank)s %(threadName)-10s  %(message)s"
-except ImportError:
-    _MPIRANK = "N/A"
-
-
-class MissingLevelName(KeyError):
-    pass
-
-
-def getLevelInt(level_name):
-    """Given a level name, return the int value"""
-    if not isinstance(level_name, basestring):
-        raise TypeError('Provided name %s is not a string (type %s)' % (level_name, type(level_name)))
-
-    level = logging.getLevelName(level_name)
-    if isinstance(level, basestring):
-        raise MissingLevelName('Unknown loglevel name %s' % level_name)
-
-    return level
-
-
-class FancyStreamHandler(logging.StreamHandler):
-    """The logging StreamHandler with uniform named arg in __init__ for selecting the stream."""
-    def __init__(self, stream=None, stdout=None):
-        """Initialize the stream (default is sys.stderr)
-            - stream : a specific stream to use
-            - stdout: if True and no stream specified, set stream to sys.stdout (False log to stderr)
-        """
-        logging.StreamHandler.__init__(self)
-        if stream is not None:
-            pass
-        elif stdout is False or stdout is None:
-            stream = sys.stderr
-        elif stdout is True:
-            stream = sys.stdout
-
-        self.stream = stream
-
-
-class FancyLogRecord(logging.LogRecord):
-    """
-    This class defines a custom log record.
-    Adding extra specifiers is as simple as adding attributes to the log record
-    """
-    def __init__(self, *args, **kwargs):
-        logging.LogRecord.__init__(self, *args, **kwargs)
-        # modify custom specifiers here
-        # we won't do this when running with -O, becuase this might be a heavy operation
-        # the __debug__ operation is actually recognised by the python compiler and it won't even do a single comparison
-        if __debug__:
-            self.className = _getCallingClassName(depth=5)
-        else:
-            self.className = 'N/A'
-        self.mpirank = _MPIRANK
-
-
-# Custom logger that uses our log record
-class FancyLogger(logging.getLoggerClass()):
-    """
-    This is a custom Logger class that uses the FancyLogRecord
-    and has extra log methods raiseException and deprecated and
-    streaming versions for debug,info,warning and error.
-    """
-    # this attribute can be checked to know if the logger is thread aware
-    _thread_aware = True
-
-    # method definition as it is in logging, can't change this
-    def makeRecord(self, name, level, pathname, lineno, msg, args, excinfo, func=None, extra=None):
-        """
-        overwrite make record to use a fancy record (with more options)
-        """
-        logrecordcls = logging.LogRecord
-        if hasattr(self, 'fancyrecord') and self.fancyrecord:
-            logrecordcls = FancyLogRecord
-        try:
-            new_msg = str(msg)
-        except UnicodeEncodeError:
-            new_msg = msg.encode('utf8', 'replace')
-        return logrecordcls(name, level, pathname, lineno, new_msg, args, excinfo)
-
-    def raiseException(self, message, exception=None, catch=False):
-        """
-        logs an exception (as warning, since it can be caught higher up and handled)
-        and raises it afterwards
-            catch: boolean, try to catch raised exception and add relevant info to message
-                (this will also happen if exception is not specified)
-        """
-        fullmessage = message
-
-        if catch or exception is None:
-            # assumes no control by codemonkey
-            # lets see if there is something more to report on
-            exc, detail, tb = sys.exc_info()
-            if exc is not None:
-                if exception is None:
-                    exception = exc
-                # extend the message with the traceback and some more details
-                # or use self.exception() instead of self.warning()?
-                tb_text = "\n".join(traceback.format_tb(tb))
-                message += " (%s)" % detail
-                fullmessage += " (%s\n%s)" % (detail, tb_text)
-
-        if exception is None:
-            exception = Exception
-
-        self.warning(fullmessage)
-        raise exception(message)
-
-    def deprecated(self, msg, cur_ver, max_ver, depth=2, exception=None, *args, **kwargs):
-        """
-        Log deprecation message, throw error if current version is passed given threshold.
-
-        Checks only major/minor version numbers (MAJ.MIN.x) by default, controlled by 'depth' argument.
-        """
-        loose_cv = LooseVersion(cur_ver)
-        loose_mv = LooseVersion(max_ver)
-
-        loose_cv.version = loose_cv.version[:depth]
-        loose_mv.version = loose_mv.version[:depth]
-
-        if loose_cv >= loose_mv:
-            self.raiseException("DEPRECATED (since v%s) functionality used: %s" % (max_ver, msg), exception=exception)
-        else:
-            deprecation_msg = "Deprecated functionality, will no longer work in v%s: %s" % (max_ver, msg)
-            self.warning(deprecation_msg)
-
-    def _handleFunction(self, function, levelno, **kwargs):
-        """
-        Walk over all handlers like callHandlers and execute function on each handler
-        """
-        c = self
-        found = 0
-        while c:
-            for hdlr in c.handlers:
-                found = found + 1
-                if levelno >= hdlr.level:
-                    function(hdlr, **kwargs)
-            if not c.propagate:
-                c = None  # break out
-            else:
-                c = c.parent
-
-    def setLevelName(self, level_name):
-        """Set the level by name."""
-        # This is supported in py27 setLevel code, but not in py24
-        self.setLevel(getLevelInt(level_name))
-
-    def streamLog(self, levelno, data):
-        """
-        Add (continuous) data to an existing message stream (eg a stream after a logging.info()
-        """
-        if isinstance(levelno, str):
-            levelno = getLevelInt(levelno)
-
-        def write_and_flush_stream(hdlr, data=None):
-            """Write to stream and flush the handler"""
-            if (not hasattr(hdlr, 'stream')) or hdlr.stream is None:
-                # no stream or not initialised.
-                raise("write_and_flush_stream failed. No active stream attribute.")
-            if data is not None:
-                hdlr.stream.write(data)
-                hdlr.flush()
-
-        # only log when appropriate (see logging.Logger.log())
-        if self.isEnabledFor(levelno):
-            self._handleFunction(write_and_flush_stream, levelno, data=data)
-
-    def streamDebug(self, data):
-        """Get a DEBUG loglevel streamLog"""
-        self.streamLog('DEBUG', data)
-
-    def streamInfo(self, data):
-        """Get a INFO loglevel streamLog"""
-        self.streamLog('INFO', data)
-
-    def streamError(self, data):
-        """Get a ERROR loglevel streamLog"""
-        self.streamLog('ERROR', data)
-
-    def _get_parent_info(self, verbose=True):
-        """Return some logger parent related information"""
-        def info(x):
-            res = [x, x.name, logging.getLevelName(x.getEffectiveLevel()), logging.getLevelName(x.level), x.disabled]
-            if verbose:
-                res.append([(h, logging.getLevelName(h.level)) for h in x.handlers])
-            return res
-
-        parentinfo = []
-        logger = self
-        parentinfo.append(info(logger))
-        while logger.parent is not None:
-            logger = logger.parent
-            parentinfo.append(info(logger))
-        return parentinfo
-
-    def get_parent_info(self, prefix, verbose=True):
-        """Return pretty text version"""
-        rev_parent_info = self._get_parent_info(verbose=verbose)
-        return ["%s %s%s" % (prefix, " " * 4 * idx, info) for idx, info in enumerate(rev_parent_info)]
-
-    def __copy__(self):
-        """Return shallow copy, in this case reference to current logger"""
-        return getLogger(self.name, fname=False, clsname=False)
-
-    def __deepcopy__(self, memo):
-        """This behaviour is undefined, fancylogger will return shallow copy, instead just crashing."""
-        return self.__copy__()
-
-
-def thread_name():
-    """
-    returns the current threads name
-    """
-    return threading.currentThread().getName()
-
-
-def getLogger(name=None, fname=False, clsname=False, fancyrecord=None):
-    """
-    returns a fancylogger
-    if fname is True, the loggers name will be 'name[.classname].functionname'
-    if clsname is True the loggers name will be 'name.classname[.functionname]'
-    This will return a logger with a fancylog record, which includes the className template for the logformat
-    This can make your code a lot slower, so this can be dissabled by setting fancyrecord to False, and
-    will also be disabled if a Name is set, and fancyrecord is not set to True
-    """
-    nameparts = [getRootLoggerName()]
-
-    if name:
-        nameparts.append(name)
-    elif fancyrecord is None or fancyrecord:  # only be fancy if fancyrecord is True or no name is given
-        fancyrecord = True
-    fancyrecord = bool(fancyrecord)  # make sure fancyrecord is a nice bool, not None
-
-    if clsname:
-        nameparts.append(_getCallingClassName())
-    if fname:
-        nameparts.append(_getCallingFunctionName())
-    fullname = ".".join(nameparts)
-
-    l = logging.getLogger(fullname)
-    l.fancyrecord = fancyrecord
-    if os.environ.get('FANCYLOGGER_GETLOGGER_DEBUG', '0').lower() in ('1', 'yes', 'true', 'y'):
-        print 'FANCYLOGGER_GETLOGGER_DEBUG',
-        print 'name', name, 'fname', fname, 'fullname', fullname,
-        print "getRootLoggerName: ", getRootLoggerName()
-        if hasattr(l, 'get_parent_info'):
-            print 'parent_info verbose'
-            print "\n".join(l.get_parent_info("FANCYLOGGER_GETLOGGER_DEBUG"))
-        sys.stdout.flush()
-    return l
-
-
-def _getCallingFunctionName():
-    """
-    returns the name of the function calling the function calling this function
-    (for internal use only)
-    """
-    try:
-        return inspect.stack()[2][3]
-    except Exception:
-        return "?"
-
-
-def _getCallingClassName(depth=2):
-    """
-    returns the name of the class calling the function calling this function
-    (for internal use only)
-    """
-    try:
-        return inspect.stack()[depth][0].f_locals['self'].__class__.__name__
-
-    except Exception:
-        return "?"
-
-
-def getRootLoggerName():
-    """
-    returns the name of the root module
-    this is the module that is actually running everything and so doing the logging
-    """
-    try:
-        return inspect.stack()[-1][1].split('/')[-1].split('.')[0]
-    except Exception:
-        return "?"
-
-
-def logToScreen(enable=True, handler=None, name=None, stdout=False):
-    """
-    enable (or disable) logging to screen
-    returns the screenhandler (this can be used to later disable logging to screen)
-
-    if you want to disable logging to screen, pass the earlier obtained screenhandler
-
-    you can also pass the name of the logger for which to log to the screen
-    otherwise you'll get all logs on the screen
-
-    by default, logToScreen will log to stderr; logging to stdout instead can be done
-    by setting the 'stdout' parameter to True
-    """
-    handleropts = {'stdout': stdout}
-
-    return _logToSomething(FancyStreamHandler,
-                           handleropts,
-                           loggeroption='logtoscreen_stdout_%s' % str(stdout),
-                           name=name,
-                           enable=enable,
-                           handler=handler,
-                           )
-
-
-def logToFile(filename, enable=True, filehandler=None, name=None, max_bytes=MAX_BYTES, backup_count=BACKUPCOUNT):
-    """
-    enable (or disable) logging to file
-    given filename
-    will log to a file with the given name using a rotatingfilehandler
-    this will let the file grow to MAX_BYTES and then rotate it
-    saving the last BACKUPCOUNT files.
-
-    returns the filehandler (this can be used to later disable logging to file)
-
-    if you want to disable logging to file, pass the earlier obtained filehandler
-    """
-    handleropts = {'filename': filename,
-                   'mode': 'a',
-                   'maxBytes': max_bytes,
-                   'backupCount': backup_count,
-                   }
-    return _logToSomething(logging.handlers.RotatingFileHandler,
-                           handleropts,
-                           loggeroption='logtofile_%s' % filename,
-                           name=name,
-                           enable=enable,
-                           handler=filehandler,
-                           )
-
-
-def logToUDP(hostname, port=5005, enable=True, datagramhandler=None, name=None):
-    """
-    enable (or disable) logging to udp
-    given hostname and port.
-
-    returns the filehandler (this can be used to later disable logging to udp)
-
-    if you want to disable logging to udp, pass the earlier obtained filehandler,
-    and set boolean = False
-    """
-    handleropts = {'hostname': hostname, 'port': port}
-    return _logToSomething(logging.handlers.DatagramHandler,
-                           handleropts,
-                           loggeroption='logtoudp_%s:%s' % (hostname, str(port)),
-                           name=name,
-                           enable=enable,
-                           handler=datagramhandler,
-                           )
-
-
-def _logToSomething(handlerclass, handleropts, loggeroption, enable=True, name=None, handler=None):
-    """
-    internal function to enable (or disable) logging to handler named handlername
-    handleropts is options dictionary passed to create the handler instance
-
-    returns the handler (this can be used to later disable logging to file)
-
-    if you want to disable logging to the handler, pass the earlier obtained handler
-    """
-    logger = getLogger(name, fname=False, clsname=False)
-
-    if not hasattr(logger, loggeroption):
-        # not set.
-        setattr(logger, loggeroption, False)  # set default to False
-
-    if enable:
-        if not getattr(logger, loggeroption):
-            if handler is None:
-                if FANCYLOG_LOGGING_FORMAT is None:
-                    f_format = DEFAULT_LOGGING_FORMAT
-                else:
-                    f_format = FANCYLOG_LOGGING_FORMAT
-                formatter = logging.Formatter(f_format)
-                handler = handlerclass(**handleropts)
-                handler.setFormatter(formatter)
-            logger.addHandler(handler)
-            setattr(logger, loggeroption, handler)
-        else:
-            handler = getattr(logger, loggeroption)
-    elif not enable:
-        # stop logging to X
-        if handler is None:
-            if len(logger.handlers) == 1:
-                # removing the last logger doesn't work
-                # it will be re-added if only one handler is present
-                # so we will just make it quiet by setting the loglevel extremely high
-                zerohandler = logger.handlers[0]
-                # no logging should be done with APOCALYPTIC, so silence happens
-                zerohandler.setLevel(getLevelInt('APOCALYPTIC'))
-            else:  # remove the handler set with this loggeroption
-                handler = getattr(logger, loggeroption)
-                logger.removeHandler(handler)
-                if hasattr(handler, 'close') and callable(handler.close):
-                    handler.close()
-        else:
-            logger.removeHandler(handler)
-        setattr(logger, loggeroption, False)
-    return handler
-
-
-def _getSysLogFacility(name=None):
-    """Look for proper syslog facility
-        typically the syslog/rsyslog config has an entry
-            # Log anything (except mail) of level info or higher.
-            # Don't log private authentication messages!
-            *.info;mail.none;authpriv.none;cron.none                /var/log/messages
-
-        name -> LOG_%s % name.upper()
-        Default log facility is user /LOG_USER
-    """
-
-    if name is None:
-        name = 'user'
-
-    facility = getattr(logging.handlers.SysLogHandler,
-                       "LOG_%s" % name.upper(), logging.handlers.SysLogHandler.LOG_USER)
-
-    return facility
-
-
-def logToDevLog(enable=True, name=None, handler=None):
-    """Log to syslog through /dev/log"""
-    devlog = '/dev/log'
-    syslogoptions = {'address': devlog,
-                     'facility': _getSysLogFacility()
-                     }
-    return _logToSomething(logging.handlers.SysLogHandler,
-                           syslogoptions, 'logtodevlog', enable=enable, name=name, handler=handler)
-
-
-#  Change loglevel
-def setLogLevel(level):
-    """
-    set a global log level (for this root logger)
-    """
-    if isinstance(level, basestring):
-        level = getLevelInt(level)
-    logger = getLogger(fname=False, clsname=False)
-    logger.setLevel(level)
-    if os.environ.get('FANCYLOGGER_LOGLEVEL_DEBUG', '0').lower() in ('1', 'yes', 'true', 'y'):
-        print "FANCYLOGGER_LOGLEVEL_DEBUG", level, logging.getLevelName(level)
-        print "\n".join(logger.get_parent_info("FANCYLOGGER_LOGLEVEL_DEBUG"))
-        sys.stdout.flush()
-
-
-def setLogLevelDebug():
-    """
-    shorthand for setting debug level
-    """
-    setLogLevel('DEBUG')
-
-
-def setLogLevelInfo():
-    """
-    shorthand for setting loglevel to Info
-    """
-    setLogLevel('INFO')
-
-
-def setLogLevelWarning():
-    """
-    shorthand for setting loglevel to Warning
-    """
-    setLogLevel('WARNING')
-
-
-def setLogLevelError():
-    """
-    shorthand for setting loglevel to Error
-    """
-    setLogLevel('ERROR')
-
-
-def getAllExistingLoggers():
-    """
-    @return: the existing loggers, in a list of C{(name, logger)} tuples
-    """
-    rootlogger = logging.getLogger(name=False)
-    # undocumented manager (in 2.4 and later)
-    manager = rootlogger.manager
-
-    loggerdict = getattr(manager, 'loggerDict')
-
-    # return list of (name,logger) tuple
-    return [x for x in loggerdict.items()]
-
-
-def getAllNonFancyloggers():
-    """
-    @return: all loggers that are not fancyloggers
-    """
-    return [x for x in getAllExistingLoggers() if not isinstance(x[1], FancyLogger)]
-
-
-def getAllFancyloggers():
-    """
-    Return all loggers that are not fancyloggers
-    """
-    return [x for x in getAllExistingLoggers() if isinstance(x[1], FancyLogger)]
-
-
-def setLogFormat(f_format):
-    """Set the log format. (Has to be set before logToSomething is called)."""
-    global FANCYLOG_LOGGING_FORMAT
-    FANCYLOG_LOGGING_FORMAT = f_format
-
-
-def setTestLogFormat():
-    """Set the log format to the test format (i.e. without timestamp)."""
-    setLogFormat(TEST_LOGGING_FORMAT)
-
-
-# Register our logger
-logging.setLoggerClass(FancyLogger)
-
-# log to a server if FANCYLOG_SERVER is set.
-_default_logTo = None
-if 'FANCYLOG_SERVER' in os.environ:
-    server = os.environ['FANCYLOG_SERVER']
-    port = DEFAULT_UDP_PORT
-    if ':' in server:
-        server, port = server.split(':')
-
-    # maybe the port was specified in the FANCYLOG_SERVER_PORT env var. this takes precedence
-    if 'FANCYLOG_SERVER_PORT' in os.environ:
-        port = int(os.environ['FANCYLOG_SERVER_PORT'])
-    port = int(port)
-
-    logToUDP(server, port)
-    _default_logTo = logToUDP
-else:
-    # log to screen by default
-    logToScreen(enable=True)
-    _default_logTo = logToScreen
-
-
-_default_handlers = logging._handlerList[:]  # There's always one
-
-
-def _enable_disable_default_handlers(enable):
-    """Interact with the default handlers to enable or disable them"""
-    if _default_logTo is None:
-        return
-    for hndlr in _default_handlers:
-        # py2.7 are weakrefs, 2.6 not
-        if isinstance(hndlr, weakref.ref):
-            handler = hndlr()
-        else:
-            handler = hndlr
-
-        try:
-            _default_logTo(enable=enable, handler=handler)
-        except:
-            pass
-
-
-def disableDefaultHandlers():
-    """Disable the default handlers on all fancyloggers
-        - if this is the last logger, it will just set the logLevel very high
-    """
-    _enable_disable_default_handlers(False)
-
-
-def enableDefaultHandlers():
-    """(re)Enable the default handlers on all fancyloggers"""
-    _enable_disable_default_handlers(True)
-
-
-def getDetailsLogLevels(fancy=True):
-    """
-    Return list of (name,loglevelname) pairs of existing loggers
-
-    @param fancy: if True, returns only Fancylogger; if False, returns non-FancyLoggers,
-                  anything else, return all loggers
-    """
-    func_map = {
-        True: getAllFancyloggers,
-        False: getAllNonFancyloggers,
-    }
-    func = func_map.get(fancy, getAllExistingLoggers)
-    res = []
-    for name, logger in func():
-        # PlaceHolder instances have no level attribute set
-        level_name = logging.getLevelName(getattr(logger, 'level', logging.NOTSET))
-        res.append((name, level_name))
-    return res
diff --git a/vsc/utils/frozendict.py b/vsc/utils/frozendict.py
deleted file mode 100644
index 21604eed7a..0000000000
--- a/vsc/utils/frozendict.py
+++ /dev/null
@@ -1,56 +0,0 @@
-# taken from https://github.com/slezica/python-frozendict on March 14th 2014 (commit ID b27053e4d1)
-#
-# Copyright (c) 2012 Santiago Lezica
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
-# documentation files (the "Software"), to deal in the Software without restriction, including without limitation
-# the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
-# and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in all copies or substantial portions
-# of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
-# TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
-# CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-# IN THE SOFTWARE
-
-import operator
-from UserDict import DictMixin
-
-
-# minor adjustments:
-# * renamed to FrozenDict
-# * deriving from DictMixin instead of collections.Mapping to make it Python 2.4 compatible
-#   see also http://docs.python.org/2/library/userdict.html#UserDict.DictMixin
-class FrozenDict(object, DictMixin):
-
-    def __init__(self, *args, **kwargs):
-        self.__dict = dict(*args, **kwargs)
-        self.__hash = None
-
-    def __getitem__(self, key):
-        return self.__dict[key]
-
-    def copy(self, **add_or_replace):
-        return FrozenDict(self, **add_or_replace)
-
-    def __iter__(self):
-        return iter(self.__dict)
-
-    def __len__(self):
-        return len(self.__dict)
-
-    def __repr__(self):
-        return '<FrozenDict %s>' % repr(self.__dict)
-
-    def __hash__(self):
-        if self.__hash is None:
-            self.__hash = reduce(operator.xor, map(hash, self.iteritems()), 0)
-
-        return self.__hash
-
-    # minor adjustment: define missing keys() method
-    def keys(self):
-        return self.__dict.keys()
diff --git a/vsc/utils/generaloption.py b/vsc/utils/generaloption.py
deleted file mode 100644
index af6d6397c0..0000000000
--- a/vsc/utils/generaloption.py
+++ /dev/null
@@ -1,1532 +0,0 @@
-#
-#
-# Copyright 2011-2014 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-#
-
-"""
-A class that can be used to generated options to python scripts in a general way.
-
-@author: Stijn De Weirdt (Ghent University)
-@author: Jens Timmerman (Ghent University)
-"""
-
-import ConfigParser
-import copy
-import inspect
-import operator
-import os
-import re
-import StringIO
-import sys
-import textwrap
-from optparse import OptionParser, OptionGroup, Option, Values, HelpFormatter
-from optparse import BadOptionError, SUPPRESS_USAGE, NO_DEFAULT, OptionValueError
-from optparse import SUPPRESS_HELP as nohelp  # supported in optparse of python v2.4
-from optparse import _ as _gettext  # this is gettext normally
-from vsc.utils.dateandtime import date_parser, datetime_parser
-from vsc.utils.fancylogger import getLogger, setLogLevel, getDetailsLogLevels
-from vsc.utils.missing import shell_quote, nub
-from vsc.utils.optcomplete import autocomplete, CompleterOption
-
-
-def set_columns(cols=None):
-    """Set os.environ COLUMNS variable
-        - only if it is not set already
-    """
-    if 'COLUMNS' in os.environ:
-        # do nothing
-        return
-
-    if cols is None:
-        stty = '/usr/bin/stty'
-        if os.path.exists(stty):
-            try:
-                cols = int(os.popen('%s size 2>/dev/null' % stty).read().strip().split(' ')[1])
-            except:
-                # do nothing
-                pass
-
-    if cols is not None:
-        os.environ['COLUMNS'] = "%s" % cols
-
-
-def what_str_list_tuple(name):
-    """Given name, return separator, class and helptext wrt separator.
-        (Currently supports strlist, strtuple, pathlist, pathtuple) 
-    """
-    sep = ','
-    helpsep = 'comma'
-    if name.startswith('path'):
-        sep = os.pathsep
-        helpsep = 'pathsep'
-
-    klass = None
-    if name.endswith('list'):
-        klass = list
-    elif name.endswith('tuple'):
-        klass = tuple
-
-    return sep, klass, helpsep
-
-def check_str_list_tuple(option, opt, value):
-    """
-    check function for strlist and strtuple type
-        assumes value is comma-separated list
-        returns list or tuple of strings
-    """
-    sep, klass, _ = what_str_list_tuple(option.type)
-    split = value.split(sep)
-
-    if klass is None:
-        err = _gettext("check_strlist_strtuple: unsupported type %s" % option.type)
-        raise OptionValueError(err)
-    else:
-        return klass(split)
-
-
-class ExtOption(CompleterOption):
-    """Extended options class
-        - enable/disable support
-
-       Actions:
-         - shorthelp : hook for shortend help messages
-         - confighelp : hook for configfile-style help messages
-         - store_debuglog : turns on fancylogger debugloglevel
-            - also: 'store_infolog', 'store_warninglog'
-         - add : add value to default (result is default + value)
-             - add_first : add default to value (result is value + default)
-             - extend : alias for add with strlist type
-             - type must support + (__add__) and one of negate (__neg__) or slicing (__getslice__)
-         - date : convert into datetime.date
-         - datetime : convert into datetime.datetime
-         - regex: compile str in regexp
-         - store_or_None
-           - set default to None if no option passed,
-           - set to default if option without value passed,
-           - set to value if option with value passed
-           
-        Types:
-          - strlist, strtuple : convert comma-separated string in a list resp. tuple of strings     
-          - pathlist, pathtuple : using os.pathsep, convert pathsep-separated string in a list resp. tuple of strings
-              - the path separator is OS-dependent
-    """
-    EXTEND_SEPARATOR = ','
-
-    ENABLE = 'enable'  # do nothing
-    DISABLE = 'disable'  # inverse action
-
-    EXTOPTION_EXTRA_OPTIONS = ('date', 'datetime', 'regex', 'add', 'add_first',)
-    EXTOPTION_STORE_OR = ('store_or_None',)  # callback type
-    EXTOPTION_LOG = ('store_debuglog', 'store_infolog', 'store_warninglog',)
-    EXTOPTION_HELP = ('shorthelp', 'confighelp',)
-
-    ACTIONS = Option.ACTIONS + EXTOPTION_EXTRA_OPTIONS + EXTOPTION_STORE_OR + EXTOPTION_LOG + EXTOPTION_HELP
-    STORE_ACTIONS = Option.STORE_ACTIONS + EXTOPTION_EXTRA_OPTIONS + EXTOPTION_LOG + ('store_or_None',)
-    TYPED_ACTIONS = Option.TYPED_ACTIONS + EXTOPTION_EXTRA_OPTIONS + EXTOPTION_STORE_OR
-    ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + EXTOPTION_EXTRA_OPTIONS
-
-    TYPE_STRLIST = ['%s%s' % (name, klass) for klass in ['list', 'tuple'] for name in ['str', 'path'] ]
-    TYPE_CHECKER = dict([(x, check_str_list_tuple) for x in TYPE_STRLIST] + Option.TYPE_CHECKER.items())
-    TYPES = tuple(TYPE_STRLIST + list(Option.TYPES))
-    BOOLEAN_ACTIONS = ('store_true', 'store_false',) + EXTOPTION_LOG
-
-    def __init__(self, *args, **kwargs):
-        """Add logger to init"""
-        CompleterOption.__init__(self, *args, **kwargs)
-        self.log = getLogger(self.__class__.__name__)
-
-    def _set_attrs(self, attrs):
-        """overwrite _set_attrs to allow store_or callbacks"""
-        Option._set_attrs(self, attrs)
-        if self.action == 'extend':
-            # alias
-            self.action = 'add'
-            self.type = 'strlist'
-        elif self.action in self.EXTOPTION_STORE_OR:
-            setattr(self, 'store_or', self.action)
-
-            def store_or(option, opt_str, value, parser, *args, **kwargs):
-                """Callback for supporting options with optional values."""
-                # see http://stackoverflow.com/questions/1229146/parsing-empty-options-in-python
-                # ugly code, optparse is crap
-                if parser.rargs and not parser.rargs[0].startswith('-'):
-                    val = option.check_value(opt_str, parser.rargs.pop(0))
-                else:
-                    val = kwargs.get('orig_default', None)
-
-                setattr(parser.values, option.dest, val)
-
-            # without the following, --x=y doesn't work; only --x y
-            self.nargs = 0  # allow 0 args, will also use 0 args
-            if self.type is None:
-                # set to not None, for takes_value to return True
-                self.type = 'string'
-
-            self.callback = store_or
-            self.callback_kwargs = {
-                'orig_default': copy.deepcopy(self.default),
-                }
-            self.action = 'callback'  # act as callback
-            if self.store_or == 'store_or_None':
-                self.default = None
-            else:
-                self.log.raiseException("_set_attrs: unknown store_or %s" % self.store_or, exception=ValueError)
-
-    def take_action(self, action, dest, opt, value, values, parser):
-        """Extended take_action"""
-        orig_action = action  # keep copy
-
-        if action == 'shorthelp':
-            parser.print_shorthelp()
-            parser.exit()
-        elif action == 'confighelp':
-            parser.print_confighelp()
-            parser.exit()
-        elif action in ('store_true', 'store_false',) + self.EXTOPTION_LOG:
-            if action in self.EXTOPTION_LOG:
-                action = 'store_true'
-
-            if opt.startswith("--%s-" % self.ENABLE):
-                # keep action
-                pass
-            elif opt.startswith("--%s-" % self.DISABLE):
-                # reverse action
-                if action in ('store_true',) + self.EXTOPTION_LOG:
-                    action = 'store_false'
-                elif action in ('store_false',):
-                    action = 'store_true'
-
-            if orig_action in self.EXTOPTION_LOG and action == 'store_true':
-                newloglevel = orig_action.split('_')[1][:-3].upper()
-                logstate = ", ".join(["(%s, %s)" % (n, l) for n, l in getDetailsLogLevels()])
-                self.log.debug("changing loglevel to %s, current state: %s" % (newloglevel, logstate))
-                setLogLevel(newloglevel)
-                self.log.debug("changed loglevel to %s, previous state: %s" % (newloglevel, logstate))
-                if hasattr(values, '_logaction_taken'):
-                    values._logaction_taken[dest] = True
-
-            Option.take_action(self, action, dest, opt, value, values, parser)
-
-        elif action in self.EXTOPTION_EXTRA_OPTIONS:
-            if action in ("add", "add_first",):
-                # determine type from lvalue
-                # set default first
-                values.ensure_value(dest, type(value)())
-                default = getattr(values, dest)
-                if not (hasattr(default, '__add__') and
-                        (hasattr(default, '__neg__') or hasattr(default, '__getslice__'))):
-                    msg = "Unsupported type %s for action %s (requires + and one of negate or slice)"
-                    self.log.raiseException(msg % (type(default), action))
-                if action == 'add':
-                    lvalue = default + value
-                elif action == 'add_first':
-                    lvalue = value + default
-            elif action == "date":
-                lvalue = date_parser(value)
-            elif action == "datetime":
-                lvalue = datetime_parser(value)
-            elif action == "regex":
-                lvalue = re.compile(r'' + value)
-            else:
-                msg = "Unknown extended option action %s (known: %s)"
-                self.log.raiseException(msg % (action, self.EXTOPTION_EXTRA_OPTIONS))
-            setattr(values, dest, lvalue)
-        else:
-            Option.take_action(self, action, dest, opt, value, values, parser)
-
-        # set flag to mark as passed by action (ie not by default)
-        # - distinguish from setting default value through option
-        if hasattr(values, '_action_taken'):
-            values._action_taken[dest] = True
-
-
-class PassThroughOptionParser(OptionParser):
-    """
-    "Pass-through" option parsing -- an OptionParser that ignores
-    unknown options and lets them pile up in the leftover argument
-    list.  Useful for programs that pass unknown options through
-    to a sub-program.
-    from http://www.koders.com/python/fid9DFF5006AF4F52BA6483C4F654E26E6A20DBC73C.aspx?s=add+one#L27
-    """
-    def __init__(self):
-        OptionParser.__init__(self, add_help_option=False, usage=SUPPRESS_USAGE)
-
-    def _process_long_opt(self, rargs, values):
-        """Extend optparse code with catch of unknown long options error"""
-        try:
-            OptionParser._process_long_opt(self, rargs, values)
-        except BadOptionError, err:
-            self.largs.append(err.opt_str)
-
-    def _process_short_opts(self, rargs, values):
-        """Process the short options, pass unknown to largs"""
-        # implementation from recent optparser
-        arg = rargs.pop(0)
-        stop = False
-        i = 1
-        for ch in arg[1:]:
-            opt = "-" + ch
-            option = self._short_opt.get(opt)
-            i += 1  # we have consumed a character
-
-            if not option:
-                # don't fail here, just append to largs
-                # raise BadOptionError(opt)
-                self.largs.append(opt)
-                return
-            if option.takes_value():
-                # Any characters left in arg?  Pretend they're the
-                # next arg, and stop consuming characters of arg.
-                if i < len(arg):
-                    rargs.insert(0, arg[i:])
-                    stop = True
-
-                nargs = option.nargs
-                if len(rargs) < nargs:
-                    if nargs == 1:
-                        self.error(_("%s option requires an argument") % opt)
-                    else:
-                        self.error(_("%s option requires %d arguments")
-                                   % (opt, nargs))
-                elif nargs == 1:
-                    value = rargs.pop(0)
-                else:
-                    value = tuple(rargs[0:nargs])
-                    del rargs[0:nargs]
-
-            else:  # option doesn't take a value
-                value = None
-
-            option.process(opt, value, values, self)
-
-            if stop:
-                break
-
-
-class ExtOptionGroup(OptionGroup):
-    """An OptionGroup with support for configfile section names"""
-    RESERVED_SECTIONS = [ConfigParser.DEFAULTSECT]
-    NO_SECTION = ('NO', 'SECTION')
-
-    def __init__(self, *args, **kwargs):
-        self.log = getLogger(self.__class__.__name__)
-        section_name = kwargs.pop('section_name', None)
-        if section_name in self.RESERVED_SECTIONS:
-            self.log.raiseException('Cannot use reserved name %s for section name.' % section_name)
-
-        OptionGroup.__init__(self, *args, **kwargs)
-        self.section_name = section_name
-        self.section_options = []
-
-    def add_option(self, *args, **kwargs):
-        """Extract configfile section info"""
-        option = OptionGroup.add_option(self, *args, **kwargs)
-        self.section_options.append(option)
-
-        return option
-
-
-class ExtOptionParser(OptionParser):
-    """
-    Make an option parser that limits the C{-h} / C{--shorthelp} to short opts only,     
-    C{-H} / C{--help} for all options.
-
-    Pass options through environment. Like:
-
-      - C{export PROGNAME_SOMEOPTION = value} will generate {--someoption=value}
-      - C{export PROGNAME_OTHEROPTION = 1} will generate {--otheroption}
-      - C{export PROGNAME_OTHEROPTION = 0} (or no or false) won't do anything
-
-    distinction is made based on option.action in TYPED_ACTIONS allow
-    C{--enable-} / C{--disable-} (using eg ExtOption option_class)
-    """
-    shorthelp = ('h', "--shorthelp",)
-    longhelp = ('H', "--help",)
-
-    VALUES_CLASS = Values
-    DESCRIPTION_DOCSTRING = False
-
-    def __init__(self, *args, **kwargs):
-        self.log = getLogger(self.__class__.__name__)
-        self.help_to_string = kwargs.pop('help_to_string', None)
-        self.help_to_file = kwargs.pop('help_to_file', None)
-        self.envvar_prefix = kwargs.pop('envvar_prefix', None)
-        self.process_env_options = kwargs.pop('process_env_options', True)
-
-        # py2.4 epilog compatibilty with py2.7 / optparse 1.5.3
-        self.epilog = kwargs.pop('epilog', None)
-
-        if not 'option_class' in kwargs:
-            kwargs['option_class'] = ExtOption
-        OptionParser.__init__(self, *args, **kwargs)
-
-        # redefine formatter for py2.4 compat
-        if not hasattr(self.formatter, 'format_epilog'):
-            setattr(self.formatter, 'format_epilog', self.formatter.format_description)
-
-        if self.epilog is None:
-            self.epilog = []
-
-        if hasattr(self.option_class, 'ENABLE') and hasattr(self.option_class, 'DISABLE'):
-            epilogtxt = 'Boolean options support %(disable)s prefix to do the inverse of the action,'
-            epilogtxt += ' e.g. option --someopt also supports --disable-someopt.'
-            self.epilog.append(epilogtxt % {'disable': self.option_class.DISABLE})
-
-        self.environment_arguments = None
-        self.commandline_arguments = None
-
-    def set_description_docstring(self):
-        """Try to find the main docstring and add it if description is not None"""
-        stack = inspect.stack()[-1]
-        try:
-            docstr = stack[0].f_globals.get('__doc__', None)
-        except:
-            self.log.debug("set_description_docstring: no docstring found in latest stack globals")
-            docstr = None
-
-        if docstr is not None:
-            indent = " "
-            # kwargs and ** magic to deal with width
-            kwargs = {
-                'initial_indent': indent * 2,
-                'subsequent_indent': indent * 2,
-                'replace_whitespace': False,
-            }
-            width = os.environ.get('COLUMNS', None)
-            if width is not None:
-                # default textwrap width
-                try:
-                    kwargs['width'] = int(width)
-                except:
-                    pass
-
-            # deal with newlines in docstring
-            final_docstr = ['']
-            for line in str(docstr).strip("\n ").split("\n"):
-                final_docstr.append(textwrap.fill(line, **kwargs))
-            final_docstr.append('')
-
-            return "\n".join(final_docstr)
-
-    def format_description(self, formatter):
-        """Extend to allow docstring as description"""
-        description = ''
-        if self.description == 'NONE_AND_NOT_NONE':
-            if self.DESCRIPTION_DOCSTRING:
-                description = self.set_description_docstring()
-        elif self.description:
-            description = formatter.format_description(self.get_description())
-
-        return str(description)
-
-    def set_usage(self, usage):
-        """Return usage and set try to set autogenerated description."""
-        usage = OptionParser.set_usage(self, usage)
-
-        if self.description is None:
-            self.description = 'NONE_AND_NOT_NONE'
-
-        return usage
-
-    def get_default_values(self):
-        """Introduce the ExtValues class with class constant
-            - make it dynamic, otherwise the class constant is shared between multiple instances
-            - class constant is used to avoid _action_taken as option in the __dict__ 
-                - only works by using reference to object
-                - same for _logaction_taken
-        """
-        values = OptionParser.get_default_values(self)
-
-        class ExtValues(self.VALUES_CLASS):
-            _action_taken = {}
-            _logaction_taken = {}
-
-        newvalues = ExtValues()
-        newvalues.__dict__ = values.__dict__.copy()
-        return newvalues
-
-    def format_help(self, formatter=None):
-        """For py2.4 compatibility reasons (missing epilog). This is the py2.7 / optparse 1.5.3 code"""
-        if formatter is None:
-            formatter = self.formatter
-        result = []
-        if self.usage:
-            result.append(self.get_usage() + "\n")
-        if self.description:
-            result.append(self.format_description(formatter) + "\n")
-        result.append(self.format_option_help(formatter))
-        result.append(self.format_epilog(formatter))
-        return "".join(result)
-
-    def format_epilog(self, formatter):
-        """Allow multiple epilog parts"""
-        res = []
-        if not isinstance(self.epilog, (list, tuple,)):
-            self.epilog = [self.epilog]
-        for epi in self.epilog:
-            res.append(formatter.format_epilog(epi))
-        return "".join(res)
-
-    def print_shorthelp(self, fh=None):
-        """Print a shortened help (no longopts)"""
-        for opt in self._get_all_options():
-            if opt._short_opts is None or len([x for x in opt._short_opts if len(x) > 0]) == 0:
-                opt.help = nohelp
-            opt._long_opts = []  # remove all long_opts
-
-        removeoptgrp = []
-        for optgrp in self.option_groups:
-            # remove all option groups that have only nohelp options
-            if reduce(operator.and_, [opt.help == nohelp for opt in optgrp.option_list]):
-                removeoptgrp.append(optgrp)
-        for optgrp in removeoptgrp:
-            self.option_groups.remove(optgrp)
-
-        self.print_help(fh)
-
-    def print_help(self, fh=None):
-        """Intercept print to file to print to string and remove the ENABLE/DISABLE options from help"""
-        if self.help_to_string:
-            self.help_to_file = StringIO.StringIO()
-        if fh is None:
-            fh = self.help_to_file
-
-        if hasattr(self.option_class, 'ENABLE') and hasattr(self.option_class, 'DISABLE'):
-            def _is_enable_disable(x):
-                """Does the option start with ENABLE/DISABLE"""
-                _e = x.startswith("--%s-" % self.option_class.ENABLE)
-                _d = x.startswith("--%s-" % self.option_class.DISABLE)
-                return _e or _d
-            for opt in self._get_all_options():
-                # remove all long_opts with ENABLE/DISABLE naming
-                opt._long_opts = [x for x in opt._long_opts if not _is_enable_disable(x)]
-
-        OptionParser.print_help(self, fh)
-
-    def print_confighelp(self, fh=None):
-        """Print help as a configfile."""
-
-        # walk through all optiongroups
-        # append where necessary, keep track of sections
-        all_groups = {}
-        sections = []
-        for gr in self.option_groups:
-            section = gr.section_name
-            if not (section is None or section == ExtOptionGroup.NO_SECTION):
-                if not section in sections:
-                    sections.append(section)
-                ag = all_groups.setdefault(section, [])
-                ag.extend(gr.section_options)
-
-        # set MAIN section first if exists
-        main_idx = sections.index('MAIN')
-        if main_idx > 0:  # not needed if it main_idx == 0
-            sections.remove('MAIN')
-            sections.insert(0, 'MAIN')
-
-        option_template = "# %(help)s\n#%(option)s=\n"
-        txt = ''
-        for section in sections:
-            txt += "[%s]\n" % section
-            for option in all_groups[section]:
-                data = {
-                    'help': option.help,
-                    'option': option.get_opt_string().lstrip('-'),
-                }
-                txt += option_template % data
-            txt += "\n"
-
-        # overwrite the format_help to be able to use the the regular print_help
-        def format_help(*args, **kwargs):
-            return txt
-        self.format_help = format_help
-        self.print_help(fh)
-
-    def _add_help_option(self):
-        """Add shorthelp and longhelp"""
-        self.add_option("-%s" % self.shorthelp[0],
-                        self.shorthelp[1],  # *self.shorthelp[1:], syntax error in Python 2.4
-                        action="shorthelp",
-                        help=_gettext("show short help message and exit"))
-        self.add_option("-%s" % self.longhelp[0],
-                        self.longhelp[1],  # *self.longhelp[1:], syntax error in Python 2.4
-                        action="help",
-                        help=_gettext("show full help message and exit"))
-        self.add_option("--confighelp",
-                        action="confighelp",
-                        help=_gettext("show help as annotated configfile"))
-
-    def _get_args(self, args):
-        """Prepend the options set through the environment"""
-        self.commandline_arguments = OptionParser._get_args(self, args)
-        self.get_env_options()
-        return self.environment_arguments + self.commandline_arguments  # prepend the environment options as longopts
-
-    def get_env_options_prefix(self):
-        """Return the prefix to use for options passed through the environment"""
-        # sys.argv[0] or the prog= argument of the optionparser, strip possible extension
-        if self.envvar_prefix is None:
-            self.envvar_prefix = self.get_prog_name().rsplit('.', 1)[0].upper()
-        return self.envvar_prefix
-
-    def get_env_options(self):
-        """Retrieve options from the environment: prefix_longopt.upper()"""
-        self.environment_arguments = []
-
-        if not self.process_env_options:
-            self.log.debug("Not processing environment for options")
-            return
-
-        if self.envvar_prefix is None:
-            self.get_env_options_prefix()
-
-        epilogprefixtxt = "All long option names can be passed as environment variables. "
-        epilogprefixtxt += "Variable name is %(prefix)s_<LONGNAME> "
-        epilogprefixtxt += "eg. --some-opt is same as setting %(prefix)s_SOME_OPT in the environment."
-        self.epilog.append(epilogprefixtxt % {'prefix': self.envvar_prefix})
-
-        for opt in self._get_all_options():
-            if opt._long_opts is None:
-                continue
-            for lo in opt._long_opts:
-                if len(lo) == 0:
-                    continue
-                env_opt_name = "%s_%s" % (self.envvar_prefix, lo.lstrip('-').replace('-', '_').upper())
-                val = os.environ.get(env_opt_name, None)
-                if not val is None:
-                    if opt.action in opt.TYPED_ACTIONS:  # not all typed actions are mandatory, but let's assume so
-                        self.environment_arguments.append("%s=%s" % (lo, val))
-                    else:
-                        # interpretation of values: 0/no/false means: don't set it
-                        if not ("%s" % val).lower() in ("0", "no", "false",):
-                            self.environment_arguments.append("%s" % lo)
-                else:
-                    self.log.debug("Environment variable %s is not set" % env_opt_name)
-
-        self.log.debug("Environment variable options with prefix %s: %s" % (self.envvar_prefix, self.environment_arguments))
-        return self.environment_arguments
-
-    def get_option_by_long_name(self, name):
-        """Return the option matching the long option name"""
-        for opt in self._get_all_options():
-            if opt._long_opts is None:
-                continue
-            for lo in opt._long_opts:
-                if len(lo) == 0:
-                    continue
-                dest = lo.lstrip('-')
-                if name == dest:
-                    return opt
-
-        return None
-
-
-class GeneralOption(object):
-    """
-    'Used-to-be simple' wrapper class for option parsing
-
-    Options with go_ prefix are for this class, the remainder is passed to the parser
-        - go_args : use these instead of of sys.argv[1:]
-        - go_columns : specify column width (in columns)
-        - go_useconfigfiles : use configfiles or not (default set by CONFIGFILES_USE)
-            if True, an option --configfiles will be added
-        - go_configfiles : list of configfiles to parse. Uses ConfigParser.read; last file wins
-        - go_configfiles_initenv : section dict of key/value dict; inserted before configfileparsing
-            As a special case, using all uppercase key in DEFAULT section with a case-sensitive 
-            configparser can be used to set "constants" for easy interpolation in all sections.
-        - go_loggername : name of logger, default classname
-        - go_mainbeforedefault : set the main options before the default ones
-        - go_autocompleter : dict with named options to pass to the autocomplete call (eg arg_completer)
-            if is None: disable autocompletion; default is {} (ie no extra args passed)
-
-    Sections starting with the string 'raw_' in the sectionname will be parsed as raw sections,
-    meaning there will be no interpolation of the strings. This comes in handy if you want to configure strings
-    with templates in them.
-
-    Options process order (last one wins)
-        0. default defined with option
-        1. value in (last) configfile (last configfile wins)
-        2. options parsed by option parser
-        In case the ExtOptionParser is used
-            0. value set through environment variable
-            1. value set through commandline option
-    """
-    OPTIONNAME_PREFIX_SEPARATOR = '-'
-
-    DEBUG_OPTIONS_BUILD = False  # enable debug mode when building the options ?
-
-    USAGE = None
-    ALLOPTSMANDATORY = True
-    PARSER = ExtOptionParser
-    INTERSPERSED = True  # mix args with options
-
-    CONFIGFILES_USE = True
-    CONFIGFILES_RAISE_MISSING = False
-    CONFIGFILES_INIT = []  # initial list of defaults, overwritten by go_configfiles options
-    CONFIGFILES_IGNORE = []
-    CONFIGFILES_MAIN_SECTION = 'MAIN'  # sectionname that contains the non-grouped/non-prefixed options
-    CONFIGFILE_PARSER = ConfigParser.SafeConfigParser
-    CONFIGFILE_CASESENSITIVE = True
-
-    METAVAR_DEFAULT = True  # generate a default metavar
-    METAVAR_MAP = None  # metvar, list of longopts map
-
-    OPTIONGROUP_SORTED_OPTIONS = True
-
-    PROCESSED_OPTIONS_PROPERTIES = ['type', 'default', 'action', 'opt_name', 'prefix', 'section_name']
-
-    VERSION = None  # set the version (will add --version)
-
-    DEFAULTSECT = ConfigParser.DEFAULTSECT
-    DEFAULT_LOGLEVEL = None
-    DEFAULT_CONFIGFILES = None
-    DEFAULT_IGNORECONFIGFILES = None
-
-    def __init__(self, **kwargs):
-        go_args = kwargs.pop('go_args', None)
-        self.no_system_exit = kwargs.pop('go_nosystemexit', None)  # unit test option
-        self.use_configfiles = kwargs.pop('go_useconfigfiles', self.CONFIGFILES_USE)  # use or ignore config files
-        self.configfiles = kwargs.pop('go_configfiles', self.CONFIGFILES_INIT[:])  # configfiles to parse
-        configfiles_initenv = kwargs.pop('go_configfiles_initenv', None)  # initial environment for configfiles to parse
-        prefixloggername = kwargs.pop('go_prefixloggername', False)  # name of logger is same as envvar prefix
-        mainbeforedefault = kwargs.pop('go_mainbeforedefault', False)  # Set the main options before the default ones
-        autocompleter = kwargs.pop('go_autocompleter', {})  # Pass these options to the autocomplete call
-
-        set_columns(kwargs.pop('go_columns', None))
-
-        kwargs.update({
-            'option_class': ExtOption,
-            'usage': kwargs.get('usage', self.USAGE),
-            'version': self.VERSION,
-        })
-        self.parser = self.PARSER(**kwargs)
-        self.parser.allow_interspersed_args = self.INTERSPERSED
-
-        self.configfile_parser = None
-        self.configfile_remainder = {}
-
-        loggername = self.__class__.__name__
-        if prefixloggername:
-            prefix = self.parser.get_env_options_prefix()
-            if prefix is not None and len(prefix) > 0:
-                loggername = prefix.replace('.', '_')  # . indicate hierarchy in logging land
-
-        self.log = getLogger(loggername)
-        self.options = None
-        self.args = None
-
-        self.autocompleter = autocompleter
-
-        self.auto_prefix = None
-        self.auto_section_name = None
-
-        self.processed_options = {}
-
-        self.config_prefix_sectionnames_map = {}
-
-        self.set_go_debug()
-
-        if mainbeforedefault:
-            self.main_options()
-            self._default_options()
-        else:
-            self._default_options()
-            self.main_options()
-
-        self.parseoptions(options_list=go_args)
-
-        if not self.options is None:
-            # None for eg usage/help
-            self.configfile_parser_init(initenv=configfiles_initenv)
-            self.parseconfigfiles()
-
-            self._set_default_loglevel()
-
-            self.postprocess()
-
-            self.validate()
-
-    def set_go_debug(self):
-        """Check if debug options are on and then set fancylogger to debug.
-        This is not the default way to set debug, it enables debug logging
-        in an earlier stage to debug generaloption itself.
-        """
-        if self.options is None:
-            if self.DEBUG_OPTIONS_BUILD:
-                setLogLevel('DEBUG')
-
-    def _default_options(self):
-        """Generate default options: debug/log and configfile"""
-        self._make_debug_options()
-        self._make_configfiles_options()
-
-    def _make_debug_options(self):
-        """Add debug/logging options: debug and info"""
-        self._logopts = {
-            'debug': ("Enable debug log mode", None, "store_debuglog", False, 'd'),
-            'info': ("Enable info log mode", None, "store_infolog", False),
-            'quiet': ("Enable quiet/warning log mode", None, "store_warninglog", False),
-        }
-
-        descr = ['Debug and logging options', '']
-        self.log.debug("Add debug and logging options descr %s opts %s (no prefix)" % (descr, self._logopts))
-        self.add_group_parser(self._logopts, descr, prefix=None)
-
-    def _set_default_loglevel(self):
-        """Set the default loglevel if no logging options are set"""
-        loglevel_set = sum([getattr(self.options, name, False) for name in self._logopts.keys()])
-        if not loglevel_set and self.DEFAULT_LOGLEVEL is not None:
-            setLogLevel(self.DEFAULT_LOGLEVEL)
-
-    def _make_configfiles_options(self):
-        """Add configfiles option"""
-        opts = {
-            'configfiles': ("Parse (additional) configfiles", "strlist", "add", self.DEFAULT_CONFIGFILES),
-            'ignoreconfigfiles': ("Ignore configfiles", "strlist", "add", self.DEFAULT_IGNORECONFIGFILES),
-        }
-        descr = ['Configfile options', '']
-        self.log.debug("Add configfiles options descr %s opts %s (no prefix)" % (descr, opts))
-        self.add_group_parser(opts, descr, prefix=None, section_name=ExtOptionGroup.NO_SECTION)
-
-    def main_options(self):
-        """Create the main options automatically"""
-        # make_init is deprecated
-        if hasattr(self, 'make_init'):
-            self.log.debug('main_options: make_init is deprecated. Rename function to main_options.')
-            getattr(self, 'make_init')()
-        else:
-            # function names which end with _options and do not start with main or _
-            reg_main_options = re.compile("^(?!_|main).*_options$")
-            names = [x for x in dir(self) if reg_main_options.search(x)]
-            if len(names) == 0:
-                self.log.error("main_options: no options functions implemented")
-            else:
-                for name in names:
-                    fn = getattr(self, name)
-                    if callable(fn):  # inspect.isfunction fails beacuse this is a boundmethod
-                        self.auto_section_name = '_'.join(name.split('_')[:-1])
-                        self.log.debug('main_options: adding options from %s (auto_section_name %s)' %
-                                       (name, self.auto_section_name))
-                        fn()
-                        self.auto_section_name = None  # reset it
-
-    def make_option_metavar(self, longopt, details):
-        """Generate the metavar for option longopt
-        @type longopt: str
-        @type details: tuple
-        """
-        if self.METAVAR_MAP is not None:
-            for metavar, longopts in self.METAVAR_MAP.items():
-                if longopt in longopts:
-                    return metavar
-
-        if self.METAVAR_DEFAULT:
-            return longopt.upper()
-
-    def add_group_parser(self, opt_dict, description, prefix=None, otherdefaults=None, section_name=None):
-        """Make a group parser from a dict
-
-
-        @type opt_dict: dict
-        @type description: a 2 element list (short and long description)
-        @section_name: str, the name of the section group in the config file.
-
-        @param opt_dict: options, with the form C{"long_opt" : value}.
-        Value is a C{tuple} containing
-        C{(help,type,action,default(,optional string=short option; list/tuple=choices; dict=add_option kwargs))}
-
-        help message passed through opt_dict will be extended with type and default
-
-        If section_name is None, prefix will be used. If prefix is None or '', 'DEFAULT' is used.
-
-        """
-        if opt_dict is None:
-            # skip opt_dict None
-            # if opt_dict is empty dict {}, the eg the descritionis added to the help
-            self.log.debug("Skipping opt_dict %s with description %s prefix %s" %
-                           (opt_dict, description, prefix))
-            return
-
-        if otherdefaults is None:
-            otherdefaults = {}
-
-        self.log.debug("add_group_parser: passed prefix %s section_name %s" % (prefix, section_name))
-        self.log.debug("add_group_parser: auto_prefix %s auto_section_name %s" %
-                       (self.auto_prefix, self.auto_section_name))
-
-        if prefix is None:
-            if self.auto_prefix is None:
-                prefix = ''
-            else:
-                prefix = self.auto_prefix
-
-        if section_name is None:
-            if prefix is not None and len(prefix) > 0 and not (prefix == self.auto_prefix):
-                section_name = prefix
-            elif self.auto_section_name is not None and len(self.auto_section_name) > 0:
-                section_name = self.auto_section_name
-            else:
-                section_name = self.CONFIGFILES_MAIN_SECTION
-
-        self.log.debug("add_group_parser: set prefix %s section_name %s" % (prefix, section_name))
-
-        # add the section name to the help output
-        if section_name is None or section_name == ExtOptionGroup.NO_SECTION:
-            section_help = ''
-        else:
-            section_help = " (configfile section %s)" % (section_name)
-
-        if description[1]:
-            short_description = description[0]
-            long_description = "%s%s" % (description[1], section_help)
-        else:
-            short_description = "%s%s" % (description[0], section_help)
-            long_description = description[1]
-
-        opt_grp = ExtOptionGroup(self.parser, short_description, long_description, section_name=section_name)
-        keys = opt_dict.keys()
-        if self.OPTIONGROUP_SORTED_OPTIONS:
-            keys.sort()  # alphabetical
-        for key in keys:
-            completer = None
-
-            details = opt_dict[key]
-
-            hlp = details[0]
-            typ = details[1]
-            action = details[2]
-            default = details[3]
-            # easy override default with otherdefault
-            if key in otherdefaults:
-                default = otherdefaults.get(key)
-
-            extra_help = []
-            if typ in ExtOption.TYPE_STRLIST:
-                sep, klass, helpsep = what_str_list_tuple(typ)
-                extra_help.append("type %s-separated %s" % (helpsep, klass.__name__))
-            elif typ is not None:
-                extra_help.append("type %s" % typ)
-
-            if default is not None:
-                if len(str(default)) == 0:
-                    extra_help.append("def ''")  # empty string
-                elif typ in ExtOption.TYPE_STRLIST:
-                    extra_help.append("def %s" % sep.join(default))
-                else:
-                    extra_help.append("def %s" % default)
-
-            if len(extra_help) > 0:
-                hlp += " (%s)" % ("; ".join(extra_help))
-
-            opt_name, opt_dest = self.make_options_option_name_and_destination(prefix, key)
-
-            args = ["--%s" % opt_name]
-
-            # this has to match PROCESSED_OPTIONS_PROPERTIES
-            self.processed_options[opt_dest] = [typ, default, action, opt_name, prefix, section_name]  # add longopt
-            if not len(self.processed_options[opt_dest]) == len(self.PROCESSED_OPTIONS_PROPERTIES):
-                self.log.raiseException("PROCESSED_OPTIONS_PROPERTIES length mismatch")
-
-            nameds = {
-                'dest': opt_dest,
-                'action': action,
-            }
-            metavar = self.make_option_metavar(key, details)
-            if metavar is not None:
-                nameds['metavar'] = metavar
-
-            if default is not None:
-                nameds['default'] = default
-
-            if typ:
-                nameds['type'] = typ
-
-            passed_kwargs = {}
-            if len(details) >= 5:
-                for extra_detail in details[4:]:
-                    if isinstance(extra_detail, (list, tuple,)):
-                        # choices
-                        nameds['choices'] = ["%s" % x for x in extra_detail]  # force to strings
-                        hlp += ' (choices: %s)' % ', '.join(nameds['choices'])
-                    elif isinstance(extra_detail, basestring) and len(extra_detail) == 1:
-                        args.insert(0, "-%s" % extra_detail)
-                    elif isinstance(extra_detail, (dict,)):
-                        # extract any optcomplete completer hints
-                        completer = extra_detail.pop('completer', None)
-
-                        # add remainder
-                        passed_kwargs.update(extra_detail)
-                    else:
-                        self.log.raiseException("add_group_parser: unknown extra detail %s" % extra_detail)
-
-            # add help
-            nameds['help'] = hlp
-
-            if hasattr(self.parser.option_class, 'ENABLE') and hasattr(self.parser.option_class, 'DISABLE'):
-                if action in self.parser.option_class.BOOLEAN_ACTIONS:
-                    args.append("--%s-%s" % (self.parser.option_class.ENABLE, opt_name))
-                    args.append("--%s-%s" % (self.parser.option_class.DISABLE, opt_name))
-
-            # force passed_kwargs as final nameds
-            nameds.update(passed_kwargs)
-            opt = opt_grp.add_option(*args, **nameds)
-
-            if completer is not None:
-                opt.completer = completer
-
-        self.parser.add_option_group(opt_grp)
-
-        # map between prefix and sectionnames
-        prefix_section_names = self.config_prefix_sectionnames_map.setdefault(prefix, [])
-        if not section_name in prefix_section_names:
-            prefix_section_names.append(section_name)
-            self.log.debug("Added prefix %s to list of sectionnames for %s" % (prefix, section_name))
-
-    def default_parseoptions(self):
-        """Return default options"""
-        return sys.argv[1:]
-
-    def autocomplete(self):
-        """Set the autocompletion magic via optcomplete"""
-        # very basic for now, no special options
-        if self.autocompleter is None:
-            self.log.debug('self.autocompleter is None, disabling autocompleter')
-        else:
-            self.log.debug('setting autocomplete with args %s' % self.autocompleter)
-            autocomplete(self.parser, **self.autocompleter)
-
-    def parseoptions(self, options_list=None):
-        """Parse the options"""
-        if options_list is None:
-            options_list = self.default_parseoptions()
-
-        self.autocomplete()
-
-        try:
-            (self.options, self.args) = self.parser.parse_args(options_list)
-        except SystemExit, err:
-            try:
-                msg = err.message
-            except AttributeError:
-                # py2.4
-                msg = str(err)
-            self.log.debug("parseoptions: parse_args err %s code %s" % (msg, err.code))
-            if self.no_system_exit:
-                return
-            else:
-                sys.exit(err.code)
-
-        self.log.debug("parseoptions: options from environment %s" % (self.parser.environment_arguments))
-        self.log.debug("parseoptions: options from commandline %s" % (self.parser.commandline_arguments))
-
-        # args should be empty, since everything is optional
-        if len(self.args) > 1:
-            self.log.debug("Found remaining args %s" % self.args)
-            if self.ALLOPTSMANDATORY:
-                self.parser.error("Invalid arguments args %s" % self.args)
-
-        self.log.debug("Found options %s args %s" % (self.options, self.args))
-
-    def configfile_parser_init(self, initenv=None):
-        """
-        Initialise the confgiparser to use.
-        
-            @params initenv: insert initial environment into the configparser. 
-                It is a dict of dicts; the first level key is the section name; 
-                the 2nd level key,value is the key=value. 
-                All section names, keys and values are converted to strings.
-        """
-        self.configfile_parser = self.CONFIGFILE_PARSER()
-
-        # make case sensitive
-        if self.CONFIGFILE_CASESENSITIVE:
-            self.log.debug('Initialise case sensitive configparser')
-            self.configfile_parser.optionxform = str
-        else:
-            self.log.debug('Initialise case insensitive configparser')
-            self.configfile_parser.optionxform = str.lower
-
-        # insert the initenv in the parser
-        if initenv is None:
-            initenv = {}
-
-        for name, section in initenv.items():
-            name = str(name)
-            if name == self.DEFAULTSECT:
-                # is protected/reserved (and hidden)
-                pass
-            elif not self.configfile_parser.has_section(name):
-                self.configfile_parser.add_section(name)
-
-            for key, value in section.items():
-                self.configfile_parser.set(name, str(key), str(value))
-
-    def parseconfigfiles(self):
-        """Parse configfiles"""
-        if not self.use_configfiles:
-            self.log.debug('parseconfigfiles: use_configfiles False, skipping configfiles')
-            return
-
-        if self.configfiles is None:
-            self.configfiles = []
-
-        self.log.debug("parseconfigfiles: configfiles initially set %s" % self.configfiles)
-
-        option_configfiles = self.options.__dict__.get('configfiles', [])  # empty list, will win so no defaults
-        option_ignoreconfigfiles = self.options.__dict__.get('ignoreconfigfiles', self.CONFIGFILES_IGNORE)
-
-        self.log.debug("parseconfigfiles: configfiles set through commandline %s" % option_configfiles)
-        self.log.debug("parseconfigfiles: ignoreconfigfiles set through commandline %s" % option_ignoreconfigfiles)
-        if option_configfiles is not None:
-            self.configfiles.extend(option_configfiles)
-
-        if option_ignoreconfigfiles is None:
-            option_ignoreconfigfiles = []
-
-        # Configparser fails on broken config files
-        # - if config file doesn't exist, it's no issue
-        configfiles = []
-        for fn in self.configfiles:
-            if not os.path.isfile(fn):
-                if self.CONFIGFILES_RAISE_MISSING:
-                    self.log.raiseException("parseconfigfiles: configfile %s not found." % fn)
-                else:
-                    self.log.debug("parseconfigfiles: configfile %s not found, will be skipped" % fn)
-
-            if fn in option_ignoreconfigfiles:
-                self.log.debug("parseconfigfiles: configfile %s will be ignored %s" % fn)
-            else:
-                configfiles.append(fn)
-
-        try:
-            parsed_files = self.configfile_parser.read(configfiles)
-        except:
-            self.log.raiseException("parseconfigfiles: problem during read")
-
-        self.log.debug("parseconfigfiles: following files were parsed %s" % parsed_files)
-        self.log.debug("parseconfigfiles: following files were NOT parsed %s" %
-                       [x for x in configfiles if not x in parsed_files])
-        self.log.debug("parseconfigfiles: sections (w/o %s) %s" %
-                       (self.DEFAULTSECT, self.configfile_parser.sections()))
-
-        # walk through list of section names
-        # - look for options set though config files
-        configfile_values = {}
-        configfile_options_default = {}
-        configfile_cmdline = []
-        configfile_cmdline_dest = []  # expected destinations
-
-        # won't parse
-        cfg_sections = self.config_prefix_sectionnames_map.values()  # without DEFAULT
-        for section in cfg_sections:
-            if not section in self.config_prefix_sectionnames_map.values():
-                self.log.warning("parseconfigfiles: found section %s, won't be parsed" % section)
-                continue
-
-        # add any non-option related configfile data to configfile_remainder dict
-        cfg_sections_flat = [name for section_names in cfg_sections for name in section_names]
-        for section in self.configfile_parser.sections():
-            if section not in cfg_sections_flat:
-                self.log.debug("parseconfigfiles: found section %s, adding to remainder" % section)
-                remainder = self.configfile_remainder.setdefault(section, {})
-                # parse the remaining options, sections starting with 'raw_'
-                # as their name will be considered raw sections
-                for opt, val in self.configfile_parser.items(section, raw=(section.startswith('raw_'))):
-                    remainder[opt] = val
-
-        # options are passed to the commandline option parser
-        for prefix, section_names in self.config_prefix_sectionnames_map.items():
-            for section in section_names:
-                # default section is treated separate in ConfigParser
-                if not self.configfile_parser.has_section(section):
-                    self.log.debug('parseconfigfiles: no section %s' % str(section))
-                    continue
-                elif section == ExtOptionGroup.NO_SECTION:
-                    self.log.debug('parseconfigfiles: ignoring NO_SECTION %s' % str(section))
-                    continue
-                elif section.lower() == 'default':
-                    self.log.debug('parseconfigfiles: ignoring default section %s' % section)
-                    continue
-
-                for opt, val in self.configfile_parser.items(section):
-                    self.log.debug('parseconfigfiles: section %s option %s val %s' % (section, opt, val))
-
-                    opt_name, opt_dest = self.make_options_option_name_and_destination(prefix, opt)
-                    actual_option = self.parser.get_option_by_long_name(opt_name)
-                    if actual_option is None:
-                        # don't fail on DEFAULT UPPERCASE options in case-sensitive mode.
-                        in_def = self.configfile_parser.has_option(self.DEFAULTSECT, opt)
-                        if in_def and self.CONFIGFILE_CASESENSITIVE and opt == opt.upper():
-                            self.log.debug(('parseconfigfiles: no option corresponding with '
-                                            'opt %s dest %s in section %s but found all uppercase '
-                                            'in DEFAULT section. Skipping.') % (opt, opt_dest, section))
-                            continue
-                        else:
-                            self.log.raiseException(('parseconfigfiles: no option corresponding with '
-                                                     'opt %s dest %s in section %s') % (opt, opt_dest, section))
-
-                    configfile_options_default[opt_dest] = actual_option.default
-
-                    # log actions require special care
-                    # if any log action was already taken before, it would precede the one from the configfile
-                    # however, multiple logactions in a configfile (or environment for that matter) have
-                    # undefined behaviour
-                    is_log_action = actual_option.action in ExtOption.EXTOPTION_LOG
-                    log_action_taken = getattr(self.options, '_logaction_taken', False)
-                    if is_log_action and log_action_taken:
-                        # value set through take_action. do not modify by configfile
-                        self.log.debug(('parseconfigfiles: log action %s (value %s) found,'
-                                        ' but log action already taken. Ignoring.') % (opt_dest, val))
-                    elif actual_option.action in ExtOption.BOOLEAN_ACTIONS:
-                        try:
-                            newval = self.configfile_parser.getboolean(section, opt)
-                            self.log.debug(('parseconfigfiles: getboolean for option %s value %s '
-                                            'in section %s returned %s') % (opt, val, section, newval))
-                        except:
-                            self.log.raiseException(('parseconfigfiles: failed to getboolean for option %s value %s '
-                                                     'in section %s') % (opt, val, section))
-                        if hasattr(self.parser.option_class, 'ENABLE') and hasattr(self.parser.option_class, 'DISABLE'):
-                            if newval:
-                                cmd_template = "--enable-%s"
-                            else:
-                                cmd_template = "--disable-%s"
-                            configfile_cmdline_dest.append(opt_dest)
-                            configfile_cmdline.append(cmd_template % opt_name)
-                        else:
-                            self.log.debug(("parseconfigfiles: no enable/disable, not trying to set boolean-valued "
-                                            "option %s via cmdline, just setting value to %s" % (opt_name, newval)))
-                            configfile_values[opt_dest] = newval
-                    else:
-                        configfile_cmdline_dest.append(opt_dest)
-                        configfile_cmdline.append("--%s" % opt_name)
-                        configfile_cmdline.append(val)
-
-        # reparse
-        self.log.debug('parseconfigfiles: going to parse options through cmdline %s' % configfile_cmdline)
-        try:
-            # can't reprocress the environment, since we are not reporcessing the commandline either
-            self.parser.process_env_options = False
-            (parsed_configfile_options, parsed_configfile_args) = self.parser.parse_args(configfile_cmdline)
-            self.parser.process_env_options = True
-        except:
-            self.log.raiseException('parseconfigfiles: failed to parse options through cmdline %s' %
-                                    configfile_cmdline)
-
-        # re-report the options as parsed via parser
-        self.log.debug("parseconfigfiles: options from configfile %s" % (self.parser.commandline_arguments))
-
-        if len(parsed_configfile_args) > 0:
-            self.log.raiseException('parseconfigfiles: not all options were parsed: %s' % parsed_configfile_args)
-
-        for opt_dest in configfile_cmdline_dest:
-            try:
-                configfile_values[opt_dest] = getattr(parsed_configfile_options, opt_dest)
-            except:
-                self.log.raiseException('parseconfigfiles: failed to retrieve dest %s from parsed_configfile_options' %
-                                        opt_dest)
-
-        self.log.debug('parseconfigfiles: parsed values from configfiles: %s' % configfile_values)
-
-        for opt_dest, val in configfile_values.items():
-            set_opt = False
-            if not hasattr(self.options, opt_dest):
-                self.log.debug('parseconfigfiles: adding new option %s with value %s' % (opt_dest, val))
-                set_opt = True
-            else:
-                if hasattr(self.options, '_action_taken') and self.options._action_taken.get(opt_dest, None):
-                    # value set through take_action. do not modify by configfile
-                    self.log.debug('parseconfigfiles: option %s already found in _action_taken' % (opt_dest))
-                else:
-                    self.log.debug('parseconfigfiles: option %s not found in _action_taken, setting to %s' %
-                                   (opt_dest, val))
-                    set_opt = True
-            if set_opt:
-                setattr(self.options, opt_dest, val)
-                if hasattr(self.options, '_action_taken'):
-                    self.options._action_taken[opt_dest] = True
-
-    def make_options_option_name_and_destination(self, prefix, key):
-        """Make the options option name"""
-        if prefix == '':
-            name = key
-        else:
-            name = "".join([prefix, self.OPTIONNAME_PREFIX_SEPARATOR, key])
-
-        # dest : replace '-' with '_'
-        dest = name.replace('-', '_')
-
-        return name, dest
-
-    def _get_options_by_property(self, prop_type, prop_value):
-        """Return all options with property type equal to value"""
-        if not prop_type in self.PROCESSED_OPTIONS_PROPERTIES:
-            self.log.raiseException('Invalid prop_type %s for PROCESSED_OPTIONS_PROPERTIES %s' %
-                                    (prop_type, self.PROCESSED_OPTIONS_PROPERTIES))
-        prop_idx = self.PROCESSED_OPTIONS_PROPERTIES.index(prop_type)
-        # get all options with prop_type
-        options = {}
-        for key in [dest for dest, props in self.processed_options.items() if props[prop_idx] == prop_value]:
-            options[key] = getattr(self.options, key, None)  # None? isn't there always a default
-
-        return options
-
-    def get_options_by_prefix(self, prefix):
-        """Get all options that set with prefix. Return a dict. The keys are stripped of the prefix."""
-        offset = 0
-        if prefix:
-            offset = len(prefix) + len(self.OPTIONNAME_PREFIX_SEPARATOR)
-
-        prefix_dict = {}
-        for dest, value in self._get_options_by_property('prefix', prefix).items():
-            new_dest = dest[offset:]
-            prefix_dict[new_dest] = value
-        return prefix_dict
-
-    def get_options_by_section(self, section):
-        """Get all options from section. Return a dict."""
-        return self._get_options_by_property('section_name', section)
-
-    def postprocess(self):
-        """Some additional processing"""
-        pass
-
-    def validate(self):
-        """Final step, allows for validating the options and/or args"""
-        pass
-
-    def dict_by_prefix(self, merge_empty_prefix=False):
-        """Break the options dict by prefix; return nested dict.
-            @param merge_empty_prefix : boolean (default False) also (try to) merge the empty
-                                        prefix in the root of the dict. If there is a non-prefixed optionname
-                                        that matches a prefix, it will be rejected and error will be logged.
-        """
-        subdict = {}
-
-        prefix_idx = self.PROCESSED_OPTIONS_PROPERTIES.index('prefix')
-        for prefix in nub([props[prefix_idx] for props in self.processed_options.values()]):
-            subdict[prefix] = self.get_options_by_prefix(prefix)
-
-        if merge_empty_prefix and '' in subdict:
-            self.log.debug("dict_by_prefix: merge_empty_prefix set")
-            for opt, val in subdict[''].items():
-                if opt in subdict:
-                    self.log.error("dict_by_prefix: non-prefixed option %s conflicts with prefix of same name." % opt)
-                else:
-                    subdict[opt] = val
-
-        self.log.debug("dict_by_prefix: subdict %s" % subdict)
-        return subdict
-
-    def generate_cmd_line(self, ignore=None, add_default=None):
-        """Create the commandline options that would create the current self.options.
-           The result is sorted on the destination names.
-
-            @param ignore : regex on destination
-            @param add_default : print value that are equal to default
-        """
-        if ignore is not None:
-            self.log.debug("generate_cmd_line ignore %s" % ignore)
-            ignore = re.compile(ignore)
-        else:
-            self.log.debug("generate_cmd_line no ignore")
-
-        args = []
-        opt_dests = self.options.__dict__.keys()
-        opt_dests.sort()
-
-        for opt_dest in opt_dests:
-            opt_value = self.options.__dict__[opt_dest]
-            # this is the action as parsed by the class, not the actual action set in option
-            # (eg action store_or_None is shown here as store_or_None, not as callback)
-            typ = self.processed_options[opt_dest][self.PROCESSED_OPTIONS_PROPERTIES.index('type')]
-            default = self.processed_options[opt_dest][self.PROCESSED_OPTIONS_PROPERTIES.index('default')]
-            action = self.processed_options[opt_dest][self.PROCESSED_OPTIONS_PROPERTIES.index('action')]
-            opt_name = self.processed_options[opt_dest][self.PROCESSED_OPTIONS_PROPERTIES.index('opt_name')]
-
-            if ignore is not None and ignore.search(opt_dest):
-                self.log.debug("generate_cmd_line adding %s value %s matches ignore. Not adding to args." %
-                               (opt_name, opt_value))
-                continue
-
-            if opt_value == default:
-                # do nothing
-                # except for store_or_None and friends
-                msg = ''
-                if not (add_default or action in ('store_or_None',)):
-                    msg = ' Not adding to args.'
-                self.log.debug("generate_cmd_line adding %s value %s default found.%s" %
-                               (opt_name, opt_value, msg))
-                if not (add_default or action in ('store_or_None',)):
-                    continue
-
-            if opt_value is None:
-                # do nothing
-                self.log.debug("generate_cmd_line adding %s value %s. None found. not adding to args." %
-                               (opt_name, opt_value))
-                continue
-
-            if action in ('store_or_None',):
-                if opt_value == default:
-                    self.log.debug("generate_cmd_line %s adding %s (value is default value %s)" %
-                                   (action, opt_name, opt_value))
-                    args.append("--%s" % (opt_name))
-                else:
-                    self.log.debug("generate_cmd_line %s adding %s non-default value %s" %
-                                   (action, opt_name, opt_value))
-                    if typ in ExtOption.TYPE_STRLIST:
-                        sep, _, _ = what_str_list_tuple(typ)
-                        args.append("--%s=%s" % (opt_name, shell_quote(sep.join(opt_value))))
-                    else:
-                        args.append("--%s=%s" % (opt_name, shell_quote(opt_value)))
-            elif action in ("store_true", "store_false",) + ExtOption.EXTOPTION_LOG:
-                # not default!
-                self.log.debug("generate_cmd_line adding %s value %s. store action found" %
-                               (opt_name, opt_value))
-                if (action in ('store_true',) + ExtOption.EXTOPTION_LOG and default is True and opt_value is False) or \
-                    (action in ('store_false',) and default is False and opt_value is True):
-                    if hasattr(self.parser.option_class, 'ENABLE') and hasattr(self.parser.option_class, 'DISABLE'):
-                        args.append("--%s-%s" % (self.parser.option_class.DISABLE, opt_name))
-                    else:
-                        self.log.error(("generate_cmd_line: %s : can't set inverse of default %s with action %s "
-                                        "with missing ENABLE/DISABLE in option_class") %
-                                       (opt_name, default, action))
-                else:
-                    if opt_value == default and ((action in ('store_true',) + ExtOption.EXTOPTION_LOG and default is False)
-                                                 or (action in ('store_false',) and default is True)):
-                        if hasattr(self.parser.option_class, 'ENABLE') and \
-                            hasattr(self.parser.option_class, 'DISABLE'):
-                            args.append("--%s-%s" % (self.parser.option_class.DISABLE, opt_name))
-                        else:
-                            self.log.debug(("generate_cmd_line: %s : action %s can only set to inverse of default %s "
-                                            "and current value is default. Not adding to args.") %
-                                           (opt_name, action, default))
-                    else:
-                        args.append("--%s" % opt_name)
-            elif action in ("add", "add_first"):
-                if default is not None:
-                    if hasattr(opt_value, '__neg__'):
-                        if action == 'add_first':
-                            opt_value = opt_value + -default
-                        else:
-                            opt_value = -default + opt_value
-                    elif hasattr(opt_value, '__getslice__'):
-                        if action == 'add_first':
-                            opt_value = opt_value[:-len(default)]
-                        else:
-                            opt_value = opt_value[len(default):]
-
-                if typ in ExtOption.TYPE_STRLIST:
-                    sep, klass, helpsep = what_str_list_tuple(typ)
-                    restype = '%s-separated %s' % (helpsep, klass.__name__)
-                    value = sep.join(opt_value)
-                else:
-                    restype = 'string'
-                    value = opt_value
-
-                if not opt_value:
-                    # empty strings, empty lists, 0
-                    self.log.debug('generate_cmd_line no value left, skipping.')
-                    continue
-
-                self.log.debug("generate_cmd_line adding %s value %s. %s action, return as %s" %
-                               (opt_name, opt_value, action, restype))
-
-                args.append("--%s=%s" % (opt_name, shell_quote(value)))
-            elif typ in ExtOption.TYPE_STRLIST:
-                sep, _, _ = what_str_list_tuple(typ)
-                args.append("--%s=%s" % (opt_name, shell_quote(sep.join(opt_value))))
-            elif action in ("append",):
-                # add multiple times
-                self.log.debug("generate_cmd_line adding %s value %s. append action, return as multiple args" %
-                               (opt_name, opt_value))
-                args.extend(["--%s=%s" % (opt_name, shell_quote(v)) for v in opt_value])
-            elif action in ("regex",):
-                self.log.debug("generate_cmd_line adding %s regex pattern %s" % (opt_name, opt_value.pattern))
-                args.append("--%s=%s" % (opt_name, shell_quote(opt_value.pattern)))
-            else:
-                self.log.debug("generate_cmd_line adding %s value %s" % (opt_name, opt_value))
-                args.append("--%s=%s" % (opt_name, shell_quote(opt_value)))
-
-        self.log.debug("commandline args %s" % args)
-        return args
-
-
-class SimpleOptionParser(ExtOptionParser):
-    DESCRIPTION_DOCSTRING = True
-
-
-class SimpleOption(GeneralOption):
-    PARSER = SimpleOptionParser
-
-    def __init__(self, go_dict=None, descr=None, short_groupdescr=None, long_groupdescr=None, config_files=None):
-        """Initialisation
-        @param go_dict : General Option option dict
-        @param short_descr : short description of main options
-        @param long_descr : longer description of main options
-        @param config_files : list of configfiles to read options from
-
-        a general options dict has as key the long option name, and is followed by a list/tuple
-        mandatory are 4 elements : option help, type, action, default
-        a 5th element is optional and is the short help name (if any)
-
-        the generated help will include the docstring
-        """
-        self.go_dict = go_dict
-        if short_groupdescr is None:
-            short_groupdescr = 'Main options'
-        if long_groupdescr is None:
-            long_groupdescr = ''
-        self.descr = [short_groupdescr, long_groupdescr]
-
-        kwargs = {
-            'go_prefixloggername': True,
-            'go_mainbeforedefault': True,
-        }
-        if config_files is not None:
-            kwargs['go_configfiles'] = config_files
-
-        super(SimpleOption, self).__init__(**kwargs)
-
-    def main_options(self):
-        if self.go_dict is not None:
-            prefix = None
-            self.add_group_parser(self.go_dict, self.descr, prefix=prefix)
-
-
-def simple_option(go_dict=None, descr=None, short_groupdescr=None, long_groupdescr=None, config_files=None):
-    """A function that returns a single level GeneralOption option parser
-
-    @param go_dict : General Option option dict
-    @param short_descr : short description of main options
-    @param long_descr : longer description of main options
-    @param config_files : list of configfiles to read options from
-
-    a general options dict has as key the long option name, and is followed by a list/tuple
-    mandatory are 4 elements : option help, type, action, default
-    a 5th element is optional and is the short help name (if any)
-
-    the generated help will include the docstring
-    """
-    return SimpleOption(go_dict, descr, short_groupdescr, long_groupdescr, config_files)
diff --git a/vsc/utils/mail.py b/vsc/utils/mail.py
deleted file mode 100644
index 318262a1f2..0000000000
--- a/vsc/utils/mail.py
+++ /dev/null
@@ -1,254 +0,0 @@
-#!/usr/bin/env python
-##
-# Copyright 2012-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-Wrapper around the standard Python mail library.
-
-  - Send a plain text message
-  - Send an HTML message, with a plain text alternative
-
-@author: Andy Georges (Ghent University)
-"""
-
-import re
-import smtplib
-from email.mime.multipart import MIMEMultipart
-from email.mime.text import MIMEText
-from email.mime.image import MIMEImage
-
-from vsc.utils import fancylogger
-
-
-class VscMailError(Exception):
-    """Raised if the sending of an email fails for some reason."""
-
-    def __init__(self, mail_host=None, mail_to=None, mail_from=None, mail_subject=None, err=None):
-        """Initialisation.
-
-        @type mail_host: string
-        @type mail_to: string
-        @type mail_from: string
-        @type mail_subject: string
-        @type err: Exception subclass
-
-        @param mail_host: the SMTP host for actually sending the mail.
-        @param mail_to: a well-formed email address of the recipient.
-        @param mail_from: a well-formed email address of the sender.
-        @param mail_subject: the subject of the mail.
-        @param err: the original exception, if any.
-        """
-        self.mail_host = mail_host
-        self.mail_to = mail_to
-        self.mail_from = mail_from
-        self.mail_subject = mail_subject
-        self.err = err
-
-
-class VscMail(object):
-    """Class providing functionality to send out mail."""
-
-    def __init__(self, mail_host=None):
-        self.mail_host = mail_host
-        self.log = fancylogger.getLogger(self.__class__.__name__)
-
-    def _send(self,
-              mail_from,
-              mail_to,
-              mail_subject,
-              msg):
-        """Actually send the mail.
-
-        @type mail_from: string representing the sender.
-        @type mail_to: string representing the recipient.
-        @type mail_subject: string representing the subject.
-        @type msg: MIME message.
-        """
-
-        try:
-            if self.mail_host:
-                self.log.debug("Using %s as the mail host" % (self.mail_host,))
-                s = smtplib.SMTP(self.mail_host)
-            else:
-                self.log.debug("Using the default mail host")
-                s = smtplib.SMTP()
-                s.connect()
-            try:
-                s.sendmail(mail_from, mail_to, msg.as_string())
-            except smtplib.SMTPHeloError, err:
-                self.log.error("Cannot get a proper response from the SMTP host" +
-                               (self.mail_host and " %s" % (self.mail_host) or ""))
-                raise
-            except smtplib.SMTPRecipientsRefused, err:
-                self.log.error("All recipients were refused by SMTP host" +
-                               (self.mail_host and " %s" % (self.mail_host) or "") +
-                               " [%s]" % (mail_to))
-                raise
-            except smtplib.SMTPSenderRefused, err:
-                self.log.error("Sender was refused by SMTP host" +
-                               (self.mail_host and " %s" % (self.mail_host) or "") +
-                               "%s" % (mail_from))
-                raise
-            except smtplib.SMTPDataError, err:
-                raise
-        except smtplib.SMTPConnectError, err:
-            self.log.exception("Cannot connect to the SMTP host" + (self.mail_host and " %s" % (self.mail_host) or ""))
-            raise VscMailError(mail_host=self.mail_host,
-                               mail_to=mail_to,
-                               mail_from=mail_from,
-                               mail_subject=mail_subject,
-                               err=err)
-        except Exception, err:
-            self.log.exception("Some unknown exception occurred in VscMail.sendTextMail. Raising a VscMailError.")
-            raise VscMailError(mail_host=self.mail_host,
-                               mail_to=mail_to,
-                               mail_from=mail_from,
-                               mail_subject=mail_subject,
-                               err=err)
-
-    def sendTextMail(self,
-                     mail_to,
-                     mail_from,
-                     reply_to,
-                     mail_subject,
-                     message):
-        """Send out the given message by mail to the given recipient(s).
-
-        @type mail_to: string or list of strings
-        @type mail_from: string
-        @type reply_to: string
-        @type mail_subject: string
-        @type message: string
-
-        @param mail_to: a valid recipient email address
-        @param mail_from: a valid sender email address.
-        @param reply_to: a valid email address for the (potential) replies.
-        @param mail_subject: the subject of the email.
-        @param message: the body of the mail.
-        """
-        self.log.info("Sending mail [%s] to %s." % (mail_subject, mail_to))
-
-        if reply_to is None:
-            reply_to = mail_from
-        msg = MIMEText(message)
-        msg['Subject'] = mail_subject
-        msg['From'] = mail_from
-        msg['To'] = mail_to
-        msg['Reply-to'] = reply_to
-
-        self._send(mail_from, mail_to, mail_subject, msg)
-
-    def _replace_images_cid(self, html, images):
-        """Replaces all occurences of the src="IMAGE" with src="cid:IMAGE" in the provided html argument.
-
-        @type html: string
-        @type images: list of strings
-
-        @param html: HTML data, containing image tags for each of the provided images
-        @param images: references to the images occuring in the HTML payload
-
-        @return: the altered HTML string.
-        """
-
-        for im in images:
-            re_src = re.compile("src=\"%s\"" % im)
-            (html, count) = re_src.subn("src=\"cid:%s\"" % im, html)
-            if count == 0:
-                self.log.raiseException("Could not find image %s in provided HTML." % im, VscMailError)
-
-        return html
-
-    def sendHTMLMail(self,
-                     mail_to,
-                     mail_from,
-                     reply_to,
-                     mail_subject,
-                     html_message,
-                     text_alternative,
-                     images=None,
-                     css=None):
-        """
-        Send an HTML email message, encoded in a MIME/multipart message.
-
-        The images and css are included in the message, and should be provided separately.
-
-        @type mail_to: string or list of strings
-        @type mail_from: string
-        @type reply_to: string
-        @type mail_subject: string
-        @type html_message: string
-        @type text_alternative: string
-        @type images: list of strings
-        @type css: string
-
-        @param mail_to: a valid recipient email addresses.
-        @param mail_from: a valid sender email address.
-        @param reply_to: a valid email address for the (potential) replies.
-        @param html_message: the actual payload, body of the mail
-        @param text_alternative: plain-text version of the mail body
-        @param images: the images that are referenced in the HTML body. These should be available as files on the
-                      filesystem in the directory where the script runs. Caveat: assume jpeg image type.
-        @param css: CSS definitions
-        """
-
-        # Create message container - the correct MIME type is multipart/alternative.
-        msg_root = MIMEMultipart('alternative')
-        msg_root['Subject'] = mail_subject
-        msg_root['From'] = mail_from
-        msg_root['To'] = mail_to
-
-        msg_root.preamble = 'This is a multi-part message in MIME format. If your email client does not support this (correctly), the first part is the plain text version.'
-
-        # Create the body of the message (a plain-text and an HTML version).
-        if images is not None:
-            html_message = self.replace_images_cid(html_message, images)
-
-        # Record the MIME types of both parts - text/plain and text/html_message.
-        msg_plain = MIMEText(text_alternative, 'plain')
-        msg_html = MIMEText(html_message, 'html_message')
-
-        # Attach parts into message container.
-        # According to RFC 2046, the last part of a multipart message, in this case
-        # the HTML message, is best and preferred.
-        msg_root.attach(msg_plain)
-        msg_alt = MIMEMultipart('related')
-        msg_alt.attach(msg_html)
-
-        if css is not None:
-            msg_html_css = MIMEText(css, 'css')
-            msg_html_css.add_header('Content-ID', '<newsletter.css>')
-            msg_alt.attach(msg_html_css)
-
-        if images is not None:
-            for im in images:
-                image_fp = open(im, 'r')
-                msg_image = MIMEImage(image_fp.read(), 'jpeg')  # FIXME: for now, we assume jpegs
-                image_fp.close()
-                msg_image.add_header('Content-ID', "<%s>" % im)
-                msg_alt.attach(msg_image)
-
-        msg_root.attach(msg_alt)
-
-        self._send(mail_from, mail_to, mail_subject, msg_root)
diff --git a/vsc/utils/missing.py b/vsc/utils/missing.py
deleted file mode 100644
index 683269cb00..0000000000
--- a/vsc/utils/missing.py
+++ /dev/null
@@ -1,444 +0,0 @@
-#!/usr/bin/env python
-# #
-# Copyright 2012-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-# #
-"""
-Various functions that are missing from the default Python library.
-
-  - nub(list): keep the unique elements in the list
-  - nub_by(list, predicate): keep the unique elements (first come, first served) that do not satisfy a given predicate
-  - find_sublist_index(list, sublist): find the index of the first
-    occurence of the sublist in the list
-  - Monoid: implementation of the monoid concept
-  - MonoidDict: dictionary that combines values upon insertiong
-    according to the given monoid
-  - RUDict: dictionary that allows recursively updating its values (if they are dicts too) with a new RUDict
-  - shell_quote / shell_unquote : convenience functions to quote / unquote strings in shell context
-
-@author: Andy Georges (Ghent University)
-@author: Stijn De Weirdt (Ghent University)
-"""
-import os
-import re
-import shlex
-import subprocess
-import sys
-import time
-
-from vsc.utils import fancylogger
-from vsc.utils.frozendict import FrozenDict
-
-
-_log = fancylogger.getLogger('vsc.utils.missing')
-
-
-def partial(func, *args, **keywords):
-    """
-    Return a new partial object which when called will behave like func called with the positional arguments args
-    and keyword arguments keywords. If more arguments are supplied to the call, they are appended to args. If additional
-    keyword arguments are supplied, they extend and override keywords.
-    new in python 2.5, from https://docs.python.org/2/library/functools.html#functools.partial
-    """
-    def newfunc(*fargs, **fkeywords):
-        newkeywords = keywords.copy()
-        newkeywords.update(fkeywords)
-        return func(*(args + fargs), **newkeywords)
-    newfunc.func = func
-    newfunc.args = args
-    newfunc.keywords = keywords
-    return newfunc
-
-
-def any(ls):
-    """Reimplementation of 'any' function, which is not available in Python 2.4 yet."""
-
-    return sum([bool(x) for x in ls]) != 0
-
-
-def all(ls):
-    """Reimplementation of 'all' function, which is not available in Python 2.4 yet."""
-
-    return sum([bool(x) for x in ls]) == len(ls)
-
-
-def nub(list_):
-    """Returns the unique items of a list of hashables, while preserving order of
-    the original list, i.e. the first unique element encoutered is
-    retained.
-
-    Code is taken from
-    http://stackoverflow.com/questions/480214/how-do-you-remove-duplicates-from-a-list-in-python-whilst-preserving-order
-
-    Supposedly, this is one of the fastest ways to determine the
-    unique elements of a list.
-
-    @type list_: a list :-)
-
-    @returns: a new list with each element from `list` appearing only once (cfr. Michelle Dubois).
-    """
-    seen = set()
-    seen_add = seen.add
-    return [x for x in list_ if x not in seen and not seen_add(x)]
-
-
-def nub_by(list_, predicate):
-    """Returns the elements of a list that fullfil the predicate.
-
-    For any pair of elements in the resulting list, the predicate does not hold. For example, the nub above
-    can be expressed as nub_by(list, lambda x, y: x == y).
-
-    @type list_: a list of items of some type t
-    @type predicate: a function that takes two elements of type t and returns a bool
-
-    @returns: the nubbed list
-    """
-    seen = set()
-    seen_add = seen.add
-    return [x for x in list_ if not any([predicate(x, y) for y in seen]) and not seen_add(x)]
-
-
-def find_sublist_index(ls, sub_ls):
-    """Find the index at which the sublist sub_ls can be found in ls.
-
-    @type ls: list
-    @type sub_ls: list
-
-    @return: index of the matching location or None if no match can be made.
-    """
-    sub_length = len(sub_ls)
-    for i in xrange(len(ls)):
-        if ls[i:(i + sub_length)] == sub_ls:
-            return i
-
-    return None
-
-
-class Monoid(object):
-    """A monoid is a mathematical object with a default element (mempty or null) and a default operation to combine
-    two elements of a given data type.
-
-    Taken from http://fmota.eu/2011/10/09/monoids-in-python.html under the do whatever you want license.
-    """
-
-    def __init__(self, null, mappend):
-        """Initialise.
-
-        @type null: default element of some data type, e.g., [] for list or 0 for int (identity element in an Abelian group)
-        @type op: mappend operation to combine two elements of the target datatype
-        """
-        self.null = null
-        self.mappend = mappend
-
-    def fold(self, xs):
-        """fold over the elements of the list, combining them into a single element of the target datatype."""
-        if hasattr(xs, "__fold__"):
-            return xs.__fold__(self)
-        else:
-            return reduce(
-                self.mappend,
-                xs,
-                self.null
-            )
-
-    def __call__(self, *args):
-        """When the monoid is called, the values are folded over and the resulting value is returned."""
-        return self.fold(args)
-
-    def star(self):
-        """Return a new similar monoid."""
-        return Monoid(self.null, self.mappend)
-
-
-class MonoidDict(dict):
-    """A dictionary with a monoid operation, that allows combining values in the dictionary according to the mappend
-    operation in the monoid.
-    """
-
-    def __init__(self, monoid, *args, **kwargs):
-        """Initialise.
-
-        @type monoid: Monoid instance
-        """
-        super(MonoidDict, self).__init__(*args, **kwargs)
-        self.monoid = monoid
-
-    def __setitem__(self, key, value):
-        """Combine the value the dict has for the key with the new value using the mappend operation."""
-        if super(MonoidDict, self).__contains__(key):
-            current = super(MonoidDict, self).__getitem__(key)
-            super(MonoidDict, self).__setitem__(key, self.monoid(current, value))
-        else:
-            super(MonoidDict, self).__setitem__(key, value)
-
-    def __getitem__(self, key):
-        """ Obtain the dictionary value for the given key. If no value is present,
-        we return the monoid's mempty (null).
-        """
-        if not super(MonoidDict, self).__contains__(key):
-            return self.monoid.null
-        else:
-            return super(MonoidDict, self).__getitem__(key)
-
-
-class RUDict(dict):
-    """Recursively updatable dictionary.
-
-    When merging with another dictionary (of the same structure), it will keep
-    updating the values as well if they are dicts or lists.
-
-    Code taken from http://stackoverflow.com/questions/6256183/combine-two-dictionaries-of-dictionaries-python.
-    """
-
-    def update(self, E=None, **F):
-        if E is not None:
-            if 'keys' in dir(E) and callable(getattr(E, 'keys')):
-                for k in E:
-                    if k in self:  # existing ...must recurse into both sides
-                        self.r_update(k, E)
-                    else:  # doesn't currently exist, just update
-                        self[k] = E[k]
-            else:
-                for (k, v) in E:
-                    self.r_update(k, {k: v})
-
-        for k in F:
-            self.r_update(k, {k: F[k]})
-
-    def r_update(self, key, other_dict):
-        """Recursive update."""
-        if isinstance(self[key], dict) and isinstance(other_dict[key], dict):
-            od = RUDict(self[key])
-            nd = other_dict[key]
-            od.update(nd)
-            self[key] = od
-        elif isinstance(self[key], list):
-            if isinstance(other_dict[key], list):
-                self[key].extend(other_dict[key])
-            else:
-                self[key] = self[key].append(other_dict[key])
-        else:
-            self[key] = other_dict[key]
-
-
-class FrozenDictKnownKeys(FrozenDict):
-    """A frozen dictionary only allowing known keys."""
-
-    # list of known keys
-    KNOWN_KEYS = []
-
-    def __init__(self, *args, **kwargs):
-        """Constructor, only way to define the contents."""
-        self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
-
-        # support ignoring of unknown keys
-        ignore_unknown_keys = kwargs.pop('ignore_unknown_keys', False)
-
-        # handle unknown keys: either ignore them or raise an exception
-        tmpdict = dict(*args, **kwargs)
-        unknown_keys = [key for key in tmpdict.keys() if not key in self.KNOWN_KEYS]
-        if unknown_keys:
-            if ignore_unknown_keys:
-                for key in unknown_keys:
-                    self.log.debug("Ignoring unknown key '%s' (value '%s')" % (key, args[0][key]))
-                    # filter key out of dictionary before creating instance
-                    del tmpdict[key]
-            else:
-                msg = "Encountered unknown keys %s (known keys: %s)" % (unknown_keys, self.KNOWN_KEYS)
-                self.log.raiseException(msg, exception=KeyError)
-
-        super(FrozenDictKnownKeys, self).__init__(tmpdict)
-
-    def __getitem__(self, key, *args, **kwargs):
-        """Redefine __getitem__ to provide a better KeyError message."""
-        try:
-            return super(FrozenDictKnownKeys, self).__getitem__(key, *args, **kwargs)
-        except KeyError, err:
-            if key in self.KNOWN_KEYS:
-                raise KeyError(err)
-            else:
-                tup = (key, self.__class__.__name__, self.KNOWN_KEYS)
-                raise KeyError("Unknown key '%s' for %s instance (known keys: %s)" % tup)
-
-
-def shell_quote(x):
-    """Add quotes so it can be apssed to shell"""
-    # use undocumented subprocess API call to quote whitespace (executed with Popen(shell=True))
-    # (see http://stackoverflow.com/questions/4748344/whats-the-reverse-of-shlex-split for alternatives if needed)
-    return subprocess.list2cmdline([str(x)])
-
-
-def shell_unquote(x):
-    """Take a literal string, remove the quotes as if it were passed by shell"""
-    # it expects a string
-    return shlex.split(str(x))[0]
-
-
-def get_class_for(modulepath, class_name):
-    """
-    Get class for a given Python class name and Python module path.
-
-    @param modulepath: Python module path (e.g., 'vsc.utils.generaloption')
-    @param class_name: Python class name (e.g., 'GeneralOption')
-    """
-    # try to import specified module path, reraise ImportError if it occurs
-    try:
-        module = __import__(modulepath, globals(), locals(), [''])
-    except ImportError, err:
-        raise ImportError(err)
-    # try to import specified class name from specified module path, throw ImportError if this fails
-    try:
-        klass = getattr(module, class_name)
-    except AttributeError, err:
-        raise ImportError("Failed to import %s from %s: %s" % (class_name, modulepath, err))
-    return klass
-
-
-def get_subclasses_dict(klass, include_base_class=False):
-    """Get dict with subclasses per classes, recursively from the specified base class."""
-    res = {}
-    subclasses = klass.__subclasses__()
-    if include_base_class:
-        res.update({klass: subclasses})
-    for subclass in subclasses:
-        # always include base class for recursive call
-        res.update(get_subclasses_dict(subclass, include_base_class=True))
-    return res
-
-
-def get_subclasses(klass, include_base_class=False):
-    """Get list of all subclasses, recursively from the specified base class."""
-    return get_subclasses_dict(klass, include_base_class=include_base_class).keys()
-
-
-def modules_in_pkg_path(pkg_path):
-    """Return list of module files in specified package path."""
-    # if the specified (relative) package path doesn't exist, try and determine the absolute path via sys.path
-    if not os.path.isabs(pkg_path) and not os.path.isdir(pkg_path):
-        _log.debug("Obtained non-existing relative package path '%s', will try to figure out absolute path" % pkg_path)
-        newpath = None
-        for sys_path_dir in sys.path:
-            abspath = os.path.join(sys_path_dir, pkg_path)
-            if os.path.isdir(abspath):
-                _log.debug("Found absolute path %s for package path %s, verifying it" % (abspath, pkg_path))
-                # also make sure an __init__.py is in place in every subdirectory
-                is_pkg = True
-                subdir = ''
-                for pkg_path_dir in pkg_path.split(os.path.sep):
-                    subdir = os.path.join(subdir, pkg_path_dir)
-                    if not os.path.isfile(os.path.join(sys_path_dir, subdir, '__init__.py')):
-                        is_pkg = False
-                        tup = (subdir, abspath, pkg_path)
-                        _log.debug("No __init__.py found in %s, %s is not a valid absolute path for pkg_path %s" % tup)
-                        break
-                if is_pkg:
-                    newpath = abspath
-                    break
-
-        if newpath is None:
-            # give up if we couldn't find an absolute path for the imported package
-            tup = (pkg_path, sys.path)
-            raise OSError("Can't browse package via non-existing relative path '%s', not found in sys.path (%s)" % tup)
-        else:
-            pkg_path = newpath
-            _log.debug("Found absolute package path %s" % pkg_path)
-
-    module_regexp = re.compile(r"^(?P<modname>[^_].*|__init__)\.py$")
-    modules = [res.group('modname') for res in map(module_regexp.match, os.listdir(pkg_path)) if res]
-    _log.debug("List of modules for package in %s: %s" % (pkg_path, modules))
-    return modules
-
-
-def avail_subclasses_in(base_class, pkg_name, include_base_class=False):
-    """Determine subclasses for specificied base classes in modules in (only) specified packages."""
-
-    def try_import(name):
-        """Try import the specified package/module."""
-        try:
-            # don't use return value of __import__ since it may not be the package itself but it's parent
-            __import__(name, globals())
-            return sys.modules[name]
-        except ImportError, err:
-            raise ImportError("avail_subclasses_in: failed to import %s: %s" % (name, err))
-
-    # import all modules in package path(s) before determining subclasses
-    pkg = try_import(pkg_name)
-    for pkg_path in pkg.__path__:
-        for mod in modules_in_pkg_path(pkg_path):
-            # no need to directly import __init__ (already done by importing package)
-            if not mod.startswith('__init__'):
-                _log.debug("Importing module '%s' from package '%s'" % (mod, pkg_name))
-                try_import('%s.%s' % (pkg_name, mod))
-
-    return get_subclasses_dict(base_class, include_base_class=include_base_class)
-
-
-class TryOrFail(object):
-    """
-    Perform the function n times, catching each exception in the exception tuple except on the last try
-    where it will be raised again.
-    """
-    def __init__(self, n, exceptions=(Exception,), sleep=0):
-        self.n = n
-        self.exceptions = exceptions
-        self.sleep = sleep
-
-    def __call__(self, function):
-        def new_function(*args, **kwargs):
-            for i in xrange(0, self.n):
-                try:
-                    return function(*args, **kwargs)
-                except self.exceptions, err:
-                    if i == self.n - 1:
-                        raise
-                    _log.exception("try_or_fail caught an exception - attempt %d: %s" % (i, err))
-                    if self.sleep > 0:
-                        _log.warning("try_or_fail is sleeping for %d seconds before the next attempt" % (self.sleep,))
-                        time.sleep(self.sleep)
-
-        return new_function
-
-
-def post_order(graph, root):
-    """
-    Walk the graph from the given root in a post-order manner by providing the corresponding generator
-    """
-    for node in graph[root]:
-        for child in post_order(graph, node):
-            yield child
-    yield root
-
-
-def topological_sort(graph):
-    """
-    Perform topological sorting of the given graph.
-
-    The graph is a dict with the values for a key being the dependencies, i.e., an arrow from key to each value.
-    """
-    visited = set()
-    for root in graph:
-        for node in post_order(graph, root):
-            if not node in visited:
-                yield node
-                visited.add(node)
diff --git a/vsc/utils/optcomplete.py b/vsc/utils/optcomplete.py
deleted file mode 100644
index 8d070786ca..0000000000
--- a/vsc/utils/optcomplete.py
+++ /dev/null
@@ -1,629 +0,0 @@
-#******************************************************************************\
-# * Copyright (c) 2003-2004, Martin Blais
-# * All rights reserved.
-# *
-# * Redistribution and use in source and binary forms, with or without
-# * modification, are permitted provided that the following conditions are
-# * met:
-# *
-# * * Redistributions of source code must retain the above copyright
-# *   notice, this list of conditions and the following disclaimer.
-# *
-# * * Redistributions in binary form must reproduce the above copyright
-# *   notice, this list of conditions and the following disclaimer in the
-# *   documentation and/or other materials provided with the distribution.
-# *
-# * * Neither the name of the Martin Blais, Furius, nor the names of its
-# *   contributors may be used to endorse or promote products derived from
-# *   this software without specific prior written permission.
-# *
-# * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-# * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-# * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-# * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-# * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#******************************************************************************\
-
-"""Automatic completion for optparse module.
-
-This module provide automatic bash completion support for programs that use the
-optparse module.  The premise is that the optparse options parser specifies
-enough information (and more) for us to be able to generate completion strings
-esily.  Another advantage of this over traditional completion schemes where the
-completion strings are hard-coded in a separate bash source file, is that the
-same code that parses the options is used to generate the completions, so the
-completions is always up-to-date with the program itself.
-
-In addition, we allow you specify a list of regular expressions or code that
-define what kinds of files should be proposed as completions to this file if
-needed.  If you want to implement more complex behaviour, you can instead
-specify a function, which will be called with the current directory as an
-argument.
-
-You need to activate bash completion using the shell script function that comes
-with optcomplete (see http://furius.ca/optcomplete for more details).
-
-@author: Martin Blais (blais@furius.ca)
-@author: Stijn De Weirdt (Ghent University)
-
-This is a copy of optcomplete.py (changeset 17:e0a9131a94cc)
-from source: https://hg.furius.ca/public/optcomplete
-
-Modification by stdweird: 
-    - cleanup
-"""
-
-# Bash Protocol Description
-# -------------------------
-# 'COMP_CWORD'
-#      An index into `${COMP_WORDS}' of the word containing the current
-#      cursor position.  This variable is available only in shell
-#      functions invoked by the programmable completion facilities (*note
-#      Programmable Completion::).
-#
-# 'COMP_LINE'
-#      The current command line.  This variable is available only in
-#      shell functions and external commands invoked by the programmable
-#      completion facilities (*note Programmable Completion::).
-#
-# 'COMP_POINT'
-#      The index of the current cursor position relative to the beginning
-#      of the current command.  If the current cursor position is at the
-#      end of the current command, the value of this variable is equal to
-#      `${#COMP_LINE}'.  This variable is available only in shell
-#      functions and external commands invoked by the programmable
-#      completion facilities (*note Programmable Completion::).
-#
-# 'COMP_WORDS'
-#      An array variable consisting of the individual words in the
-#      current command line.  This variable is available only in shell
-#      functions invoked by the programmable completion facilities (*note
-#      Programmable Completion::).
-#
-# 'COMPREPLY'
-#      An array variable from which Bash reads the possible completions
-#      generated by a shell function invoked by the programmable
-#      completion facility (*note Programmable Completion::).
-
-
-import copy
-import glob
-import logging
-import os
-import re
-import sys
-import types
-
-from optparse import OptionParser, Option
-from pprint import pformat
-
-debugfn = None  # for debugging only
-
-OPTCOMPLETE_ENVIRONMENT = 'OPTPARSE_AUTO_COMPLETE'
-
-BASH = "bash"
-
-DEFAULT_SHELL = BASH
-
-SHELL = DEFAULT_SHELL
-
-OPTION_CLASS = Option
-OPTIONPARSER_CLASS = OptionParser
-
-def set_optionparser(option_class, optionparser_class):
-    """Set the default Option and OptionParser class"""
-    global OPTION_CLASS
-    global OPTIONPARSER_CLASS
-    OPTION_CLASS = option_class
-    OPTIONPARSER_CLASS = optionparser_class
-
-def get_shell():
-    """Determine the shell, update class constant SHELL and return the shell
-    Idea is to call it just once
-    """
-    global SHELL
-    SHELL = os.path.basename(os.environ.get("SHELL", DEFAULT_SHELL))
-    return SHELL
-
-
-# get the shell
-get_shell()
-
-
-class CompleterMissingCallArgument(Exception):
-    """Exception to raise when call arg is missing"""
-
-
-class Completer(object):
-    """Base class to derive all other completer classes from.
-    It generates an empty completion list
-    """
-    CALL_ARGS = None  # list of named args that must be passed
-    CALL_ARGS_OPTIONAL = None  # list of named args that can be passed
-
-    def __call__(self, **kwargs):
-        """Check mandatory args, then return _call"""
-        all_args = []
-        if self.CALL_ARGS is not None:
-            for arg in self.CALL_ARGS:
-                all_args.append(arg)
-                if not arg in kwargs:
-                    msg = "%s __call__ missing mandatory arg %s" % (self.__class__.__name__, arg)
-                    raise CompleterMissingCallArgument(msg)
-
-        if self.CALL_ARGS_OPTIONAL is not None:
-            all_args.extend(self.CALL_ARGS_OPTIONAL)
-
-        for arg in kwargs.keys():
-            if not arg in all_args:
-                # remove it
-                kwargs.pop(arg)
-
-        return self._call(**kwargs)
-
-    def _call(self, **kwargs):
-        """Return empty list"""
-        return []
-
-
-class NoneCompleter(Completer):
-    """Generates empty completion list. For compatibility reasons."""
-    pass
-
-
-class ListCompleter(Completer):
-    """Completes by filtering using a fixed list of strings."""
-    def __init__(self, stringlist):
-        self.olist = stringlist
-
-    def _call(self, **kwargs):
-        """Return the initialised fixed list of strings"""
-        return map(str, self.olist)
-
-
-class AllCompleter(Completer):
-    """Completes by listing all possible files in current directory."""
-    CALL_ARGS_OPTIONAL = ['pwd']
-
-    def _call(self, **kwargs):
-        return os.listdir(kwargs.get('pwd', '.'))
-
-
-class FileCompleter(Completer):
-    """Completes by listing all possible files in current directory.
-       If endings are specified, then limit the files to those."""
-    CALL_ARGS_OPTIONAL = ['prefix']
-
-    def __init__(self, endings=None):
-        if isinstance(endings, basestring):
-            endings = [endings]
-        elif endings is None:
-            endings = []
-        self.endings = tuple(map(str, endings))
-
-    def _call(self, **kwargs):
-        # TODO : what does prefix do in bash?
-        prefix = kwargs.get('prefix', '')
-
-        if SHELL == BASH:
-            res = ['_filedir']
-            if self.endings:
-                res.append("'@(%s)'" % '|'.join(self.endings))
-            return " ".join(res)
-        else:
-            res = []
-            for path in glob.glob(prefix + '*'):
-                res.append(path)
-                if os.path.isdir(path):
-                    # add trailing slashes to directories
-                    res[-1] += os.path.sep
-
-            if self.endings:
-                res = [path for path in res if os.path.isdir(path) or path.endswith(self.endings)]
-
-            if len(res) == 1 and os.path.isdir(res[0]):
-                # return two options so that it completes the / but doesn't add a space
-                return [res[0] + 'a', res[0] + 'b']
-            else:
-                return res
-
-
-class DirCompleter(Completer):
-    """Completes by listing subdirectories only."""
-    CALL_ARGS_OPTIONAL = ['prefix']
-
-    def _call(self, **kwargs):
-        # TODO : what does prefix do in bash?
-        prefix = kwargs.get('prefix', '')
-
-        if SHELL == BASH:
-            return "_filedir -d"
-        else:
-            res = [path + "/" for path in glob.glob(prefix + '*') if os.path.isdir(path)]
-
-            if len(res) == 1:
-                # return two options so that it completes the / but doesn't add a space
-                return [res[0] + 'a', res[0] + 'b']
-            else:
-                return res
-
-
-class KnownHostsCompleter(Completer):
-    """Completes a list of known hostnames"""
-    def _call(self, **kwargs):
-        if SHELL == BASH:
-            return "_known_hosts"
-        else:
-            # TODO needs implementation, no autocompletion for now
-            return []
-
-
-class RegexCompleter(Completer):
-    """Completes by filtering all possible files with the given list of regexps."""
-    CALL_ARGS_OPTIONAL = ['prefix', 'pwd']
-
-    def __init__(self, regexlist, always_dirs=True):
-        self.always_dirs = always_dirs
-
-        if isinstance(regexlist, basestring):
-            regexlist = [regexlist]
-        self.regexlist = []
-        for regex in regexlist:
-            if isinstance(regex, basestring):
-                regex = re.compile(regex)
-            self.regexlist.append(regex)
-
-    def _call(self, **kwargs):
-        dn = os.path.dirname(kwargs.get('prefix', ''))
-        if dn:
-            pwd = dn
-        else:
-            pwd = kwargs.get('pwd', '.')
-
-        ofiles = []
-        for fn in os.listdir(pwd):
-            for r in self.regexlist:
-                if r.match(fn):
-                    if dn:
-                        fn = os.path.join(dn, fn)
-                    ofiles.append(fn)
-                    break
-
-            if self.always_dirs and os.path.isdir(fn):
-                ofiles.append(fn + os.path.sep)
-
-        return ofiles
-
-
-class CompleterOption(OPTION_CLASS):
-    """optparse Option class with completer attribute"""
-    def __init__(self, *args, **kwargs):
-        completer = kwargs.pop('completer', None)
-        OPTION_CLASS.__init__(self, *args, **kwargs)
-        if completer is not None:
-            self.completer = completer
-
-
-def extract_word(line, point):
-    """Return a prefix and suffix of the enclosing word.  The character under
-    the cursor is the first character of the suffix."""
-
-    if SHELL == BASH and 'IFS' in os.environ:
-        ifs = [r.group(0) for r in re.finditer(r'.', os.environ['IFS'])]
-        wsre = re.compile('|'.join(ifs))
-    else:
-        wsre = re.compile(r'\s')
-
-    if point < 0 or point > len(line):
-        return '', ''
-
-    preii = point - 1
-    while preii >= 0:
-        if wsre.match(line[preii]):
-            break
-        preii -= 1
-    preii += 1
-
-    sufii = point
-    while sufii < len(line):
-        if wsre.match(line[sufii]):
-            break
-        sufii += 1
-
-    return line[preii : point], line[point : sufii]
-
-
-def error_override(self, msg):
-    """Hack to keep OptionParser from writing to sys.stderr when
-    calling self.exit from self.error"""
-    self.exit(2, msg=None)
-
-
-def guess_first_nonoption(gparser, subcmds_map):
-    """Given a global options parser, try to guess the first non-option without
-    generating an exception. This is used for scripts that implement a
-    subcommand syntax, so that we can generate the appropriate completions for
-    the subcommand."""
-
-
-    gparser = copy.deepcopy(gparser)
-    def print_usage_nousage (self, *args, **kwargs):
-        pass
-    gparser.print_usage = print_usage_nousage
-
-    prev_interspersed = gparser.allow_interspersed_args  # save state to restore
-    gparser.disable_interspersed_args()
-
-    cwords = os.environ.get('COMP_WORDS', '').split()
-
-    # save original error_func so we can put it back after the hack
-    error_func = gparser.error
-    try:
-        try:
-            instancemethod = type(OPTIONPARSER_CLASS.error)
-            # hack to keep OptionParser from writing to sys.stderr
-            gparser.error = instancemethod(error_override, gparser, OPTIONPARSER_CLASS)
-            _, args = gparser.parse_args(cwords[1:])
-        except SystemExit:
-            return None
-    finally:
-        # undo the hack and restore original OptionParser error function
-        gparser.error = instancemethod(error_func, gparser, OPTIONPARSER_CLASS)
-
-    value = None
-    if args:
-        subcmdname = args[0]
-        try:
-            value = subcmds_map[subcmdname]
-        except KeyError:
-            pass
-
-    gparser.allow_interspersed_args = prev_interspersed  # restore state
-
-    return value  # can be None, indicates no command chosen.
-
-
-def autocomplete(parser, arg_completer=None, opt_completer=None, subcmd_completer=None, subcommands=None):
-    """Automatically detect if we are requested completing and if so generate
-    completion automatically from given parser.
-
-    'parser' is the options parser to use.
-
-    'arg_completer' is a callable object that gets invoked to produce a list of
-    completions for arguments completion (oftentimes files).
-
-    'opt_completer' is the default completer to the options that require a
-    value. 
-    
-    'subcmd_completer' is the default completer for the subcommand
-    arguments.
-
-    If 'subcommands' is specified, the script expects it to be a map of
-    command-name to an object of any kind.  We are assuming that this object is
-    a map from command name to a pair of (options parser, completer) for the
-    command. If the value is not such a tuple, the method
-    'autocomplete(completer)' is invoked on the resulting object.
-
-    This will attempt to match the first non-option argument into a subcommand
-    name and if so will use the local parser in the corresponding map entry's
-    value.  This is used to implement completion for subcommand syntax and will
-    not be needed in most cases.
-    """
-
-    # If we are not requested for complete, simply return silently, let the code
-    # caller complete. This is the normal path of execution.
-    if not os.environ.has_key(OPTCOMPLETE_ENVIRONMENT):
-        return
-    # After this point we should never return, only sys.exit(1)
-
-    # Set default completers.
-    if arg_completer is None:
-        arg_completer = NoneCompleter()
-    if opt_completer is None:
-        opt_completer = FileCompleter()
-    if subcmd_completer is None:
-        # subcmd_completer = arg_completer
-        subcmd_completer = FileCompleter()
-
-    # By default, completion will be arguments completion, unless we find out
-    # later we're trying to complete for an option.
-    completer = arg_completer
-
-    #
-    # Completing...
-    #
-
-    # Fetching inputs... not sure if we're going to use these.
-
-    # zsh's bashcompinit does not pass COMP_WORDS, replace with
-    # COMP_LINE for now...
-    if not os.environ.has_key('COMP_WORDS'):
-        os.environ['COMP_WORDS'] = os.environ['COMP_LINE']
-
-    cwords = os.environ.get('COMP_WORDS', '').split()
-    cline = os.environ.get('COMP_LINE', '')
-    cpoint = int(os.environ.get('COMP_POINT', 0))
-    cword = int(os.environ.get('COMP_CWORD', 0))
-
-    # Extract word enclosed word.
-    prefix, suffix = extract_word(cline, cpoint)
-
-    # If requested, try subcommand syntax to find an options parser for that
-    # subcommand.
-    if subcommands:
-        assert isinstance(subcommands, dict)
-        value = guess_first_nonoption(parser, subcommands)
-        if value:
-            if isinstance(value, (list, tuple)):
-                parser = value[0]
-                if len(value) > 1 and value[1]:
-                    # override completer for command if it is present.
-                    completer = value[1]
-                else:
-                    completer = subcmd_completer
-                autocomplete(parser, completer)
-            elif  hasattr(value, 'autocomplete'):
-                # Call completion method on object. This should call
-                # autocomplete() recursively with appropriate arguments.
-                value.autocomplete(subcmd_completer)
-            else:
-                # no completions for that command object
-                pass
-            sys.exit(1)
-        else:  # suggest subcommands
-            completer = ListCompleter(subcommands.keys())
-
-    # Look at previous word, if it is an option and it requires an argument,
-    # check for a local completer.  If there is no completer, what follows
-    # directly cannot be another option, so mark to not add those to
-    # completions.
-    optarg = False
-    try:
-        # Look for previous word, which will be containing word if the option
-        # has an equals sign in it.
-        prev = None
-        if cword < len(cwords):
-            mo = re.search('(--.*?)=(.*)', cwords[cword])
-            if mo:
-                prev, prefix = mo.groups()
-        if not prev:
-            prev = cwords[cword - 1]
-
-        if prev and prev.startswith('-'):
-            option = parser.get_option(prev)
-            if option:
-                if option.nargs > 0:
-                    optarg = True
-                    if hasattr(option, 'completer'):
-                        completer = option.completer
-                    elif option.choices:
-                        completer = ListCompleter(option.choices)
-                    elif option.type in ('string',):
-                        completer = opt_completer
-                    else:
-                        completer = NoneCompleter()
-                # Warn user at least, it could help him figure out the problem.
-                elif hasattr(option, 'completer'):
-                    msg = "Error: optparse option with a completer does not take arguments: %s" % (option)
-                    raise SystemExit(msg)
-    except KeyError:
-        pass
-
-    completions = []
-
-    # Options completion.
-    if not optarg and (not prefix or prefix.startswith('-')):
-        completions += parser._short_opt.keys()
-        completions += parser._long_opt.keys()
-        # Note: this will get filtered properly below.
-
-    completer_kwargs = {
-        'pwd': os.getcwd(),
-        'cline': cline,
-        'cpoint': cpoint,
-        'prefix': prefix,
-        'suffix': suffix,
-    }
-    # File completion.
-    if completer and (not prefix or not prefix.startswith('-')):
-        # Call appropriate completer depending on type.
-        if isinstance(completer, (basestring, list, tuple)):
-            completer = FileCompleter(completer)
-        elif not isinstance(completer, (types.FunctionType, types.LambdaType, types.ClassType, types.ObjectType)):
-            # TODO: what to do here?
-            pass
-
-        completions = completer(**completer_kwargs)
-
-    if isinstance(completions, basestring):
-        # is a bash command, just run it
-        if SHELL in (BASH,):  # TODO: zsh
-            print completions
-        else:
-            raise Exception("Commands are unsupported by this shell %s" % SHELL)
-    else:
-        # Filter using prefix.
-        if prefix:
-            completions = sorted(filter(lambda x: x.startswith(prefix), completions))
-        completions = ' '.join(map(str, completions))
-
-        # Save results
-        if SHELL == "bash":
-            print 'COMPREPLY=(' + completions + ')'
-        else:
-            print completions
-
-    # Print debug output (if needed).  You can keep a shell with 'tail -f' to
-    # the log file to monitor what is happening.
-    if debugfn:
-        txt = "\n".join([
-            '---------------------------------------------------------',
-            'CWORDS %s' % cwords,
-            'CLINE %s' % cline,
-            'CPOINT %s' % cpoint,
-            'CWORD %s' % cword,
-            '',
-            'Short options',
-            pformat(parser._short_opt),
-            '',
-            'Long options',
-            pformat(parser._long_opt),
-            'Prefix %s' % prefix,
-            'Suffix %s', suffix,
-            'completions %s' % completions,
-            ])
-        if isinstance(debugfn, logging.Logger):
-            debugfn.debug(txt)
-        else:
-            f = open(debugfn, 'a')
-            f.write(txt)
-            f.close()
-
-    # Exit with error code (we do not let the caller continue on purpose, this
-    # is a run for completions only.)
-    sys.exit(1)
-
-
-class CmdComplete(object):
-
-    """Simple default base class implementation for a subcommand that supports
-    command completion.  This class is assuming that there might be a method
-    addopts(self, parser) to declare options for this subcommand, and an
-    optional completer data member to contain command-specific completion.  Of
-    course, you don't really have to use this, but if you do it is convenient to
-    have it here."""
-
-    def autocomplete(self, completer=None):
-        parser = OPTIONPARSER_CLASS(self.__doc__.strip())
-        if hasattr(self, 'addopts'):
-            fnc = getattr(self, 'addopts')
-            fnc(parser)
-
-        if hasattr(self, 'completer'):
-            completer = getattr(self, 'completer')
-
-        return autocomplete(parser, completer)
-
-
-def gen_cmdline(cmd_list, partial):
-    """Create the commandline to generate simulated tabcompletion output
-    @param cmd_list: command to execute as list of strings
-    @param partial: the string to autocomplete (typically, partial is an element of the cmd_list)
-    """
-    cmdline = " ".join(cmd_list)
-
-    env = []
-    env.append("%s=1" % OPTCOMPLETE_ENVIRONMENT)
-    env.append('COMP_LINE="%s"' % cmdline)
-    env.append('COMP_WORDS=(%s)' % cmdline)
-    env.append('COMP_POINT=%s' % len(cmdline))
-    env.append('COMP_CWORD=%s' % cmd_list.index(partial))
-
-    return "%s %s" % (" ".join(env), cmd_list[0])
-
diff --git a/vsc/utils/patterns.py b/vsc/utils/patterns.py
deleted file mode 100644
index efb614551a..0000000000
--- a/vsc/utils/patterns.py
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env python
-##
-# Copyright 2012-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-Module offering the Singleton class.
-
-
-This class can be used as the C{__metaclass__} class field to ensure only a
-single instance of the class gets used in the run of an application or
-script.
-
->>> class A(object):
-...     __metaclass__ = Singleton
-
-@author: Andy Georges (Ghent University)
-"""
-
-
-class Singleton(type):
-    """Serves as  metaclass for classes that should implement the Singleton pattern.
-
-    See http://stackoverflow.com/questions/6760685/creating-a-singleton-in-python
-    """
-    _instances = {}
-
-    def __call__(cls, *args, **kwargs):
-        if cls not in cls._instances:
-            cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs)
-        return cls._instances[cls]
diff --git a/vsc/utils/rest.py b/vsc/utils/rest.py
deleted file mode 100644
index 18974a8167..0000000000
--- a/vsc/utils/rest.py
+++ /dev/null
@@ -1,288 +0,0 @@
-##
-# This file is part of agithub
-# Originally created by Jonathan Paugh
-#
-# https://github.com/jpaugh/agithub
-#
-# Copyright 2012 Jonathan Paugh
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-##
-"""
-This module contains Rest api utilities,
-Mainly the RestClient, which you can use to easily pythonify a rest api.
-
-based on https://github.com/jpaugh/agithub/commit/1e2575825b165c1cb7cbd85c22e2561fc4d434d3
-
-@author: Jonathan Paugh
-@author: Jens Timmerman
-"""
-import base64
-import urllib
-import urllib2
-try:
-    import json
-except ImportError:
-    import simplejson as json
-
-from vsc.utils import fancylogger
-
-try:
-    from functools import partial
-except ImportError:
-    from vsc.utils.missing import partial
-
-
-class Client(object):
-    """An implementation of a REST client"""
-    DELETE = 'DELETE'
-    GET = 'GET'
-    HEAD = 'HEAD'
-    PATCH = 'PATCH'
-    POST = 'POST'
-    PUT = 'PUT'
-
-    HTTP_METHODS = (
-        DELETE,
-        GET,
-        HEAD,
-        PATCH,
-        POST,
-        PUT,
-    )
-
-    USER_AGENT = 'vsc-rest-client'
-
-    def __init__(self, url, username=None, password=None, token=None, token_type='Token', user_agent=None, append_slash=False):
-        """
-        Create a Client object,
-        this client can consume a REST api hosted at host/endpoint
-
-        If a username is given a password or a token is required.
-        You can not use a password and a token.
-        token_type is the typoe fo th the authorization token text in the http authentication header, defaults to Token
-        This should be set to 'Bearer' for certain OAuth implementations.
-        """
-        self.auth_header = None
-        self.username = username
-        self.url = url
-        self.append_slash = append_slash
-
-        if not user_agent:
-            self.user_agent = self.USER_AGENT
-        else:
-            self.user_agent = user_agent
-
-        handler = urllib2.HTTPSHandler()
-        self.opener = urllib2.build_opener(handler)
-
-        if username is not None:
-            if password is None and token is None:
-                raise TypeError("You need a password or an OAuth token to authenticate as " + username)
-            if password is not None and token is not None:
-                raise TypeError("You cannot use both password and OAuth token authenication")
-
-        if password is not None:
-            self.auth_header = self.hash_pass(password, username)
-        elif token is not None:
-            self.auth_header = '%s %s' % (token_type, token)
-
-    def get(self, url, headers={}, **params):
-        """
-        Do a http get request on the given url with given headers and parameters
-        Parameters is a dictionary that will will be urlencoded
-        """
-        if self.append_slash:
-            url += '/'
-        url += self.urlencode(params)
-        return self.request(self.GET, url, None, headers)
-
-    def head(self, url, headers={}, **params):
-        """
-        Do a http head request on the given url with given headers and parameters
-        Parameters is a dictionary that will will be urlencoded
-        """
-        if self.append_slash:
-            url += '/'
-        url += self.urlencode(params)
-        return self.request(self.HEAD, url, None, headers)
-
-    def delete(self, url, headers={}, **params):
-        """
-        Do a http delete request on the given url with given headers and parameters
-        Parameters is a dictionary that will will be urlencoded
-        """
-        if self.append_slash:
-            url += '/'
-        url += self.urlencode(params)
-        return self.request(self.DELETE, url, None, headers)
-
-    def post(self, url, body=None, headers={}, **params):
-        """
-        Do a http post request on the given url with given body, headers and parameters
-        Parameters is a dictionary that will will be urlencoded
-        """
-        if self.append_slash:
-            url += '/'
-        url += self.urlencode(params)
-        headers['Content-Type'] = 'application/json'
-        return self.request(self.POST, url, json.dumps(body), headers)
-
-    def put(self, url, body=None, headers={}, **params):
-        """
-        Do a http put request on the given url with given body, headers and parameters
-        Parameters is a dictionary that will will be urlencoded
-        """
-        if self.append_slash:
-            url += '/'
-        url += self.urlencode(params)
-        headers['Content-Type'] = 'application/json'
-        return self.request(self.PUT, url, json.dumps(body), headers)
-
-    def patch(self, url, body=None, headers={}, **params):
-        """
-        Do a http patch request on the given url with given body, headers and parameters
-        Parameters is a dictionary that will will be urlencoded
-        """
-        if self.append_slash:
-            url += '/'
-        url += self.urlencode(params)
-        headers['Content-Type'] = 'application/json'
-        return self.request(self.PATCH, url, json.dumps(body), headers)
-
-    def request(self, method, url, body, headers):
-        if self.auth_header is not None:
-            headers['Authorization'] = self.auth_header
-        headers['User-Agent'] = self.user_agent
-        fancylogger.getLogger().debug('cli request: %s, %s, %s, %s', method, url, body, headers)
-        #TODO: in recent python: Context manager
-        conn = self.get_connection(method, url, body, headers)
-        status = conn.code
-        body = conn.read()
-        try:
-            pybody = json.loads(body)
-        except ValueError:
-            pybody = body
-        fancylogger.getLogger().debug('reponse len: %s ', len(pybody))
-        conn.close()
-        return status, pybody
-
-    def urlencode(self, params):
-        if not params:
-            return ''
-        return '?' + urllib.urlencode(params)
-
-    def hash_pass(self, password, username=None):
-        if not username:
-            username = self.username
-        return 'Basic ' + base64.b64encode('%s:%s' % (username, password)).strip()
-
-    def get_connection(self, method, url, body, headers):
-        if not self.url.endswith('/') and not url.startswith('/'):
-            sep = '/'
-        else:
-            sep = ''
-        request = urllib2.Request(self.url + sep + url, data=body)
-        for header, value in headers.iteritems():
-            request.add_header(header, value)
-        request.get_method = lambda: method
-        fancylogger.getLogger().debug('opening request:  %s%s%s', self.url, sep, url)
-        connection = self.opener.open(request)
-        return connection
-
-
-class RequestBuilder(object):
-    '''RequestBuilder(client).path.to.resource.method(...)
-        stands for
-    RequestBuilder(client).client.method('path/to/resource, ...)
-
-    Also, if you use an invalid path, too bad. Just be ready to catch a
-    You can use item access instead of attribute access. This is
-    convenient for using variables' values and required for numbers.
-    bad status from github.com. (Or maybe an httplib.error...)
-
-    To understand the method(...) calls, check out github.client.Client.
-    '''
-    def __init__(self, client):
-        """Constructor"""
-        self.client = client
-        self.url = ''
-
-    def __getattr__(self, key):
-        """
-        Overwrite __getattr__ to build up the equest url
-        this enables us to do bla.some.path['something']
-        and get the url bla/some/path/something
-        """
-        # make sure key is a string
-        key = str(key)
-        # our methods are lowercase, but our HTTP_METHOD constants are upercase, so check if it is in there, but only
-        # if it was a lowercase key
-        # this is here so bla.something.get() should work, and not result in bla/something/get being returned
-        if key.upper() in self.client.HTTP_METHODS and [x for x in key if x.islower()]:
-            mfun = getattr(self.client, key)
-            fun = partial(mfun, url=self.url)
-            return fun
-        self.url += '/' + key
-        return self
-
-    __getitem__ = __getattr__
-
-    def __str__(self):
-        '''If you ever stringify this, you've (probably) messed up
-        somewhere. So let's give a semi-helpful message.
-        '''
-        return "I don't know about %s, You probably want to do a get or other http request, use .get()" % self.url
-
-    def __repr__(self):
-        return '%s: %s' % (self.__class__, self.url)
-
-
-class RestClient(object):
-    """
-    A client with a request builder, so you can easily create rest requests
-    e.g. to create a github Rest API client just do
-    >>> g = RestClient('https://api.github.com', username='user', password='pass')
-    >>> g = RestClient('https://api.github.com', token='oauth token')
-    >>> status, data = g.issues.get(filter='subscribed')
-    >>> data
-    ... [ list_, of, stuff ]
-    >>> status, data = g.repos.jpaugh64.repla.issues[1].get()
-    >>> data
-    ... { 'dict': 'my issue data', }
-    >>> name, repo = 'jpaugh64', 'repla'
-    >>> status, data = g.repos[name][repo].issues[1].get()
-    ... same thing
-    >>> status, data = g.funny.I.donna.remember.that.one.get()
-    >>> status
-    ... 404
-
-    That's all there is to it. (blah.post() should work, too.)
-
-    NOTE: It is up to you to spell things correctly. Github doesn't even
-    try to validate the url you feed it. On the other hand, it
-    automatically supports the full API--so why should you care?
-    """
-    def __init__(self, *args, **kwargs):
-        """We create a client with the given arguments"""
-        self.client = Client(*args, **kwargs)
-
-    def __getattr__(self, key):
-        """Get an attribute, we will build a request with it"""
-        return RequestBuilder(self.client).__getattr__(key)
diff --git a/vsc/utils/run.py b/vsc/utils/run.py
deleted file mode 100644
index 8e61c95bf6..0000000000
--- a/vsc/utils/run.py
+++ /dev/null
@@ -1,843 +0,0 @@
-#
-# Copyright 2009-2013 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-#
-
-"""
-Python module to execute a command
-
-Historical overview of existing equivalent code
-
- - EasyBuild filetools module
-    - C{run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True, log_output=False, path=None)}
-    - C{run_cmd_qa(cmd, qa, no_qa=None, log_ok=True, log_all=False, simple=False, regexp=True, std_qa=None, path=None)}
-
- - Executes a command cmd
-    - looks for questions and tries to answer based on qa dictionary
-    - returns exitcode and stdout+stderr (mixed)
-    - no input though stdin
-    - if C{log_ok} or C{log_all} are set -> will C{log.error} if non-zero exit-code
-    - if C{simple} is C{True} -> instead of returning a tuple (output, ec) it will just return C{True} or C{False} signifying succes
-    - C{regexp} -> Regex used to check the output for errors. If C{True} will use default (see C{parselogForError})
-    - if log_output is True -> all output of command will be logged to a tempfile
-    - path is the path run_cmd should chdir to before doing anything
-
- - Q&A: support reading stdout asynchronous and replying to a question through stdin
-
- - Manage C{managecommands} module C{Command} class
-    - C{run} method
-
- - python-package-vsc-utils run module Command class
-    - C{run} method
-
- - C{mympirun} (old)
-    - C{runrun(self, cmd, returnout=False, flush=False, realcmd=False)}:
-        - C{runrunnormal(self, cmd, returnout=False, flush=False)}
-        - C{runrunfile(self, cmd, returnout=False, flush=False)}
-
- - C{hanything} commands/command module
-    - C{run} method
-        - fake pty support
-
-@author: Stijn De Weirdt (Ghent University)
-"""
-
-import errno
-import logging
-import os
-import pty
-import re
-import signal
-import sys
-import time
-
-from vsc.utils.fancylogger import getLogger, getAllExistingLoggers
-
-
-PROCESS_MODULE_ASYNCPROCESS_PATH = 'vsc.utils.asyncprocess'
-PROCESS_MODULE_SUBPROCESS_PATH = 'subprocess'
-
-RUNRUN_TIMEOUT_OUTPUT = ''
-RUNRUN_TIMEOUT_EXITCODE = 123
-RUNRUN_QA_MAX_MISS_EXITCODE = 124
-
-BASH = '/bin/bash'
-SHELL = BASH
-
-
-class DummyFunction(object):
-    def __getattr__(self, name):
-        def dummy(*args, **kwargs):
-            pass
-        return dummy
-
-
-class Run(object):
-    """Base class for static run method"""
-    INIT_INPUT_CLOSE = True
-    USE_SHELL = True
-    SHELL = SHELL  # set the shell via the module constant
-
-    @classmethod
-    def run(cls, cmd, **kwargs):
-        """static method
-            return (exitcode,output)
-        """
-        r = cls(cmd, **kwargs)
-        return r._run()
-
-    def __init__(self, cmd=None, **kwargs):
-        """
-        Handle initiliastion
-            @param cmd: command to run
-            @param input: set "simple" input
-            @param startpath: directory to change to before executing command
-            @param disable_log: use fake logger (won't log anything)
-            @param use_shell: use the subshell 
-            @param shell: change the shell
-        """
-        self.input = kwargs.pop('input', None)
-        self.startpath = kwargs.pop('startpath', None)
-        self.use_shell = kwargs.pop('use_shell', self.USE_SHELL)
-        self.shell = kwargs.pop('shell', self.SHELL)
-
-        if kwargs.pop('disable_log', None):
-            self.log = DummyFunction()  # No logging
-        if not hasattr(self, 'log'):
-            self.log = getLogger(self._get_log_name())
-
-        self.cmd = cmd  # actual command
-
-        self._cwd_before_startpath = None
-
-        self._process_module = None
-        self._process = None
-
-        self.readsize = 1024  # number of bytes to read blocking
-
-        self._shellcmd = None
-        self._popen_named_args = None
-
-        self._process_exitcode = None
-        self._process_output = None
-
-        self._post_exitcode_log_failure = self.log.error
-
-        super(Run, self).__init__(**kwargs)
-
-    def _get_log_name(self):
-        """Set the log name"""
-        return self.__class__.__name__
-
-    def _prep_module(self, modulepath=None, extendfromlist=None):
-        # these will provide the required Popen, PIPE and STDOUT
-        if modulepath is None:
-            modulepath = PROCESS_MODULE_SUBPROCESS_PATH
-
-        fromlist = ['Popen', 'PIPE', 'STDOUT']
-        if extendfromlist is not None:
-            fromlist.extend(extendfromlist)
-
-        self._process_modulepath = modulepath
-
-        self._process_module = __import__(self._process_modulepath, globals(), locals(), fromlist)
-
-    def _run(self):
-        """actual method
-        Structure
-
-         - pre
-            - convert command to shell command - DONE
-            - chdir before start - DONE
-
-            - start C{Popen} - DONE
-                - support async and subprocess - DONE
-                - support for
-                    - filehandle
-                    - PIPE - DONE
-                    - pty - DONE
-
-         - main
-            - should capture exitcode and output
-            - features
-                - separate stdout and stderr ?
-                - simple single run
-                    - no timeout/waiting - DONE
-                - flush to
-                    - stdout
-                    - logger - DONE
-                    - both stdout and logger
-                - process intermediate output
-                    - qa
-                - input
-                    - qa
-                    - from file ?
-                    - text - DONE
-
-         - post
-            - parse with regexp
-                - raise/log error on match
-         - return
-            - return output
-                - log output
-                - write to file
-                - return in string - DONE
-            - on C{ec > 0}
-                - error - DONE
-                - raiseException
-            - simple
-                - just return True/False
-        """
-        self._run_pre()
-        self._wait_for_process()
-        return self._run_post()
-
-    def _run_pre(self):
-        """Non-blocking start"""
-        if self._process_module is None:
-            self._prep_module()
-
-        if self.startpath is not None:
-            self._start_in_path()
-
-        if self._shellcmd is None:
-            self._make_shell_command()
-
-        if self._popen_named_args is None:
-            self._make_popen_named_args()
-
-        self._init_process()
-
-        self._init_input()
-
-    def _run_post(self):
-        self._cleanup_process()
-
-        self._post_exitcode()
-
-        self._post_output()
-
-        if self.startpath is not None:
-            self._return_to_previous_start_in_path()
-
-        return self._run_return()
-
-    def _start_in_path(self):
-        """Change path before the run"""
-        if self.startpath is None:
-            self.log.debug("_start_in_path: no startpath set")
-            return
-
-        if os.path.exists(self.startpath):
-            if os.path.isdir(self.startpath):
-                try:
-                    self._cwd_before_startpath = os.getcwd()  # store it some one can return to it
-                    os.chdir(self.startpath)
-                except:
-                    self.raiseException("_start_in_path: failed to change path from %s to startpath %s" %
-                                        (self._cwd_before_startpath, self.startpath))
-            else:
-                self.log.raiseExcpetion("_start_in_path: provided startpath %s exists but is no directory" %
-                                        self.startpath)
-        else:
-            self.raiseException("_start_in_path: startpath %s does not exist" % self.startpath)
-
-    def _return_to_previous_start_in_path(self):
-        """Change to original path before the change to startpath"""
-        if self._cwd_before_startpath is None:
-            self.log.warning("_return_to_previous_start_in_path: previous cwd is empty. Not trying anything")
-            return
-
-        if os.path.exists(self._cwd_before_startpath):
-            if os.path.isdir(self._cwd_before_startpath):
-                try:
-                    currentpath = os.getcwd()
-                    if not currentpath == self.startpath:
-                        self.log.warning(("_return_to_previous_start_in_path: current diretory %s does not match "
-                                          "startpath %s") % (currentpath, self.startpath))
-                    os.chdir(self._cwd_before_startpath)
-                except:
-                    self.raiseException(("_return_to_previous_start_in_path: failed to change path from current %s "
-                                         "to previous path %s") % (currentpath, self._cwd_before_startpath))
-            else:
-                self.log.raiseExcpetion(("_return_to_previous_start_in_path: provided previous cwd path %s exists "
-                                         "but is no directory") % self._cwd_before_startpath)
-        else:
-            self.raiseException("_return_to_previous_start_in_path: previous cwd path %s does not exist" %
-                                self._cwd_before_startpath)
-
-    def _make_popen_named_args(self, others=None):
-        """Create the named args for Popen"""
-        self._popen_named_args = {
-                                  'stdout': self._process_module.PIPE,
-                                  'stderr': self._process_module.STDOUT,
-                                  'stdin': self._process_module.PIPE,
-                                  'close_fds': True,
-                                  'shell': self.use_shell,
-                                  'executable': self.shell,
-                                  }
-        if others is not None:
-            self._popen_named_args.update(others)
-
-        self.log.debug("_popen_named_args %s" % self._popen_named_args)
-
-    def _make_shell_command(self):
-        """Convert cmd into shell command"""
-        if self.cmd is None:
-            self.log.raiseExcpetion("_make_shell_command: no cmd set.")
-
-        if isinstance(self.cmd, basestring):
-            self._shellcmd = self.cmd
-        elif isinstance(self.cmd, (list, tuple,)):
-            self._shellcmd = " ".join(self.cmd)
-        else:
-            self.log.raiseException("Failed to convert cmd %s (type %s) into shell command" % (self.cmd, type(self.cmd)))
-
-    def _init_process(self):
-        """Initialise the self._process"""
-        try:
-            self._process = self._process_module.Popen(self._shellcmd, **self._popen_named_args)
-        except OSError:
-            self.log.raiseException("_init_process: init Popen shellcmd %s failed: %s" % (self._shellcmd))
-
-    def _init_input(self):
-        """Handle input, if any in a simple way"""
-        if self.input is not None:  # allow empty string (whatever it may mean)
-            try:
-                self._process.stdin.write(self.input)
-            except:
-                self.log.raiseException("_init_input: Failed write input %s to process" % self.input)
-
-        if self.INIT_INPUT_CLOSE:
-            self._process.stdin.close()
-            self.log.debug("_init_input: process stdin closed")
-        else:
-            self.log.debug("_init_input: process stdin NOT closed")
-
-    def _wait_for_process(self):
-        """The main loop
-            This one has most simple loop
-        """
-        try:
-            self._process_exitcode = self._process.wait()
-            self._process_output = self._read_process(-1)  # -1 is read all
-        except:
-            self.log.raiseException("_wait_for_process: problem during wait exitcode %s output %s" %
-                                    (self._process_exitcode, self._process_output))
-
-    def _cleanup_process(self):
-        """Cleanup any leftovers from the process"""
-
-    def _read_process(self, readsize=None):
-        """Read from process, return out"""
-        if readsize is None:
-            readsize = self.readsize
-        if readsize is None:
-            readsize = -1  # read all
-        self.log.debug("_read_process: going to read with readsize %s" % readsize)
-        out = self._process.stdout.read(readsize)
-        return out
-
-    def _post_exitcode(self):
-        """Postprocess the exitcode in self._process_exitcode"""
-        if not self._process_exitcode == 0:
-            self._post_exitcode_log_failure("_post_exitcode: problem occured with cmd %s: output %s" %
-                                            (self.cmd, self._process_output))
-        else:
-            self.log.debug("_post_exitcode: success cmd %s: output %s" % (self.cmd, self._process_output))
-
-    def _post_output(self):
-        """Postprocess the output in self._process_output"""
-        pass
-
-    def _run_return(self):
-        """What to return"""
-        return self._process_exitcode, self._process_output
-
-    def _killtasks(self, tasks=None, sig=signal.SIGKILL, kill_pgid=False):
-        """
-        Kill all tasks
-            @param: tasks list of processids
-            @param: sig, signal to use to kill
-            @apram: kill_pgid, send kill to group
-        """
-        if tasks is None:
-            self.log.error("killtasks no tasks passed")
-        elif isinstance(tasks, basestring):
-            try:
-                tasks = [int(tasks)]
-            except:
-                self.log.error("killtasks failed to convert tasks string %s to int" % tasks)
-
-        for pid in tasks:
-            pgid = os.getpgid(pid)
-            try:
-                os.kill(int(pid), sig)
-                if kill_pgid:
-                    os.killpg(pgid, sig)
-                self.log.debug("Killed %s with signal %s" % (pid, sig))
-            except OSError, err:
-                # ERSCH is no such process, so no issue
-                if not err.errno == errno.ESRCH:
-                    self.log.error("Failed to kill %s: %s" % (pid, err))
-            except Exception, err:
-                self.log.error("Failed to kill %s: %s" % (pid, err))
-
-    def stop_tasks(self):
-        """Cleanup current run"""
-        self._killtasks(tasks=[self._process.pid])
-        try:
-            os.waitpid(-1, os.WNOHANG)
-        except:
-            pass
-
-
-class RunNoWorries(Run):
-    """When the exitcode is >0, log.debug instead of log.error"""
-    def __init__(self, cmd, **kwargs):
-        super(RunNoWorries, self).__init__(cmd, **kwargs)
-        self._post_exitcode_log_failure = self.log.debug
-
-
-class RunLoopException(Exception):
-    def __init__(self, code, output):
-        self.code = code
-        self.output = output
-
-    def __str__(self):
-        return "%s code %s output %s" % (self.__class__.__name__, self.code, self.output)
-
-
-class RunLoop(Run):
-    """Main process is a while loop which reads the output in blocks
-        need to read from time to time.
-        otherwise the stdout/stderr buffer gets filled and it all stops working
-    """
-    LOOP_TIMEOUT_INIT = 0.1
-    LOOP_TIMEOUT_MAIN = 1
-
-    def __init__(self, cmd, **kwargs):
-        super(RunLoop, self).__init__(cmd, **kwargs)
-        self._loop_count = None
-        self._loop_continue = None  # intial state, change this to break out the loop
-
-    def _wait_for_process(self):
-        """Loop through the process in timesteps
-            collected output is run through _loop_process_output
-        """
-        # these are initialised outside the function (cannot be forgotten, but can be overwritten)
-        self._loop_count = 0  # internal counter
-        self._loop_continue = True
-        self._process_output = ''
-
-        # further initialisation
-        self._loop_initialise()
-
-        time.sleep(self.LOOP_TIMEOUT_INIT)
-        ec = self._process.poll()
-        try:
-            while self._loop_continue and ec < 0:
-                output = self._read_process()
-                self._process_output += output
-                # process after updating the self._process_ vars
-                self._loop_process_output(output)
-
-                if len(output) == 0:
-                    time.sleep(self.LOOP_TIMEOUT_MAIN)
-                ec = self._process.poll()
-
-                self._loop_count += 1
-
-            self.log.debug("_wait_for_process: loop stopped after %s iterations (ec %s loop_continue %s)" %
-                           (self._loop_count, ec, self._loop_continue))
-
-            # read remaining data (all of it)
-            output = self._read_process(-1)
-
-            self._process_output += output
-            self._process_exitcode = ec
-
-            # process after updating the self._process_ vars
-            self._loop_process_output_final(output)
-        except RunLoopException, err:
-            self.log.debug('RunLoopException %s' % err)
-            self._process_output = err.output
-            self._process_exitcode = err.code
-
-    def _loop_initialise(self):
-        """Initialisation before the loop starts"""
-        pass
-
-    def _loop_process_output(self, output):
-        """Process the output that is read in blocks
-            simplest form: do nothing
-        """
-        pass
-
-    def _loop_process_output_final(self, output):
-        """Process the remaining output that is read
-            simplest form: do the same as _loop_process_output
-        """
-        self._loop_process_output(output)
-
-
-class RunLoopLog(RunLoop):
-    LOOP_LOG_LEVEL = logging.INFO
-
-    def _wait_for_process(self):
-        # initialise the info logger
-        self.log.info("Going to run cmd %s" % self._shellcmd)
-        super(RunLoopLog, self)._wait_for_process()
-
-    def _loop_process_output(self, output):
-        """Process the output that is read in blocks
-            send it to the logger. The logger need to be stream-like
-        """
-        self.log.streamLog(self.LOOP_LOG_LEVEL, output)
-        super(RunLoopLog, self)._loop_process_output(output)
-
-
-class RunLoopStdout(RunLoop):
-
-    def _loop_process_output(self, output):
-        """Process the output that is read in blocks
-            send it to the stdout
-        """
-        sys.stdout.write(output)
-        sys.stdout.flush()
-        super(RunLoopStdout, self)._loop_process_output(output)
-
-
-class RunAsync(Run):
-    """Async process class"""
-
-    def _prep_module(self, modulepath=None, extendfromlist=None):
-        # these will provide the required Popen, PIPE and STDOUT
-        if modulepath is None:
-            modulepath = PROCESS_MODULE_ASYNCPROCESS_PATH
-        if extendfromlist is None:
-            extendfromlist = ['send_all', 'recv_some']
-        super(RunAsync, self)._prep_module(modulepath=modulepath, extendfromlist=extendfromlist)
-
-    def _read_process(self, readsize=None):
-        """Read from async process, return out"""
-        if readsize is None:
-            readsize = self.readsize
-
-        if self._process.stdout is None:
-            # Nothing yet/anymore
-            return ''
-
-        try:
-            if readsize is not None  and readsize < 0:
-                # read all blocking (it's not why we should use async
-                out = self._process.stdout.read()
-            else:
-                # non-blocking read (readsize is a maximum to return !
-                out = self._process_module.recv_some(self._process, maxread=readsize)
-            return out
-        except (IOError, Exception):
-            # recv_some may throw Exception
-            self.log.exception("_read_process: read failed")
-            return ''
-
-
-class RunFile(Run):
-    """Popen to filehandle"""
-    def __init__(self, cmd, **kwargs):
-        self.filename = kwargs.pop('filename', None)
-        self.filehandle = None
-        super(RunFile, self).__init__(cmd, **kwargs)
-
-    def _make_popen_named_args(self, others=None):
-        if others is None:
-            if os.path.exists(self.filename):
-                if os.path.isfile(self.filename):
-                    self.log.warning("_make_popen_named_args: going to overwrite existing file %s" % self.filename)
-                elif os.path.isdir(self.filename):
-                    self.raiseException(("_make_popen_named_args: writing to filename %s impossible. Path exists and "
-                                         "is a directory.") % self.filename)
-                else:
-                    self.raiseException("_make_popen_named_args: path exists and is not a file or directory %s" %
-                                        self.filename)
-            else:
-                dirname = os.path.dirname(self.filename)
-                if dirname and not os.path.isdir(dirname):
-                    try:
-                        os.makedirs(dirname)
-                    except:
-                        self.log.raiseException(("_make_popen_named_args: dirname %s for file %s does not exists. "
-                                                 "Creating it failed.") % (dirname, self.filename))
-
-            try:
-                self.filehandle = open(self.filename, 'w')
-            except:
-                self.log.raiseException("_make_popen_named_args: failed to open filehandle for file %s" % self.filename)
-
-            others = {
-                      'stdout': self.filehandle,
-                      }
-
-        super(RunFile, self)._make_popen_named_args(others=others)
-
-    def _cleanup_process(self):
-        """Close the filehandle"""
-        try:
-            self.filehandle.close()
-        except:
-            self.log.raiseException("_cleanup_process: failed to close filehandle for filename %s" % self.filename)
-
-    def _read_process(self, readsize=None):
-        """Meaningless for filehandle"""
-        return ''
-
-
-class RunPty(Run):
-    """Pty support (eg for screen sessions)"""
-    def _read_process(self, readsize=None):
-        """This does not work for pty"""
-        return ''
-
-    def _make_popen_named_args(self, others=None):
-        if others is None:
-            (master, slave) = pty.openpty()
-            others = {
-                'stdin': slave,
-                'stdout': slave,
-                'stderr': slave
-                }
-        super(RunPty, self)._make_popen_named_args(others=others)
-
-
-class RunTimeout(RunLoop, RunAsync):
-    """Question/Answer processing"""
-
-    def __init__(self, cmd, **kwargs):
-        self.timeout = float(kwargs.pop('timeout', None))
-        self.start = time.time()
-        super(RunTimeout, self).__init__(cmd, **kwargs)
-
-    def _loop_process_output(self, output):
-        """"""
-        time_passed = time.time() - self.start
-        if self.timeout is not None and  time_passed > self.timeout:
-            self.log.debug("Time passed %s > timeout %s." % (time_passed, self.timeout))
-            self.stop_tasks()
-
-            # go out of loop
-            raise RunLoopException(RUNRUN_TIMEOUT_EXITCODE, RUNRUN_TIMEOUT_OUTPUT)
-        super(RunTimeout, self)._loop_process_output(output)
-
-
-class RunQA(RunLoop, RunAsync):
-    """Question/Answer processing"""
-    LOOP_MAX_MISS_COUNT = 20
-    INIT_INPUT_CLOSE = False
-    CYCLE_ANSWERS = True
-
-    def __init__(self, cmd, **kwargs):
-        """
-        Add  question and answer style running
-            @param qa: dict with exact questions and answers
-            @param qa_reg: dict with (named) regex-questions and answers (answers can contain named string templates)
-            @param no_qa: list of regex that can block the output, but is not seen as a question.
-
-        Regular expressions are compiled, just pass the (raw) text.
-        """
-        qa = kwargs.pop('qa', {})
-        qa_reg = kwargs.pop('qa_reg', {})
-        no_qa = kwargs.pop('no_qa', [])
-        self._loop_miss_count = None  # maximum number of misses
-        self._loop_previous_ouput_length = None  # track length of output through loop
-
-        super(RunQA, self).__init__(cmd, **kwargs)
-
-        self.qa, self.qa_reg, self.no_qa = self._parse_qa(qa, qa_reg, no_qa)
-
-    def _parse_qa(self, qa, qa_reg, no_qa):
-        """
-        process the QandA dictionary
-            - given initial set of Q and A (in dict), return dict of reg. exp. and A
-
-        - make regular expression that matches the string with
-            - replace whitespace
-            - replace newline
-        - qa_reg: question is compiled as is, and whitespace+ending is added
-        - provided answers can be either strings or lists of strings (which will be used iteratively)
-        """
-
-        def escape_special(string):
-            specials = '.*+?(){}[]|\$^'
-            return re.sub(r"([%s])" % ''.join(['\%s' % x for x in specials]), r"\\\1", string)
-
-        SPLIT = '[\s\n]+'
-        REG_SPLIT = re.compile(r"" + SPLIT)
-
-        def process_answers(answers):
-            """Construct list of newline-terminated answers (as strings)."""
-            if isinstance(answers, basestring):
-                answers = [answers]
-            elif isinstance(answers, list):
-                # list is manipulated when answering matching question, so take a copy
-                answers = answers[:]
-            else:
-                msg_tmpl = "Invalid type for answer, not a string or list: %s (%s)"
-                self.log.raiseException(msg_tmpl % (type(answers), answers), exception=TypeError)
-            # add optional split at the end
-            for i in [idx for idx, a in enumerate(answers) if not a.endswith('\n')]:
-                answers[i] += '\n'
-            return answers
-
-        def process_question(question):
-            """Convert string question to regex."""
-            split_q = [escape_special(x) for x in REG_SPLIT.split(question)]
-            reg_q_txt = SPLIT.join(split_q) + SPLIT.rstrip('+') + "*$"
-            reg_q = re.compile(r"" + reg_q_txt)
-            if reg_q.search(question):
-                return reg_q
-            else:
-                # this is just a sanity check on the created regex, can this actually occur?
-                msg_tmpl = "_parse_qa process_question: question %s converted in %s does not match itself"
-                self.log.raiseException(msg_tmpl % (question.pattern, reg_q_txt), exception=ValueError)
-
-        new_qa = {}
-        self.log.debug("new_qa: ")
-        for question, answers in qa.items():
-            reg_q = process_question(question)
-            new_qa[reg_q] = process_answers(answers)
-            self.log.debug("new_qa[%s]: %s" % (reg_q.pattern.__repr__(), answers))
-
-        new_qa_reg = {}
-        self.log.debug("new_qa_reg: ")
-        for question, answers in qa_reg.items():
-            reg_q = re.compile(r"" + question + r"[\s\n]*$")
-            new_qa_reg[reg_q] = process_answers(answers)
-            self.log.debug("new_qa_reg[%s]: %s" % (reg_q.pattern.__repr__(), answers))
-
-        # simple statements, can contain wildcards
-        new_no_qa = [re.compile(r"" + x + r"[\s\n]*$") for x in no_qa]
-        self.log.debug("new_no_qa: %s" % [x.pattern.__repr__() for x in new_no_qa])
-
-        return new_qa, new_qa_reg, new_no_qa
-
-    def _loop_initialise(self):
-        """Initialisation before the loop starts"""
-        self._loop_miss_count = 0
-        self._loop_previous_ouput_length = 0
-
-    def _loop_process_output(self, output):
-        """Process the output that is read in blocks
-            check the output passed to questions available
-        """
-        hit = False
-
-        self.log.debug('output %s all_output %s' % (output, self._process_output))
-
-        # qa first and then qa_reg
-        nr_qa = len(self.qa)
-        for idx, (question, answers) in enumerate(self.qa.items() + self.qa_reg.items()):
-            res = question.search(self._process_output)
-            if output and res:
-                answer = answers[0] % res.groupdict()
-                if len(answers) > 1:
-                    prev_answer = answers.pop(0)
-                    if self.CYCLE_ANSWERS:
-                        answers.append(prev_answer)
-                    self.log.debug("New answers list for question %s: %s" % (question.pattern, answers))
-                self.log.debug("_loop_process_output: answer %s question %s (std: %s) out %s" %
-                               (answer, question.pattern, idx >= nr_qa, self._process_output[-50:]))
-                self._process_module.send_all(self._process, answer)
-                hit = True
-                break
-
-        if not hit:
-            curoutlen = len(self._process_output)
-            if curoutlen > self._loop_previous_ouput_length:
-                # still progress in output, just continue (but don't reset miss counter either)
-                self._loop_previous_ouput_length = curoutlen
-            else:
-                noqa = False
-                for r in self.no_qa:
-                    if r.search(self._process_output):
-                        self.log.debug("_loop_process_output: no_qa found for out %s" % self._process_output[-50:])
-                        noqa = True
-                if not noqa:
-                    self._loop_miss_count += 1
-        else:
-            self._loop_miss_count = 0  # rreset miss counter on hit
-
-        if  self._loop_miss_count > self.LOOP_MAX_MISS_COUNT:
-            self.log.debug("loop_process_output: max misses LOOP_MAX_MISS_COUNT %s reached. End of output: %s" %
-                           (self.LOOP_MAX_MISS_COUNT, self._process_output[-500:]))
-            self.stop_tasks()
-
-            # go out of loop
-            raise RunLoopException(RUNRUN_QA_MAX_MISS_EXITCODE, self._process_output)
-        super(RunQA, self)._loop_process_output(output)
-
-
-class RunAsyncLoop(RunLoop, RunAsync):
-    """Async read in loop"""
-    pass
-
-
-class RunAsyncLoopLog(RunLoopLog, RunAsync):
-    """Async read, log to logger"""
-    pass
-
-
-class RunQALog(RunLoopLog, RunQA):
-    """Async loop QA with LoopLog"""
-    pass
-
-
-class RunQAStdout(RunLoopStdout, RunQA):
-    """Async loop QA with LoopLogStdout"""
-    pass
-
-
-class RunAsyncLoopStdout(RunLoopStdout, RunAsync):
-    """Async read, flush to stdout"""
-    pass
-
-
-# convenient names
-# eg: from vsc.utils.run import trivial
-
-run_simple = Run.run
-run_simple_noworries = RunNoWorries.run
-
-run_async = RunAsync.run
-run_asyncloop = RunAsyncLoop.run
-run_timeout = RunTimeout.run
-
-run_to_file = RunFile.run
-run_async_to_stdout = RunAsyncLoopStdout.run
-
-run_qa = RunQA.run
-run_qalog = RunQALog.run
-run_qastdout = RunQAStdout.run
-
-if __name__ == "__main__":
-    run_simple('echo ok')
diff --git a/vsc/utils/testing.py b/vsc/utils/testing.py
deleted file mode 100644
index 71807d5677..0000000000
--- a/vsc/utils/testing.py
+++ /dev/null
@@ -1,114 +0,0 @@
-#!/usr/bin/env python
-##
-#
-# Copyright 2014-2014 Ghent University
-#
-# This file is part of vsc-base,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/vsc-base
-#
-# vsc-base is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Library General Public License as
-# published by the Free Software Foundation, either version 2 of
-# the License, or (at your option) any later version.
-#
-# vsc-base is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Library General Public License for more details.
-#
-# You should have received a copy of the GNU Library General Public License
-# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-Test utilities.
-
-@author: Kenneth Hoste (Ghent University)
-"""
-
-import re
-import sys
-from cStringIO import StringIO
-from unittest import TestCase
-
-
-class EnhancedTestCase(TestCase):
-    """Enhanced test case, provides extra functionality (e.g. an assertErrorRegex method)."""
-
-    def setUp(self):
-        """Prepare test case."""
-        super(EnhancedTestCase, self).setUp()
-        self.orig_sys_stdout = sys.stdout
-        self.orig_sys_stderr = sys.stderr
-
-    def convert_exception_to_str(self, err):
-        """Convert an Exception instance to a string."""
-        msg = err
-        if hasattr(err, 'msg'):
-            msg = err.msg
-        elif hasattr(err, 'message'):
-            msg = err.message
-            if not msg:
-                # rely on str(msg) in case err.message is empty
-                msg = err
-        elif hasattr(err, 'args'):  # KeyError in Python 2.4 only provides message via 'args' attribute
-            msg = err.args[0]
-        else:
-            msg = err
-        try:
-            res = str(msg)
-        except UnicodeEncodeError:
-            res = msg.encode('utf8', 'replace')
-
-        return res
-
-    def assertErrorRegex(self, error, regex, call, *args, **kwargs):
-        """
-        Convenience method to match regex with the expected error message.
-        Example: self.assertErrorRegex(OSError, "No such file or directory", os.remove, '/no/such/file')
-        """
-        try:
-            call(*args, **kwargs)
-            str_kwargs = ['='.join([k, str(v)]) for (k, v) in kwargs.items()]
-            str_args = ', '.join(map(str, args) + str_kwargs)
-            self.assertTrue(False, "Expected errors with %s(%s) call should occur" % (call.__name__, str_args))
-        except error, err:
-            msg = self.convert_exception_to_str(err)
-            if isinstance(regex, basestring):
-                regex = re.compile(regex)
-            self.assertTrue(regex.search(msg), "Pattern '%s' is found in '%s'" % (regex.pattern, msg))
-
-    def mock_stdout(self, enable):
-        """Enable/disable mocking stdout."""
-        sys.stdout.flush()
-        if enable:
-            sys.stdout = StringIO()
-        else:
-            sys.stdout = self.orig_sys_stdout
-
-    def mock_stderr(self, enable):
-        """Enable/disable mocking stdout."""
-        sys.stderr.flush()
-        if enable:
-            sys.stderr = StringIO()
-        else:
-            sys.stderr = self.orig_sys_stderr
-
-    def get_stdout(self):
-        """Return output captured from stdout until now."""
-        return sys.stdout.getvalue()
-
-    def get_stderr(self):
-        """Return output captured from stderr until now."""
-        return sys.stderr.getvalue()
-
-    def tearDown(self):
-        """Cleanup after running a test."""
-        self.mock_stdout(False)
-        self.mock_stderr(False)
-        super(EnhancedTestCase, self).tearDown()
diff --git a/vsc/utils/wrapper.py b/vsc/utils/wrapper.py
deleted file mode 100644
index 537c1f252b..0000000000
--- a/vsc/utils/wrapper.py
+++ /dev/null
@@ -1,42 +0,0 @@
-"""
-This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License 
-with attribution required
-
-Original code by http://stackoverflow.com/users/416467/kindall from answer 4 of
-http://stackoverflow.com/questions/9057669/how-can-i-intercept-calls-to-pythons-magic-methods-in-new-style-classes
-"""
-class Wrapper(object):
-    """Wrapper class that provides proxy access to an instance of some
-       internal instance."""
-
-    __wraps__ = None
-    __ignore__ = "class mro new init setattr getattr getattribute"
-
-    def __init__(self, obj):
-        if self.__wraps__ is None:
-            raise TypeError("base class Wrapper may not be instantiated")
-        elif isinstance(obj, self.__wraps__):
-            self._obj = obj
-        else:
-            raise ValueError("wrapped object must be of %s" % self.__wraps__)
-
-    # provide proxy access to regular attributes of wrapped object
-    def __getattr__(self, name):
-        return getattr(self._obj, name)
-
-    # create proxies for wrapped object's double-underscore attributes
-    class __metaclass__(type):
-        def __init__(cls, name, bases, dct):
-
-            def make_proxy(name):
-                def proxy(self, *args):
-                    return getattr(self._obj, name)
-                return proxy
-
-            type.__init__(cls, name, bases, dct)
-            if cls.__wraps__:
-                ignore = set("__%s__" % n for n in cls.__ignore__.split())
-                for name in dir(cls.__wraps__):
-                    if name.startswith("__"):
-                        if name not in ignore and name not in dct:
-                            setattr(cls, name, property(make_proxy(name)))

From ac09dfc28e49ad5fb6435479506aa8d4a09df22e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Feb 2015 10:49:10 +0100
Subject: [PATCH 0497/1356] fix required Python version in setup.cfg

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index d1b2877e6d..baf390bd17 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,2 +1,2 @@
 [bdist_rpm]
-requires = environment-modules, bash, python >= 2.4, python < 3
+requires = environment-modules, bash, python >= 2.6, python < 3

From b0f7d54075b4ac2d3b4e8f9df257957930b0679f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Feb 2015 10:49:39 +0100
Subject: [PATCH 0498/1356] include vsc-base version check in main.py

---
 easybuild/main.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/easybuild/main.py b/easybuild/main.py
index f1ab88af41..837b388c60 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -39,6 +39,23 @@
 import os
 import sys
 import traceback
+from distutils.version import LooseVersion
+
+# version check of required vsc-base package
+REQ_VSC_BASE_VERSION = '2.0.1'
+vsc_base_error = None
+try:
+    from vsc.version import VERSION as VSC_BASE_VERSION
+    if LooseVersion(VSC_BASE_VERSION) < LooseVersion(REQ_VSC_BASE_VERSION):
+        tup = (VSC_BASE_VERSION, REQ_VSC_BASE_VERSION)
+        vsc_base_error = "Found vsc-base version %s, but version >= %s is required" % tup
+except ImportError:
+    vsc_base_error = "Failed to determine version of required vsc-base Python package"
+
+if vsc_base_error is not None:
+    sys.stderr.write("ERROR: %s\n" % vsc_base_error)
+    sys.exit(1)
+
 
 # IMPORTANT this has to be the first easybuild import as it customises the logging
 #  expect missing log output when this not the case!

From edab6c57b6583c0ec411ef70f05ba8196e49bc38 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Feb 2015 10:49:50 +0100
Subject: [PATCH 0499/1356] include vsc-base as a proper dependency in setup.py

---
 setup.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/setup.py b/setup.py
index 1a961f4a36..4d5a9f7352 100644
--- a/setup.py
+++ b/setup.py
@@ -35,6 +35,7 @@
 import os
 from distutils import log
 
+from easybuild.main import REQ_VSC_BASE_VERSION
 from easybuild.tools.version import VERSION
 
 API_VERSION = str(VERSION).split('.')[0]
@@ -106,4 +107,5 @@ def find_rel_test():
     provides = ["eb"] + easybuild_packages,
     test_suite = "test.framework.suite",
     zip_safe = False,
+    install_requires = ["vsc-base >= " % REQ_VSC_BASE_VERSION],
 )

From d34f288d4d425e15d7e93b19fb0f45f8327cddba Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 8 Feb 2015 17:45:30 +0100
Subject: [PATCH 0500/1356] add configure option for specifying syntax for
 module files

---
 easybuild/tools/config.py           |  1 +
 easybuild/tools/module_generator.py | 21 ++++++++++++++++++++-
 easybuild/tools/options.py          |  7 +++++--
 3 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 60af87d556..8224b01f28 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -54,6 +54,7 @@
 
 DEFAULT_LOGFILE_FORMAT = ("easybuild", "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
 DEFAULT_MNS = 'EasyBuildMNS'
+DEFAULT_MODULE_SYNTAX = 'Tcl'
 DEFAULT_MODULES_TOOL = 'EnvironmentModulesC'
 DEFAULT_PATH_SUBDIRS = {
     'buildpath': 'build',
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 4a8c03e699..d859d5d0e3 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -36,15 +36,18 @@
 import re
 import tempfile
 from vsc.utils import fancylogger
+from vsc.utils.missing import get_subclasses
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
 from easybuild.tools import config
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import mkdir
-from easybuild.tools.module_naming_scheme.utilities import det_hidden_modname
 from easybuild.tools.utilities import quote_str
 
 
+MODULE_GENERATOR_CLASS_PREFIX = 'ModuleGenerator'
+
+
 _log = fancylogger.getLogger('module_generator', fname=False)
 
 
@@ -407,3 +410,19 @@ def set_alias(self, key, value):
         """
     # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
         return 'setalias(%s,"%s")\n' % (key, quote_str(value))
+
+
+def avail_module_syntaxes():
+    """
+    Return all known module syntaxes.
+    """
+    class_dict = {}
+    for klass in get_subclasses(ModuleGenerator):
+        class_name = klass.__name__
+        if class_name.startswith(MODULE_GENERATOR_CLASS_PREFIX):
+            syntax = class_name[len(MODULE_GENERATOR_CLASS_PREFIX):]
+            class_dict.update({syntax: klass})
+        else:
+            tup = (MODULE_GENERATOR_CLASS_PREFIX, class_name)
+            _log.error("Invalid name for ModuleGenerator subclass, should start with %s: %s" % tup)
+    return class_dict
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 80fd4db664..21ec1cf4f4 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -48,13 +48,14 @@
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
-from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
-from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
+from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX, DEFAULT_MODULES_TOOL
+from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
+from easybuild.tools.module_generator import avail_module_syntaxes
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
 from easybuild.tools.ordereddict import OrderedDict
@@ -226,6 +227,8 @@ def config_options(self):
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
             'module-naming-scheme': ("Module naming scheme",
                                      'choice', 'store', DEFAULT_MNS, sorted(avail_module_naming_schemes().keys())),
+            'module-syntax': ("Syntax to be used for module files", 'choice', 'store', DEFAULT_MODULE_SYNTAX,
+                              sorted(avail_module_syntaxes().keys())),
             'moduleclasses': (("Extend supported module classes "
                                "(For more info on the default classes, use --show-default-moduleclasses)"),
                                None, 'extend', [x[0] for x in DEFAULT_MODULECLASSES]),

From 4e383b1bbb82ea01ad48a6a20972c5ab085573ad Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 8 Feb 2015 17:54:34 +0100
Subject: [PATCH 0501/1356] use module syntax selected in EasyBuild
 configuration

---
 easybuild/framework/easyblock.py    |  9 ++++-----
 easybuild/tools/config.py           |  9 ++++++++-
 easybuild/tools/module_generator.py | 13 +++++++++++--
 easybuild/tools/options.py          |  4 ++--
 4 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 4327d92fdd..910b9cd822 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -67,7 +67,7 @@
 from easybuild.tools.filetools import write_file, compute_checksum, verify_checksum
 from easybuild.tools.run import run_cmd
 from easybuild.tools.jenkins import write_to_xml
-from easybuild.tools.module_generator import ModuleGeneratorLua
+from easybuild.tools.module_generator import module_generator
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.modules import ROOT_ENV_VAR_NAME_PREFIX, VERSION_ENV_VAR_NAME_PREFIX, DEVEL_ENV_VAR_NAME_PREFIX
 from easybuild.tools.modules import get_software_root, modules_tool
@@ -132,7 +132,7 @@ def __init__(self, ec):
         # modules interface with default MODULEPATH
         self.modules_tool = modules_tool()
         # module generator
-        self.module_generator = ModuleGeneratorLua(self, fake=True)
+        self.module_generator = module_generator()
 
         # modules footer
         self.modules_footer = None
@@ -745,7 +745,6 @@ def make_devel_module(self, create_in_builddir=False):
         # load fake module
         fake_mod_data = self.load_fake_module(purge=True)
 
-        mod_gen = ModuleGeneratorLua(self)
         header = "#%Module\n"
 
         env_txt = ""
@@ -753,7 +752,7 @@ def make_devel_module(self, create_in_builddir=False):
             # check if non-empty string
             # TODO: add unset for empty vars?
             if val.strip():
-                env_txt += mod_gen.set_environment(key, val)
+                env_txt += self.module_generator.set_environment(key, val)
 
         load_txt = ""
         # capture all the EBDEVEL vars
@@ -765,7 +764,7 @@ def make_devel_module(self, create_in_builddir=False):
                     path = os.environ[key]
                     if os.path.isfile(path):
                         mod_name = path.rsplit(os.path.sep, 1)[-1]
-                        load_txt += mod_gen.load_module(mod_name)
+                        load_txt += self.module_generator.load_module(mod_name)
             elif key.startswith('SOFTDEVEL'):
                 self.log.nosupport("Environment variable SOFTDEVEL* being relied on", '2.0')
 
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 8224b01f28..d6555baa56 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -350,11 +350,18 @@ def get_modules_tool():
 
 def get_module_naming_scheme():
     """
-    Return module naming scheme (EasyBuild, ...)
+    Return module naming scheme (EasyBuildMNS, HierarchicalMNS, ...)
     """
     return ConfigurationVariables()['module_naming_scheme']
 
 
+def get_module_syntax():
+    """
+    Return module syntax (Lua, Tcl)
+    """
+    return ConfigurationVariables()['module_syntax']
+
+
 def log_file_format(return_directory=False):
     """Return the format for the logfile or the directory"""
     idx = int(not return_directory)
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index d859d5d0e3..8add16ecbf 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -40,7 +40,7 @@
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
 from easybuild.tools import config
-from easybuild.tools.config import build_option
+from easybuild.tools.config import build_option, get_module_syntax
 from easybuild.tools.filetools import mkdir
 from easybuild.tools.utilities import quote_str
 
@@ -412,7 +412,7 @@ def set_alias(self, key, value):
         return 'setalias(%s,"%s")\n' % (key, quote_str(value))
 
 
-def avail_module_syntaxes():
+def avail_module_generators():
     """
     Return all known module syntaxes.
     """
@@ -426,3 +426,12 @@ def avail_module_syntaxes():
             tup = (MODULE_GENERATOR_CLASS_PREFIX, class_name)
             _log.error("Invalid name for ModuleGenerator subclass, should start with %s: %s" % tup)
     return class_dict
+
+
+def module_generator():
+    """
+    Return interface to modules tool (environment modules (C, Tcl), or Lmod)
+    """
+    module_syntax = get_module_syntax()
+    module_generator_class = avail_module_generators().get(module_syntax)
+    return module_generator_class()
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 21ec1cf4f4..deea120161 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -55,7 +55,7 @@
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
-from easybuild.tools.module_generator import avail_module_syntaxes
+from easybuild.tools.module_generator import avail_module_generators
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
 from easybuild.tools.ordereddict import OrderedDict
@@ -228,7 +228,7 @@ def config_options(self):
             'module-naming-scheme': ("Module naming scheme",
                                      'choice', 'store', DEFAULT_MNS, sorted(avail_module_naming_schemes().keys())),
             'module-syntax': ("Syntax to be used for module files", 'choice', 'store', DEFAULT_MODULE_SYNTAX,
-                              sorted(avail_module_syntaxes().keys())),
+                              sorted(avail_module_generators().keys())),
             'moduleclasses': (("Extend supported module classes "
                                "(For more info on the default classes, use --show-default-moduleclasses)"),
                                None, 'extend', [x[0] for x in DEFAULT_MODULECLASSES]),

From 9081cd7736771269f4109c70369979cd59046c5c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 8 Feb 2015 18:06:35 +0100
Subject: [PATCH 0502/1356] make it work with module syntax = 'Lua'

---
 easybuild/framework/easyblock.py    |  2 +-
 easybuild/tools/config.py           | 17 +++++++++--------
 easybuild/tools/module_generator.py |  5 ++---
 easybuild/tools/modules.py          |  1 +
 4 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 910b9cd822..5ff1249912 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -132,7 +132,7 @@ def __init__(self, ec):
         # modules interface with default MODULEPATH
         self.modules_tool = modules_tool()
         # module generator
-        self.module_generator = module_generator()
+        self.module_generator = module_generator(self, fake=True)
 
         # modules footer
         self.modules_footer = None
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index d6555baa56..dc8bd6f4b2 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -177,20 +177,21 @@ class ConfigurationVariables(FrozenDictKnownKeys):
 
     # list of known/required keys
     REQUIRED = [
-        'config',
-        'prefix',
         'buildpath',
+        'config',
         'installpath',
-        'sourcepath',
-        'repository',
-        'repositorypath',
         'logfile_format',
-        'tmp_logdir',
         'moduleclasses',
+        'module_naming_scheme',
+        'module_syntax',
+        'modules_tool',
+        'prefix',
+        'repository',
+        'repositorypath',
+        'sourcepath',
         'subdir_modules',
         'subdir_software',
-        'modules_tool',
-        'module_naming_scheme',
+        'tmp_logdir',
     ]
     KNOWN_KEYS = REQUIRED  # KNOWN_KEYS must be defined for FrozenDictKnownKeys functionality
 
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 8add16ecbf..c9ea45d55d 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -60,7 +60,6 @@ class ModuleGenerator(object):
     CHARS_TO_ESCAPE = ["$"]
 
     def __init__(self, application, fake=False):
-        self.fake = fake
         self.app = application
         self.fake = fake
         self.tmpdir = None
@@ -428,10 +427,10 @@ def avail_module_generators():
     return class_dict
 
 
-def module_generator():
+def module_generator(app, fake=False):
     """
     Return interface to modules tool (environment modules (C, Tcl), or Lmod)
     """
     module_syntax = get_module_syntax()
     module_generator_class = avail_module_generators().get(module_syntax)
-    return module_generator_class()
+    return module_generator_class(app, fake=fake)
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index c8cd2c8914..dab0acd4dc 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -835,6 +835,7 @@ def available(self, mod_name=None):
 
     def update(self):
         """Update after new modules were added."""
+        return
         spider_cmd = os.path.join(os.path.dirname(self.cmd), 'spider')
         cmd = [spider_cmd, '-o', 'moduleT', os.environ['MODULEPATH']]
         self.log.debug("Running command '%s'..." % ' '.join(cmd))

From ce2d60662431ed3e250960b863498a6d34851a5b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 8 Feb 2015 23:17:27 +0100
Subject: [PATCH 0503/1356] properly handle module header

---
 easybuild/framework/easyblock.py    |  2 +-
 easybuild/tools/module_generator.py | 15 +++++++++++++--
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 5ff1249912..0c43a3f4b9 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -745,7 +745,7 @@ def make_devel_module(self, create_in_builddir=False):
         # load fake module
         fake_mod_data = self.load_fake_module(purge=True)
 
-        header = "#%Module\n"
+        header = self.module_generator.module_header()
 
         env_txt = ""
         for (key, val) in env.get_changes().items():
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index c9ea45d55d..1146f068f6 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -116,12 +116,19 @@ def set_fake(self, fake):
         else:
             self.module_path = config.install_path('mod')
 
+    def module_header(self):
+        """Return module header string."""
+        raise NotImplementedError
+
 
 class ModuleGeneratorTcl(ModuleGenerator):
     """
     Class for generating Tcl module files.
     """
 
+    def module_header(self):
+        """Return module header string."""
+        return "#%Module\n"
 
     def get_description(self, conflict=True):
         """
@@ -130,7 +137,6 @@ def get_description(self, conflict=True):
         description = "%s - Homepage: %s" % (self.app.cfg['description'], self.app.cfg['homepage'])
 
         lines = [
-            "#%%Module",  # double % to escape string formatting!
             "",
             "proc ModulesHelp { } {",
             "    puts stderr {   %(description)s",
@@ -161,7 +167,8 @@ def get_description(self, conflict=True):
             # - 'conflict Compiler/GCC/4.8.2/OpenMPI' for 'Compiler/GCC/4.8.2/OpenMPI/1.6.4'
             lines.append("conflict %s\n" % os.path.dirname(self.app.short_mod_name))
 
-        txt = '\n'.join(lines) % {
+        txt = self.module_header()
+        txt += '\n'.join(lines) % {
             'name': self.app.name,
             'version': self.app.version,
             'description': description,
@@ -271,6 +278,10 @@ class ModuleGeneratorLua(ModuleGenerator):
     Class for generating Lua module files.
     """
 
+    def module_header(self):
+        """Return module header string."""
+        return ''
+
     def get_description(self, conflict=True):
         """
         Generate a description.

From 383df78bf2fae92f4e874d9aa040aff494cec92c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 8 Feb 2015 23:28:15 +0100
Subject: [PATCH 0504/1356] only use .lua file suffix for module files in Lua
 syntax

---
 easybuild/framework/easyblock.py    | 2 +-
 easybuild/tools/module_generator.py | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 0c43a3f4b9..3999b3c06d 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1651,7 +1651,7 @@ def make_module_step(self, fake=False):
         txt += self.make_module_extra()
         txt += self.make_module_footer()
 
-        write_file(self.module_generator.filename+".lua", txt)
+        write_file(self.module_generator.filename, txt)
 
         self.log.info("Module file %s written" % self.module_generator.filename)
 
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 1146f068f6..71ae52498b 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -58,6 +58,7 @@ class ModuleGenerator(object):
 
     # chars we want to escape in the generated modulefiles
     CHARS_TO_ESCAPE = ["$"]
+    MODULE_SUFFIX = ''
 
     def __init__(self, application, fake=False):
         self.app = application
@@ -72,7 +73,7 @@ def prepare(self):
         Creates the absolute filename for the module.
         """
         mod_path_suffix = build_option('suffix_modules_path')
-        full_mod_name = self.app.full_mod_name
+        full_mod_name = '%s%s' % (self.app.full_mod_name, self.MODULE_SUFFIX)
         # module file goes in general moduleclass category
         self.filename = os.path.join(self.module_path, mod_path_suffix, full_mod_name)
         # make symlink in moduleclass category
@@ -278,6 +279,8 @@ class ModuleGeneratorLua(ModuleGenerator):
     Class for generating Lua module files.
     """
 
+    MODULE_SUFFIX = '.lua'
+
     def module_header(self):
         """Return module header string."""
         return ''

From e7b00f1493d4beef5c580bd2708f5c88b0011c89 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 8 Feb 2015 23:34:29 +0100
Subject: [PATCH 0505/1356] correctly handle comments in module files, in both
 Tcl and Lua syntax

---
 easybuild/framework/easyblock.py    |  3 +--
 easybuild/tools/module_generator.py | 12 ++++++++++++
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3999b3c06d..2593064e06 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -892,8 +892,7 @@ def make_module_footer(self):
         """
         Insert a footer section in the modulefile, primarily meant for contextual information
         """
-        #@todo fix this as it is lua specific
-        txt = '\n -- Built with EasyBuild version %s\n' % VERBOSE_VERSION
+        txt = '\n' + self.module_generator.comment("Built with EasyBuild version %s" % VERBOSE_VERSION)
 
         # add extra stuff for extensions (if any)
         if self.cfg['exts_list']:
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 71ae52498b..ee84147467 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -121,6 +121,10 @@ def module_header(self):
         """Return module header string."""
         raise NotImplementedError
 
+    def comment(self, msg):
+        """Return string containing given message as a comment."""
+        raise NotImplementedError
+
 
 class ModuleGeneratorTcl(ModuleGenerator):
     """
@@ -131,6 +135,10 @@ def module_header(self):
         """Return module header string."""
         return "#%Module\n"
 
+    def comment(self, msg):
+        """Return string containing given message as a comment."""
+        return "# %s\n" % msg
+
     def get_description(self, conflict=True):
         """
         Generate a description.
@@ -285,6 +293,10 @@ def module_header(self):
         """Return module header string."""
         return ''
 
+    def comment(self, msg):
+        """Return string containing given message as a comment."""
+        return " -- %s\n" % msg
+
     def get_description(self, conflict=True):
         """
         Generate a description.

From 3e338cc89baf994b4ec6e27f462422ed07d93b57 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 9 Feb 2015 07:16:43 +0100
Subject: [PATCH 0506/1356] make sure Lmod is used as modules tool when
 generating module files in Lua syntax

---
 easybuild/tools/module_generator.py | 25 ++++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index ee84147467..9931fd2904 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -42,6 +42,7 @@
 from easybuild.tools import config
 from easybuild.tools.config import build_option, get_module_syntax
 from easybuild.tools.filetools import mkdir
+from easybuild.tools.modules import Lmod, modules_tool
 from easybuild.tools.utilities import quote_str
 
 
@@ -61,12 +62,14 @@ class ModuleGenerator(object):
     MODULE_SUFFIX = ''
 
     def __init__(self, application, fake=False):
+        """ModuleGenerator constructor."""
         self.app = application
         self.fake = fake
         self.tmpdir = None
         self.filename = None
         self.class_mod_file = None
         self.module_path = None
+        self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
     def prepare(self):
         """
@@ -99,7 +102,7 @@ def create_symlinks(self):
                     os.remove(class_mod_file)
                 os.symlink(self.filename, class_mod_file)
         except OSError, err:
-            _log.error("Failed to create symlinks from %s to %s: %s" % (self.class_mod_files, self.filename, err))
+            self.log.error("Failed to create symlinks from %s to %s: %s" % (self.class_mod_files, self.filename, err))
 
     def is_fake(self):
         """Return whether this ModuleGeneratorTcl instance generates fake modules or not."""
@@ -107,12 +110,12 @@ def is_fake(self):
 
     def set_fake(self, fake):
         """Determine whether this ModuleGeneratorTcl instance should generate fake modules."""
-        _log.debug("Updating fake for this ModuleGeneratorTcl instance to %s (was %s)" % (fake, self.fake))
+        self.log.debug("Updating fake for this ModuleGeneratorTcl instance to %s (was %s)" % (fake, self.fake))
         self.fake = fake
         # fake mode: set installpath to temporary dir
         if self.fake:
             self.tmpdir = tempfile.mkdtemp()
-            _log.debug("Fake mode: using %s (instead of %s)" % (self.tmpdir, self.module_path))
+            self.log.debug("Fake mode: using %s (instead of %s)" % (self.tmpdir, self.module_path))
             self.module_path = self.tmpdir
         else:
             self.module_path = config.install_path('mod')
@@ -222,13 +225,13 @@ def prepend_paths(self, key, paths, allow_abs=False):
         template = "prepend-path\t%s\t\t%s\n"
 
         if isinstance(paths, basestring):
-            _log.info("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
+            self.log.info("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
         # make sure only relative paths are passed
         for i in xrange(len(paths)):
             if os.path.isabs(paths[i]) and not allow_abs:
-                _log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % paths[i])
+                self.log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % paths[i])
             elif not os.path.isabs(paths[i]):
                 # prepend $root (= installdir) for relative paths
                 paths[i] = "$root/%s" % paths[i]
@@ -289,6 +292,14 @@ class ModuleGeneratorLua(ModuleGenerator):
 
     MODULE_SUFFIX = '.lua'
 
+    def __init__(self, *args, **kwargs):
+        """ModuleGeneratorLua constructor."""
+        super(ModuleGeneratorLua, self).__init__(*args, **kwargs)
+
+        # make sure Lmod is being used as a modules tool
+        if not isinstance(modules_tool(), Lmod):
+            self.log.error("Only Lmod can be used as modules tool when generating module files in Lua syntax.")
+
     def module_header(self):
         """Return module header string."""
         return ''
@@ -381,13 +392,13 @@ def prepend_paths(self, key, paths, allow_abs=False):
         template = 'prepend_path(%s,%s)\n'
 
         if isinstance(paths, basestring):
-            _log.info("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
+            self.log.info("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
         # make sure only relative paths are passed
         for i in xrange(len(paths)):
             if os.path.isabs(paths[i]) and not allow_abs:
-                _log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % paths[i])
+                self.log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % paths[i])
             elif not os.path.isabs(paths[i]):
                 # prepend $root (= installdir) for relative paths
                 paths[i] = ' pathJoin(pkg.root,"%s")' % paths[i]

From 74926e65d9a7542e1890d7c398b68f1363540711 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 9 Feb 2015 08:28:25 +0100
Subject: [PATCH 0507/1356] always filter hidden deps from list of dependencies

---
 easybuild/framework/easyconfig/easyconfig.py | 21 ++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 9db79d881d..e3c0249510 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -180,6 +180,9 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         if self.validation:
             self.validate(check_osdeps=build_option('check_osdeps'))
 
+        # filter hidden dependencies from list of dependencies
+        self.filter_hidden_deps()
+
         # keep track of whether the generated module file should be hidden
         if hidden is None:
             hidden = build_option('hidden')
@@ -281,11 +284,12 @@ def handle_allowed_system_deps(self):
 
     def validate(self, check_osdeps=True):
         """
-        Validate this EasyConfig
-        - check certain variables
-        TODO: move more into here
+        Validate this easyonfig
+        - ensure certain easyconfig parameters are set to a known value (see self.validations)
+        - check OS dependencies
+        - check license
         """
-        self.log.info("Validating easy block")
+        self.log.info("Validating easyconfig")
         for attr in self.validations:
             self._validate(attr, self.validations[attr])
 
@@ -306,9 +310,6 @@ def validate(self, check_osdeps=True):
         self.log.info("Checking licenses")
         self.validate_license()
 
-        self.log.info("Checking whether list of hidden dependencies is a subset of list of dependencies")
-        self.validate_hiddendeps()
-
     def validate_license(self):
         """Validate the license"""
         lic = self._config['software_license'][0]
@@ -376,10 +377,9 @@ def validate_iterate_opts_lists(self):
 
         return True
 
-    def validate_hiddendeps(self):
+    def filter_hidden_deps(self):
         """
-        Validate that list of hidden dependencies is a subset of the list of dependencies.
-        The list of dependencies is adjusted to only include non-hidden dependencies.
+        Filter hidden dependencies from list of dependencies.
         """
         dep_mod_names = [dep['full_mod_name'] for dep in self['dependencies']]
 
@@ -394,6 +394,7 @@ def validate_hiddendeps(self):
                 # hidden dependencies must also be included in list of dependencies;
                 # this is done to try and make easyconfigs portable w.r.t. site-specific policies with minimal effort,
                 # i.e. by simply removing the 'hiddendependencies' specification
+                self.log.warning("Hidden dependency %s not in list of dependencies" % visible_mod_name)
                 faulty_deps.append(visible_mod_name)
 
         if faulty_deps:

From 914a27ee4f1b92f10e86090cbfa51de8745ec4c7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Feb 2015 08:03:40 +0100
Subject: [PATCH 0508/1356] drop version check for vsc-base, go back to only
 requiring vsc-base v2.0.0

---
 easybuild/main.py | 16 ----------------
 setup.py          |  3 +--
 2 files changed, 1 insertion(+), 18 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 837b388c60..58bfbe320d 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -41,22 +41,6 @@
 import traceback
 from distutils.version import LooseVersion
 
-# version check of required vsc-base package
-REQ_VSC_BASE_VERSION = '2.0.1'
-vsc_base_error = None
-try:
-    from vsc.version import VERSION as VSC_BASE_VERSION
-    if LooseVersion(VSC_BASE_VERSION) < LooseVersion(REQ_VSC_BASE_VERSION):
-        tup = (VSC_BASE_VERSION, REQ_VSC_BASE_VERSION)
-        vsc_base_error = "Found vsc-base version %s, but version >= %s is required" % tup
-except ImportError:
-    vsc_base_error = "Failed to determine version of required vsc-base Python package"
-
-if vsc_base_error is not None:
-    sys.stderr.write("ERROR: %s\n" % vsc_base_error)
-    sys.exit(1)
-
-
 # IMPORTANT this has to be the first easybuild import as it customises the logging
 #  expect missing log output when this not the case!
 from easybuild.tools.build_log import EasyBuildError, init_logging, print_msg, print_error, stop_logging
diff --git a/setup.py b/setup.py
index 4d5a9f7352..6e2bba4a75 100644
--- a/setup.py
+++ b/setup.py
@@ -35,7 +35,6 @@
 import os
 from distutils import log
 
-from easybuild.main import REQ_VSC_BASE_VERSION
 from easybuild.tools.version import VERSION
 
 API_VERSION = str(VERSION).split('.')[0]
@@ -107,5 +106,5 @@ def find_rel_test():
     provides = ["eb"] + easybuild_packages,
     test_suite = "test.framework.suite",
     zip_safe = False,
-    install_requires = ["vsc-base >= " % REQ_VSC_BASE_VERSION],
+    install_requires = ["vsc-base >= 2.0.0"],
 )

From 56cb4288de72f79c3fb354858e84a2af23ba2c87 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Feb 2015 08:04:07 +0100
Subject: [PATCH 0509/1356] drop unused import

---
 easybuild/main.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 58bfbe320d..f1ab88af41 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -39,7 +39,6 @@
 import os
 import sys
 import traceback
-from distutils.version import LooseVersion
 
 # IMPORTANT this has to be the first easybuild import as it customises the logging
 #  expect missing log output when this not the case!

From 48cceb3fc82a013272d81b8afce80c7e25f51c8e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Feb 2015 10:32:08 +0100
Subject: [PATCH 0510/1356] skip tests that require a GitHub token if no token
 is available

---
 test/framework/github.py  | 58 +++++++++++++++++++++------------------
 test/framework/options.py | 19 +++++++++++++
 2 files changed, 51 insertions(+), 26 deletions(-)

diff --git a/test/framework/github.py b/test/framework/github.py
index 588bc7240f..001ab22818 100644
--- a/test/framework/github.py
+++ b/test/framework/github.py
@@ -56,50 +56,56 @@ def setUp(self):
         """setup"""
         super(GithubTest, self).setUp()
         github_user = GITHUB_TEST_ACCOUNT
-        github_token = fetch_github_token(github_user)
-        if github_token is None:
+        self.github_token = fetch_github_token(github_user)
+        if self.github_token is None:
             self.ghfs = None
         else:
             self.ghfs = Githubfs(GITHUB_USER, GITHUB_REPO, GITHUB_BRANCH, github_user, None, github_token)
 
     def test_walk(self):
         """test the gitubfs walk function"""
-        # TODO: this will not work when rate limited, so we should have a test account token here
-        if self.ghfs is not None:
-            try:
-                expected = [(None, ['a_directory', 'second_dir'], ['README.md']),
-                            ('a_directory', ['a_subdirectory'], ['a_file.txt']), ('a_directory/a_subdirectory', [],
-                            ['a_file.txt']), ('second_dir', [], ['a_file.txt'])]
-                self.assertEquals([x for x in self.ghfs.walk(None)], expected)
-            except IOError:
-                pass
-        else:
+        if self.github_token is None:
             print "Skipping test_walk, no GitHub token available?"
+            return
+
+        try:
+            expected = [(None, ['a_directory', 'second_dir'], ['README.md']),
+                        ('a_directory', ['a_subdirectory'], ['a_file.txt']), ('a_directory/a_subdirectory', [],
+                        ['a_file.txt']), ('second_dir', [], ['a_file.txt'])]
+            self.assertEquals([x for x in self.ghfs.walk(None)], expected)
+        except IOError:
+            pass
 
     def test_read_api(self):
         """Test the githubfs read function"""
-        if self.ghfs is not None:
-            try:
-                self.assertEquals(self.ghfs.read("a_directory/a_file.txt").strip(), "this is a line of text")
-            except IOError:
-                pass
-        else:
+        if self.github_token is not None:
             print "Skipping test_read_api, no GitHub token available?"
+            return
+
+        try:
+            self.assertEquals(self.ghfs.read("a_directory/a_file.txt").strip(), "this is a line of text")
+        except IOError:
+            pass
 
     def test_read(self):
         """Test the githubfs read function without using the api"""
-        if self.ghfs is not None:
-            try:
-                fp = self.ghfs.read("a_directory/a_file.txt", api=False)
-                self.assertEquals(open(fp, 'r').read().strip(), "this is a line of text")
-                os.remove(fp)
-            except (IOError, OSError):
-                pass
-        else:
+        if self.github_token is None:
             print "Skipping test_read, no GitHub token available?"
+            return
+
+        try:
+            fp = self.ghfs.read("a_directory/a_file.txt", api=False)
+            self.assertEquals(open(fp, 'r').read().strip(), "this is a line of text")
+            os.remove(fp)
+        except (IOError, OSError):
+            pass
 
     def test_fetch_easyconfigs_from_pr(self):
         """Test fetch_easyconfigs_from_pr function."""
+        if self.github_token is None:
+            print "Skipping test_fetch_easyconfigs_from_pr, no GitHub token available?"
+            return
+
         tmpdir = tempfile.mkdtemp()
         # PR for ictce/6.2.5, see https://github.com/hpcugent/easybuild-easyconfigs/pull/726/files
         all_ecs = ['gzip-1.6-ictce-6.2.5.eb', 'icc-2013_sp1.2.144.eb', 'ictce-6.2.5.eb', 'ifort-2013_sp1.2.144.eb',
diff --git a/test/framework/options.py b/test/framework/options.py
index 66f75a88a1..ad38770658 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -44,16 +44,27 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import mkdir, read_file, write_file
+from easybuild.tools.github import fetch_github_token
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.options import EasyBuildOptions
 from easybuild.tools.version import VERSION
 from vsc.utils import fancylogger
 
+
+# test account, for which a token is available
+GITHUB_TEST_ACCOUNT = 'easybuild_test'
+
+
 class CommandLineOptionsTest(EnhancedTestCase):
     """Testcases for command line options."""
 
     logfile = None
 
+    def setUp(self):
+        """Set up test."""
+        super(CommandLineOptionsTest, self).setUp()
+        self.github_token = fetch_github_token(GITHUB_TEST_ACCOUNT)
+
     def test_help_short(self, txt=None):
         """Test short help message."""
 
@@ -751,6 +762,10 @@ def test_dry_run_hierarchical(self):
 
     def test_from_pr(self):
         """Test fetching easyconfigs from a PR."""
+        if self.github_token is None:
+            print "Skipping test_from_pr, no GitHub token available?"
+            return
+
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
@@ -798,6 +813,10 @@ def test_from_pr(self):
 
     def test_from_pr_listed_ecs(self):
         """Test --from-pr in combination with specifying easyconfigs on the command line."""
+        if self.github_token is None:
+            print "Skipping test_from_pr, no GitHub token available?"
+            return
+
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 

From bd7641b222922aa44caf3bf2abc68dbee98e03aa Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Tue, 10 Feb 2015 15:18:03 +0100
Subject: [PATCH 0511/1356] Adjust path_matches to ignore non-existing paths

---
 easybuild/tools/filetools.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 8b81d71d1c..6a20a977b1 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -847,7 +847,13 @@ def mkdir(path, parents=False, set_gid=None, sticky=None):
 
 def path_matches(path, paths):
     """Check whether given path matches any of the provided paths."""
-    return any([os.path.samefile(path, p) for p in paths])
+    for somepath in paths:
+        try:
+            if os.path.samefile(path, somepath):
+                return True
+        except OSError:
+            pass
+    return False
 
 
 def rmtree2(path, n=3):

From df6a34c4c98a159f7fdac89c8772e3c8929ac076 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Tue, 10 Feb 2015 15:49:00 +0100
Subject: [PATCH 0512/1356] Clean up logic

---
 easybuild/tools/filetools.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 6a20a977b1..67623e8169 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -847,12 +847,11 @@ def mkdir(path, parents=False, set_gid=None, sticky=None):
 
 def path_matches(path, paths):
     """Check whether given path matches any of the provided paths."""
+    if not os.path.exists(path):
+        return False
     for somepath in paths:
-        try:
-            if os.path.samefile(path, somepath):
-                return True
-        except OSError:
-            pass
+        if os.path.exists(somepath) and os.path.samefile(path, somepath):
+            return True
     return False
 
 

From 8b8d3632a3e1001ea642c7320ecb34b3a2bf11d3 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Tue, 10 Feb 2015 17:39:50 +0100
Subject: [PATCH 0513/1356] Let mpi_family return None if MPI is not supported
 by a toolchain rather than fail hard with an exception

---
 easybuild/tools/toolchain/toolchain.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index a4119c4592..6b9924858e 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -454,5 +454,7 @@ def comp_family(self):
         raise NotImplementedError
 
     def mpi_family(self):
-        """ Return type of MPI library used in this toolchain (abstract method)."""
-        raise NotImplementedError
+        """ Return type of MPI library used in this toolchain or 'None' if MPI is not
+            supported.
+        """
+        return None

From 4df598e71f03152e1f3d0e2ef6c4d653c76c31db Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 11 Feb 2015 00:26:53 +0100
Subject: [PATCH 0514/1356] make sure plain text keyring is used, so the tests
 can (try) to obtain the GitHub token for 'easybuild_test' without having to
 supply a password

---
 test/framework/suite.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 1ed29b598a..027e6c6e1e 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -31,6 +31,7 @@
 @author: Kenneth Hoste (Ghent University)
 """
 import glob
+import keyring
 import os
 import shutil
 import sys
@@ -38,6 +39,9 @@
 import unittest
 from vsc.utils import fancylogger
 
+# set plain text key ring to be used, so a GitHub token stored in it can be obtained with having to provide a password
+keyring.set_keyring(keyring.backends.file.PlaintextKeyring())
+
 # disable all logging to significantly speed up tests
 import easybuild.tools.build_log  # initialize EasyBuild logging, so we disable it
 fancylogger.disableDefaultHandlers()

From 32b19fb06e70fca262da38c42f5e527fbb9c6678 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@gmail.com>
Date: Wed, 11 Feb 2015 09:56:41 +0100
Subject: [PATCH 0515/1356] added a system config file, this is handy to set
 configurations on system level (e.g. when installing easybuild with an rpm,
 with Lmod as default modules tool)

---
 easybuild/tools/options.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 80fd4db664..46923ba867 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -66,7 +66,9 @@
 
 
 XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
-DEFAULT_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
+XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', os.path.join("/etc"))
+DEFAULT_SYSTEM_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild.cfg')
+DEFAULT_USER_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
 
 
 class EasyBuildOptions(GeneralOption):
@@ -74,7 +76,7 @@ class EasyBuildOptions(GeneralOption):
     VERSION = this_is_easybuild()
 
     DEFAULT_LOGLEVEL = 'INFO'
-    DEFAULT_CONFIGFILES = [DEFAULT_CONFIGFILE]
+    DEFAULT_CONFIGFILES = [DEFAULT_SYSTEM_CONFIGFILE, DEFAULT_USER_CONFIGFILE]
 
     ALLOPTSMANDATORY = False  # allow more than one argument
 
@@ -138,7 +140,7 @@ def software_options(self):
                  )
 
         opts = OrderedDict({
-            'amend':(("Specify additional search and build parameters (can be used multiple times); "
+            'amend': (("Specify additional search and build parameters (can be used multiple times); "
                       "for example: versionprefix=foo or patches=one.patch,two.patch)"),
                       None, 'append', None, {'metavar': 'VAR=VALUE[,VALUE]'}),
             'software': ("Search and build software with given name and version",
@@ -681,7 +683,7 @@ def process_software_build_specs(options):
         tryval = getattr(options, 'try_%s' % opt)
         if val or tryval:
             if val and tryval:
-                self.log.warning("Ignoring --try-%(opt)s, only using --%(opt)s specification" % {'opt': opt})
+                fancylogger.getLogger().warning("Ignoring --try-%(opt)s, only using --%(opt)s specification" % {'opt': opt})
             elif tryval:
                 try_to_generate = True
             val = val or tryval  # --try-X value is overridden by --X
@@ -707,7 +709,9 @@ def process_software_build_specs(options):
         if options.amend:
             amends += options.amend
             if options.try_amend:
-                self.log.warning("Ignoring options passed via --try-amend, only using those passed via --amend.")
+                fancylogger.getLogger().warning(
+                    "Ignoring options passed via --try-amend, only using those passed via --amend."
+                )
         if options.try_amend:
             amends += options.try_amend
             try_to_generate = True

From ea7b93e8a6aea8c9caf49812dbd627816508196a Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@gmail.com>
Date: Wed, 11 Feb 2015 10:05:40 +0100
Subject: [PATCH 0516/1356] whitespace cleanup

---
 easybuild/tools/options.py | 62 +++++++++++++++++++++-----------------
 1 file changed, 34 insertions(+), 28 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 46923ba867..55166f0f90 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -1,5 +1,5 @@
-# #
-# Copyright 2009-2014 Ghent University
+##
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -21,7 +21,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-# #
+##
 """
 Command line options for eb
 
@@ -141,10 +141,10 @@ def software_options(self):
 
         opts = OrderedDict({
             'amend': (("Specify additional search and build parameters (can be used multiple times); "
-                      "for example: versionprefix=foo or patches=one.patch,two.patch)"),
+                       "for example: versionprefix=foo or patches=one.patch,two.patch)"),
                       None, 'append', None, {'metavar': 'VAR=VALUE[,VALUE]'}),
             'software': ("Search and build software with given name and version",
-                              None, 'extend', None, {'metavar': 'NAME,VERSION'}),
+                         None, 'extend', None, {'metavar': 'NAME,VERSION'}),
             'software-name': ("Search and build software with given name",
                               None, 'store', None, {'metavar': 'NAME'}),
             'software-version': ("Search and build software with given version",
@@ -184,8 +184,10 @@ def override_options(self):
             'download_timeout': ("Timeout for initiating downloads (in seconds)", None, 'store', None),
             'easyblock': ("easyblock to use for processing the spec file or dumping the options",
                           None, 'store', None, 'e', {'metavar': 'CLASS'}),
-            'experimental': ("Allow experimental code (with behaviour that can be changed or removed at any given time).",
-                             None, 'store_true', False),
+            'experimental': (
+                "Allow experimental code (with behaviour that can be changed or removed at any given time).",
+                None, 'store_true', False
+            ),
             'group': ("Group to be used for software installations (only verified, not set)", None, 'store', None),
             'hidden': ("Install 'hidden' module file(s) by prefixing their name with '.'", None, 'store_true', False),
             'ignore-osdeps': ("Ignore any listed OS dependencies", None, 'store_true', False),
@@ -195,7 +197,7 @@ def override_options(self):
             'oldstyleconfig':   ("Look for and use the oldstyle configuration file.",
                                  None, 'store_true', True),
             'pretend': (("Does the build/installation in a test directory located in $HOME/easybuildinstall"),
-                         None, 'store_true', False, 'p'),
+                        None, 'store_true', False, 'p'),
             'set-gid-bit': ("Set group ID bit on newly created directories", None, 'store_true', False),
             'sticky-bit': ("Set sticky bit on newly created directories", None, 'store_true', False),
             'skip-test-cases': ("Skip running test cases", None, 'store_true', False, 't'),
@@ -218,11 +220,13 @@ def config_options(self):
             'avail-modules-tools': ("Show all supported module tools",
                                     None, "store_true", False,),
             'avail-repositories': ("Show all repository types (incl. non-usable)",
-                                    None, "store_true", False,),
+                                   None, "store_true", False,),
             'buildpath': ("Temporary build path", None, 'store', mk_full_default_path('buildpath')),
             'ignore-dirs': ("Directory names to ignore when searching for files/dirs",
                             'strlist', 'store', ['.git', '.svn']),
-            'installpath': ("Install path for software and modules", None, 'store', mk_full_default_path('installpath')),
+            'installpath': (
+                "Install path for software and modules", None, 'store', mk_full_default_path('installpath')
+            ),
             # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
@@ -230,14 +234,14 @@ def config_options(self):
                                      'choice', 'store', DEFAULT_MNS, sorted(avail_module_naming_schemes().keys())),
             'moduleclasses': (("Extend supported module classes "
                                "(For more info on the default classes, use --show-default-moduleclasses)"),
-                               None, 'extend', [x[0] for x in DEFAULT_MODULECLASSES]),
+                              None, 'extend', [x[0] for x in DEFAULT_MODULECLASSES]),
             'modules-footer': ("Path to file containing footer to be added to all generated module files",
                                None, 'store_or_None', None, {'metavar': "PATH"}),
             'modules-tool': ("Modules tool to use",
                              'choice', 'store', DEFAULT_MODULES_TOOL, sorted(avail_modules_tools().keys())),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
                         "(used prefix for defaults %s)" % DEFAULT_PREFIX),
-                        None, 'store', None),
+                       None, 'store', None),
             'recursive-module-unload': ("Enable generating of modules that unload recursively.",
                                         None, 'store_true', False),
             'repository': ("Repository type, using repositorypath",
@@ -245,18 +249,22 @@ def config_options(self):
             'repositorypath': (("Repository path, used by repository "
                                 "(is passed as list of arguments to create the repository instance). "
                                 "For more info, use --avail-repositories."),
-                                'strlist', 'store',
-                                [mk_full_default_path('repositorypath')]),
+                               'strlist', 'store',
+                               [mk_full_default_path('repositorypath')]),
             'show-default-moduleclasses': ("Show default module classes with description",
                                            None, 'store_true', False),
             'sourcepath': ("Path(s) to where sources should be downloaded (string, colon-separated)",
                            None, 'store', mk_full_default_path('sourcepath')),
             'subdir-modules': ("Installpath subdir for modules", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_modules']),
-            'subdir-software': ("Installpath subdir for software", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_software']),
+            'subdir-software': (
+                "Installpath subdir for software", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_software']
+            ),
             'suffix-modules-path': ("Suffix for module files install path", None, 'store', GENERAL_CLASS),
             # this one is sort of an exception, it's something jobscripts can set,
             # has no real meaning for regular eb usage
-            'testoutput': ("Path to where a job should place the output (to be set within jobscript)", None, 'store', None),
+            'testoutput': (
+                "Path to where a job should place the output (to be set within jobscript)", None, 'store', None
+            ),
             'tmp-logdir': ("Log directory where temporary log files are stored", None, 'store', None),
             'tmpdir': ('Directory to use for temporary storage', None, 'store', None),
         })
@@ -277,10 +285,10 @@ def informative_options(self):
                                           None, 'store_true', False),
             'avail-easyconfig-params': (("Show all easyconfig parameters (include "
                                          "easyblock-specific ones by using -e)"),
-                                         'choice', 'store_or_None', FORMAT_TXT, [FORMAT_RST, FORMAT_TXT], 'a'),
+                                        'choice', 'store_or_None', FORMAT_TXT, [FORMAT_RST, FORMAT_TXT], 'a'),
             'avail-easyconfig-templates': (("Show all template names and template constants "
                                             "that can be used in easyconfigs"),
-                                            None, 'store_true', False),
+                                           None, 'store_true', False),
             'dep-graph': ("Create dependency graph",
                           None, "store", None, {'metavar': 'depgraph.<ext>'}),
             'list-easyblocks': ("Show list of available easyblocks",
@@ -388,7 +396,7 @@ def postprocess(self):
                 self.options.avail_easyconfig_constants, self.options.avail_easyconfig_licenses,
                 self.options.avail_repositories, self.options.show_default_moduleclasses,
                 self.options.avail_modules_tools, self.options.avail_module_naming_schemes,
-               ]):
+                ]):
             build_easyconfig_constants_dict()  # runs the easyconfig constants sanity check
             self._postprocess_list_avail()
 
@@ -412,7 +420,7 @@ def postprocess(self):
     def _postprocess_config(self):
         """Postprocessing of configuration options"""
         if self.options.prefix is not None:
-            # prefix applies to all paths, and repository has to be reinitialised to take new repositorypath into account
+            # prefix applies to all paths, and repository has to be reinitialised to take new repositorypath in account
             # in the legacy-style configuration, repository is initialised in configuration file itself
             for dest in ['installpath', 'buildpath', 'sourcepath', 'repository', 'repositorypath']:
                 if not self.options._action_taken.get(dest, False):
@@ -544,10 +552,9 @@ def add_class(classes, cls):
             """Add a new class, and all of its subclasses."""
             children = cls.__subclasses__()
             classes.update({cls.__name__: {
-                                           'module': cls.__module__,
-                                           'children': [x.__name__ for x in children]
-                                           }
-                            })
+                'module': cls.__module__,
+                'children': [x.__name__ for x in children]
+            }})
             for child in children:
                 add_class(classes, child)
 
@@ -647,6 +654,7 @@ def process_software_build_specs(options):
 
     try_to_generate = False
     build_specs = {}
+    logger = fancylogger.getLogger()
 
     # regular options: don't try to generate easyconfig, and search
     opts_map = {
@@ -683,7 +691,7 @@ def process_software_build_specs(options):
         tryval = getattr(options, 'try_%s' % opt)
         if val or tryval:
             if val and tryval:
-                fancylogger.getLogger().warning("Ignoring --try-%(opt)s, only using --%(opt)s specification" % {'opt': opt})
+                logger.warning("Ignoring --try-%(opt)s, only using --%(opt)s specification" % {'opt': opt})
             elif tryval:
                 try_to_generate = True
             val = val or tryval  # --try-X value is overridden by --X
@@ -709,9 +717,7 @@ def process_software_build_specs(options):
         if options.amend:
             amends += options.amend
             if options.try_amend:
-                fancylogger.getLogger().warning(
-                    "Ignoring options passed via --try-amend, only using those passed via --amend."
-                )
+                logger.warning("Ignoring options passed via --try-amend, only using those passed via --amend.")
         if options.try_amend:
             amends += options.try_amend
             try_to_generate = True

From da9cce07092ebd7fc0dbcc58a29f7a95b1d19eb2 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Wed, 11 Feb 2015 12:21:46 +0100
Subject: [PATCH 0517/1356] Added unit test

---
 test/framework/toolchain.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index dc60b2c041..df7c35569f 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -381,6 +381,30 @@ def test_comp_family(self):
         tc.prepare()
         self.assertEqual(tc.comp_family(), "GCC")
 
+    def test_mpi_family(self):
+        """Test determining MPI family."""
+        # check subtoolchain w/o MPI
+        tc = self.get_toolchain("GCC", version="4.7.2")
+        tc.prepare()
+        self.assertEqual(tc.mpi_family(), None)
+        modules.modules_tool().purge()
+
+        # check full toolchain including MPI
+        tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
+        tc.prepare()
+        self.assertEqual(tc.mpi_family(), "OpenMPI")
+        modules.modules_tool().purge()
+
+        # check another one
+        tmpdir, imkl_module_path, imkl_module_txt = self.setup_sandbox_for_intel_fftw()
+        tc = self.get_toolchain("ictce", version="4.1.13")
+        tc.prepare()
+        self.assertEqual(tc.mpi_family(), "IntelMPI")
+
+        # cleanup
+        shutil.rmtree(tmpdir)
+        open(imkl_module_path, 'w').write(imkl_module_txt)
+
     def test_goolfc(self):
         """Test whether goolfc is handled properly."""
         tc = self.get_toolchain("goolfc", version="1.3.12")

From 85cbb15030afc38552032f7e5ef842c6c2aa2115 Mon Sep 17 00:00:00 2001
From: "Forai,Petar" <petar.forai@imp.ac.at>
Date: Wed, 11 Feb 2015 12:28:53 +0100
Subject: [PATCH 0518/1356] Restore checking module dependencies for Tcl
 modules for toolchain verification.

---
 easybuild/tools/module_generator.py | 19 +++++++++++++++++--
 easybuild/tools/modules.py          |  4 +---
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 9931fd2904..44917b138b 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -342,7 +342,8 @@ def get_description(self, conflict=True):
              ])
 
         elif conflict:
-            # conflicts are not needed in lua module files, as Lmod "conflict" by default
+            # conflicts are not needed in lua module files, as Lmod's one name
+            # rule and automatic swapping.
             pass
 
         txt = '\n'.join(lines) % {
@@ -436,7 +437,7 @@ def add_tcl_footer(self, tcltxt):
         """
         Append whatever Tcl code you want to your modulefile
         """
-    # nothing to do here, but this should fail in the context of generating Lua modules
+    #@todo to pass or not to pass? this should fail in the context of generating Lua modules
         pass
 
 
@@ -471,3 +472,17 @@ def module_generator(app, fake=False):
     module_syntax = get_module_syntax()
     module_generator_class = avail_module_generators().get(module_syntax)
     return module_generator_class(app, fake=fake)
+
+def return_module_loadregex(modulefile):
+    """
+    Return the right regex depending on the module file type (Lua vs Tcl) in order for 
+    to be able to figure out dependencies.
+    """
+    if (modules_tool().modulefile_path(modulefile)).endswith('.lua'):
+        loadregex = re.compile(r"^\s*load\(\"(\S+)\"", re.M)
+    else:   `
+        loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
+    return loadregex
+
+
+
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index dab0acd4dc..814557ae67 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -572,9 +572,7 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
         @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
         """
         modtxt = self.read_module_file(mod_name)
-        #@todo: this was removed for Lmod
-        #loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
-        loadregex = re.compile(r"load\(\"(\S*)\"", re.M)
+        loadregex = return_module_loadregex(mod_name)
         mods = loadregex.findall(modtxt)
 
         if depth > 0:

From 0df89a1ab4d5992f17f2f95761da088200f33caa Mon Sep 17 00:00:00 2001
From: "Forai,Petar" <petar.forai@imp.ac.at>
Date: Wed, 11 Feb 2015 12:32:01 +0100
Subject: [PATCH 0519/1356] This time for real.

---
 easybuild/tools/module_generator.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 44917b138b..aae4ded30d 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -473,16 +473,14 @@ def module_generator(app, fake=False):
     module_generator_class = avail_module_generators().get(module_syntax)
     return module_generator_class(app, fake=fake)
 
-def return_module_loadregex(modulefile):
+def return_module_loadregex(modname):
     """
     Return the right regex depending on the module file type (Lua vs Tcl) in order for 
     to be able to figure out dependencies.
     """
-    if (modules_tool().modulefile_path(modulefile)).endswith('.lua'):
+    if (modules_tool().modulefile_path(modname).endswith('.lua')):
         loadregex = re.compile(r"^\s*load\(\"(\S+)\"", re.M)
     else:   `
         loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
     return loadregex
 
-
-

From dcbabba53058c61f1964b1956fc228f12ca56ed3 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@gmail.com>
Date: Wed, 11 Feb 2015 12:40:21 +0100
Subject: [PATCH 0520/1356] using pkg_resources does not work, you never get a
 filename, installing in /etc doesn't work, fails when running as user, so
 install in the .egg and use a relative path

---
 easybuild/tools/options.py |  4 ++--
 setup.py                   | 47 +++++++++++++++++++-------------------
 2 files changed, 26 insertions(+), 25 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 55166f0f90..57407bfa9b 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -67,7 +67,7 @@
 
 XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
 XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', os.path.join("/etc"))
-DEFAULT_SYSTEM_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild.cfg')
+DEFAULT_SHIPPED_CONFIGFILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', '..', 'easybuild.cfg')
 DEFAULT_USER_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
 
 
@@ -76,7 +76,7 @@ class EasyBuildOptions(GeneralOption):
     VERSION = this_is_easybuild()
 
     DEFAULT_LOGLEVEL = 'INFO'
-    DEFAULT_CONFIGFILES = [DEFAULT_SYSTEM_CONFIGFILE, DEFAULT_USER_CONFIGFILE]
+    DEFAULT_CONFIGFILES = [DEFAULT_SHIPPED_CONFIGFILE, DEFAULT_USER_CONFIGFILE]
 
     ALLOPTSMANDATORY = False  # allow more than one argument
 
diff --git a/setup.py b/setup.py
index 1a961f4a36..40ba373e0c 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,5 @@
-# #
-# Copyright 2012-2013 Ghent University
+##
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -21,8 +21,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-# #
-
+##
 """
 This script can be used to install easybuild-framework, e.g. using:
   easy_install --user .
@@ -39,6 +38,7 @@
 
 API_VERSION = str(VERSION).split('.')[0]
 
+
 # Utility function to read README file
 def read(fname):
     return open(os.path.join(os.path.dirname(__file__), fname)).read()
@@ -55,6 +55,7 @@ def read(fname):
 
 log.info("Installing version %s (API version %s)" % (VERSION, API_VERSION))
 
+
 def find_rel_test():
     """Return list of files recursively from basedir (aka find -type f)"""
     basedir = os.path.join(os.path.dirname(__file__), "test", "framework")
@@ -78,22 +79,22 @@ def find_rel_test():
 ]
 
 setup(
-    name = "easybuild-framework",
-    version = str(VERSION),
-    author = "EasyBuild community",
-    author_email = "easybuild@lists.ugent.be",
-    description = """The EasyBuild framework supports the creation of custom easyblocks that \
+    name="easybuild-framework",
+    version=str(VERSION),
+    author="EasyBuild community",
+    author_email="easybuild@lists.ugent.be",
+    description="""The EasyBuild framework supports the creation of custom easyblocks that \
 implement support for installing particular (groups of) software packages.""",
-    license = "GPLv2",
-    keywords = "software build building installation installing compilation HPC scientific",
-    url = "http://hpcugent.github.com/easybuild",
-    packages = easybuild_packages,
-    package_dir = {'test.framework': "test/framework"},
-    package_data = {"test.framework": find_rel_test()},
-    scripts = ["eb", "optcomplete.bash", "minimal_bash_completion.bash"],
-    data_files = [],
-    long_description = read('README.rst'),
-    classifiers = [
+    license="GPLv2",
+    keywords="software build building installation installing compilation HPC scientific",
+    url="http://hpcugent.github.com/easybuild",
+    packages=easybuild_packages,
+    package_dir={'test.framework': "test/framework"},
+    package_data={"test.framework": find_rel_test()},
+    scripts=["eb", "optcomplete.bash", "minimal_bash_completion.bash"],
+    data_files=['easybuild.cfg'],
+    long_description=read('README.rst'),
+    classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Environment :: Console",
         "Intended Audience :: System Administrators",
@@ -102,8 +103,8 @@ def find_rel_test():
         "Programming Language :: Python :: 2.4",
         "Topic :: Software Development :: Build Tools",
     ],
-    platforms = "Linux",
-    provides = ["eb"] + easybuild_packages,
-    test_suite = "test.framework.suite",
-    zip_safe = False,
+    platforms="Linux",
+    provides=["eb"] + easybuild_packages,
+    test_suite="test.framework.suite",
+    zip_safe=False,
 )

From 4e84e618715a4a5ecb4f2895521ea6a8ee67c77d Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Wed, 11 Feb 2015 12:52:58 +0100
Subject: [PATCH 0521/1356] Added unit test

---
 test/framework/filetools.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 6c94e81a5d..1ad8fdcfe1 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -250,6 +250,26 @@ def check_mkdir(path, error=None, **kwargs):
 
         shutil.rmtree(tmpdir)
 
+    def test_path_matches(self):
+        # set up temporary directories
+        tmpdir = tempfile.mkdtemp()
+        path1 = os.path.join(tmpdir, 'path1')
+        ft.mkdir(path1)
+        path2 = os.path.join(tmpdir, 'path2') 
+        ft.mkdir(path1)
+        symlink = os.path.join(tmpdir, 'symlink')
+        os.symlink(path1, symlink)
+        missing = os.path.join(tmpdir, 'missing')
+
+        self.assertFalse(ft.path_matches(missing, [path1, path2]))
+        self.assertFalse(ft.path_matches(path1, [missing]))
+        self.assertFalse(ft.path_matches(path1, [missing, path2]))
+        self.assertFalse(ft.path_matches(path2, [missing, symlink]))
+        self.assertTrue(ft.path_matches(path1, [missing, symlink]))
+
+        # cleanup
+        shutil.rmtree(tmpdir)
+
     def test_read_write_file(self):
         """Test reading/writing files."""
         tmpdir = tempfile.mkdtemp()

From 7225d5bf92d62b1e6571b9848025847eeb05a1c0 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@gmail.com>
Date: Wed, 11 Feb 2015 14:59:03 +0100
Subject: [PATCH 0522/1356] add default system config again

---
 easybuild/tools/options.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 57407bfa9b..42b60963a9 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -67,6 +67,7 @@
 
 XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
 XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', os.path.join("/etc"))
+DEFAULT_SYSTEM_CONFIGFILE = os.path.join(XDG_CONFIG_DIRS, 'easybuild', 'config.fg')
 DEFAULT_SHIPPED_CONFIGFILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', '..', 'easybuild.cfg')
 DEFAULT_USER_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
 
@@ -76,7 +77,7 @@ class EasyBuildOptions(GeneralOption):
     VERSION = this_is_easybuild()
 
     DEFAULT_LOGLEVEL = 'INFO'
-    DEFAULT_CONFIGFILES = [DEFAULT_SHIPPED_CONFIGFILE, DEFAULT_USER_CONFIGFILE]
+    DEFAULT_CONFIGFILES = [DEFAULT_SHIPPED_CONFIGFILE, DEFAULT_SYSTEM_CONFIGFILE, DEFAULT_USER_CONFIGFILE]
 
     ALLOPTSMANDATORY = False  # allow more than one argument
 

From 6c37fc082b5bbb36ca14c51264d17e27410c87ea Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@gmail.com>
Date: Wed, 11 Feb 2015 15:24:21 +0100
Subject: [PATCH 0523/1356] doing things the stdweird way

---
 easybuild/tools/options.py | 6 +++---
 setup.py                   | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 42b60963a9..f8eaf55353 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -33,6 +33,7 @@
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
 """
+import glob
 import os
 import re
 import sys
@@ -67,8 +68,7 @@
 
 XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
 XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', os.path.join("/etc"))
-DEFAULT_SYSTEM_CONFIGFILE = os.path.join(XDG_CONFIG_DIRS, 'easybuild', 'config.fg')
-DEFAULT_SHIPPED_CONFIGFILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', '..', 'easybuild.cfg')
+DEFAULT_SYSTEM_CONFIGFILES = glob.glob(os.path.join(XDG_CONFIG_DIRS, 'easybuild.d', '*.cfg'))
 DEFAULT_USER_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
 
 
@@ -77,7 +77,7 @@ class EasyBuildOptions(GeneralOption):
     VERSION = this_is_easybuild()
 
     DEFAULT_LOGLEVEL = 'INFO'
-    DEFAULT_CONFIGFILES = [DEFAULT_SHIPPED_CONFIGFILE, DEFAULT_SYSTEM_CONFIGFILE, DEFAULT_USER_CONFIGFILE]
+    DEFAULT_CONFIGFILES = DEFAULT_SYSTEM_CONFIGFILES + [DEFAULT_USER_CONFIGFILE]
 
     ALLOPTSMANDATORY = False  # allow more than one argument
 
diff --git a/setup.py b/setup.py
index 40ba373e0c..3d7bb5b577 100644
--- a/setup.py
+++ b/setup.py
@@ -92,7 +92,7 @@ def find_rel_test():
     package_dir={'test.framework': "test/framework"},
     package_data={"test.framework": find_rel_test()},
     scripts=["eb", "optcomplete.bash", "minimal_bash_completion.bash"],
-    data_files=['easybuild.cfg'],
+    data_files=[],
     long_description=read('README.rst'),
     classifiers=[
         "Development Status :: 5 - Production/Stable",

From 3d715e22596793c717eb3c6626cdbf24318d42db Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Wed, 11 Feb 2015 15:27:56 +0100
Subject: [PATCH 0524/1356] Add initial support for a toolchain based module
 naming schemei, where software is installed in a directory specific to each
 toolchain, and each toolchain module extends the path. This won't work unless
 toolchains properly inherit (iccifort -> iimpi -> intel) and dependencies are
 listed appropriately in toolchains.

The other required change in easyblock.py changed the order of
statements written in the module file so that the 'module use' statement
appears after loading the dependencies. This allows the module path to
be updated in the correct order in this naming scheme.
---
 easybuild/framework/easyblock.py              |  2 +-
 .../module_naming_scheme/toolchain_mns.py     | 90 +++++++++++++++++++
 2 files changed, 91 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/tools/module_naming_scheme/toolchain_mns.py

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index a5decf677b..3f9b0259f7 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1642,8 +1642,8 @@ def make_module_step(self, fake=False):
 
         txt = ''
         txt += self.make_module_description()
-        txt += self.make_module_extend_modpath()
         txt += self.make_module_dep()
+        txt += self.make_module_extend_modpath()
         txt += self.make_module_req()
         txt += self.make_module_extra()
         txt += self.make_module_footer()
diff --git a/easybuild/tools/module_naming_scheme/toolchain_mns.py b/easybuild/tools/module_naming_scheme/toolchain_mns.py
new file mode 100644
index 0000000000..80c57ad669
--- /dev/null
+++ b/easybuild/tools/module_naming_scheme/toolchain_mns.py
@@ -0,0 +1,90 @@
+##
+# Copyright 2013-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Implementation of an example hierarchical module naming scheme.
+
+@author: Kenneth Hoste (Ghent University)
+@author: Markus Geimer (Forschungszentrum Juelich GmbH)
+"""
+
+import os
+import re
+from vsc.utils import fancylogger
+
+from easybuild.tools.module_naming_scheme.hierarchical_mns import HierarchicalMNS
+from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
+
+CORE = 'Core'
+TOOLCHAIN = 'Toolchain'
+
+MODULECLASS_TC = 'toolchain'
+
+
+class ToolchainMNS(HierarchicalMNS):
+    """Class implementing a toolchain-based hierarchical module naming scheme."""
+
+    def det_module_subdir(self, ec):
+        """
+        Determine module subdirectory, relative to the top of the module path.
+        This determines the separation between module names exposed to users, and what's part of the $MODULEPATH.
+        Examples: Core, Toolchain/gpsolf/2015.02
+        """
+
+        if ec.toolchain.name == DUMMY_TOOLCHAIN_NAME:
+
+            # toolchain is dummy/dummy, put in Core
+            subdir = CORE
+        else:
+            subdir = os.path.join(TOOLCHAIN,ec.toolchain.name,ec.toolchain.version)
+
+        return subdir
+
+
+    def det_modpath_extensions(self, ec):
+        """
+        Determine module path extensions, if any.
+        Examples: Toolchain/intel/2014.12 (for intel/2014.12 module)
+        """
+        modclass = ec['moduleclass']
+
+        paths = []
+
+
+	# Take care of the GCC corner case since it is both a compiler and a toolchain
+        if modclass == MODULECLASS_TC or ec['name'] == 'GCC':
+
+            fullver = self.det_full_version(ec)
+            paths.append(os.path.join(TOOLCHAIN,  ec['name'], fullver))
+
+        return paths
+
+    def expand_toolchain_load(self):
+        """
+        Determine whether load statements for a toolchain should be expanded to load statements for its dependencies.
+        This is useful when toolchains are not exposed to users.
+        """
+#        return True
+# In our case we have to load the toolchains because they are explicitly exposed when extending the module path
+        return False

From 3a6a8c6e17e8fb479f3a5c956c43bc419fff9477 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Wed, 11 Feb 2015 15:47:06 +0100
Subject: [PATCH 0525/1356] Clear checksums when using '--try-software-version'

---
 easybuild/framework/easyconfig/tweak.py | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 0047ae8a6d..d72fb4a95c 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -42,6 +42,7 @@
 from vsc.utils import fancylogger
 from vsc.utils.missing import nub
 
+from easybuild.framework.easyconfig.default import get_easyconfig_parameter_default
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, create_paths, process_easyconfig
 from easybuild.tools.filetools import read_file, write_file
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
@@ -162,11 +163,16 @@ def __repr__(self):
 
     additions = []
 
+    # automagically clear out list of checksums if software version is being tweaked 
+    if 'version' in tweaks and 'checksums' not in tweaks:
+        tweaks['checksums'] = []
+        _log.warning("Tweaking version: checksums cleared, verification disabled.")
+
     # we need to treat list values seperately, i.e. we prepend to the current value (if any)
     for (key, val) in tweaks.items():
 
         if isinstance(val, list):
-            regexp = re.compile(r"^(?P<key>\s*%s)\s*=\s*(?P<val>.*)$" % key, re.M)
+            regexp = re.compile(r"^(?P<key>\s*%s)\s*=\s*(?P<val>\[(.|\n)*\])\s*$" % key, re.M)
             res = regexp.search(ectxt)
             if res:
                 fval = [x for x in val if x != '']  # filter out empty strings
@@ -174,7 +180,10 @@ def __repr__(self):
                 # - input ending with comma (empty tail list element) => prepend
                 # - input starting with comma (empty head list element) => append
                 # - no empty head/tail list element => overwrite
-                if val[0] == '':
+                if not val:
+                    newval = '[]'
+                    _log.debug("Clearing %s to empty list (was: %s)" % (key, res.group('val')))
+                elif val[0] == '':
                     newval = "%s + %s" % (res.group('val'), fval)
                     _log.debug("Appending %s to %s" % (fval, key))
                 elif val[-1] == '':
@@ -185,7 +194,7 @@ def __repr__(self):
                     _log.debug("Overwriting %s with %s" % (key, fval))
                 ectxt = regexp.sub("%s = %s" % (res.group('key'), newval), ectxt)
                 _log.info("Tweaked %s list to '%s'" % (key, newval))
-            else:
+            elif get_easyconfig_parameter_default(key) != val:
                 additions.append("%s = %s" % (key, val))
 
             tweaks.pop(key)
@@ -211,7 +220,7 @@ def __repr__(self):
             if diff:
                 ectxt = regexp.sub("%s = %s" % (res.group('key'), quote_str(val)), ectxt)
                 _log.info("Tweaked '%s' to '%s'" % (key, quote_str(val)))
-        else:
+        elif get_easyconfig_parameter_default(key) != val:
             additions.append("%s = %s" % (key, quote_str(val)))
 
     if additions:

From b2f2930a6806516edfeddd47035ad36e600957a3 Mon Sep 17 00:00:00 2001
From: "Forai,Petar" <petar.forai@imp.ac.at>
Date: Wed, 11 Feb 2015 15:59:21 +0100
Subject: [PATCH 0526/1356] removed a typo

---
 easybuild/tools/module_generator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index aae4ded30d..5edd77f2e6 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -480,7 +480,7 @@ def return_module_loadregex(modname):
     """
     if (modules_tool().modulefile_path(modname).endswith('.lua')):
         loadregex = re.compile(r"^\s*load\(\"(\S+)\"", re.M)
-    else:   `
+    else:
         loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
     return loadregex
 

From bdf4b26d97db2b7dc68abd0361c27bf39fa8a76d Mon Sep 17 00:00:00 2001
From: "Forai,Petar" <petar.forai@imp.ac.at>
Date: Wed, 11 Feb 2015 16:16:14 +0100
Subject: [PATCH 0527/1356] added missing import.

---
 easybuild/tools/modules.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 814557ae67..ae8e3b6f01 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -51,6 +51,7 @@
 from easybuild.tools.filetools import convert_name, mkdir, read_file, path_matches, which
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.run import run_cmd
+from easybuild.tools.modules_generator import return_module_loadregex
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
 from vsc.utils.missing import nub
 

From ba4a6a816387098ebfb8c454b494c156f045e1a4 Mon Sep 17 00:00:00 2001
From: "Forai,Petar" <petar.forai@imp.ac.at>
Date: Wed, 11 Feb 2015 16:38:24 +0100
Subject: [PATCH 0528/1356] another typo.

---
 easybuild/tools/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index ae8e3b6f01..7bf758e492 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -51,7 +51,7 @@
 from easybuild.tools.filetools import convert_name, mkdir, read_file, path_matches, which
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.run import run_cmd
-from easybuild.tools.modules_generator import return_module_loadregex
+from easybuild.tools.module_generator import return_module_loadregex
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
 from vsc.utils.missing import nub
 

From 567c43d9db0926336878fc5dc0cb33a2952f48c3 Mon Sep 17 00:00:00 2001
From: "Forai,Petar" <petar.forai@imp.ac.at>
Date: Wed, 11 Feb 2015 17:26:05 +0100
Subject: [PATCH 0529/1356] moved bits and pieces to resolve the cyclic import
 deps.

---
 easybuild/tools/module_generator.py | 9 ++-------
 easybuild/tools/modules.py          | 2 +-
 easybuild/tools/options.py          | 3 +++
 3 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 5edd77f2e6..e97f36d73d 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -42,7 +42,6 @@
 from easybuild.tools import config
 from easybuild.tools.config import build_option, get_module_syntax
 from easybuild.tools.filetools import mkdir
-from easybuild.tools.modules import Lmod, modules_tool
 from easybuild.tools.utilities import quote_str
 
 
@@ -296,10 +295,6 @@ def __init__(self, *args, **kwargs):
         """ModuleGeneratorLua constructor."""
         super(ModuleGeneratorLua, self).__init__(*args, **kwargs)
 
-        # make sure Lmod is being used as a modules tool
-        if not isinstance(modules_tool(), Lmod):
-            self.log.error("Only Lmod can be used as modules tool when generating module files in Lua syntax.")
-
     def module_header(self):
         """Return module header string."""
         return ''
@@ -473,12 +468,12 @@ def module_generator(app, fake=False):
     module_generator_class = avail_module_generators().get(module_syntax)
     return module_generator_class(app, fake=fake)
 
-def return_module_loadregex(modname):
+def return_module_loadregex(modfilepath):
     """
     Return the right regex depending on the module file type (Lua vs Tcl) in order for 
     to be able to figure out dependencies.
     """
-    if (modules_tool().modulefile_path(modname).endswith('.lua')):
+    if (modfilepath.endswith('.lua')):
         loadregex = re.compile(r"^\s*load\(\"(\S+)\"", re.M)
     else:
         loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 7bf758e492..75be8ca69f 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -573,7 +573,7 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
         @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
         """
         modtxt = self.read_module_file(mod_name)
-        loadregex = return_module_loadregex(mod_name)
+        loadregex = return_module_loadregex(self.modulefile_path(modmod_name))
         mods = loadregex.findall(modtxt)
 
         if depth > 0:
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index deea120161..f0c89fb5ab 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -398,6 +398,9 @@ def postprocess(self):
             if not HAVE_GITHUB_API:
                 self.log.error("Required support for using GitHub API is not available (see warnings).")
 
+        if self.options.modules_syntax == 'Lua' and self.options.modules_tool !='Lmod':
+            self.log.error("Generating Lua module files requires Lmod as modules tool.")
+
         # make sure a GitHub token is available when it's required
         if self.options.upload_test_report:
             if not HAVE_KEYRING:

From 32ff7ed51648aef2ce9dbf9e13ac560887a46baa Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Wed, 11 Feb 2015 23:44:39 +0100
Subject: [PATCH 0530/1356] Some more circular deps should be gone and fixed a
 typo.

---
 easybuild/tools/module_generator.py | 9 ++++-----
 easybuild/tools/modules.py          | 5 ++---
 easybuild/tools/options.py          | 2 +-
 3 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index e97f36d73d..1701c2caff 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -40,7 +40,6 @@
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
 from easybuild.tools import config
-from easybuild.tools.config import build_option, get_module_syntax
 from easybuild.tools.filetools import mkdir
 from easybuild.tools.utilities import quote_str
 
@@ -432,7 +431,7 @@ def add_tcl_footer(self, tcltxt):
         """
         Append whatever Tcl code you want to your modulefile
         """
-    #@todo to pass or not to pass? this should fail in the context of generating Lua modules
+    	#@todo to pass or not to pass? this should fail in the context of generating Lua modules
         pass
 
 
@@ -440,10 +439,9 @@ def set_alias(self, key, value):
         """
         Generate set-alias statement in modulefile for the given key/value pair.
         """
-    # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
+    	# quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
         return 'setalias(%s,"%s")\n' % (key, quote_str(value))
 
-
 def avail_module_generators():
     """
     Return all known module syntaxes.
@@ -468,9 +466,10 @@ def module_generator(app, fake=False):
     module_generator_class = avail_module_generators().get(module_syntax)
     return module_generator_class(app, fake=fake)
 
+
 def return_module_loadregex(modfilepath):
     """
-    Return the right regex depending on the module file type (Lua vs Tcl) in order for 
+    Return the correct regex depending on the module file type (Lua vs Tcl) in order for 
     to be able to figure out dependencies.
     """
     if (modfilepath.endswith('.lua')):
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 75be8ca69f..78b5e5e2eb 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -1,4 +1,4 @@
-# #
+#
 # Copyright 2009-2014 Ghent University
 #
 # This file is part of EasyBuild,
@@ -51,7 +51,6 @@
 from easybuild.tools.filetools import convert_name, mkdir, read_file, path_matches, which
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.run import run_cmd
-from easybuild.tools.module_generator import return_module_loadregex
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
 from vsc.utils.missing import nub
 
@@ -573,7 +572,7 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
         @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
         """
         modtxt = self.read_module_file(mod_name)
-        loadregex = return_module_loadregex(self.modulefile_path(modmod_name))
+	loadregex = return_module_loadregex(self.modulefile_path(modmod_name))
         mods = loadregex.findall(modtxt)
 
         if depth > 0:
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index f0c89fb5ab..7a771e24b0 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -398,7 +398,7 @@ def postprocess(self):
             if not HAVE_GITHUB_API:
                 self.log.error("Required support for using GitHub API is not available (see warnings).")
 
-        if self.options.modules_syntax == 'Lua' and self.options.modules_tool !='Lmod':
+        if self.options.module_syntax == 'Lua' and self.options.modules_tool !='Lmod':
             self.log.error("Generating Lua module files requires Lmod as modules tool.")
 
         # make sure a GitHub token is available when it's required

From c38e9fac556ac4ef932fa318214f28fa329d6215 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 12 Feb 2015 01:51:57 +0100
Subject: [PATCH 0531/1356] fix remark w.r.t. MODULE_GENERATOR_CLASS_PREFIX

---
 easybuild/tools/module_generator.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 1701c2caff..0fc03f9a44 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -39,12 +39,13 @@
 from vsc.utils.missing import get_subclasses
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
-from easybuild.tools import config
+from easybuild.tools.config import build_option, get_module_syntax, install_path
 from easybuild.tools.filetools import mkdir
 from easybuild.tools.utilities import quote_str
 
 
-MODULE_GENERATOR_CLASS_PREFIX = 'ModuleGenerator'
+LUA_SYNTAX = 'Lua'
+TCL_SYNTAX = 'Tcl'
 
 
 _log = fancylogger.getLogger('module_generator', fname=False)
@@ -54,6 +55,7 @@ class ModuleGenerator(object):
     """
     Class for generating module files.
     """
+    SYNTAX = None
 
     # chars we want to escape in the generated modulefiles
     CHARS_TO_ESCAPE = ["$"]
@@ -116,7 +118,7 @@ def set_fake(self, fake):
             self.log.debug("Fake mode: using %s (instead of %s)" % (self.tmpdir, self.module_path))
             self.module_path = self.tmpdir
         else:
-            self.module_path = config.install_path('mod')
+            self.module_path = install_path('mod')
 
     def module_header(self):
         """Return module header string."""
@@ -131,6 +133,7 @@ class ModuleGeneratorTcl(ModuleGenerator):
     """
     Class for generating Tcl module files.
     """
+    SYNTAX = TCL_SYNTAX
 
     def module_header(self):
         """Return module header string."""
@@ -287,6 +290,7 @@ class ModuleGeneratorLua(ModuleGenerator):
     """
     Class for generating Lua module files.
     """
+    SYNTAX = LUA_SYNTAX
 
     MODULE_SUFFIX = '.lua'
 
@@ -448,13 +452,7 @@ def avail_module_generators():
     """
     class_dict = {}
     for klass in get_subclasses(ModuleGenerator):
-        class_name = klass.__name__
-        if class_name.startswith(MODULE_GENERATOR_CLASS_PREFIX):
-            syntax = class_name[len(MODULE_GENERATOR_CLASS_PREFIX):]
-            class_dict.update({syntax: klass})
-        else:
-            tup = (MODULE_GENERATOR_CLASS_PREFIX, class_name)
-            _log.error("Invalid name for ModuleGenerator subclass, should start with %s: %s" % tup)
+        class_dict.update({klass.SYNTAX: klass})
     return class_dict
 
 

From a081dd6a1dc91c228cfa192d895749f54a74e631 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 12 Feb 2015 02:16:01 +0100
Subject: [PATCH 0532/1356] fix @stdweird's remarks

---
 easybuild/tools/module_generator.py | 31 +++++++++--------------------
 easybuild/tools/modules.py          | 14 +++++++++++--
 easybuild/tools/options.py          |  5 +++--
 3 files changed, 24 insertions(+), 26 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 0fc03f9a44..3967a92321 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -313,7 +313,6 @@ def get_description(self, conflict=True):
 
         description = "%s - Homepage: %s" % (self.app.cfg['description'], self.app.cfg['homepage'])
 
-
         lines = [
             "local pkg = {}",
             "help = [["
@@ -352,7 +351,6 @@ def get_description(self, conflict=True):
             'homepage': self.app.cfg['homepage'],
         }
 
-
         return txt
 
     def load_module(self, mod_name):
@@ -414,7 +412,6 @@ def use(self, paths):
             use_statements.append('use("%s")' % path)
         return '\n'.join(use_statements)
 
-
     def set_environment(self, key, value):
 
         """
@@ -423,27 +420,24 @@ def set_environment(self, key, value):
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
         return 'setenv("%s", %s)\n' % (key, quote_str(value))
 
-
     def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.
         """
         pass
 
-
     def add_tcl_footer(self, tcltxt):
         """
         Append whatever Tcl code you want to your modulefile
         """
-    	#@todo to pass or not to pass? this should fail in the context of generating Lua modules
+        #@todo to pass or not to pass? this should fail in the context of generating Lua modules
         pass
 
-
     def set_alias(self, key, value):
         """
         Generate set-alias statement in modulefile for the given key/value pair.
         """
-    	# quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
+        # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
         return 'setalias(%s,"%s")\n' % (key, quote_str(value))
 
 def avail_module_generators():
@@ -458,21 +452,14 @@ def avail_module_generators():
 
 def module_generator(app, fake=False):
     """
-    Return interface to modules tool (environment modules (C, Tcl), or Lmod)
+    Return ModuleGenerator instance that matches the selected module file syntax to be used
     """
     module_syntax = get_module_syntax()
-    module_generator_class = avail_module_generators().get(module_syntax)
-    return module_generator_class(app, fake=fake)
-
+    available_mod_gens = avail_module_generators()
 
-def return_module_loadregex(modfilepath):
-    """
-    Return the correct regex depending on the module file type (Lua vs Tcl) in order for 
-    to be able to figure out dependencies.
-    """
-    if (modfilepath.endswith('.lua')):
-        loadregex = re.compile(r"^\s*load\(\"(\S+)\"", re.M)
-    else:
-        loadregex = re.compile(r"^\s*module\s+load\s+(\S+)", re.M)
-    return loadregex
+    if module_syntax not in available_mod_gens:
+        tup = (module_syntax, available_mod_gens)
+        _log.error("No module generator available for specified syntax '%s' (available: %s)" % tup)
 
+    module_generator_class = available_mod_gens[module_syntax]
+    return module_generator_class(app, fake=fake)
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 78b5e5e2eb..1b8cdf50d1 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -118,6 +118,17 @@
 _log = fancylogger.getLogger('modules', fname=False)
 
 
+def module_load_regex(modfilepath):
+    """
+    Return the correct (compiled) regex to extract dependencies, depending on the module file type (Lua vs Tcl)
+    """
+    if modfilepath.endswith('.lua'):
+        regex = r'^\s*load\("(\S+)"'
+    else:
+        regex = r"^\s*module\s+load\s+(\S+)"
+    return re.compile(regex, re.M)
+
+
 class ModulesTool(object):
     """An abstract interface to a tool that deals with modules."""
     # position and optionname
@@ -572,7 +583,7 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
         @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
         """
         modtxt = self.read_module_file(mod_name)
-	loadregex = return_module_loadregex(self.modulefile_path(modmod_name))
+        loadregex = module_load_regex(self.modulefile_path(mod_name))
         mods = loadregex.findall(modtxt)
 
         if depth > 0:
@@ -833,7 +844,6 @@ def available(self, mod_name=None):
 
     def update(self):
         """Update after new modules were added."""
-        return
         spider_cmd = os.path.join(os.path.dirname(self.cmd), 'spider')
         cmd = [spider_cmd, '-o', 'moduleT', os.environ['MODULEPATH']]
         self.log.debug("Running command '%s'..." % ' '.join(cmd))
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 7a771e24b0..91d4560510 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -55,9 +55,10 @@
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
-from easybuild.tools.module_generator import avail_module_generators
+from easybuild.tools.module_generator import LUA_SYNTAX, avail_module_generators
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
+from easybuild.tools.modules import Lmod
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.toolchain.utilities import search_toolchain
 from easybuild.tools.repository.repository import avail_repositories
@@ -398,7 +399,7 @@ def postprocess(self):
             if not HAVE_GITHUB_API:
                 self.log.error("Required support for using GitHub API is not available (see warnings).")
 
-        if self.options.module_syntax == 'Lua' and self.options.modules_tool !='Lmod':
+        if self.options.module_syntax == LUA_SYNTAX and self.options.modules_tool != Lmod.__name__:
             self.log.error("Generating Lua module files requires Lmod as modules tool.")
 
         # make sure a GitHub token is available when it's required

From 83ad732527110e808f6a702ecdcd0bc5393c6077 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Thu, 12 Feb 2015 11:40:34 +0100
Subject: [PATCH 0533/1356] Suppress creation of module symlinks for
 hierarchical MNS

---
 easybuild/tools/module_naming_scheme/hierarchical_mns.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 22a0342965..587397ae21 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -133,6 +133,13 @@ def det_module_subdir(self, ec):
 
         return subdir
 
+    def det_module_symlink_paths(self, ec):
+        """
+        Determine list of paths in which symlinks to module files must be created.
+        """
+        # symlinks are not very useful in the context of a hierarchical MNS
+        return []
+
     def det_modpath_extensions(self, ec):
         """
         Determine module path extensions, if any.

From f4d2b6a1aec7c0e53deaa31af28a591a097322de Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Thu, 12 Feb 2015 16:44:04 +0100
Subject: [PATCH 0534/1356] Add hierarchical module naming scheme which
 categorizes modulefiles by 'moduleclass' easyconfig parameter on each level
 of the hierarchy

---
 .../module_naming_scheme/categorized_hmns.py  | 106 ++++++++++++++++++
 1 file changed, 106 insertions(+)
 create mode 100644 easybuild/tools/module_naming_scheme/categorized_hmns.py

diff --git a/easybuild/tools/module_naming_scheme/categorized_hmns.py b/easybuild/tools/module_naming_scheme/categorized_hmns.py
new file mode 100644
index 0000000000..26279861b0
--- /dev/null
+++ b/easybuild/tools/module_naming_scheme/categorized_hmns.py
@@ -0,0 +1,106 @@
+##
+# Copyright (c) 2015 Forschungszentrum Juelich GmbH, Germany
+#
+# All rights reserved.
+#
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright
+#   notice, this list of conditions and the following disclaimer in the
+#   documentation and/or other materials provided with the distribution.
+#
+# * Neither the name of Forschungszentrum Juelich GmbH, nor the names of
+#   its contributors may be used to endorse or promote products derived
+#   from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+##
+"""
+Implementation of a hierarchical module naming scheme using module classes.
+
+@author: Markus Geimer (Forschungszentrum Juelich GmbH)
+"""
+
+import os
+
+from easybuild.tools.module_naming_scheme.hierarchical_mns import HierarchicalMNS
+from easybuild.tools.config import build_option
+
+
+class CategorizedHMNS(HierarchicalMNS):
+    """
+    Class implementing an extended hierarchical module naming scheme using the
+    'moduleclass' easyconfig parameter to categorize modulefiles on each level
+    of the hierarchy.
+    """
+
+    REQUIRED_KEYS = ['name', 'version', 'versionsuffix', 'toolchain', 'moduleclass']
+
+    def det_module_subdir(self, ec):
+        """
+        Determine module subdirectory, relative to the top of the module path.
+        This determines the separation between module names exposed to users,
+        and what's part of the $MODULEPATH. This implementation appends the
+        'moduleclass' easyconfig parameter to the base path of the corresponding
+        hierarchy level.
+
+        Examples:
+        Core/compiler, Compiler/GCC/4.8.3/mpi, MPI/GCC/4.8.3/OpenMPI/1.6.5/bio
+        """
+        moduleclass = ec['moduleclass']
+        basedir = super(CategorizedHMNS, self).det_module_subdir(ec)
+
+        return os.path.join(basedir, moduleclass)
+
+    def det_modpath_extensions(self, ec):
+        """
+        Determine module path extensions, if any. Appends all known (valid)
+        module classes to the base path of the corresponding hierarchy level.
+
+        Examples:
+        Compiler/GCC/4.8.3/<moduleclasses> (for GCC/4.8.3 module),
+        MPI/GCC/4.8.3/OpenMPI/1.6.5/<moduleclasses> (for OpenMPI/1.6.5 module)
+        """
+        known_module_classes = build_option('valid_module_classes')
+        basepaths = super(CategorizedHMNS, self).det_modpath_extensions(ec)
+
+        paths = []
+        for path in basepaths:
+            for moduleclass in known_module_classes:
+                paths.extend([os.path.join(path, moduleclass)])
+
+        return paths
+
+    def det_init_modulepaths(self, ec):
+        """
+        Determine list of initial module paths (i.e., top of the hierarchy).
+        Appends all known (valid) module classes to the top-level base path.
+
+        Examples:
+        Core/<moduleclasses>
+        """
+        known_module_classes = build_option('valid_module_classes')
+        basepaths = super(CategorizedHMNS, self).det_init_modulepaths(ec)
+
+        paths = []
+        for path in basepaths:
+            for moduleclass in known_module_classes:
+                paths.extend([os.path.join(path, moduleclass)])
+
+        return paths

From 4c60d07b7d7788af0a4cbdf77aaeda3484215eb0 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 13 Feb 2015 10:21:08 +0100
Subject: [PATCH 0535/1356] Update toolchain_mns.py

Fixed the names...added some humour
---
 easybuild/tools/module_naming_scheme/toolchain_mns.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/toolchain_mns.py b/easybuild/tools/module_naming_scheme/toolchain_mns.py
index 80c57ad669..6d9ea58bf4 100644
--- a/easybuild/tools/module_naming_scheme/toolchain_mns.py
+++ b/easybuild/tools/module_naming_scheme/toolchain_mns.py
@@ -25,8 +25,8 @@
 """
 Implementation of an example hierarchical module naming scheme.
 
-@author: Kenneth Hoste (Ghent University)
-@author: Markus Geimer (Forschungszentrum Juelich GmbH)
+@author: Alan O'Cais (Forschungszentrum Juelich GmbH)
+@author: Eric "The Knife" Gregory (Forschungszentrum Juelich GmbH)
 """
 
 import os

From 0a667215a343f5917affa41176f455ce179e4633 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 13 Feb 2015 10:47:37 +0100
Subject: [PATCH 0536/1356] Update toolchain_mns.py

Fixed comments from @boegel
---
 .../module_naming_scheme/toolchain_mns.py     | 19 +++----------------
 1 file changed, 3 insertions(+), 16 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/toolchain_mns.py b/easybuild/tools/module_naming_scheme/toolchain_mns.py
index 6d9ea58bf4..149480fe34 100644
--- a/easybuild/tools/module_naming_scheme/toolchain_mns.py
+++ b/easybuild/tools/module_naming_scheme/toolchain_mns.py
@@ -29,19 +29,12 @@
 @author: Eric "The Knife" Gregory (Forschungszentrum Juelich GmbH)
 """
 
-import os
-import re
-from vsc.utils import fancylogger
-
 from easybuild.tools.module_naming_scheme.hierarchical_mns import HierarchicalMNS
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 
-CORE = 'Core'
 TOOLCHAIN = 'Toolchain'
-
 MODULECLASS_TC = 'toolchain'
 
-
 class ToolchainMNS(HierarchicalMNS):
     """Class implementing a toolchain-based hierarchical module naming scheme."""
 
@@ -51,9 +44,7 @@ def det_module_subdir(self, ec):
         This determines the separation between module names exposed to users, and what's part of the $MODULEPATH.
         Examples: Core, Toolchain/gpsolf/2015.02
         """
-
         if ec.toolchain.name == DUMMY_TOOLCHAIN_NAME:
-
             # toolchain is dummy/dummy, put in Core
             subdir = CORE
         else:
@@ -70,11 +61,8 @@ def det_modpath_extensions(self, ec):
         modclass = ec['moduleclass']
 
         paths = []
-
-
-	# Take care of the GCC corner case since it is both a compiler and a toolchain
-        if modclass == MODULECLASS_TC or ec['name'] == 'GCC':
-
+	# Take care of the corner cases, such as GCC, where it is both a compiler and a toolchain
+        if modclass == MODULECLASS_TC or ec['name'] in ['GCC']:
             fullver = self.det_full_version(ec)
             paths.append(os.path.join(TOOLCHAIN,  ec['name'], fullver))
 
@@ -85,6 +73,5 @@ def expand_toolchain_load(self):
         Determine whether load statements for a toolchain should be expanded to load statements for its dependencies.
         This is useful when toolchains are not exposed to users.
         """
-#        return True
-# In our case we have to load the toolchains because they are explicitly exposed when extending the module path
+	# In our case we have to load the toolchains because they are explicitly exposed when extending the module path
         return False

From a8f50b8dbb4ab16dd4e6e3b1bed1ba5c37cce001 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 13 Feb 2015 10:49:30 +0100
Subject: [PATCH 0537/1356] Update toolchain_mns.py

---
 easybuild/tools/module_naming_scheme/toolchain_mns.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/toolchain_mns.py b/easybuild/tools/module_naming_scheme/toolchain_mns.py
index 149480fe34..717277ad3f 100644
--- a/easybuild/tools/module_naming_scheme/toolchain_mns.py
+++ b/easybuild/tools/module_naming_scheme/toolchain_mns.py
@@ -52,7 +52,6 @@ def det_module_subdir(self, ec):
 
         return subdir
 
-
     def det_modpath_extensions(self, ec):
         """
         Determine module path extensions, if any.

From f842f54e815f69a9728d95bf93fccbbc6ed3648a Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 13 Feb 2015 10:50:54 +0100
Subject: [PATCH 0538/1356] Update toolchain_mns.py

Final deletions
---
 easybuild/tools/module_naming_scheme/toolchain_mns.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/toolchain_mns.py b/easybuild/tools/module_naming_scheme/toolchain_mns.py
index 717277ad3f..fc8a47b9e5 100644
--- a/easybuild/tools/module_naming_scheme/toolchain_mns.py
+++ b/easybuild/tools/module_naming_scheme/toolchain_mns.py
@@ -49,7 +49,6 @@ def det_module_subdir(self, ec):
             subdir = CORE
         else:
             subdir = os.path.join(TOOLCHAIN,ec.toolchain.name,ec.toolchain.version)
-
         return subdir
 
     def det_modpath_extensions(self, ec):
@@ -58,13 +57,11 @@ def det_modpath_extensions(self, ec):
         Examples: Toolchain/intel/2014.12 (for intel/2014.12 module)
         """
         modclass = ec['moduleclass']
-
         paths = []
 	# Take care of the corner cases, such as GCC, where it is both a compiler and a toolchain
         if modclass == MODULECLASS_TC or ec['name'] in ['GCC']:
             fullver = self.det_full_version(ec)
             paths.append(os.path.join(TOOLCHAIN,  ec['name'], fullver))
-
         return paths
 
     def expand_toolchain_load(self):

From 4563a77d3ff4f31788c3431ff279b3ec559a38a6 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Fri, 13 Feb 2015 12:54:08 +0100
Subject: [PATCH 0539/1356] Add note on license and some code refactoring

---
 .../module_naming_scheme/categorized_hmns.py  | 22 +++++++++++--------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/categorized_hmns.py b/easybuild/tools/module_naming_scheme/categorized_hmns.py
index 26279861b0..5ab963ae12 100644
--- a/easybuild/tools/module_naming_scheme/categorized_hmns.py
+++ b/easybuild/tools/module_naming_scheme/categorized_hmns.py
@@ -30,6 +30,8 @@
 # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# License: 3-clause BSD
 ##
 """
 Implementation of a hierarchical module naming scheme using module classes.
@@ -77,15 +79,9 @@ def det_modpath_extensions(self, ec):
         Compiler/GCC/4.8.3/<moduleclasses> (for GCC/4.8.3 module),
         MPI/GCC/4.8.3/OpenMPI/1.6.5/<moduleclasses> (for OpenMPI/1.6.5 module)
         """
-        known_module_classes = build_option('valid_module_classes')
         basepaths = super(CategorizedHMNS, self).det_modpath_extensions(ec)
 
-        paths = []
-        for path in basepaths:
-            for moduleclass in known_module_classes:
-                paths.extend([os.path.join(path, moduleclass)])
-
-        return paths
+        return self.categorize_paths(basepaths)
 
     def det_init_modulepaths(self, ec):
         """
@@ -95,12 +91,20 @@ def det_init_modulepaths(self, ec):
         Examples:
         Core/<moduleclasses>
         """
-        known_module_classes = build_option('valid_module_classes')
         basepaths = super(CategorizedHMNS, self).det_init_modulepaths(ec)
 
+        return self.categorize_paths(basepaths)
+
+    def categorize_paths(self, basepaths):
+        """
+        Returns a list of paths where all known (valid) module classes have
+        been added to each of the given base paths.
+        """
+        valid_module_classes = build_option('valid_module_classes')
+
         paths = []
         for path in basepaths:
-            for moduleclass in known_module_classes:
+            for moduleclass in valid_module_classes:
                 paths.extend([os.path.join(path, moduleclass)])
 
         return paths

From 4442f894cdfb0ede9cecae3d884e00760ed13b73 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 13 Feb 2015 17:32:06 +0100
Subject: [PATCH 0540/1356] keep module load regex in module_generator.py +
 fixes for other small remarks

---
 easybuild/main.py                   |  6 +++++
 easybuild/tools/module_generator.py | 41 ++++++++++++++++++++---------
 easybuild/tools/modules.py          | 21 +++++++--------
 easybuild/tools/options.py          |  4 +--
 test/framework/toolchain.py         |  5 +++-
 5 files changed, 49 insertions(+), 28 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index f1ab88af41..de649ee2e1 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -53,6 +53,8 @@
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak
 from easybuild.tools.config import get_repository, get_repositorypath, set_tmpdir
 from easybuild.tools.filetools import cleanup, write_file
+from easybuild.tools.module_generator import module_load_regex
+from easybuild.tools.modules import modules_tool
 from easybuild.tools.options import process_software_build_specs
 from easybuild.tools.robot import det_robot_path, dry_run, resolve_dependencies, search_easyconfigs
 from easybuild.tools.parallelbuild import submit_jobs
@@ -208,6 +210,10 @@ def main(testing_data=(None, None, None)):
     config.init(options, config_options_dict)
     config.init_build_options(build_options=build_options, cmdline_options=options)
 
+    # inject function to determine regex for 'load' statements in modules into ModulesTool instance
+    # we need to resort to this trickery to avoid cyclic imports (while retaining top-level imports)
+    modules_tool().set_load_regex_function(module_load_regex)
+
     # update session state
     eb_config = eb_go.generate_cmd_line(add_default=True)
     modlist = session_module_list(testing=testing)  # build options must be initialized first before 'module list' works
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 3967a92321..00302c1534 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -34,20 +34,18 @@
 """
 import os
 import re
+import sys
 import tempfile
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_subclasses
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
 from easybuild.tools.config import build_option, get_module_syntax, install_path
-from easybuild.tools.filetools import mkdir
+from easybuild.tools.filetools import mkdir, read_file
+from easybuild.tools.modules import modules_tool
 from easybuild.tools.utilities import quote_str
 
 
-LUA_SYNTAX = 'Lua'
-TCL_SYNTAX = 'Tcl'
-
-
 _log = fancylogger.getLogger('module_generator', fname=False)
 
 
@@ -59,7 +57,7 @@ class ModuleGenerator(object):
 
     # chars we want to escape in the generated modulefiles
     CHARS_TO_ESCAPE = ["$"]
-    MODULE_SUFFIX = ''
+    MODULE_FILE_EXTENSION = None
 
     def __init__(self, application, fake=False):
         """ModuleGenerator constructor."""
@@ -76,7 +74,7 @@ def prepare(self):
         Creates the absolute filename for the module.
         """
         mod_path_suffix = build_option('suffix_modules_path')
-        full_mod_name = '%s%s' % (self.app.full_mod_name, self.MODULE_SUFFIX)
+        full_mod_name = '%s%s' % (self.app.full_mod_name, self.MODULE_FILE_EXTENSION)
         # module file goes in general moduleclass category
         self.filename = os.path.join(self.module_path, mod_path_suffix, full_mod_name)
         # make symlink in moduleclass category
@@ -133,7 +131,11 @@ class ModuleGeneratorTcl(ModuleGenerator):
     """
     Class for generating Tcl module files.
     """
-    SYNTAX = TCL_SYNTAX
+    MODULE_FILE_EXTENSION = ''  # no suffix for Tcl module files
+    SYNTAX = 'Tcl'
+
+    LOAD_REGEX = r"^\s*module\s+load\s+(\S+)"
+    LOAD_TEMPLATE = "module load %(mod_name)s"
 
     def module_header(self):
         """Return module header string."""
@@ -202,7 +204,7 @@ def load_module(self, mod_name):
         else:
             load_statement = [
                 "if { ![is-loaded %(mod_name)s] } {",
-                "    module load %(mod_name)s",
+                "    %s" % self.LOAD_TEMPLATE,
                 "}",
             ]
         return '\n'.join([""] + load_statement + [""]) % {'mod_name': mod_name}
@@ -290,9 +292,11 @@ class ModuleGeneratorLua(ModuleGenerator):
     """
     Class for generating Lua module files.
     """
-    SYNTAX = LUA_SYNTAX
+    MODULE_FILE_EXTENSION = '.lua'
+    SYNTAX = 'Lua'
 
-    MODULE_SUFFIX = '.lua'
+    LOAD_REGEX = r'^\s*load\("(\S+)"'
+    LOAD_TEMPLATE = 'load("%(mod_name)s")'
 
     def __init__(self, *args, **kwargs):
         """ModuleGeneratorLua constructor."""
@@ -361,11 +365,11 @@ def load_module(self, mod_name):
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the depedency "module load" is present,
             # it will get translated to "module unload"
-            load_statement = ['load("%(mod_name)s")']
+            load_statement = [LOAD_TEMPLATE]
         else:
             load_statement = [
                 'if ( not isloaded("%(mod_name)s")) then',
-                '  load("%(mod_name)s")',
+                '  %s' % LOAD_TEMPLATE,
                 'end',
             ]
         return '\n'.join([""] + load_statement + [""]) % {'mod_name': mod_name}
@@ -463,3 +467,14 @@ def module_generator(app, fake=False):
 
     module_generator_class = available_mod_gens[module_syntax]
     return module_generator_class(app, fake=fake)
+
+
+def module_load_regex(modfilepath):
+    """
+    Return the correct (compiled) regex to extract dependencies, depending on the module file type (Lua vs Tcl)
+    """
+    if modfilepath.endswith('.lua'):
+        regex = ModuleGeneratorLua.LOAD_REGEX
+    else:
+        regex = ModuleGeneratorTcl.LOAD_REGEX
+    return re.compile(regex, re.M)
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 1b8cdf50d1..2e913b9562 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -118,17 +118,6 @@
 _log = fancylogger.getLogger('modules', fname=False)
 
 
-def module_load_regex(modfilepath):
-    """
-    Return the correct (compiled) regex to extract dependencies, depending on the module file type (Lua vs Tcl)
-    """
-    if modfilepath.endswith('.lua'):
-        regex = r'^\s*load\("(\S+)"'
-    else:
-        regex = r"^\s*module\s+load\s+(\S+)"
-    return re.compile(regex, re.M)
-
-
 class ModulesTool(object):
     """An abstract interface to a tool that deals with modules."""
     # position and optionname
@@ -185,6 +174,14 @@ def __init__(self, mod_paths=None, testing=False):
         self.check_module_function(allow_mismatch=build_option('allow_modules_tool_mismatch'))
         self.set_and_check_version()
 
+        self.det_load_regex = None
+
+    def set_load_regex_function(self, det_load_regex):
+        """
+        Set function to determine regex for 'load' statements.
+        """
+        self.det_load_regex = det_load_regex
+
     def buildstats(self):
         """Return tuple with data to be included in buildstats"""
         return (self.__class__.__name__, self.cmd, self.version)
@@ -583,7 +580,7 @@ def dependencies_for(self, mod_name, depth=sys.maxint):
         @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
         """
         modtxt = self.read_module_file(mod_name)
-        loadregex = module_load_regex(self.modulefile_path(mod_name))
+        loadregex = self.det_load_regex(self.modulefile_path(mod_name))
         mods = loadregex.findall(modtxt)
 
         if depth > 0:
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 91d4560510..f6b03a970d 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -55,7 +55,7 @@
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
-from easybuild.tools.module_generator import LUA_SYNTAX, avail_module_generators
+from easybuild.tools.module_generator import ModuleGeneratorLua, avail_module_generators
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
 from easybuild.tools.modules import Lmod
@@ -399,7 +399,7 @@ def postprocess(self):
             if not HAVE_GITHUB_API:
                 self.log.error("Required support for using GitHub API is not available (see warnings).")
 
-        if self.options.module_syntax == LUA_SYNTAX and self.options.modules_tool != Lmod.__name__:
+        if self.options.module_syntax == ModuleGeneratorLua.SYNTAX and self.options.modules_tool != Lmod.__name__:
             self.log.error("Generating Lua module files requires Lmod as modules tool.")
 
         # make sure a GitHub token is available when it's required
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index dc60b2c041..c80ea9a344 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -39,6 +39,7 @@
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import write_file
+from easybuild.tools.module_generator import module_load_regex
 from easybuild.tools.toolchain.utilities import search_toolchain
 from test.framework.utilities import find_full_path
 
@@ -50,7 +51,9 @@ def setUp(self):
         super(ToolchainTest, self).setUp()
 
         # start with a clean slate
-        modules.modules_tool().purge()
+        modtool = modules.modules_tool()
+        modtool.purge()
+        modtool.set_load_regex_function(module_load_regex)
 
         # make sure path with modules for testing is added to MODULEPATH
         self.orig_modpath = os.environ.get('MODULEPATH', '')

From 027a8bf3c896514878e8d000d384700534ae30f1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 13 Feb 2015 20:23:40 +0100
Subject: [PATCH 0541/1356] fix nasty hack to inject module_load_regex function
 into ModulesTool instance

---
 easybuild/framework/easyblock.py       |  4 +++-
 easybuild/main.py                      |  6 -----
 easybuild/tools/config.py              |  3 +--
 easybuild/tools/module_generator.py    | 30 +++++++++++++++++++++---
 easybuild/tools/modules.py             | 32 --------------------------
 easybuild/tools/toolchain/toolchain.py |  4 ++--
 test/framework/toolchain.py            |  5 +---
 7 files changed, 34 insertions(+), 50 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 2593064e06..a4bb487b2c 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1640,7 +1640,9 @@ def make_module_step(self, fake=False):
         Generate a module file.
         """
         self.module_generator.set_fake(fake)
-        modpath = self.module_generator.prepare()
+
+        mod_symlink_paths = ActiveMNS().det_module_symlink_paths(self.app.cfg)
+        modpath = self.module_generator.prepare(mod_symlink_paths)
 
         txt = ''
         txt += self.make_module_description()
diff --git a/easybuild/main.py b/easybuild/main.py
index de649ee2e1..f1ab88af41 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -53,8 +53,6 @@
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak
 from easybuild.tools.config import get_repository, get_repositorypath, set_tmpdir
 from easybuild.tools.filetools import cleanup, write_file
-from easybuild.tools.module_generator import module_load_regex
-from easybuild.tools.modules import modules_tool
 from easybuild.tools.options import process_software_build_specs
 from easybuild.tools.robot import det_robot_path, dry_run, resolve_dependencies, search_easyconfigs
 from easybuild.tools.parallelbuild import submit_jobs
@@ -210,10 +208,6 @@ def main(testing_data=(None, None, None)):
     config.init(options, config_options_dict)
     config.init_build_options(build_options=build_options, cmdline_options=options)
 
-    # inject function to determine regex for 'load' statements in modules into ModulesTool instance
-    # we need to resort to this trickery to avoid cyclic imports (while retaining top-level imports)
-    modules_tool().set_load_regex_function(module_load_regex)
-
     # update session state
     eb_config = eb_go.generate_cmd_line(add_default=True)
     modlist = session_module_list(testing=testing)  # build options must be initialized first before 'module list' works
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index dc8bd6f4b2..20159cbe87 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -40,12 +40,11 @@
 import tempfile
 import time
 from vsc.utils import fancylogger
-from vsc.utils.missing import nub, FrozenDictKnownKeys
+from vsc.utils.missing import FrozenDictKnownKeys
 from vsc.utils.patterns import Singleton
 
 import easybuild.tools.build_log  # this import is required to obtain a correct (EasyBuild) logger!
 import easybuild.tools.environment as env
-from easybuild.tools.environment import read_environment as _read_environment
 from easybuild.tools.run import run_cmd
 
 
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 00302c1534..72685b7957 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -39,7 +39,6 @@
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_subclasses
 
-from easybuild.framework.easyconfig.easyconfig import ActiveMNS
 from easybuild.tools.config import build_option, get_module_syntax, install_path
 from easybuild.tools.filetools import mkdir, read_file
 from easybuild.tools.modules import modules_tool
@@ -69,7 +68,7 @@ def __init__(self, application, fake=False):
         self.module_path = None
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
-    def prepare(self):
+    def prepare(self, mod_symlink_paths):
         """
         Creates the absolute filename for the module.
         """
@@ -78,7 +77,6 @@ def prepare(self):
         # module file goes in general moduleclass category
         self.filename = os.path.join(self.module_path, mod_path_suffix, full_mod_name)
         # make symlink in moduleclass category
-        mod_symlink_paths = ActiveMNS().det_module_symlink_paths(self.app.cfg)
         self.class_mod_files = [os.path.join(self.module_path, p, full_mod_name) for p in mod_symlink_paths]
 
         # create directories and links
@@ -478,3 +476,29 @@ def module_load_regex(modfilepath):
     else:
         regex = ModuleGeneratorTcl.LOAD_REGEX
     return re.compile(regex, re.M)
+
+
+def dependencies_for(mod_name, depth=sys.maxint):
+    """
+    Obtain a list of dependencies for the given module, determined recursively, up to a specified depth (optionally)
+    @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
+    """
+    mod_filepath = modules_tool().modulefile_path(mod_name)
+    modtxt = read_file(mod_filepath)
+    loadregex = module_load_regex(mod_filepath)
+    mods = loadregex.findall(modtxt)
+
+    if depth > 0:
+        # recursively determine dependencies for these dependency modules, until depth is non-positive
+        moddeps = [dependencies_for(mod, depth=depth - 1) for mod in mods]
+    else:
+        # ignore any deeper dependencies
+        moddeps = []
+
+    # add dependencies of dependency modules only if they're not there yet
+    for moddepdeps in moddeps:
+        for dep in moddepdeps:
+            if not dep in mods:
+                mods.append(dep)
+
+    return mods
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 2e913b9562..39ba39999b 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -38,7 +38,6 @@
 import os
 import re
 import subprocess
-import sys
 from distutils.version import StrictVersion
 from subprocess import PIPE
 from vsc.utils import fancylogger
@@ -51,7 +50,6 @@
 from easybuild.tools.filetools import convert_name, mkdir, read_file, path_matches, which
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.run import run_cmd
-from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
 from vsc.utils.missing import nub
 
 # software root/version environment variable name prefixes
@@ -176,12 +174,6 @@ def __init__(self, mod_paths=None, testing=False):
 
         self.det_load_regex = None
 
-    def set_load_regex_function(self, det_load_regex):
-        """
-        Set function to determine regex for 'load' statements.
-        """
-        self.det_load_regex = det_load_regex
-
     def buildstats(self):
         """Return tuple with data to be included in buildstats"""
         return (self.__class__.__name__, self.cmd, self.version)
@@ -574,30 +566,6 @@ def read_module_file(self, mod_name):
 
         return read_file(modfilepath)
 
-    def dependencies_for(self, mod_name, depth=sys.maxint):
-        """
-        Obtain a list of dependencies for the given module, determined recursively, up to a specified depth (optionally)
-        @param depth: recursion depth (default is sys.maxint, which should be equivalent to infinite recursion depth)
-        """
-        modtxt = self.read_module_file(mod_name)
-        loadregex = self.det_load_regex(self.modulefile_path(mod_name))
-        mods = loadregex.findall(modtxt)
-
-        if depth > 0:
-            # recursively determine dependencies for these dependency modules, until depth is non-positive
-            moddeps = [self.dependencies_for(mod, depth=depth - 1) for mod in mods]
-        else:
-            # ignore any deeper dependencies
-            moddeps = []
-
-        # add dependencies of dependency modules only if they're not there yet
-        for moddepdeps in moddeps:
-            for dep in moddepdeps:
-                if not dep in mods:
-                    mods.append(dep)
-
-        return mods
-
     def modpath_extensions_for(self, mod_names):
         """
         Determine dictionary with $MODULEPATH extensions for specified modules.
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index a4119c4592..a735fdc9f7 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -32,11 +32,11 @@
 """
 
 import os
-import re
 from vsc.utils import fancylogger
 
 from easybuild.tools.config import build_option, install_path
 from easybuild.tools.environment import setvar
+from easybuild.tools.module_generator import dependencies_for
 from easybuild.tools.modules import get_software_root, get_software_version, modules_tool
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
 from easybuild.tools.toolchain.options import ToolchainOptions
@@ -353,7 +353,7 @@ def prepare(self, onlymod=None):
 
         # determine direct toolchain dependencies
         mod_name = self.det_short_module_name()
-        self.toolchain_dep_mods = self.modules_tool.dependencies_for(mod_name, depth=0)
+        self.toolchain_dep_mods = dependencies_for(mod_name, depth=0)
         self.log.debug('prepare: list of direct toolchain dependencies: %s' % self.toolchain_dep_mods)
 
         # only retain names of toolchain elements, excluding toolchain name
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index c80ea9a344..dc60b2c041 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -39,7 +39,6 @@
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import write_file
-from easybuild.tools.module_generator import module_load_regex
 from easybuild.tools.toolchain.utilities import search_toolchain
 from test.framework.utilities import find_full_path
 
@@ -51,9 +50,7 @@ def setUp(self):
         super(ToolchainTest, self).setUp()
 
         # start with a clean slate
-        modtool = modules.modules_tool()
-        modtool.purge()
-        modtool.set_load_regex_function(module_load_regex)
+        modules.modules_tool().purge()
 
         # make sure path with modules for testing is added to MODULEPATH
         self.orig_modpath = os.environ.get('MODULEPATH', '')

From c5c2dbecaf6cb09dc5fcc466d6a7c78cc9b0fa93 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 13 Feb 2015 20:39:55 +0100
Subject: [PATCH 0542/1356] fix typo

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index a4bb487b2c..f21a17b984 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1641,7 +1641,7 @@ def make_module_step(self, fake=False):
         """
         self.module_generator.set_fake(fake)
 
-        mod_symlink_paths = ActiveMNS().det_module_symlink_paths(self.app.cfg)
+        mod_symlink_paths = ActiveMNS().det_module_symlink_paths(self.cfg)
         modpath = self.module_generator.prepare(mod_symlink_paths)
 
         txt = ''

From de2c619132e07fb2884ad6600e872725d1e02427 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sat, 14 Feb 2015 12:14:14 +0100
Subject: [PATCH 0543/1356] Add unit test for module_generator

---
 test/framework/module_generator.py | 35 +++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 67db3f17e0..4f8c3c7c74 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -378,6 +378,7 @@ def test_is_short_modname_for(self):
     def test_hierarchical_mns(self):
         """Test hierarchical module naming scheme."""
 
+        moduleclasses = ['base', 'compiler', 'mpi', 'numlib', 'system', 'toolchain']
         ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         all_stops = [x[0] for x in EasyBlock.get_steps()]
         build_options = {
@@ -385,6 +386,7 @@ def test_hierarchical_mns(self):
             'robot_path': [ecs_dir],
             'valid_stops': all_stops,
             'validate': False,
+            'valid_module_classes': moduleclasses,
         }
 
         def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
@@ -399,7 +401,7 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
         os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
         init_config(build_options=build_options)
 
-        # format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions)
+        # format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions, init_modpaths)
         iccver = '2013.5.192-GCC-4.8.3'
         impi_ec = 'impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb'
         imkl_ec = 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'
@@ -421,6 +423,37 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
         ec = EasyConfig(os.path.join(ecs_dir, 'impi-4.1.3.049.eb'))
         self.assertErrorRegex(EasyBuildError, 'No compiler available.*MPI lib', ActiveMNS().det_modpath_extensions, ec)
 
+        os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'CategorizedHMNS'
+        init_config(build_options=build_options)
+
+        # format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions)
+        test_ecs = {
+            'GCC-4.7.2.eb': ('GCC/4.7.2', 'Core/compiler',
+                             ['Compiler/GCC/4.7.2/%s' % c for c in moduleclasses]),
+            'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2/mpi',
+                             ['MPI/GCC/4.7.2/OpenMPI/1.6.4/%s' % c for c in moduleclasses]),
+            'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5', 'MPI/GCC/4.7.2/OpenMPI/1.6.4/base',
+                             []),
+            'goolf-1.4.10.eb': ('goolf/1.4.10', 'Core/toolchain',
+                             []),
+            'icc-2013.5.192-GCC-4.8.3.eb': ('icc/%s' % iccver, 'Core/compiler',
+                             ['Compiler/intel/%s/%s' % (iccver, c) for c in moduleclasses]),
+            'ifort-2013.3.163.eb': ('ifort/2013.3.163', 'Core/compiler',
+                             ['Compiler/intel/2013.3.163/%s' % c for c in moduleclasses]),
+            'CUDA-5.5.22-GCC-4.8.2.eb': ('CUDA/5.5.22', 'Compiler/GCC/4.8.2/system',
+                             ['Compiler/GCC-CUDA/4.8.2-5.5.22/%s' % c for c in moduleclasses]),
+            impi_ec: ('impi/4.1.3.049', 'Compiler/intel/%s/mpi' % iccver,
+                             ['MPI/intel/%s/impi/4.1.3.049/%s' % (iccver, c) for c in moduleclasses]),
+            imkl_ec: ('imkl/11.1.2.144', 'MPI/intel/%s/impi/4.1.3.049/numlib' % iccver,
+                             []),
+        }
+        for ecfile, mns_vals in test_ecs.items():
+            test_ec(ecfile, *mns_vals, init_modpaths = ['Core/%s' % c for c in moduleclasses])
+
+        # impi with dummy toolchain, which doesn't make sense in a hierarchical context
+        ec = EasyConfig(os.path.join(ecs_dir, 'impi-4.1.3.049.eb'))
+        self.assertErrorRegex(EasyBuildError, 'No compiler available.*MPI lib', ActiveMNS().det_modpath_extensions, ec)
+
         os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
         init_config(build_options=build_options)
 

From 9ca4efb0e1091cba32f5b653da0ccc6fde8e2d86 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sat, 14 Feb 2015 13:10:08 +0100
Subject: [PATCH 0544/1356] Use write_file instead of open().write()

---
 test/framework/toolchain.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index df7c35569f..cc30bc341a 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -403,7 +403,7 @@ def test_mpi_family(self):
 
         # cleanup
         shutil.rmtree(tmpdir)
-        open(imkl_module_path, 'w').write(imkl_module_txt)
+        write_file(imkl_module_path, imkl_module_txt)
 
     def test_goolfc(self):
         """Test whether goolfc is handled properly."""
@@ -503,7 +503,7 @@ def test_ictce_toolchain(self):
 
         # cleanup
         shutil.rmtree(tmpdir)
-        open(imkl_module_path, 'w').write(imkl_module_txt)
+        write_file(imkl_module_path, imkl_module_txt)
 
     def test_toolchain_verification(self):
         """Test verification of toolchain definition."""
@@ -544,7 +544,7 @@ def test_mpi_cmd_for(self):
 
         # cleanup
         shutil.rmtree(tmpdir)
-        open(imkl_module_path, 'w').write(imkl_module_txt)
+        write_file(imkl_module_path, imkl_module_txt)
 
     def tearDown(self):
         """Cleanup."""

From fd142036749d30e7f088e0f84eaff9cb0929ff50 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 14 Feb 2015 14:44:02 +0100
Subject: [PATCH 0545/1356] remove vsc and vsc.utils from list of included
 packages

---
 setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.py b/setup.py
index 6e2bba4a75..2ff3160270 100644
--- a/setup.py
+++ b/setup.py
@@ -74,7 +74,6 @@ def find_rel_test():
     "easybuild.toolchains.fft", "easybuild.toolchains.linalg", "easybuild.tools", "easybuild.tools.deprecated",
     "easybuild.tools.toolchain", "easybuild.tools.module_naming_scheme", "easybuild.tools.repository",
     "test.framework", "test",
-    "vsc", "vsc.utils",
 ]
 
 setup(

From 2d684b2c1e81315ea616e5881000f22f1e70ab86 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sun, 15 Feb 2015 10:12:39 +0100
Subject: [PATCH 0546/1356] Adjusted affiliation to make it consistent with
 other places

---
 easybuild/tools/module_naming_scheme/categorized_hmns.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_naming_scheme/categorized_hmns.py b/easybuild/tools/module_naming_scheme/categorized_hmns.py
index 5ab963ae12..203fa4e41f 100644
--- a/easybuild/tools/module_naming_scheme/categorized_hmns.py
+++ b/easybuild/tools/module_naming_scheme/categorized_hmns.py
@@ -36,7 +36,7 @@
 """
 Implementation of a hierarchical module naming scheme using module classes.
 
-@author: Markus Geimer (Forschungszentrum Juelich GmbH)
+@author: Markus Geimer (Juelich Supercomputing Centre)
 """
 
 import os

From f89eb14235328f18f1480f90d24383ae44cdc376 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sun, 15 Feb 2015 11:03:46 +0100
Subject: [PATCH 0547/1356] Add unit tests for command-line options

---
 .../Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4      | 30 +++++++++++++
 .../Compiler/GCC/4.7.2/system/hwloc/1.6.2     | 34 ++++++++++++++
 .../framework/modules/Core/compiler/GCC/4.7.2 | 28 ++++++++++++
 .../modules/Core/toolchain/gompi/1.4.10       | 28 ++++++++++++
 .../modules/Core/toolchain/goolf/1.4.10       | 39 ++++++++++++++++
 .../GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3 | 27 ++++++++++++
 .../1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2  | 22 ++++++++++
 .../2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2         | 28 ++++++++++++
 test/framework/options.py                     | 44 ++++++++++++++++++-
 9 files changed, 278 insertions(+), 2 deletions(-)
 create mode 100644 test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4
 create mode 100644 test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2
 create mode 100644 test/framework/modules/Core/compiler/GCC/4.7.2
 create mode 100644 test/framework/modules/Core/toolchain/gompi/1.4.10
 create mode 100644 test/framework/modules/Core/toolchain/goolf/1.4.10
 create mode 100644 test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
 create mode 100644 test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
 create mode 100644 test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2

diff --git a/test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4 b/test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4
new file mode 100644
index 0000000000..4950e8551b
--- /dev/null
+++ b/test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4
@@ -0,0 +1,30 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   The Open MPI Project is an open source MPI-2 implementation. - Homepage: http://www.open-mpi.org/
+    }
+}
+
+module-whatis {Description: The Open MPI Project is an open source MPI-2 implementation. - Homepage: http://www.open-mpi.org/}
+
+set root    /tmp/software/Compiler/GCC/4.8.2/OpenMPI/1.6.5-no-OFED
+
+conflict    OpenMPI
+module use /tmp/modules/all/MPI/GCC/4.7.2/OpenMPI/1.6.4/base
+module use /tmp/modules/all/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib
+
+if { ![is-loaded hwloc/1.6.2] } {
+    module load hwloc/1.6.2
+}
+
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+prepend-path	LIBRARY_PATH		$root/lib
+prepend-path	MANPATH		$root/share/man
+prepend-path	PATH		$root/bin
+prepend-path	PKG_CONFIG_PATH		$root/lib/pkgconfig
+
+setenv	EBROOTOPENMPI		"$root"
+setenv	EBVERSIONOPENMPI		"1.6.4"
+setenv	EBDEVELOPENMPI		"$root/easybuild/Compiler-GCC-4.7.2-OpenMPI-1.6.4-easybuild-devel"
+
diff --git a/test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2 b/test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2
new file mode 100644
index 0000000000..0c3e92ed9f
--- /dev/null
+++ b/test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2
@@ -0,0 +1,34 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   The Portable Hardware Locality (hwloc) software package provides a portable abstraction
+ (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including
+ NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various
+ system attributes such as cache and memory information as well as the locality of I/O devices such as
+ network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering
+ information about modern computing hardware so as to exploit it accordingly and efficiently. - Homepage: http://www.open-mpi.org/projects/hwloc/
+    }
+}
+
+module-whatis {Description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction
+ (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including
+ NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various
+ system attributes such as cache and memory information as well as the locality of I/O devices such as
+ network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering
+ information about modern computing hardware so as to exploit it accordingly and efficiently. - Homepage: http://www.open-mpi.org/projects/hwloc/}
+
+set root    /tmp/software/Compiler/GCC/4.7.2/hwloc/1.6.2
+
+conflict    hwloc
+
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+prepend-path	LIBRARY_PATH		$root/lib
+prepend-path	MANPATH		$root/share/man
+prepend-path	PATH		$root/bin
+prepend-path	PKG_CONFIG_PATH		$root/lib/pkgconfig
+
+setenv	EBROOTHWLOC		"$root"
+setenv	EBVERSIONHWLOC		"1.8.1"
+setenv	EBDEVELHWLOC		"$root/easybuild/Compiler-GCC-4.7.2-hwloc-1.6.2-easybuild-devel"
+
diff --git a/test/framework/modules/Core/compiler/GCC/4.7.2 b/test/framework/modules/Core/compiler/GCC/4.7.2
new file mode 100644
index 0000000000..71275941af
--- /dev/null
+++ b/test/framework/modules/Core/compiler/GCC/4.7.2
@@ -0,0 +1,28 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/
+    }
+}
+
+module-whatis {Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/}
+
+set root    /tmp/software/Core/GCC/4.7.2
+
+conflict    GCC
+module use /tmp/modules/all/Compiler/GCC/4.7.2/mpi
+module use /tmp/modules/all/Compiler/GCC/4.7.2/system
+
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+prepend-path	LD_LIBRARY_PATH		$root/lib/gcc/x86_64-apple-darwin13.2.0/4.7.2
+prepend-path	LIBRARY_PATH		$root/lib
+prepend-path	MANPATH		$root/share/man
+prepend-path	PATH		$root/bin
+
+setenv	EBROOTGCC		"$root"
+setenv	EBVERSIONGCC		"4.7.2"
+setenv	EBDEVELGCC		"$root/easybuild/Core-GCC-4.7.2-easybuild-devel"
+
diff --git a/test/framework/modules/Core/toolchain/gompi/1.4.10 b/test/framework/modules/Core/toolchain/gompi/1.4.10
new file mode 100644
index 0000000000..f6b56cbee8
--- /dev/null
+++ b/test/framework/modules/Core/toolchain/gompi/1.4.10
@@ -0,0 +1,28 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   GNU Compiler Collection (GCC) based compiler toolchain,
+ including OpenMPI for MPI support. - Homepage: (none)
+    }
+}
+
+module-whatis {Description: GNU Compiler Collection (GCC) based compiler toolchain,
+ including OpenMPI for MPI support. - Homepage: (none)}
+
+set root    /tmp/software/Core/gompi/1.4.10
+
+conflict    gompi
+
+if { ![is-loaded GCC/4.7.2] } {
+    module load GCC/4.7.2
+}
+
+if { ![is-loaded OpenMPI/1.6.4] } {
+    module load OpenMPI/1.6.4
+}
+
+
+setenv	EBROOTGOMPI		"$root"
+setenv	EBVERSIONGOMPI		"1.4.10"
+setenv	EBDEVELGOMPI		"$root/easybuild/Core-gompi-1.4.10-easybuild-devel"
+
diff --git a/test/framework/modules/Core/toolchain/goolf/1.4.10 b/test/framework/modules/Core/toolchain/goolf/1.4.10
new file mode 100644
index 0000000000..b199b678fc
--- /dev/null
+++ b/test/framework/modules/Core/toolchain/goolf/1.4.10
@@ -0,0 +1,39 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   GNU Compiler Collection (GCC) based compiler toolchain,
+ including OpenMPI for MPI support. - Homepage: (none)
+    }
+}
+
+module-whatis {Description: GNU Compiler Collection (GCC) based compiler toolchain,
+ including OpenMPI for MPI support. - Homepage: (none)}
+
+set root    /tmp/software/Core/gompi/1.4.10
+
+conflict    gompi
+
+if { ![is-loaded GCC/4.7.2] } {
+    module load GCC/4.7.2
+}
+
+if { ![is-loaded OpenMPI/1.6.4] } {
+    module load OpenMPI/1.6.4
+}
+
+if { ![is-loaded FFTW/3.3.3] } {
+    module load FFTW/3.3.3
+}
+
+if { ![is-loaded OpenBLAS/0.2.6-LAPACK-3.4.2] } {
+    module load OpenBLAS/0.2.6-LAPACK-3.4.2
+}
+
+if { ![is-loaded ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2] } {
+    module load ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
+}
+
+setenv	EBROOTGOMPI		"$root"
+setenv	EBVERSIONGOMPI		"1.4.10"
+setenv	EBDEVELGOMPI		"$root/easybuild/Core-gompi-1.4.10-easybuild-devel"
+
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3 b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
new file mode 100644
index 0000000000..f5558adc35
--- /dev/null
+++ b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
@@ -0,0 +1,27 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+in one or more dimensions, of arbitrary input size, and of both real and complex data. - Homepage: http://www.fftw.org
+}
+}
+
+module-whatis {FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+in one or more dimensions, of arbitrary input size, and of both real and complex data. - Homepage: http://www.fftw.org}
+
+set root    /home-2/khoste/.local/easybuild/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/FFTW/3.3.3
+
+conflict    FFTW
+
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+prepend-path	MANPATH		$root/share/man
+prepend-path	PATH		$root/bin
+prepend-path	PKG_CONFIG_PATH		$root/lib/pkgconfig
+
+setenv	EBROOTFFTW		"$root"
+setenv	EBVERSIONFFTW		"3.3.3"
+setenv	EBDEVELFFTW		"$root/easybuild/FFTW-3.3.3-gompi-1.4.10-easybuild-devel"
+
+
+# built with EasyBuild version 1.4.0dev
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2 b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
new file mode 100644
index 0000000000..f81a3b5d44
--- /dev/null
+++ b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
@@ -0,0 +1,22 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. - Homepage: http://xianyi.github.com/OpenBLAS/
+}
+}
+
+module-whatis {OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. - Homepage: http://xianyi.github.com/OpenBLAS/}
+
+set root    /home-2/khoste/.local/easybuild/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/OpenBLAS/0.2.6-LAPACK-3.4.2
+
+conflict    OpenBLAS
+
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+
+setenv	EBROOTOPENBLAS		"$root"
+setenv	EBVERSIONOPENBLAS		"0.2.6"
+setenv	EBDEVELOPENBLAS		"$root/easybuild/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2-easybuild-devel"
+
+
+# built with EasyBuild version 1.4.0dev
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2 b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
new file mode 100644
index 0000000000..31166dc2f3
--- /dev/null
+++ b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
@@ -0,0 +1,28 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
+redesigned for distributed memory MIMD parallel computers. - Homepage: http://www.netlib.org/scalapack/
+}
+}
+
+module-whatis {The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
+redesigned for distributed memory MIMD parallel computers. - Homepage: http://www.netlib.org/scalapack/}
+
+set root    /home-2/khoste/.local/easybuild/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
+
+conflict    ScaLAPACK
+
+if { ![is-loaded OpenBLAS/0.2.6-LAPACK-3.4.2] } {
+    module load OpenBLAS/0.2.6-LAPACK-3.4.2
+}
+
+prepend-path	CPATH		$root/include
+prepend-path	LD_LIBRARY_PATH		$root/lib
+
+setenv	EBROOTSCALAPACK		"$root"
+setenv	EBVERSIONSCALAPACK		"2.0.2"
+setenv	EBDEVELSCALAPACK		"$root/easybuild/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2-easybuild-devel"
+
+
+# built with EasyBuild version 1.4.0dev
diff --git a/test/framework/options.py b/test/framework/options.py
index 66f75a88a1..3f98a7f7a6 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -436,7 +436,7 @@ def test_avail_lists(self):
 
         name_items = {
             'modules-tools': ['EnvironmentModulesC', 'Lmod'],
-            'module-naming-schemes': ['EasyBuildMNS', 'HierarchicalMNS'],
+            'module-naming-schemes': ['EasyBuildMNS', 'HierarchicalMNS', 'CategorizedHMNS'],
         }
         for (name, items) in name_items.items():
             args = [
@@ -749,6 +749,46 @@ def test_dry_run_hierarchical(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
+    def test_dry_run_categorized(self):
+        """Test dry run using a categorized hierarchical module naming scheme."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        test_ecs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        args = [
+            os.path.join(test_ecs, 'gzip-1.5-goolf-1.4.10.eb'),
+            os.path.join(test_ecs, 'OpenMPI-1.6.4-GCC-4.7.2.eb'),
+            '--dry-run',
+            '--unittest-file=%s' % self.logfile,
+            '--module-naming-scheme=CategorizedHMNS',
+            '--ignore-osdeps',
+            '--force',
+            '--debug',
+            '--robot-paths=%s' % os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs'),
+        ]
+        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True, raise_error=True)
+
+        ecs_mods = [
+            # easyconfig, module subdir, (short) module name, mark
+            ("GCC-4.7.2.eb", "Core/compiler", "GCC/4.7.2", 'x'),  # already present but not listed, so 'x'
+            ("hwloc-1.6.2-GCC-4.7.2.eb", "Compiler/GCC/4.7.2/system", "hwloc/1.6.2", 'x'),
+            ("OpenMPI-1.6.4-GCC-4.7.2.eb", "Compiler/GCC/4.7.2/mpi", "OpenMPI/1.6.4", 'F'),  # already present and listed, so 'F'
+            ("gompi-1.4.10.eb", "Core/toolchain", "gompi/1.4.10", 'x'),
+            ("OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib",
+             "OpenBLAS/0.2.6-LAPACK-3.4.2", 'x'),
+            ("FFTW-3.3.3-gompi-1.4.10.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib", "FFTW/3.3.3", 'x'),
+            ("ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib",
+             "ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2", 'x'),
+            ("goolf-1.4.10.eb", "Core/toolchain", "goolf/1.4.10", 'x'),
+            ("gzip-1.5-goolf-1.4.10.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4/base", "gzip/1.5", ' '),  # listed but not there: ' '
+        ]
+        for ec, mod_subdir, mod_name, mark in ecs_mods:
+            regex = re.compile("^ \* \[%s\] \S+%s \(module: %s \| %s\)$" % (mark, ec, mod_subdir, mod_name), re.M)
+            self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
+
+        if os.path.exists(dummylogfn):
+            os.remove(dummylogfn)
+
     def test_from_pr(self):
         """Test fetching easyconfigs from a PR."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -1216,7 +1256,7 @@ def test_recursive_try(self):
             '--dry-run',
         ]
 
-        for extra_args in [[], ['--module-naming-scheme=HierarchicalMNS']]:
+        for extra_args in [[], ['--module-naming-scheme=HierarchicalMNS', '--module-naming-scheme=CategorizedHMNS']]:
 
             outtxt = self.eb_main(args + extra_args, verbose=True, raise_error=True)
 

From e516c5e894721b3afbf64680e786c3517cbac032 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 15 Feb 2015 11:35:57 +0100
Subject: [PATCH 0548/1356] enhance test that includes hard check for use of
 '$root' in module file

---
 test/framework/easyblock.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 2657389906..2e042e24b2 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -309,7 +309,8 @@ def test_make_module_step(self):
         self.assertTrue(re.search("^#%Module", txt.split('\n')[0]))
         self.assertTrue(re.search("^conflict\s+%s$" % name, txt, re.M))
         self.assertTrue(re.search("^set\s+root\s+%s$" % eb.installdir, txt, re.M))
-        self.assertTrue(re.search('^setenv\s+EBROOT%s\s+".root"\s*$' % name.upper(), txt, re.M))
+        ebroot_regex = re.compile('^setenv\s+EBROOT%s\s+".root"\s*$' % name.upper())
+        self.assertTrue(ebroot_regex.search(txt, re.M), "%s in %s" % (ebroot_regex.pattern, txt))
         self.assertTrue(re.search('^setenv\s+EBVERSION%s\s+"%s"$' % (name.upper(), version), txt, re.M))
         for (key, val) in modextravars.items():
             regex = re.compile('^setenv\s+%s\s+"%s"$' % (key, val), re.M)

From 627c44d3cc935118db62defcdd9e48bf71497e6d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 15 Feb 2015 11:45:27 +0100
Subject: [PATCH 0549/1356] enhance test to also check filtering of hidden deps
 with validation disabled

---
 test/framework/easyconfig.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 5f662ccbf2..25d6214e29 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -557,7 +557,6 @@ def test_obtain_easyconfig(self):
         self.assertTrue(re.search(pattern, txt, re.M))
         os.remove(res[1])
 
-
         # should be able to prepend to list of patches and handle list of dependencies
         new_patches = ['two.patch', 'three.patch']
         specs.update({
@@ -611,6 +610,17 @@ def test_obtain_easyconfig(self):
         ec = EasyConfig(res[1])
         self.assertEqual(ec['patches'], specs['patches'])
         self.assertEqual(ec.dependencies(), parsed_deps)
+
+        # hidden dependencies are filtered from list of dependencies
+        self.assertFalse('test/3.2.1-GCC-4.4.5' in [d['full_mod_name'] for d in ec['dependencies']])
+        self.assertTrue('test/.3.2.1-GCC-4.4.5' in [d['full_mod_name'] for d in ec['hiddendependencies']])
+        os.remove(res[1])
+
+        # hidden dependencies are also filtered from list of dependencies when validation is skipped
+        res = obtain_ec_for(specs, [self.ec_dir], None)
+        ec = EasyConfig(res[1], validate=False)
+        self.assertFalse('test/3.2.1-GCC-4.4.5' in [d['full_mod_name'] for d in ec['dependencies']])
+        self.assertTrue('test/.3.2.1-GCC-4.4.5' in [d['full_mod_name'] for d in ec['hiddendependencies']])
         os.remove(res[1])
 
         # verify append functionality for lists

From ccd911024b2dadef33a64fafa156fbb5dd145eca Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sun, 15 Feb 2015 12:12:45 +0100
Subject: [PATCH 0550/1356] Adjust number of modulefiles

---
 test/framework/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 00cce786d7..776b493f23 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -43,7 +43,7 @@
 
 
 # number of modules included for testing purposes
-TEST_MODULES_COUNT = 50
+TEST_MODULES_COUNT = 58
 
 
 class ModulesTest(EnhancedTestCase):

From 235635a3fffcd1ea1ab98f62b42a1c86fc00893f Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sun, 15 Feb 2015 12:13:01 +0100
Subject: [PATCH 0551/1356] Modulefile cleanup

---
 test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4   | 2 +-
 test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2  | 4 ++--
 test/framework/modules/Core/compiler/GCC/4.7.2                | 2 +-
 test/framework/modules/Core/toolchain/gompi/1.4.10            | 2 +-
 test/framework/modules/Core/toolchain/goolf/1.4.10            | 2 +-
 .../modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3     | 2 +-
 .../4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2    | 2 +-
 .../1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2  | 2 +-
 8 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4 b/test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4
index 4950e8551b..a851535416 100644
--- a/test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4
+++ b/test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4
@@ -7,7 +7,7 @@ proc ModulesHelp { } {
 
 module-whatis {Description: The Open MPI Project is an open source MPI-2 implementation. - Homepage: http://www.open-mpi.org/}
 
-set root    /tmp/software/Compiler/GCC/4.8.2/OpenMPI/1.6.5-no-OFED
+set root    /tmp/software/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4-no-OFED
 
 conflict    OpenMPI
 module use /tmp/modules/all/MPI/GCC/4.7.2/OpenMPI/1.6.4/base
diff --git a/test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2 b/test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2
index 0c3e92ed9f..18dc7a1cc8 100644
--- a/test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2
+++ b/test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2
@@ -17,7 +17,7 @@ module-whatis {Description: The Portable Hardware Locality (hwloc) software pack
  network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering
  information about modern computing hardware so as to exploit it accordingly and efficiently. - Homepage: http://www.open-mpi.org/projects/hwloc/}
 
-set root    /tmp/software/Compiler/GCC/4.7.2/hwloc/1.6.2
+set root    /tmp/software/Compiler/GCC/4.7.2/system/hwloc/1.6.2
 
 conflict    hwloc
 
@@ -29,6 +29,6 @@ prepend-path	PATH		$root/bin
 prepend-path	PKG_CONFIG_PATH		$root/lib/pkgconfig
 
 setenv	EBROOTHWLOC		"$root"
-setenv	EBVERSIONHWLOC		"1.8.1"
+setenv	EBVERSIONHWLOC		"1.6.2"
 setenv	EBDEVELHWLOC		"$root/easybuild/Compiler-GCC-4.7.2-hwloc-1.6.2-easybuild-devel"
 
diff --git a/test/framework/modules/Core/compiler/GCC/4.7.2 b/test/framework/modules/Core/compiler/GCC/4.7.2
index 71275941af..7e6aa96a08 100644
--- a/test/framework/modules/Core/compiler/GCC/4.7.2
+++ b/test/framework/modules/Core/compiler/GCC/4.7.2
@@ -9,7 +9,7 @@ proc ModulesHelp { } {
 module-whatis {Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
  as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/}
 
-set root    /tmp/software/Core/GCC/4.7.2
+set root    /tmp/software/Core/compiler/GCC/4.7.2
 
 conflict    GCC
 module use /tmp/modules/all/Compiler/GCC/4.7.2/mpi
diff --git a/test/framework/modules/Core/toolchain/gompi/1.4.10 b/test/framework/modules/Core/toolchain/gompi/1.4.10
index f6b56cbee8..20bdcdcf44 100644
--- a/test/framework/modules/Core/toolchain/gompi/1.4.10
+++ b/test/framework/modules/Core/toolchain/gompi/1.4.10
@@ -9,7 +9,7 @@ proc ModulesHelp { } {
 module-whatis {Description: GNU Compiler Collection (GCC) based compiler toolchain,
  including OpenMPI for MPI support. - Homepage: (none)}
 
-set root    /tmp/software/Core/gompi/1.4.10
+set root    /tmp/software/Core/toolchain/gompi/1.4.10
 
 conflict    gompi
 
diff --git a/test/framework/modules/Core/toolchain/goolf/1.4.10 b/test/framework/modules/Core/toolchain/goolf/1.4.10
index b199b678fc..9c3483696f 100644
--- a/test/framework/modules/Core/toolchain/goolf/1.4.10
+++ b/test/framework/modules/Core/toolchain/goolf/1.4.10
@@ -9,7 +9,7 @@ proc ModulesHelp { } {
 module-whatis {Description: GNU Compiler Collection (GCC) based compiler toolchain,
  including OpenMPI for MPI support. - Homepage: (none)}
 
-set root    /tmp/software/Core/gompi/1.4.10
+set root    /tmp/software/Core/toolchain/gompi/1.4.10
 
 conflict    gompi
 
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3 b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
index f5558adc35..9590348bd7 100644
--- a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
+++ b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
@@ -9,7 +9,7 @@ in one or more dimensions, of arbitrary input size, and of both real and complex
 module-whatis {FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
 in one or more dimensions, of arbitrary input size, and of both real and complex data. - Homepage: http://www.fftw.org}
 
-set root    /home-2/khoste/.local/easybuild/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/FFTW/3.3.3
+set root    /tmp/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
 
 conflict    FFTW
 
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2 b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
index f81a3b5d44..07b044ec1a 100644
--- a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
+++ b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
@@ -7,7 +7,7 @@ proc ModulesHelp { } {
 
 module-whatis {OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. - Homepage: http://xianyi.github.com/OpenBLAS/}
 
-set root    /home-2/khoste/.local/easybuild/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/OpenBLAS/0.2.6-LAPACK-3.4.2
+set root    /tmp/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
 
 conflict    OpenBLAS
 
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2 b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
index 31166dc2f3..4a93cd6ef5 100644
--- a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
+++ b/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
@@ -9,7 +9,7 @@ redesigned for distributed memory MIMD parallel computers. - Homepage: http://ww
 module-whatis {The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
 redesigned for distributed memory MIMD parallel computers. - Homepage: http://www.netlib.org/scalapack/}
 
-set root    /home-2/khoste/.local/easybuild/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
+set root    /tmp/software/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
 
 conflict    ScaLAPACK
 

From c0da35367e198360fa765c149300058d4b94a6d5 Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sun, 15 Feb 2015 16:22:51 +0100
Subject: [PATCH 0552/1356] Move test module files for CategorizedHMNS to
 subdir

---
 test/framework/modules.py                     |  3 ++-
 .../Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4      |  0
 .../Compiler/GCC/4.7.2/system/hwloc/1.6.2     |  0
 .../Core/compiler/GCC/4.7.2                   |  0
 .../Core/toolchain/gompi/1.4.10               |  0
 .../Core/toolchain/goolf/1.4.10               |  0
 .../GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3 |  0
 .../1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2  |  0
 .../2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2         |  0
 test/framework/options.py                     |  3 ++-
 test/framework/utilities.py                   | 27 +++++++++++++++++++
 11 files changed, 31 insertions(+), 2 deletions(-)
 rename test/framework/modules/{ => CategorizedHMNS}/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4 (100%)
 rename test/framework/modules/{ => CategorizedHMNS}/Compiler/GCC/4.7.2/system/hwloc/1.6.2 (100%)
 rename test/framework/modules/{ => CategorizedHMNS}/Core/compiler/GCC/4.7.2 (100%)
 rename test/framework/modules/{ => CategorizedHMNS}/Core/toolchain/gompi/1.4.10 (100%)
 rename test/framework/modules/{ => CategorizedHMNS}/Core/toolchain/goolf/1.4.10 (100%)
 rename test/framework/modules/{ => CategorizedHMNS}/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3 (100%)
 rename test/framework/modules/{ => CategorizedHMNS}/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2 (100%)
 rename test/framework/modules/{ => CategorizedHMNS}/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2 (100%)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 776b493f23..468b3307b4 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -127,7 +127,8 @@ def test_load(self):
         self.init_testmods()
         ms = self.testmods.available()
         # exclude modules not on the top level of a hierarchy
-        ms = [m for m in ms if not (m.startswith('Core') or m.startswith('Compiler/') or m.startswith('MPI/'))]
+        ms = [m for m in ms if not (m.startswith('Core') or m.startswith('Compiler/') or m.startswith('MPI/') or
+                                    m.startswith('CategorizedHMNS'))]
 
         for m in ms:
             self.testmods.load([m])
diff --git a/test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4 b/test/framework/modules/CategorizedHMNS/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4
similarity index 100%
rename from test/framework/modules/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4
rename to test/framework/modules/CategorizedHMNS/Compiler/GCC/4.7.2/mpi/OpenMPI/1.6.4
diff --git a/test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2 b/test/framework/modules/CategorizedHMNS/Compiler/GCC/4.7.2/system/hwloc/1.6.2
similarity index 100%
rename from test/framework/modules/Compiler/GCC/4.7.2/system/hwloc/1.6.2
rename to test/framework/modules/CategorizedHMNS/Compiler/GCC/4.7.2/system/hwloc/1.6.2
diff --git a/test/framework/modules/Core/compiler/GCC/4.7.2 b/test/framework/modules/CategorizedHMNS/Core/compiler/GCC/4.7.2
similarity index 100%
rename from test/framework/modules/Core/compiler/GCC/4.7.2
rename to test/framework/modules/CategorizedHMNS/Core/compiler/GCC/4.7.2
diff --git a/test/framework/modules/Core/toolchain/gompi/1.4.10 b/test/framework/modules/CategorizedHMNS/Core/toolchain/gompi/1.4.10
similarity index 100%
rename from test/framework/modules/Core/toolchain/gompi/1.4.10
rename to test/framework/modules/CategorizedHMNS/Core/toolchain/gompi/1.4.10
diff --git a/test/framework/modules/Core/toolchain/goolf/1.4.10 b/test/framework/modules/CategorizedHMNS/Core/toolchain/goolf/1.4.10
similarity index 100%
rename from test/framework/modules/Core/toolchain/goolf/1.4.10
rename to test/framework/modules/CategorizedHMNS/Core/toolchain/goolf/1.4.10
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3 b/test/framework/modules/CategorizedHMNS/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
similarity index 100%
rename from test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
rename to test/framework/modules/CategorizedHMNS/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/FFTW/3.3.3
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2 b/test/framework/modules/CategorizedHMNS/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
similarity index 100%
rename from test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
rename to test/framework/modules/CategorizedHMNS/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/OpenBLAS/0.2.6-LAPACK-3.4.2
diff --git a/test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2 b/test/framework/modules/CategorizedHMNS/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
similarity index 100%
rename from test/framework/modules/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
rename to test/framework/modules/CategorizedHMNS/MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib/ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2
diff --git a/test/framework/options.py b/test/framework/options.py
index 3f98a7f7a6..7807ec8b59 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -754,6 +754,7 @@ def test_dry_run_categorized(self):
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
+        self.setup_categorized_modules()
         test_ecs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         args = [
             os.path.join(test_ecs, 'gzip-1.5-goolf-1.4.10.eb'),
@@ -1256,7 +1257,7 @@ def test_recursive_try(self):
             '--dry-run',
         ]
 
-        for extra_args in [[], ['--module-naming-scheme=HierarchicalMNS', '--module-naming-scheme=CategorizedHMNS']]:
+        for extra_args in [[], ['--module-naming-scheme=HierarchicalMNS']]:
 
             outtxt = self.eb_main(args + extra_args, verbose=True, raise_error=True)
 
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index f2b26c85e4..eca8615fbb 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -234,6 +234,33 @@ def setup_hierarchical_modules(self):
                               line)
                 sys.stdout.write(line)
 
+    def setup_categorized_modules(self):
+        """Setup categorized hierarchical modules to run tests on."""
+        mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
+
+        # simply copy module files under 'CategorizedHMNS/{Core,Compiler,MPI}' to test install path
+        # EasyBuild is responsible for making sure that the toolchain can be loaded using the short module name
+        mkdir(mod_prefix, parents=True)
+        for mod_subdir in ['Core', 'Compiler', 'MPI']:
+            src_mod_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                                        'modules', 'CategorizedHMNS', mod_subdir)
+            shutil.copytree(src_mod_path, os.path.join(mod_prefix, mod_subdir))
+
+        # make sure only modules in the CategorizedHMNS are available
+        self.reset_modulepath([os.path.join(mod_prefix, 'Core', 'compiler'),
+                               os.path.join(mod_prefix, 'Core', 'toolchain')])
+
+        # tweak use statements in modules to ensure correct paths
+        for modfile in [
+            os.path.join(mod_prefix, 'Core', 'compiler', 'GCC', '4.7.2'),
+            os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'mpi', 'OpenMPI', '1.6.4'),
+        ]:
+            for line in fileinput.input(modfile, inplace=1):
+                line = re.sub(r"(module\s*use\s*)/tmp/modules/all",
+                              r"\1%s/modules/all" % self.test_installpath,
+                              line)
+                sys.stdout.write(line)
+
 
 def cleanup():
     """Perform cleanup of singletons and caches."""

From b3dfce96dccb90d1b5b0cb80efedb3321ac6002f Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sun, 15 Feb 2015 17:05:00 +0100
Subject: [PATCH 0553/1356] Renamed `setup_categorized_modules` to
 `setup_categorized_hmns_modules` as suggested

---
 test/framework/options.py   | 2 +-
 test/framework/utilities.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 7807ec8b59..9714ef5b96 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -754,7 +754,7 @@ def test_dry_run_categorized(self):
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
-        self.setup_categorized_modules()
+        self.setup_categorized_hmns_modules()
         test_ecs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         args = [
             os.path.join(test_ecs, 'gzip-1.5-goolf-1.4.10.eb'),
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index eca8615fbb..e344d3f185 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -234,7 +234,7 @@ def setup_hierarchical_modules(self):
                               line)
                 sys.stdout.write(line)
 
-    def setup_categorized_modules(self):
+    def setup_categorized_hmns_modules(self):
         """Setup categorized hierarchical modules to run tests on."""
         mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
 

From fbf73d67f060265dee39bbf874c6a9a5d915c1ba Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Sun, 15 Feb 2015 18:07:29 +0100
Subject: [PATCH 0554/1356] Add unit test for path_to_top_of_module_tree under
 CategorizedHMNS

---
 test/framework/modules.py | 41 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 468b3307b4..e098f30a42 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -248,6 +248,11 @@ def test_path_to_top_of_module_tree(self):
         path = modtool.path_to_top_of_module_tree([], 'toy/0.0', '', [])
         self.assertEqual(path, [])
 
+    def test_path_to_top_of_module_tree_hierarchical_mns(self):
+        """Test function to determine path to top of the module tree for a hierarchical module naming scheme."""
+
+        modtool = modules_tool()
+
         ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
         all_stops = [x[0] for x in EasyBlock.get_steps()]
         build_options = {
@@ -278,6 +283,42 @@ def test_path_to_top_of_module_tree(self):
         path = modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
         self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
 
+    def test_path_to_top_of_module_tree_categorized_hmns(self):
+        """
+        Test function to determine path to top of the module tree for a categorized hierarchical module naming
+        scheme.
+        """
+
+        ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
+        all_stops = [x[0] for x in EasyBlock.get_steps()]
+        build_options = {
+            'check_osdeps': False,
+            'robot_path': [ecs_dir],
+            'valid_stops': all_stops,
+            'validate': False,
+        }
+        os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'CategorizedHMNS'
+        init_config(build_options=build_options)
+        self.setup_categorized_hmns_modules()
+        modtool = modules_tool()
+        mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
+        init_modpaths = [os.path.join(mod_prefix, 'Core', 'compiler'), os.path.join(mod_prefix, 'Core', 'toolchain')]
+
+        deps = ['GCC/4.7.2', 'OpenMPI/1.6.4', 'FFTW/3.3.3', 'OpenBLAS/0.2.6-LAPACK-3.4.2',
+                'ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2']
+        path = modtool.path_to_top_of_module_tree(init_modpaths, 'goolf/1.4.10', os.path.join(mod_prefix, 'Core', 'toolchain'), deps)
+        self.assertEqual(path, [])
+        path = modtool.path_to_top_of_module_tree(init_modpaths, 'GCC/4.7.2', os.path.join(mod_prefix, 'Core', 'compiler'), [])
+        self.assertEqual(path, [])
+        full_mod_subdir = os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'mpi')
+        deps = ['GCC/4.7.2', 'hwloc/1.6.2']
+        path = modtool.path_to_top_of_module_tree(init_modpaths, 'OpenMPI/1.6.4', full_mod_subdir, deps)
+        self.assertEqual(path, ['GCC/4.7.2'])
+        full_mod_subdir = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4', 'numlib')
+        deps = ['GCC/4.7.2', 'OpenMPI/1.6.4']
+        path = modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
+        self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
+
 
 def suite():
     """ returns all the testcases in this module """

From e3afeabca038ee3db41e9f2b217a0b7945e3a17f Mon Sep 17 00:00:00 2001
From: Markus Geimer <m.geimer@fz-juelich.de>
Date: Mon, 16 Feb 2015 10:13:50 +0100
Subject: [PATCH 0555/1356] Create empty module file directory to make C/Tcl
 modules happy

---
 test/framework/utilities.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index e344d3f185..272984373b 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -245,6 +245,9 @@ def setup_categorized_hmns_modules(self):
             src_mod_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
                                         'modules', 'CategorizedHMNS', mod_subdir)
             shutil.copytree(src_mod_path, os.path.join(mod_prefix, mod_subdir))
+        # create empty module file directory to make C/Tcl modules happy
+        mpi_pref = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
+        mkdir(os.path.join(mpi_pref, 'base'))
 
         # make sure only modules in the CategorizedHMNS are available
         self.reset_modulepath([os.path.join(mod_prefix, 'Core', 'compiler'),

From 23bc84d4c5a5a74c8a45a55430e15b26e40408da Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Feb 2015 16:14:10 +0100
Subject: [PATCH 0556/1356] correctly handle $XDG_CONFIG_DIRS

---
 easybuild/tools/options.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index f8eaf55353..af6c9fc037 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -67,8 +67,8 @@
 
 
 XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
-XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', os.path.join("/etc"))
-DEFAULT_SYSTEM_CONFIGFILES = glob.glob(os.path.join(XDG_CONFIG_DIRS, 'easybuild.d', '*.cfg'))
+XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', os.path.join('/etc')).split(os.pathsep)
+DEFAULT_SYSTEM_CONFIGFILES = [f for d in XDG_CONFIG_DIRS for f in glob.glob(os.path.join(d, 'easybuild.d', '*.cfg'))]
 DEFAULT_USER_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
 
 

From 57db2753596d2c90a30d94983dcda2ee6d4ba0ad Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Feb 2015 16:20:55 +0100
Subject: [PATCH 0557/1356] style fixes in options.py

---
 easybuild/tools/options.py | 23 +++++++++--------------
 1 file changed, 9 insertions(+), 14 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index af6c9fc037..f31e3aaf2f 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -67,7 +67,7 @@
 
 
 XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
-XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', os.path.join('/etc')).split(os.pathsep)
+XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', '/etc').split(os.pathsep)
 DEFAULT_SYSTEM_CONFIGFILES = [f for d in XDG_CONFIG_DIRS for f in glob.glob(os.path.join(d, 'easybuild.d', '*.cfg'))]
 DEFAULT_USER_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
 
@@ -185,10 +185,8 @@ def override_options(self):
             'download_timeout': ("Timeout for initiating downloads (in seconds)", None, 'store', None),
             'easyblock': ("easyblock to use for processing the spec file or dumping the options",
                           None, 'store', None, 'e', {'metavar': 'CLASS'}),
-            'experimental': (
-                "Allow experimental code (with behaviour that can be changed or removed at any given time).",
-                None, 'store_true', False
-            ),
+            'experimental': ("Allow experimental code (with behaviour that can be changed/removed at any given time).",
+                             None, 'store_true', False),
             'group': ("Group to be used for software installations (only verified, not set)", None, 'store', None),
             'hidden': ("Install 'hidden' module file(s) by prefixing their name with '.'", None, 'store_true', False),
             'ignore-osdeps': ("Ignore any listed OS dependencies", None, 'store_true', False),
@@ -225,9 +223,8 @@ def config_options(self):
             'buildpath': ("Temporary build path", None, 'store', mk_full_default_path('buildpath')),
             'ignore-dirs': ("Directory names to ignore when searching for files/dirs",
                             'strlist', 'store', ['.git', '.svn']),
-            'installpath': (
-                "Install path for software and modules", None, 'store', mk_full_default_path('installpath')
-            ),
+            'installpath': ("Install path for software and modules",
+                            None, 'store', mk_full_default_path('installpath')),
             # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
@@ -257,15 +254,13 @@ def config_options(self):
             'sourcepath': ("Path(s) to where sources should be downloaded (string, colon-separated)",
                            None, 'store', mk_full_default_path('sourcepath')),
             'subdir-modules': ("Installpath subdir for modules", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_modules']),
-            'subdir-software': (
-                "Installpath subdir for software", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_software']
-            ),
+            'subdir-software': ("Installpath subdir for software",
+                                None, 'store', DEFAULT_PATH_SUBDIRS['subdir_software']),
             'suffix-modules-path': ("Suffix for module files install path", None, 'store', GENERAL_CLASS),
             # this one is sort of an exception, it's something jobscripts can set,
             # has no real meaning for regular eb usage
-            'testoutput': (
-                "Path to where a job should place the output (to be set within jobscript)", None, 'store', None
-            ),
+            'testoutput': ("Path to where a job should place the output (to be set within jobscript)",
+                           None, 'store', None),
             'tmp-logdir': ("Log directory where temporary log files are stored", None, 'store', None),
             'tmpdir': ('Directory to use for temporary storage', None, 'store', None),
         })

From ed831b896dec53a7814fab0776eb74495b343f4a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Feb 2015 16:55:38 +0100
Subject: [PATCH 0558/1356] add unit test for default configuration file(s)
 based on $XDG_CONFIG*

---
 test/framework/config.py | 84 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)

diff --git a/test/framework/config.py b/test/framework/config.py
index 21ee31185a..429b29407a 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -335,7 +335,91 @@ def test_build_options(self):
         bo2 = BuildOptions()
         self.assertTrue(bo is bo2)
 
+    def test_XDG_CONFIG_env_vars(self):
+        """Test effect of XDG_CONFIG* environment variables on default configuration."""
+        self.purge_environment()
+
+        xdg_config_home = os.environ.get('XDG_CONFIG_HOME')
+        xdg_config_dirs = os.environ.get('XDG_CONFIG_DIRS')
+
+        cfg_template = '\n'.join([
+            '[config]',
+            'prefix=%s',
+        ])
+
+        homedir = os.path.join(self.test_prefix, 'homedir', '.config')
+        mkdir(os.path.join(homedir, 'easybuild'), parents=True)
+        write_file(os.path.join(homedir, 'easybuild', 'config.cfg'), cfg_template % '/home')
+
+        dir1 = os.path.join(self.test_prefix, 'dir1')
+        mkdir(os.path.join(dir1, 'easybuild.d'), parents=True)
+        write_file(os.path.join(dir1, 'easybuild.d', 'foo.cfg'), cfg_template % '/foo')
+        write_file(os.path.join(dir1, 'easybuild.d', 'bar.cfg'), cfg_template % '/bar')
+
+        dir2 = os.path.join(self.test_prefix, 'dir2')  # empty on purpose
+        mkdir(os.path.join(dir2, 'easybuild.d'), parents=True)
 
+        dir3 = os.path.join(self.test_prefix, 'dir3')
+        mkdir(os.path.join(dir3, 'easybuild.d'), parents=True)
+        write_file(os.path.join(dir3, 'easybuild.d', 'foobarbaz.cfg'), cfg_template % '/foobarbaz')
+
+        # only $XDG_CONFIG_HOME set
+        os.environ['XDG_CONFIG_HOME'] = homedir
+        cfg_files = [os.path.join(homedir, 'easybuild', 'config.cfg')]
+        reload(eboptions)
+        eb_go = eboptions.parse_options(args=[])
+        self.assertEqual(eb_go.options.configfiles, cfg_files)
+        self.assertEqual(eb_go.options.prefix, '/home')
+
+        # $XDG_CONFIG_HOME set, one directory listed in $XDG_CONFIG_DIRS
+        os.environ['XDG_CONFIG_DIRS'] = dir1
+        cfg_files = [
+            os.path.join(dir1, 'easybuild.d', 'bar.cfg'),
+            os.path.join(dir1, 'easybuild.d', 'foo.cfg'),
+            os.path.join(homedir, 'easybuild', 'config.cfg'),  # $XDG_CONFIG_HOME goes last
+        ]
+        reload(eboptions)
+        eb_go = eboptions.parse_options(args=[])
+        self.assertEqual(eb_go.options.configfiles, cfg_files)
+        self.assertEqual(eb_go.options.prefix, '/home')  # last cfgfile wins
+
+        # $XDG_CONFIG_HOME not set, multiple directories listed in $XDG_CONFIG_DIRS
+        del os.environ['XDG_CONFIG_HOME']  # unset, so should become default
+        os.environ['XDG_CONFIG_DIRS'] = os.pathsep.join([dir1, dir2, dir3])
+        cfg_files = [
+            os.path.join(dir1, 'easybuild.d', 'bar.cfg'),
+            os.path.join(dir1, 'easybuild.d', 'foo.cfg'),
+            os.path.join(dir3, 'easybuild.d', 'foobarbaz.cfg'),
+            # default config file in home dir is last (even if the file is not there)
+            os.path.join(os.path.expanduser('~'), '.config', 'easybuild', 'config.cfg'),
+        ]
+        reload(eboptions)
+        eb_go = eboptions.parse_options(args=[])
+        self.assertEqual(eb_go.options.configfiles, cfg_files)
+
+        # $XDG_CONFIG_HOME set to non-existing directory, multiple directories listed in $XDG_CONFIG_DIRS
+        os.environ['XDG_CONFIG_HOME'] = os.path.join(self.test_prefix, 'nosuchdir')
+        cfg_files = [
+            os.path.join(dir1, 'easybuild.d', 'bar.cfg'),
+            os.path.join(dir1, 'easybuild.d', 'foo.cfg'),
+            os.path.join(dir3, 'easybuild.d', 'foobarbaz.cfg'),
+            os.path.join(self.test_prefix, 'nosuchdir', 'easybuild', 'config.cfg'),
+        ]
+        reload(eboptions)
+        eb_go = eboptions.parse_options(args=[])
+        self.assertEqual(eb_go.options.configfiles, cfg_files)
+        self.assertEqual(eb_go.options.prefix, '/foobarbaz')  # last cfgfile wins
+
+        # restore $XDG_CONFIG env vars to original state
+        if xdg_config_home is None:
+            del os.environ['XDG_CONFIG_HOME']
+        else:
+            os.environ['XDG_CONFIG_HOME'] = xdg_config_home
+
+        if xdg_config_dirs is None:
+            del os.environ['XDG_CONFIG_DIRS']
+        else:
+            os.environ['XDG_CONFIG_DIRS'] = xdg_config_dirs
 
 def suite():
     return TestLoader().loadTestsFromTestCase(EasyBuildConfigTest)

From 26aea028c957f1960c59598e8e1996183e8617b0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Feb 2015 17:38:37 +0100
Subject: [PATCH 0559/1356] add unit test cases for --try-X being overridden by
 --X, and fix overriding of --try-amend by --amend

---
 easybuild/tools/options.py | 2 +-
 test/framework/options.py  | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index f31e3aaf2f..3ac38024f3 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -714,7 +714,7 @@ def process_software_build_specs(options):
             amends += options.amend
             if options.try_amend:
                 logger.warning("Ignoring options passed via --try-amend, only using those passed via --amend.")
-        if options.try_amend:
+        elif options.try_amend:
             amends += options.try_amend
             try_to_generate = True
 
diff --git a/test/framework/options.py b/test/framework/options.py
index 66f75a88a1..529636d98d 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1164,10 +1164,15 @@ def test_try(self):
             ([], 'toy/0.0'),
             (['--try-software=foo,1.2.3', '--try-toolchain=gompi,1.4.10'], 'foo/1.2.3-gompi-1.4.10'),
             (['--try-toolchain-name=gompi', '--try-toolchain-version=1.4.10'], 'toy/0.0-gompi-1.4.10'),
+            # --try-toolchain is overridden by --toolchain
+            (['--try-toolchain=gompi,1.3.12', '--toolchain=dummy,dummy'], 'toy/0.0'),
             (['--try-software-name=foo', '--try-software-version=1.2.3'], 'foo/1.2.3'),
             (['--try-toolchain-name=gompi', '--try-toolchain-version=1.4.10'], 'toy/0.0-gompi-1.4.10'),
             (['--try-software-version=1.2.3', '--try-toolchain=gompi,1.4.10'], 'toy/1.2.3-gompi-1.4.10'),
             (['--try-amend=versionsuffix=-test'], 'toy/0.0-test'),
+            # --try-amend is overridden by --amend
+            (['--amend=versionsuffix=', '--try-amend=versionsuffix=-test'], 'toy/0.0'),
+            (['--try-toolchain=gompi,1.3.12', '--toolchain=dummy,dummy'], 'toy/0.0'),
             # tweak existing list-typed value (patches)
             (['--try-amend=versionsuffix=-test2', '--try-amend=patches=1.patch,2.patch'], 'toy/0.0-test2'),
             # append to existing list-typed value (patches)

From 1537f4abddb63b29c0701ca1b87b2064e09c0d50 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Feb 2015 21:52:04 +0100
Subject: [PATCH 0560/1356] enhance bootstrap script to allow bootstrapping
 using supplied tarballs

---
 easybuild/scripts/bootstrap_eb.py | 149 ++++++++++++++++++++++--------
 1 file changed, 108 insertions(+), 41 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index cc0aca8ed5..28b070c0b8 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -42,6 +42,7 @@
 """
 
 import copy
+import glob
 import os
 import re
 import shutil
@@ -50,8 +51,7 @@
 from distutils.version import LooseVersion
 
 # set print_debug to True for detailed progress info
-print_debug = False
-#print_debug = True
+print_debug = os.environ.get('EASYBUILD_BOOTSTRAP_DEBUG', False)
 
 # clean PYTHONPATH to avoid finding readily installed stuff
 os.environ['PYTHONPATH'] = ''
@@ -91,16 +91,17 @@ def find_egg_dir_for(path, pkg):
 
     for libdir in ['lib', 'lib64']:
         full_libpath = os.path.join(path, det_lib_path(libdir))
-
         eggdir_regex = re.compile('%s-[0-9a-z.]+-py[0-9.]+.egg' % pkg.replace('-', '_'))
-        subdirs = os.listdir(full_libpath)
+        subdirs = (os.path.exists(full_libpath) and os.listdir(full_libpath)) or []
         for subdir in subdirs:
             if eggdir_regex.match(subdir):
                 eggdir = os.path.join(full_libpath, subdir)
                 debug("Found egg dir for %s at %s" % (pkg, eggdir))
                 return eggdir
 
-    error("Failed to determine egg dir path for %s in %s (subdirs: %s)" % (pkg, path, subdirs))
+    # no egg dir found
+    debug("Failed to determine egg dir path for %s in %s (subdirs: %s)" % (pkg, path, subdirs))
+    return None
 
 def prep(path):
     """Prepare for installing a Python package in the specified path."""
@@ -206,7 +207,11 @@ def stage0(tmpdir):
         error("Installing distribute which should deliver easy_install failed?")
 
     # prepend distribute egg dir to sys.path, so we know which setuptools we're using
-    sys.path.insert(0, find_egg_dir_for(tmpdir, 'distribute'))
+    distribute_egg_dir = find_egg_dir_for(tmpdir, 'distribute')
+    if distribute_egg_dir is None:
+        error("Failed to determine egg dir path for distribute_egg_dir in %s" % tmpdir)
+    else:
+        sys.path.insert(0, distribute_egg_dir)
 
     # make sure we're getting the setuptools we expect
     import setuptools
@@ -215,37 +220,71 @@ def stage0(tmpdir):
     else:
         debug("Found setuptools in expected path, good!")
 
-def stage1(tmpdir):
+    return distribute_egg_dir
+
+
+def stage1(tmpdir, sources_path):
     """STAGE 1: temporary install EasyBuild using distribute's easy_install."""
 
     info("\n\n+++ STAGE 1: installing EasyBuild in temporary dir with easy_install...\n\n")
 
+    # determine locations of source tarballs, if sources path is specified
+    source_tarballs = []
+    if sources_path is not None:
+        info("Fetching sources from %s..." % sources_path)
+        for pkg in ['vsc-base', 'easybuild-framework', 'easybuild-easyblocks', 'easybuild-easyconfigs']:
+            pkg_tarball_glob = os.path.join(sources_path, '%s*.tar.gz' % pkg)
+            pkg_tarball_paths = glob.glob(pkg_tarball_glob)
+            if len(pkg_tarball_paths) > 1:
+                error("Multiple tarballs found for %s: %s" % (pkg, pkg_tarball_paths))
+            elif len(pkg_tarball_paths) == 0:
+                if pkg != 'vsc-base':
+                    error("Missing source tarball: %s" % pkg_tarball_glob)
+            else:
+                info("Found %s" % pkg_tarball_paths[0])
+                source_tarballs.append(pkg_tarball_paths[0])
+
     from setuptools.command import easy_install
 
     # prepare install dir
     targetdir_stage1 = os.path.join(tmpdir, 'eb_stage1')
     prep(targetdir_stage1)  # set PATH, Python search path
 
-
     # install latest EasyBuild with easy_install from PyPi
     cmd = []
     cmd.append('--upgrade')  # make sure the latest version is pulled from PyPi
     cmd.append('--prefix=%s' % targetdir_stage1)
-    cmd.append('easybuild')
+
+    if sources_path:
+        # install provided source tarballs
+        cmd.extend(source_tarballs)
+    else:
+        # install meta-package easybuild from PyPI
+        cmd.append('easybuild')
+
     if not print_debug:
         cmd.insert(0, '--quiet')
-    debug("installing EasyBuild with 'easy_install %s'" % (" ".join(cmd)))
+    info("installing EasyBuild with 'easy_install %s'" % (' '.join(cmd)))
     easy_install.main(cmd)
 
     # clear the Python search path, we only want the individual eggs dirs to be in the PYTHONPATH (see below)
     # this is needed to avoid easy-install.pth controlling what Python packages are actually used
     os.environ['PYTHONPATH'] = ''
 
-    versions = {}
+    # template string to inject in template easyconfig
+    templates = {}
 
     pkg_egg_dir_framework = None
-    for pkg in ['easyconfigs', 'easyblocks', 'framework']:
-        pkg_egg_dir = find_egg_dir_for(targetdir_stage1, 'easybuild-%s' % pkg)
+    for pkg in ['vsc-base', 'easybuild-framework', 'easybuild-easyblocks', 'easybuild-easyconfigs']:
+        templates.update({pkg: ''})
+
+        pkg_egg_dir = find_egg_dir_for(targetdir_stage1, pkg)
+        if pkg_egg_dir is None:
+            if pkg == 'vsc-base':
+                # vsc-base is optional in older EasyBuild versions
+                continue
+            else:
+                error("Failed to determine egg dir path for %s in %s" % (pkg, targetdir_stage1))
 
         # prepend EasyBuild egg dirs to Python search path, so we know which EasyBuild we're using
         sys.path.insert(0, pkg_egg_dir)
@@ -253,24 +292,36 @@ def stage1(tmpdir):
         os.environ['PYTHONPATH'] = os.pathsep.join([pkg_egg_dir] + pythonpaths)
 
         # determine per-package versions based on egg dirs
-        version_regex = re.compile('easybuild_%s-([0-9a-z.-]*)-py[0-9.]*.egg' % pkg)
+        version_regex = re.compile('%s-([0-9a-z.-]*)-py[0-9.]*.egg' % pkg.replace('-', '_'))
         pkg_egg_dirname = os.path.basename(pkg_egg_dir)
         res = version_regex.search(pkg_egg_dirname)
         if res is not None:
             pkg_version = res.group(1)
-            versions.update({'%s_version' % pkg: pkg_version})
             debug("Found version for easybuild-%s: %s" % (pkg, pkg_version))
+            if sources_path is None:
+                # downloaded tarballs should be versioned
+                templates.update({pkg: "'%s-%s.tar.gz'," % (pkg, pkg_version)})
+            else:
+                # names of specified source tarballs should not contain a version
+                templates.update({pkg: "'%s.tar.gz'," % pkg})
         else:
-            error("Failed to determine version for easybuild-%s package from %s with %s" % (pkg, pkg_egg_dirname, version_regex.pattern))
+            # vsc-base is only required for EasyBuild v2.x or higher
+            if pkg != 'vsc-base':
+                tup = (pkg, pkg_egg_dirname, version_regex.pattern)
+                error("Failed to determine version for easybuild-%s package from %s with %s" % tup)
 
         if pkg == 'framework':
             pkg_egg_dir_framework = pkg_egg_dir
 
     # figure out EasyBuild version via eb command line
-    # NOTE: EasyBuild uses some magic to determine the EasyBuild version based on the versions of the individual packages
-    version_re = re.compile("This is EasyBuild (?P<version>[0-9.]*[a-z0-9]*) \(framework: [0-9.]*[a-z0-9]*, easyblocks: [0-9.]*[a-z0-9]*\)")
+    # note: EasyBuild uses some magic to determine the EasyBuild version based on the versions of the individual packages
+    pattern = "This is EasyBuild (?P<version>%(v)s) \(framework: %(v)s, easyblocks: %(v)s\)" % {'v': '[0-9.]*[a-z0-9]*'}
+    version_re = re.compile(pattern)
     version_out_file = os.path.join(tmpdir, 'eb_version.out')
-    os.system("python -S %s/easybuild/main.py --version > %s 2>&1" % (pkg_egg_dir_framework, version_out_file))
+    eb_version_cmd = 'from easybuild.tools.version import this_is_easybuild; print this_is_easybuild()'
+    cmd = "python -c '%s' > %s 2>&1" % (eb_version_cmd, version_out_file)
+    debug("Determining EasyBuild version using command '%s'" % cmd)
+    os.system(cmd)
     txt = open(version_out_file, "r").read()
     res = version_re.search(txt)
     if res:
@@ -279,7 +330,7 @@ def stage1(tmpdir):
     else:
         error("Stage 1 failed, could not determine EasyBuild version (txt: %s)." % txt)
 
-    versions.update({'version': eb_version})
+    templates.update({'version': eb_version})
 
     # clear PYTHONPATH before we go to stage2
     # PYTHONPATH doesn't need to (and shouldn't) include the stage1 egg dirs
@@ -298,21 +349,23 @@ def stage1(tmpdir):
     else:
         debug("Found easybuild-easyblocks in expected path, good!")
 
-    return versions
+    debug("templates: %s" % templates)
+    return templates
 
-def stage2(tmpdir, versions, install_path):
+def stage2(tmpdir, templates, install_path, distribute_egg_dir, sources_path):
     """STAGE 2: install EasyBuild to temporary dir with EasyBuild from stage 1."""
 
     info("\n\n+++ STAGE 2: installing EasyBuild in temporary dir with EasyBuild from stage 1...\n\n")
 
-    # make sure we still have distribute in PYTHONPATH, so we have control over which 'setup' is used
-    pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
-    os.environ['PYTHONPATH'] = os.pathsep.join([find_egg_dir_for(tmpdir, 'distribute')] + pythonpaths)
+    if distribute_egg_dir is not None:
+        # make sure we still have distribute in PYTHONPATH, so we have control over which 'setup' is used
+        pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
+        os.environ['PYTHONPATH'] = os.pathsep.join([distribute_egg_dir] + pythonpaths)
 
     # create easyconfig file
-    ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % versions['version'])
+    ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])
     f = open(ebfile, "w")
-    f.write(EB_EC_FILE % versions)
+    f.write(EB_EC_FILE % templates)
     f.close()
 
     # unset $MODULEPATH, we don't care about already installed modules
@@ -325,7 +378,7 @@ def stage2(tmpdir, versions, install_path):
 
     # make sure we don't leave any stuff behind in default path $HOME/.local/easybuild
     # and set build and install path explicitely
-    if LooseVersion(versions['version']) < LooseVersion("1.3.0"):
+    if LooseVersion(templates['version']) < LooseVersion('1.3.0'):
         os.environ['EASYBUILD_PREFIX'] = tmpdir
         os.environ['EASYBUILD_BUILDPATH'] = tmpdir
         if install_path is not None:
@@ -336,6 +389,8 @@ def stage2(tmpdir, versions, install_path):
         eb_args.append('--buildpath=%s' % tmpdir)
         if install_path is not None:
             eb_args.append('--installpath=%s' % install_path)
+        if sources_path is not None:
+            eb_args.append('--sourcepath=%s' % sources_path)
 
     debug("Running EasyBuild with arguments '%s'" % ' '.join(eb_args))
     sys.argv = eb_args
@@ -357,6 +412,12 @@ def main():
         error("Usage: %s <install path>" % sys.argv[0])
     install_path = os.path.abspath(sys.argv[1])
 
+    sources_path = os.environ.get('EASYBUILD_BOOTSTRAP_TARBALLS')
+    if sources_path is not None:
+        info("Fetching sources from %s..." % sources_path)
+
+    skip_stage0 = os.environ.get('EASYBUILD_BOOTSTRAP_SKIP_STAGE0', False)
+
     # create temporary dir for temporary installations
     tmpdir = tempfile.mkdtemp()
     debug("Going to use %s as temporary directory" % tmpdir)
@@ -387,13 +448,17 @@ def main():
     # install EasyBuild in stages
 
     # STAGE 0: install distribute, which delivers easy_install
-    stage0(tmpdir)
+    if skip_stage0:
+        distribute_egg_dir = None
+        info("Skipping stage0, using local distribute/setuptools providing easy_install")
+    else:
+        distribute_egg_dir = stage0(tmpdir)
 
     # STAGE 1: install EasyBuild using easy_install to tmp dir
-    versions = stage1(tmpdir)
+    templates = stage1(tmpdir, sources_path)
 
     # STAGE 2: install EasyBuild using EasyBuild (to final target installation dir)
-    stage2(tmpdir, versions, install_path)
+    stage2(tmpdir, templates, install_path, distribute_egg_dir, sources_path)
 
     # clean up the mess
     debug("Cleaning up %s..." % tmpdir)
@@ -404,10 +469,10 @@ def main():
     info('')
     if install_path is not None:
         info('EasyBuild v%s was installed to %s, so make sure your $MODULEPATH includes %s' % \
-             (versions['version'], install_path, os.path.join(install_path, 'modules', 'all')))
+             (templates['version'], install_path, os.path.join(install_path, 'modules', 'all')))
     else:
         info('EasyBuild v%s was installed to configured install path, make sure your $MODULEPATH is set correctly.' % \
-             versions['version'])
+             templates['version'])
         info('(default config => add "$HOME/.local/easybuild/modules/all" in $MODULEPATH)')
 
     info('')
@@ -433,16 +498,18 @@ def main():
 toolchain = {'name': 'dummy', 'version': 'dummy'}
 
 source_urls = [
-               'http://pypi.python.org/packages/source/e/easybuild-framework/',
-               'http://pypi.python.org/packages/source/e/easybuild-easyblocks/',
-               'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/',
-              ]
+    'https://pypi.python.org/packages/source/v/vsc-base/',
+    'http://pypi.python.org/packages/source/e/easybuild-framework/',
+    'http://pypi.python.org/packages/source/e/easybuild-easyblocks/',
+    'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/',
+]
 # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?)
 sources = [
-           'easybuild-framework-%(framework_version)s.tar.gz',
-           'easybuild-easyblocks-%(easyblocks_version)s.tar.gz',
-           'easybuild-easyconfigs-%(easyconfigs_version)s.tar.gz',
-          ]
+    %(vsc-base)s
+    %(easybuild-framework)s
+    %(easybuild-easyblocks)s
+    %(easybuild-easyconfigs)s
+]
 
 # EasyBuild is a (set of) Python packages, so it depends on Python
 # usually, we want to use the system Python, so no actual Python dependency is listed

From e63aa8263cc2b017fbfc515a89fecaead5bab1a8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Feb 2015 14:23:05 +0100
Subject: [PATCH 0561/1356] use https for all PyPI URLs

---
 easybuild/scripts/bootstrap_eb.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 944ad11a88..14cea85aa7 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -512,9 +512,9 @@ def main():
 
 source_urls = [
     'https://pypi.python.org/packages/source/v/vsc-base/',
-    'http://pypi.python.org/packages/source/e/easybuild-framework/',
-    'http://pypi.python.org/packages/source/e/easybuild-easyblocks/',
-    'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/',
+    'https://pypi.python.org/packages/source/e/easybuild-framework/',
+    'https://pypi.python.org/packages/source/e/easybuild-easyblocks/',
+    'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/',
 ]
 # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?)
 sources = [

From 36affeedbfec4792970ebd59cce246b19bd7d952 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Feb 2015 16:15:02 +0100
Subject: [PATCH 0562/1356] fix remarks

---
 easybuild/scripts/bootstrap_eb.py | 94 +++++++++++++++----------------
 1 file changed, 46 insertions(+), 48 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 14cea85aa7..478563b1aa 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -50,6 +50,9 @@
 import tempfile
 from distutils.version import LooseVersion
 
+VSC_BASE = 'vsc-base'
+EASYBUILD_PACKAGES = [VSC_BASE, 'easybuild-framework', 'easybuild-easyblocks', 'easybuild-easyconfigs']
+
 # set print_debug to True for detailed progress info
 print_debug = os.environ.get('EASYBUILD_BOOTSTRAP_DEBUG', False)
 
@@ -229,26 +232,29 @@ def stage0(tmpdir):
     return distribute_egg_dir
 
 
-def stage1(tmpdir, sources_path):
+def stage1(tmpdir, sourcepath):
     """STAGE 1: temporary install EasyBuild using distribute's easy_install."""
 
     info("\n\n+++ STAGE 1: installing EasyBuild in temporary dir with easy_install...\n\n")
 
     # determine locations of source tarballs, if sources path is specified
-    source_tarballs = []
-    if sources_path is not None:
-        info("Fetching sources from %s..." % sources_path)
-        for pkg in ['vsc-base', 'easybuild-framework', 'easybuild-easyblocks', 'easybuild-easyconfigs']:
-            pkg_tarball_glob = os.path.join(sources_path, '%s*.tar.gz' % pkg)
+    source_tarballs = {}
+    if sourcepath is not None:
+        info("Fetching sources from %s..." % sourcepath)
+        for pkg in EASYBUILD_PACKAGES:
+            pkg_tarball_glob = os.path.join(sourcepath, '%s*.tar.gz' % pkg)
             pkg_tarball_paths = glob.glob(pkg_tarball_glob)
             if len(pkg_tarball_paths) > 1:
                 error("Multiple tarballs found for %s: %s" % (pkg, pkg_tarball_paths))
             elif len(pkg_tarball_paths) == 0:
-                if pkg != 'vsc-base':
+                if pkg != VSC_BASE:
+                    # vsc-base package is not strictly required
+                    # it's only a dependency since EasyBuild v2.0;
+                    # with EasyBuild v2.0, it will be pulled in from PyPI when installing easybuild-framework
                     error("Missing source tarball: %s" % pkg_tarball_glob)
             else:
-                info("Found %s" % pkg_tarball_paths[0])
-                source_tarballs.append(pkg_tarball_paths[0])
+                info("Found %s for %s package" % (pkg_tarball_paths[0], pkg))
+                source_tarballs.update({pkg: pkg_tarball_paths[0]})
 
     from setuptools.command import easy_install
 
@@ -261,9 +267,9 @@ def stage1(tmpdir, sources_path):
     cmd.append('--upgrade')  # make sure the latest version is pulled from PyPi
     cmd.append('--prefix=%s' % targetdir_stage1)
 
-    if sources_path:
-        # install provided source tarballs
-        cmd.extend(source_tarballs)
+    if source_tarballs:
+        # install provided source tarballs (order matters)
+        cmd.extend([source_tarballs[pkg] for pkg in EASYBUILD_PACKAGES if pkg in source_tarballs])
     else:
         # install meta-package easybuild from PyPI
         cmd.append('easybuild')
@@ -280,45 +286,36 @@ def stage1(tmpdir, sources_path):
     # template string to inject in template easyconfig
     templates = {}
 
-    pkg_egg_dir_framework = None
-    for pkg in ['vsc-base', 'easybuild-framework', 'easybuild-easyblocks', 'easybuild-easyconfigs']:
+    for pkg in EASYBUILD_PACKAGES:
         templates.update({pkg: ''})
 
         pkg_egg_dir = find_egg_dir_for(targetdir_stage1, pkg)
         if pkg_egg_dir is None:
-            if pkg == 'vsc-base':
+            if pkg == VSC_BASE:
                 # vsc-base is optional in older EasyBuild versions
                 continue
-            else:
-                error("Failed to determine egg dir path for %s in %s" % (pkg, targetdir_stage1))
 
         # prepend EasyBuild egg dirs to Python search path, so we know which EasyBuild we're using
         sys.path.insert(0, pkg_egg_dir)
         pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
         os.environ['PYTHONPATH'] = os.pathsep.join([pkg_egg_dir] + pythonpaths)
 
-        # determine per-package versions based on egg dirs
-        version_regex = re.compile('%s-([0-9a-z.-]*)-py[0-9.]*.egg' % pkg.replace('-', '_'))
-        pkg_egg_dirname = os.path.basename(pkg_egg_dir)
-        res = version_regex.search(pkg_egg_dirname)
-        if res is not None:
-            pkg_version = res.group(1)
-            debug("Found version for easybuild-%s: %s" % (pkg, pkg_version))
-            if sources_path is None:
-                # downloaded tarballs should be versioned
+        if source_tarballs:
+            if pkg in source_tarballs:
+                templates.update({pkg: "'%s'," % os.path.basename(source_tarballs[pkg])})
+        else:
+            # determine per-package versions based on egg dirs, to use them in easyconfig template
+            version_regex = re.compile('%s-([0-9a-z.-]*)-py[0-9.]*.egg' % pkg.replace('-', '_'))
+            pkg_egg_dirname = os.path.basename(pkg_egg_dir)
+            res = version_regex.search(pkg_egg_dirname)
+            if res is not None:
+                pkg_version = res.group(1)
+                debug("Found version for easybuild-%s: %s" % (pkg, pkg_version))
                 templates.update({pkg: "'%s-%s.tar.gz'," % (pkg, pkg_version)})
             else:
-                # names of specified source tarballs should not contain a version
-                templates.update({pkg: "'%s.tar.gz'," % pkg})
-        else:
-            # vsc-base is only required for EasyBuild v2.x or higher
-            if pkg != 'vsc-base':
                 tup = (pkg, pkg_egg_dirname, version_regex.pattern)
                 error("Failed to determine version for easybuild-%s package from %s with %s" % tup)
 
-        if pkg == 'framework':
-            pkg_egg_dir_framework = pkg_egg_dir
-
     # figure out EasyBuild version via eb command line
     # note: EasyBuild uses some magic to determine the EasyBuild version based on the versions of the individual packages
     pattern = "This is EasyBuild (?P<version>%(v)s) \(framework: %(v)s, easyblocks: %(v)s\)" % {'v': '[0-9.]*[a-z0-9]*'}
@@ -358,7 +355,7 @@ def stage1(tmpdir, sources_path):
     debug("templates: %s" % templates)
     return templates
 
-def stage2(tmpdir, templates, install_path, distribute_egg_dir, sources_path):
+def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
     """STAGE 2: install EasyBuild to temporary dir with EasyBuild from stage 1."""
 
     info("\n\n+++ STAGE 2: installing EasyBuild in %s with EasyBuild from stage 1...\n\n" % install_path)
@@ -371,7 +368,7 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sources_path):
     # create easyconfig file
     ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])
     f = open(ebfile, "w")
-    f.write(EB_EC_FILE % templates)
+    f.write(EASYBUILD_EASYCONFIG_TEMPLATE % templates)
     f.close()
 
     # unset $MODULEPATH, we don't care about already installed modules
@@ -395,8 +392,8 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sources_path):
         eb_args.append('--buildpath=%s' % tmpdir)
         if install_path is not None:
             eb_args.append('--installpath=%s' % install_path)
-        if sources_path is not None:
-            eb_args.append('--sourcepath=%s' % sources_path)
+        if sourcepath is not None:
+            eb_args.append('--sourcepath=%s' % sourcepath)
 
     # make sure parent modules path already exists (Lmod trips over a non-existing entry in $MODULEPATH)
     if install_path is not None:
@@ -425,9 +422,9 @@ def main():
         error("Usage: %s <install path>" % sys.argv[0])
     install_path = os.path.abspath(sys.argv[1])
 
-    sources_path = os.environ.get('EASYBUILD_BOOTSTRAP_TARBALLS')
-    if sources_path is not None:
-        info("Fetching sources from %s..." % sources_path)
+    sourcepath = os.environ.get('EASYBUILD_BOOTSTRAP_SOURCEPATH')
+    if sourcepath is not None:
+        info("Fetching sources from %s..." % sourcepath)
 
     skip_stage0 = os.environ.get('EASYBUILD_BOOTSTRAP_SKIP_STAGE0', False)
 
@@ -468,10 +465,10 @@ def main():
         distribute_egg_dir = stage0(tmpdir)
 
     # STAGE 1: install EasyBuild using easy_install to tmp dir
-    templates = stage1(tmpdir, sources_path)
+    templates = stage1(tmpdir, sourcepath)
 
     # STAGE 2: install EasyBuild using EasyBuild (to final target installation dir)
-    stage2(tmpdir, templates, install_path, distribute_egg_dir, sources_path)
+    stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath)
 
     # clean up the mess
     debug("Cleaning up %s..." % tmpdir)
@@ -497,7 +494,7 @@ def main():
     info("See http://easybuild.readthedocs.org/en/latest/Configuration.html for details on configuring EasyBuild.")
 
 # template easyconfig file for EasyBuild
-EB_EC_FILE = """
+EASYBUILD_EASYCONFIG_TEMPLATE = """
 easyblock = 'EB_EasyBuildMeta'
 
 name = 'EasyBuild'
@@ -510,11 +507,12 @@ def main():
 
 toolchain = {'name': 'dummy', 'version': 'dummy'}
 
+pypi_source_url = 'https://pypi.python.org/packages/source'
 source_urls = [
-    'https://pypi.python.org/packages/source/v/vsc-base/',
-    'https://pypi.python.org/packages/source/e/easybuild-framework/',
-    'https://pypi.python.org/packages/source/e/easybuild-easyblocks/',
-    'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/',
+    '%%s/v/vsc-base/' %% pypi_source_url,
+    '%%s/e/easybuild-framework/' %% pypi_source_url,
+    '%%s/e/easybuild-easyblocks/' %% pypi_source_url,
+    '%%s/e/easybuild-easyconfigs/' %% pypi_source_url,
 ]
 # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?)
 sources = [

From e277ccc8a172f43d9d1f5990ebf22081ccdf5614 Mon Sep 17 00:00:00 2001
From: "Forai,Petar" <petar.forai@imp.ac.at>
Date: Wed, 18 Feb 2015 22:45:32 +0100
Subject: [PATCH 0563/1356] Reintroduced  for Tcl modules, still rendering full
 path to devel module in Lua case.

---
 easybuild/framework/easyblock.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index f21a17b984..0aab2bf6be 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -845,12 +845,17 @@ def make_module_extra(self):
 
         # EBROOT + EBVERSION + EBDEVEL
         environment_name = convert_name(self.name, upper=True)
-        #todo this is only valid for Lua now
-        # This is a bit different in Lua due to string quoting rules in Lua and in Tcl - so $root cannot be used easily.
-        # so we resort to rendering our internal variables and quote them in the set_environment() like all other values.
-        txt += self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, self.installdir)
         txt += self.module_generator.set_environment(VERSION_ENV_VAR_NAME_PREFIX + environment_name, self.version)
-        devel_path = os.path.join(self.installdir, log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
+        
+        if self.module_generator.SYNTAX == 'Lua':
+            txt += self.module_generator.self_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, self.installdir)
+            devel_path = os.path.join(self.installdir, log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
+        elif self.module_generator.SYNTAX == 'Tcl':
+            txt += self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, "$root")
+            devel_path = os.path.join("$root", log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
+        else: 
+            raise NotImplementedError
+                                                
         txt += self.module_generator.set_environment(DEVEL_ENV_VAR_NAME_PREFIX + environment_name, devel_path)
 
         txt += "\n"

From eb98c1298966623ad29bb343928c141266e28f62 Mon Sep 17 00:00:00 2001
From: "Forai,Petar" <petar.forai@imp.ac.at>
Date: Wed, 18 Feb 2015 23:08:40 +0100
Subject: [PATCH 0564/1356] Removed the Keyword section of the Lua template, as
 module keyword is looking in the whatis section.

---
 easybuild/tools/module_generator.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 72685b7957..87d89eaa77 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -325,7 +325,6 @@ def get_description(self, conflict=True):
             "whatis([[Description: %(description)s]])",
             "whatis([[Homepage: %(homepage)s]])"
             "whatis([[License: N/A ]])",
-            "whatis([[Keywords: Not set]])",
             "",
             "",
             'pkg.root="%(installdir)s"',
@@ -415,13 +414,20 @@ def use(self, paths):
         return '\n'.join(use_statements)
 
     def set_environment(self, key, value):
-
         """
-        Generate setenv statement for the given key/value pair.
+        Generate a quoted setenv statement for the given key/value pair.
         """
-        # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
+        # setting of $EBDEVELFOO modulefile path in Tcl case uses string
+        # interpolation available in Tcl, but not in Lua. Ie
+        # setenv("FOO","pkg.root/somevar") where pkg.root and somevar are
+        # variables cant be used. 
         return 'setenv("%s", %s)\n' % (key, quote_str(value))
 
+    def set_environment_unquoted(self, key, unquotedvalue):
+        """ Generate an unquoted setenv statement for the given key/value pair.
+        """
+        return 'setenv("%s",%s)\n' % (key, unquotedvalue))
+
     def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.

From 9361d63b4dff62b1fef83e573df58fb988996338 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 19 Feb 2015 10:17:40 +0100
Subject: [PATCH 0565/1356] disable updating of Lmod cache by default

---
 easybuild/framework/easyblock.py |  5 +++-
 easybuild/tools/config.py        |  1 +
 easybuild/tools/modules.py       | 47 +++++++++++++++++---------------
 easybuild/tools/options.py       |  6 ++--
 test/framework/modulestool.py    |  1 +
 5 files changed, 35 insertions(+), 25 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index a5decf677b..4bb5cbce3e 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1652,7 +1652,10 @@ def make_module_step(self, fake=False):
 
         self.log.info("Module file %s written" % self.module_generator.filename)
 
-        self.modules_tool.update()
+         # only update after generating final module file
+        if not fake:
+            self.modules_tool.update()
+
         self.module_generator.create_symlinks()
 
         if not fake:
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 60af87d556..278791512f 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -111,6 +111,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'skip_test_cases',
         'sticky_bit',
         'upload_test_report',
+        'update_modules_tool_cache',
     ],
     True: [
         'cleanup_builddir',
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 36f412a9bc..90be795902 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -63,6 +63,8 @@
 # see e.g., https://bugzilla.redhat.com/show_bug.cgi?id=719785
 LD_LIBRARY_PATH = os.getenv('LD_LIBRARY_PATH', '')
 
+LMOD_USER_CACHE_DIR = os.path.join(os.path.expanduser('~'), '.lmod.d', '.cache')
+
 output_matchers = {
     # matches whitespace and module-listing headers
     'whitespace': re.compile(r"^\s*$|^(-+).*(-+)$"),
@@ -833,31 +835,32 @@ def available(self, mod_name=None):
 
     def update(self):
         """Update after new modules were added."""
-        spider_cmd = os.path.join(os.path.dirname(self.cmd), 'spider')
-        cmd = [spider_cmd, '-o', 'moduleT', os.environ['MODULEPATH']]
-        self.log.debug("Running command '%s'..." % ' '.join(cmd))
+        if build_option('update_modules_tool_cache'):
+            spider_cmd = os.path.join(os.path.dirname(self.cmd), 'spider')
+            cmd = [spider_cmd, '-o', 'moduleT', os.environ['MODULEPATH']]
+            self.log.debug("Running command '%s'..." % ' '.join(cmd))
 
-        proc = subprocess.Popen(cmd, stdout=PIPE, stderr=PIPE, env=os.environ)
-        (stdout, stderr) = proc.communicate()
+            proc = subprocess.Popen(cmd, stdout=PIPE, stderr=PIPE, env=os.environ)
+            (stdout, stderr) = proc.communicate()
 
-        if stderr:
-            self.log.error("An error occured when running '%s': %s" % (' '.join(cmd), stderr))
+            if stderr:
+                self.log.error("An error occured when running '%s': %s" % (' '.join(cmd), stderr))
 
-        if self.testing:
-            # don't actually update local cache when testing, just return the cache contents
-            return stdout
-        else:
-            try:
-                cache_filefn = os.path.join(os.path.expanduser('~'), '.lmod.d', '.cache', 'moduleT.lua')
-                self.log.debug("Updating Lmod spider cache %s with output from '%s'" % (cache_filefn, ' '.join(cmd)))
-                cache_dir = os.path.dirname(cache_filefn)
-                if not os.path.exists(cache_dir):
-                    mkdir(cache_dir, parents=True)
-                cache_file = open(cache_filefn, 'w')
-                cache_file.write(stdout)
-                cache_file.close()
-            except (IOError, OSError), err:
-                self.log.error("Failed to update Lmod spider cache %s: %s" % (cache_filefn, err))
+            if self.testing:
+                # don't actually update local cache when testing, just return the cache contents
+                return stdout
+            else:
+                try:
+                    cache_fp = os.path.join(LMOD_USER_CACHE_DIR, 'moduleT.lua')
+                    self.log.debug("Updating Lmod spider cache %s with output from '%s'" % (cache_fp, ' '.join(cmd)))
+                    cache_dir = os.path.dirname(cache_fp)
+                    if not os.path.exists(cache_dir):
+                        mkdir(cache_dir, parents=True)
+                    cache_file = open(cache_fp, 'w')
+                    cache_file.write(stdout)
+                    cache_file.close()
+                except (IOError, OSError), err:
+                    self.log.error("Failed to update Lmod spider cache %s: %s" % (cache_fp, err))
 
     def prepend_module_path(self, path):
         # Lmod pushes a path to the front on 'module use'
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 80fd4db664..2cac7660c9 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -192,6 +192,8 @@ def override_options(self):
                             str, 'extend', None),
             'oldstyleconfig':   ("Look for and use the oldstyle configuration file.",
                                  None, 'store_true', True),
+            'optarch': ("Set architecture optimization, overriding native architecture optimizations",
+                        None, 'store', None),
             'pretend': (("Does the build/installation in a test directory located in $HOME/easybuildinstall"),
                          None, 'store_true', False, 'p'),
             'set-gid-bit': ("Set group ID bit on newly created directories", None, 'store_true', False),
@@ -199,8 +201,8 @@ def override_options(self):
             'skip-test-cases': ("Skip running test cases", None, 'store_true', False, 't'),
             'umask': ("umask to use (e.g. '022'); non-user write permissions on install directories are removed",
                       None, 'store', None),
-            'optarch': ("Set architecture optimization, overriding native architecture optimizations",
-                        None, 'store', None),
+            'update-modules-tool-cache': ("Update modules tool cache file(s) after generating module file",
+                                          None, 'store_true', False),
         })
 
         self.log.debug("override_options: descr %s opts %s" % (descr, opts))
diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index 5b92f8822a..333ef8fd1f 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -156,6 +156,7 @@ def test_lmod_specific(self):
         if lmod_abspath is not None:
             build_options = {
                 'allow_modules_tool_mismatch': True,
+                'update_modules_tool_cache': True,
             }
             init_config(build_options=build_options)
 

From ecdf327d2c0674dbc1d9482f3e6623997ab8b7f5 Mon Sep 17 00:00:00 2001
From: "Forai,Petar" <petar.forai@imp.ac.at>
Date: Thu, 19 Feb 2015 14:19:46 +0100
Subject: [PATCH 0566/1356] Removed a typo and changed the regex for  matching
 in the test.

---
 easybuild/framework/easyblock.py    | 3 +--
 easybuild/tools/module_generator.py | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 0aab2bf6be..333605f9a7 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -845,7 +845,6 @@ def make_module_extra(self):
 
         # EBROOT + EBVERSION + EBDEVEL
         environment_name = convert_name(self.name, upper=True)
-        txt += self.module_generator.set_environment(VERSION_ENV_VAR_NAME_PREFIX + environment_name, self.version)
         
         if self.module_generator.SYNTAX == 'Lua':
             txt += self.module_generator.self_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, self.installdir)
@@ -855,7 +854,7 @@ def make_module_extra(self):
             devel_path = os.path.join("$root", log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
         else: 
             raise NotImplementedError
-                                                
+        txt += self.module_generator.set_environment(VERSION_ENV_VAR_NAME_PREFIX + environment_name, self.version)
         txt += self.module_generator.set_environment(DEVEL_ENV_VAR_NAME_PREFIX + environment_name, devel_path)
 
         txt += "\n"
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 87d89eaa77..fef1a54eb6 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -426,7 +426,7 @@ def set_environment(self, key, value):
     def set_environment_unquoted(self, key, unquotedvalue):
         """ Generate an unquoted setenv statement for the given key/value pair.
         """
-        return 'setenv("%s",%s)\n' % (key, unquotedvalue))
+        return 'setenv("%s",%s)\n' % (key, unquotedvalue)
 
     def msg_on_load(self, msg):
         """

From 8ab7ef9e4a7eecaca00157a4083f8022a715ee1c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 19 Feb 2015 20:58:47 +0100
Subject: [PATCH 0567/1356] fix regex by including re.M in re.compile

---
 test/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 2e042e24b2..b61f95026a 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -309,7 +309,7 @@ def test_make_module_step(self):
         self.assertTrue(re.search("^#%Module", txt.split('\n')[0]))
         self.assertTrue(re.search("^conflict\s+%s$" % name, txt, re.M))
         self.assertTrue(re.search("^set\s+root\s+%s$" % eb.installdir, txt, re.M))
-        ebroot_regex = re.compile('^setenv\s+EBROOT%s\s+".root"\s*$' % name.upper())
+        ebroot_regex = re.compile('^setenv\s+EBROOT%s\s+".root"\s*$' % name.upper(), re.M)
         self.assertTrue(ebroot_regex.search(txt, re.M), "%s in %s" % (ebroot_regex.pattern, txt))
         self.assertTrue(re.search('^setenv\s+EBVERSION%s\s+"%s"$' % (name.upper(), version), txt, re.M))
         for (key, val) in modextravars.items():

From 6ef7de777536dbcd8d9f09170e139aa1521be2c0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 19 Feb 2015 21:01:46 +0100
Subject: [PATCH 0568/1356] remove futile re.M

---
 test/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index b61f95026a..9c0aed359a 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -310,7 +310,7 @@ def test_make_module_step(self):
         self.assertTrue(re.search("^conflict\s+%s$" % name, txt, re.M))
         self.assertTrue(re.search("^set\s+root\s+%s$" % eb.installdir, txt, re.M))
         ebroot_regex = re.compile('^setenv\s+EBROOT%s\s+".root"\s*$' % name.upper(), re.M)
-        self.assertTrue(ebroot_regex.search(txt, re.M), "%s in %s" % (ebroot_regex.pattern, txt))
+        self.assertTrue(ebroot_regex.search(txt), "%s in %s" % (ebroot_regex.pattern, txt))
         self.assertTrue(re.search('^setenv\s+EBVERSION%s\s+"%s"$' % (name.upper(), version), txt, re.M))
         for (key, val) in modextravars.items():
             regex = re.compile('^setenv\s+%s\s+"%s"$' % (key, val), re.M)

From 0979fdafb5864b3b905110c98831811645031ff9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 16:01:25 +0100
Subject: [PATCH 0569/1356] fix small issues in cmdline options, add
 dump_cfgfile_using_defaults function in options.py

---
 easybuild/tools/options.py | 82 ++++++++++++++++++++++++++++++++++++--
 1 file changed, 79 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 3ac38024f3..550e6c6e53 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -33,6 +33,7 @@
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
 """
+import copy
 import glob
 import os
 import re
@@ -66,6 +67,8 @@
 from vsc.utils.generaloption import GeneralOption
 
 
+CONFIG_ENV_VAR_PREFIX = 'EASYBUILD'
+
 XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
 XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', '/etc').split(os.pathsep)
 DEFAULT_SYSTEM_CONFIGFILES = [f for d in XDG_CONFIG_DIRS for f in glob.glob(os.path.join(d, 'easybuild.d', '*.cfg'))]
@@ -182,7 +185,7 @@ def override_options(self):
             'cleanup-builddir': ("Cleanup build dir after successful installation.", None, 'store_true', True),
             'deprecated': ("Run pretending to be (future) version, to test removal of deprecated code.",
                            None, 'store', None),
-            'download_timeout': ("Timeout for initiating downloads (in seconds)", None, 'store', None),
+            'download-timeout': ("Timeout for initiating downloads (in seconds)", None, 'store', None),
             'easyblock': ("easyblock to use for processing the spec file or dumping the options",
                           None, 'store', None, 'e', {'metavar': 'CLASS'}),
             'experimental': ("Allow experimental code (with behaviour that can be changed/removed at any given time).",
@@ -315,7 +318,7 @@ def regtest_options(self):
                                    None, 'store', None, {'metavar': 'DIR'}),
             'sequential': ("Specify this option if you want to prevent parallel build",
                            None, 'store_true', False),
-            'upload-test-report': ("Upload full test report as a gist on GitHub", None, 'store_true', None),
+            'upload-test-report': ("Upload full test report as a gist on GitHub", None, 'store_true', False),
             'test-report-env-filter': ("Regex used to filter out variables in environment dump of test report",
                                        None, 'regex', None),
         })
@@ -638,10 +641,83 @@ def parse_options(args=None):
     description = ("Builds software based on easyconfig (or parse a directory).\n"
                    "Provide one or more easyconfigs or directories, use -H or --help more information.")
 
-    eb_go = EasyBuildOptions(usage=usage, description=description, prog='eb', envvar_prefix='EASYBUILD', go_args=args)
+    eb_go = EasyBuildOptions(usage=usage, description=description, prog='eb', envvar_prefix=CONFIG_ENV_VAR_PREFIX,
+                             go_args=args)
     return eb_go
 
 
+def dump_cfgfile_using_defaults():
+    """Dump contents of configuration file with default values for all configuration options."""
+    default_cfg_txt = []
+    logger = fancylogger.getLogger()
+
+    # copy original environment to restore it later
+    orig_environ = copy.deepcopy(os.environ)
+
+    # clean up environment from unwanted $EASYBUILD_X env vars
+    for key in os.environ.keys():
+        if key.startswith('%s_' % CONFIG_ENV_VAR_PREFIX):
+            logger.debug("Undefining $%s (value: %s)" % (key, os.environ[key]))
+            del os.environ[key]
+
+    # configure while ignoring any configuration files
+    # this should provide us with the default configuration, since the environment is clean too
+    go = EasyBuildOptions(go_useconfigfiles=False)
+
+    for group in go.parser.option_groups:
+        # only consider section with a name of type 'string'
+        if isinstance(group.section_name, basestring):
+            # determine option name prefix for this group, so we can use the correct option name
+            group_prefix = None
+            if group.section_name in go.config_prefix_sectionnames_map:
+                group_prefix = group.section_name
+            logger.debug("Group prefix for group %s: %s" % (group.section_name, group_prefix))
+
+            # include section indicator
+            default_cfg_txt.append('[%s]' % group.section_name)
+
+            for opt in group.option_list:
+                # option correct option name from option destination
+                key = opt.dest.replace('_', '-')
+                # determine default value for this option by looking at current value in parsed options
+                default = getattr(go.options, opt.dest)
+
+                # correct key if there's a group prefix set
+                if group_prefix is not None:
+                    key = key[len(group_prefix)+1:]
+
+                # correct formatting of list/tuple values
+                if isinstance(default, (tuple, list)):
+                    default = ','.join(default)
+
+                # escape use of '%' in values
+                if isinstance(default, basestring):
+                    default = default.replace('%', '%%')
+
+                # uncomment options which are set to None as default
+                # resetting values to None doesn't work (yet)
+                if default is None:
+                    # resetting values to None only works with Python 2.7, just uncomment them otherwise
+                    if LooseVersion(sys.version) >= LooseVersion('2.7'):
+                        entry = '%s' % key
+                    else:
+                        entry = '#%s' % key
+                else:
+                    entry = '%s = %s' % (key, default)
+
+                default_cfg_txt.append(entry)
+        else:
+            logger.debug("Skipping section with name %s" % str(group.section_name))
+
+    # restore original environment
+    logger.debug("Restoring original environment")
+    os.environ = orig_environ
+
+    res = '\n'.join(default_cfg_txt)
+    logger.debug("Configuration file with default values for all options: %s" % res)
+    return res
+
+
 def process_software_build_specs(options):
     """
     Create a dictionary with specified software build options.

From 8a0d85550826cf1e9eea6e623e0ad9cb575d030d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 16:10:05 +0100
Subject: [PATCH 0570/1356] isolate tests from non-default configuration by
 using configuration file with all options set to default

---
 test/framework/options.py   | 22 ++++++++++++----------
 test/framework/utilities.py | 36 +++++++++++++++++++++++++++++++++++-
 2 files changed, 47 insertions(+), 11 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index edb8bef11e..68a69589d7 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -644,6 +644,7 @@ def test_dry_run_short(self):
         test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         shutil.copytree(test_ecs_dir, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
 
+        del os.environ['EASYBUILD_CONFIGFILES']
         orig_sys_path = sys.path[:]
         sys.path.insert(0, tmpdir)  # prepend to give it preference over possible other installed easyconfigs pkgs
 
@@ -1456,14 +1457,6 @@ def test_robot(self):
         mkdir(os.path.join(tmpdir, 'easybuild'), parents=True)
         shutil.copytree(test_ecs_path, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
 
-        # prepend path to test easyconfigs into Python search path, so it gets picked up as --robot-paths default
-        orig_sys_path = sys.path[:]
-        sys.path.insert(0, tmpdir)
-        self.eb_main(args, raise_error=True)
-
-        shutil.rmtree(tmpdir)
-        sys.path[:] = orig_sys_path
-
         # make sure that paths specified to --robot get preference over --robot-paths
         args = [
             eb_file,
@@ -1473,10 +1466,19 @@ def test_robot(self):
         ]
         outtxt = self.eb_main(args, raise_error=True)
 
-        for ec in ['GCC-4.6.3.eb', 'ictce-4.1.13.eb', 'toy-0.0-deps.eb', 'gzip-1.4-GCC-4.6.3.eb']:
-            ec_regex = re.compile('^\s\*\s\[[xF ]\]\s%s' % os.path.join(test_ecs_path, ec), re.M)
+        for ecfile in ['GCC-4.6.3.eb', 'ictce-4.1.13.eb', 'toy-0.0-deps.eb', 'gzip-1.4-GCC-4.6.3.eb']:
+            ec_regex = re.compile(r'^\s\*\s\[[xF ]\]\s%s' % os.path.join(test_ecs_path, ecfile), re.M)
             self.assertTrue(ec_regex.search(outtxt), "Pattern %s found in %s" % (ec_regex.pattern, outtxt))
 
+        # prepend path to test easyconfigs into Python search path, so it gets picked up as --robot-paths default
+        del os.environ['EASYBUILD_CONFIGFILES']
+        orig_sys_path = sys.path[:]
+        sys.path.insert(0, tmpdir)
+        self.eb_main(args, raise_error=True)
+
+        shutil.rmtree(tmpdir)
+        sys.path[:] = orig_sys_path
+
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 272984373b..20b3fce049 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -51,6 +51,40 @@
 from easybuild.tools.filetools import mkdir, read_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.modules import modules_tool
+from easybuild.tools.options import dump_cfgfile_using_defaults
+
+
+# make sure tests are robust against any non-default configuration settings;
+# involves ignoring any existing configuration files that are picked up, and cleaning the environment
+# this is tackled here rather than in suite.py, to make sure this is also done when test modules are ran separately
+
+# keep track of any $EASYBUILD_TEST_X environment variables
+test_env_var_prefix = 'EASYBUILD_TEST_'
+eb_test_env_vars = dict([(key, val) for (key, val) in os.environ.items() if key.startswith(test_env_var_prefix)])
+print "eb_test_env_vars: %s" % eb_test_env_vars
+
+# clean up environment from unwanted $EASYBUILD_X env vars
+for key in os.environ.keys():
+    if key.startswith('EASYBUILD_'):
+        print "Undefining $%s (value: %s)" % (key, os.environ[key])
+        del os.environ[key]
+
+# dump configuration file with default values for all options
+default_cfg_txt = dump_cfgfile_using_defaults()
+
+# put configuration file with default configuration settings in place
+TOP_TMPDIR = tempfile.mkdtemp()
+default_cfgfile = os.path.join(TOP_TMPDIR, 'default.cfg')
+fh = open(default_cfgfile, 'w')
+fh.write(default_cfg_txt)
+fh.close()
+os.environ['EASYBUILD_CONFIGFILES'] = default_cfgfile
+
+# redefine $EASYBUILD_TEST_X env vars as $EASYBUILD_X
+for testkey, val in eb_test_env_vars.items():
+    key = 'EASYBUILD_%s' % testkey[len(test_env_var_prefix):]
+    print "redefining $%s as $%s = '%s'" % (testkey, key, val)
+    os.environ[key] = val
 
 
 class EnhancedTestCase(TestCase):
@@ -85,6 +119,7 @@ def setUp(self):
         fd, self.logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')
         os.close(fd)
         self.cwd = os.getcwd()
+        self.test_prefix = tempfile.mkdtemp()
 
         # keep track of original environment to restore
         self.orig_environ = copy.deepcopy(os.environ)
@@ -100,7 +135,6 @@ def setUp(self):
 
         self.test_sourcepath = os.path.join(testdir, 'sandbox', 'sources')
         os.environ['EASYBUILD_SOURCEPATH'] = self.test_sourcepath
-        self.test_prefix = tempfile.mkdtemp()
         os.environ['EASYBUILD_PREFIX'] = self.test_prefix
         self.test_buildpath = tempfile.mkdtemp()
         os.environ['EASYBUILD_BUILDPATH'] = self.test_buildpath

From 9301b35766efdea50b770d5e8990c517f6341ab6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 16:59:26 +0100
Subject: [PATCH 0571/1356] fix issues in github unit tests

---
 test/framework/github.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/test/framework/github.py b/test/framework/github.py
index 001ab22818..b8c4d635eb 100644
--- a/test/framework/github.py
+++ b/test/framework/github.py
@@ -55,12 +55,11 @@ class GithubTest(EnhancedTestCase):
     def setUp(self):
         """setup"""
         super(GithubTest, self).setUp()
-        github_user = GITHUB_TEST_ACCOUNT
-        self.github_token = fetch_github_token(github_user)
+        self.github_token = fetch_github_token(GITHUB_TEST_ACCOUNT)
         if self.github_token is None:
             self.ghfs = None
         else:
-            self.ghfs = Githubfs(GITHUB_USER, GITHUB_REPO, GITHUB_BRANCH, github_user, None, github_token)
+            self.ghfs = Githubfs(GITHUB_USER, GITHUB_REPO, GITHUB_BRANCH, GITHUB_TEST_ACCOUNT, None, self.github_token)
 
     def test_walk(self):
         """test the gitubfs walk function"""
@@ -78,7 +77,7 @@ def test_walk(self):
 
     def test_read_api(self):
         """Test the githubfs read function"""
-        if self.github_token is not None:
+        if self.github_token is None:
             print "Skipping test_read_api, no GitHub token available?"
             return
 

From 48de142afdfe89b3debe6240f5ac70a14978c672 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 17:00:33 +0100
Subject: [PATCH 0572/1356] use $EASYBUILD_IGNORECONFIGFILES to ignore any
 existing EB cfg files, remove unused dump_cfgfile_using_defaults

---
 easybuild/tools/options.py  | 73 -------------------------------------
 test/framework/utilities.py | 15 ++------
 2 files changed, 4 insertions(+), 84 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 550e6c6e53..dcdd40ffb6 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -33,7 +33,6 @@
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
 """
-import copy
 import glob
 import os
 import re
@@ -646,78 +645,6 @@ def parse_options(args=None):
     return eb_go
 
 
-def dump_cfgfile_using_defaults():
-    """Dump contents of configuration file with default values for all configuration options."""
-    default_cfg_txt = []
-    logger = fancylogger.getLogger()
-
-    # copy original environment to restore it later
-    orig_environ = copy.deepcopy(os.environ)
-
-    # clean up environment from unwanted $EASYBUILD_X env vars
-    for key in os.environ.keys():
-        if key.startswith('%s_' % CONFIG_ENV_VAR_PREFIX):
-            logger.debug("Undefining $%s (value: %s)" % (key, os.environ[key]))
-            del os.environ[key]
-
-    # configure while ignoring any configuration files
-    # this should provide us with the default configuration, since the environment is clean too
-    go = EasyBuildOptions(go_useconfigfiles=False)
-
-    for group in go.parser.option_groups:
-        # only consider section with a name of type 'string'
-        if isinstance(group.section_name, basestring):
-            # determine option name prefix for this group, so we can use the correct option name
-            group_prefix = None
-            if group.section_name in go.config_prefix_sectionnames_map:
-                group_prefix = group.section_name
-            logger.debug("Group prefix for group %s: %s" % (group.section_name, group_prefix))
-
-            # include section indicator
-            default_cfg_txt.append('[%s]' % group.section_name)
-
-            for opt in group.option_list:
-                # option correct option name from option destination
-                key = opt.dest.replace('_', '-')
-                # determine default value for this option by looking at current value in parsed options
-                default = getattr(go.options, opt.dest)
-
-                # correct key if there's a group prefix set
-                if group_prefix is not None:
-                    key = key[len(group_prefix)+1:]
-
-                # correct formatting of list/tuple values
-                if isinstance(default, (tuple, list)):
-                    default = ','.join(default)
-
-                # escape use of '%' in values
-                if isinstance(default, basestring):
-                    default = default.replace('%', '%%')
-
-                # uncomment options which are set to None as default
-                # resetting values to None doesn't work (yet)
-                if default is None:
-                    # resetting values to None only works with Python 2.7, just uncomment them otherwise
-                    if LooseVersion(sys.version) >= LooseVersion('2.7'):
-                        entry = '%s' % key
-                    else:
-                        entry = '#%s' % key
-                else:
-                    entry = '%s = %s' % (key, default)
-
-                default_cfg_txt.append(entry)
-        else:
-            logger.debug("Skipping section with name %s" % str(group.section_name))
-
-    # restore original environment
-    logger.debug("Restoring original environment")
-    os.environ = orig_environ
-
-    res = '\n'.join(default_cfg_txt)
-    logger.debug("Configuration file with default values for all options: %s" % res)
-    return res
-
-
 def process_software_build_specs(options):
     """
     Create a dictionary with specified software build options.
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 20b3fce049..2be26dc34c 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -51,7 +51,7 @@
 from easybuild.tools.filetools import mkdir, read_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.modules import modules_tool
-from easybuild.tools.options import dump_cfgfile_using_defaults
+from easybuild.tools.options import EasyBuildOptions
 
 
 # make sure tests are robust against any non-default configuration settings;
@@ -69,16 +69,9 @@
         print "Undefining $%s (value: %s)" % (key, os.environ[key])
         del os.environ[key]
 
-# dump configuration file with default values for all options
-default_cfg_txt = dump_cfgfile_using_defaults()
-
-# put configuration file with default configuration settings in place
-TOP_TMPDIR = tempfile.mkdtemp()
-default_cfgfile = os.path.join(TOP_TMPDIR, 'default.cfg')
-fh = open(default_cfgfile, 'w')
-fh.write(default_cfg_txt)
-fh.close()
-os.environ['EASYBUILD_CONFIGFILES'] = default_cfgfile
+# ignore any existing configuration files
+go = EasyBuildOptions(go_useconfigfiles=False)
+os.environ['EASYBUILD_IGNORECONFIGFILES'] = ','.join(go.options.configfiles)
 
 # redefine $EASYBUILD_TEST_X env vars as $EASYBUILD_X
 for testkey, val in eb_test_env_vars.items():

From cb89dfd3b260e042f7d7da020da66ef849959588 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 17:02:47 +0100
Subject: [PATCH 0573/1356] revert changes made in options.py tests

---
 test/framework/options.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 68a69589d7..e919176df0 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -644,7 +644,6 @@ def test_dry_run_short(self):
         test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         shutil.copytree(test_ecs_dir, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
 
-        del os.environ['EASYBUILD_CONFIGFILES']
         orig_sys_path = sys.path[:]
         sys.path.insert(0, tmpdir)  # prepend to give it preference over possible other installed easyconfigs pkgs
 
@@ -1457,6 +1456,14 @@ def test_robot(self):
         mkdir(os.path.join(tmpdir, 'easybuild'), parents=True)
         shutil.copytree(test_ecs_path, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
 
+        # prepend path to test easyconfigs into Python search path, so it gets picked up as --robot-paths default
+        orig_sys_path = sys.path[:]
+        sys.path.insert(0, tmpdir)
+        self.eb_main(args, raise_error=True)
+
+        shutil.rmtree(tmpdir)
+        sys.path[:] = orig_sys_path
+
         # make sure that paths specified to --robot get preference over --robot-paths
         args = [
             eb_file,
@@ -1470,15 +1477,6 @@ def test_robot(self):
             ec_regex = re.compile(r'^\s\*\s\[[xF ]\]\s%s' % os.path.join(test_ecs_path, ecfile), re.M)
             self.assertTrue(ec_regex.search(outtxt), "Pattern %s found in %s" % (ec_regex.pattern, outtxt))
 
-        # prepend path to test easyconfigs into Python search path, so it gets picked up as --robot-paths default
-        del os.environ['EASYBUILD_CONFIGFILES']
-        orig_sys_path = sys.path[:]
-        sys.path.insert(0, tmpdir)
-        self.eb_main(args, raise_error=True)
-
-        shutil.rmtree(tmpdir)
-        sys.path[:] = orig_sys_path
-
 
 def suite():
     """ returns all the testcases in this module """

From 3638748644527e98b7e35577cf159e4c3ce6ef6b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 17:16:45 +0100
Subject: [PATCH 0574/1356] re-add parallelbuild unit test(s), and fix the
 broken one

---
 test/framework/parallelbuild.py | 3 ++-
 test/framework/suite.py         | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 637d56061e..7b1bdde306 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -72,6 +72,7 @@ def setUp(self):
         build_options = {
             'robot_path': os.path.join(os.path.dirname(__file__), 'easyconfigs'),
             'valid_module_classes': config.module_classes(),
+            'validate': False,
         }
         init_config(build_options=build_options)
 
@@ -84,7 +85,7 @@ def setUp(self):
     def test_build_easyconfigs_in_parallel(self):
         """Basic test for build_easyconfigs_in_parallel function."""
         easyconfig_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'gzip-1.5-goolf-1.4.10.eb')
-        easyconfigs = process_easyconfig(easyconfig_file, validate=False)
+        easyconfigs = process_easyconfig(easyconfig_file)
         ordered_ecs = resolve_dependencies(easyconfigs)
         build_easyconfigs_in_parallel("echo %(spec)s", ordered_ecs)
 
diff --git a/test/framework/suite.py b/test/framework/suite.py
index 027e6c6e1e..fa8538fd51 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -39,7 +39,7 @@
 import unittest
 from vsc.utils import fancylogger
 
-# set plain text key ring to be used, so a GitHub token stored in it can be obtained with having to provide a password
+# set plain text key ring to be used, so a GitHub token stored in it can be obtained without having to provide a password
 keyring.set_keyring(keyring.backends.file.PlaintextKeyring())
 
 # disable all logging to significantly speed up tests
@@ -100,7 +100,7 @@
 
 # call suite() for each module and then run them all
 # note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
-tests = [o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw]
+tests = [o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p]
 
 SUITE = unittest.TestSuite([x.suite() for x in tests])
 

From 12927eeef31e3b25abbce141c441a15f9e4d3ae6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 17:17:08 +0100
Subject: [PATCH 0575/1356] remove print statements in test utilities module

---
 test/framework/utilities.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 2be26dc34c..913810232e 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -61,12 +61,10 @@
 # keep track of any $EASYBUILD_TEST_X environment variables
 test_env_var_prefix = 'EASYBUILD_TEST_'
 eb_test_env_vars = dict([(key, val) for (key, val) in os.environ.items() if key.startswith(test_env_var_prefix)])
-print "eb_test_env_vars: %s" % eb_test_env_vars
 
 # clean up environment from unwanted $EASYBUILD_X env vars
 for key in os.environ.keys():
     if key.startswith('EASYBUILD_'):
-        print "Undefining $%s (value: %s)" % (key, os.environ[key])
         del os.environ[key]
 
 # ignore any existing configuration files
@@ -76,7 +74,6 @@
 # redefine $EASYBUILD_TEST_X env vars as $EASYBUILD_X
 for testkey, val in eb_test_env_vars.items():
     key = 'EASYBUILD_%s' % testkey[len(test_env_var_prefix):]
-    print "redefining $%s as $%s = '%s'" % (testkey, key, val)
     os.environ[key] = val
 
 

From 95843a00f2d37450420661e0156a063b34b0337e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 17:35:18 +0100
Subject: [PATCH 0576/1356] fix remark w.r.t. source_urls/sources in easyconfig
 template in bootstrap script

---
 easybuild/scripts/bootstrap_eb.py | 22 ++++++++--------------
 1 file changed, 8 insertions(+), 14 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 478563b1aa..9cfb05c6c6 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -50,6 +50,8 @@
 import tempfile
 from distutils.version import LooseVersion
 
+PYPI_SOURCE_URL = 'https://pypi.python.org/packages/source'
+
 VSC_BASE = 'vsc-base'
 EASYBUILD_PACKAGES = [VSC_BASE, 'easybuild-framework', 'easybuild-easyblocks', 'easybuild-easyconfigs']
 
@@ -368,6 +370,10 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
     # create easyconfig file
     ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])
     f = open(ebfile, "w")
+    templates.update({
+        'source_urls': '\n'.join(["'%s/%s/%s'," % (PYPI_SOURCE_URL, pkg[0], pkg) for pkg in EASYBUILD_PACKAGES]),
+        'sources': "%(vsc-base)s%(easybuild-framework)s%(easybuild-easyblocks)s%(easybuild-easyconfigs)s" % templates,
+    })
     f.write(EASYBUILD_EASYCONFIG_TEMPLATE % templates)
     f.close()
 
@@ -507,20 +513,8 @@ def main():
 
 toolchain = {'name': 'dummy', 'version': 'dummy'}
 
-pypi_source_url = 'https://pypi.python.org/packages/source'
-source_urls = [
-    '%%s/v/vsc-base/' %% pypi_source_url,
-    '%%s/e/easybuild-framework/' %% pypi_source_url,
-    '%%s/e/easybuild-easyblocks/' %% pypi_source_url,
-    '%%s/e/easybuild-easyconfigs/' %% pypi_source_url,
-]
-# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?)
-sources = [
-    %(vsc-base)s
-    %(easybuild-framework)s
-    %(easybuild-easyblocks)s
-    %(easybuild-easyconfigs)s
-]
+source_urls = [%(source_urls)s]
+sources = [%(sources)s]
 
 # EasyBuild is a (set of) Python packages, so it depends on Python
 # usually, we want to use the system Python, so no actual Python dependency is listed

From 3d5794a0d7e70ecfc28d798231af9f7bf2095aae Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 20:15:48 +0100
Subject: [PATCH 0577/1356] bump vsc-base dep version

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 08ee69b456..9fde7b7d1a 100644
--- a/setup.py
+++ b/setup.py
@@ -106,5 +106,5 @@ def find_rel_test():
     provides=["eb"] + easybuild_packages,
     test_suite="test.framework.suite",
     zip_safe=False,
-    install_requires=["vsc-base >= 2.0.0"],
+    install_requires=["vsc-base >= 2.0.2"],
 )

From 962e47c610a94eff252e65a25b8cd1dcf367c399 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 22:12:57 +0100
Subject: [PATCH 0578/1356] fix test for build_easyconfigs_in_parallel, avoid
 that it downloads sources

---
 easybuild/tools/parallelbuild.py | 7 ++++---
 test/framework/parallelbuild.py  | 3 ++-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index f71de69a5f..18bca84e48 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -50,7 +50,7 @@
 _log = fancylogger.getLogger('parallelbuild', fname=False)
 
 
-def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
+def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None, prepare_first=True):
     """
     easyconfigs is a list of easyconfigs which can be built (e.g. they have no unresolved dependencies)
     this function will build them in parallel by submitting jobs
@@ -79,10 +79,11 @@ def tokey(dep):
         return ActiveMNS().det_full_module_name(dep)
 
     for ec in easyconfigs:
-        # This is very important, otherwise we might have race conditions
+        # this is very important, otherwise we might have race conditions
         # e.g. GCC-4.5.3 finds cloog.tar.gz but it was incorrectly downloaded by GCC-4.6.3
         # running this step here, prevents this
-        prepare_easyconfig(ec)
+        if prepare_first:
+            prepare_easyconfig(ec)
 
         # the new job will only depend on already submitted jobs
         _log.info("creating job for ec: %s" % str(ec))
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 7b1bdde306..27635e0c6f 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -87,7 +87,8 @@ def test_build_easyconfigs_in_parallel(self):
         easyconfig_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'gzip-1.5-goolf-1.4.10.eb')
         easyconfigs = process_easyconfig(easyconfig_file)
         ordered_ecs = resolve_dependencies(easyconfigs)
-        build_easyconfigs_in_parallel("echo %(spec)s", ordered_ecs)
+        jobs = build_easyconfigs_in_parallel("echo %(spec)s", ordered_ecs, prepare_first=False)
+        self.assertEqual(len(jobs), 8)
 
 def suite():
     """ returns all the testcases in this module """

From 3869d27b80239009e8aadba88478832cf55787b5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 22:52:01 +0100
Subject: [PATCH 0579/1356] make test_fetch_easyconfigs_from_pr robust against
 offline testing

---
 test/framework/github.py | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/test/framework/github.py b/test/framework/github.py
index b8c4d635eb..fb6cdbecb2 100644
--- a/test/framework/github.py
+++ b/test/framework/github.py
@@ -33,6 +33,7 @@
 import tempfile
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
+from urllib2 import URLError
 
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.github import Githubfs, fetch_github_token, fetch_easyconfigs_from_pr
@@ -109,14 +110,19 @@ def test_fetch_easyconfigs_from_pr(self):
         # PR for ictce/6.2.5, see https://github.com/hpcugent/easybuild-easyconfigs/pull/726/files
         all_ecs = ['gzip-1.6-ictce-6.2.5.eb', 'icc-2013_sp1.2.144.eb', 'ictce-6.2.5.eb', 'ifort-2013_sp1.2.144.eb',
                    'imkl-11.1.2.144.eb', 'impi-4.1.3.049.eb']
-        ec_files = fetch_easyconfigs_from_pr(726, path=tmpdir, github_user=GITHUB_TEST_ACCOUNT)
-        self.assertEqual(all_ecs, sorted([os.path.basename(f) for f in ec_files]))
-        self.assertEqual(all_ecs, sorted(os.listdir(tmpdir)))
-        shutil.rmtree(tmpdir)
+        try:
+            ec_files = fetch_easyconfigs_from_pr(726, path=tmpdir, github_user=GITHUB_TEST_ACCOUNT)
+            self.assertEqual(all_ecs, sorted([os.path.basename(f) for f in ec_files]))
+            self.assertEqual(all_ecs, sorted(os.listdir(tmpdir)))
+
+            # PR for EasyBuild v1.13.0 release (250+ commits, 218 files changed)
+            err_msg = "PR #897 contains more than .* commits, can't obtain last commit"
+            self.assertErrorRegex(EasyBuildError, err_msg, fetch_easyconfigs_from_pr, 897, github_user=GITHUB_TEST_ACCOUNT)
 
-        # PR for EasyBuild v1.13.0 release (250+ commits, 218 files changed)
-        err_msg = "PR #897 contains more than .* commits, can't obtain last commit"
-        self.assertErrorRegex(EasyBuildError, err_msg, fetch_easyconfigs_from_pr, 897, github_user=GITHUB_TEST_ACCOUNT)
+        except URLError, err:
+            print "Ignoring URLError '%s' in test_fetch_easyconfigs_from_pr" % err
+
+        shutil.rmtree(tmpdir)
 
 
 def suite():

From aa8a18917054dcfd08abeef755b638f8f6545e76 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 22:58:55 +0100
Subject: [PATCH 0580/1356] make test_obtain_file robust against offline
 testing

---
 test/framework/easyblock.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 2657389906..b3657f448d 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -472,18 +472,22 @@ def test_obtain_file(self):
         init_config(args=["--sourcepath=%s:/no/such/dir:%s" % (tmpdir, sandbox_sources)])
         file_url = "http://hpcugent.github.io/easybuild/index.html"
         fn = os.path.basename(file_url)
+        res = None
         try:
             res = eb.obtain_file(file_url)
+        except EasyBuildError, err:
+            # if this fails, it should be because there's no online access
+            download_fail_regex = re.compile('socket error')
+            self.assertTrue(download_fail_regex.search(str(err)))
+
+        # result may be None during offline testing
+        if res is not None:
             loc = os.path.join(tmpdir, 't', 'toy', fn)
             self.assertEqual(res, loc)
             self.assertTrue(os.path.exists(loc), "%s file is found at %s" % (fn, loc))
             txt = open(loc, 'r').read()
             eb_regex = re.compile("EasyBuild: building software with ease")
             self.assertTrue(eb_regex.search(txt))
-        except EasyBuildError, err:
-            # if this fails, it should be because there's no online access
-            download_fail_regex = re.compile('socket error')
-            self.assertTrue(download_fail_regex.search(str(err)))
 
         shutil.rmtree(tmpdir)
 

From f05c69bb2153228823391c21852557a0d57a68d5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 23:06:40 +0100
Subject: [PATCH 0581/1356] make test_gitrepo robust against offline testing

---
 test/framework/easyblock.py  |  2 ++
 test/framework/repository.py | 14 ++++++++++----
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index b3657f448d..890cc86f28 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -488,6 +488,8 @@ def test_obtain_file(self):
             txt = open(loc, 'r').read()
             eb_regex = re.compile("EasyBuild: building software with ease")
             self.assertTrue(eb_regex.search(txt))
+        else:
+            print "ignoring failure to download %s in test_obtain_file, testing offline?" % file_url
 
         shutil.rmtree(tmpdir)
 
diff --git a/test/framework/repository.py b/test/framework/repository.py
index dbb86d9d1f..08ee4ac151 100644
--- a/test/framework/repository.py
+++ b/test/framework/repository.py
@@ -28,11 +28,13 @@
 @author: Toon Willems (Ghent University)
 """
 import os
+import re
 import shutil
 import tempfile
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.repository.filerepo import FileRepository
 from easybuild.tools.repository.gitrepo import GitRepository
 from easybuild.tools.repository.svnrepo import SvnRepository
@@ -75,10 +77,14 @@ def test_gitrepo(self):
 
         # URL
         repo = GitRepository(test_repo_url)
-        repo.init()
-        self.assertEqual(os.path.basename(repo.wc), 'testrepository')
-        self.assertTrue(os.path.exists(os.path.join(repo.wc, 'README.md')))
-        shutil.rmtree(repo.wc)
+        try:
+            repo.init()
+            self.assertEqual(os.path.basename(repo.wc), 'testrepository')
+            self.assertTrue(os.path.exists(os.path.join(repo.wc, 'README.md')))
+            shutil.rmtree(repo.wc)
+        except EasyBuildError, err:
+            print "ignoring failed subtest in test_gitrepo, testing offline?"
+            self.assertTrue(re.search("pull in working copy .* went wrong", str(err)))
 
         # filepath
         tmpdir = tempfile.mkdtemp()

From b178cdbe0b9e823cb2c625b440f615cb55ac7256 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Feb 2015 23:11:35 +0100
Subject: [PATCH 0582/1356] include '.' in $PYTHONPATH when testing
 generate_software_list script

---
 test/framework/scripts.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 1776f8cdc1..ae4b21296e 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -46,7 +46,7 @@ def test_generate_software_list(self):
         # adjust $PYTHONPATH such that test easyblocks are found by the script
         eb_blocks_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'sandbox'))
         pythonpath = os.environ.get('PYTHONPATH', '.')
-        os.environ['PYTHONPATH'] = "%s:%s" % (pythonpath, eb_blocks_path)
+        os.environ['PYTHONPATH'] = ".:%s:%s" % (pythonpath, eb_blocks_path)
 
         testdir = os.path.dirname(__file__)
         topdir = os.path.dirname(os.path.dirname(testdir))

From 2545e3d31bd00a764fe2d6afe5ef23f0c26f8832 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 21 Feb 2015 10:56:07 +0100
Subject: [PATCH 0583/1356] use GITHUB_TEST_ACCOUNT constant in options.py
 tests

---
 test/framework/options.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index e919176df0..1847bd2453 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -818,7 +818,7 @@ def test_from_pr(self):
             # an argument must be specified to --robot, since easybuild-easyconfigs may not be installed
             '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
             '--unittest-file=%s' % self.logfile,
-            '--github-user=easybuild_test',  # a GitHub token should be available for this user
+            '--github-user=%s' % GITHUB_TEST_ACCOUNT,  # a GitHub token should be available for this user
             '--tmpdir=%s' % tmpdir,
         ]
         try:
@@ -881,7 +881,7 @@ def test_from_pr_listed_ecs(self):
             # an argument must be specified to --robot, since easybuild-easyconfigs may not be installed
             '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
             '--unittest-file=%s' % self.logfile,
-            '--github-user=easybuild_test',  # a GitHub token should be available for this user
+            '--github-user=%s' % GITHUB_TEST_ACCOUNT,  # a GitHub token should be available for this user
             '--tmpdir=%s' % tmpdir,
         ]
         try:

From 65b3d6a905ce12abc30933cf4ab9c9e73fd76d28 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 21 Feb 2015 12:09:07 +0100
Subject: [PATCH 0584/1356] wrap 'import keyring' in try-except in suite.py

---
 test/framework/suite.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index fa8538fd51..1a656890ce 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -31,7 +31,6 @@
 @author: Kenneth Hoste (Ghent University)
 """
 import glob
-import keyring
 import os
 import shutil
 import sys
@@ -40,7 +39,11 @@
 from vsc.utils import fancylogger
 
 # set plain text key ring to be used, so a GitHub token stored in it can be obtained without having to provide a password
-keyring.set_keyring(keyring.backends.file.PlaintextKeyring())
+try:
+    import keyring
+    keyring.set_keyring(keyring.backends.file.PlaintextKeyring())
+except ImportError:
+    pass
 
 # disable all logging to significantly speed up tests
 import easybuild.tools.build_log  # initialize EasyBuild logging, so we disable it

From ec0c8a1dc882e5e88012e74c52e7e473a596fac2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 21 Feb 2015 14:06:05 +0100
Subject: [PATCH 0585/1356] fix redefining $PYTHONPATH in scripts tests

---
 test/framework/scripts.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index ae4b21296e..86cb80e422 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -44,9 +44,10 @@ def test_generate_software_list(self):
         """Test for generate_software_list.py script."""
 
         # adjust $PYTHONPATH such that test easyblocks are found by the script
-        eb_blocks_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'sandbox'))
-        pythonpath = os.environ.get('PYTHONPATH', '.')
-        os.environ['PYTHONPATH'] = ".:%s:%s" % (pythonpath, eb_blocks_path)
+        test_dir = os.path.abspath(os.path.dirname(__file__))
+        eb_blocks_path = os.path.join(test_dir, 'sandbox')
+        pythonpath = os.environ.get('PYTHONPATH', os.path.dirname(test_dir))
+        os.environ['PYTHONPATH'] = os.pathsep.join([pythonpath, eb_blocks_path])
 
         testdir = os.path.dirname(__file__)
         topdir = os.path.dirname(os.path.dirname(testdir))

From d1c19ad5b781c4532483ea88f7901e73fa193f46 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 21 Feb 2015 14:15:06 +0100
Subject: [PATCH 0586/1356] use EnhancedTestCase provided by vsc.utils.testing

---
 test/framework/utilities.py | 29 ++++-------------------------
 1 file changed, 4 insertions(+), 25 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 913810232e..a6b54e7a68 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -34,9 +34,9 @@
 import shutil
 import sys
 import tempfile
-from unittest import TestCase
 from vsc.utils import fancylogger
 from vsc.utils.patterns import Singleton
+from vsc.utils.testing import EnhancedTestCase as _EnhancedTestCase
 
 import easybuild.tools.build_log as eb_build_log
 import easybuild.tools.options as eboptions
@@ -77,34 +77,12 @@
     os.environ[key] = val
 
 
-class EnhancedTestCase(TestCase):
+class EnhancedTestCase(_EnhancedTestCase):
     """Enhanced test case, provides extra functionality (e.g. an assertErrorRegex method)."""
 
-    def assertErrorRegex(self, error, regex, call, *args, **kwargs):
-        """Convenience method to match regex with the expected error message"""
-        try:
-            call(*args, **kwargs)
-            str_kwargs = ', '.join(['='.join([k,str(v)]) for (k,v) in kwargs.items()])
-            str_args = ', '.join(map(str, args) + [str_kwargs])
-            self.assertTrue(False, "Expected errors with %s(%s) call should occur" % (call.__name__, str_args))
-        except error, err:
-            if hasattr(err, 'msg'):
-                msg = err.msg
-            elif hasattr(err, 'message'):
-                msg = err.message
-            elif hasattr(err, 'args'):  # KeyError in Python 2.4 only provides message via 'args' attribute
-                msg = err.args[0]
-            else:
-                msg = err
-            try:
-                msg = str(msg)
-            except UnicodeEncodeError:
-                msg = msg.encode('utf8', 'replace')
-            self.assertTrue(re.search(regex, msg), "Pattern '%s' is found in '%s'" % (regex, msg))
-            self.assertTrue(re.search(regex, msg), "Pattern '%s' is found in '%s'" % (regex, msg))
-
     def setUp(self):
         """Set up testcase."""
+        super(EnhancedTestCase, self).setUp()
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
         fd, self.logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')
         os.close(fd)
@@ -155,6 +133,7 @@ def setUp(self):
 
     def tearDown(self):
         """Clean up after running testcase."""
+        super(EnhancedTestCase, self).tearDown()
         os.chdir(self.cwd)
         modify_env(os.environ, self.orig_environ)
         tempfile.tempdir = None

From 5c15f47154778e9776c7737af4d84719d0269d5b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 21 Feb 2015 16:13:15 +0100
Subject: [PATCH 0587/1356] fix minor remark

---
 easybuild/tools/modules.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 90be795902..b1e99c92fe 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -63,8 +63,6 @@
 # see e.g., https://bugzilla.redhat.com/show_bug.cgi?id=719785
 LD_LIBRARY_PATH = os.getenv('LD_LIBRARY_PATH', '')
 
-LMOD_USER_CACHE_DIR = os.path.join(os.path.expanduser('~'), '.lmod.d', '.cache')
-
 output_matchers = {
     # matches whitespace and module-listing headers
     'whitespace': re.compile(r"^\s*$|^(-+).*(-+)$"),
@@ -136,6 +134,8 @@ class ModulesTool(object):
     REQ_VERSION = None
     # the regexp, should have a "version" group (multiline search)
     VERSION_REGEXP = None
+    # modules tool user cache directory
+    USER_CACHE_DIR = None
 
     __metaclass__ = Singleton
 
@@ -794,6 +794,7 @@ class Lmod(ModulesTool):
     # we need at least Lmod v5.6.3 (and it can't be a release candidate)
     REQ_VERSION = '5.6.3'
     VERSION_REGEXP = r"^Modules\s+based\s+on\s+Lua:\s+Version\s+(?P<version>\d\S*)\s"
+    USER_CACHE_DIR = os.path.join(os.path.expanduser('~'), '.lmod.d', '.cache')
 
     def __init__(self, *args, **kwargs):
         """Constructor, set lmod-specific class variable values."""
@@ -851,7 +852,7 @@ def update(self):
                 return stdout
             else:
                 try:
-                    cache_fp = os.path.join(LMOD_USER_CACHE_DIR, 'moduleT.lua')
+                    cache_fp = os.path.join(self.USER_CACHE_DIR, 'moduleT.lua')
                     self.log.debug("Updating Lmod spider cache %s with output from '%s'" % (cache_fp, ' '.join(cmd)))
                     cache_dir = os.path.dirname(cache_fp)
                     if not os.path.exists(cache_dir):

From bcb5fdc5e624c15e1b0d518c2df03856db33b33f Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Sat, 21 Feb 2015 17:29:21 +0200
Subject: [PATCH 0588/1356] initial commit.

---
 easybuild/framework/easyblock.py              |   2 +
 easybuild/framework/easyconfig/default.py     |   2 +-
 .../scripts/generate_crayprgenv_toolchains.py | 141 ++++++++++++++++++
 .../toolchains/compiler/craypewrappers.py     |  96 ++++++++++++
 easybuild/toolchains/compiler/gcc.py          |   4 +-
 easybuild/toolchains/cpec.py                  |  35 +++++
 easybuild/toolchains/cpeg.py                  |  34 +++++
 easybuild/toolchains/cpei.py                  |  34 +++++
 easybuild/tools/run.py                        |  24 +--
 easybuild/tools/toolchain/toolchain.py        |   7 +-
 10 files changed, 362 insertions(+), 17 deletions(-)
 create mode 100755 easybuild/scripts/generate_crayprgenv_toolchains.py
 create mode 100644 easybuild/toolchains/compiler/craypewrappers.py
 create mode 100644 easybuild/toolchains/cpec.py
 create mode 100644 easybuild/toolchains/cpeg.py
 create mode 100644 easybuild/toolchains/cpei.py

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index ba37110e6b..4423353afd 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1316,8 +1316,10 @@ def prepare_step(self):
         """
         self.cfg['unwanted_env_vars'] = env.unset_env_vars(self.cfg['unwanted_env_vars'])
         self.toolchain.prepare(self.cfg['onlytcmod'])
+        self.modules_tool.load(self.cfg['system_modules']) 
         self.guess_start_dir()
 
+
     def configure_step(self):
         """Configure build  (abstract method)."""
         raise NotImplementedError
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index acc99c33eb..26756c36ce 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -147,7 +147,7 @@
     'dependencies': [[], "List of dependencies", DEPENDENCIES],
     'hiddendependencies': [[], "List of dependencies available as hidden modules", DEPENDENCIES],
     'osdependencies': [[], "OS dependencies that should be present on the system", DEPENDENCIES],
-
+    'system_modules': [[], "System module dependencies that should be present on the system", DEPENDENCIES],
     # LICENSE easyconfig parameters
     'group': [None, "Name of the user group for which the software should be available", LICENSE],
     'key': [None, 'Key for installing software', LICENSE],
diff --git a/easybuild/scripts/generate_crayprgenv_toolchains.py b/easybuild/scripts/generate_crayprgenv_toolchains.py
new file mode 100755
index 0000000000..68e862a569
--- /dev/null
+++ b/easybuild/scripts/generate_crayprgenv_toolchains.py
@@ -0,0 +1,141 @@
+#!/usr/bin/env python
+# #
+# Copyright 2014 Petar Forai
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+
+
+import easybuild.tools.modules as modules
+import easybuild.tools.config as config
+import easybuild.tools.options as eboptions
+
+import easybuild.tools.options as eboptions
+from easybuild.tools import config, modules
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import build_option
+from easybuild.tools.filetools import which
+from easybuild.tools.modules import modules_tool, Lmod
+from easybuild.tools.config import build_option, get_modules_tool
+
+from collections import namedtuple
+import tempfile, os
+
+#_log = fancylogger.getLogger('craytcgenerator', fname=False)
+
+
+EB_EC_FILE_TMPLT = """
+easyblock = 'Toolchain'
+
+name = '%(name)s'
+version = '%(version)s'
+
+homepage = 'http://hpcugent.github.io/easybuild/'
+description = \"\"\"This is a shim module for having EB pick up the Cray
+Programming Environment (PrgEnv-*) modules. This module implements the EB
+toolchain module for each of the cray modules.\"\"\"
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = []
+sources = []
+dependencies = []
+
+moduleclass = 'toolchain'
+
+modtclfooter = \"\"\"
+module load %(craymodule)s/%(version)s
+module load %(craypetarget)s
+\"\"\"
+
+"""
+
+eb_go = eboptions.parse_options()
+config.init(eb_go.options, eb_go.get_options_by_section('config'))
+
+config.init_build_options({'suffix_modules_path':'all'})
+config.set_tmpdir()
+
+
+
+#FIXME: This needs to be usable from not only Lmod, but other environment modules tool in EasyBuild.
+# from easybuild.tools.modules import get_software_root, modules_tool
+# use something like self.modules_tool = modules_tool()
+ml = modules_tool()
+
+prgenvmods = []
+
+print "Running module avail commands for the Cray compiler wrappers."
+#print "using modules tool " + str(ml.__class__.__name__)
+
+prgenvmods = ml.available("PrgEnv")
+
+if len(prgenvmods) == 0:
+    print """No Cray Programming Environment modules are visible in the modules tool.\n
+             Make sure to include them in $MODULEPATH or this is not a Cray system."""
+
+print prgenvmods
+
+craymod_to_tc = {'PrgEnv-cray': 'cpec',
+                 'PrgEnv-intel': 'cpei',
+                 'PrgEnv-gnu': 'cpeg',
+                 'PrgEnv-pgi': 'cpep', }
+
+tc_to_craymod = {'cpec': 'PrgEnv-cray',
+                 'cpei': 'PrgEnv-intel',
+                 'cpeg': 'PrgEnv-gnu',
+                 'cpep': 'PrgEnv-pgi', }
+
+
+def modToTC(m):
+    modname, version = m.split('/')
+    if modname not in craymod_to_tc:
+        print "Can't map Cray module name to EasyBuild toolchain name module."
+    else:
+        # The TC name for a given cray module name is defined to be the mapping table craymod_to_tc
+        # and the EB toolchain version is identical to the version of the PrgEnv module itself.
+        # Cray already does all the work of coming up with numbers, so let's use this.
+        toolchain = namedtuple('toolchain', 'toolchainname , toolchainversion')
+        return toolchain(toolchainname=craymod_to_tc[modname], toolchainversion=version)
+
+
+def generate_EB_config(tmpdir, craytc):
+    name = craytc.toolchainname
+    version = craytc.toolchainversion
+    ebconfigfile = os.path.join(tmpdir, '%s-%s.eb' % (name, version))
+    print "Generating file ", ebconfigfile
+    f = open(ebconfigfile, "w")
+    f.write(EB_EC_FILE_TMPLT % {'name': name,
+                                'version': version,
+                                'craymodule': tc_to_craymod[name],
+                                'craypetarget': 'craype-haswell', #@todo this needs to ne somehow better or at least an option!
+    })
+    f.close()
+
+
+tmpdir = tempfile.mkdtemp()
+print tmpdir
+os.chdir(tmpdir)
+
+for mod in prgenvmods:
+    toolchain = modToTC(mod)
+    generate_EB_config(tmpdir, toolchain)
diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
new file mode 100644
index 0000000000..7b137ad2dd
--- /dev/null
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -0,0 +1,96 @@
+##
+# Copyright 2012-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Support for the Cray Programming Environment Wrappers (aka cc, CC, ftn).
+The Cray compiler wrappers are actually way more than just a compiler drivers.
+
+The basic concept is that the compiler driver knows how to invoke the true underlying
+compiler with the compiler's specific options tuned to cray systems.
+
+That means that certain defaults are set that are specific to Cray's computers.
+
+The compiler wrappers are quite similar to EB toolchains as they include
+linker and compiler directives to use the Cray libraries for their MPI (and network drivers)
+Cray's LibSci (BLAS/LAPACK et al), FFT library, etc.
+
+
+@author: Petar Forai
+"""
+
+from easybuild.tools.toolchain.compiler import Compiler
+from easybuild.toolchains.compiler.gcc import Gcc
+from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+
+TC_CONSTANT_CRAYPEWRAPPER = "CRAYPEWRAPPER"
+
+
+class CrayPEWrapper(Compiler):
+    """Base CrayPE compiler class"""
+
+    COMPILER_MODULE_NAME = ['PrgEnv']
+
+    COMPILER_FAMILY = TC_CONSTANT_CRAYPEWRAPPER
+
+    COMPILER_UNIQUE_OPTS = {
+        'verbose' : (False, "Enable verbose calls to real compiler driver."),
+        'dynamic' : (False, "Enables dynamic code generation."),
+	}
+
+    COMPILER_UNIQUE_OPTION_MAP = {
+        'verbose': 'craype-verbose',
+	    'dynamic': 'dynamic',
+    }
+
+    COMPILER_OPT_FLAGS = []
+    COMPILER_PREC_FLAGS = []
+
+    COMPILER_CC = 'cc'
+    COMPILER_CXX = 'CC'
+    COMPILER_C_UNIQUE_FLAGS = []
+
+
+    COMPILER_F77 = 'ftn'
+    COMPILER_F90 = 'ftn'
+    COMPILER_F_UNIQUE_FLAGS = []
+
+
+#    def _set_compiler_vars(self):
+#        super(CrayPEWrapper, self)._set_compiler_vars()
+
+#Gcc's base is Compiler
+class CrayPEWrapperGNU(Gcc):
+    """Base Cray Programming Environment GNU compiler class"""
+
+    COMPILER_MODULE_NAME = ['PrgEnv-gnu']
+
+    #COMPILER_FAMILY = TC_CONSTANT_GCC #@todo does this make sense?
+
+
+class CrayPEWrapperIntel(CrayPEWrapper,IntelIccIfort):
+    COMPILER_MODULE_NAME = ['PrgEnv-intel']
+
+
+class CrayPEWrapperCray(CrayPEWrapper):
+    pass
\ No newline at end of file
diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py
index e47a9c4778..9b1886d96b 100644
--- a/easybuild/toolchains/compiler/gcc.py
+++ b/easybuild/toolchains/compiler/gcc.py
@@ -95,5 +95,5 @@ def _set_compiler_vars(self):
         # append lib dir paths to LDFLAGS (only if the paths are actually there)
         # Note: hardcode 'GCC' here; we can not reuse COMPILER_MODULE_NAME because
         # it can be redefined by combining GCC with other compilers (e.g., Clang).
-        gcc_root = self.get_software_root('GCC')[0]
-        self.variables.append_subdirs("LDFLAGS", gcc_root, subdirs=["lib64", "lib"])
+        #gcc_root = self.get_software_root('GCC')[0]
+        #self.variables.append_subdirs("LDFLAGS", gcc_root, subdirs=["lib64", "lib"])
diff --git a/easybuild/toolchains/cpec.py b/easybuild/toolchains/cpec.py
new file mode 100644
index 0000000000..e183c1dbdf
--- /dev/null
+++ b/easybuild/toolchains/cpec.py
@@ -0,0 +1,35 @@
+##
+# Copyright 2014 Petar Forai
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+@author: Petar Forai
+"""
+
+
+from easybuild.toolchains.compiler.craypewrappers import *
+
+class cpec(CrayPEWrapperCray):
+    """Compiler toolchain with Cray cc,CC,ftn,LibSci,MPT,SHMEM."""
+    NAME = 'cpec'
+
diff --git a/easybuild/toolchains/cpeg.py b/easybuild/toolchains/cpeg.py
new file mode 100644
index 0000000000..770bac48d1
--- /dev/null
+++ b/easybuild/toolchains/cpeg.py
@@ -0,0 +1,34 @@
+##
+# Copyright 2014 Petar Forai
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+@author: Petar Forai
+"""
+
+
+from easybuild.toolchains.compiler.craypewrappers import *
+
+class cpeg(CrayPEWrapperGNU):
+    """Compiler toolchain with Cray cc,CC,ftn,LibSci,MPT,SHMEM."""
+    NAME = 'cpeg'
diff --git a/easybuild/toolchains/cpei.py b/easybuild/toolchains/cpei.py
new file mode 100644
index 0000000000..8d1d65c255
--- /dev/null
+++ b/easybuild/toolchains/cpei.py
@@ -0,0 +1,34 @@
+##
+# Copyright 2014 Petar Forai
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+@author: Petar Forai
+"""
+
+
+from easybuild.toolchains.compiler.craypewrappers import *
+
+class cpei(CrayPEWrapperIntel):
+    """Compiler toolchain with Cray cc,CC,ftn,LibSci,MPT,SHMEM."""
+    NAME = 'cpei'
diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index 9b42b159fe..522c3dcd43 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -64,19 +64,19 @@ def adjust_cmd(func):
     """Make adjustments to given command, if required."""
 
     def inner(cmd, *args, **kwargs):
-        # SuSE hack
+	# SuSE hack
         # - profile is not resourced, and functions (e.g. module) is not inherited
-        if 'PROFILEREAD' in os.environ and (len(os.environ['PROFILEREAD']) > 0):
-            filepaths = ['/etc/profile.d/modules.sh']
-            extra = ''
-            for fp in filepaths:
-                if os.path.exists(fp):
-                    extra = ". %s &&%s" % (fp, extra)
-                else:
-                    _log.warning("Can't find file %s" % fp)
-
-            cmd = "%s %s" % (extra, cmd)
-
+        #if 'PROFILEREAD' in os.environ and (len(os.environ['PROFILEREAD']) > 0):
+        #    filepaths = ['/etc/profile.d/modules.sh']
+        #    extra = ''
+        #    for fp in filepaths:
+        #        if os.path.exists(fp):
+        #            extra = ". %s &&%s" % (fp, extra)
+        #        else:
+        #            _log.warning("Can't find file %s" % fp)
+	#
+        extra = ''
+	cmd = "%s %s" % (extra, cmd)
         return func(cmd, *args, **kwargs)
 
     return inner
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 75c5a29c85..563977b672 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -336,10 +336,13 @@ def prepare(self, onlymod=None):
         if not self._toolchain_exists():
             self.log.raiseException("No module found for toolchain name '%s' (%s)" % (self.name, self.version))
 
-        if self.name == DUMMY_TOOLCHAIN_NAME:
+        
+	if self.name == DUMMY_TOOLCHAIN_NAME:
             if self.version == DUMMY_TOOLCHAIN_VERSION:
                 self.log.info('prepare: toolchain dummy mode, dummy version; not loading dependencies')
-            else:
+		#@todo I keep this is as, but want dummy to do the same as a regular toolchain. Need to think this through.
+        	self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
+	    else:
                 self.log.info('prepare: toolchain dummy mode and loading dependencies')
                 self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
             return

From 7e027dffc53bb230707398814f0c26bb2bc4db6a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 21 Feb 2015 16:58:35 +0100
Subject: [PATCH 0589/1356] check early for a noexec on location for temporary
 files

---
 easybuild/tools/config.py |  7 +++++--
 test/framework/suite.py   | 23 +++++++++--------------
 2 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 60af87d556..a159794402 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -439,7 +439,7 @@ def read_environment(env_vars, strict=False):
     _log.nosupport("read_environment has moved to easybuild.tools.environment", '2.0')
 
 
-def set_tmpdir(tmpdir=None):
+def set_tmpdir(tmpdir=None, raise_error=False):
     """Set temporary directory to be used by tempfile and others."""
     try:
         if tmpdir is not None:
@@ -468,7 +468,10 @@ def set_tmpdir(tmpdir=None):
         if not run_cmd(tmptest_file, simple=True, log_ok=False, regexp=False):
             msg = "The temporary directory (%s) does not allow to execute files. " % tempfile.gettempdir()
             msg += "This can cause problems in the build process, consider using --tmpdir."
-            _log.warning(msg)
+            if raise_error:
+                _log.error(msg)
+            else:
+                _log.warning(msg)
         else:
             _log.debug("Temporary directory %s allows to execute files, good!" % tempfile.gettempdir())
         os.remove(tmptest_file)
diff --git a/test/framework/suite.py b/test/framework/suite.py
index 1a656890ce..598be0106a 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -32,12 +32,15 @@
 """
 import glob
 import os
-import shutil
 import sys
 import tempfile
 import unittest
 from vsc.utils import fancylogger
 
+# initialize EasyBuild logging, so we disable it
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import set_tmpdir
+
 # set plain text key ring to be used, so a GitHub token stored in it can be obtained without having to provide a password
 try:
     import keyring
@@ -46,7 +49,6 @@
     pass
 
 # disable all logging to significantly speed up tests
-import easybuild.tools.build_log  # initialize EasyBuild logging, so we disable it
 fancylogger.disableDefaultHandlers()
 fancylogger.setLogLevelError()
 
@@ -81,18 +83,11 @@
 
 
 # make sure temporary files can be created/used
-fd, fn = tempfile.mkstemp()
-os.close(fd)
-os.remove(fn)
-testdir = tempfile.mkdtemp()
-for test_fn in [fn, os.path.join(testdir, 'test')]:
-    try:
-        open(fn, 'w').write('test')
-    except IOError, err:
-        sys.stderr.write("ERROR: Can't write to temporary file %s, set $TMPDIR to a writeable directory (%s)" % (fn, err))
-        sys.exit(1)
-os.remove(fn)
-shutil.rmtree(testdir)
+try:
+    set_tmpdir(raise_error=True)
+except EasyBuildError, err:
+    sys.stderr.write("No execution rights on temporary files, specify another location via $TMPDIR: %s\n" % err)
+    sys.exit(1)
 
 # initialize logger for all the unit tests
 fd, log_fn = tempfile.mkstemp(prefix='easybuild-tests-', suffix='.log')

From d3476b136b592b24c59811d69f8cb158decc04e1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 21 Feb 2015 19:20:20 +0100
Subject: [PATCH 0590/1356] bump version of vsc-base dep

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 08ee69b456..627008004e 100644
--- a/setup.py
+++ b/setup.py
@@ -106,5 +106,5 @@ def find_rel_test():
     provides=["eb"] + easybuild_packages,
     test_suite="test.framework.suite",
     zip_safe=False,
-    install_requires=["vsc-base >= 2.0.0"],
+    install_requires=["vsc-base >= 2.0.3"],
 )

From 6c789d59f2deff097cdae2333d4bcd0218a6fda4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 21 Feb 2015 19:37:03 +0100
Subject: [PATCH 0591/1356] sort all lists obtained via glob.glob, since they
 are in arbitrary order

---
 easybuild/framework/easyblock.py        | 2 +-
 easybuild/framework/easyconfig/tweak.py | 2 +-
 easybuild/tools/jenkins.py              | 2 +-
 easybuild/tools/options.py              | 6 +++---
 easybuild/tools/utilities.py            | 2 +-
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index a5decf677b..dbe2c60b63 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -937,7 +937,7 @@ def make_module_req(self):
             txt = "\n"
             for key in sorted(requirements):
                 for path in requirements[key]:
-                    paths = glob.glob(path)
+                    paths = sorted(glob.glob(path))
                     if paths:
                         txt += self.module_generator.prepend_paths(key, paths)
             try:
diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 0047ae8a6d..010a411699 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -302,7 +302,7 @@ def find_matching_easyconfigs(name, installver, paths):
     for path in paths:
         patterns = create_paths(path, name, installver)
         for pattern in patterns:
-            more_ec_files = filter(os.path.isfile, glob.glob(pattern))
+            more_ec_files = filter(os.path.isfile, sorted(glob.glob(pattern)))
             _log.debug("Including files that match glob pattern '%s': %s" % (pattern, more_ec_files))
             ec_files.extend(more_ec_files)
 
diff --git a/easybuild/tools/jenkins.py b/easybuild/tools/jenkins.py
index fe8e9cf242..625984f0b5 100644
--- a/easybuild/tools/jenkins.py
+++ b/easybuild/tools/jenkins.py
@@ -142,7 +142,7 @@ def aggregate_xml_in_dirs(base_dir, output_filename):
     total = 0
 
     for d in dirs:
-        xml_file = glob.glob(os.path.join(d, "*.xml"))
+        xml_file = sorted(glob.glob(os.path.join(d, "*.xml")))
         if xml_file:
             # take the first one (should be only one present)
             xml_file = xml_file[0]
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 3ac38024f3..c79a10d7eb 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -68,8 +68,8 @@
 
 XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
 XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', '/etc').split(os.pathsep)
-DEFAULT_SYSTEM_CONFIGFILES = [f for d in XDG_CONFIG_DIRS for f in glob.glob(os.path.join(d, 'easybuild.d', '*.cfg'))]
-DEFAULT_USER_CONFIGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
+DEFAULT_SYS_CFGFILES = [f for d in XDG_CONFIG_DIRS for f in sorted(glob.glob(os.path.join(d, 'easybuild.d', '*.cfg')))]
+DEFAULT_USER_CFGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
 
 
 class EasyBuildOptions(GeneralOption):
@@ -77,7 +77,7 @@ class EasyBuildOptions(GeneralOption):
     VERSION = this_is_easybuild()
 
     DEFAULT_LOGLEVEL = 'INFO'
-    DEFAULT_CONFIGFILES = DEFAULT_SYSTEM_CONFIGFILES + [DEFAULT_USER_CONFIGFILE]
+    DEFAULT_CONFIGFILES = DEFAULT_SYS_CFGFILES + [DEFAULT_USER_CFGFILE]
 
     ALLOPTSMANDATORY = False  # allow more than one argument
 
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 7c8a959319..096766e127 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -94,7 +94,7 @@ def import_available_modules(namespace):
     """
     modules = []
     for path in sys.path:
-        for module in glob.glob(os.path.sep.join([path] + namespace.split('.') + ['*.py'])):
+        for module in sorted(glob.glob(os.path.sep.join([path] + namespace.split('.') + ['*.py']))):
             if not module.endswith('__init__.py'):
                 mod_name = module.split(os.path.sep)[-1].split('.')[0]
                 modpath = '.'.join([namespace, mod_name])

From 13877938c49b663ccb5b7f685c3cf082a98d6455 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 21 Feb 2015 20:40:06 +0100
Subject: [PATCH 0592/1356] unset *all* $EASYBUILD_X env vars in
 purge_environment method in config.py tests

---
 test/framework/config.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index 429b29407a..36de96ad16 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -59,9 +59,8 @@ def setUp(self):
 
     def purge_environment(self):
         """Remove any leftover easybuild variables"""
-        for path in ['buildpath', 'installpath', 'sourcepath', 'prefix']:
-            var = 'EASYBUILD_%s' % path.upper()
-            if var in os.environ:
+        for var in os.environ.keys():
+            if var.startswith('EASYBUILD_'):
                 del os.environ[var]
 
     def tearDown(self):

From a1f2600774002e2237077d31cffe57426174d8c6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 22 Feb 2015 09:35:17 +0100
Subject: [PATCH 0593/1356] empty test install dir before running test to check
 permissions

---
 test/framework/toy_build.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 95eb21b03b..5d0aef6add 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -401,6 +401,9 @@ def test_toy_permissions(self):
             ('030', None, curr_grp, 0740, 0640, 0740),  # no write for group, with specified group
             ('077', None, None, 0700, 0600, 0700),  # no access for other/group
         ]:
+            # empty the install directory, to ensure any created directories adher to the permissions
+            shutil.rmtree(self.test_installpath)
+
             if cfg_group is None and ec_group is None:
                 allargs = [toy_ec_file]
             elif ec_group is not None:
@@ -450,9 +453,6 @@ def test_toy_permissions(self):
                     path_gid = os.stat(fullpath).st_gid
                     self.assertEqual(path_gid, grp.getgrnam(group).gr_gid)
 
-            # cleanup for next iteration
-            shutil.rmtree(self.test_installpath)
-
         # restore original umask
         os.umask(orig_umask)
 

From e334beb8b09a185f29f1ca9f3e70517fb2ff5a66 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 22 Feb 2015 22:32:48 +0100
Subject: [PATCH 0594/1356] set $EASYBUILD_ROBOT_PATHS in setUp, unset it where
 needed

---
 test/framework/options.py   | 6 ++++++
 test/framework/utilities.py | 3 +++
 2 files changed, 9 insertions(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 1847bd2453..36f500906d 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -633,6 +633,9 @@ def test_dry_run(self):
 
     def test_dry_run_short(self):
         """Test dry run (short format)."""
+        # unset $EASYBUILD_ROBOT_PATHS that was defined in setUp
+        del os.environ['EASYBUILD_ROBOT_PATHS']
+
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
@@ -1425,6 +1428,9 @@ def toy(extra_args=None):
 
     def test_robot(self):
         """Test --robot and --robot-paths command line options."""
+        # unset $EASYBUILD_ROBOT_PATHS that was defined in setUp
+        del os.environ['EASYBUILD_ROBOT_PATHS']
+
         test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         eb_file = os.path.join(test_ecs_path, 'gzip-1.4-GCC-4.6.3.eb')  # includes 'toy/.0.0-deps' as a dependency
 
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index a6b54e7a68..efb5500bdf 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -109,6 +109,9 @@ def setUp(self):
         self.test_installpath = tempfile.mkdtemp()
         os.environ['EASYBUILD_INSTALLPATH'] = self.test_installpath
 
+        # make sure that the tests only pick up easyconfigs provided with the tests
+        os.environ['EASYBUILD_ROBOT_PATHS'] = os.path.join(testdir, 'easyconfigs')
+
         # make sure no deprecated behaviour is being triggered (unless intended by the test)
         # trip *all* log.deprecated statements by setting deprecation version ridiculously high
         self.orig_current_version = eb_build_log.CURRENT_VERSION

From b15b3950a4344dd94b4f5a1a8a94da6efde8b974 Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Mon, 23 Feb 2015 14:58:46 +0200
Subject: [PATCH 0595/1356] Pre Kenneth fixes.

---
 .../toolchains/compiler/craypewrappers.py     | 143 +++++++++++++++---
 easybuild/toolchains/compiler/gcc.py          |   4 +-
 easybuild/toolchains/cpec.py                  |   2 +-
 easybuild/toolchains/cpeg.py                  |   2 +-
 easybuild/toolchains/cpei.py                  |   2 +-
 5 files changed, 128 insertions(+), 25 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 7b137ad2dd..35bd1e970f 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -43,54 +43,157 @@
 from easybuild.toolchains.compiler.gcc import Gcc
 from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
 
+import easybuild.tools.systemtools as systemtools
+
 TC_CONSTANT_CRAYPEWRAPPER = "CRAYPEWRAPPER"
 
 
 class CrayPEWrapper(Compiler):
     """Base CrayPE compiler class"""
 
-    COMPILER_MODULE_NAME = ['PrgEnv']
-
+    COMPILER_MODULE_NAME = None
     COMPILER_FAMILY = TC_CONSTANT_CRAYPEWRAPPER
 
     COMPILER_UNIQUE_OPTS = {
-        'verbose' : (False, "Enable verbose calls to real compiler driver."),
-        'dynamic' : (False, "Enables dynamic code generation."),
-	}
+        'mpich-mt': (False, """Directs the driver to link in an alternate version of the Cray-MPICH library which
+                                 provides fine-grained multi-threading support to applications that perform
+                                 MPI operations within threaded regions."""),
+        'dynamic': (True, "Directs the compiler driver to link dynamic libraries at runtime."),
+        'usewrappedcompiler': (False, "Use the embedded compiler instead of the wrapper"),
+    }
 
     COMPILER_UNIQUE_OPTION_MAP = {
+        'dynamic': 'dynamic',
+        'shared': 'shared',
+        'static': 'static',
+        'verbose': 'craype-verbose',
+        'mpich-mt': 'craympich-mt',
+        'pic': 'dynamic',
+    }
+
+    COMPILER_SHARED_OPTION_MAP = {
+        'dynamic': 'dynamic',
+        'pic': 'dynamic',
         'verbose': 'craype-verbose',
-	    'dynamic': 'dynamic',
+        'static': 'static',
     }
 
-    COMPILER_OPT_FLAGS = []
-    COMPILER_PREC_FLAGS = []
+    # @todo this is BS.
+    COMPILER_OPTIMAL_ARCHITECTURE_OPTION = {
+        systemtools.INTEL: 'march=native',
+        systemtools.AMD: 'march=native'
+    }
+
+    #COMPILER_PREC_FLAGS = ['strict', 'precise', 'defaultprec', 'loose', 'veryloose']  # precision flags, ordered !
 
     COMPILER_CC = 'cc'
     COMPILER_CXX = 'CC'
-    COMPILER_C_UNIQUE_FLAGS = []
-
 
     COMPILER_F77 = 'ftn'
     COMPILER_F90 = 'ftn'
-    COMPILER_F_UNIQUE_FLAGS = []
 
+    def _set_compiler_vars(self):
+        super(CrayPEWrapper, self)._set_compiler_vars()
+
+    def _get_optimal_architecture(self):
+        """On a Cray system we assume that the optimal architecture is controlled
+           by loading a craype module that instructs the compiler to generate backend code
+           for that particular target"""
+        pass
+
+    def _set_compiler_flags(self):
+        """Collect the flags set, and add them as variables too"""
+        flags = [self.options.option(x) for x in self.COMPILER_FLAGS if self.options.get(x, False)]
+        cflags = [self.options.option(x) for x in self.COMPILER_C_FLAGS + self.COMPILER_C_UNIQUE_FLAGS \
+                  if self.options.get(x, False)]
+        fflags = [self.options.option(x) for x in self.COMPILER_F_FLAGS + self.COMPILER_F_UNIQUE_FLAGS \
+                  if self.options.get(x, False)]
+
+        # 1st one is the one to use. add default at the end so len is at least 1
+        # optflags = [self.options.option(x) for x in self.COMPILER_OPT_FLAGS if self.options.get(x, False)] + \
+        #            [self.options.option('defaultopt')]
+        #
+        # optarchflags = [self.options.option(x) for x in ['optarch'] if self.options.get(x, False)]
+        #
+        # precflags = [self.options.option(x) for x in self.COMPILER_PREC_FLAGS if self.options.get(x, False)] + \
+        #             [self.options.option('defaultprec')]
+        #
+        # self.variables.nextend('OPTFLAGS', optflags[:1] + optarchflags)
+        # self.variables.nextend('PRECFLAGS', precflags[:1])
+
+        # precflags last
+        self.variables.nappend('CFLAGS', flags)
+        self.variables.nappend('CFLAGS', cflags)
+        self.variables.join('CFLAGS', )  # 'OPTFLAGS', 'PRECFLAGS')
+
+        self.variables.nappend('CXXFLAGS', flags)
+        self.variables.nappend('CXXFLAGS', cflags)
+        self.variables.join('CXXFLAGS', )  # 'OPTFLAGS', 'PRECFLAGS')
+
+        self.variables.nappend('FFLAGS', flags)
+        self.variables.nappend('FFLAGS', fflags)
+        self.variables.join('FFLAGS', )  # 'OPTFLAGS', 'PRECFLAGS')
+
+        self.variables.nappend('F90FLAGS', flags)
+        self.variables.nappend('F90FLAGS', fflags)
+        self.variables.join('F90FLAGS', )  # 'OPTFLAGS', 'PRECFLAGS')
+
+
+# Gcc's base is Compiler
+class CrayPEWrapperGNU(CrayPEWrapper):
+    """Base Cray Programming Environment GNU compiler class"""
+    COMPILER_MODULE_NAME = ['PrgEnv-gnu']
+    TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_GNU'
 
-#    def _set_compiler_vars(self):
-#        super(CrayPEWrapper, self)._set_compiler_vars()
 
-#Gcc's base is Compiler
-class CrayPEWrapperGNU(Gcc):
-    """Base Cray Programming Environment GNU compiler class"""
+    def _set_compiler_vars(self):
+        if self.options.option('usewrappedcompiler'):
 
-    COMPILER_MODULE_NAME = ['PrgEnv-gnu']
+            COMPILER_UNIQUE_OPTS = Gcc.COMPILER_UNIQUE_OPTS
+            COMPILER_UNIQUE_OPTION_MAP = Gcc.COMPILER_UNIQUE_OPTION_MAP
+
+            COMPILER_CC = Gcc.COMPILER_CC
+            COMPILER_CXX = Gcc.COMPILER_CXX
+            COMPILER_C_UNIQUE_FLAGS = []
+
+            COMPILER_F77 = Gcc.COMPILER_F77
+            COMPILER_F90 = Gcc.COMPILER_F90
+            COMPILER_F_UNIQUE_FLAGS = Gcc.COMPILER_F_UNIQUE_FLAGS
 
-    #COMPILER_FAMILY = TC_CONSTANT_GCC #@todo does this make sense?
+            super(CrayPEWrapperGNU, self)._set_compiler_vars()
+        else:
+            super(CrayPEWrapper, self)._set_compiler_vars()
 
 
-class CrayPEWrapperIntel(CrayPEWrapper,IntelIccIfort):
+class CrayPEWrapperIntel(CrayPEWrapper):
+    TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_INTEL'
+
     COMPILER_MODULE_NAME = ['PrgEnv-intel']
 
+    def _set_compiler_vars(self):
+        if self.options.option("usewrappedcompiler"):
+            COMPILER_UNIQUE_OPTS = IntelIccIfort.COMPILER_UNIQUE_OPTS
+            COMPILER_UNIQUE_OPTION_MAP = IntelIccIfort.COMPILER_UNIQUE_OPTION_MAP
+
+            COMPILER_CC = IntelIccIfort.COMPILER_CC
+
+            COMPILER_CXX = IntelIccIfort.COMPILER_CXX
+            COMPILER_C_UNIQUE_FLAGS = IntelIccIfort.COMPILER_C_UNIQUE_FLAGS
+
+            COMPILER_F77 = IntelIccIfort.COMPILER_F77
+            COMPILER_F90 = IntelIccIfort.COMPILER_F90
+            COMPILER_F_UNIQUE_FLAGS = IntelIccIfort.COMPILER_F_UNIQUE_FLAGS
+
+            LINKER_TOGGLE_STATIC_DYNAMIC = IntelIccIfort.LINKER_TOGGLE_STATIC_DYNAMIC
+
+            super(CrayPEWrapperIntel, self).set_compiler_vars()
+        else:
+            super(CrayPEWrapper, self)._set_compiler_vars()
+
 
 class CrayPEWrapperCray(CrayPEWrapper):
-    pass
\ No newline at end of file
+    TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_CRAY'
+    COMPILER_MODULE_NAME = ['PrgEnv-cray']
+
+    def _set_compiler_vars(self):
+        super(CrayPEWrapperCray, self)._set_compiler_vars()
\ No newline at end of file
diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py
index 9b1886d96b..e47a9c4778 100644
--- a/easybuild/toolchains/compiler/gcc.py
+++ b/easybuild/toolchains/compiler/gcc.py
@@ -95,5 +95,5 @@ def _set_compiler_vars(self):
         # append lib dir paths to LDFLAGS (only if the paths are actually there)
         # Note: hardcode 'GCC' here; we can not reuse COMPILER_MODULE_NAME because
         # it can be redefined by combining GCC with other compilers (e.g., Clang).
-        #gcc_root = self.get_software_root('GCC')[0]
-        #self.variables.append_subdirs("LDFLAGS", gcc_root, subdirs=["lib64", "lib"])
+        gcc_root = self.get_software_root('GCC')[0]
+        self.variables.append_subdirs("LDFLAGS", gcc_root, subdirs=["lib64", "lib"])
diff --git a/easybuild/toolchains/cpec.py b/easybuild/toolchains/cpec.py
index e183c1dbdf..f6d2c79041 100644
--- a/easybuild/toolchains/cpec.py
+++ b/easybuild/toolchains/cpec.py
@@ -27,7 +27,7 @@
 """
 
 
-from easybuild.toolchains.compiler.craypewrappers import *
+from easybuild.toolchains.compiler.craypewrappers import CrayPEWrapperCray
 
 class cpec(CrayPEWrapperCray):
     """Compiler toolchain with Cray cc,CC,ftn,LibSci,MPT,SHMEM."""
diff --git a/easybuild/toolchains/cpeg.py b/easybuild/toolchains/cpeg.py
index 770bac48d1..90b51084ef 100644
--- a/easybuild/toolchains/cpeg.py
+++ b/easybuild/toolchains/cpeg.py
@@ -27,7 +27,7 @@
 """
 
 
-from easybuild.toolchains.compiler.craypewrappers import *
+from easybuild.toolchains.compiler.craypewrappers import CrayPEWrapperGNU
 
 class cpeg(CrayPEWrapperGNU):
     """Compiler toolchain with Cray cc,CC,ftn,LibSci,MPT,SHMEM."""
diff --git a/easybuild/toolchains/cpei.py b/easybuild/toolchains/cpei.py
index 8d1d65c255..00e0411e0e 100644
--- a/easybuild/toolchains/cpei.py
+++ b/easybuild/toolchains/cpei.py
@@ -27,7 +27,7 @@
 """
 
 
-from easybuild.toolchains.compiler.craypewrappers import *
+from easybuild.toolchains.compiler.craypewrappers import CrayPEWrapperIntel
 
 class cpei(CrayPEWrapperIntel):
     """Compiler toolchain with Cray cc,CC,ftn,LibSci,MPT,SHMEM."""

From d0a8c5b822e07b498f761662fb52e2c66eba5c09 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 24 Feb 2015 14:33:59 +0100
Subject: [PATCH 0596/1356] use TEST_EASYBUILD_ prefix for environment
 variables picked by unit tests to configure EasyBuild

---
 test/framework/utilities.py | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index efb5500bdf..733de7e469 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -51,31 +51,30 @@
 from easybuild.tools.filetools import mkdir, read_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.modules import modules_tool
-from easybuild.tools.options import EasyBuildOptions
+from easybuild.tools.options import CONFIG_ENV_VAR_PREFIX, EasyBuildOptions
 
 
 # make sure tests are robust against any non-default configuration settings;
 # involves ignoring any existing configuration files that are picked up, and cleaning the environment
 # this is tackled here rather than in suite.py, to make sure this is also done when test modules are ran separately
 
-# keep track of any $EASYBUILD_TEST_X environment variables
-test_env_var_prefix = 'EASYBUILD_TEST_'
-eb_test_env_vars = dict([(key, val) for (key, val) in os.environ.items() if key.startswith(test_env_var_prefix)])
-
 # clean up environment from unwanted $EASYBUILD_X env vars
 for key in os.environ.keys():
-    if key.startswith('EASYBUILD_'):
+    if key.startswith('%s_' % CONFIG_ENV_VAR_PREFIX):
         del os.environ[key]
 
 # ignore any existing configuration files
 go = EasyBuildOptions(go_useconfigfiles=False)
 os.environ['EASYBUILD_IGNORECONFIGFILES'] = ','.join(go.options.configfiles)
 
-# redefine $EASYBUILD_TEST_X env vars as $EASYBUILD_X
-for testkey, val in eb_test_env_vars.items():
-    key = 'EASYBUILD_%s' % testkey[len(test_env_var_prefix):]
-    os.environ[key] = val
-
+# redefine $TEST_EASYBUILD_X env vars as $EASYBUILD_X
+test_env_var_prefix = 'TEST_EASYBUILD_'
+for key in os.environ.keys():
+    if key.startswith(test_env_var_prefix):
+        val = os.environ[key]
+        del os.environ[key]
+        key = '%s_%s' % (CONFIG_ENV_VAR_PREFIX, key[len(test_env_var_prefix):])
+        os.environ[key] = val
 
 class EnhancedTestCase(_EnhancedTestCase):
     """Enhanced test case, provides extra functionality (e.g. an assertErrorRegex method)."""

From 1a20ea61551a0b844c6d4c9d83f8b7aa4fe795aa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 24 Feb 2015 14:39:01 +0100
Subject: [PATCH 0597/1356] tiny style fix

---
 test/framework/utilities.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 733de7e469..8a7278f2ad 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -73,8 +73,8 @@
     if key.startswith(test_env_var_prefix):
         val = os.environ[key]
         del os.environ[key]
-        key = '%s_%s' % (CONFIG_ENV_VAR_PREFIX, key[len(test_env_var_prefix):])
-        os.environ[key] = val
+        newkey = '%s_%s' % (CONFIG_ENV_VAR_PREFIX, key[len(test_env_var_prefix):])
+        os.environ[newkey] = val
 
 class EnhancedTestCase(_EnhancedTestCase):
     """Enhanced test case, provides extra functionality (e.g. an assertErrorRegex method)."""

From 00bfdb55427ffdf06b577d51d794fd43bb00fca0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 09:06:41 +0100
Subject: [PATCH 0598/1356] clean up implementation of get_cpu_speed

---
 easybuild/tools/systemtools.py | 90 ++++++++++++++++------------------
 1 file changed, 41 insertions(+), 49 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 77dc04b996..ea72b64156 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -58,6 +58,9 @@
 
 UNKNOWN = 'UNKNOWN'
 
+MAX_FREQ_FP = '/sys/devices/system/cpu/cpu0/cpufreq/scaling_max_freq'
+PROC_CPUINFO_FP = '/proc/cpuinfo'
+
 
 class SystemToolsException(Exception):
     """raised when systemtools fails"""
@@ -89,7 +92,7 @@ def count_bits(n):
 
         # determine total number of cores via /proc/cpuinfo
         try:
-            txt = read_file('/proc/cpuinfo', log_error=False)
+            txt = read_file(PROC_CPUINFO_FP, log_error=False)
             # sometimes this is uppercase
             max_num_cores = txt.lower().count('processor\t:')
         except IOError, err:
@@ -146,7 +149,7 @@ def get_cpu_vendor():
 
     if os_type == LINUX:
         try:
-            txt = read_file('/proc/cpuinfo', log_error=False)
+            txt = read_file(PROC_CPUINFO_FP, log_error=False)
             arch = UNKNOWN
             # vendor_id might not be in the /proc/cpuinfo, so this might fail
             res = regexp.search(txt)
@@ -191,7 +194,7 @@ def get_cpu_model():
     if os_type == LINUX:
         regexp = re.compile(r"^model name\s+:\s*(?P<modelname>.+)\s*$", re.M)
         try:
-            txt = read_file('/proc/cpuinfo', log_error=False)
+            txt = read_file(PROC_CPUINFO_FP, log_error=False)
             if txt is not None:
                 res = regexp.search(txt)
                 if res is not None:
@@ -213,58 +216,47 @@ def get_cpu_speed():
     Returns the (maximum) cpu speed in MHz, as a float value.
     In case of throttling, the highest cpu speed is returns.
     """
+    cpu_freq = None
     os_type = get_os_type()
+
     if os_type == LINUX:
-        try:
-            # Linux with cpu scaling
-            max_freq_fp = '/sys/devices/system/cpu/cpu0/cpufreq/scaling_max_freq'
-            _log.debug("Trying to determine CPU frequency via %s" % max_freq_fp)
-            try:
-                f = open(max_freq_fp, 'r')
-                cpu_freq = float(f.read())/1000
-                f.close()
-                return cpu_freq
-            except IOError, err:
-                _log.debug("Failed to read %s to determine max. CPU clock frequency with CPU scaling: %s" % (max_freq_fp, err))
-
-            # Linux without cpu scaling
-            cpuinfo_fp = '/proc/cpuinfo'
-            _log.debug("Trying to determine CPU frequency via %s" % cpuinfo_fp)
-            try:
-                cpu_freq = None
-                cpuinfo_txt = open(cpuinfo_fp, 'r').read()
-                cpu_freq_patterns = [
-                    r"^cpu MHz\s*:\s*(?P<cpu_freq>[0-9.]+)",  # Linux x86 & more
-                    r"^clock\s*:\s*(?P<cpu_freq>[0-9.]+)",  # Linux on POWER
-                ]
-                for cpu_freq_pattern in cpu_freq_patterns:
-                    cpu_freq_re = re.compile(cpu_freq_pattern, re.M)
-                    res = cpu_freq_re.search(cpuinfo_txt)
-                    if res:
-                        cpu_freq = res.group('cpu_freq')
-                        _log.debug("Found CPU frequency using regex '%s': %s" % (cpu_freq_pattern, cpu_freq))
-                        break
-                    else:
-                        _log.debug("Failed to determine CPU frequency using regex '%s'" % cpu_freq_re.pattern)
-                if cpu_freq is None:
-                    raise SystemToolsException("Failed to determine CPU frequency from %s" % cpuinfo_fp)
-                else:
-                    return float(cpu_freq)
-            except IOError, err:
-                _log.debug("Failed to read %s to determine CPU clock frequency: %s" % (cpuinfo_fp, err))
-
-        except (IOError, OSError), err:
-            raise SystemToolsException("Determining CPU speed failed, exception occured: %s" % err)
+        # Linux with cpu scaling
+        if os.path.exists(MAX_FREQ_FP):
+            _log.debug("Trying to determine CPU frequency on Linux via %s" % MAX_FREQ_FP)
+            txt = read_file(MAX_FREQ_FP)
+            cpu_freq = float(txt)/1000
+
+        # Linux without cpu scaling
+        elif os.path.exists(PROC_CPUINFO_FP):
+            _log.debug("Trying to determine CPU frequency on Linux via %s" % PROC_CPUINFO_FP)
+            cpuinfo_txt = read_file(PROC_CPUINFO_FP)
+            cpu_freq_regex = r"(%s)" % '|'.join([
+                r"^cpu MHz\s*:\s*(?P<cpu_freq_x86>[0-9.]+)",  # Linux x86 & more
+                r"^clock\s*:\s*(?P<cpu_freq_POWER>[0-9.]+)",  # Linux on POWER
+            ])
+            res = re.search(cpu_freq_regex, cpuinfo_txt, re.M)
+            if res:
+                cpu_freq = res.group('cpu_freq_x86') or res.group('cpu_freq_POWER')
+            if cpu_freq is not None:
+                cpu_freq = float(cpu_freq)
+                _log.debug("Found CPU frequency using regex '%s': %s" % (cpu_freq_regex, cpu_freq))
+            else:
+                raise SystemToolsException("Failed to determine CPU frequency from %s" % PROC_CPUINFO_FP)
+        else:
+            _log.debug("%s not found to determine max. CPU clock frequency without CPU scaling: %s" % PROC_CPUINFO_FP)
 
     elif os_type == DARWIN:
-        # OS X
-        out, ec = run_cmd("sysctl -n hw.cpufrequency_max")
-        # returns clock frequency in cycles/sec, but we want MHz
-        mhz = float(out.strip())/(1000**2)
+        cmd = "sysctl -n hw.cpufrequency_max"
+        _log.debug("Trying to determine CPU frequency on Darwin via cmd '%s'" % cmd)
+        out, ec = run_cmd(cmd)
         if ec == 0:
-            return mhz
+            # returns clock frequency in cycles/sec, but we want MHz
+            cpu_freq = float(out.strip())/(1000**2)
+
+    else:
+        raise SystemToolsException("Could not determine CPU clock frequency (OS: %s)." % os_type)
 
-    raise SystemToolsException("Could not determine CPU clock frequency (OS: %s)." % os_type)
+    return cpu_freq
 
 
 def get_kernel_name():

From 6f900a40f576e0e07c1df7ef2be2d5fa5a9cbfe1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 09:08:38 +0100
Subject: [PATCH 0599/1356] thoroughly test possible code paths in
 get_cpu_speed by mocking used functions

---
 test/framework/systemtools.py | 155 +++++++++++++++++++++++++++++++++-
 1 file changed, 153 insertions(+), 2 deletions(-)

diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index 8447913dc7..95c7bbf81b 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -28,19 +28,144 @@
 @author: Kenneth hoste (Ghent University)
 """
 import os
-from test.framework.utilities import EnhancedTestCase, init_config
+from os.path import exists as orig_os_path_exists
+from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
 
+import easybuild.tools.systemtools as st
+from easybuild.tools.filetools import read_file
+from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import AMD, ARM, DARWIN, INTEL, LINUX, UNKNOWN
-from easybuild.tools.systemtools import get_avail_core_count, get_core_count
+from easybuild.tools.systemtools import get_avail_core_count
 from easybuild.tools.systemtools import get_cpu_model, get_cpu_speed, get_cpu_vendor, get_glibc_version
 from easybuild.tools.systemtools import get_os_type, get_os_name, get_os_version, get_platform_name, get_shared_lib_ext
 from easybuild.tools.systemtools import get_system_info
 
 
+MAX_FREQ_FP = '/sys/devices/system/cpu/cpu0/cpufreq/scaling_max_freq'
+PROC_CPUINFO_FP = '/proc/cpuinfo'
+
+PROC_CPUINFO_TXT = None
+PROC_CPUINFO_TXT_X86 = """processor	: 0
+vendor_id	: GenuineIntel
+cpu family	: 6
+model		: 45
+model name	: Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
+stepping	: 7
+microcode	: 1808
+cpu MHz		: 2600.075
+cache size	: 20480 KB
+physical id	: 0
+siblings	: 8
+core id		: 0
+cpu cores	: 8
+apicid		: 0
+initial apicid	: 0
+fpu		: yes
+fpu_exception	: yes
+cpuid level	: 13
+wp		: yes
+flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx lahf_lm ida arat xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid
+bogomips	: 5200.15
+clflush size	: 64
+cache_alignment	: 64
+address sizes	: 46 bits physical, 48 bits virtual
+power management:
+
+processor	: 1
+vendor_id	: GenuineIntel
+cpu family	: 6
+model		: 45
+model name	: Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
+stepping	: 7
+microcode	: 1808
+cpu MHz		: 2600.075
+cache size	: 20480 KB
+physical id	: 1
+siblings	: 8
+core id		: 0
+cpu cores	: 8
+apicid		: 32
+initial apicid	: 32
+fpu		: yes
+fpu_exception	: yes
+cpuid level	: 13
+wp		: yes
+flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx lahf_lm ida arat xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid
+bogomips	: 5200.04
+clflush size	: 64
+cache_alignment	: 64
+address sizes	: 46 bits physical, 48 bits virtual
+power management:
+"""
+PROC_CPUINFO_TXT_POWER = """
+processor	: 0
+cpu		: POWER7 (architected), altivec supported
+clock		: 3550.000000MHz
+revision	: 2.3 (pvr 003f 0203)
+ 
+processor	: 13
+cpu		: POWER7 (architected), altivec supported
+clock		: 3550.000000MHz
+revision	: 2.3 (pvr 003f 0203)
+ 
+timebase	: 512000000
+platform	: pSeries
+model		: IBM,8205-E6C
+machine		: CHRP IBM,8205-E6C
+"""
+
+
+def mocked_read_file(fp):
+    """Mocked version of read_file, with specified contents for known filenames."""
+    known_fps = {
+        MAX_FREQ_FP:  '2850000',
+        PROC_CPUINFO_FP: PROC_CPUINFO_TXT,
+    }
+    if fp in known_fps:
+        return known_fps[fp]
+    else:
+        return read_file(fp)
+
+def mocked_os_path_exists(mocked_fp, fp):
+    """Mocked version of os.path.exists, returns True for a particular specified filepath."""
+    if fp == mocked_fp:
+        return True
+    else:
+        orig_os_path_exists(fp)
+
+def mocked_run_cmd(cmd, **kwargs):
+    """Mocked version of run_cmd, with specified output for known commands."""
+    known_cmds = {
+        "sysctl -n hw.cpufrequency_max": "2400000000",
+    }
+    if cmd in known_cmds:
+        if 'simple' in kwargs and kwargs['simple']:
+            return True
+        else:
+            return (known_cmds[cmd], 0)
+    else:
+        return run_cmd(cmd, **kwargs)
+
+
 class SystemToolsTest(EnhancedTestCase):
     """ very basis FileRepository test, we don't want git / svn dependency """
 
+    def setUp(self):
+        """Set up systemtools test."""
+        super(SystemToolsTest, self).setUp()
+        self.orig_get_os_type = st.get_os_type
+        self.orig_os_path_exists = st.os.path.exists
+        self.orig_read_file = st.read_file
+        self.orig_run_cmd = st.run_cmd
+
+    def tearDown(self):
+        """Cleanup after systemtools test."""
+        st.os.path.exists = self.orig_os_path_exists
+        st.read_file = self.orig_read_file
+        st.get_os_type = self.orig_get_os_type
+        super(SystemToolsTest, self).tearDown()
+
     def test_avail_core_count(self):
         """Test getting core count."""
         core_count = get_avail_core_count()
@@ -58,6 +183,32 @@ def test_cpu_speed(self):
         self.assertTrue(isinstance(cpu_speed, float))
         self.assertTrue(cpu_speed > 0.0)
 
+        # test for particular type of system by mocking used functions
+        st.get_os_type = lambda: st.LINUX
+        st.read_file = mocked_read_file
+        st.os.path.exists = lambda fp: mocked_os_path_exists(PROC_CPUINFO_FP, fp)
+
+        # tweak global constant used by mocked_read_file
+        global PROC_CPUINFO_TXT
+
+        # /proc/cpuinfo on Linux x86 (no cpufreq)
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_X86
+        self.assertEqual(get_cpu_speed(), 2600.075)
+
+        # /proc/cpuinfo on Linux POWER
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_POWER
+        self.assertEqual(get_cpu_speed(), 3550.0)
+
+        # Linux (x86) with cpufreq
+        st.os.path.exists = lambda fp: mocked_os_path_exists(MAX_FREQ_FP, fp)
+        self.assertEqual(get_cpu_speed(), 2850.0)
+
+        # OS X
+        st.os.path.exists = self.orig_os_path_exists
+        st.get_os_type = lambda: st.DARWIN
+        st.run_cmd = mocked_run_cmd
+        self.assertEqual(get_cpu_speed(), 2400.0)
+
     def test_cpu_vendor(self):
         """Test getting CPU vendor."""
         cpu_vendor = get_cpu_vendor()

From 82f3b4a6eafab5cc5506f10a96517d8577056c68 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 09:27:06 +0100
Subject: [PATCH 0600/1356] clean up get_avail_core_count, enhance testing for
 it

---
 easybuild/tools/systemtools.py | 70 +++++++---------------------------
 test/framework/systemtools.py  | 13 +++++++
 2 files changed, 27 insertions(+), 56 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index ea72b64156..086bc62088 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -36,11 +36,7 @@
 import sys
 from socket import gethostname
 from vsc.utils import fancylogger
-try:
-    # this import fails with Python 2.4 because it requires the ctypes module (only in Python 2.5+)
-    from vsc.utils.affinity import sched_getaffinity
-except ImportError:
-    pass
+from vsc.utils.affinity import sched_getaffinity
 
 from easybuild.tools.filetools import read_file, which
 from easybuild.tools.run import run_cmd
@@ -52,6 +48,7 @@
 AMD = 'AMD'
 ARM = 'ARM'
 INTEL = 'Intel'
+PPC = 'PPC'
 
 LINUX = 'Linux'
 DARWIN = 'Darwin'
@@ -70,64 +67,25 @@ def get_avail_core_count():
     """
     Returns the number of available CPUs, according to cgroups and taskssets limits
     """
-    # tiny inner function to help figure out number of available cores in a cpuset
-    def count_bits(n):
-        """Count the number of set bits for a given integer."""
-        bit_cnt = 0
-        while n > 0:
-            n &= n - 1
-            bit_cnt += 1
-        return bit_cnt
-
+    core_cnt = None
     os_type = get_os_type()
-    if os_type == LINUX:
-        try:
-            # the preferred approach is via sched_getaffinity (yields a long, so cast it down to int)
-            num_cores = int(sum(sched_getaffinity().cpus))
-            return num_cores
-        except NameError:
-            pass
-
-        # in case sched_getaffinity isn't available, fall back to relying on /proc/cpuinfo
-
-        # determine total number of cores via /proc/cpuinfo
-        try:
-            txt = read_file(PROC_CPUINFO_FP, log_error=False)
-            # sometimes this is uppercase
-            max_num_cores = txt.lower().count('processor\t:')
-        except IOError, err:
-            raise SystemToolsException("An error occured while determining total core count: %s" % err)
 
-        # determine cpuset we're in (if any)
-        mypid = os.getpid()
-        try:
-            f = open("/proc/%s/status" % mypid, 'r')
-            txt = f.read()
-            f.close()
-            cpuset = re.search("^Cpus_allowed:\s*([0-9,a-f]+)", txt, re.M | re.I)
-        except IOError:
-            cpuset = None
-
-        if cpuset is not None:
-            # use cpuset mask to determine actual number of available cores
-            mask_as_int = long(cpuset.group(1).replace(',', ''), 16)
-            num_cores_in_cpuset = count_bits((2**max_num_cores - 1) & mask_as_int)
-            _log.info("In cpuset with %s CPUs" % num_cores_in_cpuset)
-            return num_cores_in_cpuset
-        else:
-            _log.debug("No list of allowed CPUs found, not in a cpuset.")
-            return max_num_cores
+    if os_type == LINUX:
+        # simple use available sched_getaffinity() function (yields a long, so cast it down to int)
+        core_cnt = int(sum(sched_getaffinity().cpus))
     else:
-        # BSD
+        # BSD-type systems
+        out, _ = run_cmd('sysctl -n hw.ncpu')
         try:
-            out, _ = run_cmd('sysctl -n hw.ncpu')
-            num_cores = int(out)
-            if num_cores > 0:
-                return num_cores
+            if int(out) > 0:
+                core_cnt = int(out)
         except ValueError:
             pass
 
-    raise SystemToolsException('Can not determine number of cores on this system')
+    if core_cnt is None:
+        raise SystemToolsException('Can not determine number of cores on this system')
+    else:
+        return core_cnt
 
 
 def get_core_count():
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index 95c7bbf81b..472247dc98 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -138,6 +138,7 @@ def mocked_run_cmd(cmd, **kwargs):
     """Mocked version of run_cmd, with specified output for known commands."""
     known_cmds = {
         "sysctl -n hw.cpufrequency_max": "2400000000",
+        "sysctl -n hw.ncpu": '10',
     }
     if cmd in known_cmds:
         if 'simple' in kwargs and kwargs['simple']:
@@ -172,6 +173,18 @@ def test_avail_core_count(self):
         self.assertTrue(isinstance(core_count, int), "core_count has type int: %s, %s" % (core_count, type(core_count)))
         self.assertTrue(core_count > 0, "core_count %d > 0" % core_count)
 
+        st.get_os_type = lambda: st.LINUX
+        orig_sched_getaffinity = st.sched_getaffinity
+        class MockedSchedGetaffinity(object):
+            cpus = [1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L]
+        st.sched_getaffinity = lambda: MockedSchedGetaffinity()
+        self.assertEqual(get_avail_core_count(), 6)
+        st.sched_getaffinity = orig_sched_getaffinity
+
+        st.get_os_type = lambda: st.DARWIN
+        st.run_cmd = mocked_run_cmd
+        self.assertEqual(get_avail_core_count(), 10)
+
     def test_cpu_model(self):
         """Test getting CPU model."""
         cpu_model = get_cpu_model()

From 526c4fe2587d13dd87063068acc3fbe48a0f8c08 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 09:53:40 +0100
Subject: [PATCH 0601/1356] clean up get_cpu_vendor and enhance dedicated test
 for it

---
 easybuild/tools/systemtools.py | 76 +++++++++++++++++-----------------
 test/framework/systemtools.py  | 68 +++++++++++++++++++++++-------
 2 files changed, 91 insertions(+), 53 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 086bc62088..daff28ccae 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -58,6 +58,11 @@
 MAX_FREQ_FP = '/sys/devices/system/cpu/cpu0/cpufreq/scaling_max_freq'
 PROC_CPUINFO_FP = '/proc/cpuinfo'
 
+VENDORS = {
+    'GenuineIntel': INTEL,
+    'AuthenticAMD': AMD,
+}
+
 
 class SystemToolsException(Exception):
     """raised when systemtools fails"""
@@ -94,52 +99,49 @@ def get_core_count():
 
 
 def get_cpu_vendor():
-    """Try to detect the cpu identifier
+    """
+    Try to detect the CPU vendor
 
-    will return INTEL, ARM or AMD constant
+    @return: INTEL, ARM or AMD constant
     """
-    regexp = re.compile(r"^vendor_id\s+:\s*(?P<vendorid>\S+)\s*$", re.M)
-    VENDORS = {
-        'GenuineIntel': INTEL,
-        'AuthenticAMD': AMD,
-    }
+    vendor = None
     os_type = get_os_type()
 
-    if os_type == LINUX:
-        try:
-            txt = read_file(PROC_CPUINFO_FP, log_error=False)
-            arch = UNKNOWN
-            # vendor_id might not be in the /proc/cpuinfo, so this might fail
-            res = regexp.search(txt)
-            if res:
-                arch = res.groupdict().get('vendorid', UNKNOWN)
-            if arch in VENDORS:
-                return VENDORS[arch]
-
-            # some embeded linux on arm behaves differently (e.g. raspbian)
-            regexp = re.compile(r"^Processor\s+:\s*(?P<vendorid>ARM\S+)\s*", re.M)
-            res = regexp.search(txt)
-            if res:
-                arch = res.groupdict().get('vendorid', UNKNOWN)
-            if ARM in arch:
-                return ARM
-        except IOError, err:
-            raise SystemToolsException("An error occured while determining CPU vendor since: %s" % err)
+    if os_type == LINUX and os.path.exists(PROC_CPUINFO_FP):
+        txt = read_file(PROC_CPUINFO_FP)
+        arch = UNKNOWN
+
+        # vendor_id might not be in the /proc/cpuinfo, so this might fail
+        vendor_regex = re.compile(r"^vendor_id\s+:\s*(?P<vendorid>\S+)\s*$", re.M)
+        res = vendor_regex.search(txt)
+        if res:
+            arch = res.group('vendorid')
+        if arch in VENDORS:
+            vendor = VENDORS[arch]
+            tup = (vendor, vendor_regex.pattern, PROC_CPUINFO_FP)
+            _log.debug("Determined CPU vendor on Linux as being '%s' via regex '%s' in %s" % tup)
+
+        # embedded Linux on ARM behaves differently (e.g. Raspbian)
+        vendor_regex = re.compile(r".*:\s*(?P<vendorid>ARM\S+)\s*", re.M)
+        res = vendor_regex.search(txt)
+        if res:
+            vendor = ARM
+            tup = (vendor, vendor_regex.pattern, PROC_CPUINFO_FP)
+            _log.debug("Determined CPU vendor on Linux as being '%s' via regex '%s' in %s" % tup)
 
     elif os_type == DARWIN:
-        out, exitcode = run_cmd("sysctl -n machdep.cpu.vendor")
+        cmd = "sysctl -n machdep.cpu.vendor"
+        out, ec = run_cmd(cmd)
         out = out.strip()
-        if not exitcode and out and out in VENDORS:
-            return VENDORS[out]
+        if ec == 0 and out and out in VENDORS:
+            vendor = VENDORS[out]
+            _log.debug("Determined CPU vendor on DARWIN as being '%s' via cmd '%s" % (vendor, cmd))
 
-    else:
-        # BSD
-        out, exitcode = run_cmd("sysctl -n hw.model")
-        out = out.strip()
-        if not exitcode and out:
-            return out.split(' ')[0]
+    if vendor is None:
+        vendor = UNKNOWN
+        _log.warning("Could not determine CPU vendor on %s, returning %s" % (os_type, vendor))
 
-    return UNKNOWN
+    return vendor
 
 
 def get_cpu_model():
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index 472247dc98..f49c38c90a 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -46,6 +46,41 @@
 PROC_CPUINFO_FP = '/proc/cpuinfo'
 
 PROC_CPUINFO_TXT = None
+PROC_CPUINFO_TXT_ARM = """processor : 0
+model name : ARMv7 Processor rev 5 (v7l)
+BogoMIPS : 57.60
+Features : half thumb fastmult vfp edsp neon vfpv3 tls vfpv4 idiva idivt vfpd32 lpae evtstrm
+CPU implementer : 0x41
+CPU architecture: 7
+CPU variant : 0x0
+CPU part : 0xc07
+CPU revision : 5
+ 
+processor : 1
+model name : ARMv7 Processor rev 5 (v7l)
+BogoMIPS : 57.60
+Features : half thumb fastmult vfp edsp neon vfpv3 tls vfpv4 idiva idivt vfpd32 lpae evtstrm
+CPU implementer : 0x41
+CPU architecture: 7
+CPU variant : 0x0
+CPU part : 0xc07
+CPU revision : 5 
+"""
+PROC_CPUINFO_TXT_POWER = """processor	: 0
+cpu		: POWER7 (architected), altivec supported
+clock		: 3550.000000MHz
+revision	: 2.3 (pvr 003f 0203)
+ 
+processor	: 13
+cpu		: POWER7 (architected), altivec supported
+clock		: 3550.000000MHz
+revision	: 2.3 (pvr 003f 0203)
+ 
+timebase	: 512000000
+platform	: pSeries
+model		: IBM,8205-E6C
+machine		: CHRP IBM,8205-E6C
+"""
 PROC_CPUINFO_TXT_X86 = """processor	: 0
 vendor_id	: GenuineIntel
 cpu family	: 6
@@ -98,22 +133,6 @@
 address sizes	: 46 bits physical, 48 bits virtual
 power management:
 """
-PROC_CPUINFO_TXT_POWER = """
-processor	: 0
-cpu		: POWER7 (architected), altivec supported
-clock		: 3550.000000MHz
-revision	: 2.3 (pvr 003f 0203)
- 
-processor	: 13
-cpu		: POWER7 (architected), altivec supported
-clock		: 3550.000000MHz
-revision	: 2.3 (pvr 003f 0203)
- 
-timebase	: 512000000
-platform	: pSeries
-model		: IBM,8205-E6C
-machine		: CHRP IBM,8205-E6C
-"""
 
 
 def mocked_read_file(fp):
@@ -139,6 +158,7 @@ def mocked_run_cmd(cmd, **kwargs):
     known_cmds = {
         "sysctl -n hw.cpufrequency_max": "2400000000",
         "sysctl -n hw.ncpu": '10',
+        "sysctl -n machdep.cpu.vendor": 'GenuineIntel',
     }
     if cmd in known_cmds:
         if 'simple' in kwargs and kwargs['simple']:
@@ -227,6 +247,22 @@ def test_cpu_vendor(self):
         cpu_vendor = get_cpu_vendor()
         self.assertTrue(cpu_vendor in [AMD, ARM, INTEL, UNKNOWN])
 
+        st.get_os_type = lambda: st.LINUX
+        st.read_file = mocked_read_file
+        st.os.path.exists = lambda fp: mocked_os_path_exists(PROC_CPUINFO_FP, fp)
+
+        global PROC_CPUINFO_TXT
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_X86
+        self.assertEqual(get_cpu_vendor(), INTEL)
+
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_ARM
+        self.assertEqual(get_cpu_vendor(), ARM)
+
+        st.os.path.exists = self.orig_os_path_exists
+        st.get_os_type = lambda: st.DARWIN
+        st.run_cmd = mocked_run_cmd
+        self.assertEqual(get_cpu_vendor(), INTEL)
+
     def test_os_type(self):
         """Test getting OS type."""
         os_type = get_os_type()

From 793af55e4e5d35438a7ad602c0a2f31450229339 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 10:34:28 +0100
Subject: [PATCH 0602/1356] clean up get_cpu_model and enhance dedicated test
 for it

---
 easybuild/tools/systemtools.py | 42 ++++++++++++++++++++--------------
 test/framework/systemtools.py  | 25 ++++++++++++++++----
 2 files changed, 46 insertions(+), 21 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index daff28ccae..52d8525ace 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -146,27 +146,35 @@ def get_cpu_vendor():
 
 def get_cpu_model():
     """
-    returns cpu model
-    f.ex Intel(R) Core(TM) i5-2540M CPU @ 2.60GHz
+    Determine CPU model
+    for example: Intel(R) Core(TM) i5-2540M CPU @ 2.60GHz
     """
-    model = UNKNOWN
+    model = None
     os_type = get_os_type()
-    if os_type == LINUX:
-        regexp = re.compile(r"^model name\s+:\s*(?P<modelname>.+)\s*$", re.M)
-        try:
-            txt = read_file(PROC_CPUINFO_FP, log_error=False)
-            if txt is not None:
-                res = regexp.search(txt)
-                if res is not None:
-                    model = res.group('modelname').strip()
-        except IOError, err:
-            raise SystemToolsException("An error occured when determining CPU model: %s" % err)
+
+    if os_type == LINUX and os.path.exists(PROC_CPUINFO_FP):
+        # consider 'model name' first, use 'model' as a fallback
+        # 'model name' is not there for Linux/POWER, but 'model' has the right info
+        for key in [r'model\s*name', 'model']:
+            model_regex = re.compile(r"^%s\s+:\s*(?P<model>.+)\s*$" % key, re.M)
+            txt = read_file(PROC_CPUINFO_FP)
+            res = model_regex.search(txt)
+            if res is not None:
+                model = res.group('model').strip()
+                tup = (model_regex.pattern, PROC_CPUINFO_FP, model)
+                _log.debug("Determined CPU model on Linux using regex '%s' in %s: %s" % tup)
+                break
 
     elif os_type == DARWIN:
-        out, exitcode = run_cmd("sysctl -n machdep.cpu.brand_string")
-        out = out.strip()
-        if not exitcode:
-            model = out
+        cmd = "sysctl -n machdep.cpu.brand_string"
+        out, ec = run_cmd(cmd)
+        if ec == 0:
+            model = out.strip()
+            _log.debug("Determined CPU model on Darwin using cmd '%s': %s" % (cmd, model))
+
+    if model is None:
+        model = UNKNOWN
+        _log.warning("Failed to determine CPU model, returning %s" % model)
 
     return model
 
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index f49c38c90a..091e19309b 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -148,16 +148,14 @@ def mocked_read_file(fp):
 
 def mocked_os_path_exists(mocked_fp, fp):
     """Mocked version of os.path.exists, returns True for a particular specified filepath."""
-    if fp == mocked_fp:
-        return True
-    else:
-        orig_os_path_exists(fp)
+    return fp == mocked_fp or orig_os_path_exists(fp)
 
 def mocked_run_cmd(cmd, **kwargs):
     """Mocked version of run_cmd, with specified output for known commands."""
     known_cmds = {
         "sysctl -n hw.cpufrequency_max": "2400000000",
         "sysctl -n hw.ncpu": '10',
+        "sysctl -n machdep.cpu.brand_string": "Intel(R) Core(TM) i5-4258U CPU @ 2.40GHz",
         "sysctl -n machdep.cpu.vendor": 'GenuineIntel',
     }
     if cmd in known_cmds:
@@ -210,6 +208,25 @@ def test_cpu_model(self):
         cpu_model = get_cpu_model()
         self.assertTrue(isinstance(cpu_model, basestring))
 
+        st.get_os_type = lambda: st.LINUX
+        st.read_file = mocked_read_file
+        st.os.path.exists = lambda fp: mocked_os_path_exists(PROC_CPUINFO_FP, fp)
+        global PROC_CPUINFO_TXT
+
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_X86
+        self.assertEqual(get_cpu_model(), "Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz")
+
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_POWER
+        self.assertEqual(get_cpu_model(), "IBM,8205-E6C")
+
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_ARM
+        self.assertEqual(get_cpu_model(), "ARMv7 Processor rev 5 (v7l)")
+
+        st.os.path.exists = self.orig_os_path_exists
+        st.get_os_type = lambda: st.DARWIN
+        st.run_cmd = mocked_run_cmd
+        self.assertEqual(get_cpu_model(), "Intel(R) Core(TM) i5-4258U CPU @ 2.40GHz")
+
     def test_cpu_speed(self):
         """Test getting CPU speed."""
         cpu_speed = get_cpu_speed()

From d6b33a0eedaa9e19d0cd1c3a25aad9d2b05e0a94 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 10:47:10 +0100
Subject: [PATCH 0603/1356] enhance error message in get_glibc_version

---
 easybuild/tools/systemtools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 52d8525ace..e89bffd809 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -398,7 +398,7 @@ def get_glibc_version():
             return glibc_version
         else:
             tup = (glibc_ver_str, glibc_ver_regex.pattern)
-            _log.error("Failed to determine version from '%s' using pattern '%s'." % tup)
+            _log.error("Failed to determine glibc version from '%s' using pattern '%s'." % tup)
     else:
         # no glibc on OS X standard
         _log.debug("No glibc on a non-Linux system, so can't determine version.")

From 708de3eb9bf54b2b0b37eaaf272b3975c64a1a28 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 10:59:03 +0100
Subject: [PATCH 0604/1356] moar systemtools testing via mocking used functions

---
 test/framework/systemtools.py | 49 +++++++++++++++++++++++++++++++++--
 1 file changed, 47 insertions(+), 2 deletions(-)

diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index 091e19309b..d0567fafb9 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -27,7 +27,7 @@
 
 @author: Kenneth hoste (Ghent University)
 """
-import os
+import re
 from os.path import exists as orig_os_path_exists
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
@@ -36,7 +36,7 @@
 from easybuild.tools.filetools import read_file
 from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import AMD, ARM, DARWIN, INTEL, LINUX, UNKNOWN
-from easybuild.tools.systemtools import get_avail_core_count
+from easybuild.tools.systemtools import det_parallelism, get_avail_core_count
 from easybuild.tools.systemtools import get_cpu_model, get_cpu_speed, get_cpu_vendor, get_glibc_version
 from easybuild.tools.systemtools import get_os_type, get_os_name, get_os_version, get_platform_name, get_shared_lib_ext
 from easybuild.tools.systemtools import get_system_info
@@ -153,10 +153,12 @@ def mocked_os_path_exists(mocked_fp, fp):
 def mocked_run_cmd(cmd, **kwargs):
     """Mocked version of run_cmd, with specified output for known commands."""
     known_cmds = {
+        "ldd --version" : "ldd (GNU libc) 2.12",
         "sysctl -n hw.cpufrequency_max": "2400000000",
         "sysctl -n hw.ncpu": '10',
         "sysctl -n machdep.cpu.brand_string": "Intel(R) Core(TM) i5-4258U CPU @ 2.40GHz",
         "sysctl -n machdep.cpu.vendor": 'GenuineIntel',
+        "ulimit -u": '40',
     }
     if cmd in known_cmds:
         if 'simple' in kwargs and kwargs['simple']:
@@ -290,6 +292,12 @@ def test_shared_lib_ext(self):
         ext = get_shared_lib_ext()
         self.assertTrue(ext in ['dylib', 'so'])
 
+        st.get_os_type = lambda: st.LINUX
+        self.assertEqual(get_shared_lib_ext(), 'so')
+
+        st.get_os_type = lambda: st.DARWIN
+        self.assertEqual(get_shared_lib_ext(), 'dylib')
+
     def test_platform_name(self):
         """Test getting platform name."""
         platform_name_nover = get_platform_name()
@@ -303,6 +311,12 @@ def test_platform_name(self):
         self.assertTrue(platform_name_ver.startswith(platform_name_ver))
         self.assertTrue(len_ver >= len_nover)
 
+        st.get_os_type = lambda: st.LINUX
+        self.assertTrue(re.match('.*-unknown-linux$', get_platform_name()))
+
+        st.get_os_type = lambda: st.DARWIN
+        self.assertTrue(re.match('.*-apple-darwin$', get_platform_name()))
+
     def test_os_name(self):
         """Test getting OS name."""
         os_name = get_os_name()
@@ -318,11 +332,42 @@ def test_glibc_version(self):
         glibc_version = get_glibc_version()
         self.assertTrue(isinstance(glibc_version, basestring) or glibc_version == UNKNOWN)
 
+        st.get_os_type = lambda: st.LINUX
+        st.run_cmd = mocked_run_cmd
+        self.assertEqual(get_glibc_version(), '2.12')
+
+        st.get_os_type = lambda: st.DARWIN
+        self.assertEqual(get_glibc_version(), UNKNOWN)
+
     def test_system_info(self):
         """Test getting system info."""
         system_info = get_system_info()
         self.assertTrue(isinstance(system_info, dict))
 
+    def test_det_parallelism(self):
+        """Test det_parallelism function."""
+        self.assertTrue(det_parallelism(None, None) > 0)
+        # specified parallellism
+        self.assertEqual(det_parallelism(5, None), 5)
+        # max parallellism caps
+        self.assertEqual(det_parallelism(None, 1), 1)
+        self.assertEqual(det_parallelism(16, 1), 1)
+        self.assertEqual(det_parallelism(5, 2), 2)
+        self.assertEqual(det_parallelism(5, 10), 5)
+
+        orig_get_avail_core_count = st.get_avail_core_count
+
+        # mock number of available cores to 8
+        st.get_avail_core_count = lambda: 8
+        self.assertTrue(det_parallelism(None, None), 8)
+        # make 'ulimit -u' return '40', which should result in default (max) parallelism of 4 ((40-15)/6)
+        st.run_cmd = mocked_run_cmd
+        self.assertTrue(det_parallelism(None, None), 4)
+        self.assertTrue(det_parallelism(6, None), 4)
+        self.assertTrue(det_parallelism(2, None), 2)
+
+        st.get_avail_core_count = orig_get_avail_core_count
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(SystemToolsTest)

From 1a9f9a3d02d329c74268ead145efc402a95f6413 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 11:50:44 +0100
Subject: [PATCH 0605/1356] add get_cpu_family() function in systemtools.py +
 dedicated test for it

---
 easybuild/tools/systemtools.py | 30 +++++++++++++++++++++++++++++-
 test/framework/systemtools.py  | 29 +++++++++++++++++++++++++++--
 2 files changed, 56 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index e89bffd809..00624b3e4d 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -48,7 +48,7 @@
 AMD = 'AMD'
 ARM = 'ARM'
 INTEL = 'Intel'
-PPC = 'PPC'
+POWER = 'POWER'
 
 LINUX = 'Linux'
 DARWIN = 'Darwin'
@@ -58,6 +58,7 @@
 MAX_FREQ_FP = '/sys/devices/system/cpu/cpu0/cpufreq/scaling_max_freq'
 PROC_CPUINFO_FP = '/proc/cpuinfo'
 
+CPU_FAMILIES = [ARM, AMD, INTEL, POWER]
 VENDORS = {
     'GenuineIntel': INTEL,
     'AuthenticAMD': AMD,
@@ -144,6 +145,33 @@ def get_cpu_vendor():
     return vendor
 
 
+def get_cpu_family():
+    """
+    Determine CPU family.
+    @return: one of the AMD, ARM, INTEL, POWER constants
+    """
+    family = None
+    vendor = get_cpu_vendor()
+    if vendor in CPU_FAMILIES:
+        family = vendor
+        _log.debug("Using vendor as CPU family: %s" % family)
+
+    else:
+        # POWER family needs to be determined indirectly via 'cpu' in /proc/cpuinfo
+        if os.path.exists(PROC_CPUINFO_FP):
+            cpuinfo_txt = read_file(PROC_CPUINFO_FP)
+            power_regex = re.compile(r"^cpu\s+:\s*POWER.*", re.M)
+            if power_regex.search(cpuinfo_txt):
+                family = POWER
+                tup = (power_regex.pattern, PROC_CPUINFO_FP, family)
+                _log.debug("Determined CPU family using regex '%s' in %s: %s" % tup)
+
+    if family is None:
+        family = UNKNOWN
+        _log.warning("Failed to determine CPU family, returning %s" % family)
+
+    return family
+
 def get_cpu_model():
     """
     Determine CPU model
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index d0567fafb9..d1d01beec5 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -35,8 +35,8 @@
 import easybuild.tools.systemtools as st
 from easybuild.tools.filetools import read_file
 from easybuild.tools.run import run_cmd
-from easybuild.tools.systemtools import AMD, ARM, DARWIN, INTEL, LINUX, UNKNOWN
-from easybuild.tools.systemtools import det_parallelism, get_avail_core_count
+from easybuild.tools.systemtools import CPU_FAMILIES, AMD, ARM, DARWIN, INTEL, LINUX, POWER, UNKNOWN
+from easybuild.tools.systemtools import det_parallelism, get_avail_core_count, get_cpu_family
 from easybuild.tools.systemtools import get_cpu_model, get_cpu_speed, get_cpu_vendor, get_glibc_version
 from easybuild.tools.systemtools import get_os_type, get_os_name, get_os_version, get_platform_name, get_shared_lib_ext
 from easybuild.tools.systemtools import get_system_info
@@ -185,6 +185,7 @@ def tearDown(self):
         st.os.path.exists = self.orig_os_path_exists
         st.read_file = self.orig_read_file
         st.get_os_type = self.orig_get_os_type
+        st.run_cmd = self.orig_run_cmd
         super(SystemToolsTest, self).tearDown()
 
     def test_avail_core_count(self):
@@ -282,6 +283,30 @@ def test_cpu_vendor(self):
         st.run_cmd = mocked_run_cmd
         self.assertEqual(get_cpu_vendor(), INTEL)
 
+    def test_cpu_family(self):
+        """Test get_cpu_family function."""
+        cpu_family = get_cpu_family()
+        self.assertTrue(cpu_family in CPU_FAMILIES or cpu_family == UNKNOWN)
+
+        st.get_os_type = lambda: st.LINUX
+        st.read_file = mocked_read_file
+        st.os.path.exists = lambda fp: mocked_os_path_exists(PROC_CPUINFO_FP, fp)
+
+        global PROC_CPUINFO_TXT
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_X86
+        self.assertEqual(get_cpu_family(), INTEL)
+
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_ARM
+        self.assertEqual(get_cpu_family(), ARM)
+
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_POWER
+        self.assertEqual(get_cpu_family(), POWER)
+
+        st.os.path.exists = self.orig_os_path_exists
+        st.get_os_type = lambda: st.DARWIN
+        st.run_cmd = mocked_run_cmd
+        self.assertEqual(get_cpu_family(), INTEL)
+
     def test_os_type(self):
         """Test getting OS type."""
         os_type = get_os_type()

From b6f57c3ad90ae87d5bf11a4570bca1372dcccbe4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 11:51:52 +0100
Subject: [PATCH 0606/1356] use get_cpu_family() rather than get_cpu_vendor()
 for picking optarch flag

---
 easybuild/tools/toolchain/compiler.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/toolchain/compiler.py b/easybuild/tools/toolchain/compiler.py
index 9b72f621af..3946eca9ba 100644
--- a/easybuild/tools/toolchain/compiler.py
+++ b/easybuild/tools/toolchain/compiler.py
@@ -260,7 +260,7 @@ def _set_compiler_flags(self):
     def _get_optimal_architecture(self):
         """ Get options for the current architecture """
         if self.arch is None:
-            self.arch = systemtools.get_cpu_vendor()
+            self.arch = systemtools.get_cpu_family()
 
         optarch = None
         if build_option('optarch') is not None:
@@ -272,7 +272,7 @@ def _get_optimal_architecture(self):
             self.log.info("_get_optimal_architecture: using %s as optarch for %s." % (optarch, self.arch))
             self.options.options_map['optarch'] = optarch
 
-        if 'optarch' in self.options.options_map and self.options.options_map.get('optarch', None) is None:
+        if self.options.options_map.get('optarch', None) is None:
             self.log.raiseException("_get_optimal_architecture: don't know how to set optarch for %s." % self.arch)
 
     def comp_family(self, prefix=None):

From c977b3e71502759f7d1680c8578387de424d444c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 11:52:17 +0100
Subject: [PATCH 0607/1356] use -mcpu=native for GCC/Clang on POWER

---
 easybuild/toolchains/compiler/clang.py | 56 +++++++++++++-------------
 easybuild/toolchains/compiler/gcc.py   | 43 ++++++++++----------
 test/framework/toolchain.py            | 10 ++++-
 3 files changed, 57 insertions(+), 52 deletions(-)

diff --git a/easybuild/toolchains/compiler/clang.py b/easybuild/toolchains/compiler/clang.py
index b78919bba1..d5b676bde1 100644
--- a/easybuild/toolchains/compiler/clang.py
+++ b/easybuild/toolchains/compiler/clang.py
@@ -53,38 +53,38 @@ class Clang(Compiler):
         'loop-vectorize': ['fvectorize'],
         'basic-block-vectorize': ['fslp-vectorize'],
         'optarch':'march=native',
-
-    # Clang's options do not map well onto these precision modes.  The flags enable and disable certain classes of
-    # optimizations.
-    # 
-    # -fassociative-math: allow re-association of operands in series of floating-point operations, violates the
-    # ISO C and C++ language standard by possibly changing computation result.
-    # -freciprocal-math: allow optimizations to use the reciprocal of an argument rather than perform division.
-    # -fsigned-zeros: do not allow optimizations to treat the sign of a zero argument or result as insignificant.
-    # -fhonor-infinities: disallow optimizations to assume that arguments and results are not +/- Infs.
-    # -fhonor-nans: disallow optimizations to assume that arguments and results are not +/- NaNs.
-    # -ffinite-math-only: allow optimizations for floating-point arithmetic that assume that arguments and results
-    # are not NaNs or +-Infs (equivalent to -fno-honor-nans -fno-honor-infinities)
-    # -funsafe-math-optimizations: allow unsafe math optimizations (implies -fassociative-math, -fno-signed-zeros,
-    # -freciprocal-math).
-    # -ffast-math: an umbrella flag that enables all optimizations listed above, provides preprocessor macro
-    # __FAST_MATH__.
-    #
-    # Using -fno-fast-math is equivalent to disabling all individual optimizations, see
-    # http://llvm.org/viewvc/llvm-project/cfe/trunk/lib/Driver/Tools.cpp?view=markup (lines 2100 and following)
-    #
-    # 'strict', 'precise' and 'defaultprec' are all ISO C++ and IEEE complaint, but we explicitly specify details
-    # flags for strict and precise for robustness against future changes.
-    'strict': ['fno-fast-math'],
-    'precise': ['fno-unsafe-math-optimizations'],
-    'defaultprec': [],
-    'loose': ['ffast-math', 'fno-unsafe-math-optimizations'],
-    'veryloose': ['ffast-math'],
+        # Clang's options do not map well onto these precision modes.  The flags enable and disable certain classes of
+        # optimizations.
+        # 
+        # -fassociative-math: allow re-association of operands in series of floating-point operations, violates the
+        # ISO C and C++ language standard by possibly changing computation result.
+        # -freciprocal-math: allow optimizations to use the reciprocal of an argument rather than perform division.
+        # -fsigned-zeros: do not allow optimizations to treat the sign of a zero argument or result as insignificant.
+        # -fhonor-infinities: disallow optimizations to assume that arguments and results are not +/- Infs.
+        # -fhonor-nans: disallow optimizations to assume that arguments and results are not +/- NaNs.
+        # -ffinite-math-only: allow optimizations for floating-point arithmetic that assume that arguments and results
+        # are not NaNs or +-Infs (equivalent to -fno-honor-nans -fno-honor-infinities)
+        # -funsafe-math-optimizations: allow unsafe math optimizations (implies -fassociative-math, -fno-signed-zeros,
+        # -freciprocal-math).
+        # -ffast-math: an umbrella flag that enables all optimizations listed above, provides preprocessor macro
+        # __FAST_MATH__.
+        #
+        # Using -fno-fast-math is equivalent to disabling all individual optimizations, see
+        # http://llvm.org/viewvc/llvm-project/cfe/trunk/lib/Driver/Tools.cpp?view=markup (lines 2100 and following)
+        #
+        # 'strict', 'precise' and 'defaultprec' are all ISO C++ and IEEE complaint, but we explicitly specify details
+        # flags for strict and precise for robustness against future changes.
+        'strict': ['fno-fast-math'],
+        'precise': ['fno-unsafe-math-optimizations'],
+        'defaultprec': [],
+        'loose': ['ffast-math', 'fno-unsafe-math-optimizations'],
+        'veryloose': ['ffast-math'],
     }
 
     COMPILER_OPTIMAL_ARCHITECTURE_OPTION = {
         systemtools.INTEL : 'march=native',
-        systemtools.AMD : 'march=native'
+        systemtools.AMD : 'march=native',
+        systemtools.POWER: 'mcpu=native',  # no support for march=native on POWER
     }
 
     COMPILER_CC = 'clang'
diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py
index e47a9c4778..3ec1888438 100644
--- a/easybuild/toolchains/compiler/gcc.py
+++ b/easybuild/toolchains/compiler/gcc.py
@@ -43,31 +43,30 @@ class Gcc(Compiler):
 
     COMPILER_FAMILY = TC_CONSTANT_GCC
     COMPILER_UNIQUE_OPTS = {
-                            'loop': (False, "Automatic loop parallellisation"),
-                            'f2c': (False, "Generate code compatible with f2c and f77"),
-                            'lto':(False, "Enable Link Time Optimization"),
-                            }
+        'loop': (False, "Automatic loop parallellisation"),
+        'f2c': (False, "Generate code compatible with f2c and f77"),
+        'lto':(False, "Enable Link Time Optimization"),
+    }
     COMPILER_UNIQUE_OPTION_MAP = {
-                                  'i8': 'fdefault-integer-8',
-                                  'r8': 'fdefault-real-8',
-                                  'unroll': 'funroll-loops',
-                                  'f2c': 'ff2c',
-                                  'loop': ['ftree-switch-conversion', 'floop-interchange',
-                                            'floop-strip-mine', 'floop-block'],
-                                  'lto':'flto',
-                                  'optarch':'march=native',
-                                  'openmp':'fopenmp',
-                                  'strict': ['mieee-fp', 'mno-recip'],
-                                  'precise':['mno-recip'],
-                                  'defaultprec':[],
-                                  'loose': ['mrecip', 'mno-ieee-fp'],
-                                  'veryloose': ['mrecip=all', 'mno-ieee-fp'],
-                                  }
+        'i8': 'fdefault-integer-8',
+        'r8': 'fdefault-real-8',
+        'unroll': 'funroll-loops',
+        'f2c': 'ff2c',
+        'loop': ['ftree-switch-conversion', 'floop-interchange', 'floop-strip-mine', 'floop-block'],
+        'lto': 'flto',
+        'openmp': 'fopenmp',
+        'strict': ['mieee-fp', 'mno-recip'],
+        'precise':['mno-recip'],
+        'defaultprec':[],
+        'loose': ['mrecip', 'mno-ieee-fp'],
+        'veryloose': ['mrecip=all', 'mno-ieee-fp'],
+    }
 
     COMPILER_OPTIMAL_ARCHITECTURE_OPTION = {
-                                            systemtools.INTEL : 'march=native',
-                                            systemtools.AMD : 'march=native'
-                                           }
+        systemtools.AMD : 'march=native',
+        systemtools.INTEL : 'march=native',
+        systemtools.POWER: 'mcpu=native',  # no support for march=native on POWER
+    }
 
     COMPILER_CC = 'gcc'
     COMPILER_CXX = 'g++'
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index dc60b2c041..fe1c238412 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -42,6 +42,10 @@
 from easybuild.tools.toolchain.utilities import search_toolchain
 from test.framework.utilities import find_full_path
 
+from easybuild.tools import systemtools as st
+import easybuild.tools.toolchain.compiler
+easybuild.tools.toolchain.compiler.systemtools.get_compiler_family = lambda: st.POWER
+
 class ToolchainTest(EnhancedTestCase):
     """ Baseclass for toolchain testcases """
 
@@ -295,6 +299,7 @@ def test_misc_flags_unique(self):
 
     def test_override_optarch(self):
         """Test whether overriding the optarch flag works."""
+        print st.get_compiler_family()
         flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']
         for optarch_var in ['march=lovelylovelysandybridge', None]:
             build_options = {'optarch': optarch_var}
@@ -307,7 +312,8 @@ def test_override_optarch(self):
                 if optarch_var is not None:
                     flag = '-%s' % optarch_var
                 else:
-                    flag = '-march=native'
+                    # default optarch flag
+                    flag = tc.COMPILER_OPTIMAL_ARCHITECTURE_OPTION[tc.arch]
 
                 for var in flag_vars:
                     flags = tc.get_variable(var)
@@ -389,7 +395,7 @@ def test_goolfc(self):
         tc.prepare()
 
         nvcc_flags = r' '.join([
-            r'-Xcompiler="-O2 -march=native"',
+            r'-Xcompiler="-O2 -%s"' % tc.COMPILER_OPTIMAL_ARCHITECTURE_OPTION[tc.arch],
             # the use of -lcudart in -Xlinker is a bit silly but hard to avoid
             r'-Xlinker=".* -lm -lrt -lcudart -lpthread"',
             r' '.join(["-gencode %s" % x for x in opts['cuda_gencode']]),

From 9bde497864a70c49a08c2589486f4a1d74349753 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 12:09:57 +0100
Subject: [PATCH 0608/1356] split up systemtools tests into smaller ones
 (native vs mocked)

---
 easybuild/tools/systemtools.py |  1 +
 test/framework/systemtools.py  | 61 +++++++++++++++++++++++++---------
 2 files changed, 47 insertions(+), 15 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 00624b3e4d..9d910675a6 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -172,6 +172,7 @@ def get_cpu_family():
 
     return family
 
+
 def get_cpu_model():
     """
     Determine CPU model
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index d1d01beec5..fdec5a05db 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -188,12 +188,14 @@ def tearDown(self):
         st.run_cmd = self.orig_run_cmd
         super(SystemToolsTest, self).tearDown()
 
-    def test_avail_core_count(self):
+    def test_avail_core_count_native(self):
         """Test getting core count."""
         core_count = get_avail_core_count()
         self.assertTrue(isinstance(core_count, int), "core_count has type int: %s, %s" % (core_count, type(core_count)))
         self.assertTrue(core_count > 0, "core_count %d > 0" % core_count)
 
+    def test_avail_core_count_linux(self):
+        """Test getting core count (mocked for Linux)."""
         st.get_os_type = lambda: st.LINUX
         orig_sched_getaffinity = st.sched_getaffinity
         class MockedSchedGetaffinity(object):
@@ -202,15 +204,19 @@ class MockedSchedGetaffinity(object):
         self.assertEqual(get_avail_core_count(), 6)
         st.sched_getaffinity = orig_sched_getaffinity
 
+    def test_avail_core_count_darwin(self):
+        """Test getting core count (mocked for Darwin)."""
         st.get_os_type = lambda: st.DARWIN
         st.run_cmd = mocked_run_cmd
         self.assertEqual(get_avail_core_count(), 10)
 
-    def test_cpu_model(self):
+    def test_cpu_model_native(self):
         """Test getting CPU model."""
         cpu_model = get_cpu_model()
         self.assertTrue(isinstance(cpu_model, basestring))
 
+    def test_cpu_model_linux(self):
+        """Test getting CPU model (mocked for Linux)."""
         st.get_os_type = lambda: st.LINUX
         st.read_file = mocked_read_file
         st.os.path.exists = lambda fp: mocked_os_path_exists(PROC_CPUINFO_FP, fp)
@@ -225,17 +231,20 @@ def test_cpu_model(self):
         PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_ARM
         self.assertEqual(get_cpu_model(), "ARMv7 Processor rev 5 (v7l)")
 
-        st.os.path.exists = self.orig_os_path_exists
+    def test_cpu_model_darwin(self):
+        """Test getting CPU model (mocked for Darwin)."""
         st.get_os_type = lambda: st.DARWIN
         st.run_cmd = mocked_run_cmd
         self.assertEqual(get_cpu_model(), "Intel(R) Core(TM) i5-4258U CPU @ 2.40GHz")
 
-    def test_cpu_speed(self):
+    def test_cpu_speed_native(self):
         """Test getting CPU speed."""
         cpu_speed = get_cpu_speed()
         self.assertTrue(isinstance(cpu_speed, float))
         self.assertTrue(cpu_speed > 0.0)
 
+    def test_cpu_speed_linux(self):
+        """Test getting CPU speed (mocked for Linux)."""
         # test for particular type of system by mocking used functions
         st.get_os_type = lambda: st.LINUX
         st.read_file = mocked_read_file
@@ -256,8 +265,8 @@ def test_cpu_speed(self):
         st.os.path.exists = lambda fp: mocked_os_path_exists(MAX_FREQ_FP, fp)
         self.assertEqual(get_cpu_speed(), 2850.0)
 
-        # OS X
-        st.os.path.exists = self.orig_os_path_exists
+    def test_cpu_speed_darwin(self):
+        """Test getting CPU speed (mocked for Darwin)."""
         st.get_os_type = lambda: st.DARWIN
         st.run_cmd = mocked_run_cmd
         self.assertEqual(get_cpu_speed(), 2400.0)
@@ -267,6 +276,8 @@ def test_cpu_vendor(self):
         cpu_vendor = get_cpu_vendor()
         self.assertTrue(cpu_vendor in [AMD, ARM, INTEL, UNKNOWN])
 
+    def test_cpu_vendor_linux(self):
+        """Test getting CPU vendor (mocked for Linux)."""
         st.get_os_type = lambda: st.LINUX
         st.read_file = mocked_read_file
         st.os.path.exists = lambda fp: mocked_os_path_exists(PROC_CPUINFO_FP, fp)
@@ -278,21 +289,24 @@ def test_cpu_vendor(self):
         PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_ARM
         self.assertEqual(get_cpu_vendor(), ARM)
 
-        st.os.path.exists = self.orig_os_path_exists
+    def test_cpu_vendor_darwin(self):
+        """Test getting CPU vendor (mocked for Darwin)."""
         st.get_os_type = lambda: st.DARWIN
         st.run_cmd = mocked_run_cmd
         self.assertEqual(get_cpu_vendor(), INTEL)
 
-    def test_cpu_family(self):
+    def test_cpu_family_native(self):
         """Test get_cpu_family function."""
         cpu_family = get_cpu_family()
         self.assertTrue(cpu_family in CPU_FAMILIES or cpu_family == UNKNOWN)
 
+    def test_cpu_family_linux(self):
+        """Test get_cpu_family function (mocked for Linux)."""
         st.get_os_type = lambda: st.LINUX
         st.read_file = mocked_read_file
         st.os.path.exists = lambda fp: mocked_os_path_exists(PROC_CPUINFO_FP, fp)
-
         global PROC_CPUINFO_TXT
+
         PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_X86
         self.assertEqual(get_cpu_family(), INTEL)
 
@@ -302,7 +316,8 @@ def test_cpu_family(self):
         PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_POWER
         self.assertEqual(get_cpu_family(), POWER)
 
-        st.os.path.exists = self.orig_os_path_exists
+    def test_cpu_family_darwin(self):
+        """Test get_cpu_family function (mocked for Darwin)."""
         st.get_os_type = lambda: st.DARWIN
         st.run_cmd = mocked_run_cmd
         self.assertEqual(get_cpu_family(), INTEL)
@@ -312,18 +327,22 @@ def test_os_type(self):
         os_type = get_os_type()
         self.assertTrue(os_type in [DARWIN, LINUX])
 
-    def test_shared_lib_ext(self):
+    def test_shared_lib_ext_native(self):
         """Test getting extension for shared libraries."""
         ext = get_shared_lib_ext()
         self.assertTrue(ext in ['dylib', 'so'])
 
+    def test_shared_lib_ext_native(self):
+        """Test getting extension for shared libraries (mocked for Linux)."""
         st.get_os_type = lambda: st.LINUX
         self.assertEqual(get_shared_lib_ext(), 'so')
 
+    def test_shared_lib_ext_native(self):
+        """Test getting extension for shared libraries (mocked for Darwin)."""
         st.get_os_type = lambda: st.DARWIN
         self.assertEqual(get_shared_lib_ext(), 'dylib')
 
-    def test_platform_name(self):
+    def test_platform_name_native(self):
         """Test getting platform name."""
         platform_name_nover = get_platform_name()
         self.assertTrue(isinstance(platform_name_nover, basestring))
@@ -336,11 +355,17 @@ def test_platform_name(self):
         self.assertTrue(platform_name_ver.startswith(platform_name_ver))
         self.assertTrue(len_ver >= len_nover)
 
+    def test_platform_name_linux(self):
+        """Test getting platform name (mocked for Linux)."""
         st.get_os_type = lambda: st.LINUX
         self.assertTrue(re.match('.*-unknown-linux$', get_platform_name()))
+        self.assertTrue(re.match('.*-unknown-linux-gnu$', get_platform_name(withversion=True)))
 
+    def test_platform_name_darwin(self):
+        """Test getting platform name (mocked for Darwin)."""
         st.get_os_type = lambda: st.DARWIN
         self.assertTrue(re.match('.*-apple-darwin$', get_platform_name()))
+        self.assertTrue(re.match('.*-apple-darwin.*$', get_platform_name(withversion=True)))
 
     def test_os_name(self):
         """Test getting OS name."""
@@ -352,15 +377,19 @@ def test_os_version(self):
         os_version = get_os_version()
         self.assertTrue(isinstance(os_version, basestring) or os_version == UNKNOWN)
 
-    def test_glibc_version(self):
+    def test_glibc_version_native(self):
         """Test getting glibc version."""
         glibc_version = get_glibc_version()
         self.assertTrue(isinstance(glibc_version, basestring) or glibc_version == UNKNOWN)
 
+    def test_glibc_version_linux(self):
+        """Test getting glibc version (mocked for Linux)."""
         st.get_os_type = lambda: st.LINUX
         st.run_cmd = mocked_run_cmd
         self.assertEqual(get_glibc_version(), '2.12')
 
+    def test_glibc_version_darwin(self):
+        """Test getting glibc version (mocked for Darwin)."""
         st.get_os_type = lambda: st.DARWIN
         self.assertEqual(get_glibc_version(), UNKNOWN)
 
@@ -369,8 +398,8 @@ def test_system_info(self):
         system_info = get_system_info()
         self.assertTrue(isinstance(system_info, dict))
 
-    def test_det_parallelism(self):
-        """Test det_parallelism function."""
+    def test_det_parallelism_native(self):
+        """Test det_parallelism function (native calls)."""
         self.assertTrue(det_parallelism(None, None) > 0)
         # specified parallellism
         self.assertEqual(det_parallelism(5, None), 5)
@@ -380,6 +409,8 @@ def test_det_parallelism(self):
         self.assertEqual(det_parallelism(5, 2), 2)
         self.assertEqual(det_parallelism(5, 10), 5)
 
+    def test_det_parallelism_mocked(self):
+        """Test det_parallelism function (with mocked ulimit/get_avail_core_count)."""
         orig_get_avail_core_count = st.get_avail_core_count
 
         # mock number of available cores to 8

From 0f8b5839e81f217acb1b8164513e9854757df0aa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 12:16:43 +0100
Subject: [PATCH 0609/1356] re-add code that shouldn't have been removed in
 compiler.py

---
 easybuild/tools/toolchain/compiler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/toolchain/compiler.py b/easybuild/tools/toolchain/compiler.py
index 3946eca9ba..fda05be513 100644
--- a/easybuild/tools/toolchain/compiler.py
+++ b/easybuild/tools/toolchain/compiler.py
@@ -272,7 +272,7 @@ def _get_optimal_architecture(self):
             self.log.info("_get_optimal_architecture: using %s as optarch for %s." % (optarch, self.arch))
             self.options.options_map['optarch'] = optarch
 
-        if self.options.options_map.get('optarch', None) is None:
+        if 'optarch' in self.options.options_map and self.options.options_map.get('optarch', None) is None:
             self.log.raiseException("_get_optimal_architecture: don't know how to set optarch for %s." % self.arch)
 
     def comp_family(self, prefix=None):

From 297dea1641208a8999a4c55304a718878668f2c1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 13:17:23 +0100
Subject: [PATCH 0610/1356] fix broken test

---
 test/framework/toolchain.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index b7d6571f29..e6e80ff5e4 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -288,7 +288,10 @@ def test_misc_flags_unique(self):
                 tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
                 tc.set_options({opt: enable})
                 tc.prepare()
-                flag = '-%s' % tc.COMPILER_UNIQUE_OPTION_MAP[opt]
+                if opt == 'optarch':
+                    flag = '-%s' % tc.COMPILER_OPTIMAL_ARCHITECTURE_OPTION[tc.arch]
+                else:
+                    flag = '-%s' % tc.COMPILER_UNIQUE_OPTION_MAP[opt]
                 for var in flag_vars:
                     flags = tc.get_variable(var)
                     if enable:
@@ -299,7 +302,6 @@ def test_misc_flags_unique(self):
 
     def test_override_optarch(self):
         """Test whether overriding the optarch flag works."""
-        print st.get_compiler_family()
         flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']
         for optarch_var in ['march=lovelylovelysandybridge', None]:
             build_options = {'optarch': optarch_var}

From dc0c202935531c9e5183db625aa736c3b0e06066 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@gmail.com>
Date: Wed, 25 Feb 2015 13:40:31 +0100
Subject: [PATCH 0611/1356] added instructions on best way to get graphviz with
 python bindings on os X

---
 easybuild/framework/easyconfig/tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index da3af771ac..9a99136861 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -64,7 +64,7 @@
     sys.path.append('/usr/lib64/graphviz/python/')
     import gv
 except ImportError, err:
-    graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz")
+    graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz, or brew install graphviz --with-bindings")
 
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS

From b26840a389b8a985200e5020004bed33c688a3af Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 15:53:24 +0100
Subject: [PATCH 0612/1356] flesh out --fix-broken-easyconfigs into stand-alone
 script fix_broken_easyconfigs.py

---
 easybuild/framework/easyconfig/easyconfig.py  |  33 +----
 .../easyconfig/format/pyheaderconfigobj.py    |   2 +-
 easybuild/framework/easyconfig/parser.py      |  41 +-----
 easybuild/scripts/fix_broken_easyconfigs.py   | 136 ++++++++++++++++++
 easybuild/tools/config.py                     |   1 -
 easybuild/tools/options.py                    |   2 -
 test/framework/easyconfig.py                  |  46 +-----
 test/framework/scripts.py                     | 105 ++++++++++++++
 8 files changed, 255 insertions(+), 111 deletions(-)
 create mode 100755 easybuild/scripts/fix_broken_easyconfigs.py

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 97fea27897..0712c7c5d2 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -39,7 +39,6 @@
 import difflib
 import os
 import re
-import tempfile
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_class_for, nub
 from vsc.utils.patterns import Singleton
@@ -47,7 +46,7 @@
 import easybuild.tools.environment as env
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_module_naming_scheme
-from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file, write_file
+from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
 from easybuild.tools.module_naming_scheme.utilities import det_hidden_modname, is_valid_module_name
@@ -62,7 +61,7 @@
 from easybuild.framework.easyconfig.format.one import retrieve_blocks_in_spec
 from easybuild.framework.easyconfig.licenses import EASYCONFIG_LICENSES_DICT, License
 from easybuild.framework.easyconfig.parser import DEPRECATED_PARAMETERS, REPLACED_PARAMETERS
-from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig, fix_broken_easyconfig
+from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.templates import template_constant_dict
 
 
@@ -135,9 +134,6 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         # obtain name and easyblock specifications from raw easyconfig contents
         self.software_name, self.easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['name', 'easyblock'])
 
-        # try and fix potentially broken easyconfig, if requested
-        self.fix_broken()
-
         # determine line of extra easyconfig parameters
         if extra_options is None:
             easyblock_class = get_easyblock_class(self.easyblock, name=self.software_name)
@@ -219,25 +215,6 @@ def update(self, key, value):
         else:
             self.log.error("Can't update configuration value for %s, because it's not a string or list." % key)
 
-    def fix_broken(self):
-        """
-        Try and fix this easyconfig's raw contents, if it's broken and fixing is requested.
-        """
-        if build_option('fix_broken_easyconfigs'):
-            derived_easyblock_class = get_easyblock_class(self.easyblock, name=self.software_name, default_fallback=False)
-            fixed_rawtxt = fix_broken_easyconfig(self.rawtxt, derived_easyblock_class)
-            if self.rawtxt != fixed_rawtxt:
-                self.rawtxt = fixed_rawtxt
-                self.path = os.path.join(tempfile.gettempdir(), os.path.basename(self.path))
-                write_file(self.path, self.rawtxt)
-                self.log.info("Replacing broken supplied easyconfig with fixed copy %s" % self.path)
-                self.log.info("Contents of fixed easyconfig file: %s" % self.rawtxt)
-
-                # redetermine easyblock from easyconfig, since it may have changed
-                self.easyblock = fetch_parameters_from_easyconfig(self.rawtxt, ['easyblock'])[0]
-            else:
-                self.log.debug("Nothing broken detected in supplied easyconfig %s, so nothing fixed" % self.path)
-
     def parse(self):
         """
         Parse the file and set options
@@ -252,14 +229,14 @@ def parse(self):
             self.log.error("Specifications should be specified using a dictionary, got %s" % type(self.build_specs))
         self.log.debug("Obtained specs dict %s" % arg_specs)
 
-        self.log.info("Parsing easyconfig file %s" % self.path)
-        parser = EasyConfigParser(self.path)
+        self.log.info("Parsing easyconfig file %s with rawcontent: %s" % (self.path, self.rawtxt))
+        parser = EasyConfigParser(filename=self.path, rawcontent=self.rawtxt)
         parser.set_specifications(arg_specs)
         local_vars = parser.get_config_dict()
         self.log.debug("Parsed easyconfig as a dictionary: %s" % local_vars)
 
         # make sure all mandatory parameters are defined
-        # this includes both generic mandatory parameters, as software-specific parameters defined via extra_options
+        # this includes both generic mandatory parameters and software-specific parameters defined via extra_options
         missing_mandatory_keys = [key for key in self.mandatory if key not in local_vars]
         if missing_mandatory_keys:
             self.log.error("mandatory parameters not provided in %s: %s" % (self.path, missing_mandatory_keys))
diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index f76266f7c5..026392824a 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -227,7 +227,7 @@ def _validate_pyheader(self):
         """
         Basic validation of pyheader localvars.
         This takes parameter names from the PYHEADER_BLACKLIST and PYHEADER_MANDATORY;
-        blacklisted vparameter are not allowed, mandatory vparameter are mandatory unless blacklisted
+        blacklisted parameters are not allowed, mandatory parameters are mandatory unless blacklisted
         """
         if self.pyheader_localvars is None:
             self.log.error("self.pyheader_localvars must be initialized")
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 215b65f7aa..376b2e436f 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -72,46 +72,12 @@ def fetch_parameters_from_easyconfig(rawtxt, params):
     return param_values
 
 
-def fix_broken_easyconfig(ectxt, easyblock_class):
-    """
-    Fix easyconfig file at specified location, that may be broken due to non-backwards-compatible changes.
-    @param ectxt: raw contents of easyconfig to fix
-    @param easyblock_class: easyblock class, as derived from software name/specified easyblock
-    """
-    _log.debug("Raw contents of potentially broken easyconfig file to fix: %s" % ectxt)
-
-    subs = {
-        # replace former 'magic' variable shared_lib_ext with SHLIB_EXT constant
-        'shared_lib_ext': 'SHLIB_EXT',
-        'name': 'name',
-    }
-    # include replaced easyconfig parameters
-    subs.update(REPLACED_PARAMETERS)
-
-    # check whether any substitions need to be made
-    for old, new in subs.items():
-        regex = re.compile(r'(\W)%s(\W)' % old)
-        if regex.search(ectxt):
-            tup = (regex.pattern, old, new)
-            _log.info("Broken stuff detected using regex pattern '%s', replacing '%s' with '%s'" % tup)
-            ectxt = regex.sub(r'\1%s\2' % new, ectxt)
-
-    # check whether missing "easyblock = 'ConfigureMake'" needs to be inserted
-    if easyblock_class is None:
-        # prepend "easyblock = 'ConfigureMake'" to line containing "name =..."
-        easyblock_spec = "easyblock = 'ConfigureMake'"
-        _log.info("Inserting \"%s\", since no easyblock class was derived from easyconfig parameters" % easyblock_spec)
-        ectxt = re.sub(r'(\s*)(name\s*=)', r"\1%s\n\n\2" % easyblock_spec, ectxt, re.M)
-
-    return ectxt
-
-
 class EasyConfigParser(object):
     """Read the easyconfig file, return a parsed config object
         Can contain references to multiple version and toolchain/toolchain versions
     """
 
-    def __init__(self, filename=None, format_version=None):
+    def __init__(self, filename=None, format_version=None, rawcontent=None):
         """Initialise the EasyConfigParser class"""
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
@@ -126,6 +92,11 @@ def __init__(self, filename=None, format_version=None):
         if filename is not None:
             self._check_filename(filename)
             self.process()
+        elif rawcontent is not None:
+            self.rawcontent = rawcontent
+            self._set_formatter()
+        else:
+            self.log.error("Neither filename nor rawcontent provided to EasyConfigParser")
 
     def process(self, filename=None):
         """Create an instance"""
diff --git a/easybuild/scripts/fix_broken_easyconfigs.py b/easybuild/scripts/fix_broken_easyconfigs.py
new file mode 100755
index 0000000000..3daf26ed61
--- /dev/null
+++ b/easybuild/scripts/fix_broken_easyconfigs.py
@@ -0,0 +1,136 @@
+#!/usr/bin/env python
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+import os
+import re
+import sys
+import tempfile
+from vsc.utils import fancylogger
+from vsc.utils.generaloption import simple_option
+
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
+from easybuild.framework.easyconfig.parser import REPLACED_PARAMETERS, fetch_parameters_from_easyconfig
+from easybuild.tools.filetools import find_easyconfigs, read_file, write_file
+
+from test.framework.utilities import init_config
+
+
+log = fancylogger.getLogger('main')
+fancylogger.logToScreen(enable=True, stdout=True)
+log.setLevel('INFO')
+
+
+def fix_broken_easyconfig(ectxt, easyblock_class):
+    """
+    Fix provided easyconfig file, that may be broken due to non-backwards-compatible changes.
+    @param ectxt: raw contents of easyconfig to fix
+    @param easyblock_class: easyblock class, as derived from software name/specified easyblock
+    """
+    log.debug("Raw contents of potentially broken easyconfig file to fix: %s" % ectxt)
+
+    subs = {
+        # replace former 'magic' variable shared_lib_ext with SHLIB_EXT constant
+        'shared_lib_ext': 'SHLIB_EXT',
+    }
+    # include replaced easyconfig parameters
+    subs.update(REPLACED_PARAMETERS)
+
+    # check whether any substitions need to be made
+    for old, new in subs.items():
+        regex = re.compile(r'(\W)%s(\W)' % old)
+        if regex.search(ectxt):
+            tup = (regex.pattern, old, new)
+            log.debug("Broken stuff detected using regex pattern '%s', replacing '%s' with '%s'" % tup)
+            ectxt = regex.sub(r'\1%s\2' % new, ectxt)
+
+    # check whether missing "easyblock = 'ConfigureMake'" needs to be inserted
+    if easyblock_class is None:
+        # prepend "easyblock = 'ConfigureMake'" to line containing "name =..."
+        easyblock_spec = "easyblock = 'ConfigureMake'"
+        log.debug("Inserting \"%s\", since no easyblock class was derived from easyconfig parameters" % easyblock_spec)
+        ectxt = re.sub(r'(\s*)(name\s*=)', r"\1%s\n\n\2" % easyblock_spec, ectxt, re.M)
+
+    return ectxt
+
+
+# MAIN
+
+def main():
+
+    try:
+        import easybuild.easyblocks.generic.configuremake
+    except ImportError, err:
+        log.error("easyblocks are not available in Python search path: %s" % err)
+
+    options = {
+        'backup': ("Backup up easyconfigs before modifying them", None, 'store_true', True, 'b'),
+    }
+    go = simple_option(options)
+
+    init_config(args=['--quiet'])
+
+    for path in go.args:
+        if not os.path.exists(path):
+            log.error("Non-existing path %s specified" % path)
+
+    ec_files = [ec for p in go.args for ec in find_easyconfigs(p)]
+    if not ec_files:
+        log.error("No easyconfig files specified")
+
+    log.info("Processing %d easyconfigs" % len(ec_files))
+    for ec_file in ec_files:
+
+        ectxt = read_file(ec_file)
+        name, easyblock = fetch_parameters_from_easyconfig(ectxt, ['name', 'easyblock'])
+        derived_easyblock_class = get_easyblock_class(easyblock, name=name, default_fallback=False)
+
+        fixed_ectxt = fix_broken_easyconfig(ectxt, derived_easyblock_class)
+
+        if ectxt != fixed_ectxt:
+            if go.options.backup:
+                try:
+                    backup_ec_file = '%s.bk' % ec_file
+                    i = 1
+                    while os.path.exists(backup_ec_file):
+                        backup_ec_file = '%s.bk%d' % (ec_file, i)
+                        i += 1
+                    os.rename(ec_file, backup_ec_file)
+                    log.info("Backed up %s to %s" % (ec_file, backup_ec_file))
+                except OSError, err:
+                    log.error("Failed to backup %s before rewriting it: %s" % (ec_file, err))
+
+            write_file(path, fixed_ectxt)
+            log.debug("Contents of fixed easyconfig file: %s" % fixed_ectxt)
+
+            log.info("%s: fixed" % ec_file)
+        else:
+            log.info("%s: nothing to fix" % ec_file)
+
+
+if __name__ == '__main__':
+    try:
+        main()
+    except EasyBuildError, err:
+        sys.exit(1)
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index a7b5387323..9e2108143c 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -103,7 +103,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'allow_modules_tool_mismatch',
         'debug',
         'experimental',
-        'fix_broken_easyconfigs',
         'force',
         'hidden',
         'robot',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 4c5371a20f..ebb608c169 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -189,8 +189,6 @@ def override_options(self):
                           None, 'store', None, 'e', {'metavar': 'CLASS'}),
             'experimental': ("Allow experimental code (with behaviour that can be changed/removed at any given time).",
                              None, 'store_true', False),
-            'fix-broken-easyconfigs': ("Fix easyconfig files that were broken due to non-backwards-compatible changes",
-                                       None, 'store_true', False),
             'group': ("Group to be used for software installations (only verified, not set)", None, 'store', None),
             'hidden': ("Install 'hidden' module file(s) by prefixing their name with '.'", None, 'store_true', False),
             'ignore-osdeps': ("Ignore any listed OS dependencies", None, 'store_true', False),
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index a95a432f1b..e82d768112 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -43,9 +43,9 @@
 import easybuild.framework.easyconfig as easyconfig
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
-from easybuild.framework.easyconfig.easyconfig import create_paths, det_installversion
+from easybuild.framework.easyconfig.easyconfig import create_paths
 from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file, get_easyblock_class
-from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig, fix_broken_easyconfig
+from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak_one
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import module_classes
@@ -53,7 +53,6 @@
 from easybuild.tools.module_naming_scheme.toolchain import det_toolchain_compilers, det_toolchain_mpi
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.systemtools import get_shared_lib_ext
-from easybuild.tools.utilities import quote_str
 from test.framework.utilities import find_full_path
 
 
@@ -1016,47 +1015,6 @@ def foo(key):
         easyconfig.easyconfig.EasyConfig = orig_EasyConfig
         easyconfig.easyconfig.ActiveMNS = orig_ActiveMNS
 
-    def test_fix_broken_easyconfig(self):
-        """Test fix_broken_easyconfig function."""
-        # local import, since test easyblocks need to be made available first by setUp
-        from easybuild.easyblocks.toy import EB_toy
-
-        broken_ec_txt = '\n'.join([
-            "# licenseheader",
-            "name = 'foo'",
-            "version = '1.2.3'",
-            '',
-            "description = 'foo'",
-            "homepage = 'http://example.com'",
-            '',
-            "toolchain = {'name': 'bar', 'version': '3.2.1'}",
-            '',
-            "premakeopts = 'FOO=libfoo.%s' % shared_lib_ext",
-            "makeopts = 'CC=gcc'",
-            '',
-            "license = 'foo.lic'",
-        ])
-        fixed_ec_txt = '\n'.join([
-            "# licenseheader",
-            "name = 'foo'",
-            "version = '1.2.3'",
-            '',
-            "description = 'foo'",
-            "homepage = 'http://example.com'",
-            '',
-            "toolchain = {'name': 'bar', 'version': '3.2.1'}",
-            '',
-            "prebuildopts = 'FOO=libfoo.%s' % SHLIB_EXT",
-            "buildopts = 'CC=gcc'",
-            '',
-            "license_file = 'foo.lic'",
-        ])
-        self.assertEqual(fix_broken_easyconfig(broken_ec_txt, EB_toy), fixed_ec_txt)
-
-        lines = fixed_ec_txt.split('\n')
-        fixed_ec_txt = '\n'.join([lines[0], "easyblock = 'ConfigureMake'", ''] + lines[1:])
-        self.assertEqual(fix_broken_easyconfig(broken_ec_txt, None), fixed_ec_txt)
-
     def test_unknown_easyconfig_parameter(self):
         """Check behaviour when unknown easyconfig parameters are used."""
         self.contents = '\n'.join([
diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 86cb80e422..975c730542 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -34,6 +34,8 @@
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
 
+from easybuild.framework.easyconfig.easyconfig import EasyConfig
+from easybuild.tools.filetools import read_file, write_file
 from easybuild.tools.run import run_cmd
 
 
@@ -91,6 +93,109 @@ def test_generate_software_list(self):
         shutil.rmtree(tmpdir)
         os.environ['PYTHONPATH'] = pythonpath
 
+    def test_fix_broken_easyconfig(self):
+        """Test fix_broken_easyconfigs.py script."""
+        testdir = os.path.dirname(__file__)
+        topdir = os.path.dirname(os.path.dirname(testdir))
+        script = os.path.join(topdir, 'easybuild', 'scripts', 'fix_broken_easyconfigs.py')
+        test_easyblocks = os.path.join(testdir, 'sandbox')
+
+        broken_ec_txt_tmpl = '\n'.join([
+            "# licenseheader",
+            "%sname = '%s'",
+            "version = '1.2.3'",
+            '',
+            "description = 'foo'",
+            "homepage = 'http://example.com'",
+            '',
+            "toolchain = {'name': 'bar', 'version': '3.2.1'}",
+            '',
+            "premakeopts = 'FOO=libfoo.%%s' %% shared_lib_ext",
+            "makeopts = 'CC=gcc'",
+            '',
+            "license = 'foo.lic'",
+        ])
+        fixed_ec_txt_tmpl = '\n'.join([
+            "# licenseheader",
+            "%sname = '%s'",
+            "version = '1.2.3'",
+            '',
+            "description = 'foo'",
+            "homepage = 'http://example.com'",
+            '',
+            "toolchain = {'name': 'bar', 'version': '3.2.1'}",
+            '',
+            "prebuildopts = 'FOO=libfoo.%%s' %% SHLIB_EXT",
+            "buildopts = 'CC=gcc'",
+            '',
+            "license_file = 'foo.lic'",
+        ])
+        broken_ec_tmpl = os.path.join(self.test_prefix, '%s.eb')
+
+        # don't change it if it isn't broken
+        broken_ec = broken_ec_tmpl % 'notbroken'
+        script_cmd = "%s %s" % (script, broken_ec)
+        fixed_ec_txt = fixed_ec_txt_tmpl % ("easyblock = 'ConfigureMake'\n\n", 'foo')
+
+        write_file(broken_ec, fixed_ec_txt)
+        # (dummy) ConfigureMake easyblock is available in test sandbox
+        script_cmd = "PYTHONPATH=%s:$PYTHONPATH:%s %s %s" % (topdir, test_easyblocks, script, broken_ec)
+        new_ec_txt = read_file(broken_ec)
+        self.assertEqual(new_ec_txt, fixed_ec_txt)
+        self.assertTrue(EasyConfig(None, rawtxt=new_ec_txt))
+        self.assertFalse(os.path.exists('%s.bk' % broken_ec))  # no backup created if nothing was fixed
+
+        broken_ec = broken_ec_tmpl % 'nosuchsoftware'
+        script_cmd = "%s %s" % (script, broken_ec)
+        broken_ec_txt = broken_ec_txt_tmpl % ('', 'nosuchsoftware')
+        fixed_ec_txt = fixed_ec_txt_tmpl % ("easyblock = 'ConfigureMake'\n\n", 'nosuchsoftware')
+
+        # broken easyconfig is fixed in place, original file is backed up
+        write_file(broken_ec, broken_ec_txt)
+        run_cmd(script_cmd)
+        new_ec_txt = read_file(broken_ec)
+        self.assertEqual(new_ec_txt, fixed_ec_txt)
+        self.assertTrue(EasyConfig(None, rawtxt=new_ec_txt))
+        self.assertEqual(read_file('%s.bk' % broken_ec), broken_ec_txt)
+        self.assertFalse(os.path.exists('%s.bk1' % broken_ec))
+
+        # broken easyconfig is fixed in place, original file is backed up, existing backup is not overwritten
+        write_file(broken_ec, broken_ec_txt)
+        write_file('%s.bk' % broken_ec, 'thisshouldnot\nbechanged')
+        run_cmd(script_cmd)
+        new_ec_txt = read_file(broken_ec)
+        self.assertEqual(new_ec_txt, fixed_ec_txt)
+        self.assertTrue(EasyConfig(None, rawtxt=new_ec_txt))
+        self.assertEqual(read_file('%s.bk' % broken_ec), 'thisshouldnot\nbechanged')
+        self.assertEqual(read_file('%s.bk1' % broken_ec), broken_ec_txt)
+
+        # if easyblock is specified, that part is left untouched
+        broken_ec = broken_ec_tmpl % 'footoy'
+        script_cmd = "PYTHONPATH=%s:$PYTHONPATH:%s %s %s" % (topdir, test_easyblocks, script, broken_ec)
+        broken_ec_txt = broken_ec_txt_tmpl % ("easyblock = 'EB_toy'\n\n", 'foo')
+        fixed_ec_txt = fixed_ec_txt_tmpl % ("easyblock = 'EB_toy'\n\n", 'foo')
+
+        write_file(broken_ec, broken_ec_txt)
+        run_cmd(script_cmd)
+        new_ec_txt = read_file(broken_ec)
+        self.assertEqual(new_ec_txt, fixed_ec_txt)
+        self.assertTrue(EasyConfig(None, rawtxt=new_ec_txt))
+        self.assertEqual(read_file('%s.bk' % broken_ec), broken_ec_txt)
+
+        # for existing easyblocks, "easyblock = 'ConfigureMake'" should *not* be added
+        # EB_toy easyblock is available in test sandbox
+        test_easyblocks = os.path.join(testdir, 'sandbox')
+        broken_ec = broken_ec_tmpl % 'toy'
+        # path to test easyblocks must be *appended* to PYTHONPATH (due to flattening in easybuild-easyblocks repo)
+        script_cmd = "PYTHONPATH=%s:$PYTHONPATH:%s %s %s" % (topdir, test_easyblocks, script, broken_ec)
+        broken_ec_txt = broken_ec_txt_tmpl % ('', 'toy')
+        fixed_ec_txt = fixed_ec_txt_tmpl % ('', 'toy')
+        write_file(broken_ec, broken_ec_txt)
+        run_cmd(script_cmd)
+        new_ec_txt = read_file(broken_ec)
+        self.assertEqual(new_ec_txt, fixed_ec_txt)
+        self.assertTrue(EasyConfig(None, rawtxt=new_ec_txt))
+        self.assertEqual(read_file('%s.bk' % broken_ec), broken_ec_txt)
 
 def suite():
     """ returns all the testcases in this module """

From 772bcf8dfef1c0cc59cefbb3dae663d67ea4b7c1 Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@ugent.be>
Date: Wed, 25 Feb 2015 16:20:06 +0100
Subject: [PATCH 0613/1356] Update tools.py

---
 easybuild/framework/easyconfig/tools.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 9a99136861..93bf23f188 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -64,7 +64,9 @@
     sys.path.append('/usr/lib64/graphviz/python/')
     import gv
 except ImportError, err:
-    graph_errors.append("Failed to import graphviz: try yum install graphviz-python, or apt-get install python-pygraphviz, or brew install graphviz --with-bindings")
+    graph_errors.append("Failed to import graphviz: try yum install graphviz-python,"
+                        "or apt-get install python-pygraphviz,"
+                        "or brew install graphviz --with-bindings")
 
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS

From 11d199b56d85d146e74625e39f754b87d3bc69a9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 16:22:33 +0100
Subject: [PATCH 0614/1356] fix small remark

---
 easybuild/tools/systemtools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 9d910675a6..58d0adcef9 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -134,7 +134,7 @@ def get_cpu_vendor():
         cmd = "sysctl -n machdep.cpu.vendor"
         out, ec = run_cmd(cmd)
         out = out.strip()
-        if ec == 0 and out and out in VENDORS:
+        if ec == 0 and out in VENDORS:
             vendor = VENDORS[out]
             _log.debug("Determined CPU vendor on DARWIN as being '%s' via cmd '%s" % (vendor, cmd))
 

From eab31539a108aaaaf97d322363223e0ab243a4f9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 16:49:50 +0100
Subject: [PATCH 0615/1356] add support for letting get_cpu_vendor return IBM +
 code cleanup

---
 easybuild/tools/systemtools.py | 22 ++++++++++------------
 test/framework/systemtools.py  |  5 ++++-
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 58d0adcef9..1414044a57 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -47,6 +47,7 @@
 # constants
 AMD = 'AMD'
 ARM = 'ARM'
+IBM = 'IBM'
 INTEL = 'Intel'
 POWER = 'POWER'
 
@@ -60,8 +61,10 @@
 
 CPU_FAMILIES = [ARM, AMD, INTEL, POWER]
 VENDORS = {
-    'GenuineIntel': INTEL,
+    'ARM': ARM,
     'AuthenticAMD': AMD,
+    'GenuineIntel': INTEL,
+    'IBM': IBM,
 }
 
 
@@ -112,24 +115,19 @@ def get_cpu_vendor():
         txt = read_file(PROC_CPUINFO_FP)
         arch = UNKNOWN
 
-        # vendor_id might not be in the /proc/cpuinfo, so this might fail
-        vendor_regex = re.compile(r"^vendor_id\s+:\s*(?P<vendorid>\S+)\s*$", re.M)
+        vendor_regexes = [
+            r"^vendor_id\s+:\s*(\S+)\s*$",  # Linux/x86
+            r".*:\s*(ARM|IBM).*$",  # Linux/ARM (e.g., Raspbian), Linux/POWER
+        ]
+        vendor_regex = re.compile('|'.join(vendor_regexes), re.M)
         res = vendor_regex.search(txt)
         if res:
-            arch = res.group('vendorid')
+            arch = res.group(1) or res.group(2)
         if arch in VENDORS:
             vendor = VENDORS[arch]
             tup = (vendor, vendor_regex.pattern, PROC_CPUINFO_FP)
             _log.debug("Determined CPU vendor on Linux as being '%s' via regex '%s' in %s" % tup)
 
-        # embedded Linux on ARM behaves differently (e.g. Raspbian)
-        vendor_regex = re.compile(r".*:\s*(?P<vendorid>ARM\S+)\s*", re.M)
-        res = vendor_regex.search(txt)
-        if res:
-            vendor = ARM
-            tup = (vendor, vendor_regex.pattern, PROC_CPUINFO_FP)
-            _log.debug("Determined CPU vendor on Linux as being '%s' via regex '%s' in %s" % tup)
-
     elif os_type == DARWIN:
         cmd = "sysctl -n machdep.cpu.vendor"
         out, ec = run_cmd(cmd)
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index fdec5a05db..fdebc3a118 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -35,7 +35,7 @@
 import easybuild.tools.systemtools as st
 from easybuild.tools.filetools import read_file
 from easybuild.tools.run import run_cmd
-from easybuild.tools.systemtools import CPU_FAMILIES, AMD, ARM, DARWIN, INTEL, LINUX, POWER, UNKNOWN
+from easybuild.tools.systemtools import CPU_FAMILIES, AMD, ARM, DARWIN, IBM, INTEL, LINUX, POWER, UNKNOWN
 from easybuild.tools.systemtools import det_parallelism, get_avail_core_count, get_cpu_family
 from easybuild.tools.systemtools import get_cpu_model, get_cpu_speed, get_cpu_vendor, get_glibc_version
 from easybuild.tools.systemtools import get_os_type, get_os_name, get_os_version, get_platform_name, get_shared_lib_ext
@@ -286,6 +286,9 @@ def test_cpu_vendor_linux(self):
         PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_X86
         self.assertEqual(get_cpu_vendor(), INTEL)
 
+        PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_POWER
+        self.assertEqual(get_cpu_vendor(), IBM)
+
         PROC_CPUINFO_TXT = PROC_CPUINFO_TXT_ARM
         self.assertEqual(get_cpu_vendor(), ARM)
 

From 70243528534f61fdcd559423a4f09ff1058a8e31 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 16:57:29 +0100
Subject: [PATCH 0616/1356] fix test for fix_broken_easyconfigs.py script, in
 case the easybuild-easyblocks repo isn't around

---
 test/framework/scripts.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 975c730542..3b78519baa 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -131,22 +131,23 @@ def test_fix_broken_easyconfig(self):
             "license_file = 'foo.lic'",
         ])
         broken_ec_tmpl = os.path.join(self.test_prefix, '%s.eb')
+        script_cmd_tmpl = "PYTHONPATH=%s:$PYTHONPATH:%s %s %%s" % (topdir, test_easyblocks, script)
 
         # don't change it if it isn't broken
         broken_ec = broken_ec_tmpl % 'notbroken'
-        script_cmd = "%s %s" % (script, broken_ec)
+        script_cmd = script_cmd_tmpl % broken_ec
         fixed_ec_txt = fixed_ec_txt_tmpl % ("easyblock = 'ConfigureMake'\n\n", 'foo')
 
         write_file(broken_ec, fixed_ec_txt)
         # (dummy) ConfigureMake easyblock is available in test sandbox
-        script_cmd = "PYTHONPATH=%s:$PYTHONPATH:%s %s %s" % (topdir, test_easyblocks, script, broken_ec)
+        script_cmd = script_cmd_tmpl % broken_ec
         new_ec_txt = read_file(broken_ec)
         self.assertEqual(new_ec_txt, fixed_ec_txt)
         self.assertTrue(EasyConfig(None, rawtxt=new_ec_txt))
         self.assertFalse(os.path.exists('%s.bk' % broken_ec))  # no backup created if nothing was fixed
 
         broken_ec = broken_ec_tmpl % 'nosuchsoftware'
-        script_cmd = "%s %s" % (script, broken_ec)
+        script_cmd = script_cmd_tmpl % broken_ec
         broken_ec_txt = broken_ec_txt_tmpl % ('', 'nosuchsoftware')
         fixed_ec_txt = fixed_ec_txt_tmpl % ("easyblock = 'ConfigureMake'\n\n", 'nosuchsoftware')
 
@@ -171,7 +172,7 @@ def test_fix_broken_easyconfig(self):
 
         # if easyblock is specified, that part is left untouched
         broken_ec = broken_ec_tmpl % 'footoy'
-        script_cmd = "PYTHONPATH=%s:$PYTHONPATH:%s %s %s" % (topdir, test_easyblocks, script, broken_ec)
+        script_cmd = script_cmd_tmpl % broken_ec
         broken_ec_txt = broken_ec_txt_tmpl % ("easyblock = 'EB_toy'\n\n", 'foo')
         fixed_ec_txt = fixed_ec_txt_tmpl % ("easyblock = 'EB_toy'\n\n", 'foo')
 
@@ -187,7 +188,7 @@ def test_fix_broken_easyconfig(self):
         test_easyblocks = os.path.join(testdir, 'sandbox')
         broken_ec = broken_ec_tmpl % 'toy'
         # path to test easyblocks must be *appended* to PYTHONPATH (due to flattening in easybuild-easyblocks repo)
-        script_cmd = "PYTHONPATH=%s:$PYTHONPATH:%s %s %s" % (topdir, test_easyblocks, script, broken_ec)
+        script_cmd = script_cmd_tmpl % broken_ec
         broken_ec_txt = broken_ec_txt_tmpl % ('', 'toy')
         fixed_ec_txt = fixed_ec_txt_tmpl % ('', 'toy')
         write_file(broken_ec, broken_ec_txt)

From cdc875dd70a5b96a28c787def641a8234a76f84f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 17:31:55 +0100
Subject: [PATCH 0617/1356] fix test_cpu_vendors test

---
 test/framework/systemtools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index fdebc3a118..faf6f14265 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -35,7 +35,7 @@
 import easybuild.tools.systemtools as st
 from easybuild.tools.filetools import read_file
 from easybuild.tools.run import run_cmd
-from easybuild.tools.systemtools import CPU_FAMILIES, AMD, ARM, DARWIN, IBM, INTEL, LINUX, POWER, UNKNOWN
+from easybuild.tools.systemtools import CPU_FAMILIES, ARM, DARWIN, IBM, INTEL, LINUX, POWER, UNKNOWN, VENDORS
 from easybuild.tools.systemtools import det_parallelism, get_avail_core_count, get_cpu_family
 from easybuild.tools.systemtools import get_cpu_model, get_cpu_speed, get_cpu_vendor, get_glibc_version
 from easybuild.tools.systemtools import get_os_type, get_os_name, get_os_version, get_platform_name, get_shared_lib_ext
@@ -274,7 +274,7 @@ def test_cpu_speed_darwin(self):
     def test_cpu_vendor(self):
         """Test getting CPU vendor."""
         cpu_vendor = get_cpu_vendor()
-        self.assertTrue(cpu_vendor in [AMD, ARM, INTEL, UNKNOWN])
+        self.assertTrue(cpu_vendor in VENDORS.values() + [UNKNOWN])
 
     def test_cpu_vendor_linux(self):
         """Test getting CPU vendor (mocked for Linux)."""

From 403acbaa3726d82ec667c45153457520493f3304 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 17:35:11 +0100
Subject: [PATCH 0618/1356] fix mocked version of os.path.exists in systemtools
 tests, only return True for specified path

---
 test/framework/systemtools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index faf6f14265..c33319e96a 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -148,7 +148,7 @@ def mocked_read_file(fp):
 
 def mocked_os_path_exists(mocked_fp, fp):
     """Mocked version of os.path.exists, returns True for a particular specified filepath."""
-    return fp == mocked_fp or orig_os_path_exists(fp)
+    return fp == mocked_fp
 
 def mocked_run_cmd(cmd, **kwargs):
     """Mocked version of run_cmd, with specified output for known commands."""

From 89b5cfbeb02a218d92e833f52944dfb049a277af Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 18:43:55 +0100
Subject: [PATCH 0619/1356] bump to v2.0.0 + update release notes

---
 RELEASE_NOTES              | 43 ++++++++++++++++++++++++++++++++++++++
 easybuild/tools/version.py |  2 +-
 2 files changed, 44 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 13ef17e9cc..408bddcf75 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,6 +3,49 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
+v2.0.0 (March 2nd 2015)
+-----------------------
+
+(requires vsc-base v2.0.3 or more recent)
+
+feature + bugfix release
+- drop support for behaviour that was deprecated for EasyBuild version 2.0 (#1143)
+    - the provided fix_broken_easyconfigs.py script can be used to update easyconfig files suffering from this (#1151)
+- stop including a crippled copy of vsc-base, include vsc-base as a proper dependency instead (#1160)
+- various other enhancements, including:
+    - add support for Linux/POWER systems (#1044)
+    - major cleanup in tools/systemtools.py + significantly enhanced tests (#1044)
+    - add support for 'eb -a rst', list available easyconfig parameters in ReST format (#1131)
+    - add support for specifying one or more easyconfigs in combination with --from-pr (#1132)
+    - define __contains__ in EasyConfig class (#1155)
+    - restore support for downloading over a proxy (#1158)
+        - i.e., use urllib2 rather than urllib
+        - this involved sacrificing the download progress report (which was only visible in the log file)
+    - let mpi_family return None if MPI is not supported by a toolchain (#1164)
+    - include support for specifying system-level configuration files for EasyBuild via $XDG_CONFIG_DIRS (#1166)
+        - see http://easybuild.readthedocs.org/en/develop/Configuration.html#default-configuration-files
+    - make unit tests more robust (#1167)
+    - add hierarchical module naming scheme categorizing modules by 'moduleclass' (#1176)
+    - enhance bootstrap script to allow bootstrapping using supplied tarballs (#1184)
+    - disable updating of Lmod cache by default (#1185)
+- various bug fixes, including:
+    - stop triggering deprecated/no longer support functionality in unit tests (#1126)
+    - fix from_pr test by including dummy easyblocks for HPL and ScaLAPACK (#1133)
+    - escape use of '%' in string with command line options with --job (#1135)
+    - fix handling specified patch level 0 (+ enhance tests for fetch_patches method) (#1139)
+    - fix formatting issues in generated easyconfig file obtained via --try-X (#1144)
+    - use log.error in tools/toolchain/toolchain.py where applicable (#1145)
+    - stop hardcoding /tmp in mpi_cmd_for function (#1146)
+    - correctly determine variable name for EBEXTLIST when generating module file (#1156)
+    - do not ignore exit code of failing postinstall commands (#1157)
+    - fix rare case in which used easyconfig and copied easyconfig are the same (#1159)
+    - always filter hidden deps from list of dependencies (#1161)
+    - fix implementation of path_matches function in tools/filetools.py (#1163)
+        - make sure that the specified paths exist before checking whether they point to the same file
+    - make sure plain text keyring is used by unit tests (#1165)
+    - suppress creation of module symlinks for hierarchical MNS (#1173)
+    - sort all lists obtained via glob.glob, since they are in arbitrary order (#1187)
+
 v1.16.1 (December 19th 2014)
 ----------------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 1bd1419af5..fc2af74096 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("2.0.0dev")
+VERSION = LooseVersion("2.0.0")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 8d601c5680978761306809fe1f88a4fc8ba0225a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 25 Feb 2015 20:07:00 +0100
Subject: [PATCH 0620/1356] add links for existing documentation updates,
 include FIXMEs for the ones that need to be taken care of

---
 RELEASE_NOTES | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 408bddcf75..67a87d00a0 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -11,7 +11,10 @@ v2.0.0 (March 2nd 2015)
 feature + bugfix release
 - drop support for behaviour that was deprecated for EasyBuild version 2.0 (#1143)
     - the provided fix_broken_easyconfigs.py script can be used to update easyconfig files suffering from this (#1151)
+    - FIXME: link to docs: No-longer-support-functionality.html + Usage-of-stand-alone-scripts.html#fix-broken-easyconfigs
 - stop including a crippled copy of vsc-base, include vsc-base as a proper dependency instead (#1160)
+    - FIXME: link to docs w.r.t. development setup
+    - FIXME: update requires dependencies to mention vsc-base
 - various other enhancements, including:
     - add support for Linux/POWER systems (#1044)
     - major cleanup in tools/systemtools.py + significantly enhanced tests (#1044)
@@ -23,11 +26,14 @@ feature + bugfix release
         - this involved sacrificing the download progress report (which was only visible in the log file)
     - let mpi_family return None if MPI is not supported by a toolchain (#1164)
     - include support for specifying system-level configuration files for EasyBuild via $XDG_CONFIG_DIRS (#1166)
-        - see http://easybuild.readthedocs.org/en/develop/Configuration.html#default-configuration-files
+        - see http://easybuild.readthedocs.org/en/latest/Configuration.html#default-configuration-files
     - make unit tests more robust (#1167)
+        - FIXME link to docs on running unit tests
     - add hierarchical module naming scheme categorizing modules by 'moduleclass' (#1176)
     - enhance bootstrap script to allow bootstrapping using supplied tarballs (#1184)
-    - disable updating of Lmod cache by default (#1185)
+        - see http://easybuild.readthedocs.org/en/latest/Installation.html#advanced-bootstrapping-options
+    - disable updating of Lmod user cache by default, add configuration option --update-modules-tool-cache (#1185)
+        - for now, only the Lmod user cache can be updated using --update-modules-tool-cache
 - various bug fixes, including:
     - stop triggering deprecated/no longer support functionality in unit tests (#1126)
     - fix from_pr test by including dummy easyblocks for HPL and ScaLAPACK (#1133)
@@ -41,9 +47,8 @@ feature + bugfix release
     - fix rare case in which used easyconfig and copied easyconfig are the same (#1159)
     - always filter hidden deps from list of dependencies (#1161)
     - fix implementation of path_matches function in tools/filetools.py (#1163)
-        - make sure that the specified paths exist before checking whether they point to the same file
     - make sure plain text keyring is used by unit tests (#1165)
-    - suppress creation of module symlinks for hierarchical MNS (#1173)
+    - suppress creation of module symlinks for HierarchicalMNS (#1173)
     - sort all lists obtained via glob.glob, since they are in arbitrary order (#1187)
 
 v1.16.1 (December 19th 2014)

From 0b19f94b951ccb30bb1b6e446a3e497d4f09f042 Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Wed, 25 Feb 2015 23:11:14 +0200
Subject: [PATCH 0621/1356] Some TC dickery.

---
 easybuild/toolchains/compiler/craypewrappers.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 35bd1e970f..0cb466a5aa 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -72,7 +72,6 @@ class CrayPEWrapper(Compiler):
     }
 
     COMPILER_SHARED_OPTION_MAP = {
-        'dynamic': 'dynamic',
         'pic': 'dynamic',
         'verbose': 'craype-verbose',
         'static': 'static',

From 06ec32a53617738f1bca670ca74efd38a3ede8d5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 26 Feb 2015 11:24:22 +0100
Subject: [PATCH 0622/1356] fix remarks in systemtools.py

---
 easybuild/tools/systemtools.py | 31 +++++++++++--------------------
 1 file changed, 11 insertions(+), 20 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 1414044a57..4f0d52a7be 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -106,7 +106,7 @@ def get_cpu_vendor():
     """
     Try to detect the CPU vendor
 
-    @return: INTEL, ARM or AMD constant
+    @return: a value from the VENDORS dict
     """
     vendor = None
     os_type = get_os_type()
@@ -115,14 +115,10 @@ def get_cpu_vendor():
         txt = read_file(PROC_CPUINFO_FP)
         arch = UNKNOWN
 
-        vendor_regexes = [
-            r"^vendor_id\s+:\s*(\S+)\s*$",  # Linux/x86
-            r".*:\s*(ARM|IBM).*$",  # Linux/ARM (e.g., Raspbian), Linux/POWER
-        ]
-        vendor_regex = re.compile('|'.join(vendor_regexes), re.M)
+        vendor_regex = re.compile(r"(vendor_id.*?)?\s*:\s*(?P<vendor>(?(1)\S+|(?:IBM|ARM)))")
         res = vendor_regex.search(txt)
         if res:
-            arch = res.group(1) or res.group(2)
+            arch = res.group('vendor')
         if arch in VENDORS:
             vendor = VENDORS[arch]
             tup = (vendor, vendor_regex.pattern, PROC_CPUINFO_FP)
@@ -146,7 +142,7 @@ def get_cpu_vendor():
 def get_cpu_family():
     """
     Determine CPU family.
-    @return: one of the AMD, ARM, INTEL, POWER constants
+    @return: a value from the CPU_FAMILIES list
     """
     family = None
     vendor = get_cpu_vendor()
@@ -173,14 +169,13 @@ def get_cpu_family():
 
 def get_cpu_model():
     """
-    Determine CPU model
-    for example: Intel(R) Core(TM) i5-2540M CPU @ 2.60GHz
+    Determine CPU model, e.g., Intel(R) Core(TM) i5-2540M CPU @ 2.60GHz
     """
     model = None
     os_type = get_os_type()
 
     if os_type == LINUX and os.path.exists(PROC_CPUINFO_FP):
-        # consider 'model name' first, use 'model' as a fallback
+        # we need 'model name' on Linux/x86, but 'model' is there first with different info
         # 'model name' is not there for Linux/POWER, but 'model' has the right info
         for key in [r'model\s*name', 'model']:
             model_regex = re.compile(r"^%s\s+:\s*(?P<model>.+)\s*$" % key, re.M)
@@ -225,16 +220,12 @@ def get_cpu_speed():
         elif os.path.exists(PROC_CPUINFO_FP):
             _log.debug("Trying to determine CPU frequency on Linux via %s" % PROC_CPUINFO_FP)
             cpuinfo_txt = read_file(PROC_CPUINFO_FP)
-            cpu_freq_regex = r"(%s)" % '|'.join([
-                r"^cpu MHz\s*:\s*(?P<cpu_freq_x86>[0-9.]+)",  # Linux x86 & more
-                r"^clock\s*:\s*(?P<cpu_freq_POWER>[0-9.]+)",  # Linux on POWER
-            ])
-            res = re.search(cpu_freq_regex, cpuinfo_txt, re.M)
+            # 'cpu MHz' on Linux/x86 (& more), 'clock' on Linux/POWER
+            cpu_freq_regex = re.compile(r"^(?:cpu MHz|clock)\s*:\s*(?P<cpu_freq>\d+(?:\.\d+)?)", re.M)
+            res = cpu_freq_regex.search(cpuinfo_txt)
             if res:
-                cpu_freq = res.group('cpu_freq_x86') or res.group('cpu_freq_POWER')
-            if cpu_freq is not None:
-                cpu_freq = float(cpu_freq)
-                _log.debug("Found CPU frequency using regex '%s': %s" % (cpu_freq_regex, cpu_freq))
+                cpu_freq = float(res.group('cpu_freq'))
+                _log.debug("Found CPU frequency using regex '%s': %s" % (cpu_freq_regex.pattern, cpu_freq))
             else:
                 raise SystemToolsException("Failed to determine CPU frequency from %s" % PROC_CPUINFO_FP)
         else:

From b5d67f0b88b2f54cb6aee21f747bd55110838fd2 Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Thu, 26 Feb 2015 12:33:30 +0200
Subject: [PATCH 0623/1356] First working version of using the wrappers
 internal compiler.

---
 .../toolchains/compiler/craypewrappers.py     | 76 +++++++------------
 1 file changed, 26 insertions(+), 50 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 0cb466a5aa..411d0fed31 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -55,32 +55,19 @@ class CrayPEWrapper(Compiler):
     COMPILER_FAMILY = TC_CONSTANT_CRAYPEWRAPPER
 
     COMPILER_UNIQUE_OPTS = {
+	    'dynamic': (True, """Generate dynamically linked executables and libraries."""),
         'mpich-mt': (False, """Directs the driver to link in an alternate version of the Cray-MPICH library which
                                  provides fine-grained multi-threading support to applications that perform
                                  MPI operations within threaded regions."""),
-        'dynamic': (True, "Directs the compiler driver to link dynamic libraries at runtime."),
         'usewrappedcompiler': (False, "Use the embedded compiler instead of the wrapper"),
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-        'dynamic': 'dynamic',
-        'shared': 'shared',
-        'static': 'static',
+	    'pic': 'shared',
+        'shared': 'dynamic',
+	    'static': 'static',
         'verbose': 'craype-verbose',
         'mpich-mt': 'craympich-mt',
-        'pic': 'dynamic',
-    }
-
-    COMPILER_SHARED_OPTION_MAP = {
-        'pic': 'dynamic',
-        'verbose': 'craype-verbose',
-        'static': 'static',
-    }
-
-    # @todo this is BS.
-    COMPILER_OPTIMAL_ARCHITECTURE_OPTION = {
-        systemtools.INTEL: 'march=native',
-        systemtools.AMD: 'march=native'
     }
 
     #COMPILER_PREC_FLAGS = ['strict', 'precise', 'defaultprec', 'loose', 'veryloose']  # precision flags, ordered !
@@ -91,8 +78,9 @@ class CrayPEWrapper(Compiler):
     COMPILER_F77 = 'ftn'
     COMPILER_F90 = 'ftn'
 
-    def _set_compiler_vars(self):
-        super(CrayPEWrapper, self)._set_compiler_vars()
+    COMPILER_FLAGS = []  # we dont have this for the wrappers
+    COMPILER_OPT_FLAGS = []  # or those
+    COMPILER_PREC_FLAGS = []  # and those for sure not !
 
     def _get_optimal_architecture(self):
         """On a Cray system we assume that the optimal architecture is controlled
@@ -102,40 +90,26 @@ def _get_optimal_architecture(self):
 
     def _set_compiler_flags(self):
         """Collect the flags set, and add them as variables too"""
+
         flags = [self.options.option(x) for x in self.COMPILER_FLAGS if self.options.get(x, False)]
         cflags = [self.options.option(x) for x in self.COMPILER_C_FLAGS + self.COMPILER_C_UNIQUE_FLAGS \
                   if self.options.get(x, False)]
         fflags = [self.options.option(x) for x in self.COMPILER_F_FLAGS + self.COMPILER_F_UNIQUE_FLAGS \
                   if self.options.get(x, False)]
 
-        # 1st one is the one to use. add default at the end so len is at least 1
-        # optflags = [self.options.option(x) for x in self.COMPILER_OPT_FLAGS if self.options.get(x, False)] + \
-        #            [self.options.option('defaultopt')]
-        #
-        # optarchflags = [self.options.option(x) for x in ['optarch'] if self.options.get(x, False)]
-        #
-        # precflags = [self.options.option(x) for x in self.COMPILER_PREC_FLAGS if self.options.get(x, False)] + \
-        #             [self.options.option('defaultprec')]
-        #
-        # self.variables.nextend('OPTFLAGS', optflags[:1] + optarchflags)
-        # self.variables.nextend('PRECFLAGS', precflags[:1])
 
         # precflags last
         self.variables.nappend('CFLAGS', flags)
         self.variables.nappend('CFLAGS', cflags)
-        self.variables.join('CFLAGS', )  # 'OPTFLAGS', 'PRECFLAGS')
 
         self.variables.nappend('CXXFLAGS', flags)
         self.variables.nappend('CXXFLAGS', cflags)
-        self.variables.join('CXXFLAGS', )  # 'OPTFLAGS', 'PRECFLAGS')
 
         self.variables.nappend('FFLAGS', flags)
         self.variables.nappend('FFLAGS', fflags)
-        self.variables.join('FFLAGS', )  # 'OPTFLAGS', 'PRECFLAGS')
 
         self.variables.nappend('F90FLAGS', flags)
         self.variables.nappend('F90FLAGS', fflags)
-        self.variables.join('F90FLAGS', )  # 'OPTFLAGS', 'PRECFLAGS')
 
 
 # Gcc's base is Compiler
@@ -144,24 +118,26 @@ class CrayPEWrapperGNU(CrayPEWrapper):
     COMPILER_MODULE_NAME = ['PrgEnv-gnu']
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_GNU'
 
-
     def _set_compiler_vars(self):
         if self.options.option('usewrappedcompiler'):
+            self.COMPILER_UNIQUE_OPTS = Gcc.COMPILER_UNIQUE_OPTS
+            self.COMPILER_UNIQUE_OPTION_MAP = Gcc.COMPILER_UNIQUE_OPTION_MAP
 
-            COMPILER_UNIQUE_OPTS = Gcc.COMPILER_UNIQUE_OPTS
-            COMPILER_UNIQUE_OPTION_MAP = Gcc.COMPILER_UNIQUE_OPTION_MAP
+            self.COMPILER_CC = Gcc.COMPILER_CC
+            self.COMPILER_CXX = Gcc.COMPILER_CXX
+            self.COMPILER_C_UNIQUE_FLAGS = []
 
-            COMPILER_CC = Gcc.COMPILER_CC
-            COMPILER_CXX = Gcc.COMPILER_CXX
-            COMPILER_C_UNIQUE_FLAGS = []
+            self.COMPILER_F77 = Gcc.COMPILER_F77
+            self.COMPILER_F90 = Gcc.COMPILER_F90
+            self.COMPILER_F_UNIQUE_FLAGS = Gcc.COMPILER_F_UNIQUE_FLAGS
 
-            COMPILER_F77 = Gcc.COMPILER_F77
-            COMPILER_F90 = Gcc.COMPILER_F90
-            COMPILER_F_UNIQUE_FLAGS = Gcc.COMPILER_F_UNIQUE_FLAGS
-
-            super(CrayPEWrapperGNU, self)._set_compiler_vars()
         else:
-            super(CrayPEWrapper, self)._set_compiler_vars()
+            pass
+
+        super(CrayPEWrapperGNU,self)._set_compiler_vars()
+
+
+
 
 
 class CrayPEWrapperIntel(CrayPEWrapper):
@@ -169,7 +145,7 @@ class CrayPEWrapperIntel(CrayPEWrapper):
 
     COMPILER_MODULE_NAME = ['PrgEnv-intel']
 
-    def _set_compiler_vars(self):
+    def _set_compiler_flags(self):
         if self.options.option("usewrappedcompiler"):
             COMPILER_UNIQUE_OPTS = IntelIccIfort.COMPILER_UNIQUE_OPTS
             COMPILER_UNIQUE_OPTION_MAP = IntelIccIfort.COMPILER_UNIQUE_OPTION_MAP
@@ -185,9 +161,9 @@ def _set_compiler_vars(self):
 
             LINKER_TOGGLE_STATIC_DYNAMIC = IntelIccIfort.LINKER_TOGGLE_STATIC_DYNAMIC
 
-            super(CrayPEWrapperIntel, self).set_compiler_vars()
+            super(CrayPEWrapperIntel, self).set_compiler_flags()
         else:
-            super(CrayPEWrapper, self)._set_compiler_vars()
+            super(CrayPEWrapper, self)._set_compiler_flags()
 
 
 class CrayPEWrapperCray(CrayPEWrapper):
@@ -195,4 +171,4 @@ class CrayPEWrapperCray(CrayPEWrapper):
     COMPILER_MODULE_NAME = ['PrgEnv-cray']
 
     def _set_compiler_vars(self):
-        super(CrayPEWrapperCray, self)._set_compiler_vars()
\ No newline at end of file
+        super(CrayPEWrapperCray, self)._set_compiler_vars()

From 7ff551129f090d8123f64f559d12dcf5897e6989 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 26 Feb 2015 12:54:15 +0100
Subject: [PATCH 0624/1356] use a single regex for obtaining model name

---
 easybuild/tools/systemtools.py | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 4f0d52a7be..921c8e926e 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -177,15 +177,13 @@ def get_cpu_model():
     if os_type == LINUX and os.path.exists(PROC_CPUINFO_FP):
         # we need 'model name' on Linux/x86, but 'model' is there first with different info
         # 'model name' is not there for Linux/POWER, but 'model' has the right info
-        for key in [r'model\s*name', 'model']:
-            model_regex = re.compile(r"^%s\s+:\s*(?P<model>.+)\s*$" % key, re.M)
-            txt = read_file(PROC_CPUINFO_FP)
-            res = model_regex.search(txt)
-            if res is not None:
-                model = res.group('model').strip()
-                tup = (model_regex.pattern, PROC_CPUINFO_FP, model)
-                _log.debug("Determined CPU model on Linux using regex '%s' in %s: %s" % tup)
-                break
+        model_regex = re.compile(r"^model(?:\s+name)?\s+:\s*(?P<model>.*[A-Za-z].+)\s*$", re.M)
+        txt = read_file(PROC_CPUINFO_FP)
+        res = model_regex.search(txt)
+        if res is not None:
+            model = res.group('model').strip()
+            tup = (model_regex.pattern, PROC_CPUINFO_FP, model)
+            _log.debug("Determined CPU model on Linux using regex '%s' in %s: %s" % tup)
 
     elif os_type == DARWIN:
         cmd = "sysctl -n machdep.cpu.brand_string"

From 460c84fb9c9e58c75353ab7826a4a2c886606e69 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 26 Feb 2015 15:19:23 +0100
Subject: [PATCH 0625/1356] fix remarks

---
 easybuild/framework/easyconfig/easyconfig.py | 13 ++--
 easybuild/framework/easyconfig/parser.py     |  8 +-
 easybuild/scripts/fix_broken_easyconfigs.py  | 77 +++++++++++---------
 test/framework/easyconfigparser.py           | 24 ++++++
 4 files changed, 79 insertions(+), 43 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 0712c7c5d2..99a94ddb8c 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -101,11 +101,12 @@ class EasyConfig(object):
     def __init__(self, path, extra_options=None, build_specs=None, validate=True, hidden=None, rawtxt=None):
         """
         initialize an easyconfig.
-        @param path: path to easyconfig file to be parsed
+        @param path: path to easyconfig file to be parsed (ignored if rawtxt is specified)
         @param extra_options: dictionary with extra variables that can be set for this specific instance
         @param build_specs: dictionary of build specifications (see EasyConfig class, default: {})
         @param validate: indicates whether validation should be performed (note: combined with 'validate' build option)
         @param hidden: indicate whether corresponding module file should be installed hidden ('.'-prefixed)
+        @param rawtxt: raw contents of easyconfig file
         """
         self.template_values = None
         self.enable_templating = True  # a boolean to control templating
@@ -116,13 +117,14 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
             self.log.error("EasyConfig __init__ expected a valid path")
 
         # read easyconfig file contents (or use provided rawtxt), so it can be passed down to avoid multiple re-reads
-        self.path = path
+        self.path = None
         if rawtxt is None:
+            self.path = path
             self.rawtxt = read_file(path)
-            self.log.info("Raw contents from supplied easyconfig file %s: %s" % (path, self.rawtxt))
+            self.log.debug("Raw contents from supplied easyconfig file %s: %s" % (path, self.rawtxt))
         else:
             self.rawtxt = rawtxt
-            self.log.info("Supplied easyconfig: %s" % self.rawtxt)
+            self.log.debug("Supplied raw easyconfig contents: %s" % self.rawtxt)
 
         # use legacy module classes as default
         self.valid_module_classes = build_option('valid_module_classes')
@@ -698,7 +700,8 @@ def fetch_parameter_from_easyconfig_file(path, param):
     old = 'fetch_parameter_from_easyconfig_file'
     new = 'fetch_parameters_from_easyconfig'
     _log.deprecated("%s is replaced by %s from easybuild.framework.easyconfig.parser" % (old, new), '3.0')
-    return fetch_parameters_from_easyconfig(read_file(path), [param])[0]
+    ectxt = read_file(path)
+    return fetch_parameters_from_easyconfig(ectxt, [param])[0]
 
 
 def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_failed_import=True):
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 376b2e436f..3b4c5ce318 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -89,12 +89,12 @@ def __init__(self, filename=None, format_version=None, rawcontent=None):
         self.format_version = format_version
         self._formatter = None
 
-        if filename is not None:
-            self._check_filename(filename)
-            self.process()
-        elif rawcontent is not None:
+        if rawcontent is not None:
             self.rawcontent = rawcontent
             self._set_formatter()
+        elif filename is not None:
+            self._check_filename(filename)
+            self.process()
         else:
             self.log.error("Neither filename nor rawcontent provided to EasyConfigParser")
 
diff --git a/easybuild/scripts/fix_broken_easyconfigs.py b/easybuild/scripts/fix_broken_easyconfigs.py
index 3daf26ed61..2144eefbb6 100755
--- a/easybuild/scripts/fix_broken_easyconfigs.py
+++ b/easybuild/scripts/fix_broken_easyconfigs.py
@@ -22,6 +22,11 @@
 # You should have received a copy of the GNU General Public License
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
+"""
+Script to fix easyconfigs that broke due to support for deprecated functionality being dropped in EasyBuild 2.0
+
+@author: Kenneth Hoste (Ghent University)
+"""
 import os
 import re
 import sys
@@ -37,9 +42,11 @@
 from test.framework.utilities import init_config
 
 
-log = fancylogger.getLogger('main')
-fancylogger.logToScreen(enable=True, stdout=True)
-log.setLevel('INFO')
+options = {
+    'backup': ("Backup up easyconfigs before modifying them", None, 'store_true', True, 'b'),
+}
+go = simple_option(options)
+log = go.log
 
 
 def fix_broken_easyconfig(ectxt, easyblock_class):
@@ -75,20 +82,47 @@ def fix_broken_easyconfig(ectxt, easyblock_class):
     return ectxt
 
 
+def process_easyconfig_file(ec_file):
+    """Process an easyconfig file: fix if it's broken, back it up before fixing it inline (if requested)."""
+    ectxt = read_file(ec_file)
+    name, easyblock = fetch_parameters_from_easyconfig(ectxt, ['name', 'easyblock'])
+    derived_easyblock_class = get_easyblock_class(easyblock, name=name, default_fallback=False)
+
+    fixed_ectxt = fix_broken_easyconfig(ectxt, derived_easyblock_class)
+
+    if ectxt != fixed_ectxt:
+        if go.options.backup:
+            try:
+                backup_ec_file = '%s.bk' % ec_file
+                i = 1
+                while os.path.exists(backup_ec_file):
+                    backup_ec_file = '%s.bk%d' % (ec_file, i)
+                    i += 1
+                os.rename(ec_file, backup_ec_file)
+                log.info("Backed up %s to %s" % (ec_file, backup_ec_file))
+            except OSError, err:
+                log.error("Failed to backup %s before rewriting it: %s" % (ec_file, err))
+
+        write_file(ec_file, fixed_ectxt)
+        log.debug("Contents of fixed easyconfig file: %s" % fixed_ectxt)
+
+        log.info("%s: fixed" % ec_file)
+    else:
+        log.info("%s: nothing to fix" % ec_file)
+
 # MAIN
 
 def main():
+    """Main script functionality."""
+
+    fancylogger.logToScreen(enable=True, stdout=True)
+    log.setLevel('INFO')
 
     try:
         import easybuild.easyblocks.generic.configuremake
     except ImportError, err:
         log.error("easyblocks are not available in Python search path: %s" % err)
 
-    options = {
-        'backup': ("Backup up easyconfigs before modifying them", None, 'store_true', True, 'b'),
-    }
-    go = simple_option(options)
-
     init_config(args=['--quiet'])
 
     for path in go.args:
@@ -101,32 +135,7 @@ def main():
 
     log.info("Processing %d easyconfigs" % len(ec_files))
     for ec_file in ec_files:
-
-        ectxt = read_file(ec_file)
-        name, easyblock = fetch_parameters_from_easyconfig(ectxt, ['name', 'easyblock'])
-        derived_easyblock_class = get_easyblock_class(easyblock, name=name, default_fallback=False)
-
-        fixed_ectxt = fix_broken_easyconfig(ectxt, derived_easyblock_class)
-
-        if ectxt != fixed_ectxt:
-            if go.options.backup:
-                try:
-                    backup_ec_file = '%s.bk' % ec_file
-                    i = 1
-                    while os.path.exists(backup_ec_file):
-                        backup_ec_file = '%s.bk%d' % (ec_file, i)
-                        i += 1
-                    os.rename(ec_file, backup_ec_file)
-                    log.info("Backed up %s to %s" % (ec_file, backup_ec_file))
-                except OSError, err:
-                    log.error("Failed to backup %s before rewriting it: %s" % (ec_file, err))
-
-            write_file(path, fixed_ectxt)
-            log.debug("Contents of fixed easyconfig file: %s" % fixed_ectxt)
-
-            log.info("%s: fixed" % ec_file)
-        else:
-            log.info("%s: nothing to fix" % ec_file)
+        process_easyconfig_file(ec_file)
 
 
 if __name__ == '__main__':
diff --git a/test/framework/easyconfigparser.py b/test/framework/easyconfigparser.py
index fa4194b9d1..5d0d4c5959 100644
--- a/test/framework/easyconfigparser.py
+++ b/test/framework/easyconfigparser.py
@@ -36,6 +36,8 @@
 from easybuild.framework.easyconfig.format.format import Dependency
 from easybuild.framework.easyconfig.format.version import EasyVersion
 from easybuild.framework.easyconfig.parser import EasyConfigParser
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import read_file
 
 
 TESTDIRBASE = os.path.join(os.path.dirname(__file__), 'easyconfigs')
@@ -146,6 +148,28 @@ def test_v20_deps(self):
         # restore
         easybuild.tools.build_log.EXPERIMENTAL = orig_experimental
 
+    def test_raw(self):
+        """Test passing of raw contents to EasyConfigParser."""
+        ec_file1 = os.path.join(TESTDIRBASE, 'v1.0', 'GCC-4.6.3.eb')
+        ec_txt1 = read_file(ec_file1)
+        ec_file2 = os.path.join(TESTDIRBASE, 'v1.0', 'gzip-1.5-goolf-1.4.10.eb')
+        ec_txt2 = read_file(ec_file2)
+
+        ecparser = EasyConfigParser(ec_file1)
+        self.assertEqual(ecparser.rawcontent, ec_txt1)
+
+        ecparser = EasyConfigParser(rawcontent=ec_txt2)
+        self.assertEqual(ecparser.rawcontent, ec_txt2)
+
+        # rawcontent supersedes passed filepath
+        ecparser = EasyConfigParser(ec_file1, rawcontent=ec_txt2)
+        self.assertEqual(ecparser.rawcontent, ec_txt2)
+        ec = ecparser.get_config_dict()
+        self.assertEqual(ec['name'], 'gzip')
+        self.assertEqual(ec['toolchain']['name'], 'goolf')
+
+        self.assertErrorRegex(EasyBuildError, "Neither filename nor rawcontent provided", EasyConfigParser)
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(EasyConfigParserTest)

From c00c4dc3a3d3419ad5462d7781a6cd9c420a9689 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 26 Feb 2015 17:00:48 +0100
Subject: [PATCH 0626/1356] drop custom setUp/tearDown in toolchain tests which
 are hard modifying $MODULEPATH

---
 test/framework/toolchain.py | 22 ----------------------
 1 file changed, 22 deletions(-)

diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index e6e80ff5e4..01b6ce5769 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -49,17 +49,6 @@
 class ToolchainTest(EnhancedTestCase):
     """ Baseclass for toolchain testcases """
 
-    def setUp(self):
-        """Set up everything for a unit test."""
-        super(ToolchainTest, self).setUp()
-
-        # start with a clean slate
-        modules.modules_tool().purge()
-
-        # make sure path with modules for testing is added to MODULEPATH
-        self.orig_modpath = os.environ.get('MODULEPATH', '')
-        os.environ['MODULEPATH'] = find_full_path(os.path.join('test', 'framework', 'modules'))
-
     def get_toolchain(self, name, version=None):
         """Get a toolchain object instance to test with."""
         tc_class, _ = search_toolchain(name)
@@ -554,17 +543,6 @@ def test_mpi_cmd_for(self):
         shutil.rmtree(tmpdir)
         write_file(imkl_module_path, imkl_module_txt)
 
-    def tearDown(self):
-        """Cleanup."""
-        # purge any loaded modules before restoring $MODULEPATH
-        modules.modules_tool().purge()
-
-        super(ToolchainTest, self).tearDown()
-
-        os.environ['MODULEPATH'] = self.orig_modpath
-        # reinitialize modules tool after touching $MODULEPATH
-        modules.modules_tool()
-
 def suite():
     """ return all the tests"""
     return TestLoader().loadTestsFromTestCase(ToolchainTest)

From 7ad8032fa903d00cfe509d8065a0eaacb2f51f22 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Feb 2015 09:08:30 +0100
Subject: [PATCH 0627/1356] include PR #1191 in v2.0 release notes

---
 RELEASE_NOTES | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 67a87d00a0..8ded9a94b1 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -42,7 +42,7 @@ feature + bugfix release
     - fix formatting issues in generated easyconfig file obtained via --try-X (#1144)
     - use log.error in tools/toolchain/toolchain.py where applicable (#1145)
     - stop hardcoding /tmp in mpi_cmd_for function (#1146)
-    - correctly determine variable name for EBEXTLIST when generating module file (#1156)
+    - correctly determine variable name for $EBEXTLIST when generating module file (#1156)
     - do not ignore exit code of failing postinstall commands (#1157)
     - fix rare case in which used easyconfig and copied easyconfig are the same (#1159)
     - always filter hidden deps from list of dependencies (#1161)
@@ -50,6 +50,7 @@ feature + bugfix release
     - make sure plain text keyring is used by unit tests (#1165)
     - suppress creation of module symlinks for HierarchicalMNS (#1173)
     - sort all lists obtained via glob.glob, since they are in arbitrary order (#1187)
+    - stop modifying $MODULEPATH directly in setUp/tearDown of toolchain tests (#1191)
 
 v1.16.1 (December 19th 2014)
 ----------------------------

From 1a998c25080fa09ee308c97dd98675eb9338afa2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Feb 2015 09:09:30 +0100
Subject: [PATCH 0628/1356] use available which() function, rather than running
 'which' via run_cmd

---
 easybuild/framework/easyconfig/tools.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 93bf23f188..82ad8d0ab0 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -73,11 +73,10 @@
 from easybuild.framework.easyconfig.easyconfig import process_easyconfig
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import find_easyconfigs, search_file, write_file
+from easybuild.tools.filetools import find_easyconfigs, which, write_file
 from easybuild.tools.github import fetch_easyconfigs_from_pr
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.ordereddict import OrderedDict
-from easybuild.tools.run import run_cmd
 from easybuild.tools.utilities import quote_str
 
 
@@ -203,12 +202,12 @@ def get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None):
     path_list.extend(sys.path)
 
     # figure out installation prefix, e.g. distutils install path for easyconfigs
-    (out, ec) = run_cmd("which eb", simple=False, log_all=False, log_ok=False)
-    if ec:
-        _log.warning("eb not found (%s), failed to determine installation prefix" % out)
+    eb_path = which('eb')
+    if eb_path is None:
+        _log.warning("'eb' not found in $PATH, failed to determine installation prefix")
     else:
         # eb should reside in <install_prefix>/bin/eb
-        install_prefix = os.path.dirname(os.path.dirname(out))
+        install_prefix = os.path.dirname(os.path.dirname(eb_path))
         path_list.append(install_prefix)
         _log.debug("Also considering installation prefix %s..." % install_prefix)
 

From 9aa5e2772623f574222e96e65905ced569788f4d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Feb 2015 12:18:46 +0100
Subject: [PATCH 0629/1356] include PR #1192 in v2.0 release notes

---
 RELEASE_NOTES | 1 +
 1 file changed, 1 insertion(+)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 8ded9a94b1..053701ffe7 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -34,6 +34,7 @@ feature + bugfix release
         - see http://easybuild.readthedocs.org/en/latest/Installation.html#advanced-bootstrapping-options
     - disable updating of Lmod user cache by default, add configuration option --update-modules-tool-cache (#1185)
         - for now, only the Lmod user cache can be updated using --update-modules-tool-cache
+    - use available which() function, rather than running 'which' via run_cmd (#1192)
 - various bug fixes, including:
     - stop triggering deprecated/no longer support functionality in unit tests (#1126)
     - fix from_pr test by including dummy easyblocks for HPL and ScaLAPACK (#1133)

From e909a3c3a612ccfeef82ba0a6700c3cb55f504c1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Feb 2015 18:31:53 +0100
Subject: [PATCH 0630/1356] fix install-EasyBuild-develop.sh script w.r.t.
 vsc-base dependency

---
 .../scripts/install-EasyBuild-develop.sh      | 25 ++++++++++++-------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/easybuild/scripts/install-EasyBuild-develop.sh b/easybuild/scripts/install-EasyBuild-develop.sh
index 5474adb48b..e4fd5acbb0 100644
--- a/easybuild/scripts/install-EasyBuild-develop.sh
+++ b/easybuild/scripts/install-EasyBuild-develop.sh
@@ -10,11 +10,11 @@ set -e
 # Print script help
 print_usage()
 {
-    echo "Usage: $0 github_username install_directory"
+    echo "Usage: $0 <github_username> <install_dir>"
     echo
-    echo "    github_username:     username on GitHub for which the easybuild repositories should be cloned"
+    echo "    github_username:     username on GitHub for which the EasyBuild repositories should be cloned"
     echo
-    echo "    install_directory:   directory were all the EasyBuild files will be installed"
+    echo "    install_dir:         directory were all the EasyBuild files will be installed"
     echo
 }
 
@@ -25,17 +25,17 @@ github_clone_branch()
     BRANCH="$2"
 
     cd "${INSTALL_DIR}"
-    echo "=== Cloning ${REPO} ..."
+    echo "=== Cloning ${GITHUB_USERNAME}/${REPO} ..."
     git clone git@github.com:${GITHUB_USERNAME}/${REPO}.git
 
-    echo "=== Add and fetch HPC UGent GitHub repository"
+    echo "=== Adding and fetching HPC-UGent GitHub repository @ hpcugent/{$REPO} ..."
     cd "${REPO}"
     git remote add "github_hpcugent" "git@github.com:hpcugent/${REPO}.git"
     git fetch github_hpcugent
     
     # If branch is not 'master', track and checkout it
     if [ "$BRANCH" != "master" ] ; then
-        echo "=== Checking out the '${BRANCH}' branch"
+        echo "=== Checking out the '${BRANCH}' branch ..."
         git branch --track "${BRANCH}" "github_hpcugent/${BRANCH}"
         git checkout "${BRANCH}"
     fi
@@ -69,6 +69,7 @@ conflict    EasyBuild
 
 prepend-path    PATH            "\$root/easybuild-framework"
 
+prepend-path    PYTHONPATH      "\$root/vsc-base"
 prepend-path    PYTHONPATH      "\$root/easybuild-framework"
 prepend-path    PYTHONPATH      "\$root/easybuild-easyblocks"
 prepend-path    PYTHONPATH      "\$root/easybuild-easyconfigs"
@@ -107,6 +108,9 @@ mkdir -p "${INSTALL_DIR}"
 cd "${INSTALL_DIR}"
 INSTALL_DIR="${PWD}" # get the full path
 
+# Clone repository for vsc-base dependency with 'master' branch
+github_clone_branch "vsc-base"   "master"
+
 # Clone code repositories with the 'develop' branch
 github_clone_branch "easybuild-framework"   "develop"
 github_clone_branch "easybuild-easyblocks"  "develop"
@@ -119,11 +123,14 @@ github_clone_branch "easybuild" "master"
 github_clone_branch "easybuild-wiki" "master"
 
 # Create the module file
-EB_DEVEL_MODULE="${INSTALL_DIR}/module-EasyBuild-develop"
+EB_DEVEL_MODULE_NAME="EasyBuild-develop"
+EB_DEVEL_MODULE="${INSTALL_DIR}/${EB_DEVEL_MODULE_NAME}"
 print_devel_module > "${EB_DEVEL_MODULE}"
 echo 
-echo "=== Run 'module load ${EB_DEVEL_MODULE}' to use your development version of EasyBuild."
-echo "=== (you can add a symlink in your MODULEPATH to make this module appear together with the others)"
+echo "=== Run 'module use ${INSTALL_DIR}' and 'module load ${EB_DEVEL_MODULE_NAME}' to use your development version of EasyBuild."
+echo "=== (you can append ${INSTALL_DIR} to your MODULEPATH to make this module always available for loading)"
+echo
+echo "=== To update each repository, run 'git pull origin' in each subdirectory of ${INSTALL_DIR}"
 echo
 
 exit 0

From 6c25ca4d9b0890f3f83ef62d2b0177152e667432 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Feb 2015 18:52:44 +0100
Subject: [PATCH 0631/1356] add test to make sure vsc-base is imported from
 outside of framework location

---
 test/framework/suite.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 598be0106a..fdfcfd71e0 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -35,12 +35,23 @@
 import sys
 import tempfile
 import unittest
+import vsc
 from vsc.utils import fancylogger
 
 # initialize EasyBuild logging, so we disable it
+import easybuild.framework
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import set_tmpdir
 
+# easybuild.framework.__file__ provides location to <prefix>/easybuild/framework/__init__.py
+FRAMEWORK_LOC = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(easybuild.framework.__file__))))
+# vsc.__file__ provides location to <prefix>/vsc/__init__.py
+VSC_LOC = os.path.dirname(os.path.dirname(os.path.abspath(vsc.__file__)))
+# make sure vsc is being imported from outside of framework
+if os.path.samefile(FRAMEWORK_LOC, VSC_LOC):
+    sys.stderr.write("ERROR: Use of vsc-base at same location as easybuild-framework detected: %s\n" % VSC_LOC)
+    sys.exit(1)
+
 # set plain text key ring to be used, so a GitHub token stored in it can be obtained without having to provide a password
 try:
     import keyring

From 902be120c8036ff23906a41c49efde3d37095f27 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 2 Mar 2015 09:04:05 +0100
Subject: [PATCH 0632/1356] flesh out check for vsc import location into new
 test module test/framework/general.py

---
 test/framework/general.py | 59 +++++++++++++++++++++++++++++++++++++++
 test/framework/suite.py   | 14 ++--------
 2 files changed, 61 insertions(+), 12 deletions(-)
 create mode 100644 test/framework/general.py

diff --git a/test/framework/general.py b/test/framework/general.py
new file mode 100644
index 0000000000..d50b854d4d
--- /dev/null
+++ b/test/framework/general.py
@@ -0,0 +1,59 @@
+##
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Unit tests for general aspects of the EasyBuild framework
+
+@author: Kenneth hoste (Ghent University)
+"""
+import os
+from test.framework.utilities import EnhancedTestCase
+from unittest import TestLoader, main
+
+import vsc
+
+import easybuild.framework
+
+
+class GeneralTest(EnhancedTestCase):
+    """Test for general aspects of EasyBuild framework."""
+
+    def test_vsc_location(self):
+        """Make sure location of imported vsc module is not the framework itself."""
+        # cfr. https://github.com/hpcugent/easybuild-framework/pull/1160
+        # easybuild.framework.__file__ provides location to <prefix>/easybuild/framework/__init__.py
+        framework_loc = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(easybuild.framework.__file__))))
+        # vsc.__file__ provides location to <prefix>/vsc/__init__.py
+        vsc_loc = os.path.dirname(os.path.dirname(os.path.abspath(vsc.__file__)))
+        # make sure vsc is being imported from outside of framework
+        msg = "vsc-base is not provided by EasyBuild framework itself, found location: %s" % vsc_loc
+        self.assertFalse(os.path.samefile(framework_loc, vsc_loc), msg)
+
+
+def suite():
+    """ returns all the testcases in this module """
+    return TestLoader().loadTestsFromTestCase(GeneralTest)
+
+if __name__ == '__main__':
+    main()
diff --git a/test/framework/suite.py b/test/framework/suite.py
index fdfcfd71e0..f854208879 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -35,23 +35,12 @@
 import sys
 import tempfile
 import unittest
-import vsc
 from vsc.utils import fancylogger
 
 # initialize EasyBuild logging, so we disable it
-import easybuild.framework
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import set_tmpdir
 
-# easybuild.framework.__file__ provides location to <prefix>/easybuild/framework/__init__.py
-FRAMEWORK_LOC = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(easybuild.framework.__file__))))
-# vsc.__file__ provides location to <prefix>/vsc/__init__.py
-VSC_LOC = os.path.dirname(os.path.dirname(os.path.abspath(vsc.__file__)))
-# make sure vsc is being imported from outside of framework
-if os.path.samefile(FRAMEWORK_LOC, VSC_LOC):
-    sys.stderr.write("ERROR: Use of vsc-base at same location as easybuild-framework detected: %s\n" % VSC_LOC)
-    sys.exit(1)
-
 # set plain text key ring to be used, so a GitHub token stored in it can be obtained without having to provide a password
 try:
     import keyring
@@ -74,6 +63,7 @@
 import test.framework.easyconfigversion as ev
 import test.framework.filetools as f
 import test.framework.format_convert as f_c
+import test.framework.general as gen
 import test.framework.github as g
 import test.framework.license as l
 import test.framework.module_generator as mg
@@ -109,7 +99,7 @@
 
 # call suite() for each module and then run them all
 # note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
-tests = [o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p]
+tests = [gen, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p]
 
 SUITE = unittest.TestSuite([x.suite() for x in tests])
 

From 345131861fa19a1862fee1951c578cb859020446 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 2 Mar 2015 10:13:34 +0100
Subject: [PATCH 0633/1356] isolate unit tests from available easyblocks other
 than those included in the tests

---
 test/framework/options.py   | 3 ++-
 test/framework/utilities.py | 5 +++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 36f500906d..ae2273a1d1 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1429,7 +1429,7 @@ def toy(extra_args=None):
     def test_robot(self):
         """Test --robot and --robot-paths command line options."""
         # unset $EASYBUILD_ROBOT_PATHS that was defined in setUp
-        del os.environ['EASYBUILD_ROBOT_PATHS']
+        os.environ['EASYBUILD_ROBOT_PATHS'] = self.test_prefix
 
         test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         eb_file = os.path.join(test_ecs_path, 'gzip-1.4-GCC-4.6.3.eb')  # includes 'toy/.0.0-deps' as a dependency
@@ -1463,6 +1463,7 @@ def test_robot(self):
         shutil.copytree(test_ecs_path, os.path.join(tmpdir, 'easybuild', 'easyconfigs'))
 
         # prepend path to test easyconfigs into Python search path, so it gets picked up as --robot-paths default
+        del os.environ['EASYBUILD_ROBOT_PATHS']
         orig_sys_path = sys.path[:]
         sys.path.insert(0, tmpdir)
         self.eb_main(args, raise_error=True)
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 8a7278f2ad..5754c71760 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -118,6 +118,11 @@ def setUp(self):
 
         init_config()
 
+        # remove any entries in Python search path that seem to provide easyblocks
+        for path in sys.path[:]:
+            if os.path.exists(os.path.join(path, 'easybuild', 'easyblocks', '__init__.py')):
+                sys.path.remove(path)
+
         # add test easyblocks to Python search path and (re)import and reload easybuild modules
         import easybuild
         sys.path.append(os.path.join(testdir, 'sandbox'))

From a2d29ffae49b5bd4ee2ab382c386184a3d88c656 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 2 Mar 2015 13:32:17 +0100
Subject: [PATCH 0634/1356] fix issues in updated install-EasyBuild-develop.sh
 script

---
 easybuild/scripts/install-EasyBuild-develop.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/scripts/install-EasyBuild-develop.sh b/easybuild/scripts/install-EasyBuild-develop.sh
index e4fd5acbb0..83e93031ed 100644
--- a/easybuild/scripts/install-EasyBuild-develop.sh
+++ b/easybuild/scripts/install-EasyBuild-develop.sh
@@ -26,7 +26,7 @@ github_clone_branch()
 
     cd "${INSTALL_DIR}"
     echo "=== Cloning ${GITHUB_USERNAME}/${REPO} ..."
-    git clone git@github.com:${GITHUB_USERNAME}/${REPO}.git
+    git clone --branch master git@github.com:${GITHUB_USERNAME}/${REPO}.git
 
     echo "=== Adding and fetching HPC-UGent GitHub repository @ hpcugent/{$REPO} ..."
     cd "${REPO}"
@@ -69,7 +69,7 @@ conflict    EasyBuild
 
 prepend-path    PATH            "\$root/easybuild-framework"
 
-prepend-path    PYTHONPATH      "\$root/vsc-base"
+prepend-path    PYTHONPATH      "\$root/vsc-base/lib"
 prepend-path    PYTHONPATH      "\$root/easybuild-framework"
 prepend-path    PYTHONPATH      "\$root/easybuild-easyblocks"
 prepend-path    PYTHONPATH      "\$root/easybuild-easyconfigs"

From dd8f439e29a32b3dfaef07dfa095b94aa0873d09 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 13 Aug 2014 17:55:44 +0200
Subject: [PATCH 0635/1356] Confine job-related functionality into a single
 "job backend" module.

* `tools.parallelbuild` is now parametric on a job factory object,
  which encapsulates all functionality needed to create and manage
  jobs.  By swapping the factory, we can change the job backend.

* the `--job` option now accepts an (optional) argument, naming the
  backend to use.  ATM, only the `pbs` backend is selectable.
---
 easybuild/main.py                |   3 +-
 easybuild/tools/options.py       |   2 +-
 easybuild/tools/parallelbuild.py |  55 +++++++++------
 easybuild/tools/pbs_job.py       | 112 +++++++++++++++++++------------
 easybuild/tools/testing.py       |   2 +-
 5 files changed, 108 insertions(+), 66 deletions(-)
 mode change 100644 => 100755 easybuild/main.py

diff --git a/easybuild/main.py b/easybuild/main.py
old mode 100644
new mode 100755
index f1ab88af41..17b8c6ea59
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -292,7 +292,8 @@ def main(testing_data=(None, None, None)):
 
     # submit build as job(s), clean up and exit
     if options.job:
-        job_info_txt = submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
+        job_info_txt = submit_jobs(ordered_ecs, eb_go.generate_cmd_line(),
+                                   backend=options.job, testing=testing)
         if not testing:
             print_msg("Submitted parallel build jobs, exiting now: %s" % job_info_txt)
             cleanup(logfile, eb_tmpdir, testing)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ebb608c169..e607d643be 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -116,7 +116,7 @@ def basic_options(self):
             'dry-run-short': ("Print build overview incl. dependencies (short paths)", None, 'store_true', False, 'D'),
             'force': ("Force to rebuild software even if it's already installed (i.e. if it can be found as module)",
                       None, 'store_true', False, 'f'),
-            'job': ("Submit the build as a job", None, 'store_true', False),
+            'job': ("Submit the build as a job", 'choice', 'store_or_None', 'pbs', ['pbs']),
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 18bca84e48..71ef43a206 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -42,22 +42,33 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
-from easybuild.tools.pbs_job import PbsJob, connect_to_server, disconnect_from_server, get_ppn
+from easybuild.tools.pbs_job import PbsJobFactory
+#from easybuild.tools.gc3pie_job import GC3PieJobFactory
 from easybuild.tools.repository.repository import init_repository
 from vsc.utils import fancylogger
 
 
 _log = fancylogger.getLogger('parallelbuild', fname=False)
 
+# map `--job=name` to a Python class we can use
+_job_submission_backends = {
+#    'gc3pie': GC3PieJobFactory,
+    'pbs': PbsJobFactory,
+}
 
-def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None, prepare_first=True):
+def build_easyconfigs_in_parallel(backend, build_command, easyconfigs, output_dir=None):
     """
-    easyconfigs is a list of easyconfigs which can be built (e.g. they have no unresolved dependencies)
-    this function will build them in parallel by submitting jobs
+    Build easyconfigs in parallel by submitting jobs to a batch-queuing system.
+    Return list of jobs submitted.
+
+    Argument `easyconfigs` is a list of easyconfigs which can be
+    built: e.g. they have no unresolved dependencies.  This function
+    will build them in parallel by submitting jobs.
+
+    @param backend: name of the job processing backend to use (currently 'pbs' only)
     @param build_command: build command to use
     @param easyconfigs: list of easyconfig files
     @param output_dir: output directory
-    returns the jobs
     """
     _log.info("going to build these easyconfigs in parallel: %s", easyconfigs)
     job_ids = {}
@@ -65,14 +76,14 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None, p
     # so one can linearly walk over the list and use previous job id's
     jobs = []
 
-    # create a single connection, and reuse it
-    conn = connect_to_server()
-    if conn is None:
-        _log.error("connect_to_server returned %s, can't submit jobs." % (conn))
-
-    # determine ppn once, and pass is to each job being created
-    # this avoids having to figure out ppn over and over again, every time creating a temp connection to the server
-    ppn = get_ppn()
+    assert backend in _job_submission_backends
+    try:
+        job_factory = _job_submission_backends[backend]()
+        job_factory.connect_to_server()
+    except RuntimeError, err:
+        _log.error("connection to server failed (%s: %s), can't submit jobs."
+                   % (err.__class__.__name__, err))
+        return None # XXX: should this `raise` instead?
 
     def tokey(dep):
         """Determine key for specified dependency."""
@@ -87,7 +98,7 @@ def tokey(dep):
 
         # the new job will only depend on already submitted jobs
         _log.info("creating job for ec: %s" % str(ec))
-        new_job = create_job(build_command, ec, output_dir=output_dir, conn=conn, ppn=ppn)
+        new_job = create_job(job_factory, build_command, ec, output_dir=output_dir)
 
         # sometimes unresolved_deps will contain things, not needed to be build
         job_deps = [job_ids[dep] for dep in map(tokey, ec['unresolved_deps']) if dep in job_ids]
@@ -115,16 +126,18 @@ def tokey(dep):
             _log.info("releasing hold on job %s" % job.jobid)
             job.release_hold()
 
-    disconnect_from_server(conn)
+    job_factory.disconnect_from_server()
 
     return jobs
 
 
-def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
+def submit_jobs(ordered_ecs, cmd_line_opts, backend='pbs', testing=False):
     """
     Submit jobs.
     @param ordered_ecs: list of easyconfigs, in the order they should be processed
     @param cmd_line_opts: list of command line options (in 'longopt=value' form)
+    @param backend: job submission backend to use (either 'pbs' or 'gc3pie')
+    @param testing: If `True`, skip actual job submission
     """
     curdir = os.getcwd()
 
@@ -143,16 +156,18 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
     if testing:
         _log.debug("Skipping actual submission of jobs since testing mode is enabled")
     else:
-        jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
+        jobs = build_easyconfigs_in_parallel(backend, command, ordered_ecs)
         job_info_lines = ["List of submitted jobs:"]
         job_info_lines.extend(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in jobs])
         job_info_lines.append("(%d jobs submitted)" % len(jobs))
         return '\n'.join(job_info_lines)
 
 
-def create_job(build_command, easyconfig, output_dir=None, conn=None, ppn=None):
+def create_job(job_factory, build_command, easyconfig, output_dir=None):
     """
-    Creates a job, to build a *single* easyconfig
+    Creates a job to build a *single* easyconfig.
+
+    @param job_factory: A factory object for querying server parameters and creating actual job objects
     @param build_command: format string for command, full path to an easyconfig file will be substituted in it
     @param easyconfig: easyconfig as processed by process_easyconfig
     @param output_dir: optional output path; --regtest-output-dir will be used inside the job with this variable
@@ -195,7 +210,7 @@ def create_job(build_command, easyconfig, output_dir=None, conn=None, ppn=None):
         previous_time = buildstats[-1]['build_time']
         resources['hours'] = int(math.ceil(previous_time * 2 / 60))
 
-    job = PbsJob(command, name, easybuild_vars, resources=resources, conn=conn, ppn=ppn)
+    job = job_factory.make_job(command, name, easybuild_vars, resources)
     job.module = easyconfig['ec'].full_mod_name
 
     return job
diff --git a/easybuild/tools/pbs_job.py b/easybuild/tools/pbs_job.py
index 55774cd474..d37b6162c4 100644
--- a/easybuild/tools/pbs_job.py
+++ b/easybuild/tools/pbs_job.py
@@ -30,6 +30,7 @@
 @author: Kenneth Hoste (Ghent University)
 """
 
+from functools import wraps
 import os
 import tempfile
 import time
@@ -50,50 +51,75 @@
     from PBSQuery import PBSQuery
     import pbs
     KNOWN_HOLD_TYPES = [pbs.USER_HOLD, pbs.OTHER_HOLD, pbs.SYSTEM_HOLD]
+    # `pbs_python` available, no need guard against import errors
+    def only_if_pbs_import_successful(fn):
+        return fn
 except ImportError:
-    _log.debug("Failed to import pbs from pbs_python. Silently ignoring, is only a real issue with --job")
-    pbs_import_failed = ("PBSQuery or pbs modules not available. "
-                         "Please make sure pbs_python is installed and usable.")
-
-
-def connect_to_server(pbs_server=None):
-    """Connect to PBS server and return connection."""
-    if pbs_import_failed:
-        _log.error(pbs_import_failed)
-        return None
-
-    if not pbs_server:
-        pbs_server = pbs.pbs_default()
-    return pbs.pbs_connect(pbs_server)
-
-
-def disconnect_from_server(conn):
-    """Disconnect a given connection."""
-    if pbs_import_failed:
-        _log.error(pbs_import_failed)
-        return None
-
-    pbs.pbs_disconnect(conn)
-
-
-def get_ppn():
-    """Guess the ppn for full node"""
-
-    log = fancylogger.getLogger('pbs_job.get_ppn')
-
-    pq = PBSQuery()
-    node_vals = pq.getnodes().values()  # only the values, not the names
-    interesting_nodes = ('free', 'job-exclusive',)
-    res = {}
-    for np in [int(x['np'][0]) for x in node_vals if x['state'][0] in interesting_nodes]:
-        res.setdefault(np, 0)
-        res[np] += 1
-
-    # return most frequent
-    freq_count, freq_np = max([(j, i) for i, j in res.items()])
-    log.debug("Found most frequent np %s (%s times) in interesting nodes %s" % (freq_np, freq_count, interesting_nodes))
-
-    return freq_np
+    _log.debug("Failed to import pbs from pbs_python."
+               " Silently ignoring, this is a real issue only with --job=pbs")
+    # no `pbs_python` available, turn function into a no-op
+    def only_if_pbs_import_successful(fn):
+        @wraps(fn)
+        def instead(*args, **kwargs):
+            """This is a no-op since `pbs_python` is not available."""
+            _log.error("PBSQuery or pbs modules not available."
+                       " Please make sure `pbs_python` is installed and usable.")
+            return None
+        return instead
+
+
+class PbsJobFactory(object):
+    """
+    Manage PBS server communication and create `PbsJob` objects.
+    """
+
+    def __init__(self, pbs_server=None):
+        self.pbs_server = pbs_server or pbs.pbs_default()
+        self.conn = None
+        self._ppn = None
+
+    @only_if_pbs_import_successful
+    def connect_to_server(self):
+        """Connect to PBS server, set and return connection."""
+        if not self.conn:
+            self.conn = pbs.pbs_connect(self.pbs_server)
+        return self.conn
+
+    @only_if_pbs_import_successful
+    def disconnect_from_server(self):
+        """Disconnect current connection."""
+        pbs.pbs_disconnect(self.conn)
+        self.conn = None
+
+    @property
+    def ppn(self):
+        """PBS' `ppn` value for a full node."""
+        # cache this value as it's not likely going to change over the
+        # `eb` script runtime ...
+        if not self._ppn:
+            log = fancylogger.getLogger('pbs_job.PbsJobFactory.ppn')
+
+            pq = PBSQuery()
+            node_vals = pq.getnodes().values()  # only the values, not the names
+            interesting_nodes = ('free', 'job-exclusive',)
+            res = {}
+            for np in [int(x['np'][0]) for x in node_vals if x['state'][0] in interesting_nodes]:
+                res.setdefault(np, 0)
+                res[np] += 1
+
+            # return most frequent
+            freq_count, freq_np = max([(j, i) for i, j in res.items()])
+            log.debug("Found most frequent np %s (%s times) in interesting nodes %s" % (freq_np, freq_count, interesting_nodes))
+
+            self._ppn = freq_np
+
+        return self._ppn
+
+
+    def make_job(self, script, name, env_vars=None, resources={}):
+        """Create and return a `PbsJob` object with the given parameters."""
+        return PbsJob(script, name, env_vars, resources,
+                      conn=self.conn, ppn=self.ppn)
 
 
 class PbsJob(object):
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index 8bebbf3612..683f607e4a 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -124,7 +124,7 @@ def regtest(easyconfig_paths, build_specs=None):
         # retry twice in case of failure, to avoid fluke errors
         command += "if [ $? -ne 0 ]; then %(cmd)s --force && %(cmd)s --force; fi" % {'cmd': cmd}
 
-        jobs = build_easyconfigs_in_parallel(command, resolved, output_dir=output_dir)
+        jobs = build_easyconfigs_in_parallel('pbs', command, resolved, output_dir=output_dir)
 
         print "List of submitted jobs:"
         for job in jobs:

From 772c3c2d11ae4fe7492b376ed084abda636df4be Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 13 Aug 2014 21:51:01 +0200
Subject: [PATCH 0636/1356] Ensure `PbsJobFactory` raises a `RuntimeError` if
 no connection to the server can be made.

---
 easybuild/tools/pbs_job.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/pbs_job.py b/easybuild/tools/pbs_job.py
index d37b6162c4..f67d154f4f 100644
--- a/easybuild/tools/pbs_job.py
+++ b/easybuild/tools/pbs_job.py
@@ -62,9 +62,10 @@ def only_if_pbs_import_successful(fn):
         @wraps(fn)
         def instead(*args, **kwargs):
             """This is a no-op since `pbs_python` is not available."""
-            _log.error("PBSQuery or pbs modules not available."
-                       " Please make sure `pbs_python` is installed and usable.")
-            return None
+            errmsg = ("PBSQuery or pbs modules not available."
+                      " Please make sure `pbs_python` is installed and usable.")
+            _log.error(errmsg)
+            raise RuntimeError(errmsg)
         return instead
 
 

From 2f66b0745275bfc0915abd5e5766c2201a306879 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 13 Aug 2014 21:51:25 +0200
Subject: [PATCH 0637/1356] Remove use of `functools.wrap` to stay compatible
 with Py 2.4

---
 easybuild/tools/pbs_job.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/tools/pbs_job.py b/easybuild/tools/pbs_job.py
index f67d154f4f..ee5336c63e 100644
--- a/easybuild/tools/pbs_job.py
+++ b/easybuild/tools/pbs_job.py
@@ -30,7 +30,6 @@
 @author: Kenneth Hoste (Ghent University)
 """
 
-from functools import wraps
 import os
 import tempfile
 import time
@@ -59,7 +58,6 @@ def only_if_pbs_import_successful(fn):
                " Silently ignoring, this is a real issue only with --job=pbs")
     # no `pbs_python` available, turn function into a no-op
     def only_if_pbs_import_successful(fn):
-        @wraps(fn)
         def instead(*args, **kwargs):
             """This is a no-op since `pbs_python` is not available."""
             errmsg = ("PBSQuery or pbs modules not available."

From c01460986cf14e46cf049b2d22cc614879fca04d Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 13 Aug 2014 21:58:41 +0200
Subject: [PATCH 0638/1356] Avoid closures when possible, module-level
 functions are faster.

---
 easybuild/tools/parallelbuild.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 71ef43a206..38de2c67bf 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -56,6 +56,10 @@
     'pbs': PbsJobFactory,
 }
 
+def _to_key(dep):
+    """Determine key for specified dependency."""
+    return ActiveMNS().det_full_module_name(dep)
+
 def build_easyconfigs_in_parallel(backend, build_command, easyconfigs, output_dir=None):
     """
     Build easyconfigs in parallel by submitting jobs to a batch-queuing system.
@@ -71,10 +75,6 @@ def build_easyconfigs_in_parallel(backend, build_command, easyconfigs, output_di
     @param output_dir: output directory
     """
     _log.info("going to build these easyconfigs in parallel: %s", easyconfigs)
-    job_ids = {}
-    # dependencies have already been resolved,
-    # so one can linearly walk over the list and use previous job id's
-    jobs = []
 
     assert backend in _job_submission_backends
     try:
@@ -85,9 +85,10 @@ def build_easyconfigs_in_parallel(backend, build_command, easyconfigs, output_di
                    % (err.__class__.__name__, err))
         return None # XXX: should this `raise` instead?
 
-    def tokey(dep):
-        """Determine key for specified dependency."""
-        return ActiveMNS().det_full_module_name(dep)
+    job_ids = {}
+    # dependencies have already been resolved,
+    # so one can linearly walk over the list and use previous job id's
+    jobs = []
 
     for ec in easyconfigs:
         # this is very important, otherwise we might have race conditions
@@ -101,7 +102,7 @@ def tokey(dep):
         new_job = create_job(job_factory, build_command, ec, output_dir=output_dir)
 
         # sometimes unresolved_deps will contain things, not needed to be build
-        job_deps = [job_ids[dep] for dep in map(tokey, ec['unresolved_deps']) if dep in job_ids]
+        job_deps = [job_ids[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in job_ids]
         new_job.add_dependencies(job_deps)
 
         # place user hold on job to prevent it from starting too quickly,

From 6a7112153db78d567ae924779b0d5b12128a2958 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 13 Aug 2014 22:15:43 +0200
Subject: [PATCH 0639/1356] More Python 2.4 compatibility.

---
 easybuild/tools/pbs_job.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/pbs_job.py b/easybuild/tools/pbs_job.py
index ee5336c63e..d409f8eb0d 100644
--- a/easybuild/tools/pbs_job.py
+++ b/easybuild/tools/pbs_job.py
@@ -90,9 +90,8 @@ def disconnect_from_server(self):
         pbs.pbs_disconnect(self.conn)
         self.conn = None
 
-    @property
-    def ppn(self):
-        """PBS' `ppn` value for a full node."""
+    def _get_ppn(self):
+        """Guess PBS' `ppn` value for a full node."""
         # cache this value as it's not likely going to change over the
         # `eb` script runtime ...
         if not self._ppn:
@@ -114,6 +113,8 @@ def ppn(self):
 
         return self._ppn
 
+    ppn = property(_get_ppn)
+
 
     def make_job(self, script, name, env_vars=None, resources={}):
         """Create and return a `PbsJob` object with the given parameters."""

From 00f440b2b4c44966f3c5d88d47d9af85d05db97d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Feb 2015 11:34:13 +0100
Subject: [PATCH 0640/1356] add new pkg tools.job, move --job support relying
 on pbs_python in it

---
 easybuild/tools/job/__init__.py                   | 0
 easybuild/tools/job/gc3pie.py                     | 0
 easybuild/tools/{pbs_job.py => job/pbs_python.py} | 0
 setup.py                                          | 2 +-
 4 files changed, 1 insertion(+), 1 deletion(-)
 create mode 100644 easybuild/tools/job/__init__.py
 create mode 100644 easybuild/tools/job/gc3pie.py
 rename easybuild/tools/{pbs_job.py => job/pbs_python.py} (100%)

diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/easybuild/tools/pbs_job.py b/easybuild/tools/job/pbs_python.py
similarity index 100%
rename from easybuild/tools/pbs_job.py
rename to easybuild/tools/job/pbs_python.py
diff --git a/setup.py b/setup.py
index 627008004e..fcb6f4b2dd 100644
--- a/setup.py
+++ b/setup.py
@@ -73,7 +73,7 @@ def find_rel_test():
     "easybuild", "easybuild.framework", "easybuild.framework.easyconfig", "easybuild.framework.easyconfig.format",
     "easybuild.toolchains", "easybuild.toolchains.compiler", "easybuild.toolchains.mpi",
     "easybuild.toolchains.fft", "easybuild.toolchains.linalg", "easybuild.tools", "easybuild.tools.deprecated",
-    "easybuild.tools.toolchain", "easybuild.tools.module_naming_scheme", "easybuild.tools.repository",
+    "easybuild.tools.job", "easybuild.tools.toolchain", "easybuild.tools.module_naming_scheme", "easybuild.tools.repository",
     "test.framework", "test",
 ]
 

From 21f031766b681d41b965096ebc11e547d2f553ec Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Feb 2015 11:51:04 +0100
Subject: [PATCH 0641/1356] flesh out ideas to restructure --job support to add
 GC3Pie backend

---
 easybuild/tools/job/gc3pie.py     | 32 +++++++++++++++++++++++++++++++
 easybuild/tools/job/job.py        | 29 ++++++++++++++++++++++++++++
 easybuild/tools/job/pbs_python.py |  4 +++-
 easybuild/tools/parallelbuild.py  |  4 ++--
 4 files changed, 66 insertions(+), 3 deletions(-)
 create mode 100644 easybuild/tools/job/job.py

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index e69de29bb2..cce0772bdf 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -0,0 +1,32 @@
+##
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""Interface for submitting jobs via gc3pie"""
+
+from easybuild.tools.job.job import Job
+
+
+# eb --job=GC3Pie
+class GC3Pie(Job):
+    pass
diff --git a/easybuild/tools/job/job.py b/easybuild/tools/job/job.py
new file mode 100644
index 0000000000..b7c2f0cb22
--- /dev/null
+++ b/easybuild/tools/job/job.py
@@ -0,0 +1,29 @@
+##
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""Abstract interface for submitting jobs"""
+
+
+class Job(object):
+    pass
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index d409f8eb0d..e12f01df04 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -35,6 +35,8 @@
 import time
 from vsc.utils import fancylogger
 
+from easybuild.tools.job.job import Job
+
 
 _log = fancylogger.getLogger('pbs_job', fname=False)
 
@@ -122,7 +124,7 @@ def make_job(self, script, name, env_vars=None, resources={}):
                       conn=self.conn, ppn=self.ppn)
 
 
-class PbsJob(object):
+class Pbs_python(Job):
     """Interaction with TORQUE"""
 
     def __init__(self, script, name, env_vars=None, resources={}, conn=None, ppn=None):
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 38de2c67bf..abfa055a3f 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -42,7 +42,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
-from easybuild.tools.pbs_job import PbsJobFactory
+from easybuild.tools.job.job import job_factory
 #from easybuild.tools.gc3pie_job import GC3PieJobFactory
 from easybuild.tools.repository.repository import init_repository
 from vsc.utils import fancylogger
@@ -78,7 +78,7 @@ def build_easyconfigs_in_parallel(backend, build_command, easyconfigs, output_di
 
     assert backend in _job_submission_backends
     try:
-        job_factory = _job_submission_backends[backend]()
+        job_factory = GC3PieFactory()  #job_factory()
         job_factory.connect_to_server()
     except RuntimeError, err:
         _log.error("connection to server failed (%s: %s), can't submit jobs."

From 9e593b86009b2e6ab45fc8c6e31e4de833dfef88 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 10 Feb 2015 16:31:27 +0100
Subject: [PATCH 0642/1356] Get job backend setting via the
 `easybuild.tools.config` method.

No need to pass the backend setting all the way down from the top-level.
This is what is done, e.g., for the "module naming scheme".
---
 easybuild/main.py                |  3 +--
 easybuild/tools/config.py        | 13 +++++++++++
 easybuild/tools/job/__init__.py  | 38 ++++++++++++++++++++++++++++++++
 easybuild/tools/parallelbuild.py | 18 ++++-----------
 4 files changed, 56 insertions(+), 16 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 17b8c6ea59..f1ab88af41 100755
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -292,8 +292,7 @@ def main(testing_data=(None, None, None)):
 
     # submit build as job(s), clean up and exit
     if options.job:
-        job_info_txt = submit_jobs(ordered_ecs, eb_go.generate_cmd_line(),
-                                   backend=options.job, testing=testing)
+        job_info_txt = submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
         if not testing:
             print_msg("Submitted parallel build jobs, exiting now: %s" % job_info_txt)
             cleanup(logfile, eb_tmpdir, testing)
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 9e2108143c..43b89c6665 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -355,6 +355,19 @@ def get_module_naming_scheme():
     return ConfigurationVariables()['module_naming_scheme']
 
 
+# XXX: from the code writer perspective, this would more appropriately
+# named `get_job_factory` or `get_job_backend`; from the
+# user/command-line viewpoint, however, `--job` is just fine so if we
+# stick with the convention that the accessor for command-line option
+# `--foo` is named `get_foo`, we should name this `get_job()`.
+# And so be it.
+def get_job():
+    """
+    Return job execution backend (PBS, GC3Pie, ...)
+    """
+    return ConfigurationVariables()['job']
+
+
 def log_file_format(return_directory=False):
     """Return the format for the logfile or the directory"""
     idx = int(not return_directory)
diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index e69de29bb2..ac1afb86f7 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -0,0 +1,38 @@
+# #
+# This file is part of EasyBuild, see:
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+
+
+from vsc.utils.missing import get_subclasses
+
+from easybuild.tools.config import get_job
+
+
+def avail_job_factories():
+    """
+    Return all known job execution backends.
+    """
+    class_dict = dict([(x.__name__, x) for x in get_subclasses(Job)])
+    return class_dict
+
+
+def job_factory(testing=False):
+    """
+    Return interface to job factory.
+    """
+    job_factory = get_job()
+    job_factory_class = avail_job_factories().get(job_factory)
+    return job_factory_class(testing=testing)
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index abfa055a3f..d1d5134f03 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -43,24 +43,17 @@
 from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.job.job import job_factory
-#from easybuild.tools.gc3pie_job import GC3PieJobFactory
 from easybuild.tools.repository.repository import init_repository
 from vsc.utils import fancylogger
 
 
 _log = fancylogger.getLogger('parallelbuild', fname=False)
 
-# map `--job=name` to a Python class we can use
-_job_submission_backends = {
-#    'gc3pie': GC3PieJobFactory,
-    'pbs': PbsJobFactory,
-}
-
 def _to_key(dep):
     """Determine key for specified dependency."""
     return ActiveMNS().det_full_module_name(dep)
 
-def build_easyconfigs_in_parallel(backend, build_command, easyconfigs, output_dir=None):
+def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
     """
     Build easyconfigs in parallel by submitting jobs to a batch-queuing system.
     Return list of jobs submitted.
@@ -69,16 +62,14 @@ def build_easyconfigs_in_parallel(backend, build_command, easyconfigs, output_di
     built: e.g. they have no unresolved dependencies.  This function
     will build them in parallel by submitting jobs.
 
-    @param backend: name of the job processing backend to use (currently 'pbs' only)
     @param build_command: build command to use
     @param easyconfigs: list of easyconfig files
     @param output_dir: output directory
     """
     _log.info("going to build these easyconfigs in parallel: %s", easyconfigs)
 
-    assert backend in _job_submission_backends
+    job_factory = job_factory()
     try:
-        job_factory = GC3PieFactory()  #job_factory()
         job_factory.connect_to_server()
     except RuntimeError, err:
         _log.error("connection to server failed (%s: %s), can't submit jobs."
@@ -132,12 +123,11 @@ def build_easyconfigs_in_parallel(backend, build_command, easyconfigs, output_di
     return jobs
 
 
-def submit_jobs(ordered_ecs, cmd_line_opts, backend='pbs', testing=False):
+def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
     """
     Submit jobs.
     @param ordered_ecs: list of easyconfigs, in the order they should be processed
     @param cmd_line_opts: list of command line options (in 'longopt=value' form)
-    @param backend: job submission backend to use (either 'pbs' or 'gc3pie')
     @param testing: If `True`, skip actual job submission
     """
     curdir = os.getcwd()
@@ -157,7 +147,7 @@ def submit_jobs(ordered_ecs, cmd_line_opts, backend='pbs', testing=False):
     if testing:
         _log.debug("Skipping actual submission of jobs since testing mode is enabled")
     else:
-        jobs = build_easyconfigs_in_parallel(backend, command, ordered_ecs)
+        jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
         job_info_lines = ["List of submitted jobs:"]
         job_info_lines.extend(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in jobs])
         job_info_lines.append("(%d jobs submitted)" % len(jobs))

From 2a9af158fcd69a3dbd5d6d428ee7f5f13c424515 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 10 Feb 2015 16:37:49 +0100
Subject: [PATCH 0643/1356] Merge all abstract and generic job-related code
 into `easybuild.tools.job`.

It was previously scattered across the two files
`easybuild/tools/job/__init__.py` and `easybuild/tools/job/job.py`.
---
 easybuild/tools/job/__init__.py   | 19 ++++++++++++++++---
 easybuild/tools/job/gc3pie.py     |  2 +-
 easybuild/tools/job/job.py        | 29 -----------------------------
 easybuild/tools/job/pbs_python.py |  2 +-
 easybuild/tools/parallelbuild.py  |  2 +-
 5 files changed, 19 insertions(+), 35 deletions(-)
 delete mode 100644 easybuild/tools/job/job.py

diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index ac1afb86f7..494c4165d7 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -1,5 +1,13 @@
-# #
-# This file is part of EasyBuild, see:
+##
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
 # http://github.com/hpcugent/easybuild
 #
 # EasyBuild is free software: you can redistribute it and/or modify
@@ -13,7 +21,8 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-# #
+##
+"""Abstract interface for submitting jobs and related utilities."""
 
 
 from vsc.utils.missing import get_subclasses
@@ -21,6 +30,10 @@
 from easybuild.tools.config import get_job
 
 
+class Job(object):
+    pass
+
+
 def avail_job_factories():
     """
     Return all known job execution backends.
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index cce0772bdf..c8f3dc86c9 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -24,7 +24,7 @@
 ##
 """Interface for submitting jobs via gc3pie"""
 
-from easybuild.tools.job.job import Job
+from easybuild.tools.job import Job
 
 
 # eb --job=GC3Pie
diff --git a/easybuild/tools/job/job.py b/easybuild/tools/job/job.py
deleted file mode 100644
index b7c2f0cb22..0000000000
--- a/easybuild/tools/job/job.py
+++ /dev/null
@@ -1,29 +0,0 @@
-##
-# Copyright 2015-2015 Ghent University
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-##
-"""Abstract interface for submitting jobs"""
-
-
-class Job(object):
-    pass
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index e12f01df04..5bb436c5f7 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -35,7 +35,7 @@
 import time
 from vsc.utils import fancylogger
 
-from easybuild.tools.job.job import Job
+from easybuild.tools.job import Job
 
 
 _log = fancylogger.getLogger('pbs_job', fname=False)
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index d1d5134f03..e8660b7893 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -42,7 +42,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
-from easybuild.tools.job.job import job_factory
+from easybuild.tools.job import job_factory
 from easybuild.tools.repository.repository import init_repository
 from vsc.utils import fancylogger
 

From 3bc286630413f27ee3fbe339f083a5fd671da37d Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 10 Feb 2015 17:02:42 +0100
Subject: [PATCH 0644/1356] Submit *all* jobs with a user hold, and then
 release them all.

Since jobs with dependencies will have a dependency hold set anyway, we
can spare ourselves the check.
---
 easybuild/tools/job/pbs_python.py | 17 ++++++++---------
 easybuild/tools/parallelbuild.py  | 11 ++---------
 2 files changed, 10 insertions(+), 18 deletions(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 5bb436c5f7..7201169806 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -198,7 +198,7 @@ def add_dependencies(self, job_ids):
 
         self.deps.extend(job_ids)
 
-    def submit(self, with_hold=False):
+    def submit(self):
         """Submit the jobscript txt, set self.jobid"""
         txt = self.script
         self.log.debug("Going to submit script %s" % txt)
@@ -226,14 +226,13 @@ def submit(self, with_hold=False):
             pbs_attributes.extend(deps_attributes)
             self.log.debug("Job deps attributes: %s" % deps_attributes[0].value)
 
-        # submit job with (user) hold if requested
-        if with_hold:
-            hold_attributes = pbs.new_attropl(1)
-            hold_attributes[0].name = pbs.ATTR_h
-            hold_attributes[0].value = pbs.USER_HOLD
-            pbs_attributes.extend(hold_attributes)
-            self.holds.append(pbs.USER_HOLD)
-            self.log.debug("Job hold attributes: %s" % hold_attributes[0].value)
+        # submit job with (user) hold
+        hold_attributes = pbs.new_attropl(1)
+        hold_attributes[0].name = pbs.ATTR_h
+        hold_attributes[0].value = pbs.USER_HOLD
+        pbs_attributes.extend(hold_attributes)
+        self.holds.append(pbs.USER_HOLD)
+        self.log.debug("Job hold attributes: %s" % hold_attributes[0].value)
 
         # add a bunch of variables (added by qsub)
         # also set PBS_O_WORKDIR to os.getcwd()
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index e8660b7893..db3d4a3234 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -96,15 +96,8 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
         job_deps = [job_ids[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in job_ids]
         new_job.add_dependencies(job_deps)
 
-        # place user hold on job to prevent it from starting too quickly,
-        # we might still need it in the queue to set it as a dependency for another job;
-        # only set hold for job without dependencies, other jobs have a dependency hold set anyway
-        with_hold = False
-        if not job_deps:
-            with_hold = True
-
         # actually (try to) submit job
-        new_job.submit(with_hold)
+        new_job.submit()
         _log.info("job for module %s has been submitted (job id: %s)" % (new_job.module, new_job.jobid))
 
         # update dictionary
@@ -115,7 +108,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
     # release all user holds on jobs after submission is completed
     for job in jobs:
         if job.has_holds():
-            _log.info("releasing hold on job %s" % job.jobid)
+            _log.info("releasing user hold on job %s" % job.jobid)
             job.release_hold()
 
     job_factory.disconnect_from_server()

From 54bfd56c68810412b39d2903637857e87bc4b7d1 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 10 Feb 2015 17:20:01 +0100
Subject: [PATCH 0645/1356] Use job object themselves as dependencies.

This adaptation is needed in view of the GC3Pie job backend: GC3Pie
manages dependencies internally *before submission* so there is no job
ID to rely upon.
---
 easybuild/tools/job/pbs_python.py | 13 +++++--------
 easybuild/tools/parallelbuild.py  |  8 +++++---
 2 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 7201169806..c7b01c5f89 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -187,16 +187,13 @@ def __init__(self, script, name, env_vars=None, resources={}, conn=None, ppn=Non
         # list of holds that are placed on this job
         self.holds = []
 
-    def add_dependencies(self, job_ids):
+    def add_dependencies(self, jobs):
         """
         Add dependencies to this job.
-        job_ids is an array of job ids (e.g.: 8453.master2.gengar....)
-        if only one job_id is provided this function will also work
-        """
-        if isinstance(job_ids, str):
-            job_ids = list(job_ids)
 
-        self.deps.extend(job_ids)
+        Argument `jobs` is a sequence of `PbsJob` objects.
+        """
+        self.deps.extend(jobs)
 
     def submit(self):
         """Submit the jobscript txt, set self.jobid"""
@@ -222,7 +219,7 @@ def submit(self):
         if self.deps:
             deps_attributes = pbs.new_attropl(1)
             deps_attributes[0].name = pbs.ATTR_depend
-            deps_attributes[0].value = ",".join(["afterany:%s" % dep for dep in self.deps])
+            deps_attributes[0].value = ",".join(["afterany:%s" % dep.jobid for dep in self.deps])
             pbs_attributes.extend(deps_attributes)
             self.log.debug("Job deps attributes: %s" % deps_attributes[0].value)
 
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index db3d4a3234..4621eb6d0f 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -76,11 +76,13 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
                    % (err.__class__.__name__, err))
         return None # XXX: should this `raise` instead?
 
-    job_ids = {}
     # dependencies have already been resolved,
     # so one can linearly walk over the list and use previous job id's
     jobs = []
 
+    # keep track of which job builds which module
+    module_to_job = {}
+
     for ec in easyconfigs:
         # this is very important, otherwise we might have race conditions
         # e.g. GCC-4.5.3 finds cloog.tar.gz but it was incorrectly downloaded by GCC-4.6.3
@@ -93,7 +95,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
         new_job = create_job(job_factory, build_command, ec, output_dir=output_dir)
 
         # sometimes unresolved_deps will contain things, not needed to be build
-        job_deps = [job_ids[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in job_ids]
+        job_deps = [module_to_job[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in module_to_job]
         new_job.add_dependencies(job_deps)
 
         # actually (try to) submit job
@@ -101,7 +103,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
         _log.info("job for module %s has been submitted (job id: %s)" % (new_job.module, new_job.jobid))
 
         # update dictionary
-        job_ids[new_job.module] = new_job.jobid
+        module_to_job[new_job.module] = new_job
         new_job.cleanup()
         jobs.append(new_job)
 

From edf92b95eb62e5b19f31f4f3497ccdde3c8ca722 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 10 Feb 2015 17:22:56 +0100
Subject: [PATCH 0646/1356] Cosmetic changes.

---
 easybuild/tools/job/pbs_python.py | 12 ++++++------
 easybuild/tools/parallelbuild.py  | 12 +++---------
 2 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index c7b01c5f89..25dfdc9c13 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -124,7 +124,7 @@ def make_job(self, script, name, env_vars=None, resources={}):
                       conn=self.conn, ppn=self.ppn)
 
 
-class Pbs_python(Job):
+class PbsJob(Job):
     """Interaction with TORQUE"""
 
     def __init__(self, script, name, env_vars=None, resources={}, conn=None, ppn=None):
@@ -206,14 +206,14 @@ def submit(self):
         pbs_attributes[0].value = self.name
 
         # set resource requirements
-        resourse_attributes = pbs.new_attropl(len(self.resources))
+        resource_attributes = pbs.new_attropl(len(self.resources))
         idx = 0
         for k, v in self.resources.items():
-            resourse_attributes[idx].name = pbs.ATTR_l  # Resource_List
-            resourse_attributes[idx].resource = k
-            resourse_attributes[idx].value = v
+            resource_attributes[idx].name = pbs.ATTR_l  # Resource_List
+            resource_attributes[idx].resource = k
+            resource_attributes[idx].value = v
             idx += 1
-        pbs_attributes.extend(resourse_attributes)
+        pbs_attributes.extend(resource_attributes)
 
         # add job dependencies to attributes
         if self.deps:
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 4621eb6d0f..518fdae6a0 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -149,7 +149,7 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
         return '\n'.join(job_info_lines)
 
 
-def create_job(job_factory, build_command, easyconfig, output_dir=None):
+def create_job(job_factory, build_command, easyconfig, output_dir='easybuild-build'):
     """
     Creates a job to build a *single* easyconfig.
 
@@ -157,22 +157,16 @@ def create_job(job_factory, build_command, easyconfig, output_dir=None):
     @param build_command: format string for command, full path to an easyconfig file will be substituted in it
     @param easyconfig: easyconfig as processed by process_easyconfig
     @param output_dir: optional output path; --regtest-output-dir will be used inside the job with this variable
-    @param conn: open connection to PBS server
-    @param ppn: ppn setting to use (# 'processors' (cores) per node to use)
+
     returns the job
     """
-    if output_dir is None:
-        output_dir = 'easybuild-build'
-
     # capture PYTHONPATH, MODULEPATH and all variables starting with EASYBUILD
     easybuild_vars = {}
     for name in os.environ:
         if name.startswith("EASYBUILD"):
             easybuild_vars[name] = os.environ[name]
 
-    others = ["PYTHONPATH", "MODULEPATH"]
-
-    for env_var in others:
+    for env_var in ["PYTHONPATH", "MODULEPATH"]:
         if env_var in os.environ:
             easybuild_vars[env_var] = os.environ[env_var]
 

From 13999bf3e4e7323529018cd9cd52d6d8dd64c10c Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 10 Feb 2015 18:52:37 +0100
Subject: [PATCH 0647/1356] First attempt at an abstract `JobServer` interface
 that could be implemented by several backends.

The interface prototype emerges from a refactoring of
`build_easyconfigs_in_parallel()` (in `parallelbuild.py`) and all around
`pbs_python.py`.
---
 easybuild/tools/config.py         |   2 +-
 easybuild/tools/job/__init__.py   | 101 +++++++++++++++++++++++++++---
 easybuild/tools/job/pbs_python.py |  55 ++++++++--------
 easybuild/tools/parallelbuild.py  |  25 +++-----
 4 files changed, 131 insertions(+), 52 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 43b89c6665..e2321bbac4 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -356,7 +356,7 @@ def get_module_naming_scheme():
 
 
 # XXX: from the code writer perspective, this would more appropriately
-# named `get_job_factory` or `get_job_backend`; from the
+# named `get_job_server` or `get_job_backend`; from the
 # user/command-line viewpoint, however, `--job` is just fine so if we
 # stick with the convention that the accessor for command-line option
 # `--foo` is named `get_foo`, we should name this `get_job()`.
diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 494c4165d7..2e76f17cdb 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -25,16 +25,103 @@
 """Abstract interface for submitting jobs and related utilities."""
 
 
+from abc import ABCMeta, abstractmethod
+
 from vsc.utils.missing import get_subclasses
 
 from easybuild.tools.config import get_job
 
 
 class Job(object):
-    pass
+    __metaclass__ = ABCMeta
+
+    @abstractmethod
+    def __init__(self, server, script, name, env_vars=None, resources={}):
+        """
+        Create a new `Job` object.
+
+        First argument `server` is an instance of the corresponding
+        `JobServer` class.
+
+        Second argument `script` is the content of the job script
+        itself, i.e., the sequence of shell commands that will be
+        executed.
+
+        Third argument `name` sets the job human-readable name.
+
+        Fourth (optional) argument `env_vars` is a dictionary with key-value pairs
+        of environment variables that should be passed on to the job.
+
+        Fifth (optional) argument `resources` is a dictionary with
+        optional keys: ['hours', 'cores'] both of which should be
+        integer values:
+        * hours can be up to 1 - MAX_WALLTIME,;
+        * cores depends on which cluster the job is being run.
+
+        Concrete subclasses may add more optional parameters.
+        """
+        pass
+
+    @abstractmethod
+    def add_dependencies(self, jobs):
+        """
+        Add dependencies to this job.
+
+        Argument `jobs` is a sequence of `Job` objects,
+        which must actually be instances of the exact same
+        class as the dependent job.
+        """
+        pass
+
+
+class JobServer(object):
+    __metaclass__ = ABCMeta
+
+    @abstractmethod
+    def begin(self):
+        """
+        Start a bulk job submission.
+
+        Jobs may be queued and only actually submitted when `commit()`
+        is called.
+        """
+        pass
+
+    @abstractmethod
+    def make_job(self, script, name, env_vars=None, resources={}):
+        """
+        Create and return a `Job` object with the given parameters.
+
+        See the `Job`:class: constructor for an explanation of what
+        the arguments are.
+        """
+        pass
+
+    @abstractmethod
+    def submit(self, job):
+        """
+        Submit a job to the batch-queueing system.
+
+        Note that actual submission may be delayed until `commit()` is
+        called.
+        """
+        pass
+
+    @abstractmethod
+    def commit(self):
+        """
+        End a bulk job submission.
+
+        Releases any jobs that were possibly queued since the last
+        `begin()` call.
+
+        No more job submissions should be attempted after `commit()`
+        has been called, until a `begin()` is invoked again.
+        """
+        pass
 
 
-def avail_job_factories():
+def avail_job_servers():
     """
     Return all known job execution backends.
     """
@@ -42,10 +129,10 @@ def avail_job_factories():
     return class_dict
 
 
-def job_factory(testing=False):
+def job_server(testing=False):
     """
-    Return interface to job factory.
+    Return interface to job server.
     """
-    job_factory = get_job()
-    job_factory_class = avail_job_factories().get(job_factory)
-    return job_factory_class(testing=testing)
+    job_server = get_job()
+    job_server_class = avail_job_servers().get(job_server)
+    return job_server_class(testing=testing)
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 25dfdc9c13..67b19ec6b6 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -69,7 +69,7 @@ def instead(*args, **kwargs):
         return instead
 
 
-class PbsJobFactory(object):
+class PbsJobServer(object):
     """
     Manage PBS server communication and create `PbsJob` objects.
     """
@@ -79,6 +79,10 @@ def __init__(self, pbs_server=None):
         self.conn = None
         self._ppn = None
 
+    def begin(self):
+        self.connect_to_server()
+        self._submitted = []
+
     @only_if_pbs_import_successful
     def connect_to_server(self):
         """Connect to PBS server, set and return connection."""
@@ -86,6 +90,19 @@ def connect_to_server(self):
             self.conn = pbs.pbs_connect(self.pbs_server)
         return self.conn
 
+    def submit(self, job):
+        assert isinstance(job, PbsJob)
+        job._submit()
+        self._submitted.append(job)
+
+    def commit(self):
+        # release all user holds on jobs after submission is completed
+        for job in self._submitted:
+            if job.has_holds():
+                _log.info("releasing user hold on job %s" % job.jobid)
+                job.release_hold()
+        self.disconnect_from_server()
+
     @only_if_pbs_import_successful
     def disconnect_from_server(self):
         """Disconnect current connection."""
@@ -97,7 +114,7 @@ def _get_ppn(self):
         # cache this value as it's not likely going to change over the
         # `eb` script runtime ...
         if not self._ppn:
-            log = fancylogger.getLogger('pbs_job.PbsJobFactory.ppn')
+            log = fancylogger.getLogger('pbs_job.PbsServer.ppn')
 
             pq = PBSQuery()
             node_vals = pq.getnodes().values()  # only the values, not the names
@@ -117,25 +134,25 @@ def _get_ppn(self):
 
     ppn = property(_get_ppn)
 
-
     def make_job(self, script, name, env_vars=None, resources={}):
         """Create and return a `PbsJob` object with the given parameters."""
-        return PbsJob(script, name, env_vars, resources,
+        return PbsJob(self, script, name, env_vars, resources,
                       conn=self.conn, ppn=self.ppn)
 
 
 class PbsJob(Job):
     """Interaction with TORQUE"""
 
-    def __init__(self, script, name, env_vars=None, resources={}, conn=None, ppn=None):
+    def __init__(self, server, script, name, env_vars=None, resources={}, conn=None, ppn=None):
         """
         create a new Job to be submitted to PBS
         env_vars is a dictionary with key-value pairs of environment variables that should be passed on to the job
         resources is a dictionary with optional keys: ['hours', 'cores'] both of these should be integer values.
         hours can be 1 - MAX_WALLTIME, cores depends on which cluster it is being run.
         """
-        self.clean_conn = True
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
+
+        self._server = server
         self.script = script
         if env_vars:
             self.env_vars = env_vars.copy()
@@ -143,18 +160,11 @@ def __init__(self, script, name, env_vars=None, resources={}, conn=None, ppn=Non
             self.env_vars = {}
         self.name = name
 
-        if pbs_import_failed:
-            self.log.error(pbs_import_failed)
-
         try:
-            self.pbs_server = pbs.pbs_default()
-            if conn:
-                self.pbsconn = conn
-                self.clean_conn = False
-            else:
-                self.pbsconn = pbs.pbs_connect(self.pbs_server)
+            self.pbsconn = self._server.connect_to_server()
         except Exception, err:
-            self.log.error("Failed to connect to the default pbs server: %s" % err)
+            self.log.error("Failed to connect to PBS server: %s" % err)
+            raise
 
         # setup the resources requested
 
@@ -195,7 +205,7 @@ def add_dependencies(self, jobs):
         """
         self.deps.extend(jobs)
 
-    def submit(self):
+    def _submit(self):
         """Submit the jobscript txt, set self.jobid"""
         txt = self.script
         self.log.debug("Going to submit script %s" % txt)
@@ -381,11 +391,6 @@ def info(self, types=None):
             for idx, attr in enumerate(types):
                 jobattr[idx].name = attr
 
-
-        # get a new connection (otherwise this seems to fail)
-        if self.clean_conn:
-            pbs.pbs_disconnect(self.pbsconn)
-            self.pbsconn = pbs.pbs_connect(self.pbs_server)
         jobs = pbs.pbs_statjob(self.pbsconn, self.jobid, jobattr, NULL)
         if len(jobs) == 0:
             # no job found, return None info
@@ -413,9 +418,3 @@ def remove(self):
             self.log.error("Failed to delete job %s: error %s" % (self.jobid, result))
         else:
             self.log.debug("Succesfully deleted job %s" % self.jobid)
-
-    def cleanup(self):
-        """Cleanup: disconnect from server."""
-        if self.clean_conn:
-            self.log.debug("Disconnecting from server.")
-            pbs.pbs_disconnect(self.pbsconn)
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 518fdae6a0..b515f0dcf1 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -42,7 +42,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
-from easybuild.tools.job import job_factory
+from easybuild.tools.job import job_server
 from easybuild.tools.repository.repository import init_repository
 from vsc.utils import fancylogger
 
@@ -68,9 +68,9 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
     """
     _log.info("going to build these easyconfigs in parallel: %s", easyconfigs)
 
-    job_factory = job_factory()
+    job_server = job_server()
     try:
-        job_factory.connect_to_server()
+        job_server.begin()
     except RuntimeError, err:
         _log.error("connection to server failed (%s: %s), can't submit jobs."
                    % (err.__class__.__name__, err))
@@ -92,28 +92,21 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
 
         # the new job will only depend on already submitted jobs
         _log.info("creating job for ec: %s" % str(ec))
-        new_job = create_job(job_factory, build_command, ec, output_dir=output_dir)
+        new_job = create_job(job_server, build_command, ec, output_dir=output_dir)
 
         # sometimes unresolved_deps will contain things, not needed to be build
         job_deps = [module_to_job[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in module_to_job]
         new_job.add_dependencies(job_deps)
 
         # actually (try to) submit job
-        new_job.submit()
+        job_server.submit(new_job)
         _log.info("job for module %s has been submitted (job id: %s)" % (new_job.module, new_job.jobid))
 
         # update dictionary
         module_to_job[new_job.module] = new_job
-        new_job.cleanup()
         jobs.append(new_job)
 
-    # release all user holds on jobs after submission is completed
-    for job in jobs:
-        if job.has_holds():
-            _log.info("releasing user hold on job %s" % job.jobid)
-            job.release_hold()
-
-    job_factory.disconnect_from_server()
+    job_server.commit()
 
     return jobs
 
@@ -149,11 +142,11 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
         return '\n'.join(job_info_lines)
 
 
-def create_job(job_factory, build_command, easyconfig, output_dir='easybuild-build'):
+def create_job(job_server, build_command, easyconfig, output_dir='easybuild-build'):
     """
     Creates a job to build a *single* easyconfig.
 
-    @param job_factory: A factory object for querying server parameters and creating actual job objects
+    @param job_server: A factory object for querying server parameters and creating actual job objects
     @param build_command: format string for command, full path to an easyconfig file will be substituted in it
     @param easyconfig: easyconfig as processed by process_easyconfig
     @param output_dir: optional output path; --regtest-output-dir will be used inside the job with this variable
@@ -190,7 +183,7 @@ def create_job(job_factory, build_command, easyconfig, output_dir='easybuild-bui
         previous_time = buildstats[-1]['build_time']
         resources['hours'] = int(math.ceil(previous_time * 2 / 60))
 
-    job = job_factory.make_job(command, name, easybuild_vars, resources)
+    job = job_server.make_job(command, name, easybuild_vars, resources)
     job.module = easyconfig['ec'].full_mod_name
 
     return job

From f8815e0d003a341e240dee176e603a1ce86eba04 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 10 Feb 2015 19:01:04 +0100
Subject: [PATCH 0648/1356] Use separate parameters `hours` and `cores` when
 building `Job` objects.

Do not conflate them into a single `resources` dictionary: it just makes
the code less readable.
---
 easybuild/tools/job/__init__.py   |  9 ++++-----
 easybuild/tools/job/pbs_python.py | 15 +++++++++------
 easybuild/tools/parallelbuild.py  |  6 +++---
 3 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 2e76f17cdb..81fa826b7b 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -36,7 +36,7 @@ class Job(object):
     __metaclass__ = ABCMeta
 
     @abstractmethod
-    def __init__(self, server, script, name, env_vars=None, resources={}):
+    def __init__(self, server, script, name, env_vars=None, hours=None, cores=None):
         """
         Create a new `Job` object.
 
@@ -52,10 +52,9 @@ def __init__(self, server, script, name, env_vars=None, resources={}):
         Fourth (optional) argument `env_vars` is a dictionary with key-value pairs
         of environment variables that should be passed on to the job.
 
-        Fifth (optional) argument `resources` is a dictionary with
-        optional keys: ['hours', 'cores'] both of which should be
+        Fifth and sith (optional) arguments `hours` and `cores` should be
         integer values:
-        * hours can be up to 1 - MAX_WALLTIME,;
+        * hours must be in the range 1 .. MAX_WALLTIME;
         * cores depends on which cluster the job is being run.
 
         Concrete subclasses may add more optional parameters.
@@ -88,7 +87,7 @@ def begin(self):
         pass
 
     @abstractmethod
-    def make_job(self, script, name, env_vars=None, resources={}):
+    def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         """
         Create and return a `Job` object with the given parameters.
 
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 67b19ec6b6..3062a09b19 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -134,20 +134,21 @@ def _get_ppn(self):
 
     ppn = property(_get_ppn)
 
-    def make_job(self, script, name, env_vars=None, resources={}):
+    def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         """Create and return a `PbsJob` object with the given parameters."""
-        return PbsJob(self, script, name, env_vars, resources,
+        return PbsJob(self, script, name, env_vars, hours, cores,
                       conn=self.conn, ppn=self.ppn)
 
 
 class PbsJob(Job):
     """Interaction with TORQUE"""
 
-    def __init__(self, server, script, name, env_vars=None, resources={}, conn=None, ppn=None):
+    def __init__(self, server, script, name, env_vars=None,
+                 hours=None, cores=None, conn=None, ppn=None):
         """
         create a new Job to be submitted to PBS
         env_vars is a dictionary with key-value pairs of environment variables that should be passed on to the job
-        resources is a dictionary with optional keys: ['hours', 'cores'] both of these should be integer values.
+        hours and cores should be integer values.
         hours can be 1 - MAX_WALLTIME, cores depends on which cluster it is being run.
         """
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
@@ -169,7 +170,8 @@ def __init__(self, server, script, name, env_vars=None, resources={}, conn=None,
         # setup the resources requested
 
         # validate requested resources!
-        hours = resources.get('hours', MAX_WALLTIME)
+        if hours is None:
+            hours = MAX_WALLTIME
         if hours > MAX_WALLTIME:
             self.log.warn("Specified %s hours, but this is impossible. (resetting to %s hours)" % (hours, MAX_WALLTIME))
             hours = MAX_WALLTIME
@@ -178,7 +180,8 @@ def __init__(self, server, script, name, env_vars=None, resources={}, conn=None,
             max_cores = get_ppn()
         else:
             max_cores = ppn
-        cores = resources.get('cores', max_cores)
+        if cores is None:
+            cores = max_cores
         if cores > max_cores:
             self.log.warn("number of requested cores (%s) was greater than available (%s) " % (cores, max_cores))
             cores = max_cores
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index b515f0dcf1..f3470e1806 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -178,12 +178,12 @@ def create_job(job_server, build_command, easyconfig, output_dir='easybuild-buil
     # just use latest build stats
     repo = init_repository(get_repository(), get_repositorypath())
     buildstats = repo.get_buildstats(*ec_tuple)
-    resources = {}
+    extra = {}
     if buildstats:
         previous_time = buildstats[-1]['build_time']
-        resources['hours'] = int(math.ceil(previous_time * 2 / 60))
+        extra['hours'] = int(math.ceil(previous_time * 2 / 60))
 
-    job = job_server.make_job(command, name, easybuild_vars, resources)
+    job = job_server.make_job(command, name, easybuild_vars, **extra)
     job.module = easyconfig['ec'].full_mod_name
 
     return job

From efb602a8c0fd209ce7abbc61fe1ea24a27c7ff20 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 12:41:36 +0100
Subject: [PATCH 0649/1356] Remove unused and outdated `PbsJob` import in
 `parallelbuild` tests.

This is preventing Jenkins from getting to the more signigicant and
juicy error messages.
---
 test/framework/parallelbuild.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 27635e0c6f..76d9b90715 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -34,7 +34,7 @@
 
 from easybuild.framework.easyconfig.tools import process_easyconfig
 from easybuild.tools import config, parallelbuild
-from easybuild.tools.parallelbuild import PbsJob, build_easyconfigs_in_parallel
+from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
 from easybuild.tools.robot import resolve_dependencies
 
 

From 5b65eeb24352a6a7f0087a919922bc37968af15f Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 14:04:40 +0100
Subject: [PATCH 0650/1356] Use separate options `--job` and `--job-backend`.

The former is a boolean option, selecting *whether* to use asynchronous
jobs to compile/build.

The latter selects which actual job submission backend to use.  Its
value must be the name of a `easybuild.tools.job.JobServer` subclass.
---
 easybuild/tools/config.py         | 11 +++--------
 easybuild/tools/job/__init__.py   | 10 +++++-----
 easybuild/tools/job/pbs_python.py |  4 ++--
 easybuild/tools/options.py        |  8 ++++++--
 4 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index e2321bbac4..cb4d6613c7 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -53,6 +53,7 @@
 
 
 DEFAULT_LOGFILE_FORMAT = ("easybuild", "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
+DEFAULT_JOB_SERVER = 'Pbs'
 DEFAULT_MNS = 'EasyBuildMNS'
 DEFAULT_MODULES_TOOL = 'EnvironmentModulesC'
 DEFAULT_PATH_SUBDIRS = {
@@ -355,17 +356,11 @@ def get_module_naming_scheme():
     return ConfigurationVariables()['module_naming_scheme']
 
 
-# XXX: from the code writer perspective, this would more appropriately
-# named `get_job_server` or `get_job_backend`; from the
-# user/command-line viewpoint, however, `--job` is just fine so if we
-# stick with the convention that the accessor for command-line option
-# `--foo` is named `get_foo`, we should name this `get_job()`.
-# And so be it.
-def get_job():
+def get_job_backend():
     """
     Return job execution backend (PBS, GC3Pie, ...)
     """
-    return ConfigurationVariables()['job']
+    return ConfigurationVariables()['job_backend']
 
 
 def log_file_format(return_directory=False):
diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 81fa826b7b..568e7b697b 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -29,7 +29,7 @@
 
 from vsc.utils.missing import get_subclasses
 
-from easybuild.tools.config import get_job
+from easybuild.tools.config import get_job_backend
 
 
 class Job(object):
@@ -124,14 +124,14 @@ def avail_job_servers():
     """
     Return all known job execution backends.
     """
-    class_dict = dict([(x.__name__, x) for x in get_subclasses(Job)])
+    class_dict = dict([(x.__name__, x) for x in get_subclasses(JobServer)])
     return class_dict
 
 
-def job_server(testing=False):
+def job_server():
     """
     Return interface to job server.
     """
-    job_server = get_job()
+    job_server = get_job_backend()
     job_server_class = avail_job_servers().get(job_server)
-    return job_server_class(testing=testing)
+    return job_server_class()
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 3062a09b19..9bc9b41dc1 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -35,7 +35,7 @@
 import time
 from vsc.utils import fancylogger
 
-from easybuild.tools.job import Job
+from easybuild.tools.job import Job, JobServer
 
 
 _log = fancylogger.getLogger('pbs_job', fname=False)
@@ -69,7 +69,7 @@ def instead(*args, **kwargs):
         return instead
 
 
-class PbsJobServer(object):
+class Pbs(JobServer):
     """
     Manage PBS server communication and create `PbsJob` objects.
     """
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index e607d643be..23d920f101 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -49,12 +49,14 @@
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
-from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
+from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_JOB_SERVER
+from easybuild.tools.config import DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
 from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
+from easybuild.tools.job import avail_job_servers
 from easybuild.tools.modules import avail_modules_tools
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
@@ -116,7 +118,9 @@ def basic_options(self):
             'dry-run-short': ("Print build overview incl. dependencies (short paths)", None, 'store_true', False, 'D'),
             'force': ("Force to rebuild software even if it's already installed (i.e. if it can be found as module)",
                       None, 'store_true', False, 'f'),
-            'job': ("Submit the build as a job", 'choice', 'store_or_None', 'pbs', ['pbs']),
+            'job': ("Submit the build as a job", None, 'store_true', False),
+            'job-backend': ("What job runner to use", 'choice', 'store',
+                            DEFAULT_JOB_SERVER, (avail_job_servers().keys())),
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",

From 72cf63c8944401b44380f30d3b9773bb90e93269 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 14:06:51 +0100
Subject: [PATCH 0651/1356] Cosmetic changes.

---
 easybuild/tools/job/__init__.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 568e7b697b..f59820c7f6 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -49,8 +49,9 @@ def __init__(self, server, script, name, env_vars=None, hours=None, cores=None):
 
         Third argument `name` sets the job human-readable name.
 
-        Fourth (optional) argument `env_vars` is a dictionary with key-value pairs
-        of environment variables that should be passed on to the job.
+        Fourth (optional) argument `env_vars` is a dictionary with
+        key-value pairs of environment variables that should be passed
+        on to the job.
 
         Fifth and sith (optional) arguments `hours` and `cores` should be
         integer values:

From f2a2f6c0e23b608b05d71790c9c8c639480fff19 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 14:59:56 +0100
Subject: [PATCH 0652/1356] Job dependencies are now specified at submission
 time.

Again, this makes it easier to write the GC3Pie code and does not really
affect the "PBS direct" one in a significant way.
---
 easybuild/tools/job/__init__.py   | 17 +++++------------
 easybuild/tools/job/pbs_python.py |  4 +++-
 easybuild/tools/parallelbuild.py  |  3 +--
 3 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index f59820c7f6..a1daa4bfb3 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -62,17 +62,6 @@ def __init__(self, server, script, name, env_vars=None, hours=None, cores=None):
         """
         pass
 
-    @abstractmethod
-    def add_dependencies(self, jobs):
-        """
-        Add dependencies to this job.
-
-        Argument `jobs` is a sequence of `Job` objects,
-        which must actually be instances of the exact same
-        class as the dependent job.
-        """
-        pass
-
 
 class JobServer(object):
     __metaclass__ = ABCMeta
@@ -98,10 +87,14 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         pass
 
     @abstractmethod
-    def submit(self, job):
+    def submit(self, job, after=frozenset()):
         """
         Submit a job to the batch-queueing system.
 
+        If second optional argument `after` is given, it must be a
+        sequence of jobs that must be successfully terminated before
+        the new job can run.
+
         Note that actual submission may be delayed until `commit()` is
         called.
         """
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 9bc9b41dc1..92f94a8166 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -90,8 +90,10 @@ def connect_to_server(self):
             self.conn = pbs.pbs_connect(self.pbs_server)
         return self.conn
 
-    def submit(self, job):
+    def submit(self, job, after=frozenset()):
         assert isinstance(job, PbsJob)
+        if after:
+            job.add_dependencies(after)
         job._submit()
         self._submitted.append(job)
 
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index f3470e1806..7e78da135d 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -96,10 +96,9 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
 
         # sometimes unresolved_deps will contain things, not needed to be build
         job_deps = [module_to_job[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in module_to_job]
-        new_job.add_dependencies(job_deps)
 
         # actually (try to) submit job
-        job_server.submit(new_job)
+        job_server.submit(new_job, job_deps)
         _log.info("job for module %s has been submitted (job id: %s)" % (new_job.module, new_job.jobid))
 
         # update dictionary

From d03a2c1deacf527034c76229da441a449e5def01 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 15:08:05 +0100
Subject: [PATCH 0653/1356] Remove the now useless `Job` abstract class.

All the job submission and control work is done through the
`easybuild.tools.job.JobServer` class; we do not need a public interface
for what is basically an internal implementation detail of each job
submission backend.
---
 easybuild/tools/job/__init__.py   | 31 -------------------------------
 easybuild/tools/job/pbs_python.py |  4 ++--
 2 files changed, 2 insertions(+), 33 deletions(-)

diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index a1daa4bfb3..0eac6a958c 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -32,37 +32,6 @@
 from easybuild.tools.config import get_job_backend
 
 
-class Job(object):
-    __metaclass__ = ABCMeta
-
-    @abstractmethod
-    def __init__(self, server, script, name, env_vars=None, hours=None, cores=None):
-        """
-        Create a new `Job` object.
-
-        First argument `server` is an instance of the corresponding
-        `JobServer` class.
-
-        Second argument `script` is the content of the job script
-        itself, i.e., the sequence of shell commands that will be
-        executed.
-
-        Third argument `name` sets the job human-readable name.
-
-        Fourth (optional) argument `env_vars` is a dictionary with
-        key-value pairs of environment variables that should be passed
-        on to the job.
-
-        Fifth and sith (optional) arguments `hours` and `cores` should be
-        integer values:
-        * hours must be in the range 1 .. MAX_WALLTIME;
-        * cores depends on which cluster the job is being run.
-
-        Concrete subclasses may add more optional parameters.
-        """
-        pass
-
-
 class JobServer(object):
     __metaclass__ = ABCMeta
 
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 92f94a8166..25001439ab 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -35,7 +35,7 @@
 import time
 from vsc.utils import fancylogger
 
-from easybuild.tools.job import Job, JobServer
+from easybuild.tools.job import JobServer
 
 
 _log = fancylogger.getLogger('pbs_job', fname=False)
@@ -142,7 +142,7 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
                       conn=self.conn, ppn=self.ppn)
 
 
-class PbsJob(Job):
+class PbsJob(object):
     """Interaction with TORQUE"""
 
     def __init__(self, server, script, name, env_vars=None,

From 6fb7d0868b9648059ceef6e69198647cfed2bc25 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 16:05:17 +0100
Subject: [PATCH 0654/1356] Make `easybuild.tools.job.avail_job_servers()`
 actually work.

Fix "OptionValueError: option --job-backend: invalid choice:
'Pbs' (choose from )" happening when invoking `eb` since last commit.
---
 easybuild/tools/job/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 0eac6a958c..30f4caf4a8 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -30,6 +30,7 @@
 from vsc.utils.missing import get_subclasses
 
 from easybuild.tools.config import get_job_backend
+from easybuild.tools.utilities import import_available_modules
 
 
 class JobServer(object):
@@ -87,6 +88,7 @@ def avail_job_servers():
     """
     Return all known job execution backends.
     """
+    import_available_modules('easybuild.tools.job')
     class_dict = dict([(x.__name__, x) for x in get_subclasses(JobServer)])
     return class_dict
 

From aa586ca44e0172cca47e5aec9d7c4a44223e09ce Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 16:06:36 +0100
Subject: [PATCH 0655/1356] First draft GC3Pie code.

---
 easybuild/tools/job/gc3pie.py | 119 ++++++++++++++++++++++++++++++++--
 1 file changed, 115 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index c8f3dc86c9..b7126eb533 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -1,5 +1,6 @@
 ##
 # Copyright 2015-2015 Ghent University
+# Copyright 2015 S3IT, University of Zurich
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -24,9 +25,119 @@
 ##
 """Interface for submitting jobs via gc3pie"""
 
-from easybuild.tools.job import Job
 
+from gc3libs import Application, Run, create_engine
+from gc3libs.core import Engine
+from gc3libs.quantity import hours as hr
+from gc3libs.workflow import DependentTaskCollection
 
-# eb --job=GC3Pie
-class GC3Pie(Job):
-    pass
+from easybuild.tools.job import JobServer
+
+
+# eb --job --job-backend=GC3Pie
+class GC3Pie(JobServer):
+    """
+    Use the GC3Pie__ framework to submit and monitor compilation jobs.
+
+    In contrast with acessing an external service, GC3Pie implements
+    its own workflow manager, which means ``eb --job
+    --job-backend=GC3Pie`` will keep running until all jobs have
+    terminated.
+
+    .. __: http://gc3pie.googlecode.com/
+    """
+
+    def begin(self):
+        """
+        Start a bulk job submission.
+
+        Removes any reference to previously-submitted jobs.
+        """
+        self._jobs = DependentTaskCollection()
+
+    def make_job(self, server, script, name, env_vars=None, hours=None, cores=None):
+        """
+        Create and return a job object with the given parameters.
+
+        First argument `server` is an instance of the corresponding
+        `JobServer` class, i.e., a `GC3Pie`:class: instance in this case.
+
+        Second argument `script` is the content of the job script
+        itself, i.e., the sequence of shell commands that will be
+        executed.
+
+        Third argument `name` sets the job human-readable name.
+
+        Fourth (optional) argument `env_vars` is a dictionary with
+        key-value pairs of environment variables that should be passed
+        on to the job.
+
+        Fifth and sith (optional) arguments `hours` and `cores` should be
+        integer values:
+        * hours must be in the range 1 .. MAX_WALLTIME;
+        * cores depends on which cluster the job is being run.
+        """
+        extra_args = {}
+        if env_vars:
+            extra_args['environment'] = env_vars
+        if hours:
+            extra_args['requested_walltime'] = hours*hr
+        if cores:
+            extra_args['requested_cores'] = cores
+        return Application(
+            # arguments
+            arguments=script.split(), # FIXME: breaks if args contain spaces!
+            # no need to stage files in or out
+            inputs=[],
+            outputs=[],
+            # where should the output (STDOUT/STDERR) files be downloaded to?
+            output_dir=('/tmp/%s' % name),
+            # capture STDOUT and STDERR
+            stdout='stdout.log',
+            join=True,
+            **extra_args
+            )
+
+    def submit(self, job, after=frozenset()):
+        """
+        Submit a job to the batch-queueing system, optionally specifying dependencies.
+
+        If second optional argument `after` is given, it must be a
+        sequence of jobs that must be successfully terminated before
+        the new job can run.
+
+        Actual submission is delayed until `commit()` is called.
+        """
+        self._jobs.add(job, after)
+
+    def commit(self):
+        """
+        End a bulk job submission.
+
+        Releases any jobs that were possibly queued since the last
+        `begin()` call.
+
+        No more job submissions should be attempted after `commit()`
+        has been called, until `begin()` is invoked again.
+        """
+        # Create an instance of `Engine` using the configuration file present
+        # in your home directory.
+        engine = gc3libs.create_engine()
+
+        # Add your application to the engine. This will NOT submit
+        # your application yet, but will make the engine *aware* of
+        # the application.
+        engine.add(self._jobs)
+
+        # in case you want to select a specific resource, call
+        # `Engine.select_resource(<resource_name>)`
+
+        # Periodically check the status of your application.
+        while self._jobs.execution.state != Run.State.TERMINATED:
+            # `Engine.progress()` will do the GC3Pie magic:
+            # submit new jobs, update status of submitted jobs, get
+            # results of terminating jobs etc...
+            engine.progress()
+
+            # Wait a few seconds...
+            time.sleep(1)

From 4deb8783afc2dff4e38879fea3527bcf7f0412b7 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 16:21:06 +0100
Subject: [PATCH 0656/1356] Fix detection of available job backends.

---
 easybuild/tools/job/__init__.py   |  8 ++++++--
 easybuild/tools/job/gc3pie.py     | 14 ++++++++++----
 easybuild/tools/job/pbs_python.py |  5 ++++-
 3 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 30f4caf4a8..763190b22c 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -36,6 +36,8 @@
 class JobServer(object):
     __metaclass__ = ABCMeta
 
+    USABLE = False
+
     @abstractmethod
     def begin(self):
         """
@@ -84,12 +86,14 @@ def commit(self):
         pass
 
 
-def avail_job_servers():
+def avail_job_servers(check_usable=True):
     """
     Return all known job execution backends.
     """
     import_available_modules('easybuild.tools.job')
-    class_dict = dict([(x.__name__, x) for x in get_subclasses(JobServer)])
+    class_dict = dict([(x.__name__, x)
+                       for x in get_subclasses(JobServer)
+                       if (x.USABLE or not check_usable)])
     return class_dict
 
 
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index b7126eb533..ab86feab38 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -26,10 +26,14 @@
 """Interface for submitting jobs via gc3pie"""
 
 
-from gc3libs import Application, Run, create_engine
-from gc3libs.core import Engine
-from gc3libs.quantity import hours as hr
-from gc3libs.workflow import DependentTaskCollection
+try:
+    from gc3libs import Application, Run, create_engine
+    from gc3libs.core import Engine
+    from gc3libs.quantity import hours as hr
+    from gc3libs.workflow import DependentTaskCollection
+    HAVE_GC3PIE = True
+except ImportError:
+    HAVE_GC3PIE = False
 
 from easybuild.tools.job import JobServer
 
@@ -47,6 +51,8 @@ class GC3Pie(JobServer):
     .. __: http://gc3pie.googlecode.com/
     """
 
+    USABLE = HAVE_GC3PIE
+
     def begin(self):
         """
         Start a bulk job submission.
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 25001439ab..4f71bd677f 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -47,7 +47,6 @@
 # list of known hold types
 KNOWN_HOLD_TYPES = []
 
-pbs_import_failed = None
 try:
     from PBSQuery import PBSQuery
     import pbs
@@ -55,6 +54,7 @@
     # `pbs_python` available, no need guard against import errors
     def only_if_pbs_import_successful(fn):
         return fn
+    HAVE_PBS_PYTHON = True
 except ImportError:
     _log.debug("Failed to import pbs from pbs_python."
                " Silently ignoring, this is a real issue only with --job=pbs")
@@ -67,6 +67,7 @@ def instead(*args, **kwargs):
             _log.error(errmsg)
             raise RuntimeError(errmsg)
         return instead
+    HAVE_PBS_PYTHON = False
 
 
 class Pbs(JobServer):
@@ -74,6 +75,8 @@ class Pbs(JobServer):
     Manage PBS server communication and create `PbsJob` objects.
     """
 
+    USABLE = HAVE_PBS_PYTHON
+
     def __init__(self, pbs_server=None):
         self.pbs_server = pbs_server or pbs.pbs_default()
         self.conn = None

From 156cc3410dfce1bcb815d33130c629fa53821ae7 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 16:37:27 +0100
Subject: [PATCH 0657/1356] Fix handling of `--job-backend` when the default
 value is not installed.

Instead of relying on a fixed default, we build a preference list:
the first available backend (in order of preference) is used as
the default value for `--job-backend`.
---
 easybuild/tools/config.py       |  3 ++-
 easybuild/tools/job/__init__.py | 14 ++++++++++++++
 easybuild/tools/options.py      |  7 ++++---
 3 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index cb4d6613c7..82657100b3 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -53,7 +53,6 @@
 
 
 DEFAULT_LOGFILE_FORMAT = ("easybuild", "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
-DEFAULT_JOB_SERVER = 'Pbs'
 DEFAULT_MNS = 'EasyBuildMNS'
 DEFAULT_MODULES_TOOL = 'EnvironmentModulesC'
 DEFAULT_PATH_SUBDIRS = {
@@ -67,6 +66,8 @@
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
 
+PREFERRED_JOB_SERVERS = ['Pbs', 'GC3Pie']
+
 
 # utility function for obtaining default paths
 def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 763190b22c..1be6e7a302 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -30,6 +30,7 @@
 from vsc.utils.missing import get_subclasses
 
 from easybuild.tools.config import get_job_backend
+from easybuild.tools.config import PREFERRED_JOB_SERVERS
 from easybuild.tools.utilities import import_available_modules
 
 
@@ -104,3 +105,16 @@ def job_server():
     job_server = get_job_backend()
     job_server_class = avail_job_servers().get(job_server)
     return job_server_class()
+
+
+def preferred_job_server(order=PREFERRED_JOB_SERVERS):
+    """
+    Return name of preferred concrete `JobServer` instance, or `None`
+    if none is available.
+    """
+    available_backends = avail_job_servers()
+    for backend in order:
+        if backend in available_backends:
+            return backend
+            break
+    return None
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 23d920f101..c31294f5b4 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -49,14 +49,15 @@
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
-from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_JOB_SERVER
+from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT
 from easybuild.tools.config import DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
 from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
+from easybuild.tools.config import PREFERRED_JOB_SERVERS
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
-from easybuild.tools.job import avail_job_servers
+from easybuild.tools.job import avail_job_servers, preferred_job_server
 from easybuild.tools.modules import avail_modules_tools
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
@@ -120,7 +121,7 @@ def basic_options(self):
                       None, 'store_true', False, 'f'),
             'job': ("Submit the build as a job", None, 'store_true', False),
             'job-backend': ("What job runner to use", 'choice', 'store',
-                            DEFAULT_JOB_SERVER, (avail_job_servers().keys())),
+                            preferred_job_server(), (avail_job_servers().keys())),
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",

From 50d79bf1fcdc595bd83acb2ff905172a88e94a93 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 16:57:41 +0100
Subject: [PATCH 0658/1356] More hacks to get `--job-backend` working.

---
 easybuild/tools/config.py        |  6 ++++--
 easybuild/tools/job/__init__.py  | 20 +++++++++++---------
 easybuild/tools/options.py       |  6 +++---
 easybuild/tools/parallelbuild.py |  7 +++++--
 4 files changed, 23 insertions(+), 16 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 82657100b3..e330bef6d9 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -66,7 +66,7 @@
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
 
-PREFERRED_JOB_SERVERS = ['Pbs', 'GC3Pie']
+PREFERRED_JOB_BACKENDS = ['Pbs', 'GC3Pie']
 
 
 # utility function for obtaining default paths
@@ -183,6 +183,7 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'prefix',
         'buildpath',
         'installpath',
+        'job_backend',
         'sourcepath',
         'repository',
         'repositorypath',
@@ -361,7 +362,8 @@ def get_job_backend():
     """
     Return job execution backend (PBS, GC3Pie, ...)
     """
-    return ConfigurationVariables()['job_backend']
+    # 'job_backend' key will only be present after EasyBuild config is initialized
+    return ConfigurationVariables().get('job_backend', None)
 
 
 def log_file_format(return_directory=False):
diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 1be6e7a302..5d11408053 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -30,7 +30,7 @@
 from vsc.utils.missing import get_subclasses
 
 from easybuild.tools.config import get_job_backend
-from easybuild.tools.config import PREFERRED_JOB_SERVERS
+from easybuild.tools.config import PREFERRED_JOB_BACKENDS
 from easybuild.tools.utilities import import_available_modules
 
 
@@ -87,7 +87,7 @@ def commit(self):
         pass
 
 
-def avail_job_servers(check_usable=True):
+def avail_job_backends(check_usable=True):
     """
     Return all known job execution backends.
     """
@@ -98,21 +98,23 @@ def avail_job_servers(check_usable=True):
     return class_dict
 
 
-def job_server():
+def job_backend():
     """
-    Return interface to job server.
+    Return interface to job server, or `None` if none is available.
     """
-    job_server = get_job_backend()
-    job_server_class = avail_job_servers().get(job_server)
-    return job_server_class()
+    job_backend = get_job_backend()
+    if job_backend is None:
+        return None
+    job_backend_class = avail_job_backends().get(job_backend)
+    return job_backend_class()
 
 
-def preferred_job_server(order=PREFERRED_JOB_SERVERS):
+def preferred_job_backend(order=PREFERRED_JOB_BACKENDS):
     """
     Return name of preferred concrete `JobServer` instance, or `None`
     if none is available.
     """
-    available_backends = avail_job_servers()
+    available_backends = avail_job_backends()
     for backend in order:
         if backend in available_backends:
             return backend
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index c31294f5b4..c285365679 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -54,10 +54,10 @@
 from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
-from easybuild.tools.config import PREFERRED_JOB_SERVERS
+from easybuild.tools.config import PREFERRED_JOB_BACKENDS
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
-from easybuild.tools.job import avail_job_servers, preferred_job_server
+from easybuild.tools.job import avail_job_backends, preferred_job_backend
 from easybuild.tools.modules import avail_modules_tools
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
@@ -121,7 +121,7 @@ def basic_options(self):
                       None, 'store_true', False, 'f'),
             'job': ("Submit the build as a job", None, 'store_true', False),
             'job-backend': ("What job runner to use", 'choice', 'store',
-                            preferred_job_server(), (avail_job_servers().keys())),
+                            preferred_job_backend(), (avail_job_backends().keys())),
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 7e78da135d..8143bd368e 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -42,7 +42,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
-from easybuild.tools.job import job_server
+from easybuild.tools.job import job_backend
 from easybuild.tools.repository.repository import init_repository
 from vsc.utils import fancylogger
 
@@ -68,7 +68,10 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
     """
     _log.info("going to build these easyconfigs in parallel: %s", easyconfigs)
 
-    job_server = job_server()
+    job_server = job_backend()
+    if job_server is None:
+        _log.error("Cannot use --job if no job backend is available.")
+
     try:
         job_server.begin()
     except RuntimeError, err:

From 58c17361d03d22498ca30b8262891997398dd4b1 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 17:10:26 +0100
Subject: [PATCH 0659/1356] Option `--job-backend` needs to be defined in
 `config_opts()` in order for it to appear within `ConfigurationVariables`.

---
 easybuild/tools/options.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index c285365679..5429603d37 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -120,8 +120,6 @@ def basic_options(self):
             'force': ("Force to rebuild software even if it's already installed (i.e. if it can be found as module)",
                       None, 'store_true', False, 'f'),
             'job': ("Submit the build as a job", None, 'store_true', False),
-            'job-backend': ("What job runner to use", 'choice', 'store',
-                            preferred_job_backend(), (avail_job_backends().keys())),
             'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
             'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
@@ -234,6 +232,8 @@ def config_options(self):
                             'strlist', 'store', ['.git', '.svn']),
             'installpath': ("Install path for software and modules",
                             None, 'store', mk_full_default_path('installpath')),
+            'job-backend': ("What job runner to use", 'choice', 'store',
+                            preferred_job_backend(), (avail_job_backends().keys())),
             # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),

From d0e85133ae2921c93cf0c8a27196b67af3db25a7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 11 Feb 2015 17:11:26 +0100
Subject: [PATCH 0660/1356] include parallelbuild tests in suite

---
 test/framework/suite.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 test/framework/suite.py

diff --git a/test/framework/suite.py b/test/framework/suite.py
old mode 100644
new mode 100755

From d890fde9e6cb28b73ff971c6435f239505106698 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 17:12:57 +0100
Subject: [PATCH 0661/1356] Set default output directory for jobs to
 `easybuild-build` everywhere.

Fix "AttributeError: 'NoneType' object has no attribute 'startswith'"
---
 easybuild/tools/parallelbuild.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 8143bd368e..bc82e19eda 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -53,7 +53,7 @@ def _to_key(dep):
     """Determine key for specified dependency."""
     return ActiveMNS().det_full_module_name(dep)
 
-def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None):
+def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybuild-build'):
     """
     Build easyconfigs in parallel by submitting jobs to a batch-queuing system.
     Return list of jobs submitted.

From 810a05fe6fb17c3e51f61beec22937d95e9519e4 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 17:19:00 +0100
Subject: [PATCH 0662/1356] Use `str()` to print job ID or other infos about
 the job. In the case of PBS jobs, we print the job ID if available; for
 GC3Pie jobs, this should print the persistent ID.

Fix "AttributeError: 'Application' object has no attribute 'jobid'"
---
 easybuild/tools/job/pbs_python.py | 5 +++++
 easybuild/tools/parallelbuild.py  | 4 +++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 4f71bd677f..f0799fc8d5 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -205,6 +205,11 @@ def __init__(self, server, script, name, env_vars=None,
         # list of holds that are placed on this job
         self.holds = []
 
+    def __str__(self):
+        """Return the job ID as a string."""
+        return (str(self.jobid) if self.jobid is not None
+                else repr(self))
+
     def add_dependencies(self, jobs):
         """
         Add dependencies to this job.
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index bc82e19eda..83ee731787 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -102,7 +102,9 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybu
 
         # actually (try to) submit job
         job_server.submit(new_job, job_deps)
-        _log.info("job for module %s has been submitted (job id: %s)" % (new_job.module, new_job.jobid))
+        _log.info(
+            "job %s for module %s has been submitted"
+            % (new_job, new_job.module))
 
         # update dictionary
         module_to_job[new_job.module] = new_job

From f622e5b37b40a001021702b0bce2229b305b3ac3 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 17:24:55 +0100
Subject: [PATCH 0663/1356] Fix "NameError: global name 'gc3libs' is not
 defined"

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index ab86feab38..23dddba1ce 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -128,7 +128,7 @@ def commit(self):
         """
         # Create an instance of `Engine` using the configuration file present
         # in your home directory.
-        engine = gc3libs.create_engine()
+        engine = create_engine()
 
         # Add your application to the engine. This will NOT submit
         # your application yet, but will make the engine *aware* of

From b806fc81aae2544943a106481b52b13701b7d6de Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Wed, 11 Feb 2015 17:32:00 +0100
Subject: [PATCH 0664/1356] Fix "NameError: global name 'time' is not defined"
 in `gc3pie.py`

---
 easybuild/tools/job/gc3pie.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 23dddba1ce..a4b8dfd82c 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -26,6 +26,8 @@
 """Interface for submitting jobs via gc3pie"""
 
 
+import time
+
 try:
     from gc3libs import Application, Run, create_engine
     from gc3libs.core import Engine

From 4e34b9af4e7e791b4c94c7a6e39f4c8909c41677 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 12 Feb 2015 08:52:15 +0100
Subject: [PATCH 0665/1356] gc3pie.py: Make handling of log.error compatible
 with stdlib logging

---
 easybuild/tools/job/gc3pie.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index a4b8dfd82c..b6210317a5 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -29,11 +29,14 @@
 import time
 
 try:
+    import gc3libs
     from gc3libs import Application, Run, create_engine
     from gc3libs.core import Engine
     from gc3libs.quantity import hours as hr
     from gc3libs.workflow import DependentTaskCollection
     HAVE_GC3PIE = True
+    # make handling of log.error compatible with stdlib logging
+    gc3libs.log.raiseError = False
 except ImportError:
     HAVE_GC3PIE = False
 

From e80dec9ede5b0d0af8b1dcb97e3db7e56de1147d Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 12 Feb 2015 12:34:58 +0100
Subject: [PATCH 0666/1356] Fix varargs formatting in `EasyBuildLog.error`.

---
 easybuild/tools/build_log.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index 1472e00e5e..24178b9f84 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -107,8 +107,9 @@ def nosupport(self, msg, ver):
 
     def error(self, msg, *args, **kwargs):
         """Print error message and raise an EasyBuildError."""
-        newMsg = "EasyBuild crashed with an error %s: %s" % (self.caller_info(), msg)
-        fancylogger.FancyLogger.error(self, newMsg, *args, **kwargs)
+        newMsg = ("EasyBuild crashed with an error %s: %s"
+                  % (self.caller_info(), (msg % args)))
+        fancylogger.FancyLogger.error(self, newMsg, **kwargs)
         if self.raiseError:
             raise EasyBuildError(newMsg)
 

From cbad0592a969ebcb5f2494cccd780549b0447883 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 12 Feb 2015 14:27:56 +0100
Subject: [PATCH 0667/1356] Use `str(job)` to represent the job "ID" in
 user-facing messages.

`str(job)` expands to a backend-dependent ID: the job number on PBS,
the persistent ID in GC3Pie.
---
 easybuild/tools/parallelbuild.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 83ee731787..27d736f262 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -141,7 +141,8 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
     else:
         jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
         job_info_lines = ["List of submitted jobs:"]
-        job_info_lines.extend(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in jobs])
+        job_info_lines.extend([("%s (%s): %s" % (job.name, job.module, job))
+                               for job in jobs])
         job_info_lines.append("(%d jobs submitted)" % len(jobs))
         return '\n'.join(job_info_lines)
 

From 355646d3f3eb4a15b138a069cee1d9875932b0b2 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 12 Feb 2015 14:28:22 +0100
Subject: [PATCH 0668/1356] Do not pass the `--job-backend` option down to
 build jobs.

---
 easybuild/tools/parallelbuild.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 27d736f262..c864ae25ef 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -125,7 +125,7 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
     curdir = os.getcwd()
 
     # the options to ignore (help options can't reach here)
-    ignore_opts = ['robot', 'job']
+    ignore_opts = ['robot', 'job', 'job-backend']
 
     # generate_cmd_line returns the options in form --longopt=value
     opts = [x for x in cmd_line_opts if not x.split('=')[0] in ['--%s' % y for y in ignore_opts]]

From a02f193c165ff18c0ffaab698f7076e901ec6470 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 12 Feb 2015 14:30:33 +0100
Subject: [PATCH 0669/1356] Set job name in GC3Pie backend

---
 easybuild/tools/job/gc3pie.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index b6210317a5..413fe4791e 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -88,7 +88,9 @@ def make_job(self, server, script, name, env_vars=None, hours=None, cores=None):
         * hours must be in the range 1 .. MAX_WALLTIME;
         * cores depends on which cluster the job is being run.
         """
-        extra_args = {}
+        extra_args = {
+            'jobname': name,
+        }
         if env_vars:
             extra_args['environment'] = env_vars
         if hours:

From 65ddd86c8a1d386a0c7a5a31e791603eba4503e7 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 12 Feb 2015 14:31:09 +0100
Subject: [PATCH 0670/1356] Collect all GC3Pie jobs output into directory
 `easybuild-jobs`.

---
 easybuild/tools/job/gc3pie.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 413fe4791e..d80be0bdd8 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -26,6 +26,7 @@
 """Interface for submitting jobs via gc3pie"""
 
 
+import os
 import time
 
 try:
@@ -104,7 +105,7 @@ def make_job(self, server, script, name, env_vars=None, hours=None, cores=None):
             inputs=[],
             outputs=[],
             # where should the output (STDOUT/STDERR) files be downloaded to?
-            output_dir=('/tmp/%s' % name),
+            output_dir=('%s/easybuild-jobs/%s' % (os.getcwd(), name)),
             # capture STDOUT and STDERR
             stdout='stdout.log',
             join=True,

From e8e4e520ebd8005fd2c176239b66ccfac7467d67 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 12 Feb 2015 14:32:02 +0100
Subject: [PATCH 0671/1356] Run build command line through `sh -c`.

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index d80be0bdd8..c7b42f24e9 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -100,7 +100,7 @@ def make_job(self, server, script, name, env_vars=None, hours=None, cores=None):
             extra_args['requested_cores'] = cores
         return Application(
             # arguments
-            arguments=script.split(), # FIXME: breaks if args contain spaces!
+            ['/bin/sh', '-c', script],
             # no need to stage files in or out
             inputs=[],
             outputs=[],

From 2878dad228a1ffdfd06bbd2c5894e1a65fba2537 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 12 Feb 2015 14:46:38 +0100
Subject: [PATCH 0672/1356] Correct argument list of `GC3Pie.make_jobs()`

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index c7b42f24e9..5c34255fa9 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -67,7 +67,7 @@ def begin(self):
         """
         self._jobs = DependentTaskCollection()
 
-    def make_job(self, server, script, name, env_vars=None, hours=None, cores=None):
+    def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         """
         Create and return a job object with the given parameters.
 

From e974c2eee46873434bc9e46f6898b12c7d57dd82 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 12 Feb 2015 16:13:21 +0100
Subject: [PATCH 0673/1356] gc3pie: Hard-code a 30 seconds polling time.

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 5c34255fa9..a8db421c80 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -154,4 +154,4 @@ def commit(self):
             engine.progress()
 
             # Wait a few seconds...
-            time.sleep(1)
+            time.sleep(30)

From 02195fe8b146937510f3ad2621445e04529ae9b5 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Fri, 13 Feb 2015 15:05:55 +0100
Subject: [PATCH 0674/1356] Use EasyBuild's logger for module-level logging.

Also correct usage of the `log=...` parameter in `print_msg`.
---
 easybuild/tools/job/gc3pie.py | 37 +++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index a8db421c80..89a6bb76a3 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -41,8 +41,14 @@
 except ImportError:
     HAVE_GC3PIE = False
 
+from easybuild.tools.build_log import print_msg
 from easybuild.tools.job import JobServer
 
+from vsc.utils import fancylogger
+
+
+_log = fancylogger.getLogger('gc3pie', fname=False)
+
 
 # eb --job --job-backend=GC3Pie
 class GC3Pie(JobServer):
@@ -153,5 +159,36 @@ def commit(self):
             # results of terminating jobs etc...
             engine.progress()
 
+            # report progress
+            stats = engine.stats()
+            print_msg(
+                "build jobs: "
+                + str.join(", ", [
+                    ("%d %s" % (stats[state], state.lower()))
+                    for state in [
+                            'total',
+                            'SUBMITTED',
+                            'RUNNING',
+                            'ok',
+                            'failed',
+                    ]
+                    if stats[state] > 0
+                ]))
+
             # Wait a few seconds...
             time.sleep(30)
+
+        # final status report
+        stats = engine.stats()
+        print_msg(
+            "build jobs: "
+            + str.join(", ", [
+                ("%d %s" % (stats[state], state.lower()))
+                for state in [
+                        'total',
+                        'ok',
+                        'failed',
+                ]
+                if stats[state] > 0
+            ]),
+            log=_log)

From bab1afb59afd7f26e7dc1db9622e820f924e7326 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Fri, 13 Feb 2015 15:07:43 +0100
Subject: [PATCH 0675/1356] pbs_python: Change logger name to match module
 name.

---
 easybuild/tools/job/pbs_python.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index f0799fc8d5..bc5ec415eb 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -38,7 +38,7 @@
 from easybuild.tools.job import JobServer
 
 
-_log = fancylogger.getLogger('pbs_job', fname=False)
+_log = fancylogger.getLogger('pbs_python', fname=False)
 
 
 MAX_WALLTIME = 72

From a2c033660a91bfb43040d5988d80153c921398c7 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Fri, 13 Feb 2015 15:09:28 +0100
Subject: [PATCH 0676/1356] gc3pie: Correctly capitalize GC3Pie in docstring.

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 89a6bb76a3..76427aac38 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -23,7 +23,7 @@
 # You should have received a copy of the GNU General Public License
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
-"""Interface for submitting jobs via gc3pie"""
+"""Interface for submitting jobs via GC3Pie"""
 
 
 import os

From f3bcd4ad269ebf88756a589ee783304f4d30b4c7 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Mon, 16 Feb 2015 15:19:13 +0100
Subject: [PATCH 0677/1356] gc3pie: Only report stats for `Application` (job)
 objects.

---
 easybuild/tools/job/gc3pie.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 76427aac38..a71d0eee4f 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -36,8 +36,6 @@
     from gc3libs.quantity import hours as hr
     from gc3libs.workflow import DependentTaskCollection
     HAVE_GC3PIE = True
-    # make handling of log.error compatible with stdlib logging
-    gc3libs.log.raiseError = False
 except ImportError:
     HAVE_GC3PIE = False
 
@@ -46,8 +44,10 @@
 
 from vsc.utils import fancylogger
 
-
-_log = fancylogger.getLogger('gc3pie', fname=False)
+# inject EasyBuild logger into GC3Pie
+gc3libs.log = fancylogger.getLogger('gc3pie', fname=False)
+# make handling of log.error compatible with stdlib logging
+gc3libs.log.raiseError = False
 
 
 # eb --job --job-backend=GC3Pie
@@ -96,7 +96,8 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         * cores depends on which cluster the job is being run.
         """
         extra_args = {
-            'jobname': name,
+            'jobname': name, # job name in GC3Pie
+            'name':    name, # same in EasyBuild
         }
         if env_vars:
             extra_args['environment'] = env_vars
@@ -160,7 +161,7 @@ def commit(self):
             engine.progress()
 
             # report progress
-            stats = engine.stats()
+            stats = engine.stats(only=Application)
             print_msg(
                 "build jobs: "
                 + str.join(", ", [
@@ -179,7 +180,7 @@ def commit(self):
             time.sleep(30)
 
         # final status report
-        stats = engine.stats()
+        stats = engine.stats(only=Application)
         print_msg(
             "build jobs: "
             + str.join(", ", [
@@ -191,4 +192,4 @@ def commit(self):
                 ]
                 if stats[state] > 0
             ]),
-            log=_log)
+            log=gc3libs.log)

From 8f4dd37502e765092b91e0fdc77a9bacb96bc2b0 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Mon, 16 Feb 2015 15:43:21 +0100
Subject: [PATCH 0678/1356] parallelbuild: Make `submit_jobs()` report
 backend-agnostic.

The former output only made sense for the PBS backend: in the GC3Pie
case, since jobs are managed by the GC3Pie engine *within* EasyBuild, it
makes little sense to report about "submitted" jobs after they have all
run...

Therefore, move PBS job reporting into `Pbs.commit()` and use a neutral
report text in `submit_jobs()`.
---
 easybuild/tools/job/pbs_python.py | 4 ++++
 easybuild/tools/parallelbuild.py  | 6 +-----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index bc5ec415eb..7fa6dc64ef 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -107,6 +107,10 @@ def commit(self):
                 _log.info("releasing user hold on job %s" % job.jobid)
                 job.release_hold()
         self.disconnect_from_server()
+        if self._submitted:
+            _log.info("List of submitted jobs:")
+            for job in self._submitted:
+                _log.info("* %s (%s): %s", job.name, job.module, job.jobid)
 
     @only_if_pbs_import_successful
     def disconnect_from_server(self):
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index c864ae25ef..4397f8a6a6 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -140,11 +140,7 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
         _log.debug("Skipping actual submission of jobs since testing mode is enabled")
     else:
         jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
-        job_info_lines = ["List of submitted jobs:"]
-        job_info_lines.extend([("%s (%s): %s" % (job.name, job.module, job))
-                               for job in jobs])
-        job_info_lines.append("(%d jobs submitted)" % len(jobs))
-        return '\n'.join(job_info_lines)
+        return ("%d jobs required for build." % (len(jobs),))
 
 
 def create_job(job_server, build_command, easyconfig, output_dir='easybuild-build'):

From aa324d32ed4858631e4d1d70ca95c0fd14987ef3 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 19 Feb 2015 11:36:33 +0100
Subject: [PATCH 0679/1356] Make `PREFERRED_JOB_BACKENDS` immutable.

---
 easybuild/tools/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index e330bef6d9..0f3782dc11 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -66,7 +66,7 @@
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
 
-PREFERRED_JOB_BACKENDS = ['Pbs', 'GC3Pie']
+PREFERRED_JOB_BACKENDS = ('Pbs', 'GC3Pie')
 
 
 # utility function for obtaining default paths

From 61e34fef903b155d9a68cfd82a9f67d27408b9b5 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 19 Feb 2015 11:53:33 +0100
Subject: [PATCH 0680/1356] Add author and affiliation in
 `easybuild.tools.job.gc3pie`

---
 easybuild/tools/job/gc3pie.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index a71d0eee4f..0cfe9e7bbd 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -23,7 +23,11 @@
 # You should have received a copy of the GNU General Public License
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
-"""Interface for submitting jobs via GC3Pie"""
+"""
+Interface for submitting jobs via GC3Pie.
+
+@author: Riccardo Murri (University of Zurich)
+"""
 
 
 import os

From 90ff4cb3d07e7268d0641c06325983598fdf6b16 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 19 Feb 2015 11:54:46 +0100
Subject: [PATCH 0681/1356] Fix typos in docstring.

---
 easybuild/tools/job/gc3pie.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 0cfe9e7bbd..b507500daa 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -59,7 +59,7 @@ class GC3Pie(JobServer):
     """
     Use the GC3Pie__ framework to submit and monitor compilation jobs.
 
-    In contrast with acessing an external service, GC3Pie implements
+    In contrast with accessing an external service, GC3Pie implements
     its own workflow manager, which means ``eb --job
     --job-backend=GC3Pie`` will keep running until all jobs have
     terminated.
@@ -94,7 +94,7 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         key-value pairs of environment variables that should be passed
         on to the job.
 
-        Fifth and sith (optional) arguments `hours` and `cores` should be
+        Fifth and sixth (optional) arguments `hours` and `cores` should be
         integer values:
         * hours must be in the range 1 .. MAX_WALLTIME;
         * cores depends on which cluster the job is being run.

From 81ff17326a161fff5a71467518c1dca0ea1a10e6 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 19 Feb 2015 12:08:30 +0100
Subject: [PATCH 0682/1356] Address @stdweird's coding style remarks.

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index b507500daa..d069700696 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -116,7 +116,7 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
             inputs=[],
             outputs=[],
             # where should the output (STDOUT/STDERR) files be downloaded to?
-            output_dir=('%s/easybuild-jobs/%s' % (os.getcwd(), name)),
+            output_dir=os.path.join(os.getcwd(), 'easybuild-jobs', name),
             # capture STDOUT and STDERR
             stdout='stdout.log',
             join=True,

From 6eb83173570f5cdf3c3a6a141a45b9461591988f Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 19 Feb 2015 12:08:36 +0100
Subject: [PATCH 0683/1356] Correctly report the total number of jobs from the
 start.

Also address @stdweird's coding style concerns regarding `str.join()`
and factoring out common print expressions into a single method.
---
 easybuild/tools/job/gc3pie.py | 58 +++++++++++++++++++----------------
 1 file changed, 32 insertions(+), 26 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index d069700696..1639b7ecdb 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -145,14 +145,16 @@ def commit(self):
         No more job submissions should be attempted after `commit()`
         has been called, until `begin()` is invoked again.
         """
+        total = len(self._jobs)
+
         # Create an instance of `Engine` using the configuration file present
         # in your home directory.
-        engine = create_engine()
+        self._engine = create_engine()
 
         # Add your application to the engine. This will NOT submit
         # your application yet, but will make the engine *aware* of
         # the application.
-        engine.add(self._jobs)
+        self._engine.add(self._jobs)
 
         # in case you want to select a specific resource, call
         # `Engine.select_resource(<resource_name>)`
@@ -162,38 +164,42 @@ def commit(self):
             # `Engine.progress()` will do the GC3Pie magic:
             # submit new jobs, update status of submitted jobs, get
             # results of terminating jobs etc...
-            engine.progress()
+            self._engine.progress()
 
             # report progress
-            stats = engine.stats(only=Application)
-            print_msg(
-                "build jobs: "
-                + str.join(", ", [
-                    ("%d %s" % (stats[state], state.lower()))
-                    for state in [
-                            'total',
-                            'SUBMITTED',
-                            'RUNNING',
-                            'ok',
-                            'failed',
-                    ]
-                    if stats[state] > 0
-                ]))
+            self._print_status_report([
+                'total',
+                'SUBMITTED',
+                'RUNNING',
+                'ok',
+                'failed',
+            ], total=total)
 
             # Wait a few seconds...
             time.sleep(30)
 
         # final status report
-        stats = engine.stats(only=Application)
+        self._print_status_report(['total', 'ok', 'failed'], total=total)
+
+    def _print_status_report(self, states=('total', 'ok', 'failed'), **override):
+        """
+        Print a job status report to STDOUT and the log file.
+
+        The number of jobs in any of the given states is reported; the
+        figures are extracted from the `stats()` method of the
+        currently-running GC3Pie engine.  Additional keyword arguments
+        can override specific stats; this is used, e.g., to correctly
+        report the number of total jobs right from the start.
+        """
+        stats = self._engine.stats(only=Application)
         print_msg(
             "build jobs: "
-            + str.join(", ", [
-                ("%d %s" % (stats[state], state.lower()))
-                for state in [
-                        'total',
-                        'ok',
-                        'failed',
-                ]
+            + ", ".join([
+                ("%d %s" % (
+                    override.get(state, stats[state]),
+                    state.lower(),
+                ))
+                for state in states
                 if stats[state] > 0
             ]),
-            log=gc3libs.log)
+            log=override.get('log', gc3libs.log))

From 11f97c9ab5dd9ae6f249e87cdb9eee9e65eee4b7 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 19 Feb 2015 12:26:03 +0100
Subject: [PATCH 0684/1356] Fix reference to renamed function `get_ppn()`.

Used to be a top-level function in the `pbs_job` module, it's now a
property in the `PbsJobServer` class.
---
 easybuild/tools/job/pbs_python.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 7fa6dc64ef..5251a24682 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -186,7 +186,7 @@ def __init__(self, server, script, name, env_vars=None,
             hours = MAX_WALLTIME
 
         if ppn is None:
-            max_cores = get_ppn()
+            max_cores = server.ppn
         else:
             max_cores = ppn
         if cores is None:

From b96c2210a335333d333f9bc9a9b1c68bcb3f3635 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 19 Feb 2015 12:28:13 +0100
Subject: [PATCH 0685/1356] Don't use a new specific logger in
 `PbsJobServer._get_ppn()`.

---
 easybuild/tools/job/pbs_python.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 5251a24682..d79af3cff9 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -123,8 +123,6 @@ def _get_ppn(self):
         # cache this value as it's not likely going to change over the
         # `eb` script runtime ...
         if not self._ppn:
-            log = fancylogger.getLogger('pbs_job.PbsServer.ppn')
-
             pq = PBSQuery()
             node_vals = pq.getnodes().values()  # only the values, not the names
             interesting_nodes = ('free', 'job-exclusive',)
@@ -135,7 +133,7 @@ def _get_ppn(self):
 
             # return most frequent
             freq_count, freq_np = max([(j, i) for i, j in res.items()])
-            log.debug("Found most frequent np %s (%s times) in interesting nodes %s" % (freq_np, freq_count, interesting_nodes))
+            _log.debug("Found most frequent np %s (%s times) in interesting nodes %s" % (freq_np, freq_count, interesting_nodes))
 
             self._ppn = freq_np
 

From 6160ef9ed0b7a9a226e315305c6064d8b9cd7f21 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 19 Feb 2015 12:30:28 +0100
Subject: [PATCH 0686/1356] Consolidate PBS job submission report in a single
 line.

---
 easybuild/tools/job/pbs_python.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index d79af3cff9..0a10b3f572 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -108,9 +108,12 @@ def commit(self):
                 job.release_hold()
         self.disconnect_from_server()
         if self._submitted:
-            _log.info("List of submitted jobs:")
-            for job in self._submitted:
-                _log.info("* %s (%s): %s", job.name, job.module, job.jobid)
+            _log.info(
+                "List of submitted jobs:"
+                + "; ".join([
+                    ("%s (%s): %s" % (job.name, job.module, job.jobid))
+                    for job in self._submitted
+                ]))
 
     @only_if_pbs_import_successful
     def disconnect_from_server(self):

From 7f0839521ad71fd66d4658f80e75dc20f971ec45 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 3 Mar 2015 17:06:58 +0100
Subject: [PATCH 0687/1356] keep $I_MPI_MPD_TMPDIR short to avoid
 'socket.error: AF_UNIX path too long'

---
 easybuild/tools/toolchain/mpi.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index 7a9694de8c..13b618e4cd 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -191,7 +191,8 @@ def mpi_cmd_for(self, cmd, nr_ranks):
             tmpdir = tempfile.mkdtemp(prefix='eb-mpi_cmd_for-')
 
             # set temporary dir for mdp
-            env.setvar('I_MPI_MPD_TMPDIR', tmpdir)
+            # note: this needs to be kept *short*, to avoid mpirun failing with "socket.error: AF_UNIX path too long"
+            env.setvar('I_MPI_MPD_TMPDIR', tempfile.gettempdir())
 
             # set PBS_ENVIRONMENT, so that --file option for mpdboot isn't stripped away
             env.setvar('PBS_ENVIRONMENT', "PBS_BATCH_MPI")

From dc1a198c80eb29c18547b052cc9b4684cade31c9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Mar 2015 07:36:38 +0100
Subject: [PATCH 0688/1356] keep tmpdir suffix short by cutting 'easybuild-'
 prefix down to 'eb-'

---
 easybuild/tools/config.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 9e2108143c..10a0aaccae 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -446,10 +446,10 @@ def set_tmpdir(tmpdir=None, raise_error=False):
         if tmpdir is not None:
             if not os.path.exists(tmpdir):
                 os.makedirs(tmpdir)
-            current_tmpdir = tempfile.mkdtemp(prefix='easybuild-', dir=tmpdir)
+            current_tmpdir = tempfile.mkdtemp(prefix='eb-', dir=tmpdir)
         else:
             # use tempfile default parent dir
-            current_tmpdir = tempfile.mkdtemp(prefix='easybuild-')
+            current_tmpdir = tempfile.mkdtemp(prefix='eb-')
     except OSError, err:
         _log.error("Failed to create temporary directory (tmpdir: %s): %s" % (tmpdir, err))
 

From ca3d04a0f3d1abc811de7b8dd697b127d8cddea7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Mar 2015 07:37:04 +0100
Subject: [PATCH 0689/1356] check length of $I_MPI_MPD_TMPDIR, issue warning
 when it seems rather long

---
 easybuild/tools/toolchain/mpi.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index 13b618e4cd..dc0fd5d461 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -188,11 +188,16 @@ def mpi_cmd_for(self, cmd, nr_ranks):
         # Intel MPI mpirun needs more work
         if mpi_family == toolchain.INTELMPI:  # @UndefinedVariable
 
-            tmpdir = tempfile.mkdtemp(prefix='eb-mpi_cmd_for-')
-
             # set temporary dir for mdp
             # note: this needs to be kept *short*, to avoid mpirun failing with "socket.error: AF_UNIX path too long"
+            # exact limit is unknown, but ~20 characters seems to be OK
             env.setvar('I_MPI_MPD_TMPDIR', tempfile.gettempdir())
+            mpd_tmpdir = os.environ['I_MPI_MPD_TMPDIR']
+            if len(mpd_tmpdir) > 20:
+                self.log.warning("$I_MPI_MPD_TMPDIR should be (very) short to avoid problems: %s" % mpd_tmpdir)
+
+            # temporary location for mpdboot and nodes files
+            tmpdir = tempfile.mkdtemp(prefix='eb-mpi_cmd_for-')
 
             # set PBS_ENVIRONMENT, so that --file option for mpdboot isn't stripped away
             env.setvar('PBS_ENVIRONMENT', "PBS_BATCH_MPI")

From b4b11ebb776a904eead8565aa36d1c500cbcd3c8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Mar 2015 15:56:44 +0100
Subject: [PATCH 0690/1356] also consider robot search path when looking for
 specified easyconfigs

---
 easybuild/framework/easyconfig/tools.py | 20 +++++++++-----------
 easybuild/main.py                       |  7 +++++--
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 82ad8d0ab0..c9e55290e8 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -240,15 +240,14 @@ def alt_easyconfig_paths(tmpdir, tweaked_ecs=False, from_pr=False):
     return tweaked_ecs_path, pr_path
 
 
-def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
+def det_easyconfig_paths(orig_paths):
     """
     Determine paths to easyconfig files.
     @param orig_paths: list of original easyconfig paths
-    @param from_pr: pull request number to fetch easyconfigs from
-    @param easyconfigs_pkg_paths: paths to installed easyconfigs package
+    @return: list of paths to easyconfig files
     """
-    if easyconfigs_pkg_paths is None:
-        easyconfigs_pkg_paths = []
+    from_pr = build_option('from_pr')
+    robot_path = build_option('robot_path')
 
     # list of specified easyconfig files
     ec_files = orig_paths[:]
@@ -266,8 +265,8 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
             # if no easyconfigs are specified, use all the ones touched in the PR
             ec_files = [path for path in pr_files if path.endswith('.eb')]
 
-    if ec_files and easyconfigs_pkg_paths:
-        # look for easyconfigs with relative paths in easybuild-easyconfigs package,
+    if ec_files and robot_path:
+        # look for easyconfigs with relative paths in robot search path,
         # unless they were found at the given relative paths
 
         # determine which easyconfigs files need to be found, if any
@@ -277,8 +276,8 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
                 ecs_to_find.append((idx, ec_file))
         _log.debug("List of easyconfig files to find: %s" % ecs_to_find)
 
-        # find missing easyconfigs by walking paths with installed easyconfig files
-        for path in easyconfigs_pkg_paths:
+        # find missing easyconfigs by walking paths in robot search path
+        for path in robot_path:
             _log.debug("Looking for missing easyconfig files (%d left) in %s..." % (len(ecs_to_find), path))
             for (subpath, dirnames, filenames) in os.walk(path, topdown=True):
                 for idx, orig_path in ecs_to_find[:]:
@@ -300,8 +299,7 @@ def det_easyconfig_paths(orig_paths, from_pr=None, easyconfigs_pkg_paths=None):
             if not ecs_to_find:
                 break
 
-    # indicate that specified paths do not contain generated easyconfig files
-    return [(ec_file, False) for ec_file in ec_files]
+    return ec_files
 
 
 def parse_easyconfigs(paths):
diff --git a/easybuild/main.py b/easybuild/main.py
index f1ab88af41..bba788bf85 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -226,8 +226,11 @@ def main(testing_data=(None, None, None)):
         _log.warning("Failed to determine install path for easybuild-easyconfigs package.")
 
     # determine paths to easyconfigs
-    paths = det_easyconfig_paths(orig_paths, options.from_pr, easyconfigs_pkg_paths)
-    if not paths:
+    paths = det_easyconfig_paths(orig_paths)
+    if paths:
+        # transform paths into tuples, use 'False' to indicate the corresponding easyconfig files were not generated
+        paths = [(p, False) for p in paths]
+    else:
         if 'name' in build_specs:
             # try to obtain or generate an easyconfig file via build specifications if a software name is provided
             paths = find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=testing)

From 3c20845f3dbbb5b8605b6e6c089266085e9b5efe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Mar 2015 15:58:01 +0100
Subject: [PATCH 0691/1356] add tests to check for changed det_easyconfig_paths
 behaviour

---
 test/framework/robot.py | 126 ++++++++++++++++++++++++++++++++++++----
 1 file changed, 115 insertions(+), 11 deletions(-)

diff --git a/test/framework/robot.py b/test/framework/robot.py
index c157a25fad..e5e166f65d 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -29,6 +29,9 @@
 """
 
 import os
+import re
+import shutil
+import tempfile
 from copy import deepcopy
 from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader
@@ -39,9 +42,15 @@
 from easybuild.framework.easyconfig.tools import skip_available
 from easybuild.tools import config, modules
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import read_file, write_file
+from easybuild.tools.github import fetch_github_token
 from easybuild.tools.robot import resolve_dependencies
 from test.framework.utilities import find_full_path
 
+
+# test account, for which a token is available
+GITHUB_TEST_ACCOUNT = 'easybuild_test'
+
 ORIG_MODULES_TOOL = modules.modules_tool
 ORIG_ECTOOLS_MODULES_TOOL = ectools.modules_tool
 ORIG_ROBOT_MODULES_TOOL = robot.modules_tool
@@ -79,8 +88,12 @@ class RobotTest(EnhancedTestCase):
     """ Testcase for the robot dependency resolution """
 
     def setUp(self):
-        """Set up everything for a unit test."""
+        """Set up test."""
         super(RobotTest, self).setUp()
+        self.github_token = fetch_github_token(GITHUB_TEST_ACCOUNT)
+
+    def xtest_resolve_dependencies(self):
+        """ Test with some basic testcases (also check if he can find dependencies inside the given directory """
 
         # replace Modules class with something we have control over
         config.modules_tool = mock_module
@@ -88,11 +101,9 @@ def setUp(self):
         robot.modules_tool = mock_module
         os.environ['module'] = "() {  eval `/bin/echo $*`\n}"
 
-        self.base_easyconfig_dir = find_full_path(os.path.join("test", "framework", "easyconfigs"))
-        self.assertTrue(self.base_easyconfig_dir)
+        base_easyconfig_dir = find_full_path(os.path.join("test", "framework", "easyconfigs"))
+        self.assertTrue(base_easyconfig_dir)
 
-    def test_resolve_dependencies(self):
-        """ Test with some basic testcases (also check if he can find dependencies inside the given directory """
         easyconfig = {
             'spec': '_',
             'full_mod_name': 'name/version',
@@ -128,7 +139,7 @@ def test_resolve_dependencies(self):
             }],
             'parsed': True,
         }
-        build_options.update({'robot': True, 'robot_path': self.base_easyconfig_dir})
+        build_options.update({'robot': True, 'robot_path': base_easyconfig_dir})
         init_config(build_options=build_options)
         res = resolve_dependencies([deepcopy(easyconfig_dep)])
         # dependency should be found, order should be correct
@@ -188,7 +199,7 @@ def test_resolve_dependencies(self):
             'hidden': False,
         }]
         ecs = [deepcopy(easyconfig_dep)]
-        build_options.update({'robot_path': self.base_easyconfig_dir})
+        build_options.update({'robot_path': base_easyconfig_dir})
         init_config(build_options=build_options)
         res = resolve_dependencies([deepcopy(easyconfig_dep)])
 
@@ -288,10 +299,6 @@ def test_resolve_dependencies(self):
         self.assertEqual('goolf/1.4.10', res[2]['full_mod_name'])
         self.assertEqual('foo/1.2.3', res[3]['full_mod_name'])
 
-    def tearDown(self):
-        """ reset the Modules back to its original """
-        super(RobotTest, self).tearDown()
-
         config.modules_tool = ORIG_MODULES_TOOL
         ectools.modules_tool = ORIG_ECTOOLS_MODULES_TOOL
         robot.modules_tool = ORIG_ROBOT_MODULES_TOOL
@@ -301,6 +308,103 @@ def tearDown(self):
             if 'module' in os.environ:
                 del os.environ['module']
 
+    def test_det_easyconfig_paths(self):
+        """Test det_easyconfig_paths function (without --from-pr)."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+
+        test_ec = 'toy-0.0-deps.eb'
+        shutil.copy2(os.path.join(test_ecs_path, test_ec), self.test_prefix)
+        shutil.copy2(os.path.join(test_ecs_path, 'ictce-4.1.13.eb'), self.test_prefix)
+        self.assertFalse(os.path.exists(test_ec))
+
+        args = [
+            os.path.join(test_ecs_path, 'toy-0.0.eb'),
+            test_ec,  # relative path, should be resolved via robot search path
+            # PR for foss/2015a, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1239/files
+            #'--from-pr=1239',
+            '--dry-run',
+            '--debug',
+            '--robot',
+            '--robot-paths=%s' % self.test_prefix,  # override $EASYBUILD_ROBOT_PATHS
+            '--unittest-file=%s' % self.logfile,
+            '--github-user=%s' % GITHUB_TEST_ACCOUNT,  # a GitHub token should be available for this user
+            '--tmpdir=%s' % self.test_prefix,
+        ]
+        outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True)
+
+        modules = [
+            (test_ecs_path, 'toy/0.0'),  # specified easyconfigs, available at given location
+            (self.test_prefix, 'ictce/4.1.13'),  # dependency, found in robot search path
+            (self.test_prefix, 'toy/0.0-deps'),  # specified easyconfig, found in robot search path
+        ]
+        for path_prefix, module in modules:
+            ec_fn = "%s.eb" % '-'.join(module.split('/'))
+            regex = re.compile(r"^ \* \[.\] %s.*%s \(module: %s\)$" % (path_prefix, ec_fn, module), re.M)
+            self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
+
+    def test_det_easyconfig_paths_from_pr(self):
+        """Test det_easyconfig_paths function, with --from-pr enabled as well."""
+        if self.github_token is None:
+            print "Skipping test_from_pr, no GitHub token available?"
+            return
+
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+
+        test_ec = 'toy-0.0-deps.eb'
+        shutil.copy2(os.path.join(test_ecs_path, test_ec), self.test_prefix)
+        shutil.copy2(os.path.join(test_ecs_path, 'ictce-4.1.13.eb'), self.test_prefix)
+        self.assertFalse(os.path.exists(test_ec))
+
+        gompi_2015a_txt = '\n'.join([
+            "easyblock = 'Toolchain'",
+            "name = 'gompi'",
+            "version = '2015a'",
+            "versionsuffix = '-test'",
+            "homepage = 'foo'",
+            "description = 'bar'",
+            "toolchain = {'name': 'dummy', 'version': 'dummy'}",
+        ])
+        write_file(os.path.join(self.test_prefix, 'gompi-2015a-test.eb'), gompi_2015a_txt)
+        # put gompi-2015a.eb easyconfig in place that shouldn't be considered (paths via --from-pr have precedence)
+        write_file(os.path.join(self.test_prefix, 'gompi-2015a.eb'), gompi_2015a_txt)
+
+        args = [
+            os.path.join(test_ecs_path, 'toy-0.0.eb'),
+            test_ec,  # relative path, should be resolved via robot search path
+            # PR for foss/2015a, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1239/files
+            '--from-pr=1239',
+            'FFTW-3.3.4-gompi-2015a.eb',
+            'gompi-2015a-test.eb',  # relative path, available in robot search path
+            '--dry-run',
+            '--robot',
+            '--robot=%s' % self.test_prefix,
+            '--unittest-file=%s' % self.logfile,
+            '--github-user=%s' % GITHUB_TEST_ACCOUNT,  # a GitHub token should be available for this user
+            '--tmpdir=%s' % self.test_prefix,
+        ]
+        outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True)
+
+        from_pr_prefix = os.path.join(self.test_prefix, '.*', 'files_pr1239')
+        modules = [
+            (test_ecs_path, 'toy/0.0'),  # specified easyconfigs, available at given location
+            (self.test_prefix, 'ictce/4.1.13'),  # dependency, found in robot search path
+            (self.test_prefix, 'toy/0.0-deps'),  # specified easyconfig, found in robot search path
+            (self.test_prefix, 'gompi/2015a-test'),  # specified easyconfig, found in robot search path
+            (from_pr_prefix, 'FFTW/3.3.4-gompi-2015a'),  # part of PR easyconfigs
+            (from_pr_prefix, 'gompi/2015a'),  # part of PR easyconfigs
+            (test_ecs_path, 'GCC/4.9.2'),  # dependency for PR easyconfigs, found in robot search path
+        ]
+        for path_prefix, module in modules:
+            ec_fn = "%s.eb" % '-'.join(module.split('/'))
+            regex = re.compile(r"^ \* \[.\] %s.*%s \(module: %s\)$" % (path_prefix, ec_fn, module), re.M)
+            self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
+
 
 def suite():
     """ returns all the testcases in this module """

From 6429586595e1769015e304cf59d7dec2b4f9691f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Mar 2015 15:58:13 +0100
Subject: [PATCH 0692/1356] fix broken test due to changed behaviour

---
 test/framework/options.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index ae2273a1d1..dc02cc8e24 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -882,7 +882,7 @@ def test_from_pr_listed_ecs(self):
             '--from-pr=1239',
             '--dry-run',
             # an argument must be specified to --robot, since easybuild-easyconfigs may not be installed
-            '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+            '--robot=%s' % test_ecs_path,
             '--unittest-file=%s' % self.logfile,
             '--github-user=%s' % GITHUB_TEST_ACCOUNT,  # a GitHub token should be available for this user
             '--tmpdir=%s' % tmpdir,
@@ -890,13 +890,13 @@ def test_from_pr_listed_ecs(self):
         try:
             outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True)
             modules = [
-                (ecstmpdir, 'toy/0.0'),
-                ('.*', 'GCC/4.9.2'),  # not included in PR
+                (test_ecs_path, 'toy/0.0'),  # not included in PR
+                (test_ecs_path, 'GCC/4.9.2'),  # not included in PR
                 (tmpdir, 'hwloc/1.10.0-GCC-4.9.2'),
                 (tmpdir, 'numactl/2.0.10-GCC-4.9.2'),
                 (tmpdir, 'OpenMPI/1.8.4-GCC-4.9.2'),
                 (tmpdir, 'gompi/2015a'),
-                ('.*', 'GCC/4.6.3'),
+                (test_ecs_path, 'GCC/4.6.3'),  # not included in PR
             ]
             for path_prefix, module in modules:
                 ec_fn = "%s.eb" % '-'.join(module.split('/'))

From 25ec16d175528fe528caa3a7de0f4489f30a7584 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Mar 2015 16:54:49 +0100
Subject: [PATCH 0693/1356] drop 'eb-' in prefix for tmpdir for files created
 in mpi_cmd_for

---
 easybuild/tools/toolchain/mpi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index dc0fd5d461..21e034b6a7 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -197,7 +197,7 @@ def mpi_cmd_for(self, cmd, nr_ranks):
                 self.log.warning("$I_MPI_MPD_TMPDIR should be (very) short to avoid problems: %s" % mpd_tmpdir)
 
             # temporary location for mpdboot and nodes files
-            tmpdir = tempfile.mkdtemp(prefix='eb-mpi_cmd_for-')
+            tmpdir = tempfile.mkdtemp(prefix='mpi_cmd_for-')
 
             # set PBS_ENVIRONMENT, so that --file option for mpdboot isn't stripped away
             env.setvar('PBS_ENVIRONMENT', "PBS_BATCH_MPI")

From 5cb9bc868f3d906738e386b3b478a6d1bf06647b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Mar 2015 17:05:40 +0100
Subject: [PATCH 0694/1356] fix broken tests due to changed prefix for tmpdir

---
 test/framework/config.py    |  8 ++++----
 test/framework/options.py   | 14 +++++++-------
 test/framework/toy_build.py |  4 ++--
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index 36de96ad16..49ff090b88 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -257,13 +257,13 @@ def test_set_tmpdir(self):
             mytmpdir = set_tmpdir(tmpdir=tmpdir)
 
             for var in ['TMPDIR', 'TEMP', 'TMP']:
-                self.assertTrue(os.environ[var].startswith(os.path.join(parent, 'easybuild-')))
+                self.assertTrue(os.environ[var].startswith(os.path.join(parent, 'eb-')))
                 self.assertEqual(os.environ[var], mytmpdir)
-            self.assertTrue(tempfile.gettempdir().startswith(os.path.join(parent, 'easybuild-')))
+            self.assertTrue(tempfile.gettempdir().startswith(os.path.join(parent, 'eb-')))
             tempfile_tmpdir = tempfile.mkdtemp()
-            self.assertTrue(tempfile_tmpdir.startswith(os.path.join(parent, 'easybuild-')))
+            self.assertTrue(tempfile_tmpdir.startswith(os.path.join(parent, 'eb-')))
             fd, tempfile_tmpfile = tempfile.mkstemp()
-            self.assertTrue(tempfile_tmpfile.startswith(os.path.join(parent, 'easybuild-')))
+            self.assertTrue(tempfile_tmpfile.startswith(os.path.join(parent, 'eb-')))
 
             # tmp_logdir follows tmpdir
             self.assertEqual(get_build_log_path(), mytmpdir)
diff --git a/test/framework/options.py b/test/framework/options.py
index ae2273a1d1..0a6c7c91f2 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -848,7 +848,7 @@ def test_from_pr(self):
             regex = re.compile(r"^ \* \[.\] .*/(?P<filepath>.*) \(module: (?P<module>.*)\)$", re.M)
             self.assertTrue(sorted(regex.findall(outtxt)), sorted(modules))
 
-            pr_tmpdir = os.path.join(tmpdir, 'easybuild-\S{6}', 'files_pr1239')
+            pr_tmpdir = os.path.join(tmpdir, 'eb-\S{6}', 'files_pr1239')
             regex = re.compile("Prepended list of robot search paths with %s:" % pr_tmpdir, re.M)
             self.assertTrue(regex.search(outtxt), "Found pattern %s in %s" % (regex.pattern, outtxt))
         except URLError, err:
@@ -1009,17 +1009,17 @@ def test_tmpdir(self):
         ]
         outtxt = self.eb_main(args, do_build=True)
 
-        tmpdir_msg = r"Using %s\S+ as temporary directory" % os.path.join(tmpdir, 'easybuild-')
+        tmpdir_msg = r"Using %s\S+ as temporary directory" % os.path.join(tmpdir, 'eb-')
         found = re.search(tmpdir_msg, outtxt, re.M)
         self.assertTrue(found, "Log message for tmpdir found in outtxt: %s" % outtxt)
 
         for var in ['TMPDIR', 'TEMP', 'TMP']:
-            self.assertTrue(os.environ[var].startswith(os.path.join(tmpdir, 'easybuild-')))
-        self.assertTrue(tempfile.gettempdir().startswith(os.path.join(tmpdir, 'easybuild-')))
+            self.assertTrue(os.environ[var].startswith(os.path.join(tmpdir, 'eb-')))
+        self.assertTrue(tempfile.gettempdir().startswith(os.path.join(tmpdir, 'eb-')))
         tempfile_tmpdir = tempfile.mkdtemp()
-        self.assertTrue(tempfile_tmpdir.startswith(os.path.join(tmpdir, 'easybuild-')))
+        self.assertTrue(tempfile_tmpdir.startswith(os.path.join(tmpdir, 'eb-')))
         fd, tempfile_tmpfile = tempfile.mkstemp()
-        self.assertTrue(tempfile_tmpfile.startswith(os.path.join(tmpdir, 'easybuild-')))
+        self.assertTrue(tempfile_tmpfile.startswith(os.path.join(tmpdir, 'eb-')))
 
         # cleanup
         os.close(fd)
@@ -1303,7 +1303,7 @@ def test_recursive_try(self):
                     mod = ec_name.replace('-', '/')
                 else:
                     mod = '%s-gompi-1.4.10' % ec_name.replace('-', '/')
-                mod_regex = re.compile("^ \* \[ \] \S+/easybuild-\S+/%s \(module: .*%s\)$" % (ec, mod), re.M)
+                mod_regex = re.compile("^ \* \[ \] \S+/eb-\S+/%s \(module: .*%s\)$" % (ec, mod), re.M)
                 #mod_regex = re.compile("%s \(module: .*%s\)$" % (ec, mod), re.M)
                 self.assertTrue(mod_regex.search(outtxt), "Pattern %s found in %s" % (mod_regex.pattern, outtxt))
 
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 5d0aef6add..28166d722d 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -180,11 +180,11 @@ def test_toy_broken(self):
                               verify=False, fails=True, verbose=False, raise_error=True)
 
         # make sure log file is retained, also for failed build
-        log_path_pattern = os.path.join(tmpdir, 'easybuild-*', 'easybuild-toy-0.0*.log')
+        log_path_pattern = os.path.join(tmpdir, 'eb-*', 'easybuild-toy-0.0*.log')
         self.assertTrue(len(glob.glob(log_path_pattern)) == 1, "Log file found at %s" % log_path_pattern)
 
         # make sure individual test report is retained, also for failed build
-        test_report_fp_pattern = os.path.join(tmpdir, 'easybuild-*', 'easybuild-toy-0.0*test_report.md')
+        test_report_fp_pattern = os.path.join(tmpdir, 'eb-*', 'easybuild-toy-0.0*test_report.md')
         self.assertTrue(len(glob.glob(test_report_fp_pattern)) == 1, "Test report %s found" % test_report_fp_pattern)
 
         # test dumping full test report (doesn't raise an exception)

From 8143a01b7a4bbc652d14e455dafa957a459f6aa0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Mar 2015 21:13:36 +0100
Subject: [PATCH 0695/1356] update copyright line in headers to 2015

---
 easybuild/__init__.py                                      | 2 +-
 easybuild/framework/__init__.py                            | 2 +-
 easybuild/framework/easyblock.py                           | 2 +-
 easybuild/framework/easyconfig/__init__.py                 | 2 +-
 easybuild/framework/easyconfig/constants.py                | 2 +-
 easybuild/framework/easyconfig/default.py                  | 2 +-
 easybuild/framework/easyconfig/easyconfig.py               | 2 +-
 easybuild/framework/easyconfig/format/__init__.py          | 2 +-
 easybuild/framework/easyconfig/format/convert.py           | 2 +-
 easybuild/framework/easyconfig/format/format.py            | 2 +-
 easybuild/framework/easyconfig/format/one.py               | 2 +-
 easybuild/framework/easyconfig/format/pyheaderconfigobj.py | 2 +-
 easybuild/framework/easyconfig/format/two.py               | 2 +-
 easybuild/framework/easyconfig/format/version.py           | 2 +-
 easybuild/framework/easyconfig/licenses.py                 | 2 +-
 easybuild/framework/easyconfig/parser.py                   | 2 +-
 easybuild/framework/easyconfig/templates.py                | 2 +-
 easybuild/framework/easyconfig/tools.py                    | 2 +-
 easybuild/framework/easyconfig/tweak.py                    | 2 +-
 easybuild/framework/extension.py                           | 2 +-
 easybuild/framework/extensioneasyblock.py                  | 2 +-
 easybuild/main.py                                          | 2 +-
 easybuild/scripts/add_header.py                            | 2 +-
 easybuild/scripts/bootstrap_eb.py                          | 2 +-
 easybuild/scripts/generate_software_list.py                | 2 +-
 easybuild/scripts/mk_tmpl_easyblock_for.py                 | 2 +-
 easybuild/scripts/port_easyblock.py                        | 2 +-
 easybuild/scripts/prep_for_release.py                      | 2 +-
 easybuild/scripts/repo_setup.py                            | 2 +-
 easybuild/toolchains/__init__.py                           | 2 +-
 easybuild/toolchains/cgmpich.py                            | 2 +-
 easybuild/toolchains/cgmpolf.py                            | 2 +-
 easybuild/toolchains/cgmvapich2.py                         | 2 +-
 easybuild/toolchains/cgmvolf.py                            | 2 +-
 easybuild/toolchains/cgompi.py                             | 2 +-
 easybuild/toolchains/cgoolf.py                             | 2 +-
 easybuild/toolchains/clanggcc.py                           | 2 +-
 easybuild/toolchains/compiler/__init__.py                  | 2 +-
 easybuild/toolchains/compiler/clang.py                     | 2 +-
 easybuild/toolchains/compiler/cuda.py                      | 2 +-
 easybuild/toolchains/compiler/dummycompiler.py             | 2 +-
 easybuild/toolchains/compiler/gcc.py                       | 2 +-
 easybuild/toolchains/compiler/inteliccifort.py             | 2 +-
 easybuild/toolchains/dummy.py                              | 2 +-
 easybuild/toolchains/fft/__init__.py                       | 2 +-
 easybuild/toolchains/fft/fftw.py                           | 2 +-
 easybuild/toolchains/fft/intelfftw.py                      | 2 +-
 easybuild/toolchains/foss.py                               | 2 +-
 easybuild/toolchains/gcc.py                                | 2 +-
 easybuild/toolchains/gcccuda.py                            | 2 +-
 easybuild/toolchains/gimkl.py                              | 2 +-
 easybuild/toolchains/gimpi.py                              | 2 +-
 easybuild/toolchains/gmacml.py                             | 2 +-
 easybuild/toolchains/gmpich.py                             | 2 +-
 easybuild/toolchains/gmpich2.py                            | 2 +-
 easybuild/toolchains/gmpolf.py                             | 2 +-
 easybuild/toolchains/gmvapich2.py                          | 2 +-
 easybuild/toolchains/gmvolf.py                             | 2 +-
 easybuild/toolchains/goalf.py                              | 2 +-
 easybuild/toolchains/gompi.py                              | 2 +-
 easybuild/toolchains/gompic.py                             | 2 +-
 easybuild/toolchains/goolf.py                              | 2 +-
 easybuild/toolchains/goolfc.py                             | 2 +-
 easybuild/toolchains/gpsmpi.py                             | 2 +-
 easybuild/toolchains/gpsolf.py                             | 2 +-
 easybuild/toolchains/gqacml.py                             | 2 +-
 easybuild/toolchains/iccifort.py                           | 2 +-
 easybuild/toolchains/ictce.py                              | 2 +-
 easybuild/toolchains/iimpi.py                              | 2 +-
 easybuild/toolchains/iiqmpi.py                             | 2 +-
 easybuild/toolchains/impich.py                             | 2 +-
 easybuild/toolchains/impmkl.py                             | 2 +-
 easybuild/toolchains/intel-para.py                         | 2 +-
 easybuild/toolchains/intel.py                              | 2 +-
 easybuild/toolchains/iomkl.py                              | 2 +-
 easybuild/toolchains/iompi.py                              | 2 +-
 easybuild/toolchains/ipsmpi.py                             | 2 +-
 easybuild/toolchains/iqacml.py                             | 2 +-
 easybuild/toolchains/ismkl.py                              | 2 +-
 easybuild/toolchains/linalg/__init__.py                    | 2 +-
 easybuild/toolchains/linalg/acml.py                        | 2 +-
 easybuild/toolchains/linalg/atlas.py                       | 2 +-
 easybuild/toolchains/linalg/blacs.py                       | 2 +-
 easybuild/toolchains/linalg/flame.py                       | 2 +-
 easybuild/toolchains/linalg/gotoblas.py                    | 2 +-
 easybuild/toolchains/linalg/intelmkl.py                    | 2 +-
 easybuild/toolchains/linalg/lapack.py                      | 2 +-
 easybuild/toolchains/linalg/openblas.py                    | 2 +-
 easybuild/toolchains/linalg/scalapack.py                   | 2 +-
 easybuild/toolchains/mpi/__init__.py                       | 2 +-
 easybuild/toolchains/mpi/intelmpi.py                       | 2 +-
 easybuild/toolchains/mpi/mpich.py                          | 2 +-
 easybuild/toolchains/mpi/mpich2.py                         | 2 +-
 easybuild/toolchains/mpi/mvapich2.py                       | 2 +-
 easybuild/toolchains/mpi/openmpi.py                        | 2 +-
 easybuild/toolchains/mpi/qlogicmpi.py                      | 2 +-
 easybuild/tools/__init__.py                                | 2 +-
 easybuild/tools/asyncprocess.py                            | 2 +-
 easybuild/tools/build_details.py                           | 2 +-
 easybuild/tools/build_log.py                               | 2 +-
 easybuild/tools/config.py                                  | 2 +-
 easybuild/tools/convert.py                                 | 2 +-
 easybuild/tools/deprecated/__init__.py                     | 2 +-
 easybuild/tools/docs.py                                    | 2 +-
 easybuild/tools/environment.py                             | 2 +-
 easybuild/tools/filetools.py                               | 2 +-
 easybuild/tools/github.py                                  | 2 +-
 easybuild/tools/jenkins.py                                 | 2 +-
 easybuild/tools/module_generator.py                        | 2 +-
 easybuild/tools/module_naming_scheme/__init__.py           | 2 +-
 easybuild/tools/module_naming_scheme/easybuild_mns.py      | 2 +-
 easybuild/tools/module_naming_scheme/hierarchical_mns.py   | 2 +-
 easybuild/tools/module_naming_scheme/mns.py                | 2 +-
 easybuild/tools/module_naming_scheme/toolchain.py          | 2 +-
 easybuild/tools/module_naming_scheme/utilities.py          | 2 +-
 easybuild/tools/modules.py                                 | 2 +-
 easybuild/tools/parallelbuild.py                           | 2 +-
 easybuild/tools/pbs_job.py                                 | 2 +-
 easybuild/tools/repository/__init__.py                     | 2 +-
 easybuild/tools/repository/filerepo.py                     | 2 +-
 easybuild/tools/repository/gitrepo.py                      | 2 +-
 easybuild/tools/repository/repository.py                   | 2 +-
 easybuild/tools/repository/svnrepo.py                      | 2 +-
 easybuild/tools/robot.py                                   | 2 +-
 easybuild/tools/run.py                                     | 2 +-
 easybuild/tools/systemtools.py                             | 2 +-
 easybuild/tools/testing.py                                 | 2 +-
 easybuild/tools/toolchain/__init__.py                      | 2 +-
 easybuild/tools/toolchain/compiler.py                      | 2 +-
 easybuild/tools/toolchain/constants.py                     | 2 +-
 easybuild/tools/toolchain/fft.py                           | 2 +-
 easybuild/tools/toolchain/linalg.py                        | 2 +-
 easybuild/tools/toolchain/mpi.py                           | 2 +-
 easybuild/tools/toolchain/options.py                       | 2 +-
 easybuild/tools/toolchain/toolchain.py                     | 2 +-
 easybuild/tools/toolchain/toolchainvariables.py            | 2 +-
 easybuild/tools/toolchain/utilities.py                     | 2 +-
 easybuild/tools/toolchain/variables.py                     | 2 +-
 easybuild/tools/utilities.py                               | 2 +-
 easybuild/tools/variables.py                               | 2 +-
 easybuild/tools/version.py                                 | 2 +-
 141 files changed, 141 insertions(+), 141 deletions(-)

diff --git a/easybuild/__init__.py b/easybuild/__init__.py
index 2b217b34bc..6bdfdf13a4 100644
--- a/easybuild/__init__.py
+++ b/easybuild/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2014 Ghent University
+# Copyright 2011-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/__init__.py b/easybuild/framework/__init__.py
index 20b1669d93..bd67a8111f 100644
--- a/easybuild/framework/__init__.py
+++ b/easybuild/framework/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 008857c8ac..1f403bfacc 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/__init__.py b/easybuild/framework/easyconfig/__init__.py
index 24e58f0208..906b4eb0d3 100644
--- a/easybuild/framework/easyconfig/__init__.py
+++ b/easybuild/framework/easyconfig/__init__.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/constants.py b/easybuild/framework/easyconfig/constants.py
index 7183c0c9fb..5cdb3168b4 100644
--- a/easybuild/framework/easyconfig/constants.py
+++ b/easybuild/framework/easyconfig/constants.py
@@ -1,5 +1,5 @@
 #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 0d33bd8388..feb1bdd5e9 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 99a94ddb8c..b0a98bcd61 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/format/__init__.py b/easybuild/framework/easyconfig/format/__init__.py
index d9929739b2..0daff8a9cc 100644
--- a/easybuild/framework/easyconfig/format/__init__.py
+++ b/easybuild/framework/easyconfig/format/__init__.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/format/convert.py b/easybuild/framework/easyconfig/format/convert.py
index 4f03522275..df3259a871 100644
--- a/easybuild/framework/easyconfig/format/convert.py
+++ b/easybuild/framework/easyconfig/format/convert.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2014-2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/format/format.py b/easybuild/framework/easyconfig/format/format.py
index 7fb06cc2f9..d13386386f 100644
--- a/easybuild/framework/easyconfig/format/format.py
+++ b/easybuild/framework/easyconfig/format/format.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index a4cc036826..7a613ad0dc 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index 026392824a..901efc4966 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/format/two.py b/easybuild/framework/easyconfig/format/two.py
index ea48707c99..62be586bc4 100644
--- a/easybuild/framework/easyconfig/format/two.py
+++ b/easybuild/framework/easyconfig/format/two.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/format/version.py b/easybuild/framework/easyconfig/format/version.py
index cb9efe28ce..e04e228afe 100644
--- a/easybuild/framework/easyconfig/format/version.py
+++ b/easybuild/framework/easyconfig/format/version.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/licenses.py b/easybuild/framework/easyconfig/licenses.py
index ce49c3d5dc..7485cfd549 100644
--- a/easybuild/framework/easyconfig/licenses.py
+++ b/easybuild/framework/easyconfig/licenses.py
@@ -1,5 +1,5 @@
 #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 3b4c5ce318..f47e550403 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/templates.py b/easybuild/framework/easyconfig/templates.py
index 57b973aca2..21762fecf5 100644
--- a/easybuild/framework/easyconfig/templates.py
+++ b/easybuild/framework/easyconfig/templates.py
@@ -1,5 +1,5 @@
 #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index c9e55290e8..f5440ed2b4 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 010a411699..dd14805b85 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/extension.py b/easybuild/framework/extension.py
index a50781e9b3..ee240db57c 100644
--- a/easybuild/framework/extension.py
+++ b/easybuild/framework/extension.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/framework/extensioneasyblock.py b/easybuild/framework/extensioneasyblock.py
index a7a5ba6488..691b283d70 100644
--- a/easybuild/framework/extensioneasyblock.py
+++ b/easybuild/framework/extensioneasyblock.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of the University of Ghent (http://ugent.be/hpc).
diff --git a/easybuild/main.py b/easybuild/main.py
index bba788bf85..c110727529 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/scripts/add_header.py b/easybuild/scripts/add_header.py
index a7d48f6214..090350e297 100644
--- a/easybuild/scripts/add_header.py
+++ b/easybuild/scripts/add_header.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC-UGent team.
diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 9cfb05c6c6..149739eb3d 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/scripts/generate_software_list.py b/easybuild/scripts/generate_software_list.py
index 94018d05d6..f7957e2334 100644
--- a/easybuild/scripts/generate_software_list.py
+++ b/easybuild/scripts/generate_software_list.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of the University of Ghent (http://ugent.be/hpc).
diff --git a/easybuild/scripts/mk_tmpl_easyblock_for.py b/easybuild/scripts/mk_tmpl_easyblock_for.py
index 0d57f13f35..e3b1b3e220 100755
--- a/easybuild/scripts/mk_tmpl_easyblock_for.py
+++ b/easybuild/scripts/mk_tmpl_easyblock_for.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/scripts/port_easyblock.py b/easybuild/scripts/port_easyblock.py
index 7fbe90a2d9..515e29edcc 100644
--- a/easybuild/scripts/port_easyblock.py
+++ b/easybuild/scripts/port_easyblock.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/scripts/prep_for_release.py b/easybuild/scripts/prep_for_release.py
index ffc4045807..60b7651e60 100644
--- a/easybuild/scripts/prep_for_release.py
+++ b/easybuild/scripts/prep_for_release.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/scripts/repo_setup.py b/easybuild/scripts/repo_setup.py
index 23686cdd73..2cf4686821 100644
--- a/easybuild/scripts/repo_setup.py
+++ b/easybuild/scripts/repo_setup.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/__init__.py b/easybuild/toolchains/__init__.py
index 9c05df7c2b..b0a226866d 100644
--- a/easybuild/toolchains/__init__.py
+++ b/easybuild/toolchains/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/cgmpich.py b/easybuild/toolchains/cgmpich.py
index af3a4e9dbf..dd7f96b3aa 100644
--- a/easybuild/toolchains/cgmpich.py
+++ b/easybuild/toolchains/cgmpich.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/cgmpolf.py b/easybuild/toolchains/cgmpolf.py
index 86668d28bd..fa6a958ab7 100644
--- a/easybuild/toolchains/cgmpolf.py
+++ b/easybuild/toolchains/cgmpolf.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/cgmvapich2.py b/easybuild/toolchains/cgmvapich2.py
index 61a764c40e..3ef8902633 100644
--- a/easybuild/toolchains/cgmvapich2.py
+++ b/easybuild/toolchains/cgmvapich2.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/cgmvolf.py b/easybuild/toolchains/cgmvolf.py
index 682853b2be..dcfc7740f2 100644
--- a/easybuild/toolchains/cgmvolf.py
+++ b/easybuild/toolchains/cgmvolf.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/cgompi.py b/easybuild/toolchains/cgompi.py
index b39c6a0c23..c988a62db3 100644
--- a/easybuild/toolchains/cgompi.py
+++ b/easybuild/toolchains/cgompi.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/cgoolf.py b/easybuild/toolchains/cgoolf.py
index a02cbb7b94..abc073c41b 100644
--- a/easybuild/toolchains/cgoolf.py
+++ b/easybuild/toolchains/cgoolf.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/clanggcc.py b/easybuild/toolchains/clanggcc.py
index 17208be047..1fe2beb801 100644
--- a/easybuild/toolchains/clanggcc.py
+++ b/easybuild/toolchains/clanggcc.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/compiler/__init__.py b/easybuild/toolchains/compiler/__init__.py
index 79d806fe7e..95a05537f5 100644
--- a/easybuild/toolchains/compiler/__init__.py
+++ b/easybuild/toolchains/compiler/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/compiler/clang.py b/easybuild/toolchains/compiler/clang.py
index d5b676bde1..bd5590e463 100644
--- a/easybuild/toolchains/compiler/clang.py
+++ b/easybuild/toolchains/compiler/clang.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/compiler/cuda.py b/easybuild/toolchains/compiler/cuda.py
index 7304b8b1f2..9397a9a584 100644
--- a/easybuild/toolchains/compiler/cuda.py
+++ b/easybuild/toolchains/compiler/cuda.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/compiler/dummycompiler.py b/easybuild/toolchains/compiler/dummycompiler.py
index f99b687c49..9296ac85d5 100644
--- a/easybuild/toolchains/compiler/dummycompiler.py
+++ b/easybuild/toolchains/compiler/dummycompiler.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py
index 3ec1888438..9146f8c773 100644
--- a/easybuild/toolchains/compiler/gcc.py
+++ b/easybuild/toolchains/compiler/gcc.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index 3804343c6d..8aa6fd89c5 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/dummy.py b/easybuild/toolchains/dummy.py
index c7791744fe..c641b89952 100644
--- a/easybuild/toolchains/dummy.py
+++ b/easybuild/toolchains/dummy.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/fft/__init__.py b/easybuild/toolchains/fft/__init__.py
index 8490061d53..0e74f343d7 100644
--- a/easybuild/toolchains/fft/__init__.py
+++ b/easybuild/toolchains/fft/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/fft/fftw.py b/easybuild/toolchains/fft/fftw.py
index 1d36693733..9b901e7e16 100644
--- a/easybuild/toolchains/fft/fftw.py
+++ b/easybuild/toolchains/fft/fftw.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index a6eb1e1eaa..ee56497367 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/foss.py b/easybuild/toolchains/foss.py
index d67dd5267c..1a8b7c69c4 100755
--- a/easybuild/toolchains/foss.py
+++ b/easybuild/toolchains/foss.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gcc.py b/easybuild/toolchains/gcc.py
index 749dd7cd9c..60115094d7 100644
--- a/easybuild/toolchains/gcc.py
+++ b/easybuild/toolchains/gcc.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gcccuda.py b/easybuild/toolchains/gcccuda.py
index 9bd72024bb..c76c53d200 100644
--- a/easybuild/toolchains/gcccuda.py
+++ b/easybuild/toolchains/gcccuda.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gimkl.py b/easybuild/toolchains/gimkl.py
index 894eda83af..a9ae8db870 100644
--- a/easybuild/toolchains/gimkl.py
+++ b/easybuild/toolchains/gimkl.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gimpi.py b/easybuild/toolchains/gimpi.py
index 0ac2345266..fb525d962b 100644
--- a/easybuild/toolchains/gimpi.py
+++ b/easybuild/toolchains/gimpi.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gmacml.py b/easybuild/toolchains/gmacml.py
index b76b3e3838..d64d715c90 100644
--- a/easybuild/toolchains/gmacml.py
+++ b/easybuild/toolchains/gmacml.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gmpich.py b/easybuild/toolchains/gmpich.py
index 4527db29f2..8640dc68ca 100644
--- a/easybuild/toolchains/gmpich.py
+++ b/easybuild/toolchains/gmpich.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gmpich2.py b/easybuild/toolchains/gmpich2.py
index caf6e0af5b..b70848a354 100644
--- a/easybuild/toolchains/gmpich2.py
+++ b/easybuild/toolchains/gmpich2.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gmpolf.py b/easybuild/toolchains/gmpolf.py
index 35a0d0b899..e849650be2 100644
--- a/easybuild/toolchains/gmpolf.py
+++ b/easybuild/toolchains/gmpolf.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/gmvapich2.py b/easybuild/toolchains/gmvapich2.py
index 03c4b94366..438d209d07 100644
--- a/easybuild/toolchains/gmvapich2.py
+++ b/easybuild/toolchains/gmvapich2.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gmvolf.py b/easybuild/toolchains/gmvolf.py
index 9e8d9ee34d..90ba0e39e1 100644
--- a/easybuild/toolchains/gmvolf.py
+++ b/easybuild/toolchains/gmvolf.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/goalf.py b/easybuild/toolchains/goalf.py
index 8c71ee927b..28a087887b 100644
--- a/easybuild/toolchains/goalf.py
+++ b/easybuild/toolchains/goalf.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gompi.py b/easybuild/toolchains/gompi.py
index 18698f9cd7..cbea82b54c 100644
--- a/easybuild/toolchains/gompi.py
+++ b/easybuild/toolchains/gompi.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gompic.py b/easybuild/toolchains/gompic.py
index 0a331d5daf..984ea26272 100644
--- a/easybuild/toolchains/gompic.py
+++ b/easybuild/toolchains/gompic.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/goolf.py b/easybuild/toolchains/goolf.py
index 2970099d71..6b51b34e66 100644
--- a/easybuild/toolchains/goolf.py
+++ b/easybuild/toolchains/goolf.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/goolfc.py b/easybuild/toolchains/goolfc.py
index 96e2f49574..184272a6f0 100644
--- a/easybuild/toolchains/goolfc.py
+++ b/easybuild/toolchains/goolfc.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gpsmpi.py b/easybuild/toolchains/gpsmpi.py
index b1dc8e0ab5..0109d0b389 100644
--- a/easybuild/toolchains/gpsmpi.py
+++ b/easybuild/toolchains/gpsmpi.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/gpsolf.py b/easybuild/toolchains/gpsolf.py
index f454620df8..592556f148 100644
--- a/easybuild/toolchains/gpsolf.py
+++ b/easybuild/toolchains/gpsolf.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
diff --git a/easybuild/toolchains/gqacml.py b/easybuild/toolchains/gqacml.py
index 9731a5bfc7..f7426a9055 100644
--- a/easybuild/toolchains/gqacml.py
+++ b/easybuild/toolchains/gqacml.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/iccifort.py b/easybuild/toolchains/iccifort.py
index 748fc8b4b1..4c688d4eb5 100644
--- a/easybuild/toolchains/iccifort.py
+++ b/easybuild/toolchains/iccifort.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/ictce.py b/easybuild/toolchains/ictce.py
index 9cf59a1eaf..468741937d 100644
--- a/easybuild/toolchains/ictce.py
+++ b/easybuild/toolchains/ictce.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/iimpi.py b/easybuild/toolchains/iimpi.py
index 781223ca34..ef5dddeafe 100644
--- a/easybuild/toolchains/iimpi.py
+++ b/easybuild/toolchains/iimpi.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/iiqmpi.py b/easybuild/toolchains/iiqmpi.py
index 58141a9471..4ef089d181 100644
--- a/easybuild/toolchains/iiqmpi.py
+++ b/easybuild/toolchains/iiqmpi.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/impich.py b/easybuild/toolchains/impich.py
index efe9c513a2..f837f77325 100644
--- a/easybuild/toolchains/impich.py
+++ b/easybuild/toolchains/impich.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/impmkl.py b/easybuild/toolchains/impmkl.py
index 383753d1db..7c8f3eaad2 100644
--- a/easybuild/toolchains/impmkl.py
+++ b/easybuild/toolchains/impmkl.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/intel-para.py b/easybuild/toolchains/intel-para.py
index 35e23da99a..31e12d638b 100644
--- a/easybuild/toolchains/intel-para.py
+++ b/easybuild/toolchains/intel-para.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2013 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/intel.py b/easybuild/toolchains/intel.py
index 25a88b6100..02c2bd6618 100644
--- a/easybuild/toolchains/intel.py
+++ b/easybuild/toolchains/intel.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2013 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/iomkl.py b/easybuild/toolchains/iomkl.py
index 57f41d7e35..a13fb71cea 100644
--- a/easybuild/toolchains/iomkl.py
+++ b/easybuild/toolchains/iomkl.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/iompi.py b/easybuild/toolchains/iompi.py
index fd757a3c92..b64cc8e759 100644
--- a/easybuild/toolchains/iompi.py
+++ b/easybuild/toolchains/iompi.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/ipsmpi.py b/easybuild/toolchains/ipsmpi.py
index 8b99018284..de8b8806a1 100644
--- a/easybuild/toolchains/ipsmpi.py
+++ b/easybuild/toolchains/ipsmpi.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/iqacml.py b/easybuild/toolchains/iqacml.py
index dc6505112a..9529746985 100644
--- a/easybuild/toolchains/iqacml.py
+++ b/easybuild/toolchains/iqacml.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/ismkl.py b/easybuild/toolchains/ismkl.py
index de3c965a46..41afc4a4f9 100644
--- a/easybuild/toolchains/ismkl.py
+++ b/easybuild/toolchains/ismkl.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/__init__.py b/easybuild/toolchains/linalg/__init__.py
index 9fdd109ac1..26041ec702 100644
--- a/easybuild/toolchains/linalg/__init__.py
+++ b/easybuild/toolchains/linalg/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index 62c18c0ef7..eb32da15f7 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/atlas.py b/easybuild/toolchains/linalg/atlas.py
index 33313b4ae6..f1320600ac 100644
--- a/easybuild/toolchains/linalg/atlas.py
+++ b/easybuild/toolchains/linalg/atlas.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/blacs.py b/easybuild/toolchains/linalg/blacs.py
index 9bdebdf2e8..e7e708e392 100644
--- a/easybuild/toolchains/linalg/blacs.py
+++ b/easybuild/toolchains/linalg/blacs.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/flame.py b/easybuild/toolchains/linalg/flame.py
index e48848649e..e276e67327 100644
--- a/easybuild/toolchains/linalg/flame.py
+++ b/easybuild/toolchains/linalg/flame.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/gotoblas.py b/easybuild/toolchains/linalg/gotoblas.py
index 48719dcf73..c196d2fe5b 100644
--- a/easybuild/toolchains/linalg/gotoblas.py
+++ b/easybuild/toolchains/linalg/gotoblas.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index af8cca4739..00aa18f44b 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/lapack.py b/easybuild/toolchains/linalg/lapack.py
index d8933bb158..0a95b9f456 100644
--- a/easybuild/toolchains/linalg/lapack.py
+++ b/easybuild/toolchains/linalg/lapack.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/openblas.py b/easybuild/toolchains/linalg/openblas.py
index 798c63e7ac..1d1c6d4790 100644
--- a/easybuild/toolchains/linalg/openblas.py
+++ b/easybuild/toolchains/linalg/openblas.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/linalg/scalapack.py b/easybuild/toolchains/linalg/scalapack.py
index b3859346c2..eea44b1b45 100644
--- a/easybuild/toolchains/linalg/scalapack.py
+++ b/easybuild/toolchains/linalg/scalapack.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/mpi/__init__.py b/easybuild/toolchains/mpi/__init__.py
index 3f868dff91..e67a5cb97e 100644
--- a/easybuild/toolchains/mpi/__init__.py
+++ b/easybuild/toolchains/mpi/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/mpi/intelmpi.py b/easybuild/toolchains/mpi/intelmpi.py
index f2bb79a926..a8fb512964 100644
--- a/easybuild/toolchains/mpi/intelmpi.py
+++ b/easybuild/toolchains/mpi/intelmpi.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/mpi/mpich.py b/easybuild/toolchains/mpi/mpich.py
index 8c61e8fdf7..b173148137 100644
--- a/easybuild/toolchains/mpi/mpich.py
+++ b/easybuild/toolchains/mpi/mpich.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/mpi/mpich2.py b/easybuild/toolchains/mpi/mpich2.py
index 21dc78de60..d68b7917d9 100644
--- a/easybuild/toolchains/mpi/mpich2.py
+++ b/easybuild/toolchains/mpi/mpich2.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/mpi/mvapich2.py b/easybuild/toolchains/mpi/mvapich2.py
index b9cbf3561a..000be188a1 100644
--- a/easybuild/toolchains/mpi/mvapich2.py
+++ b/easybuild/toolchains/mpi/mvapich2.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/mpi/openmpi.py b/easybuild/toolchains/mpi/openmpi.py
index 12e1a9ade0..8a2137e0f1 100644
--- a/easybuild/toolchains/mpi/openmpi.py
+++ b/easybuild/toolchains/mpi/openmpi.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/toolchains/mpi/qlogicmpi.py b/easybuild/toolchains/mpi/qlogicmpi.py
index 9118550664..2a7db39666 100644
--- a/easybuild/toolchains/mpi/qlogicmpi.py
+++ b/easybuild/toolchains/mpi/qlogicmpi.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/__init__.py b/easybuild/tools/__init__.py
index 15512e2f9c..6badf9fb34 100644
--- a/easybuild/tools/__init__.py
+++ b/easybuild/tools/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/asyncprocess.py b/easybuild/tools/asyncprocess.py
index 797478f70a..58e83de980 100644
--- a/easybuild/tools/asyncprocess.py
+++ b/easybuild/tools/asyncprocess.py
@@ -1,6 +1,6 @@
 ##
 # Copyright 2005 Josiah Carlson
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # The Asynchronous Python Subprocess recipe was originally created by Josiah Carlson.
 # and released under the GPL v2 on March 14, 2012
diff --git a/easybuild/tools/build_details.py b/easybuild/tools/build_details.py
index 44475ec9e8..4b6df10d39 100644
--- a/easybuild/tools/build_details.py
+++ b/easybuild/tools/build_details.py
@@ -1,4 +1,4 @@
-# Copyright 2014-2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index 1472e00e5e..2c3bbc9a1b 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 10a0aaccae..054b109d26 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/convert.py b/easybuild/tools/convert.py
index b9b845bfe3..16a3189417 100644
--- a/easybuild/tools/convert.py
+++ b/easybuild/tools/convert.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2014-2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/deprecated/__init__.py b/easybuild/tools/deprecated/__init__.py
index 8c26fd6795..379c01f066 100644
--- a/easybuild/tools/deprecated/__init__.py
+++ b/easybuild/tools/deprecated/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index c8033be791..628d6d5b2f 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/environment.py b/easybuild/tools/environment.py
index 384c65febd..45b5b2bc44 100644
--- a/easybuild/tools/environment.py
+++ b/easybuild/tools/environment.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 67623e8169..49b05f1191 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 1ff47d1555..c87ee21aa1 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/jenkins.py b/easybuild/tools/jenkins.py
index 625984f0b5..fb9ed78fec 100644
--- a/easybuild/tools/jenkins.py
+++ b/easybuild/tools/jenkins.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index ee8046caba..5488329789 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/module_naming_scheme/__init__.py b/easybuild/tools/module_naming_scheme/__init__.py
index 964cf582aa..084cf7f165 100644
--- a/easybuild/tools/module_naming_scheme/__init__.py
+++ b/easybuild/tools/module_naming_scheme/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2014 Ghent University
+# Copyright 2011-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/module_naming_scheme/easybuild_mns.py b/easybuild/tools/module_naming_scheme/easybuild_mns.py
index 864002431f..801ac6b4d5 100644
--- a/easybuild/tools/module_naming_scheme/easybuild_mns.py
+++ b/easybuild/tools/module_naming_scheme/easybuild_mns.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index 587397ae21..c0f303ad4f 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/module_naming_scheme/mns.py b/easybuild/tools/module_naming_scheme/mns.py
index ce6de596c1..99bd1f1222 100644
--- a/easybuild/tools/module_naming_scheme/mns.py
+++ b/easybuild/tools/module_naming_scheme/mns.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2014 Ghent University
+# Copyright 2011-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/module_naming_scheme/toolchain.py b/easybuild/tools/module_naming_scheme/toolchain.py
index d835fcf2a9..a4f1b419c8 100644
--- a/easybuild/tools/module_naming_scheme/toolchain.py
+++ b/easybuild/tools/module_naming_scheme/toolchain.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/module_naming_scheme/utilities.py b/easybuild/tools/module_naming_scheme/utilities.py
index 8bd5053231..da3711ad00 100644
--- a/easybuild/tools/module_naming_scheme/utilities.py
+++ b/easybuild/tools/module_naming_scheme/utilities.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index b1e99c92fe..d70bffa424 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 18bca84e48..136ac83d31 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/pbs_job.py b/easybuild/tools/pbs_job.py
index 55774cd474..d8eac9e928 100644
--- a/easybuild/tools/pbs_job.py
+++ b/easybuild/tools/pbs_job.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/repository/__init__.py b/easybuild/tools/repository/__init__.py
index 25f9cc1ca8..ebdc3c10b6 100644
--- a/easybuild/tools/repository/__init__.py
+++ b/easybuild/tools/repository/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2014 Ghent University
+# Copyright 2011-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/repository/filerepo.py b/easybuild/tools/repository/filerepo.py
index 4c1a58fe17..4cd314c08e 100644
--- a/easybuild/tools/repository/filerepo.py
+++ b/easybuild/tools/repository/filerepo.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/repository/gitrepo.py b/easybuild/tools/repository/gitrepo.py
index ab6a5f07ca..c70d12efba 100644
--- a/easybuild/tools/repository/gitrepo.py
+++ b/easybuild/tools/repository/gitrepo.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/repository/repository.py b/easybuild/tools/repository/repository.py
index a8dca02326..cc588f4191 100644
--- a/easybuild/tools/repository/repository.py
+++ b/easybuild/tools/repository/repository.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/repository/svnrepo.py b/easybuild/tools/repository/svnrepo.py
index 31f38abdc9..65394deb91 100644
--- a/easybuild/tools/repository/svnrepo.py
+++ b/easybuild/tools/repository/svnrepo.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index 99a3f6b9fa..22fc8f3c37 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index ba13928464..5309db63af 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 921c8e926e..f8e6950df5 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2014 Ghent University
+# Copyright 2011-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index 8bebbf3612..113ec2e747 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/__init__.py b/easybuild/tools/toolchain/__init__.py
index fb2a99459a..4c2abb3e18 100644
--- a/easybuild/tools/toolchain/__init__.py
+++ b/easybuild/tools/toolchain/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/compiler.py b/easybuild/tools/toolchain/compiler.py
index fda05be513..06d0860aae 100644
--- a/easybuild/tools/toolchain/compiler.py
+++ b/easybuild/tools/toolchain/compiler.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/constants.py b/easybuild/tools/toolchain/constants.py
index ddf0f9f4c5..7c9cbf30d1 100644
--- a/easybuild/tools/toolchain/constants.py
+++ b/easybuild/tools/toolchain/constants.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/fft.py b/easybuild/tools/toolchain/fft.py
index 192e418d06..f665e35f40 100644
--- a/easybuild/tools/toolchain/fft.py
+++ b/easybuild/tools/toolchain/fft.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/linalg.py b/easybuild/tools/toolchain/linalg.py
index 7086b0de4c..e5d9b18607 100644
--- a/easybuild/tools/toolchain/linalg.py
+++ b/easybuild/tools/toolchain/linalg.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index 21e034b6a7..64038d9849 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/options.py b/easybuild/tools/toolchain/options.py
index 9b0a5faaa8..f9835b7777 100644
--- a/easybuild/tools/toolchain/options.py
+++ b/easybuild/tools/toolchain/options.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 6b9924858e..5a5e1d4530 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/toolchainvariables.py b/easybuild/tools/toolchain/toolchainvariables.py
index 0c94c8874c..a9c4682152 100644
--- a/easybuild/tools/toolchain/toolchainvariables.py
+++ b/easybuild/tools/toolchain/toolchainvariables.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/utilities.py b/easybuild/tools/toolchain/utilities.py
index 633e10accb..a1ab08074b 100644
--- a/easybuild/tools/toolchain/utilities.py
+++ b/easybuild/tools/toolchain/utilities.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/variables.py b/easybuild/tools/toolchain/variables.py
index b9fb56d00e..7b2722e7bf 100644
--- a/easybuild/tools/toolchain/variables.py
+++ b/easybuild/tools/toolchain/variables.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 096766e127..fb3ac98fe0 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/variables.py b/easybuild/tools/variables.py
index bee298f6ce..7b686a8cf4 100644
--- a/easybuild/tools/variables.py
+++ b/easybuild/tools/variables.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 1bd1419af5..ca8d3e139a 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

From 57c9e387289f0d7406a56cb73767cbdb002bea5e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 4 Mar 2015 21:15:36 +0100
Subject: [PATCH 0696/1356] update copyright line in test headers to 2015

---
 test/__init__.py                                                | 2 +-
 test/framework/__init__.py                                      | 2 +-
 test/framework/asyncprocess.py                                  | 2 +-
 test/framework/config.py                                        | 2 +-
 test/framework/easyblock.py                                     | 2 +-
 test/framework/easyconfig.py                                    | 2 +-
 test/framework/easyconfigformat.py                              | 2 +-
 test/framework/easyconfigparser.py                              | 2 +-
 test/framework/easyconfigversion.py                             | 2 +-
 test/framework/ebconfigobj.py                                   | 2 +-
 test/framework/filetools.py                                     | 2 +-
 test/framework/format_convert.py                                | 2 +-
 test/framework/github.py                                        | 2 +-
 test/framework/license.py                                       | 2 +-
 test/framework/module_generator.py                              | 2 +-
 test/framework/modules.py                                       | 2 +-
 test/framework/modulestool.py                                   | 2 +-
 test/framework/options.py                                       | 2 +-
 test/framework/repository.py                                    | 2 +-
 test/framework/robot.py                                         | 2 +-
 test/framework/run.py                                           | 2 +-
 test/framework/sandbox/easybuild/easyblocks/foo.py              | 2 +-
 test/framework/sandbox/easybuild/easyblocks/foofoo.py           | 2 +-
 test/framework/sandbox/easybuild/easyblocks/generic/bar.py      | 2 +-
 .../sandbox/easybuild/easyblocks/generic/configuremake.py       | 2 +-
 .../sandbox/easybuild/easyblocks/generic/dummyextension.py      | 2 +-
 .../framework/sandbox/easybuild/easyblocks/generic/toolchain.py | 2 +-
 .../sandbox/easybuild/easyblocks/generic/toy_extension.py       | 2 +-
 test/framework/sandbox/easybuild/easyblocks/hpl.py              | 2 +-
 test/framework/sandbox/easybuild/easyblocks/scalapack.py        | 2 +-
 test/framework/sandbox/easybuild/easyblocks/toy.py              | 2 +-
 test/framework/sandbox/easybuild/easyblocks/toy_buggy.py        | 2 +-
 test/framework/sandbox/easybuild/tools/__init__.py              | 2 +-
 .../sandbox/easybuild/tools/module_naming_scheme/__init__.py    | 2 +-
 .../tools/module_naming_scheme/test_module_naming_scheme.py     | 2 +-
 .../module_naming_scheme/test_module_naming_scheme_more.py      | 2 +-
 test/framework/suite.py                                         | 2 +-
 test/framework/systemtools.py                                   | 2 +-
 test/framework/toolchain.py                                     | 2 +-
 test/framework/toolchainvariables.py                            | 2 +-
 test/framework/toy_build.py                                     | 2 +-
 test/framework/utilities.py                                     | 2 +-
 test/framework/variables.py                                     | 2 +-
 43 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/test/__init__.py b/test/__init__.py
index 9459a6d90a..8df00ef461 100644
--- a/test/__init__.py
+++ b/test/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/__init__.py b/test/framework/__init__.py
index f7e235f8d2..d6e0a952fc 100644
--- a/test/framework/__init__.py
+++ b/test/framework/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/asyncprocess.py b/test/framework/asyncprocess.py
index c70b4b1dd4..d8637fecf5 100644
--- a/test/framework/asyncprocess.py
+++ b/test/framework/asyncprocess.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/config.py b/test/framework/config.py
index 49ff090b88..c0959b40e2 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 890cc86f28..72081983bb 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index e82d768112..45e14c8f27 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/easyconfigformat.py b/test/framework/easyconfigformat.py
index 393cd3c4f4..e52175461e 100644
--- a/test/framework/easyconfigformat.py
+++ b/test/framework/easyconfigformat.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/easyconfigparser.py b/test/framework/easyconfigparser.py
index 5d0d4c5959..e163c9f0e0 100644
--- a/test/framework/easyconfigparser.py
+++ b/test/framework/easyconfigparser.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/easyconfigversion.py b/test/framework/easyconfigversion.py
index 21411c7be2..a7331b4d45 100644
--- a/test/framework/easyconfigversion.py
+++ b/test/framework/easyconfigversion.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2014-2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/ebconfigobj.py b/test/framework/ebconfigobj.py
index 667d1ba7b0..cad6b30e73 100644
--- a/test/framework/ebconfigobj.py
+++ b/test/framework/ebconfigobj.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2014-2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 1ad8fdcfe1..4c6d476ef8 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/format_convert.py b/test/framework/format_convert.py
index 84c5c0f067..a9ae19f51e 100644
--- a/test/framework/format_convert.py
+++ b/test/framework/format_convert.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2014-2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/github.py b/test/framework/github.py
index fb6cdbecb2..819b1d9a6e 100644
--- a/test/framework/github.py
+++ b/test/framework/github.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/license.py b/test/framework/license.py
index 55c389a3db..026b0a722a 100644
--- a/test/framework/license.py
+++ b/test/framework/license.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 4f8c3c7c74..180580297b 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/modules.py b/test/framework/modules.py
index e098f30a42..af492ec78f 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index 333ef8fd1f..f6ca56b8a8 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2014-2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/options.py b/test/framework/options.py
index 9dae532db1..0f381055a0 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/repository.py b/test/framework/repository.py
index 08ee4ac151..405a7125b8 100644
--- a/test/framework/repository.py
+++ b/test/framework/repository.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/robot.py b/test/framework/robot.py
index e5e166f65d..5898160f9c 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/run.py b/test/framework/run.py
index ba8cb3c491..48b33efcdd 100644
--- a/test/framework/run.py
+++ b/test/framework/run.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/foo.py b/test/framework/sandbox/easybuild/easyblocks/foo.py
index 769f2a7e5a..8f1145fe72 100644
--- a/test/framework/sandbox/easybuild/easyblocks/foo.py
+++ b/test/framework/sandbox/easybuild/easyblocks/foo.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/foofoo.py b/test/framework/sandbox/easybuild/easyblocks/foofoo.py
index 511953a0fe..94ec86ef89 100644
--- a/test/framework/sandbox/easybuild/easyblocks/foofoo.py
+++ b/test/framework/sandbox/easybuild/easyblocks/foofoo.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/bar.py b/test/framework/sandbox/easybuild/easyblocks/generic/bar.py
index 2dcc4c5c01..6d62238e39 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/bar.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/bar.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/configuremake.py b/test/framework/sandbox/easybuild/easyblocks/generic/configuremake.py
index 8304b9e42c..7fba52ca5b 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/configuremake.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/configuremake.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py b/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py
index 8024520f32..59d96675e1 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/dummyextension.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py b/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py
index 7ba202cbdc..f8212fdf96 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/toolchain.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/generic/toy_extension.py b/test/framework/sandbox/easybuild/easyblocks/generic/toy_extension.py
index b6e15d6347..f41a63c580 100644
--- a/test/framework/sandbox/easybuild/easyblocks/generic/toy_extension.py
+++ b/test/framework/sandbox/easybuild/easyblocks/generic/toy_extension.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/hpl.py b/test/framework/sandbox/easybuild/easyblocks/hpl.py
index 1ef029f6c1..ba6bfe42f7 100644
--- a/test/framework/sandbox/easybuild/easyblocks/hpl.py
+++ b/test/framework/sandbox/easybuild/easyblocks/hpl.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/scalapack.py b/test/framework/sandbox/easybuild/easyblocks/scalapack.py
index 4534a5cd10..3ed062e7d0 100644
--- a/test/framework/sandbox/easybuild/easyblocks/scalapack.py
+++ b/test/framework/sandbox/easybuild/easyblocks/scalapack.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/toy.py b/test/framework/sandbox/easybuild/easyblocks/toy.py
index b03b6d9959..49fcc4b1d4 100644
--- a/test/framework/sandbox/easybuild/easyblocks/toy.py
+++ b/test/framework/sandbox/easybuild/easyblocks/toy.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/easyblocks/toy_buggy.py b/test/framework/sandbox/easybuild/easyblocks/toy_buggy.py
index 07658b64fd..74df658f3d 100644
--- a/test/framework/sandbox/easybuild/easyblocks/toy_buggy.py
+++ b/test/framework/sandbox/easybuild/easyblocks/toy_buggy.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/tools/__init__.py b/test/framework/sandbox/easybuild/tools/__init__.py
index 15512e2f9c..6badf9fb34 100644
--- a/test/framework/sandbox/easybuild/tools/__init__.py
+++ b/test/framework/sandbox/easybuild/tools/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2014 Ghent University
+# Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/tools/module_naming_scheme/__init__.py b/test/framework/sandbox/easybuild/tools/module_naming_scheme/__init__.py
index 1a66de17e0..5a2060c2d0 100644
--- a/test/framework/sandbox/easybuild/tools/module_naming_scheme/__init__.py
+++ b/test/framework/sandbox/easybuild/tools/module_naming_scheme/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2011-2014 Ghent University
+# Copyright 2011-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py
index 1fa5865941..ccd03960ca 100644
--- a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py
+++ b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py
index 8e8d74e0c8..b8b95a9dda 100644
--- a/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py
+++ b/test/framework/sandbox/easybuild/tools/module_naming_scheme/test_module_naming_scheme_more.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/suite.py b/test/framework/suite.py
index f854208879..abe486da15 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -1,6 +1,6 @@
 #!/usr/bin/python
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index c33319e96a..0bda1e2e2c 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 01b6ce5769..217b60977e 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/toolchainvariables.py b/test/framework/toolchainvariables.py
index 9d7b996b33..5a9f8c369e 100644
--- a/test/framework/toolchainvariables.py
+++ b/test/framework/toolchainvariables.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 28166d722d..abecae9f89 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2013-2014 Ghent University
+# Copyright 2013-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 5754c71760..4ddbc3bf34 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/test/framework/variables.py b/test/framework/variables.py
index 8d337173ad..9f92769275 100644
--- a/test/framework/variables.py
+++ b/test/framework/variables.py
@@ -1,5 +1,5 @@
 # #
-# Copyright 2012-2014 Ghent University
+# Copyright 2012-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

From c7d6df6e786f70a1a076670d5cac936ed53b37d2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 5 Mar 2015 16:08:55 +0100
Subject: [PATCH 0697/1356] remove fetch_parameter_from_easyconfig_file rather
 than deprecating it, since it's internal to the EasyBuild framework

---
 easybuild/framework/easyconfig/easyconfig.py | 12 ------------
 test/framework/easyconfig.py                 |  7 +------
 2 files changed, 1 insertion(+), 18 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index b0a98bcd61..7aac218a73 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -692,18 +692,6 @@ def det_installversion(version, toolchain_name, toolchain_version, prefix, suffi
     _log.nosupport('Use det_full_ec_version from easybuild.tools.module_generator instead of %s' % old_fn, '2.0')
 
 
-def fetch_parameter_from_easyconfig_file(path, param):
-    """
-    Fetch parameter specification from given easyconfig file.
-    DEPRECATED: use fetch_parameters_from_easyconfig from easybuild.framework.easyconfigs.parser instead
-    """
-    old = 'fetch_parameter_from_easyconfig_file'
-    new = 'fetch_parameters_from_easyconfig'
-    _log.deprecated("%s is replaced by %s from easybuild.framework.easyconfig.parser" % (old, new), '3.0')
-    ectxt = read_file(path)
-    return fetch_parameters_from_easyconfig(ectxt, [param])[0]
-
-
 def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_failed_import=True):
     """
     Get class for a particular easyblock (or use default)
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 45e14c8f27..f0f6b76937 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -44,7 +44,7 @@
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.framework.easyconfig.easyconfig import create_paths
-from easybuild.framework.easyconfig.easyconfig import fetch_parameter_from_easyconfig_file, get_easyblock_class
+from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak_one
 from easybuild.tools.build_log import EasyBuildError
@@ -874,11 +874,6 @@ def test_fetch_parameters_from_easyconfig(self):
 
         self.assertEqual(fetch_parameters_from_easyconfig(read_file(toy_ec_file), ['description'])[0], "Toy C program.")
 
-        # also check deprecated function fetch_parameter_from_easyconfig_file
-        os.environ['EASYBUILD_DEPRECATED'] = '2.0'
-        init_config()
-        self.assertEqual(fetch_parameter_from_easyconfig_file(toy_ec_file, 'description'), "Toy C program.")
-
     def test_get_easyblock_class(self):
         """Test get_easyblock_class function."""
         from easybuild.easyblocks.generic.configuremake import ConfigureMake

From f405eec92b21a34f690424e7f1ea5ce53df7b937 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 5 Mar 2015 16:52:44 +0100
Subject: [PATCH 0698/1356] allow multiple arguments, fix --help, get rid of
 silly main() function

---
 easybuild/scripts/fix_broken_easyconfigs.py | 33 ++++++++++-----------
 1 file changed, 15 insertions(+), 18 deletions(-)

diff --git a/easybuild/scripts/fix_broken_easyconfigs.py b/easybuild/scripts/fix_broken_easyconfigs.py
index 2144eefbb6..0547411188 100755
--- a/easybuild/scripts/fix_broken_easyconfigs.py
+++ b/easybuild/scripts/fix_broken_easyconfigs.py
@@ -32,21 +32,18 @@
 import sys
 import tempfile
 from vsc.utils import fancylogger
-from vsc.utils.generaloption import simple_option
+from vsc.utils.generaloption import SimpleOption
 
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import init_build_options
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.framework.easyconfig.parser import REPLACED_PARAMETERS, fetch_parameters_from_easyconfig
 from easybuild.tools.filetools import find_easyconfigs, read_file, write_file
 
-from test.framework.utilities import init_config
 
-
-options = {
-    'backup': ("Backup up easyconfigs before modifying them", None, 'store_true', True, 'b'),
-}
-go = simple_option(options)
-log = go.log
+class FixBrokenEasyconfigsOption(SimpleOption):
+    """Custom option parser for this script."""
+    ALLOPTSMANDATORY = False
 
 
 def fix_broken_easyconfig(ectxt, easyblock_class):
@@ -112,8 +109,14 @@ def process_easyconfig_file(ec_file):
 
 # MAIN
 
-def main():
-    """Main script functionality."""
+try:
+    init_build_options()
+
+    options = {
+        'backup': ("Backup up easyconfigs before modifying them", None, 'store_true', True, 'b'),
+    }
+    go = FixBrokenEasyconfigsOption(options)
+    log = go.log
 
     fancylogger.logToScreen(enable=True, stdout=True)
     log.setLevel('INFO')
@@ -123,8 +126,6 @@ def main():
     except ImportError, err:
         log.error("easyblocks are not available in Python search path: %s" % err)
 
-    init_config(args=['--quiet'])
-
     for path in go.args:
         if not os.path.exists(path):
             log.error("Non-existing path %s specified" % path)
@@ -137,9 +138,5 @@ def main():
     for ec_file in ec_files:
         process_easyconfig_file(ec_file)
 
-
-if __name__ == '__main__':
-    try:
-        main()
-    except EasyBuildError, err:
-        sys.exit(1)
+except EasyBuildError, err:
+    sys.exit(1)

From dcd364055feb94113b8819300229f87ce69a88ca Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Mar 2015 15:44:07 +0100
Subject: [PATCH 0699/1356] last update to release notes

---
 RELEASE_NOTES | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 053701ffe7..a746954533 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -6,20 +6,23 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en
 v2.0.0 (March 2nd 2015)
 -----------------------
 
-(requires vsc-base v2.0.3 or more recent)
-
 feature + bugfix release
-- drop support for behaviour that was deprecated for EasyBuild version 2.0 (#1143)
-    - the provided fix_broken_easyconfigs.py script can be used to update easyconfig files suffering from this (#1151)
-    - FIXME: link to docs: No-longer-support-functionality.html + Usage-of-stand-alone-scripts.html#fix-broken-easyconfigs
-- stop including a crippled copy of vsc-base, include vsc-base as a proper dependency instead (#1160)
-    - FIXME: link to docs w.r.t. development setup
-    - FIXME: update requires dependencies to mention vsc-base
+- requires vsc-base v2.0.3 or more recent
+    - avoid deprecation warnings w.r.t. use of 'message' attribute (hpcugent/vsc-base#155)
+    - fix typo in log message rendering --ignoreconfigfiles unusable (hpcugent/vsc-base#158)
+- removed functionality that was deprecated for EasyBuild version 2.0 (#1143)
+    - see http://easybuild.readthedocs.org/en/latest/Removed-functionality.html
+    - the fix_broken_easyconfigs.py script can be used to update easyconfig files suffering from this (#1151, #1206, #1207)
+    - for more information about this script, see http://easybuild.readthedocs.org/en/latest/Useful-scripts.html#fix-broken-easyconfigs-py
+- stop including a crippled copy of vsc-base, include vsc-base as a proper dependency instead (#1160, #1194)
+    - vsc-base is automatically installed as a dependency for easybuild-framework, if a Python installation tool is used
+    - see http://easybuild.readthedocs.org/en/latest/Installation.html#required-python-packages
 - various other enhancements, including:
     - add support for Linux/POWER systems (#1044)
     - major cleanup in tools/systemtools.py + significantly enhanced tests (#1044)
     - add support for 'eb -a rst', list available easyconfig parameters in ReST format (#1131)
     - add support for specifying one or more easyconfigs in combination with --from-pr (#1132)
+        - see http://easybuild.readthedocs.org/en/latest/Integration_with_GitHub.html#using-easyconfigs-from-pull-requests-via-from-pr
     - define __contains__ in EasyConfig class (#1155)
     - restore support for downloading over a proxy (#1158)
         - i.e., use urllib2 rather than urllib
@@ -27,14 +30,17 @@ feature + bugfix release
     - let mpi_family return None if MPI is not supported by a toolchain (#1164)
     - include support for specifying system-level configuration files for EasyBuild via $XDG_CONFIG_DIRS (#1166)
         - see http://easybuild.readthedocs.org/en/latest/Configuration.html#default-configuration-files
-    - make unit tests more robust (#1167)
-        - FIXME link to docs on running unit tests
+    - make unit tests more robust (#1167, #1196)
+        - see http://easybuild.readthedocs.org/en/latest/Unit-tests.html
     - add hierarchical module naming scheme categorizing modules by 'moduleclass' (#1176)
     - enhance bootstrap script to allow bootstrapping using supplied tarballs (#1184)
         - see http://easybuild.readthedocs.org/en/latest/Installation.html#advanced-bootstrapping-options
     - disable updating of Lmod user cache by default, add configuration option --update-modules-tool-cache (#1185)
         - for now, only the Lmod user cache can be updated using --update-modules-tool-cache
     - use available which() function, rather than running 'which' via run_cmd (#1192)
+    - fix install-EasyBuild-develop.sh script w.r.t. vsc-base dependency (#1193)
+    - also consider robot search path when looking for specified easyconfigs (#1201)
+        - see http://easybuild.readthedocs.org/en/latest/Using_the_EasyBuild_command_line.html#specifying-easyconfigs
 - various bug fixes, including:
     - stop triggering deprecated/no longer support functionality in unit tests (#1126)
     - fix from_pr test by including dummy easyblocks for HPL and ScaLAPACK (#1133)
@@ -42,7 +48,7 @@ feature + bugfix release
     - fix handling specified patch level 0 (+ enhance tests for fetch_patches method) (#1139)
     - fix formatting issues in generated easyconfig file obtained via --try-X (#1144)
     - use log.error in tools/toolchain/toolchain.py where applicable (#1145)
-    - stop hardcoding /tmp in mpi_cmd_for function (#1146)
+    - stop hardcoding /tmp in mpi_cmd_for function (#1146, #1200)
     - correctly determine variable name for $EBEXTLIST when generating module file (#1156)
     - do not ignore exit code of failing postinstall commands (#1157)
     - fix rare case in which used easyconfig and copied easyconfig are the same (#1159)

From 6ed94f8ed537cc641bd912de3cca37c7936d67a5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Mar 2015 15:48:16 +0100
Subject: [PATCH 0700/1356] fix date in release notes for v2.0.0

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index a746954533..1f499303dc 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,7 +3,7 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-v2.0.0 (March 2nd 2015)
+v2.0.0 (March 6th 2015)
 -----------------------
 
 feature + bugfix release

From f9bdd1f844573104d2af97fc33fe697f646f11af Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Mar 2015 21:02:08 +0100
Subject: [PATCH 0701/1356] bump version to v1.16.2, update release notes

---
 RELEASE_NOTES              | 5 +++++
 easybuild/tools/version.py | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 13ef17e9cc..19c0795a11 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,6 +3,11 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
+v1.16.2 (March 6th 2015)
+------------------------
+
+(no changes compared to v1.16.2, simple version bump to stay in sync with easybuild-easyblocks)
+
 v1.16.1 (December 19th 2014)
 ----------------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 224892d87b..55ec19bde8 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("1.16.1")
+VERSION = LooseVersion("1.16.2")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From c3ac33eea51c8ae46e8f6466955ffc669c2af41d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Mar 2015 21:05:45 +0100
Subject: [PATCH 0702/1356] fix typo in v1.16.2 release notes

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 19c0795a11..914d939e64 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -6,7 +6,7 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en
 v1.16.2 (March 6th 2015)
 ------------------------
 
-(no changes compared to v1.16.2, simple version bump to stay in sync with easybuild-easyblocks)
+(no changes compared to v1.16.1, simple version bump to stay in sync with easybuild-easyblocks)
 
 v1.16.1 (December 19th 2014)
 ----------------------------

From 4fd96007819ca97b9796523ab28c58d18aeef9c1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Mar 2015 22:26:50 +0100
Subject: [PATCH 0703/1356] make bootstrap script robust against having
 'vsc-base' already available in Python search path

---
 easybuild/scripts/bootstrap_eb.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 149739eb3d..7be78ce457 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -447,8 +447,8 @@ def main():
     sys.path = []
     for path in orig_sys_path:
         include_path = True
-        # exclude path if it's potentially an EasyBuild package
-        if 'easybuild' in path:
+        # exclude path if it's potentially an EasyBuild package or vsc-base
+        if 'easybuild' in path or 'vsc-base' in path:
             include_path = False
         # exclude path if it contain an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):

From 103a730004ba64e7f52ce0c1179608923f37ed51 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Mar 2015 22:27:48 +0100
Subject: [PATCH 0704/1356] bump version to 2.1.0dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 7fdf6841d5..1a243e6bba 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("2.0.0")
+VERSION = LooseVersion("2.1.0dev")
 UNKNOWN = "UNKNOWN"
 
 def get_git_revision():

From 90017272c6cb9879a835473a1136c35a44730f57 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 09:00:54 +0100
Subject: [PATCH 0705/1356] check for 'easybuild' or 'vsc' subdirectories
 rather than substring in path to filter sys.path

---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 7be78ce457..214f0d9cb0 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -448,7 +448,7 @@ def main():
     for path in orig_sys_path:
         include_path = True
         # exclude path if it's potentially an EasyBuild package or vsc-base
-        if 'easybuild' in path or 'vsc-base' in path:
+        if os.path.exists(os.path.join(path, 'easybuild')) or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):

From ecd1d9259aa389b667b1f6c8c8f89465ebcb265c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 11:40:37 +0100
Subject: [PATCH 0706/1356] check both substring in path and subdirectory in
 path

---
 easybuild/scripts/bootstrap_eb.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 214f0d9cb0..1ac051a4f9 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -447,8 +447,10 @@ def main():
     sys.path = []
     for path in orig_sys_path:
         include_path = True
-        # exclude path if it's potentially an EasyBuild package or vsc-base
-        if os.path.exists(os.path.join(path, 'easybuild')) or os.path.exists(os.path.join(path, 'vsc')):
+        # exclude path if it's potentially an EasyBuild package
+        if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
+            include_path = False
+        if 'vsc_base' in path or os.path.exists(os.path.join(path, 'vsc', 'utils')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):

From 2c617c95a0aafce3058895433a8a47fcaf207d4d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 12:01:25 +0100
Subject: [PATCH 0707/1356] exclude *all* vsc pkgs from sys.path

---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 1ac051a4f9..ee2fad6f3b 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -450,7 +450,7 @@ def main():
         # exclude path if it's potentially an EasyBuild package
         if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
             include_path = False
-        if 'vsc_base' in path or os.path.exists(os.path.join(path, 'vsc', 'utils')):
+        if '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):

From 926b5d57e0ffac00c8783a76568272b3cd7c6b56 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 13:43:22 +0100
Subject: [PATCH 0708/1356] set $PYTHONNOUSERSITE to not add user site
 directory to sys.path

---
 easybuild/scripts/bootstrap_eb.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index ee2fad6f3b..d1c0a1b137 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -58,6 +58,9 @@
 # set print_debug to True for detailed progress info
 print_debug = os.environ.get('EASYBUILD_BOOTSTRAP_DEBUG', False)
 
+# don't add user site directory to sys.path (equivalent to python -s)
+os.environ['PYTHONNOUSERSITE'] = '1'
+
 # clean PYTHONPATH to avoid finding readily installed stuff
 os.environ['PYTHONPATH'] = ''
 

From 7b28caf83cd6d5c24a4a39f97d0a0293c2c0f137 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:01:31 +0100
Subject: [PATCH 0709/1356] inject path to distribute from stage0 in sys.path

---
 easybuild/scripts/bootstrap_eb.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index d1c0a1b137..75b9328e5b 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -369,6 +369,7 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
         # make sure we still have distribute in PYTHONPATH, so we have control over which 'setup' is used
         pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
         os.environ['PYTHONPATH'] = os.pathsep.join([distribute_egg_dir] + pythonpaths)
+        sys.path.insert(0, distribute_egg_dir)
 
     # create easyconfig file
     ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])

From a5fe60793f9f9a3f66b0eab832ecee28034d70ec Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:16:33 +0100
Subject: [PATCH 0710/1356] also exclude path for 'distribute' from sys.path

---
 easybuild/scripts/bootstrap_eb.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 75b9328e5b..52a103a997 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -454,10 +454,13 @@ def main():
         # exclude path if it's potentially an EasyBuild package
         if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
             include_path = False
-        if '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
+        elif '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
+            include_path = False
+        # exclude path if it provides 'distribute' package
+        elif 'distribute' in path or os.path.exists(os.path.join(path, 'distribute')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
-        if os.path.exists(os.path.join(path, 'easy-install.pth')):
+        elif os.path.exists(os.path.join(path, 'easy-install.pth')):
             include_path = False
 
         if include_path:

From 103ba0e8378b5e36c4f1d3b973048f457d347beb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:23:50 +0100
Subject: [PATCH 0711/1356] should be distutils, not distribute

---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 52a103a997..1b108d59ac 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -457,7 +457,7 @@ def main():
         elif '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it provides 'distribute' package
-        elif 'distribute' in path or os.path.exists(os.path.join(path, 'distribute')):
+        elif 'distutils' in path or os.path.exists(os.path.join(path, 'distutils')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         elif os.path.exists(os.path.join(path, 'easy-install.pth')):

From 3a1836d53de1e3a3ab40a2d4b7d4e5061afb35ea Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:41:38 +0100
Subject: [PATCH 0712/1356] Revert "should be distutils, not distribute"

This reverts commit 103ba0e8378b5e36c4f1d3b973048f457d347beb.
---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 1b108d59ac..52a103a997 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -457,7 +457,7 @@ def main():
         elif '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it provides 'distribute' package
-        elif 'distutils' in path or os.path.exists(os.path.join(path, 'distutils')):
+        elif 'distribute' in path or os.path.exists(os.path.join(path, 'distribute')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         elif os.path.exists(os.path.join(path, 'easy-install.pth')):

From afe53c13b5504eebd1836d51b0a1aedb9be25346 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:41:49 +0100
Subject: [PATCH 0713/1356] Revert "also exclude path for 'distribute' from
 sys.path"

This reverts commit a5fe60793f9f9a3f66b0eab832ecee28034d70ec.
---
 easybuild/scripts/bootstrap_eb.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 52a103a997..75b9328e5b 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -454,13 +454,10 @@ def main():
         # exclude path if it's potentially an EasyBuild package
         if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
             include_path = False
-        elif '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
-            include_path = False
-        # exclude path if it provides 'distribute' package
-        elif 'distribute' in path or os.path.exists(os.path.join(path, 'distribute')):
+        if '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
-        elif os.path.exists(os.path.join(path, 'easy-install.pth')):
+        if os.path.exists(os.path.join(path, 'easy-install.pth')):
             include_path = False
 
         if include_path:

From 1e1d64bab4a5ec60548073198340e690879fe3e4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:46:07 +0100
Subject: [PATCH 0714/1356] set site.ENABLE_USER_SITE to False

---
 easybuild/scripts/bootstrap_eb.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 75b9328e5b..d01746cb0b 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -46,6 +46,7 @@
 import os
 import re
 import shutil
+import site
 import sys
 import tempfile
 from distutils.version import LooseVersion
@@ -58,8 +59,9 @@
 # set print_debug to True for detailed progress info
 print_debug = os.environ.get('EASYBUILD_BOOTSTRAP_DEBUG', False)
 
-# don't add user site directory to sys.path (equivalent to python -s)
+# don't add user site directory to sys.path (equivalent to python -s), see https://www.python.org/dev/peps/pep-0370/
 os.environ['PYTHONNOUSERSITE'] = '1'
+site.ENABLE_USER_SITE = False
 
 # clean PYTHONPATH to avoid finding readily installed stuff
 os.environ['PYTHONPATH'] = ''

From 6505dbfa76f608a749f0140c604d7aee9fe3295f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 9 Mar 2015 11:54:08 +0100
Subject: [PATCH 0715/1356] drop useless sys.path.insert, add debug info for
 $PYTHONPATH in stage2

---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index d01746cb0b..9ffa7a2d8a 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -371,7 +371,7 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
         # make sure we still have distribute in PYTHONPATH, so we have control over which 'setup' is used
         pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
         os.environ['PYTHONPATH'] = os.pathsep.join([distribute_egg_dir] + pythonpaths)
-        sys.path.insert(0, distribute_egg_dir)
+    debug("stage 2 $PYTHONPATH: %s" % os.environ)
 
     # create easyconfig file
     ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])

From 27b8691d31354ec4576040b5546e976b66d4a4d0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 9 Mar 2015 12:53:16 +0100
Subject: [PATCH 0716/1356] include stage 1's distribute in $PYTHONPATH via
 preinstallopts

---
 easybuild/scripts/bootstrap_eb.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 9ffa7a2d8a..3d3f275ad1 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -367,11 +367,15 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
 
     info("\n\n+++ STAGE 2: installing EasyBuild in %s with EasyBuild from stage 1...\n\n" % install_path)
 
-    if distribute_egg_dir is not None:
-        # make sure we still have distribute in PYTHONPATH, so we have control over which 'setup' is used
-        pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
-        os.environ['PYTHONPATH'] = os.pathsep.join([distribute_egg_dir] + pythonpaths)
-    debug("stage 2 $PYTHONPATH: %s" % os.environ)
+    # inject path to distribute installed in stage 1 into $PYTHONPATH via preinstallopts
+    # other approaches are not reliable, since EasyBuildMeta easyblock unsets $PYTHONPATH
+    if distribute_egg_dir is None:
+        preinstallopts = ''
+    else:
+        preinstallopts = 'PYTHONPATH=%s:$PYTHONPATH' % distribute_egg_dir
+    templates.update({
+        'preinstallopts': preinstallopts,
+    })
 
     # create easyconfig file
     ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])
@@ -379,6 +383,7 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
     templates.update({
         'source_urls': '\n'.join(["'%s/%s/%s'," % (PYPI_SOURCE_URL, pkg[0], pkg) for pkg in EASYBUILD_PACKAGES]),
         'sources': "%(vsc-base)s%(easybuild-framework)s%(easybuild-easyblocks)s%(easybuild-easyconfigs)s" % templates,
+        'pythonpath': distribute_egg_dir,
     })
     f.write(EASYBUILD_EASYCONFIG_TEMPLATE % templates)
     f.close()
@@ -527,6 +532,8 @@ def main():
 # EasyBuild is a (set of) Python packages, so it depends on Python
 # usually, we want to use the system Python, so no actual Python dependency is listed
 allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+preinstallopts = '%(preinstallopts)s'
 """
 
 # distribute_setup.py script (https://pypi.python.org/pypi/distribute)

From 433bf016df6cb7fe0428ddbad1ec0d28a8cd447b Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Mon, 9 Mar 2015 14:09:29 +0100
Subject: [PATCH 0717/1356] Sort the results of a filesearch

---
 easybuild/tools/filetools.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 49b05f1191..34ad0f2810 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -367,6 +367,7 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
             dirnames[:] = [d for d in dirnames if not d in ignore_dirs]
 
         if hits:
+            hits.sort()
             common_prefix = det_common_path_prefix(hits)
             if short and common_prefix is not None and len(common_prefix) > len(var) * 2:
                 var_lines.append("%s=%s" % (var, common_prefix))

From 976cb63246931f01e791a439f81414c0bfae1ff5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Mar 2015 22:01:38 +0100
Subject: [PATCH 0718/1356] fix remark w.r.t. checking for EasyBuild/VSC pkgs
 to exclude from sys.path

---
 easybuild/scripts/bootstrap_eb.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 3d3f275ad1..a23a1279ef 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -458,12 +458,10 @@ def main():
     sys.path = []
     for path in orig_sys_path:
         include_path = True
-        # exclude path if it's potentially an EasyBuild package
-        if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
+        # exclude path if it's potentially an EasyBuild/VSC package, providing the 'easybuild'/'vsc' namespace, resp.
+        if any([os.path.exists(os.path.join(path, pkg, '__init__.py')) for pkg in ['easybuild', 'vsc']]):
             include_path = False
-        if '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
-            include_path = False
-        # exclude path if it contain an easy-install.pth file
+        # exclude any path that contains an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):
             include_path = False
 

From 3fe3254fccd58fb423c5e13228cfc3c94f8ddad6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 11 Mar 2015 07:58:25 +0100
Subject: [PATCH 0719/1356] also exclude all .egg entries in sys.path

---
 easybuild/scripts/bootstrap_eb.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index a23a1279ef..115f92121f 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -461,6 +461,9 @@ def main():
         # exclude path if it's potentially an EasyBuild/VSC package, providing the 'easybuild'/'vsc' namespace, resp.
         if any([os.path.exists(os.path.join(path, pkg, '__init__.py')) for pkg in ['easybuild', 'vsc']]):
             include_path = False
+        # exclude any .egg paths
+        if path.endswith('.egg'):
+            include_path = False
         # exclude any path that contains an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):
             include_path = False

From 45509a756fb4363cb70e72281ebab76d8799badf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 6 Mar 2015 22:26:50 +0100
Subject: [PATCH 0720/1356] make bootstrap script robust against having
 'vsc-base' already available in Python search path

---
 easybuild/scripts/bootstrap_eb.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 149739eb3d..7be78ce457 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -447,8 +447,8 @@ def main():
     sys.path = []
     for path in orig_sys_path:
         include_path = True
-        # exclude path if it's potentially an EasyBuild package
-        if 'easybuild' in path:
+        # exclude path if it's potentially an EasyBuild package or vsc-base
+        if 'easybuild' in path or 'vsc-base' in path:
             include_path = False
         # exclude path if it contain an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):

From 81e020ccf8f7384d65b923fce01a1dc0316522fe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 09:00:54 +0100
Subject: [PATCH 0721/1356] check for 'easybuild' or 'vsc' subdirectories
 rather than substring in path to filter sys.path

---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 7be78ce457..214f0d9cb0 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -448,7 +448,7 @@ def main():
     for path in orig_sys_path:
         include_path = True
         # exclude path if it's potentially an EasyBuild package or vsc-base
-        if 'easybuild' in path or 'vsc-base' in path:
+        if os.path.exists(os.path.join(path, 'easybuild')) or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):

From c295454e03868855146db2a5d1d8fe1f4a6a4624 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 11:40:37 +0100
Subject: [PATCH 0722/1356] check both substring in path and subdirectory in
 path

---
 easybuild/scripts/bootstrap_eb.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 214f0d9cb0..1ac051a4f9 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -447,8 +447,10 @@ def main():
     sys.path = []
     for path in orig_sys_path:
         include_path = True
-        # exclude path if it's potentially an EasyBuild package or vsc-base
-        if os.path.exists(os.path.join(path, 'easybuild')) or os.path.exists(os.path.join(path, 'vsc')):
+        # exclude path if it's potentially an EasyBuild package
+        if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
+            include_path = False
+        if 'vsc_base' in path or os.path.exists(os.path.join(path, 'vsc', 'utils')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):

From ed3c355c775598fc89c0814e343fe73445b0788d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 12:01:25 +0100
Subject: [PATCH 0723/1356] exclude *all* vsc pkgs from sys.path

---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 1ac051a4f9..ee2fad6f3b 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -450,7 +450,7 @@ def main():
         # exclude path if it's potentially an EasyBuild package
         if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
             include_path = False
-        if 'vsc_base' in path or os.path.exists(os.path.join(path, 'vsc', 'utils')):
+        if '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):

From 2038eb836801d30f3e5f40c5b1d9492218b0c5f1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 13:43:22 +0100
Subject: [PATCH 0724/1356] set $PYTHONNOUSERSITE to not add user site
 directory to sys.path

---
 easybuild/scripts/bootstrap_eb.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index ee2fad6f3b..d1c0a1b137 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -58,6 +58,9 @@
 # set print_debug to True for detailed progress info
 print_debug = os.environ.get('EASYBUILD_BOOTSTRAP_DEBUG', False)
 
+# don't add user site directory to sys.path (equivalent to python -s)
+os.environ['PYTHONNOUSERSITE'] = '1'
+
 # clean PYTHONPATH to avoid finding readily installed stuff
 os.environ['PYTHONPATH'] = ''
 

From 58bcd47c9baa7afba3f601279b81283e12d0f745 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:01:31 +0100
Subject: [PATCH 0725/1356] inject path to distribute from stage0 in sys.path

---
 easybuild/scripts/bootstrap_eb.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index d1c0a1b137..75b9328e5b 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -369,6 +369,7 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
         # make sure we still have distribute in PYTHONPATH, so we have control over which 'setup' is used
         pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
         os.environ['PYTHONPATH'] = os.pathsep.join([distribute_egg_dir] + pythonpaths)
+        sys.path.insert(0, distribute_egg_dir)
 
     # create easyconfig file
     ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])

From 8386c859698c02727c48ecdbce8f58b9033b4268 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:16:33 +0100
Subject: [PATCH 0726/1356] also exclude path for 'distribute' from sys.path

---
 easybuild/scripts/bootstrap_eb.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 75b9328e5b..52a103a997 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -454,10 +454,13 @@ def main():
         # exclude path if it's potentially an EasyBuild package
         if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
             include_path = False
-        if '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
+        elif '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
+            include_path = False
+        # exclude path if it provides 'distribute' package
+        elif 'distribute' in path or os.path.exists(os.path.join(path, 'distribute')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
-        if os.path.exists(os.path.join(path, 'easy-install.pth')):
+        elif os.path.exists(os.path.join(path, 'easy-install.pth')):
             include_path = False
 
         if include_path:

From 37de0fbe8c46b0126751f67e82d9a73eba12bd50 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:23:50 +0100
Subject: [PATCH 0727/1356] should be distutils, not distribute

---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 52a103a997..1b108d59ac 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -457,7 +457,7 @@ def main():
         elif '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it provides 'distribute' package
-        elif 'distribute' in path or os.path.exists(os.path.join(path, 'distribute')):
+        elif 'distutils' in path or os.path.exists(os.path.join(path, 'distutils')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         elif os.path.exists(os.path.join(path, 'easy-install.pth')):

From 2388120daef302d6bf71106ff243f191aed87c26 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:41:38 +0100
Subject: [PATCH 0728/1356] Revert "should be distutils, not distribute"

This reverts commit 103ba0e8378b5e36c4f1d3b973048f457d347beb.
---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 1b108d59ac..52a103a997 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -457,7 +457,7 @@ def main():
         elif '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it provides 'distribute' package
-        elif 'distutils' in path or os.path.exists(os.path.join(path, 'distutils')):
+        elif 'distribute' in path or os.path.exists(os.path.join(path, 'distribute')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
         elif os.path.exists(os.path.join(path, 'easy-install.pth')):

From c289bb8e06fea2d343043a03ef769c9722f38358 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:41:49 +0100
Subject: [PATCH 0729/1356] Revert "also exclude path for 'distribute' from
 sys.path"

This reverts commit a5fe60793f9f9a3f66b0eab832ecee28034d70ec.
---
 easybuild/scripts/bootstrap_eb.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 52a103a997..75b9328e5b 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -454,13 +454,10 @@ def main():
         # exclude path if it's potentially an EasyBuild package
         if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
             include_path = False
-        elif '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
-            include_path = False
-        # exclude path if it provides 'distribute' package
-        elif 'distribute' in path or os.path.exists(os.path.join(path, 'distribute')):
+        if '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
             include_path = False
         # exclude path if it contain an easy-install.pth file
-        elif os.path.exists(os.path.join(path, 'easy-install.pth')):
+        if os.path.exists(os.path.join(path, 'easy-install.pth')):
             include_path = False
 
         if include_path:

From 962ac853bdc0c3bab5b7dbb45a07028b4628c663 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 7 Mar 2015 14:46:07 +0100
Subject: [PATCH 0730/1356] set site.ENABLE_USER_SITE to False

---
 easybuild/scripts/bootstrap_eb.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 75b9328e5b..d01746cb0b 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -46,6 +46,7 @@
 import os
 import re
 import shutil
+import site
 import sys
 import tempfile
 from distutils.version import LooseVersion
@@ -58,8 +59,9 @@
 # set print_debug to True for detailed progress info
 print_debug = os.environ.get('EASYBUILD_BOOTSTRAP_DEBUG', False)
 
-# don't add user site directory to sys.path (equivalent to python -s)
+# don't add user site directory to sys.path (equivalent to python -s), see https://www.python.org/dev/peps/pep-0370/
 os.environ['PYTHONNOUSERSITE'] = '1'
+site.ENABLE_USER_SITE = False
 
 # clean PYTHONPATH to avoid finding readily installed stuff
 os.environ['PYTHONPATH'] = ''

From 211bfb0a8dcebdd7bdd20b4e2ed6d8c7ea7a4e4b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 9 Mar 2015 11:54:08 +0100
Subject: [PATCH 0731/1356] drop useless sys.path.insert, add debug info for
 $PYTHONPATH in stage2

---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index d01746cb0b..9ffa7a2d8a 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -371,7 +371,7 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
         # make sure we still have distribute in PYTHONPATH, so we have control over which 'setup' is used
         pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
         os.environ['PYTHONPATH'] = os.pathsep.join([distribute_egg_dir] + pythonpaths)
-        sys.path.insert(0, distribute_egg_dir)
+    debug("stage 2 $PYTHONPATH: %s" % os.environ)
 
     # create easyconfig file
     ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])

From 05895b1e699788fda666a1f4c5081166605b814f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 9 Mar 2015 12:53:16 +0100
Subject: [PATCH 0732/1356] include stage 1's distribute in $PYTHONPATH via
 preinstallopts

---
 easybuild/scripts/bootstrap_eb.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 9ffa7a2d8a..3d3f275ad1 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -367,11 +367,15 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
 
     info("\n\n+++ STAGE 2: installing EasyBuild in %s with EasyBuild from stage 1...\n\n" % install_path)
 
-    if distribute_egg_dir is not None:
-        # make sure we still have distribute in PYTHONPATH, so we have control over which 'setup' is used
-        pythonpaths = [x for x in os.environ.get('PYTHONPATH', '').split(os.pathsep) if len(x) > 0]
-        os.environ['PYTHONPATH'] = os.pathsep.join([distribute_egg_dir] + pythonpaths)
-    debug("stage 2 $PYTHONPATH: %s" % os.environ)
+    # inject path to distribute installed in stage 1 into $PYTHONPATH via preinstallopts
+    # other approaches are not reliable, since EasyBuildMeta easyblock unsets $PYTHONPATH
+    if distribute_egg_dir is None:
+        preinstallopts = ''
+    else:
+        preinstallopts = 'PYTHONPATH=%s:$PYTHONPATH' % distribute_egg_dir
+    templates.update({
+        'preinstallopts': preinstallopts,
+    })
 
     # create easyconfig file
     ebfile = os.path.join(tmpdir, 'EasyBuild-%s.eb' % templates['version'])
@@ -379,6 +383,7 @@ def stage2(tmpdir, templates, install_path, distribute_egg_dir, sourcepath):
     templates.update({
         'source_urls': '\n'.join(["'%s/%s/%s'," % (PYPI_SOURCE_URL, pkg[0], pkg) for pkg in EASYBUILD_PACKAGES]),
         'sources': "%(vsc-base)s%(easybuild-framework)s%(easybuild-easyblocks)s%(easybuild-easyconfigs)s" % templates,
+        'pythonpath': distribute_egg_dir,
     })
     f.write(EASYBUILD_EASYCONFIG_TEMPLATE % templates)
     f.close()
@@ -527,6 +532,8 @@ def main():
 # EasyBuild is a (set of) Python packages, so it depends on Python
 # usually, we want to use the system Python, so no actual Python dependency is listed
 allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+preinstallopts = '%(preinstallopts)s'
 """
 
 # distribute_setup.py script (https://pypi.python.org/pypi/distribute)

From e8374527cbda321561534d12055cc88d4eda59fd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Mar 2015 22:01:38 +0100
Subject: [PATCH 0733/1356] fix remark w.r.t. checking for EasyBuild/VSC pkgs
 to exclude from sys.path

---
 easybuild/scripts/bootstrap_eb.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 3d3f275ad1..a23a1279ef 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -458,12 +458,10 @@ def main():
     sys.path = []
     for path in orig_sys_path:
         include_path = True
-        # exclude path if it's potentially an EasyBuild package
-        if 'easybuild' in path or os.path.exists(os.path.join(path, 'easybuild')):
+        # exclude path if it's potentially an EasyBuild/VSC package, providing the 'easybuild'/'vsc' namespace, resp.
+        if any([os.path.exists(os.path.join(path, pkg, '__init__.py')) for pkg in ['easybuild', 'vsc']]):
             include_path = False
-        if '/vsc_' in path or os.path.exists(os.path.join(path, 'vsc')):
-            include_path = False
-        # exclude path if it contain an easy-install.pth file
+        # exclude any path that contains an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):
             include_path = False
 

From 3db2269f0b53a93fe23abfc312d6f41c0727dcf1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 11 Mar 2015 07:58:25 +0100
Subject: [PATCH 0734/1356] also exclude all .egg entries in sys.path

---
 easybuild/scripts/bootstrap_eb.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index a23a1279ef..115f92121f 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -461,6 +461,9 @@ def main():
         # exclude path if it's potentially an EasyBuild/VSC package, providing the 'easybuild'/'vsc' namespace, resp.
         if any([os.path.exists(os.path.join(path, pkg, '__init__.py')) for pkg in ['easybuild', 'vsc']]):
             include_path = False
+        # exclude any .egg paths
+        if path.endswith('.egg'):
+            include_path = False
         # exclude any path that contains an easy-install.pth file
         if os.path.exists(os.path.join(path, 'easy-install.pth')):
             include_path = False

From 950c2cf1489c9cbeb406197614551182143b503c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 11 Mar 2015 17:26:08 +0100
Subject: [PATCH 0735/1356] enhance test w.r.t. use of templates in cfgfile

---
 test/framework/config.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index c0959b40e2..c1dfaa6c66 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -213,7 +213,8 @@ def test_generaloption_config_file(self):
         cfgtxt = '\n'.join([
             '[config]',
             'buildpath = %s' % testpath1,
-            'robot-paths = /tmp/foo:%(DEFAULT_ROBOT_PATHS)s',
+            'repositorypath = /tmp/ebrepo',
+            'robot-paths=/tmp/foo:%(repositorypath)s:%(DEFAULT_ROBOT_PATHS)s',
         ])
         write_file(config_file, cfgtxt)
 
@@ -227,8 +228,7 @@ def test_generaloption_config_file(self):
         self.assertEqual(install_path(), os.path.join(os.getenv('HOME'), '.local', 'easybuild', 'software'))  # default
         self.assertEqual(source_paths(), [testpath2])  # via command line
         self.assertEqual(build_path(), testpath1)  # via config file
-        self.assertTrue('/tmp/foo' in options.robot_paths)
-        self.assertTrue(os.path.join(tmpdir, 'easybuild', 'easyconfigs') in options.robot_paths)
+        self.assertEqual(options.robot_paths[:3], ['/tmp/foo', '/tmp/ebrepo', os.path.join(tmpdir, 'easybuild', 'easyconfigs')])
 
         testpath3 = os.path.join(self.tmpdir, 'testTHREE')
         os.environ['EASYBUILD_SOURCEPATH'] = testpath2

From c941056776a5d5fd51dc8a78f9a00c785e60ec1c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 11 Mar 2015 20:52:09 +0100
Subject: [PATCH 0736/1356] derive EasyBuildError from LoggedException,
 deprecate raising EasyBuildError in log.error/log.exception

---
 easybuild/tools/build_log.py | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index 2c3bbc9a1b..9ffc0cac5c 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -36,6 +36,7 @@
 import tempfile
 from copy import copy
 from vsc.utils import fancylogger
+from vsc.utils.exceptions import LoggedException
 
 from easybuild.tools.version import VERSION
 
@@ -52,7 +53,7 @@
 DEPRECATED_DOC_URL = 'http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html'
 
 
-class EasyBuildError(Exception):
+class EasyBuildError(LoggedException):
     """
     EasyBuildError is thrown when EasyBuild runs into something horribly wrong.
     """
@@ -94,7 +95,7 @@ def experimental(self, msg, *args, **kwargs):
             self.warning(msg, *args, **kwargs)
         else:
             msg = 'Experimental functionality. Behaviour might change/be removed later (use --experimental option to enable). ' + msg
-            self.error(msg, *args)
+            raise EasyBuildError(msg % args)
 
     def deprecated(self, msg, max_ver):
         """Print deprecation warning or raise an EasyBuildError, depending on max version allowed."""
@@ -103,25 +104,28 @@ def deprecated(self, msg, max_ver):
 
     def nosupport(self, msg, ver):
         """Print error message for no longer supported behaviour, and raise an EasyBuildError."""
-        self.error("NO LONGER SUPPORTED since v%s: %s; see %s for more information" % (ver, msg, DEPRECATED_DOC_URL))
+        msg = "NO LONGER SUPPORTED since v%s: %s; see %s for more information" % (ver, msg, DEPRECATED_DOC_URL)
+        raise EasyBuildError(msg)
 
     def error(self, msg, *args, **kwargs):
         """Print error message and raise an EasyBuildError."""
-        newMsg = "EasyBuild crashed with an error %s: %s" % (self.caller_info(), msg)
-        fancylogger.FancyLogger.error(self, newMsg, *args, **kwargs)
+        new_msg = "EasyBuild crashed with an error %s: %s" % (self.caller_info(), msg)
+        fancylogger.FancyLogger.error(self, new_msg, *args, **kwargs)
         if self.raiseError:
-            raise EasyBuildError(newMsg)
+            self.deprecated("Automatically raising EasybuildError in error() logging method", '3.0')
+            raise EasyBuildError(new_msg)
 
     def exception(self, msg, *args):
         """Print exception message and raise EasyBuildError."""
         # don't raise the exception from within error
-        newMsg = "EasyBuild encountered an exception %s: %s" % (self.caller_info(), msg)
+        new_msg = "EasyBuild encountered an exception %s: %s" % (self.caller_info(), msg)
 
         self.raiseError = False
-        fancylogger.FancyLogger.exception(self, newMsg, *args)
+        fancylogger.FancyLogger.exception(self, new_msg, *args)
         self.raiseError = True
 
-        raise EasyBuildError(newMsg)
+        self.deprecated("Automatically raising EasybuildError in exception() logging method", '3.0')
+        raise EasyBuildError(new_msg)
 
 
 # set format for logger
@@ -198,7 +202,7 @@ def print_error(message, log=None, exitCode=1, opt_parser=None, exit_on_error=Tr
             sys.stderr.write("ERROR: %s\n" % message)
         sys.exit(exitCode)
     elif log is not None:
-        log.error(message)
+        raise EasyBuildError(message)
 
 
 def print_warning(message, silent=False):

From e1323c487448f1fac9ac3f3d9beb1f402b024262 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 11 Mar 2015 20:52:31 +0100
Subject: [PATCH 0737/1356] replace use of log.error in tools/robot.py by raise
 EasyBuildError (PoC)

---
 easybuild/tools/robot.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index 22fc8f3c37..8a1c2e49b4 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -38,6 +38,7 @@
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS, process_easyconfig, robot_find_easyconfig
 from easybuild.framework.easyconfig.tools import find_resolved_modules, skip_available
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import det_common_path_prefix, search_file
 from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS
@@ -154,7 +155,7 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
         if loopcnt > maxloopcnt:
             tup = (maxloopcnt, unprocessed, irresolvable)
             msg = "Maximum loop cnt %s reached, so quitting (unprocessed: %s, irresolvable: %s)" % tup
-            _log.error(msg)
+            raise EasyBuildError(msg)
 
         # first try resolving dependencies without using external dependencies
         last_processed_count = -1
@@ -206,7 +207,7 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
                         dep_mod_name = ActiveMNS().det_full_module_name(cand_dep)
                         if not dep_mod_name in mods:
                             tup = (path, dep_mod_name, mods)
-                            _log.error("easyconfig file %s does not contain module %s (mods: %s)" % tup)
+                            raise EasyBuildError("easyconfig file %s does not contain module %s (mods: %s)" % tup)
 
                         for ec in processed_ecs:
                             if not ec in unprocessed + additional:
@@ -229,7 +230,7 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
         irresolvable_mods_eb = [EasyBuildMNS().det_full_module_name(dep) for dep in irresolvable]
         _log.warning("Irresolvable dependencies (EasyBuild module names): %s" % ', '.join(irresolvable_mods_eb))
         irresolvable_mods = [ActiveMNS().det_full_module_name(dep) for dep in irresolvable]
-        _log.error('Irresolvable dependencies encountered: %s' % ', '.join(irresolvable_mods))
+        raise EasyBuildError('Irresolvable dependencies encountered: %s' % ', '.join(irresolvable_mods))
 
     _log.info("Dependency resolution complete, building as follows:\n%s" % ordered_ecs)
     return ordered_ecs

From b2314fc8ed287816124ac115f79593e450307d56 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 11 Mar 2015 21:58:52 +0100
Subject: [PATCH 0738/1356] Use sorted instead of .sort()

---
 easybuild/tools/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 34ad0f2810..4c46fb50f7 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -367,7 +367,7 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
             dirnames[:] = [d for d in dirnames if not d in ignore_dirs]
 
         if hits:
-            hits.sort()
+            hits = sorted(hits)
             common_prefix = det_common_path_prefix(hits)
             if short and common_prefix is not None and len(common_prefix) > len(var) * 2:
                 var_lines.append("%s=%s" % (var, common_prefix))

From a3cb8966935ac053149337915e440e334cfdf991 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 11 Mar 2015 22:25:37 +0100
Subject: [PATCH 0739/1356] Move sort outside the if

---
 easybuild/tools/filetools.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 4c46fb50f7..5bcec5bf6a 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -366,8 +366,9 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
             # see http://stackoverflow.com/questions/13454164/os-walk-without-hidden-folders
             dirnames[:] = [d for d in dirnames if not d in ignore_dirs]
 
+        hits = sorted(hits)
+
         if hits:
-            hits = sorted(hits)
             common_prefix = det_common_path_prefix(hits)
             if short and common_prefix is not None and len(common_prefix) > len(var) * 2:
                 var_lines.append("%s=%s" % (var, common_prefix))

From 2629de78937acf7632371f930a95e0b40f6d4373 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Wed, 11 Mar 2015 22:37:01 +0100
Subject: [PATCH 0740/1356] Moved CHARS_TO_IGNORE to base class with None, move
 Syntax specifics into derived classes.

---
 easybuild/tools/module_generator.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index fef1a54eb6..3e62cdc705 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -55,7 +55,7 @@ class ModuleGenerator(object):
     SYNTAX = None
 
     # chars we want to escape in the generated modulefiles
-    CHARS_TO_ESCAPE = ["$"]
+    CHARS_TO_ESCAPE = None
     MODULE_FILE_EXTENSION = None
 
     def __init__(self, application, fake=False):
@@ -131,6 +131,7 @@ class ModuleGeneratorTcl(ModuleGenerator):
     """
     MODULE_FILE_EXTENSION = ''  # no suffix for Tcl module files
     SYNTAX = 'Tcl'
+    CHARS_TO_ESCAPE = ["$"]
 
     LOAD_REGEX = r"^\s*module\s+load\s+(\S+)"
     LOAD_TEMPLATE = "module load %(mod_name)s"
@@ -292,6 +293,7 @@ class ModuleGeneratorLua(ModuleGenerator):
     """
     MODULE_FILE_EXTENSION = '.lua'
     SYNTAX = 'Lua'
+    CHARS_TO_ESCAPE = ["%"]
 
     LOAD_REGEX = r'^\s*load\("(\S+)"'
     LOAD_TEMPLATE = 'load("%(mod_name)s")'

From db7d4af912bf6e4c2963d601c617c4b7c331b719 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Wed, 11 Mar 2015 22:38:55 +0100
Subject: [PATCH 0741/1356] Removed the code for conflicts for Lua modules as
 it doesnt make sense.

---
 easybuild/tools/module_generator.py | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 3e62cdc705..b69a274bc8 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -333,19 +333,6 @@ def get_description(self, conflict=True):
             "",
             ]
 
-        #@todo check if this is really needed, imho Lmod doesnt need this at all.
-        if self.app.cfg['moduleloadnoconflict']:
-            lines.extend([
-             'if ( not isloaded("%(name)s/%(version)s")) then',
-             '  load("%(name)s/%(version)s")',
-             'end',
-             ])
-
-        elif conflict:
-            # conflicts are not needed in lua module files, as Lmod's one name
-            # rule and automatic swapping.
-            pass
-
         txt = '\n'.join(lines) % {
             'name': self.app.name,
             'version': self.app.version,

From 7fad3b5a7f93afacad2d7a8d077f32cfbb67573c Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Wed, 11 Mar 2015 22:40:57 +0100
Subject: [PATCH 0742/1356] Adressed remark regarding a use of info where it
 should be debug.

---
 easybuild/tools/module_generator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index b69a274bc8..7db490e480 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -379,7 +379,7 @@ def prepend_paths(self, key, paths, allow_abs=False):
         template = 'prepend_path(%s,%s)\n'
 
         if isinstance(paths, basestring):
-            self.log.info("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
+            self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
         # make sure only relative paths are passed

From 3243a827cd936ab352505b504bc7cb2a402356fe Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Wed, 11 Mar 2015 22:43:02 +0100
Subject: [PATCH 0743/1356] Added param's requirements to docstring for use()

---
 easybuild/tools/module_generator.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 7db490e480..de22aeb24a 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -396,6 +396,7 @@ def prepend_paths(self, key, paths, allow_abs=False):
     def use(self, paths):
         """
         Generate module use statements for given list of module paths.
+        @param paths: list of module path extensions to generate use statements for
         """
         use_statements = []
         for path in paths:

From 70770e8be80ab70c0c1a93b3c5b1751b8a5d720f Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Wed, 11 Mar 2015 22:44:17 +0100
Subject: [PATCH 0744/1356] rewrite use() as one liner as suggested in remarks.

---
 easybuild/tools/module_generator.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index de22aeb24a..832ad010eb 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -398,10 +398,7 @@ def use(self, paths):
         Generate module use statements for given list of module paths.
         @param paths: list of module path extensions to generate use statements for
         """
-        use_statements = []
-        for path in paths:
-            use_statements.append('use("%s")' % path)
-        return '\n'.join(use_statements)
+        return '\n'.join(['use("%s")' % p for p in paths] + [''])
 
     def set_environment(self, key, value):
         """

From b10dec93a8fc9ac2272f21326ba5cbdacc876687 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Wed, 11 Mar 2015 22:45:20 +0100
Subject: [PATCH 0745/1356] rewrite avail_module_generators() as one liner to
 address remarks.

---
 easybuild/tools/module_generator.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 832ad010eb..c58a193b24 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -439,10 +439,7 @@ def avail_module_generators():
     """
     Return all known module syntaxes.
     """
-    class_dict = {}
-    for klass in get_subclasses(ModuleGenerator):
-        class_dict.update({klass.SYNTAX: klass})
-    return class_dict
+    return dict([(k.SYNTAX, k) for k in get_subclasses(ModuleGenerator)])
 
 
 def module_generator(app, fake=False):

From e81bc5c3013b2dfc0d72f44924ced08d440bae96 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 12 Mar 2015 15:18:06 +0100
Subject: [PATCH 0746/1356] define %(DEFAULT_REPOSITORYPATH)s template for
 cfgfiles

---
 easybuild/tools/options.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ebb608c169..8a643e2770 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -86,11 +86,13 @@ class EasyBuildOptions(GeneralOption):
     def __init__(self, *args, **kwargs):
         """Constructor."""
 
+        self.default_repositorypath = [mk_full_default_path('repositorypath')]
         self.default_robot_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None) or []
 
         # set up constants to seed into config files parser, by section
         self.go_cfg_constants = {
             self.DEFAULTSECT: {
+                'DEFAULT_REPOSITORYPATH': (self.default_repositorypath[0], "Default easyconfigs repository path"),
                 'DEFAULT_ROBOT_PATHS': (os.pathsep.join(self.default_robot_paths),
                                         "List of default robot paths ('%s'-separated)" % os.pathsep),
             }
@@ -251,8 +253,7 @@ def config_options(self):
             'repositorypath': (("Repository path, used by repository "
                                 "(is passed as list of arguments to create the repository instance). "
                                 "For more info, use --avail-repositories."),
-                               'strlist', 'store',
-                               [mk_full_default_path('repositorypath')]),
+                               'strlist', 'store', self.default_repositorypath),
             'show-default-moduleclasses': ("Show default module classes with description",
                                            None, 'store_true', False),
             'sourcepath': ("Path(s) to where sources should be downloaded (string, colon-separated)",
@@ -427,7 +428,9 @@ def _postprocess_config(self):
                     if dest == 'repository':
                         setattr(self.options, dest, DEFAULT_REPOSITORY)
                     elif dest == 'repositorypath':
-                        setattr(self.options, dest, [mk_full_default_path(dest, prefix=self.options.prefix)])
+                        repositorypath = [mk_full_default_path(dest, prefix=self.options.prefix)]
+                        setattr(self.options, dest, repositorypath)
+                        self.go_cfg_constants[self.DEFAULTSECT]['DEFAULT_REPOSITORYPATH'] = repositorypath
                     else:
                         setattr(self.options, dest, mk_full_default_path(dest, prefix=self.options.prefix))
                     # LEGACY this line is here for oldstyle config reasons
@@ -595,7 +598,7 @@ def avail_toolchains(self):
 
     def avail_repositories(self):
         """Show list of known repository types."""
-        repopath_defaults = mk_full_default_path('repositorypath')
+        repopath_defaults = self.default_repositorypath
         all_repos = avail_repositories(check_useable=False)
         usable_repos = avail_repositories(check_useable=True).keys()
 

From 53972a0f3f30350a6c6143a4fdbe40c58a73bc41 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 12 Mar 2015 15:18:25 +0100
Subject: [PATCH 0747/1356] enhance tests to also test
 %(DEFAULT_REPOSITORYPATH)s

---
 test/framework/config.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index c1dfaa6c66..e91337f25b 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -213,8 +213,9 @@ def test_generaloption_config_file(self):
         cfgtxt = '\n'.join([
             '[config]',
             'buildpath = %s' % testpath1,
-            'repositorypath = /tmp/ebrepo',
-            'robot-paths=/tmp/foo:%(repositorypath)s:%(DEFAULT_ROBOT_PATHS)s',
+            'sourcepath = %(DEFAULT_REPOSITORYPATH)s',
+            'repositorypath = %(DEFAULT_REPOSITORYPATH)s,somesubdir',
+            'robot-paths=/tmp/foo:%(sourcepath)s:%(DEFAULT_ROBOT_PATHS)s',
         ])
         write_file(config_file, cfgtxt)
 
@@ -225,10 +226,17 @@ def test_generaloption_config_file(self):
         ]
         options = init_config(args=args)
 
-        self.assertEqual(install_path(), os.path.join(os.getenv('HOME'), '.local', 'easybuild', 'software'))  # default
+        topdir = os.path.join(os.getenv('HOME'), '.local', 'easybuild')
+        self.assertEqual(install_path(), os.path.join(topdir, 'software'))  # default
         self.assertEqual(source_paths(), [testpath2])  # via command line
         self.assertEqual(build_path(), testpath1)  # via config file
-        self.assertEqual(options.robot_paths[:3], ['/tmp/foo', '/tmp/ebrepo', os.path.join(tmpdir, 'easybuild', 'easyconfigs')])
+        self.assertEqual(get_repositorypath(), [os.path.join(topdir, 'ebfiles_repo'), 'somesubdir'])  # via config file
+        robot_paths = [
+            '/tmp/foo',
+            os.path.join(os.getenv('HOME'), '.local', 'easybuild', 'ebfiles_repo'),
+            os.path.join(tmpdir, 'easybuild', 'easyconfigs'),
+        ]
+        self.assertEqual(options.robot_paths[:3], robot_paths)
 
         testpath3 = os.path.join(self.tmpdir, 'testTHREE')
         os.environ['EASYBUILD_SOURCEPATH'] = testpath2

From 1c77858a01b68dd87e063e78428da2d46ccb025b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 13 Mar 2015 18:53:37 +0100
Subject: [PATCH 0748/1356] fix remarks

---
 easybuild/tools/build_log.py | 35 ++++++++++++++++++++++++++---------
 1 file changed, 26 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index 9ffc0cac5c..42060f1f74 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -53,12 +53,29 @@
 DEPRECATED_DOC_URL = 'http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html'
 
 
+# 1st argument (a LoggedException instance) is ignored
+def log_error_no_raise(_, logger, msg):
+    """Utility function to log an error with raising an exception."""
+    if hasattr(logger, 'raiseError'):
+        orig_raise_error = logger.raiseError
+        logger.raiseError = False
+
+    logger.error(msg)
+
+    if hasattr(logger, 'raiseError'):
+        logger.raiseError = orig_raise_error
+
+
 class EasyBuildError(LoggedException):
     """
     EasyBuildError is thrown when EasyBuild runs into something horribly wrong.
     """
-    def __init__(self, msg):
-        Exception.__init__(self, msg)
+    # make sure EasyBuildError isn't being raised again to avoid infinite recursion
+    LOGGING_METHOD = log_error_no_raise
+
+    def __init__(self, msg, *args):
+        msg = msg % args
+        LoggedException.__init__(self, msg)
         self.msg = msg
 
     def __str__(self):
@@ -95,7 +112,7 @@ def experimental(self, msg, *args, **kwargs):
             self.warning(msg, *args, **kwargs)
         else:
             msg = 'Experimental functionality. Behaviour might change/be removed later (use --experimental option to enable). ' + msg
-            raise EasyBuildError(msg % args)
+            raise EasyBuildError(msg, *args)
 
     def deprecated(self, msg, max_ver):
         """Print deprecation warning or raise an EasyBuildError, depending on max version allowed."""
@@ -104,16 +121,16 @@ def deprecated(self, msg, max_ver):
 
     def nosupport(self, msg, ver):
         """Print error message for no longer supported behaviour, and raise an EasyBuildError."""
-        msg = "NO LONGER SUPPORTED since v%s: %s; see %s for more information" % (ver, msg, DEPRECATED_DOC_URL)
-        raise EasyBuildError(msg)
+        nosupport_msg = "NO LONGER SUPPORTED since v%s: %s; see %s for more information"
+        raise EasyBuildError(nosupport_msg, ver, msg, DEPRECATED_DOC_URL)
 
     def error(self, msg, *args, **kwargs):
         """Print error message and raise an EasyBuildError."""
         new_msg = "EasyBuild crashed with an error %s: %s" % (self.caller_info(), msg)
         fancylogger.FancyLogger.error(self, new_msg, *args, **kwargs)
         if self.raiseError:
-            self.deprecated("Automatically raising EasybuildError in error() logging method", '3.0')
-            raise EasyBuildError(new_msg)
+            self.deprecated("Use 'raise EasyBuildError' rather than error() logging method that raises", '3.0')
+            raise EasyBuildError(new_msg, *args)
 
     def exception(self, msg, *args):
         """Print exception message and raise EasyBuildError."""
@@ -124,8 +141,8 @@ def exception(self, msg, *args):
         fancylogger.FancyLogger.exception(self, new_msg, *args)
         self.raiseError = True
 
-        self.deprecated("Automatically raising EasybuildError in exception() logging method", '3.0')
-        raise EasyBuildError(new_msg)
+        self.deprecated("Use 'raise EasyBuildError' rather than exception() logging method that raises", '3.0')
+        raise EasyBuildError(new_msg, *args)
 
 
 # set format for logger

From 7c3ef4ce3647d91b0a889e2d12952b6a60eb7de9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 16 Mar 2015 17:21:05 +0100
Subject: [PATCH 0749/1356] also reset $LD_PRELOAD when running module commands

---
 easybuild/tools/modules.py | 47 +++++++++++++++++++-------------------
 1 file changed, 24 insertions(+), 23 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index d70bffa424..dc730b9295 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -59,9 +59,10 @@
 VERSION_ENV_VAR_NAME_PREFIX = "EBVERSION"
 DEVEL_ENV_VAR_NAME_PREFIX = "EBDEVEL"
 
-# keep track of original LD_LIBRARY_PATH, because we can change it by loading modules and break modulecmd
+# keep track of original $LD_LIBRARY_PATH/$LD_PRELOAD, because it can change by loading modules and break module command
 # see e.g., https://bugzilla.redhat.com/show_bug.cgi?id=719785
-LD_LIBRARY_PATH = os.getenv('LD_LIBRARY_PATH', '')
+LD_ENV_VAR_KEYS = ['LD_LIBRARY_PATH', 'LD_PRELOAD']
+ORIG_ENVIRON = dict([(key, os.getenv(key, '')) for key in LD_ENV_VAR_KEYS])
 
 output_matchers = {
     # matches whitespace and module-listing headers
@@ -451,9 +452,9 @@ def modulefile_path(self, mod_name):
         modpath_re = re.compile('^\s*(?P<modpath>[^/\n]*/[^ ]+):$', re.M)
         return self.get_value_from_modulefile(mod_name, modpath_re)
 
-    def set_ld_library_path(self, ld_library_paths):
-        """Set $LD_LIBRARY_PATH to the given list of paths."""
-        os.environ['LD_LIBRARY_PATH'] = ':'.join(ld_library_paths)
+    def set_path_env_var(self, key, paths):
+        """Set path environment variable to the given list of paths."""
+        os.environ[key] = os.pathsep.join(paths)
 
     def run_module(self, *args, **kwargs):
         """
@@ -478,12 +479,11 @@ def run_module(self, *args, **kwargs):
 
         self.log.debug('Current MODULEPATH: %s' % os.environ.get('MODULEPATH', ''))
 
-        # change our LD_LIBRARY_PATH here
+        # change to original $LD_LIBRARY_PATH and $LD_PRELOAD before running module command
         environ = os.environ.copy()
-        environ['LD_LIBRARY_PATH'] = LD_LIBRARY_PATH
-        cur_ld_library_path = os.environ.get('LD_LIBRARY_PATH', '')
-        new_ld_library_path = environ['LD_LIBRARY_PATH']
-        self.log.debug("Adjusted LD_LIBRARY_PATH from '%s' to '%s'" % (cur_ld_library_path, new_ld_library_path))
+        for key in LD_ENV_VAR_KEYS:
+            environ[key] = ORIG_ENVIRON[key]
+            self.log.debug("Adjusted %s from '%s' to '%s'" % (key, os.environ.get(key, ''), environ[key]))
 
         # prefix if a particular shell is specified, using shell argument to Popen doesn't work (no output produced (?))
         cmdlist = [self.cmd, 'python']
@@ -504,11 +504,12 @@ def run_module(self, *args, **kwargs):
         if kwargs.get('return_output', False):
             return stdout + stderr
         else:
-            # the module command was run with an outdated LD_LIBRARY_PATH, which will be adjusted on loading a module
+            # the module command was run with an outdated $LD_LIBRARY_PATH and $LD_PRELOAD,
+            # which will be adjusted on loading a module;
             # this needs to be taken into account when updating the environment via produced output, see below
 
-            # keep track of current LD_LIBRARY_PATH, so we can correct the adjusted LD_LIBRARY_PATH below
-            prev_ld_library_path = os.environ.get('LD_LIBRARY_PATH', '').split(':')[::-1]
+            # keep track of current $LD_LIBRARY_PATH/$LD_PRELOAD, so we can correct the adjusted values below
+            prev_ld_values = dict([(key, os.environ.get(key, '').split(os.pathsep)[::-1]) for key in LD_ENV_VAR_KEYS])
 
             # Change the environment
             try:
@@ -520,14 +521,14 @@ def run_module(self, *args, **kwargs):
                 out = "stdout: %s, stderr: %s" % (stdout, stderr)
                 raise EasyBuildError("Changing environment as dictated by module failed: %s (%s)" % (err, out))
 
-            # correct LD_LIBRARY_PATH as yielded by the adjustments made
+            # correct $LD_LIBRARY_PATH and $LD_PRELOAD as yielded by the adjustments made
             # make sure we get the order right (reverse lists with [::-1])
-            curr_ld_library_path = os.environ.get('LD_LIBRARY_PATH', '').split(':')
-            new_ld_library_path = [x for x in nub(prev_ld_library_path + curr_ld_library_path[::-1]) if len(x)][::-1]
+            for key in LD_ENV_VAR_KEYS:
+                curr_ld_val = os.environ.get(key, '').split(os.pathsep)
+                new_ld_val = [x for x in nub(prev_ld_values[key] + curr_ld_val[::-1]) if len(x)][::-1]
 
-            self.log.debug("Correcting paths in LD_LIBRARY_PATH from %s to %s" %
-                           (curr_ld_library_path, new_ld_library_path))
-            self.set_ld_library_path(new_ld_library_path)
+                self.log.debug("Correcting paths in $%s from %s to %s" % (key, curr_ld_val, new_ld_val))
+                self.set_path_env_var(key, new_ld_val)
 
             # Process stderr
             result = []
@@ -732,11 +733,11 @@ class EnvironmentModulesTcl(EnvironmentModulesC):
     REQ_VERSION = None
     VERSION_REGEXP = r'^Modules\s+Release\s+Tcl\s+(?P<version>\d\S*)\s'
 
-    def set_ld_library_path(self, ld_library_paths):
-        """Set $LD_LIBRARY_PATH to the given list of paths."""
-        super(EnvironmentModulesTcl, self).set_ld_library_path(ld_library_paths)
+    def set_path_env_var(self, key, paths):
+        """Set $LD_X environment variable to the given list of paths."""
+        super(EnvironmentModulesTcl, self).set_path_env_var(paths)
         # for Tcl environment modules, we need to make sure the _modshare env var is kept in sync
-        os.environ['LD_LIBRARY_PATH_modshare'] = ':1:'.join(ld_library_paths)
+        os.environ['%s_modshare' % key] = ':1:'.join(paths)
 
     def run_module(self, *args, **kwargs):
         """

From 630ccc47695ee34204dc5a90bcd54deba76ca305 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Mon, 16 Mar 2015 22:33:59 +0100
Subject: [PATCH 0750/1356] Change another instance of log info to debug to
 address remarks.

---
 easybuild/tools/module_generator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 7ee78d8ebb..92c19d17b1 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -227,7 +227,7 @@ def prepend_paths(self, key, paths, allow_abs=False):
         template = "prepend-path\t%s\t\t%s\n"
 
         if isinstance(paths, basestring):
-            self.log.info("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
+            self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
         # make sure only relative paths are passed

From aecd9d6eed79d3b77ed541ed67130a732f75c674 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Mon, 16 Mar 2015 23:06:18 +0100
Subject: [PATCH 0751/1356] Chagned xrange to enumerate to address remarks,
 also dont modify paths[], but use new list that only contains relative paths.

---
 easybuild/tools/module_generator.py | 29 +++++++++++++++--------------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 92c19d17b1..89efd44120 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -230,15 +230,16 @@ def prepend_paths(self, key, paths, allow_abs=False):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
-        # make sure only relative paths are passed
-        for i in xrange(len(paths)):
-            if os.path.isabs(paths[i]) and not allow_abs:
-                self.log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % paths[i])
-            elif not os.path.isabs(paths[i]):
+        relpaths=[]
+        for i, path in enumerate(paths):
+            if os.path.isabs(path) and not allow_abs:
+                print "Absolute path %s passed to prepend_paths which only expects relative paths." % path
+            elif not os.path.isabs(path):
                 # prepend $root (= installdir) for relative paths
-                paths[i] = "$root/%s" % paths[i]
+                relpaths.append("$root/%s" % path)
 
-        statements = [template % (key, p) for p in paths]
+
+        statements = [template % (key, p) for p in relpaths]
         return ''.join(statements)
 
 
@@ -382,15 +383,15 @@ def prepend_paths(self, key, paths, allow_abs=False):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
-        # make sure only relative paths are passed
-        for i in xrange(len(paths)):
-            if os.path.isabs(paths[i]) and not allow_abs:
-                self.log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % paths[i])
-            elif not os.path.isabs(paths[i]):
+        relpaths=[]
+        for i, path in enumerate(paths):
+            if os.path.isabs(path) and not allow_abs:
+                print "Absolute path %s passed to prepend_paths which only expects relative paths." % path
+            elif not os.path.isabs(path):
                 # prepend $root (= installdir) for relative paths
-                paths[i] = ' pathJoin(pkg.root,"%s")' % paths[i]
+                relpaths.append(' pathJoin(pkg.root,"%s")' % path)
 
-        statements = [template % (quote_str(key), p) for p in paths]
+        statements = [template % (quote_str(key), p) for p in relpaths]
         return ''.join(statements)
 
     def use(self, paths):

From 1f37d72d3fec3b7550f0371e5c4a0716ba362d39 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Mon, 16 Mar 2015 23:21:44 +0100
Subject: [PATCH 0752/1356] Added luafooter to make the implementation between
 Tcl and Lau symmetrical.

---
 easybuild/tools/module_generator.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 89efd44120..4e2609316e 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -277,7 +277,6 @@ def add_tcl_footer(self, tcltxt):
         """
         Append whatever Tcl code you want to your modulefile
         """
-        # nothing to do here, but this should fail in the context of generating Lua modules
         return tcltxt
 
     def set_alias(self, key, value):
@@ -423,11 +422,13 @@ def msg_on_load(self, msg):
         pass
 
     def add_tcl_footer(self, tcltxt):
+        raise NotImplementedError
+
+    def add_lua_footer(self,luatxt):
         """
-        Append whatever Tcl code you want to your modulefile
+        Append whatever Lua code you want to your modulefile
         """
-        #@todo to pass or not to pass? this should fail in the context of generating Lua modules
-        pass
+        return luatxt
 
     def set_alias(self, key, value):
         """

From 0e3c928e8f2a8649851ac42ceaea0be451f2645d Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Mon, 16 Mar 2015 23:47:41 +0100
Subject: [PATCH 0753/1356] Repair prepend paths for abs_path=True and restore
 logger.

---
 easybuild/tools/module_generator.py | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 4e2609316e..0e525831d0 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -230,16 +230,17 @@ def prepend_paths(self, key, paths, allow_abs=False):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
-        relpaths=[]
+        newpaths=[]
         for i, path in enumerate(paths):
             if os.path.isabs(path) and not allow_abs:
-                print "Absolute path %s passed to prepend_paths which only expects relative paths." % path
+                self.log.info("Absolute path %s passed to prepend_paths which only expects relative paths." % path)
+                newpaths.append("%s" %path)
             elif not os.path.isabs(path):
                 # prepend $root (= installdir) for relative paths
-                relpaths.append("$root/%s" % path)
+                newpaths.append("$root/%s" % path)
 
 
-        statements = [template % (key, p) for p in relpaths]
+        statements = [template % (key, p) for p in newpaths]
         return ''.join(statements)
 
 
@@ -382,15 +383,16 @@ def prepend_paths(self, key, paths, allow_abs=False):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
-        relpaths=[]
+        newpaths=[]
         for i, path in enumerate(paths):
             if os.path.isabs(path) and not allow_abs:
-                print "Absolute path %s passed to prepend_paths which only expects relative paths." % path
+                self.log.info("Absolute path %s passed to prepend_paths which only expects relative paths." % path)
+                newpaths.append(' "%s"' % path)
             elif not os.path.isabs(path):
-                # prepend $root (= installdir) for relative paths
-                relpaths.append(' pathJoin(pkg.root,"%s")' % path)
+                # use pathJoin(pkg.root, path) for relative paths
+                newpaths.append(' pathJoin(pkg.root,"%s")' % path)
 
-        statements = [template % (quote_str(key), p) for p in relpaths]
+        statements = [template % (quote_str(key), p) for p in newpaths]
         return ''.join(statements)
 
     def use(self, paths):

From a2c6560c1da5725e2dedf211083214e48c88c834 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Tue, 17 Mar 2015 00:38:09 +0100
Subject: [PATCH 0754/1356] Repair prepend paths for abs_path=True for real.

---
 easybuild/tools/module_generator.py | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 0e525831d0..c2a217525e 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -230,17 +230,16 @@ def prepend_paths(self, key, paths, allow_abs=False):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
-        newpaths=[]
+
         for i, path in enumerate(paths):
             if os.path.isabs(path) and not allow_abs:
-                self.log.info("Absolute path %s passed to prepend_paths which only expects relative paths." % path)
-                newpaths.append("%s" %path)
+                self.log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % path)
             elif not os.path.isabs(path):
                 # prepend $root (= installdir) for relative paths
-                newpaths.append("$root/%s" % path)
+                paths[i]="$root/%s" % path
 
 
-        statements = [template % (key, p) for p in newpaths]
+        statements = [template % (key, p) for p in paths]
         return ''.join(statements)
 
 
@@ -383,16 +382,14 @@ def prepend_paths(self, key, paths, allow_abs=False):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
-        newpaths=[]
         for i, path in enumerate(paths):
             if os.path.isabs(path) and not allow_abs:
-                self.log.info("Absolute path %s passed to prepend_paths which only expects relative paths." % path)
-                newpaths.append(' "%s"' % path)
+                self.log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % path)
             elif not os.path.isabs(path):
                 # use pathJoin(pkg.root, path) for relative paths
-                newpaths.append(' pathJoin(pkg.root,"%s")' % path)
+                paths[i]=' pathJoin(pkg.root,"%s")' % path
 
-        statements = [template % (quote_str(key), p) for p in newpaths]
+        statements = [template % (quote_str(key), p) for p in paths]
         return ''.join(statements)
 
     def use(self, paths):

From 570045596c51e6ddf22786aa1ea449e084c71c59 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Mar 2015 13:15:53 +0100
Subject: [PATCH 0755/1356] run module_generator tests for both Lua and Tcl
 syntax

---
 test/framework/module_generator.py | 37 ++++++++++++++++++++++--------
 1 file changed, 27 insertions(+), 10 deletions(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index c8538d9c88..76b9322018 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -34,14 +34,14 @@
 import sys
 import tempfile
 from test.framework.utilities import EnhancedTestCase, init_config
-from unittest import TestLoader, main
+from unittest import TestLoader, TestSuite, TextTestRunner, main
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 from vsc.utils.missing import get_subclasses
 
 import easybuild.tools.module_generator
 from easybuild.framework.easyconfig.tools import process_easyconfig
 from easybuild.tools import config
-from easybuild.tools.module_generator import ModuleGeneratorTcl
+from easybuild.tools.module_generator import ModuleGeneratorLua, ModuleGeneratorTcl
 from easybuild.tools.module_naming_scheme.utilities import is_valid_module_name
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS
@@ -50,10 +50,12 @@
 
 
 class ModuleGeneratorTest(EnhancedTestCase):
-    """ testcase for ModuleGeneratorTcl """
+    """Tests for module_generator module."""
+
+    MODULE_GENERATOR_CLASS = None
 
     def setUp(self):
-        """ initialize ModuleGeneratorTcl with test Application """
+        """Test setup."""
         super(ModuleGeneratorTest, self).setUp()
         # find .eb file
         eb_path = os.path.join(os.path.join(os.path.dirname(__file__), 'easyconfigs'), 'gzip-1.4.eb')
@@ -62,13 +64,13 @@ def setUp(self):
 
         ec = EasyConfig(eb_full_path)
         self.eb = EasyBlock(ec)
-        self.modgen = ModuleGeneratorTcl(self.eb)
+        self.modgen = self.MODULE_GENERATOR_CLASS(self.eb)
         self.modgen.app.installdir = tempfile.mkdtemp(prefix='easybuild-modgen-test-')
         
         self.orig_module_naming_scheme = config.get_module_naming_scheme()
 
     def tearDown(self):
-        """cleanup"""
+        """Test cleanup."""
         super(ModuleGeneratorTest, self).tearDown()
         os.remove(self.eb.logfile)
         shutil.rmtree(self.modgen.app.installdir)
@@ -183,8 +185,11 @@ def test_load_msg(self):
 
     def test_tcl_footer(self):
         """Test including a Tcl footer."""
-        tcltxt = 'puts stderr "foo"'
-        self.assertEqual(tcltxt, self.modgen.add_tcl_footer(tcltxt))
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            tcltxt = 'puts stderr "foo"'
+            self.assertEqual(tcltxt, self.modgen.add_tcl_footer(tcltxt))
+        else:
+            pass
 
     def test_module_naming_scheme(self):
         """Test using default module naming scheme."""
@@ -467,13 +472,25 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
         for ecfile, mns_vals in test_ecs.items():
             test_ec(ecfile, *mns_vals)
 
+class TclModuleGeneratorTest(ModuleGeneratorTest):
+    """Test for module_generator module for Tcl syntax."""
+    MODULE_GENERATOR_CLASS = ModuleGeneratorTcl
+
+
+class LuaModuleGeneratorTest(ModuleGeneratorTest):
+    """Test for module_generator module for Tcl syntax."""
+    MODULE_GENERATOR_CLASS = ModuleGeneratorLua
+
 
 def suite():
     """ returns all the testcases in this module """
-    return TestLoader().loadTestsFromTestCase(ModuleGeneratorTest)
+    suite = TestSuite()
+    suite.addTests(TestLoader().loadTestsFromTestCase(TclModuleGeneratorTest))
+    suite.addTests(TestLoader().loadTestsFromTestCase(LuaModuleGeneratorTest))
+    return suite
 
 
 if __name__ == '__main__':
     #logToScreen(enable=True)
     #setLogLevelDebug()
-    main()
+    TextTestRunner().run(suite())

From b54ee496d81983075094af2a5e3379cd24b3d9d2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Mar 2015 17:14:28 +0100
Subject: [PATCH 0756/1356] fix remarks

---
 easybuild/framework/easyconfig/tools.py |  2 +-
 easybuild/tools/build_log.py            | 50 +++++++------
 easybuild/tools/robot.py                | 11 ++-
 test/framework/build_log.py             | 96 +++++++++++++++++++++++++
 test/framework/suite.py                 |  3 +-
 5 files changed, 133 insertions(+), 29 deletions(-)
 create mode 100644 test/framework/build_log.py

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index f5440ed2b4..a207b11ea9 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -314,7 +314,7 @@ def parse_easyconfigs(paths):
         # keep track of whether any files were generated
         generated_ecs |= generated
         if not os.path.exists(path):
-            _log.error("Can't find path %s" % path)
+            _log.error("Can't find path %s", path)
         try:
             ec_files = find_easyconfigs(path, ignore_dirs=build_option('ignore_dirs'))
             for ec_file in ec_files:
diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index 42060f1f74..bafd1ace68 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -53,32 +53,23 @@
 DEPRECATED_DOC_URL = 'http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html'
 
 
-# 1st argument (a LoggedException instance) is ignored
-def log_error_no_raise(_, logger, msg):
-    """Utility function to log an error with raising an exception."""
-    if hasattr(logger, 'raiseError'):
-        orig_raise_error = logger.raiseError
-        logger.raiseError = False
-
-    logger.error(msg)
-
-    if hasattr(logger, 'raiseError'):
-        logger.raiseError = orig_raise_error
-
-
 class EasyBuildError(LoggedException):
     """
     EasyBuildError is thrown when EasyBuild runs into something horribly wrong.
     """
-    # make sure EasyBuildError isn't being raised again to avoid infinite recursion
-    LOGGING_METHOD = log_error_no_raise
+    # use custom error logging method, to make sure EasyBuildError isn't being raised again to avoid infinite recursion
+    # only required because 'error' log method raises (should no longer be needed in EB v3.x)
+    LOGGING_METHOD_NAME = '_error_no_raise'
 
     def __init__(self, msg, *args):
+        """Constructor: initialise EasyBuildError instance."""
         msg = msg % args
         LoggedException.__init__(self, msg)
         self.msg = msg
 
     def __str__(self):
+        """Return string representation of this EasyBuildError instance."""
+        print '__str__'
         return repr(self.msg)
 
 
@@ -126,23 +117,40 @@ def nosupport(self, msg, ver):
 
     def error(self, msg, *args, **kwargs):
         """Print error message and raise an EasyBuildError."""
-        new_msg = "EasyBuild crashed with an error %s: %s" % (self.caller_info(), msg)
-        fancylogger.FancyLogger.error(self, new_msg, *args, **kwargs)
+        ebmsg = "EasyBuild crashed with an error %s: " + msg
+        args = (self.caller_info(),) + args
+
+        fancylogger.FancyLogger.error(self, ebmsg, *args, **kwargs)
+
         if self.raiseError:
             self.deprecated("Use 'raise EasyBuildError' rather than error() logging method that raises", '3.0')
-            raise EasyBuildError(new_msg, *args)
+            raise EasyBuildError(ebmsg, *args)
+
+    # note: self is deliberatly ignored
+    def _error_no_raise(self, msg):
+        """Utility function to log an error with raising an exception."""
+        # make sure raising of error is disabled
+        orig_raise_error = self.raiseError
+        self.raiseError = False
+
+        self.deprecated("Use of dedicated _error_no_raise log method", '3.0')
+        self.error(msg)
+
+        # reinstate previous raiseError setting
+        self.raiseError = orig_raise_error
 
     def exception(self, msg, *args):
         """Print exception message and raise EasyBuildError."""
         # don't raise the exception from within error
-        new_msg = "EasyBuild encountered an exception %s: %s" % (self.caller_info(), msg)
+        ebmsg = "EasyBuild encountered an exception %s: " + msg
+        args = (self.caller_info(),) + args
 
         self.raiseError = False
-        fancylogger.FancyLogger.exception(self, new_msg, *args)
+        fancylogger.FancyLogger.exception(self, ebmsg, *args)
         self.raiseError = True
 
         self.deprecated("Use 'raise EasyBuildError' rather than exception() logging method that raises", '3.0')
-        raise EasyBuildError(new_msg, *args)
+        raise EasyBuildError(ebmsg, *args)
 
 
 # set format for logger
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index 8a1c2e49b4..c872fbd2ef 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -153,9 +153,8 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
         # make sure this stops, we really don't want to get stuck in an infinite loop
         loopcnt += 1
         if loopcnt > maxloopcnt:
-            tup = (maxloopcnt, unprocessed, irresolvable)
-            msg = "Maximum loop cnt %s reached, so quitting (unprocessed: %s, irresolvable: %s)" % tup
-            raise EasyBuildError(msg)
+            msg = "Maximum loop cnt %s reached, so quitting (unprocessed: %s, irresolvable: %s)"
+            raise EasyBuildError(msg, maxloopcnt, unprocessed, irresolvable)
 
         # first try resolving dependencies without using external dependencies
         last_processed_count = -1
@@ -206,8 +205,8 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
                         mods = [spec['ec'].full_mod_name for spec in processed_ecs]
                         dep_mod_name = ActiveMNS().det_full_module_name(cand_dep)
                         if not dep_mod_name in mods:
-                            tup = (path, dep_mod_name, mods)
-                            raise EasyBuildError("easyconfig file %s does not contain module %s (mods: %s)" % tup)
+                            msg = "easyconfig file %s does not contain module %s (mods: %s)"
+                            raise EasyBuildError(msg, path, dep_mod_name, mods)
 
                         for ec in processed_ecs:
                             if not ec in unprocessed + additional:
@@ -230,7 +229,7 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
         irresolvable_mods_eb = [EasyBuildMNS().det_full_module_name(dep) for dep in irresolvable]
         _log.warning("Irresolvable dependencies (EasyBuild module names): %s" % ', '.join(irresolvable_mods_eb))
         irresolvable_mods = [ActiveMNS().det_full_module_name(dep) for dep in irresolvable]
-        raise EasyBuildError('Irresolvable dependencies encountered: %s' % ', '.join(irresolvable_mods))
+        raise EasyBuildError('Irresolvable dependencies encountered: %s', ', '.join(irresolvable_mods))
 
     _log.info("Dependency resolution complete, building as follows:\n%s" % ordered_ecs)
     return ordered_ecs
diff --git a/test/framework/build_log.py b/test/framework/build_log.py
new file mode 100644
index 0000000000..ffd47a7b68
--- /dev/null
+++ b/test/framework/build_log.py
@@ -0,0 +1,96 @@
+# #
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Unit tests for EasyBuild log infrastructure
+
+@author: Kenneth Hoste (Ghent University)
+"""
+import os
+import re
+import tempfile
+from test.framework.utilities import EnhancedTestCase, init_config
+from unittest import TestLoader
+from unittest import main as unittestmain
+from vsc.utils.fancylogger import getLogger, getRootLoggerName, logToFile, setLogFormat
+
+from easybuild.tools.build_log import EasyBuildError
+
+
+def raise_easybuilderror(msg, *args, **kwargs):
+    """Utility function: just raise a EasyBuildError."""
+    raise EasyBuildError(msg, *args, **kwargs)
+
+
+class BuildLogTest(EnhancedTestCase):
+    """Tests for EasyBuild log infrastructure."""
+
+    def test_easybuilderror(self):
+        """Tests for EasyBuildError."""
+        fd, tmplog = tempfile.mkstemp()
+        os.close(fd)
+
+        # auto-logging on raised EasyBuildError relies on deprecated functionality being used
+        # this should be removed for testing EasyBuild v3.x
+        os.environ['EASYBUILD_DEPRECATED'] = '2.1'
+        init_config()
+
+        # set log format, for each regex searching
+        setLogFormat("%(name)s :: %(message)s")
+
+        # if no logger is available, and no logger is specified, use default 'root' fancylogger
+        logToFile(tmplog, enable=True)
+        self.assertErrorRegex(EasyBuildError, 'BOOM', raise_easybuilderror, 'BOOM')
+        logToFile(tmplog, enable=False)
+
+        # replace log_re for EasyBuild v3.x
+        #log_re = re.compile("^%s :: EasyBuild crashed .*: BOOM$" % getRootLoggerName(), re.M)
+        root = getRootLoggerName()
+        log_re = re.compile("^%(root)s :: .*\n%(root)s :: EasyBuild crashed .*: BOOM$" % {'root': root}, re.M)
+        logtxt = open(tmplog, 'r').read()
+        self.assertTrue(log_re.match(logtxt), "%s matches %s" % (log_re.pattern, logtxt))
+
+        # test formatting of message
+        self.assertErrorRegex(EasyBuildError, 'BOOMBAF', raise_easybuilderror, 'BOOM%s', 'BAF')
+
+        os.remove(tmplog)
+
+    def test_easybuildlog(self):
+        """Tests for EasyBuildLog."""
+        log = getLogger('test_easybuildlog')
+
+        # test deprecated behaviour: raise EasyBuildError on log.error and log.exception
+        os.environ['EASYBUILD_DEPRECATED'] = '2.1'
+        init_config()
+
+        log.warning("No raise for warnings")
+        self.assertErrorRegex(EasyBuildError, 'EasyBuild crashed with an error', log.error, 'foo')
+        self.assertErrorRegex(EasyBuildError, 'EasyBuild encountered an exception', log.exception, 'bar')
+
+def suite():
+    """ returns all the testcases in this module """
+    return TestLoader().loadTestsFromTestCase(BuildLogTest)
+
+if __name__ == '__main__':
+    unittestmain()
diff --git a/test/framework/suite.py b/test/framework/suite.py
index abe486da15..2b6001221f 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -54,6 +54,7 @@
 
 # toolkit should be first to allow hacks to work
 import test.framework.asyncprocess as a
+import test.framework.build_log as bl
 import test.framework.config as c
 import test.framework.easyblock as b
 import test.framework.easyconfig as e
@@ -99,7 +100,7 @@
 
 # call suite() for each module and then run them all
 # note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
-tests = [gen, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p]
+tests = [gen, bl, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p]
 
 SUITE = unittest.TestSuite([x.suite() for x in tests])
 

From 820c2e7dc3bff90e3ff2accf1935654d8cb85d03 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Mar 2015 20:09:32 +0100
Subject: [PATCH 0757/1356] remove nonsense comment

---
 easybuild/tools/build_log.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index bafd1ace68..d43e147a90 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -126,7 +126,6 @@ def error(self, msg, *args, **kwargs):
             self.deprecated("Use 'raise EasyBuildError' rather than error() logging method that raises", '3.0')
             raise EasyBuildError(ebmsg, *args)
 
-    # note: self is deliberatly ignored
     def _error_no_raise(self, msg):
         """Utility function to log an error with raising an exception."""
         # make sure raising of error is disabled

From 3db747c377000cbb03c6b8d320e66af2b94fc67d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Mar 2015 20:20:18 +0100
Subject: [PATCH 0758/1356] remove print in __str__

---
 easybuild/tools/build_log.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index d43e147a90..f6a52cc7ce 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -69,7 +69,6 @@ def __init__(self, msg, *args):
 
     def __str__(self):
         """Return string representation of this EasyBuildError instance."""
-        print '__str__'
         return repr(self.msg)
 
 

From c869aff75809133f0691a6c246107b2fb25a28c2 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Tue, 17 Mar 2015 23:29:14 +0100
Subject: [PATCH 0759/1356] Initial support for non-EB generated system module
 files.

---
 easybuild/framework/easyblock.py          | 3 ++-
 easybuild/framework/easyconfig/default.py | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 1f403bfacc..8ab91c6dd6 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1305,7 +1305,8 @@ def prepare_step(self):
         Pre-configure step. Set's up the builddir just before starting configure
         """
         self.cfg['unwanted_env_vars'] = env.unset_env_vars(self.cfg['unwanted_env_vars'])
-        self.toolchain.prepare(self.cfg['onlytcmod'])
+        self.modules_tool.load(self.cfg['system_modules']) 
+	self.toolchain.prepare(self.cfg['onlytcmod'])
         self.guess_start_dir()
 
     def configure_step(self):
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index feb1bdd5e9..c075060ed5 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -137,7 +137,7 @@
     'dependencies': [[], "List of dependencies", DEPENDENCIES],
     'hiddendependencies': [[], "List of dependencies available as hidden modules", DEPENDENCIES],
     'osdependencies': [[], "OS dependencies that should be present on the system", DEPENDENCIES],
-
+    'system_modules': [[], "System module dependencies that should be present on the system", DEPENDENCIES],
     # LICENSE easyconfig parameters
     'group': [None, "Name of the user group for which the software should be available", LICENSE],
     'key': [None, 'Key for installing software', LICENSE],

From 22103745eeb121c8fd1aeda3e1c1b6a0762678c0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 09:02:29 +0100
Subject: [PATCH 0760/1356] drop log.deprecated from _error_no_raise

---
 easybuild/tools/build_log.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index f6a52cc7ce..b64b5f648e 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -125,13 +125,14 @@ def error(self, msg, *args, **kwargs):
             self.deprecated("Use 'raise EasyBuildError' rather than error() logging method that raises", '3.0')
             raise EasyBuildError(ebmsg, *args)
 
+    # FIXME: remove this when error() no longer raises EasyBuildError
     def _error_no_raise(self, msg):
         """Utility function to log an error with raising an exception."""
+
         # make sure raising of error is disabled
         orig_raise_error = self.raiseError
         self.raiseError = False
 
-        self.deprecated("Use of dedicated _error_no_raise log method", '3.0')
         self.error(msg)
 
         # reinstate previous raiseError setting

From c838840ea83a112c4f2a58ae0b9e97edfafd5aa8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 10:51:24 +0100
Subject: [PATCH 0761/1356] enhance tests for log methods

---
 test/framework/build_log.py | 67 ++++++++++++++++++++++++++++++++-----
 1 file changed, 58 insertions(+), 9 deletions(-)

diff --git a/test/framework/build_log.py b/test/framework/build_log.py
index ffd47a7b68..0d89b25a02 100644
--- a/test/framework/build_log.py
+++ b/test/framework/build_log.py
@@ -36,6 +36,7 @@
 from vsc.utils.fancylogger import getLogger, getRootLoggerName, logToFile, setLogFormat
 
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import read_file, write_file
 
 
 def raise_easybuilderror(msg, *args, **kwargs):
@@ -51,11 +52,6 @@ def test_easybuilderror(self):
         fd, tmplog = tempfile.mkstemp()
         os.close(fd)
 
-        # auto-logging on raised EasyBuildError relies on deprecated functionality being used
-        # this should be removed for testing EasyBuild v3.x
-        os.environ['EASYBUILD_DEPRECATED'] = '2.1'
-        init_config()
-
         # set log format, for each regex searching
         setLogFormat("%(name)s :: %(message)s")
 
@@ -64,10 +60,7 @@ def test_easybuilderror(self):
         self.assertErrorRegex(EasyBuildError, 'BOOM', raise_easybuilderror, 'BOOM')
         logToFile(tmplog, enable=False)
 
-        # replace log_re for EasyBuild v3.x
-        #log_re = re.compile("^%s :: EasyBuild crashed .*: BOOM$" % getRootLoggerName(), re.M)
-        root = getRootLoggerName()
-        log_re = re.compile("^%(root)s :: .*\n%(root)s :: EasyBuild crashed .*: BOOM$" % {'root': root}, re.M)
+        log_re = re.compile("^%s :: EasyBuild crashed .*: BOOM$" % getRootLoggerName(), re.M)
         logtxt = open(tmplog, 'r').read()
         self.assertTrue(log_re.match(logtxt), "%s matches %s" % (log_re.pattern, logtxt))
 
@@ -78,7 +71,63 @@ def test_easybuilderror(self):
 
     def test_easybuildlog(self):
         """Tests for EasyBuildLog."""
+        fd, tmplog = tempfile.mkstemp()
+        os.close(fd)
+
+        # set log format, for each regex searching
+        setLogFormat("%(name)s [%(levelname)s] :: %(message)s")
+
+        # test basic log methods
+        logToFile(tmplog, enable=True)
         log = getLogger('test_easybuildlog')
+        log.setLevelName('DEBUG')
+        log.debug("123 debug")
+        log.info("foobar info")
+        log.warn("justawarning")
+        log.raiseError = False
+        log.error("kaput")
+        log.raiseError = True
+        try:
+            log.exception("oops")
+        except EasyBuildError:
+            pass
+        logToFile(tmplog, enable=False)
+        logtxt = read_file(tmplog)
+
+        expected_logtxt = '\n'.join([
+            r"runpy.test_easybuildlog \[DEBUG\] :: 123 debug",
+            r"runpy.test_easybuildlog \[INFO\] :: foobar info",
+            r"runpy.test_easybuildlog \[WARNING\] :: justawarning",
+            r"runpy.test_easybuildlog \[ERROR\] :: EasyBuild crashed with an error \(at .* in .*\): kaput",
+            r"runpy.test_easybuildlog \[ERROR\] :: .*EasyBuild encountered an exception \(at .* in .*\): oops",
+            '',
+        ])
+        logtxt_regex = re.compile(r'^%s' % expected_logtxt, re.M)
+        self.assertTrue(logtxt_regex.search(logtxt), "Pattern '%s' found in %s" % (logtxt_regex.pattern, logtxt))
+
+        # wipe log so we can reuse it
+        write_file(tmplog, '')
+
+        # test formatting log messages by providing extra arguments
+        logToFile(tmplog, enable=True)
+        log.warn("%s", "bleh"),
+        log.info("%s+%s = %d", '4', '2', 42)
+        args = ['this', 'is', 'just', 'a', 'test']
+        log.debug("%s %s %s %s %s", *args)
+        log.raiseError = False
+        log.error("foo %s baz", 'baz')
+        log.raiseError = True
+        logToFile(tmplog, enable=False)
+        logtxt = read_file(tmplog)
+        expected_logtxt = '\n'.join([
+            r"runpy.test_easybuildlog \[WARNING\] :: bleh",
+            r"runpy.test_easybuildlog \[INFO\] :: 4\+2 = 42",
+            r"runpy.test_easybuildlog \[DEBUG\] :: this is just a test",
+            r"runpy.test_easybuildlog \[ERROR\] :: EasyBuild crashed with an error \(at .* in .*\): foo baz baz",
+            '',
+        ])
+        logtxt_regex = re.compile(r'^%s' % expected_logtxt, re.M)
+        self.assertTrue(logtxt_regex.search(logtxt), "Pattern '%s' found in %s" % (logtxt_regex.pattern, logtxt))
 
         # test deprecated behaviour: raise EasyBuildError on log.error and log.exception
         os.environ['EASYBUILD_DEPRECATED'] = '2.1'

From 449684a26bc06167d455e33b7cf75a91085d2514 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 10:52:17 +0100
Subject: [PATCH 0762/1356] bump required vsc-base version to 2.1 to have
 LoggedException around

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 627008004e..2407249b3c 100644
--- a/setup.py
+++ b/setup.py
@@ -106,5 +106,5 @@ def find_rel_test():
     provides=["eb"] + easybuild_packages,
     test_suite="test.framework.suite",
     zip_safe=False,
-    install_requires=["vsc-base >= 2.0.3"],
+    install_requires=["vsc-base >= 2.1.0"],
 )

From 30e1c1e3b12a405ab260691b91dbb6ecfdd71b6c Mon Sep 17 00:00:00 2001
From: Jens Timmerman <jens.timmerman@ugent.be>
Date: Wed, 18 Mar 2015 11:47:36 +0100
Subject: [PATCH 0763/1356] unpack_options should default to '' instead of None

---
 easybuild/framework/easyconfig/default.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 6c64f08dd9..90b072b38c 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -116,7 +116,7 @@
     'stop': [None, 'Keyword to halt the build process after a certain step.', BUILD],
     'tests': [[], ("List of test-scripts to run after install. A test script should return a "
                    "non-zero exit status to fail"), BUILD],
-    'unpack_options': [None, "Extra options for unpacking source", BUILD],
+    'unpack_options': ['', "Extra options for unpacking source", BUILD],
     'unwanted_env_vars': [[], "List of environment variables that shouldn't be set during build", BUILD],
     'versionprefix': ['', ('Additional prefix for software version '
                            '(placed before version and toolchain name)'), BUILD],

From 7222406d8e7b18305fbe0143af739e54c0723579 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 12:00:42 +0100
Subject: [PATCH 0764/1356] add support for --system-modules + unit test for
 use of system modules via EB config/easyconfig

---
 easybuild/framework/easyblock.py          | 14 ++++++++++--
 easybuild/framework/easyconfig/default.py |  1 +
 easybuild/tools/config.py                 |  1 +
 easybuild/tools/options.py                |  1 +
 test/framework/modules.py                 | 28 +++++++++++++++++++++++
 5 files changed, 43 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 8ab91c6dd6..d33754d388 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1305,8 +1305,18 @@ def prepare_step(self):
         Pre-configure step. Set's up the builddir just before starting configure
         """
         self.cfg['unwanted_env_vars'] = env.unset_env_vars(self.cfg['unwanted_env_vars'])
-        self.modules_tool.load(self.cfg['system_modules']) 
-	self.toolchain.prepare(self.cfg['onlytcmod'])
+
+        # load system modules first, before loading toolchain and dependencies
+        system_modules = build_option('system_modules')
+        if system_modules is None:
+            system_modules = []
+
+        self.log.info("Loading specified system modules: %s + %s", system_modules, self.cfg['system_modules'])
+        self.modules_tool.load(system_modules + self.cfg['system_modules'])
+
+        # prepare toolchain: load toolchain module and dependencies, set up build environment
+        self.toolchain.prepare(self.cfg['onlytcmod'])
+
         self.guess_start_dir()
 
     def configure_step(self):
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index c075060ed5..10a6be17d3 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -138,6 +138,7 @@
     'hiddendependencies': [[], "List of dependencies available as hidden modules", DEPENDENCIES],
     'osdependencies': [[], "OS dependencies that should be present on the system", DEPENDENCIES],
     'system_modules': [[], "System module dependencies that should be present on the system", DEPENDENCIES],
+
     # LICENSE easyconfig parameters
     'group': [None, "Name of the user group for which the software should be available", LICENSE],
     'key': [None, 'Key for installing software', LICENSE],
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 054b109d26..e50be2b03e 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -95,6 +95,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'skip',
         'stop',
         'suffix_modules_path',
+        'system_modules',
         'test_report_env_filter',
         'testoutput',
         'umask',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 8a643e2770..65659c8cfd 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -206,6 +206,7 @@ def override_options(self):
             'set-gid-bit': ("Set group ID bit on newly created directories", None, 'store_true', False),
             'sticky-bit': ("Set sticky bit on newly created directories", None, 'store_true', False),
             'skip-test-cases': ("Skip running test cases", None, 'store_true', False, 't'),
+            'system-modules': ("System modules to load", 'strlist', 'store', None),
             'umask': ("umask to use (e.g. '022'); non-user write permissions on install directories are removed",
                       None, 'store', None),
             'update-modules-tool-cache': ("Update modules tool cache file(s) after generating module file",
diff --git a/test/framework/modules.py b/test/framework/modules.py
index af492ec78f..2b8ea94fbf 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -38,7 +38,10 @@
 from unittest import TestLoader, main
 
 from easybuild.framework.easyblock import EasyBlock
+from easybuild.framework.easyconfig.easyconfig import EasyConfig
+from easybuild.tools import config
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import read_file, write_file
 from easybuild.tools.modules import get_software_root, get_software_version, get_software_libdir, modules_tool
 
 
@@ -319,6 +322,31 @@ def test_path_to_top_of_module_tree_categorized_hmns(self):
         path = modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
         self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
 
+    def test_system_modules(self):
+        """Test use of system modules."""
+        ectxt = read_file(os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb'))
+        toy_ec = os.path.join(self.test_prefix, 'toy-0.0-system-modules.eb')
+
+        # just specify some of the test modules we ship, doesn't matter where they come from
+        ectxt += "\nsystem_modules = ['GCC/4.6.4', 'ifort/2011.13.367']"
+        ectxt += "\nstart_dir = '%s'" % self.test_prefix  # require to be able to call prepare_step() method
+        write_file(toy_ec, ectxt)
+
+        opts = init_config(args=["--system-modules=CUDA/5.0.35-1,toy/0.0"])
+        self.assertEqual(opts.system_modules, ['CUDA/5.0.35-1', 'toy/0.0'])
+
+        build_options = {
+            'system_modules': opts.system_modules,
+            'valid_module_classes': config.module_classes(),
+        }
+        init_config(build_options=build_options)
+
+        ec = EasyConfig(toy_ec)
+        eb = EasyBlock(ec)
+
+        eb.prepare_step()
+        expected_modules = ['CUDA/5.0.35-1', 'toy/0.0', 'GCC/4.6.4', 'ifort/2011.13.367']
+        self.assertEqual(expected_modules, [x['mod_name'] for x in eb.modules_tool.list()])
 
 def suite():
     """ returns all the testcases in this module """

From f0ce2af542b7241901ccd6f75e56ddd56994f813 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 14:54:52 +0100
Subject: [PATCH 0765/1356] add unit test for self.cfg.update

---
 test/framework/easyconfig.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index f0f6b76937..a00524bbcf 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1031,6 +1031,27 @@ def set_ec_key(key):
         self.assertErrorRegex(EasyBuildError, error_regex, set_ec_key, 'therenosucheasyconfigparameterlikethis')
 
 
+    def test_update(self):
+        """Test use of update() method for EasyConfig instances."""
+        toy_ebfile = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb')
+        ec = EasyConfig(toy_ebfile)
+
+        # for string values: append
+        ec.update('unpack_options', '--strip-components=1')
+        self.assertEqual(ec['unpack_options'].strip(), '--strip-components=1')
+
+        ec.update('description', "- just a test")
+        self.assertEqual(ec['description'].strip(), "Toy C program. - just a test")
+
+        # spaces in between multiple updates for stirng values
+        ec.update('configopts', 'CC="$CC"')
+        ec.update('configopts', 'CXX="$CXX"')
+        self.assertTrue(ec['configopts'].strip().endswith('CC="$CC"  CXX="$CXX"'))
+
+        # for list values: extend
+        ec.update('patches', ['foo.patch', 'bar.patch'])
+        self.assertEqual(ec['patches'], ['toy-0.0_typo.patch', 'foo.patch', 'bar.patch'])
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(EasyConfigTest)

From 440922a83be3646faa813ccc77f628f627ab751e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 15:50:12 +0100
Subject: [PATCH 0766/1356] remove system_modules stuff

---
 easybuild/framework/easyblock.py          | 2 --
 easybuild/framework/easyconfig/default.py | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 023712dc25..1f403bfacc 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1306,10 +1306,8 @@ def prepare_step(self):
         """
         self.cfg['unwanted_env_vars'] = env.unset_env_vars(self.cfg['unwanted_env_vars'])
         self.toolchain.prepare(self.cfg['onlytcmod'])
-        self.modules_tool.load(self.cfg['system_modules']) 
         self.guess_start_dir()
 
-
     def configure_step(self):
         """Configure build  (abstract method)."""
         raise NotImplementedError
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index c075060ed5..feb1bdd5e9 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -137,7 +137,7 @@
     'dependencies': [[], "List of dependencies", DEPENDENCIES],
     'hiddendependencies': [[], "List of dependencies available as hidden modules", DEPENDENCIES],
     'osdependencies': [[], "OS dependencies that should be present on the system", DEPENDENCIES],
-    'system_modules': [[], "System module dependencies that should be present on the system", DEPENDENCIES],
+
     # LICENSE easyconfig parameters
     'group': [None, "Name of the user group for which the software should be available", LICENSE],
     'key': [None, 'Key for installing software', LICENSE],

From 87ca854473300712b2ef6389989f38699cb218a5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 16:01:48 +0100
Subject: [PATCH 0767/1356] rename Cray toolchains

---
 .../scripts/generate_crayprgenv_toolchains.py  | 18 +++++++++---------
 easybuild/toolchains/{cpec.py => craycce.py}   |  7 +++----
 easybuild/toolchains/{cpeg.py => craygnu.py}   |  6 +++---
 easybuild/toolchains/{cpei.py => crayintel.py} |  6 +++---
 4 files changed, 18 insertions(+), 19 deletions(-)
 rename easybuild/toolchains/{cpec.py => craycce.py} (87%)
 rename easybuild/toolchains/{cpeg.py => craygnu.py} (88%)
 rename easybuild/toolchains/{cpei.py => crayintel.py} (87%)

diff --git a/easybuild/scripts/generate_crayprgenv_toolchains.py b/easybuild/scripts/generate_crayprgenv_toolchains.py
index 68e862a569..58df605f6d 100755
--- a/easybuild/scripts/generate_crayprgenv_toolchains.py
+++ b/easybuild/scripts/generate_crayprgenv_toolchains.py
@@ -95,15 +95,15 @@
 
 print prgenvmods
 
-craymod_to_tc = {'PrgEnv-cray': 'cpec',
-                 'PrgEnv-intel': 'cpei',
-                 'PrgEnv-gnu': 'cpeg',
-                 'PrgEnv-pgi': 'cpep', }
-
-tc_to_craymod = {'cpec': 'PrgEnv-cray',
-                 'cpei': 'PrgEnv-intel',
-                 'cpeg': 'PrgEnv-gnu',
-                 'cpep': 'PrgEnv-pgi', }
+craymod_to_tc = {'PrgEnv-cray': 'CrayCCE',
+                 'PrgEnv-intel': 'CrayIntel',
+                 'PrgEnv-gnu': 'CrayGNU',
+                 'PrgEnv-pgi': 'CrayPGI', }
+
+tc_to_craymod = {'CrayCCE': 'PrgEnv-cray',
+                 'CrayIntel': 'PrgEnv-intel',
+                 'CrayGCC': 'PrgEnv-gnu',
+                 'CrayPGI': 'PrgEnv-pgi', }
 
 
 def modToTC(m):
diff --git a/easybuild/toolchains/cpec.py b/easybuild/toolchains/craycce.py
similarity index 87%
rename from easybuild/toolchains/cpec.py
rename to easybuild/toolchains/craycce.py
index f6d2c79041..612d28c58e 100644
--- a/easybuild/toolchains/cpec.py
+++ b/easybuild/toolchains/craycce.py
@@ -29,7 +29,6 @@
 
 from easybuild.toolchains.compiler.craypewrappers import CrayPEWrapperCray
 
-class cpec(CrayPEWrapperCray):
-    """Compiler toolchain with Cray cc,CC,ftn,LibSci,MPT,SHMEM."""
-    NAME = 'cpec'
-
+class CrayCCE(CrayPEWrapperCray):
+    """Compiler toolchain for Cray Programming Environment for Cray Compiling Environment (CCE) (PrgEnv-cray)."""
+    NAME = 'CrayCCE'
diff --git a/easybuild/toolchains/cpeg.py b/easybuild/toolchains/craygnu.py
similarity index 88%
rename from easybuild/toolchains/cpeg.py
rename to easybuild/toolchains/craygnu.py
index 90b51084ef..eb8cdeed41 100644
--- a/easybuild/toolchains/cpeg.py
+++ b/easybuild/toolchains/craygnu.py
@@ -29,6 +29,6 @@
 
 from easybuild.toolchains.compiler.craypewrappers import CrayPEWrapperGNU
 
-class cpeg(CrayPEWrapperGNU):
-    """Compiler toolchain with Cray cc,CC,ftn,LibSci,MPT,SHMEM."""
-    NAME = 'cpeg'
+class CrayGNU(CrayPEWrapperGNU):
+    """Compiler toolchain for Cray Programming Environment for GCC compilers (PrgEnv-gnu)."""
+    NAME = 'CrayGNU'
diff --git a/easybuild/toolchains/cpei.py b/easybuild/toolchains/crayintel.py
similarity index 87%
rename from easybuild/toolchains/cpei.py
rename to easybuild/toolchains/crayintel.py
index 00e0411e0e..8d546bf1c4 100644
--- a/easybuild/toolchains/cpei.py
+++ b/easybuild/toolchains/crayintel.py
@@ -29,6 +29,6 @@
 
 from easybuild.toolchains.compiler.craypewrappers import CrayPEWrapperIntel
 
-class cpei(CrayPEWrapperIntel):
-    """Compiler toolchain with Cray cc,CC,ftn,LibSci,MPT,SHMEM."""
-    NAME = 'cpei'
+class CrayIntel(CrayPEWrapperIntel):
+    """Compiler toolchain for Cray Programming Environment for Intel compilers (PrgEnv-intel)."""
+    NAME = 'CrayIntel'

From 456a9d7d82f3e4e650bbf5d0228bd25b85a1c808 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 16:35:25 +0100
Subject: [PATCH 0768/1356] tabs are evil

---
 easybuild/toolchains/compiler/craypewrappers.py | 6 +++---
 easybuild/toolchains/craygnu.py                 | 1 +
 easybuild/tools/run.py                          | 6 +++---
 easybuild/tools/toolchain/toolchain.py          | 8 ++++----
 4 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 411d0fed31..221d7fcbb4 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -55,7 +55,7 @@ class CrayPEWrapper(Compiler):
     COMPILER_FAMILY = TC_CONSTANT_CRAYPEWRAPPER
 
     COMPILER_UNIQUE_OPTS = {
-	    'dynamic': (True, """Generate dynamically linked executables and libraries."""),
+        'dynamic': (True, """Generate dynamically linked executables and libraries."""),
         'mpich-mt': (False, """Directs the driver to link in an alternate version of the Cray-MPICH library which
                                  provides fine-grained multi-threading support to applications that perform
                                  MPI operations within threaded regions."""),
@@ -63,9 +63,9 @@ class CrayPEWrapper(Compiler):
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-	    'pic': 'shared',
+        'pic': 'shared',
         'shared': 'dynamic',
-	    'static': 'static',
+        'static': 'static',
         'verbose': 'craype-verbose',
         'mpich-mt': 'craympich-mt',
     }
diff --git a/easybuild/toolchains/craygnu.py b/easybuild/toolchains/craygnu.py
index eb8cdeed41..e3b5660b9d 100644
--- a/easybuild/toolchains/craygnu.py
+++ b/easybuild/toolchains/craygnu.py
@@ -32,3 +32,4 @@
 class CrayGNU(CrayPEWrapperGNU):
     """Compiler toolchain for Cray Programming Environment for GCC compilers (PrgEnv-gnu)."""
     NAME = 'CrayGNU'
+    PRGENV_MODULE = 'PrgEnv-gnu/%(version)s'
diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index 6ccf1c1d77..90ff511d9c 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -64,7 +64,7 @@ def adjust_cmd(func):
     """Make adjustments to given command, if required."""
 
     def inner(cmd, *args, **kwargs):
-	# SuSE hack
+        # SuSE hack
         # - profile is not resourced, and functions (e.g. module) is not inherited
         #if 'PROFILEREAD' in os.environ and (len(os.environ['PROFILEREAD']) > 0):
         #    filepaths = ['/etc/profile.d/modules.sh']
@@ -74,9 +74,9 @@ def inner(cmd, *args, **kwargs):
         #            extra = ". %s &&%s" % (fp, extra)
         #        else:
         #            _log.warning("Can't find file %s" % fp)
-	#
+        #
         extra = ''
-	cmd = "%s %s" % (extra, cmd)
+        cmd = "%s %s" % (extra, cmd)
         return func(cmd, *args, **kwargs)
 
     return inner
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index afa2890e92..a912477604 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -334,12 +334,12 @@ def prepare(self, onlymod=None):
             self.log.error("No module found for toolchain: %s" % self.mod_short_name)
 
         
-	if self.name == DUMMY_TOOLCHAIN_NAME:
+        if self.name == DUMMY_TOOLCHAIN_NAME:
             if self.version == DUMMY_TOOLCHAIN_VERSION:
                 self.log.info('prepare: toolchain dummy mode, dummy version; not loading dependencies')
-		#@todo I keep this is as, but want dummy to do the same as a regular toolchain. Need to think this through.
-        	self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
-	    else:
+                #@todo I keep this is as, but want dummy to do the same as a regular toolchain. Need to think this through.
+                self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
+            else:
                 self.log.info('prepare: toolchain dummy mode and loading dependencies')
                 self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
             return

From 69854f1a46ad70cce1065de85d66ac44ada9960e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 16:57:35 +0100
Subject: [PATCH 0769/1356] load PrgEnv module via toolchain.prepare method

---
 easybuild/toolchains/compiler/craypewrappers.py | 14 ++++++++++++++
 easybuild/toolchains/craycce.py                 |  1 +
 easybuild/toolchains/craygnu.py                 |  2 +-
 easybuild/toolchains/crayintel.py               |  1 +
 easybuild/tools/toolchain/toolchain.py          |  6 ++++++
 5 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 221d7fcbb4..b04dbebb63 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -82,6 +82,20 @@ class CrayPEWrapper(Compiler):
     COMPILER_OPT_FLAGS = []  # or those
     COMPILER_PREC_FLAGS = []  # and those for sure not !
 
+    # name suffix for PrgEnv module that matches this toolchain
+    # e.g. 'gnu' => 'PrgEnv-gnu/<version>'
+    PRGENV_MODULE_NAME_TEMPLATE = 'PrgEnv-%(suffix)s/%(version)s'
+    PRGENV_MODULE_NAME_SUFFIX = None
+
+    def _pre_preprare(self):
+        """Load PrgEnv module."""
+        prgenv_mod_name = self.PRGENV_MODULE_NAME_TEMPLATE % {
+            'suffix': self.PRGENV_MODULE_NAME_SUFFIX,
+            'version': self.version,
+        }
+        self.log.info("Loading PrgEnv module '%s' for Cray toolchain %s" % (prgenv_mod_name, self.mod_short_name))
+        self.modules_tool.load([prgenv_mod_name])
+
     def _get_optimal_architecture(self):
         """On a Cray system we assume that the optimal architecture is controlled
            by loading a craype module that instructs the compiler to generate backend code
diff --git a/easybuild/toolchains/craycce.py b/easybuild/toolchains/craycce.py
index 612d28c58e..e3b2737a3d 100644
--- a/easybuild/toolchains/craycce.py
+++ b/easybuild/toolchains/craycce.py
@@ -32,3 +32,4 @@
 class CrayCCE(CrayPEWrapperCray):
     """Compiler toolchain for Cray Programming Environment for Cray Compiling Environment (CCE) (PrgEnv-cray)."""
     NAME = 'CrayCCE'
+    PRGENV_MODULE_NAME_SUFFIX = 'cray'
diff --git a/easybuild/toolchains/craygnu.py b/easybuild/toolchains/craygnu.py
index e3b5660b9d..aa89c5b51d 100644
--- a/easybuild/toolchains/craygnu.py
+++ b/easybuild/toolchains/craygnu.py
@@ -32,4 +32,4 @@
 class CrayGNU(CrayPEWrapperGNU):
     """Compiler toolchain for Cray Programming Environment for GCC compilers (PrgEnv-gnu)."""
     NAME = 'CrayGNU'
-    PRGENV_MODULE = 'PrgEnv-gnu/%(version)s'
+    PRGENV_MODULE_NAME_SUFFIX = 'gnu'
diff --git a/easybuild/toolchains/crayintel.py b/easybuild/toolchains/crayintel.py
index 8d546bf1c4..0917e11286 100644
--- a/easybuild/toolchains/crayintel.py
+++ b/easybuild/toolchains/crayintel.py
@@ -32,3 +32,4 @@
 class CrayIntel(CrayPEWrapperIntel):
     """Compiler toolchain for Cray Programming Environment for Intel compilers (PrgEnv-intel)."""
     NAME = 'CrayIntel'
+    PRGENV_MODULE_NAME_SUFFIX = 'intel'
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index a912477604..36c51fe905 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -317,6 +317,10 @@ def is_dep_in_toolchain_module(self, name):
         """Check whether a specific software name is listed as a dependency in the module for this toolchain."""
         return any(map(lambda m: self.mns.is_short_modname_for(m, name), self.toolchain_dep_mods))
 
+    def _pre_prepare(self):
+        """Toolchain-specific preparations thay should be done first."""
+        pass
+
     def prepare(self, onlymod=None):
         """
         Prepare a set of environment parameters based on name/version of toolchain
@@ -333,6 +337,8 @@ def prepare(self, onlymod=None):
         if not self._toolchain_exists():
             self.log.error("No module found for toolchain: %s" % self.mod_short_name)
 
+        # preliminary preparations first
+        self._pre_prepare()
         
         if self.name == DUMMY_TOOLCHAIN_NAME:
             if self.version == DUMMY_TOOLCHAIN_VERSION:

From 64d7da719cb4ce9cb22dc2cda0b4ec0adfe2fd9b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 17:11:17 +0100
Subject: [PATCH 0770/1356] pick craype module based on 'optarch' build option,
 and load it

---
 .../toolchains/compiler/craypewrappers.py     | 22 +++++++++++++------
 easybuild/tools/toolchain/compiler.py         | 10 ++++-----
 2 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index b04dbebb63..05763f7c72 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -36,9 +36,11 @@
 Cray's LibSci (BLAS/LAPACK et al), FFT library, etc.
 
 
-@author: Petar Forai
+@author: Petar Forai (IMP/IMBA, Austria)
+@author: Kenneth Hoste (Ghent University)
 """
 
+from easybuild.tools.config import build_option
 from easybuild.tools.toolchain.compiler import Compiler
 from easybuild.toolchains.compiler.gcc import Gcc
 from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
@@ -82,11 +84,14 @@ class CrayPEWrapper(Compiler):
     COMPILER_OPT_FLAGS = []  # or those
     COMPILER_PREC_FLAGS = []  # and those for sure not !
 
-    # name suffix for PrgEnv module that matches this toolchain
+    # template and name suffix for PrgEnv module that matches this toolchain
     # e.g. 'gnu' => 'PrgEnv-gnu/<version>'
     PRGENV_MODULE_NAME_TEMPLATE = 'PrgEnv-%(suffix)s/%(version)s'
     PRGENV_MODULE_NAME_SUFFIX = None
 
+    # template for craype module (determines code generator backend of Cray compiler wrappers)
+    CRAYPE_MODULE_NAME_TEMPLATE = 'craype-%(optarch)s'
+
     def _pre_preprare(self):
         """Load PrgEnv module."""
         prgenv_mod_name = self.PRGENV_MODULE_NAME_TEMPLATE % {
@@ -96,11 +101,14 @@ def _pre_preprare(self):
         self.log.info("Loading PrgEnv module '%s' for Cray toolchain %s" % (prgenv_mod_name, self.mod_short_name))
         self.modules_tool.load([prgenv_mod_name])
 
-    def _get_optimal_architecture(self):
-        """On a Cray system we assume that the optimal architecture is controlled
-           by loading a craype module that instructs the compiler to generate backend code
-           for that particular target"""
-        pass
+    def _set_optimal_architecture(self):
+        """Load craype module specified via 'optarch' build option."""
+        optarch = build_option('optarch')
+        if optarch is None:
+            # FIXME: try and guess which craype module to load? is there a way to do so?
+            raise NotImplementedError
+        else:
+            self.modules_tool.load([self.CRAYPE_MODULE_NAME_TEMPLATE % optarch])
 
     def _set_compiler_flags(self):
         """Collect the flags set, and add them as variables too"""
diff --git a/easybuild/tools/toolchain/compiler.py b/easybuild/tools/toolchain/compiler.py
index 06d0860aae..edae05d5ff 100644
--- a/easybuild/tools/toolchain/compiler.py
+++ b/easybuild/tools/toolchain/compiler.py
@@ -157,10 +157,8 @@ def _set_compiler_toolchainoptions(self):
                 getattr(self, 'COMPILER_%sUNIQUE_OPTS' % infix, None),
                 getattr(self, 'COMPILER_%sUNIQUE_OPTION_MAP' % infix, None),
             )
-            #print "added options for prefix %s" % prefix
 
-        # redefine optarch
-        self._get_optimal_architecture()
+        self._set_optimal_architecture()
 
     def _set_compiler_vars(self):
         """Set the compiler variables"""
@@ -257,7 +255,7 @@ def _set_compiler_flags(self):
         self.variables.nappend('F90FLAGS', fflags)
         self.variables.join('F90FLAGS', 'OPTFLAGS', 'PRECFLAGS')
 
-    def _get_optimal_architecture(self):
+    def _set_optimal_architecture(self):
         """ Get options for the current architecture """
         if self.arch is None:
             self.arch = systemtools.get_cpu_family()
@@ -269,11 +267,11 @@ def _get_optimal_architecture(self):
             optarch = self.COMPILER_OPTIMAL_ARCHITECTURE_OPTION[self.arch]
 
         if optarch is not None:
-            self.log.info("_get_optimal_architecture: using %s as optarch for %s." % (optarch, self.arch))
+            self.log.info("_set_optimal_architecture: using %s as optarch for %s." % (optarch, self.arch))
             self.options.options_map['optarch'] = optarch
 
         if 'optarch' in self.options.options_map and self.options.options_map.get('optarch', None) is None:
-            self.log.raiseException("_get_optimal_architecture: don't know how to set optarch for %s." % self.arch)
+            self.log.raiseException("_set_optimal_architecture: don't know how to set optarch for %s." % self.arch)
 
     def comp_family(self, prefix=None):
         """

From 6dc04a50df70c701d2f513e81888dfd451688c05 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 17:18:50 +0100
Subject: [PATCH 0771/1356] fix format issue for craype module

---
 easybuild/toolchains/compiler/craypewrappers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 05763f7c72..852f30f066 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -108,7 +108,7 @@ def _set_optimal_architecture(self):
             # FIXME: try and guess which craype module to load? is there a way to do so?
             raise NotImplementedError
         else:
-            self.modules_tool.load([self.CRAYPE_MODULE_NAME_TEMPLATE % optarch])
+            self.modules_tool.load([self.CRAYPE_MODULE_NAME_TEMPLATE % {'optarch': optarch}])
 
     def _set_compiler_flags(self):
         """Collect the flags set, and add them as variables too"""

From 5825143a62f1d8a6ade8344811ee9b1e1c2f60e6 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Wed, 18 Mar 2015 17:20:25 +0100
Subject: [PATCH 0772/1356] Move module path extension in module file

This is something that is required if you are using a Toolchain based name space. An example would be gpsmpi, where GCC is a dependency, this ensure that the path is extended by GCC before being extended by gpsmpi
---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 1f403bfacc..cfef7f5808 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1642,8 +1642,8 @@ def make_module_step(self, fake=False):
 
         txt = ''
         txt += self.make_module_description()
-        txt += self.make_module_extend_modpath()
         txt += self.make_module_dep()
+        txt += self.make_module_extend_modpath()
         txt += self.make_module_req()
         txt += self.make_module_extra()
         txt += self.make_module_footer()

From 8227cda3cb4f3eb5191eff0973faf4fbba5b60c8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 17:24:20 +0100
Subject: [PATCH 0773/1356] fix COMPILER_MODULE_NAME for Cray toolchains

---
 easybuild/toolchains/compiler/craypewrappers.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 852f30f066..1f676e4796 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -53,7 +53,9 @@
 class CrayPEWrapper(Compiler):
     """Base CrayPE compiler class"""
 
-    COMPILER_MODULE_NAME = None
+    # no toolchain components, so no modules to list here (empty toolchain definition w.r.t. components)
+    # the PrgEnv and craype are loaded, but are not considered actual toolchain components
+    COMPILER_MODULE_NAME = []
     COMPILER_FAMILY = TC_CONSTANT_CRAYPEWRAPPER
 
     COMPILER_UNIQUE_OPTS = {
@@ -137,7 +139,6 @@ def _set_compiler_flags(self):
 # Gcc's base is Compiler
 class CrayPEWrapperGNU(CrayPEWrapper):
     """Base Cray Programming Environment GNU compiler class"""
-    COMPILER_MODULE_NAME = ['PrgEnv-gnu']
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_GNU'
 
     def _set_compiler_vars(self):
@@ -165,8 +166,6 @@ def _set_compiler_vars(self):
 class CrayPEWrapperIntel(CrayPEWrapper):
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_INTEL'
 
-    COMPILER_MODULE_NAME = ['PrgEnv-intel']
-
     def _set_compiler_flags(self):
         if self.options.option("usewrappedcompiler"):
             COMPILER_UNIQUE_OPTS = IntelIccIfort.COMPILER_UNIQUE_OPTS
@@ -190,7 +189,6 @@ def _set_compiler_flags(self):
 
 class CrayPEWrapperCray(CrayPEWrapper):
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_CRAY'
-    COMPILER_MODULE_NAME = ['PrgEnv-cray']
 
     def _set_compiler_vars(self):
         super(CrayPEWrapperCray, self)._set_compiler_vars()

From 92e33c94f24ee7e5f320d48e852a37ae82028b14 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 18:23:25 +0100
Subject: [PATCH 0774/1356] move definitions of PRGENV_MODULE_NAME_SUFFIX to
 right location

---
 easybuild/toolchains/compiler/craypewrappers.py | 6 ++++++
 easybuild/toolchains/craycce.py                 | 1 -
 easybuild/toolchains/craygnu.py                 | 1 -
 easybuild/toolchains/crayintel.py               | 1 -
 4 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 1f676e4796..8c8a7ec16e 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -141,6 +141,8 @@ class CrayPEWrapperGNU(CrayPEWrapper):
     """Base Cray Programming Environment GNU compiler class"""
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_GNU'
 
+    PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
+
     def _set_compiler_vars(self):
         if self.options.option('usewrappedcompiler'):
             self.COMPILER_UNIQUE_OPTS = Gcc.COMPILER_UNIQUE_OPTS
@@ -166,6 +168,8 @@ def _set_compiler_vars(self):
 class CrayPEWrapperIntel(CrayPEWrapper):
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_INTEL'
 
+    PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
+
     def _set_compiler_flags(self):
         if self.options.option("usewrappedcompiler"):
             COMPILER_UNIQUE_OPTS = IntelIccIfort.COMPILER_UNIQUE_OPTS
@@ -190,5 +194,7 @@ def _set_compiler_flags(self):
 class CrayPEWrapperCray(CrayPEWrapper):
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_CRAY'
 
+    PRGENV_MODULE_NAME_SUFFIX = 'cray'  # PrgEnv-cray
+
     def _set_compiler_vars(self):
         super(CrayPEWrapperCray, self)._set_compiler_vars()
diff --git a/easybuild/toolchains/craycce.py b/easybuild/toolchains/craycce.py
index e3b2737a3d..612d28c58e 100644
--- a/easybuild/toolchains/craycce.py
+++ b/easybuild/toolchains/craycce.py
@@ -32,4 +32,3 @@
 class CrayCCE(CrayPEWrapperCray):
     """Compiler toolchain for Cray Programming Environment for Cray Compiling Environment (CCE) (PrgEnv-cray)."""
     NAME = 'CrayCCE'
-    PRGENV_MODULE_NAME_SUFFIX = 'cray'
diff --git a/easybuild/toolchains/craygnu.py b/easybuild/toolchains/craygnu.py
index aa89c5b51d..eb8cdeed41 100644
--- a/easybuild/toolchains/craygnu.py
+++ b/easybuild/toolchains/craygnu.py
@@ -32,4 +32,3 @@
 class CrayGNU(CrayPEWrapperGNU):
     """Compiler toolchain for Cray Programming Environment for GCC compilers (PrgEnv-gnu)."""
     NAME = 'CrayGNU'
-    PRGENV_MODULE_NAME_SUFFIX = 'gnu'
diff --git a/easybuild/toolchains/crayintel.py b/easybuild/toolchains/crayintel.py
index 0917e11286..8d546bf1c4 100644
--- a/easybuild/toolchains/crayintel.py
+++ b/easybuild/toolchains/crayintel.py
@@ -32,4 +32,3 @@
 class CrayIntel(CrayPEWrapperIntel):
     """Compiler toolchain for Cray Programming Environment for Intel compilers (PrgEnv-intel)."""
     NAME = 'CrayIntel'
-    PRGENV_MODULE_NAME_SUFFIX = 'intel'

From 7df15fca6ad64449ec226f7a41d6c868889b1035 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 19:02:45 +0100
Subject: [PATCH 0775/1356] error out when optarch build option is not set for
 Cray toolchain

---
 easybuild/toolchains/compiler/craypewrappers.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 8c8a7ec16e..38701abdde 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -107,8 +107,7 @@ def _set_optimal_architecture(self):
         """Load craype module specified via 'optarch' build option."""
         optarch = build_option('optarch')
         if optarch is None:
-            # FIXME: try and guess which craype module to load? is there a way to do so?
-            raise NotImplementedError
+            self.log.error("Don't know which 'craype' module to load, 'optarch' build option is unspecified.")
         else:
             self.modules_tool.load([self.CRAYPE_MODULE_NAME_TEMPLATE % {'optarch': optarch}])
 

From b77ff5ec4587634c966e1c66e8bd556e6da32621 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Mar 2015 19:18:52 +0100
Subject: [PATCH 0776/1356] style cleanup and FIXMEs

---
 .../toolchains/compiler/craypewrappers.py     | 71 +++++++------------
 1 file changed, 27 insertions(+), 44 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 38701abdde..9a08806258 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2012-2014 Ghent University
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -27,7 +27,7 @@
 The Cray compiler wrappers are actually way more than just a compiler drivers.
 
 The basic concept is that the compiler driver knows how to invoke the true underlying
-compiler with the compiler's specific options tuned to cray systems.
+compiler with the compiler's specific options tuned to Cray systems.
 
 That means that certain defaults are set that are specific to Cray's computers.
 
@@ -45,13 +45,12 @@
 from easybuild.toolchains.compiler.gcc import Gcc
 from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
 
-import easybuild.tools.systemtools as systemtools
 
 TC_CONSTANT_CRAYPEWRAPPER = "CRAYPEWRAPPER"
 
 
 class CrayPEWrapper(Compiler):
-    """Base CrayPE compiler class"""
+    """Generic support for using Cray compiler wrappers"""
 
     # no toolchain components, so no modules to list here (empty toolchain definition w.r.t. components)
     # the PrgEnv and craype are loaded, but are not considered actual toolchain components
@@ -59,10 +58,11 @@ class CrayPEWrapper(Compiler):
     COMPILER_FAMILY = TC_CONSTANT_CRAYPEWRAPPER
 
     COMPILER_UNIQUE_OPTS = {
-        'dynamic': (True, """Generate dynamically linked executables and libraries."""),
-        'mpich-mt': (False, """Directs the driver to link in an alternate version of the Cray-MPICH library which
-                                 provides fine-grained multi-threading support to applications that perform
-                                 MPI operations within threaded regions."""),
+        # FIXME: (kehoste) how is this different from the existing 'shared' toolchain option? just map 'shared' to '-dynamic'? (already done)
+        'dynamic': (True, "Generate dynamically linked executables and libraries."),
+        'mpich-mt': (False, "Directs the driver to link in an alternate version of the Cray-MPICH library which \
+                             provides fine-grained multi-threading support to applications that perform \
+                             MPI operations within threaded regions."),
         'usewrappedcompiler': (False, "Use the embedded compiler instead of the wrapper"),
     }
 
@@ -74,14 +74,13 @@ class CrayPEWrapper(Compiler):
         'mpich-mt': 'craympich-mt',
     }
 
-    #COMPILER_PREC_FLAGS = ['strict', 'precise', 'defaultprec', 'loose', 'veryloose']  # precision flags, ordered !
-
     COMPILER_CC = 'cc'
     COMPILER_CXX = 'CC'
 
     COMPILER_F77 = 'ftn'
     COMPILER_F90 = 'ftn'
 
+    # FIXME (kehoste) hmmmm, really? then how do you control optimisation, precision when using the Cray wrappers?
     COMPILER_FLAGS = []  # we dont have this for the wrappers
     COMPILER_OPT_FLAGS = []  # or those
     COMPILER_PREC_FLAGS = []  # and those for sure not !
@@ -111,6 +110,8 @@ def _set_optimal_architecture(self):
         else:
             self.modules_tool.load([self.CRAYPE_MODULE_NAME_TEMPLATE % {'optarch': optarch}])
 
+    # FIXME: (kehoste) is it really needed to customise this?
+    # this looks like a workaround for setting the COMPILER_*_FLAGS lists empty?
     def _set_compiler_flags(self):
         """Collect the flags set, and add them as variables too"""
 
@@ -137,63 +138,45 @@ def _set_compiler_flags(self):
 
 # Gcc's base is Compiler
 class CrayPEWrapperGNU(CrayPEWrapper):
-    """Base Cray Programming Environment GNU compiler class"""
+    """Support for using the Cray GNU compiler wrappers."""
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_GNU'
 
     PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
 
     def _set_compiler_vars(self):
+        """Set compiler variables, either for the compiler wrapper, or the underlying compiler."""
         if self.options.option('usewrappedcompiler'):
-            self.COMPILER_UNIQUE_OPTS = Gcc.COMPILER_UNIQUE_OPTS
-            self.COMPILER_UNIQUE_OPTION_MAP = Gcc.COMPILER_UNIQUE_OPTION_MAP
-
-            self.COMPILER_CC = Gcc.COMPILER_CC
-            self.COMPILER_CXX = Gcc.COMPILER_CXX
-            self.COMPILER_C_UNIQUE_FLAGS = []
+            self.log.info("Using underlying compiler, as specified by the %s class" % Gcc)
 
-            self.COMPILER_F77 = Gcc.COMPILER_F77
-            self.COMPILER_F90 = Gcc.COMPILER_F90
-            self.COMPILER_F_UNIQUE_FLAGS = Gcc.COMPILER_F_UNIQUE_FLAGS
-
-        else:
-            pass
+            comp_attrs = ['UNIQUE_OPTS', 'UNIQUE_OPTION_MAP', 'CC', 'CXX', 'C_UNIQUE_FLAGS',
+                          'F77', 'F90', 'F_UNIQUE_FLAGS']
+            for attr_name in ['COMPILER_%s' % a for a in comp_attrs]:
+                setattr(self, attr_name, getattr(IntelIccIfort, attr_name))
 
         super(CrayPEWrapperGNU,self)._set_compiler_vars()
 
 
-
-
-
 class CrayPEWrapperIntel(CrayPEWrapper):
+    """Support for using the Cray Intel compiler wrappers."""
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_INTEL'
 
     PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
 
     def _set_compiler_flags(self):
+        """Set compiler variables, either for the compiler wrapper, or the underlying compiler."""
         if self.options.option("usewrappedcompiler"):
-            COMPILER_UNIQUE_OPTS = IntelIccIfort.COMPILER_UNIQUE_OPTS
-            COMPILER_UNIQUE_OPTION_MAP = IntelIccIfort.COMPILER_UNIQUE_OPTION_MAP
+            self.log.info("Using underlying compiler, as specified by the %s class" % IntelIccIfort)
 
-            COMPILER_CC = IntelIccIfort.COMPILER_CC
+            comp_attrs = ['UNIQUE_OPTS', 'UNIQUE_OPTION_MAP', 'CC', 'CXX', 'C_UNIQUE_FLAGS',
+                          'F77', 'F90', 'F_UNIQUE_FLAGS']
+            for attr_name in ['COMPILER_%s' % a for a in comp_attrs] + ['LINKER_TOGGLE_STATIC_DYNAMIC']:
+                setattr(self, attr_name, getattr(IntelIccIfort, attr_name))
 
-            COMPILER_CXX = IntelIccIfort.COMPILER_CXX
-            COMPILER_C_UNIQUE_FLAGS = IntelIccIfort.COMPILER_C_UNIQUE_FLAGS
-
-            COMPILER_F77 = IntelIccIfort.COMPILER_F77
-            COMPILER_F90 = IntelIccIfort.COMPILER_F90
-            COMPILER_F_UNIQUE_FLAGS = IntelIccIfort.COMPILER_F_UNIQUE_FLAGS
-
-            LINKER_TOGGLE_STATIC_DYNAMIC = IntelIccIfort.LINKER_TOGGLE_STATIC_DYNAMIC
-
-            super(CrayPEWrapperIntel, self).set_compiler_flags()
-        else:
-            super(CrayPEWrapper, self)._set_compiler_flags()
+        super(CrayPEWrapperIntel, self).set_compiler_flags()
 
 
 class CrayPEWrapperCray(CrayPEWrapper):
+    """Support for using the Cray CCE compiler wrappers."""
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_CRAY'
 
     PRGENV_MODULE_NAME_SUFFIX = 'cray'  # PrgEnv-cray
-
-    def _set_compiler_vars(self):
-        super(CrayPEWrapperCray, self)._set_compiler_vars()

From f57e704cb8cf20d78c431235c19777e2180e1a0e Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Wed, 18 Mar 2015 23:48:10 +0200
Subject: [PATCH 0777/1356] Removed the script to initially generated the TC
 configs as this isnt needed at all.

---
 .../scripts/generate_crayprgenv_toolchains.py | 141 ------------------
 1 file changed, 141 deletions(-)
 delete mode 100755 easybuild/scripts/generate_crayprgenv_toolchains.py

diff --git a/easybuild/scripts/generate_crayprgenv_toolchains.py b/easybuild/scripts/generate_crayprgenv_toolchains.py
deleted file mode 100755
index 58df605f6d..0000000000
--- a/easybuild/scripts/generate_crayprgenv_toolchains.py
+++ /dev/null
@@ -1,141 +0,0 @@
-#!/usr/bin/env python
-# #
-# Copyright 2014 Petar Forai
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-##
-
-
-import easybuild.tools.modules as modules
-import easybuild.tools.config as config
-import easybuild.tools.options as eboptions
-
-import easybuild.tools.options as eboptions
-from easybuild.tools import config, modules
-from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.config import build_option
-from easybuild.tools.filetools import which
-from easybuild.tools.modules import modules_tool, Lmod
-from easybuild.tools.config import build_option, get_modules_tool
-
-from collections import namedtuple
-import tempfile, os
-
-#_log = fancylogger.getLogger('craytcgenerator', fname=False)
-
-
-EB_EC_FILE_TMPLT = """
-easyblock = 'Toolchain'
-
-name = '%(name)s'
-version = '%(version)s'
-
-homepage = 'http://hpcugent.github.io/easybuild/'
-description = \"\"\"This is a shim module for having EB pick up the Cray
-Programming Environment (PrgEnv-*) modules. This module implements the EB
-toolchain module for each of the cray modules.\"\"\"
-
-toolchain = {'name': 'dummy', 'version': 'dummy'}
-
-source_urls = []
-sources = []
-dependencies = []
-
-moduleclass = 'toolchain'
-
-modtclfooter = \"\"\"
-module load %(craymodule)s/%(version)s
-module load %(craypetarget)s
-\"\"\"
-
-"""
-
-eb_go = eboptions.parse_options()
-config.init(eb_go.options, eb_go.get_options_by_section('config'))
-
-config.init_build_options({'suffix_modules_path':'all'})
-config.set_tmpdir()
-
-
-
-#FIXME: This needs to be usable from not only Lmod, but other environment modules tool in EasyBuild.
-# from easybuild.tools.modules import get_software_root, modules_tool
-# use something like self.modules_tool = modules_tool()
-ml = modules_tool()
-
-prgenvmods = []
-
-print "Running module avail commands for the Cray compiler wrappers."
-#print "using modules tool " + str(ml.__class__.__name__)
-
-prgenvmods = ml.available("PrgEnv")
-
-if len(prgenvmods) == 0:
-    print """No Cray Programming Environment modules are visible in the modules tool.\n
-             Make sure to include them in $MODULEPATH or this is not a Cray system."""
-
-print prgenvmods
-
-craymod_to_tc = {'PrgEnv-cray': 'CrayCCE',
-                 'PrgEnv-intel': 'CrayIntel',
-                 'PrgEnv-gnu': 'CrayGNU',
-                 'PrgEnv-pgi': 'CrayPGI', }
-
-tc_to_craymod = {'CrayCCE': 'PrgEnv-cray',
-                 'CrayIntel': 'PrgEnv-intel',
-                 'CrayGCC': 'PrgEnv-gnu',
-                 'CrayPGI': 'PrgEnv-pgi', }
-
-
-def modToTC(m):
-    modname, version = m.split('/')
-    if modname not in craymod_to_tc:
-        print "Can't map Cray module name to EasyBuild toolchain name module."
-    else:
-        # The TC name for a given cray module name is defined to be the mapping table craymod_to_tc
-        # and the EB toolchain version is identical to the version of the PrgEnv module itself.
-        # Cray already does all the work of coming up with numbers, so let's use this.
-        toolchain = namedtuple('toolchain', 'toolchainname , toolchainversion')
-        return toolchain(toolchainname=craymod_to_tc[modname], toolchainversion=version)
-
-
-def generate_EB_config(tmpdir, craytc):
-    name = craytc.toolchainname
-    version = craytc.toolchainversion
-    ebconfigfile = os.path.join(tmpdir, '%s-%s.eb' % (name, version))
-    print "Generating file ", ebconfigfile
-    f = open(ebconfigfile, "w")
-    f.write(EB_EC_FILE_TMPLT % {'name': name,
-                                'version': version,
-                                'craymodule': tc_to_craymod[name],
-                                'craypetarget': 'craype-haswell', #@todo this needs to ne somehow better or at least an option!
-    })
-    f.close()
-
-
-tmpdir = tempfile.mkdtemp()
-print tmpdir
-os.chdir(tmpdir)
-
-for mod in prgenvmods:
-    toolchain = modToTC(mod)
-    generate_EB_config(tmpdir, toolchain)

From bef539c5e4766916ac9c6f52c1f9faa14ff9761e Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Wed, 18 Mar 2015 23:55:04 +0200
Subject: [PATCH 0778/1356] Cleanup for PR, restored dummy dummy semantics.

---
 easybuild/tools/toolchain/toolchain.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 36c51fe905..2a6d284085 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -343,8 +343,6 @@ def prepare(self, onlymod=None):
         if self.name == DUMMY_TOOLCHAIN_NAME:
             if self.version == DUMMY_TOOLCHAIN_VERSION:
                 self.log.info('prepare: toolchain dummy mode, dummy version; not loading dependencies')
-                #@todo I keep this is as, but want dummy to do the same as a regular toolchain. Need to think this through.
-                self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
             else:
                 self.log.info('prepare: toolchain dummy mode and loading dependencies')
                 self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])

From 0a3627cccaa4ae0e5028d88f7fa602743ce2e7e0 Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Thu, 19 Mar 2015 00:00:41 +0200
Subject: [PATCH 0779/1356] Restored run.py for cleanup.

---
 easybuild/tools/run.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index 90ff511d9c..5309db63af 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -66,17 +66,17 @@ def adjust_cmd(func):
     def inner(cmd, *args, **kwargs):
         # SuSE hack
         # - profile is not resourced, and functions (e.g. module) is not inherited
-        #if 'PROFILEREAD' in os.environ and (len(os.environ['PROFILEREAD']) > 0):
-        #    filepaths = ['/etc/profile.d/modules.sh']
-        #    extra = ''
-        #    for fp in filepaths:
-        #        if os.path.exists(fp):
-        #            extra = ". %s &&%s" % (fp, extra)
-        #        else:
-        #            _log.warning("Can't find file %s" % fp)
-        #
-        extra = ''
-        cmd = "%s %s" % (extra, cmd)
+        if 'PROFILEREAD' in os.environ and (len(os.environ['PROFILEREAD']) > 0):
+            filepaths = ['/etc/profile.d/modules.sh']
+            extra = ''
+            for fp in filepaths:
+                if os.path.exists(fp):
+                    extra = ". %s &&%s" % (fp, extra)
+                else:
+                    _log.warning("Can't find file %s" % fp)
+
+            cmd = "%s %s" % (extra, cmd)
+
         return func(cmd, *args, **kwargs)
 
     return inner

From 0fe7e1b5d4000610d04006a65e6defa0043fd3c7 Mon Sep 17 00:00:00 2001
From: ocaisa <a.ocais@fz-juelich.de>
Date: Fri, 20 Mar 2015 07:44:23 +0100
Subject: [PATCH 0780/1356] expand_toolchain_load still required

We currently still need to expand the toolchain load because of the current lack of support for subtoolchains within the framework
---
 easybuild/tools/module_naming_scheme/toolchain_mns.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/module_naming_scheme/toolchain_mns.py b/easybuild/tools/module_naming_scheme/toolchain_mns.py
index fc8a47b9e5..03397c52eb 100644
--- a/easybuild/tools/module_naming_scheme/toolchain_mns.py
+++ b/easybuild/tools/module_naming_scheme/toolchain_mns.py
@@ -69,5 +69,5 @@ def expand_toolchain_load(self):
         Determine whether load statements for a toolchain should be expanded to load statements for its dependencies.
         This is useful when toolchains are not exposed to users.
         """
-	# In our case we have to load the toolchains because they are explicitly exposed when extending the module path
-        return False
+	# In our case we still have to load the toolchains because they are explicitly exposed when extending the module path
+        return True

From 2571ebf09e0a11d56d6f1eb331afd5f1a4fea3c3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 23 Mar 2015 18:52:31 +0100
Subject: [PATCH 0781/1356] let tools.environment keep track of original
 environment, try and avoid confusing between *original* environemt and other
 os.environ copies

---
 easybuild/framework/easyblock.py | 30 +++++++++++++++---------------
 easybuild/main.py                |  4 ++--
 easybuild/tools/environment.py   |  6 ++++++
 easybuild/tools/modules.py       | 27 +++++++++++++--------------
 4 files changed, 36 insertions(+), 31 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 1f403bfacc..e3e1b94b0a 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -158,9 +158,6 @@ def __init__(self, ec):
         self.logdebug = build_option('debug')
         self.postmsg = ''  # allow a post message to be set, which can be shown as last output
 
-        # original environ will be set later
-        self.orig_environ = {}
-
         # list of loaded modules
         self.loaded_modules = []
 
@@ -176,8 +173,8 @@ def __init__(self, ec):
         # original module path
         self.orig_modulepath = os.getenv('MODULEPATH')
 
-        # keep track of original environment, so we restore it if needed
-        self.orig_environ = copy.deepcopy(os.environ)
+        # keep track of initial environment we start in, so we can restore it if needed
+        self.initial_environ = copy.deepcopy(os.environ)
 
         # initialize logger
         self._init_log()
@@ -973,7 +970,7 @@ def load_module(self, mod_paths=None, purge=True):
                 mod_paths = []
             all_mod_paths = mod_paths + ActiveMNS().det_init_modulepaths(self.cfg)
             mods = [self.full_mod_name]
-            self.modules_tool.load(mods, mod_paths=all_mod_paths, purge=purge, orig_env=self.orig_environ)
+            self.modules_tool.load(mods, mod_paths=all_mod_paths, purge=purge, init_env=self.initial_environ)
         else:
             self.log.warning("Not loading module, since self.full_mod_name is not set.")
 
@@ -981,9 +978,8 @@ def load_fake_module(self, purge=False):
         """
         Create and load fake module.
         """
-
-        # take a copy of the environment before loading the fake module, so we can restore it
-        orig_env = copy.deepcopy(os.environ)
+        # take a copy of the current environment before loading the fake module, so we can restore it
+        env = copy.deepcopy(os.environ)
 
         # create fake module
         fake_mod_path = self.make_module_step(True)
@@ -993,13 +989,13 @@ def load_fake_module(self, purge=False):
         modtool.prepend_module_path(fake_mod_path)
         self.load_module(purge=purge)
 
-        return (fake_mod_path, orig_env)
+        return (fake_mod_path, env)
 
     def clean_up_fake_module(self, fake_mod_data):
         """
         Clean up fake module.
         """
-        fake_mod_path, orig_env = fake_mod_data
+        fake_mod_path, env = fake_mod_data
         # unload module and remove temporary module directory
         # self.full_mod_name might not be set (e.g. during unit tests)
         if fake_mod_path and self.full_mod_name is not None:
@@ -1014,7 +1010,7 @@ def clean_up_fake_module(self, fake_mod_data):
             self.log.warning("Not unloading module, since self.full_mod_name is not set.")
 
         # restore original environment
-        restore_env(orig_env)
+        restore_env(env)
 
     def load_dependency_modules(self):
         """Load dependency modules."""
@@ -1828,11 +1824,11 @@ def run_all_steps(self, run_test_cases):
         return True
 
 
-def build_and_install_one(ecdict, orig_environ):
+def build_and_install_one(ecdict, init_env):
     """
     Build the software
     @param ecdict: dictionary contaning parsed easyconfig + metadata
-    @param orig_environ: original environment (used to reset environment)
+    @param init_env: original environment (used to reset environment)
     """
     silent = build_option('silent')
 
@@ -1845,7 +1841,7 @@ def build_and_install_one(ecdict, orig_environ):
     # restore original environment
     _log.info("Resetting environment")
     filetools.errors_found_in_log = 0
-    restore_env(orig_environ)
+    restore_env(init_env)
 
     cwd = os.getcwd()
 
@@ -2039,6 +2035,10 @@ def perform_step(step, obj, method, logfile):
         apps.append(instance)
 
     base_dir = os.getcwd()
+
+    # keep track of environment right before initiating builds
+    # note: may be different from ORIG_OS_ENVIRON, since EasyBuild may have defined additional env vars itself by now
+    # e.g. via easyconfig.handle_allowed_system_deps
     base_env = copy.deepcopy(os.environ)
     succes = []
 
diff --git a/easybuild/main.py b/easybuild/main.py
index c110727529..22b095eacf 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -100,13 +100,13 @@ def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
     # obtain a copy of the starting environment so each build can start afresh
     # we shouldn't use the environment from init_session_state, since relevant env vars might have been set since
     # e.g. via easyconfig.handle_allowed_system_deps
-    orig_environ = copy.deepcopy(os.environ)
+    init_env = copy.deepcopy(os.environ)
 
     res = []
     for ec in ecs:
         ec_res = {}
         try:
-            (ec_res['success'], app_log, err) = build_and_install_one(ec, orig_environ)
+            (ec_res['success'], app_log, err) = build_and_install_one(ec, init_env)
             ec_res['log_file'] = app_log
             if not ec_res['success']:
                 ec_res['err'] = EasyBuildError(err)
diff --git a/easybuild/tools/environment.py b/easybuild/tools/environment.py
index 45b5b2bc44..d919acf567 100644
--- a/easybuild/tools/environment.py
+++ b/easybuild/tools/environment.py
@@ -28,11 +28,16 @@
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
 """
+import copy
 import os
 from vsc.utils import fancylogger
 from vsc.utils.missing import shell_quote
 
 
+# take copy of original environemt, so we can restore (parts of) it later
+ORIG_OS_ENVIRON = copy.deepcopy(os.environ)
+
+
 _log = fancylogger.getLogger('environment', fname=False)
 
 _changes = {}
@@ -71,6 +76,7 @@ def get_changes():
     """
     return _changes
 
+
 def setvar(key, value):
     """
     put key in the environment with value
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index dc730b9295..2b1b05e253 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -47,7 +47,7 @@
 
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_modules_tool, install_path
-from easybuild.tools.environment import restore_env
+from easybuild.tools.environment import ORIG_OS_ENVIRON, restore_env
 from easybuild.tools.filetools import convert_name, mkdir, read_file, path_matches, which
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.run import run_cmd
@@ -59,10 +59,9 @@
 VERSION_ENV_VAR_NAME_PREFIX = "EBVERSION"
 DEVEL_ENV_VAR_NAME_PREFIX = "EBDEVEL"
 
-# keep track of original $LD_LIBRARY_PATH/$LD_PRELOAD, because it can change by loading modules and break module command
+# environment variables to reset/restore when running a module command (to avoid breaking it)
 # see e.g., https://bugzilla.redhat.com/show_bug.cgi?id=719785
 LD_ENV_VAR_KEYS = ['LD_LIBRARY_PATH', 'LD_PRELOAD']
-ORIG_ENVIRON = dict([(key, os.getenv(key, '')) for key in LD_ENV_VAR_KEYS])
 
 output_matchers = {
     # matches whitespace and module-listing headers
@@ -375,14 +374,14 @@ def exists(self, mod_name):
         """NO LONGER SUPPORTED: use exist method instead"""
         self.log.nosupport("exists(<mod_name>) is not supported anymore, use exist([<mod_name>]) instead", '2.0')
 
-    def load(self, modules, mod_paths=None, purge=False, orig_env=None):
+    def load(self, modules, mod_paths=None, purge=False, init_env=None):
         """
         Load all requested modules.
 
         @param modules: list of modules to load
         @param mod_paths: list of module paths to activate before loading
         @param purge: whether or not a 'module purge' should be run before loading
-        @param orig_env: original environment to restore after running 'module purge'
+        @param init_env: original environment to restore after running 'module purge'
         """
         if mod_paths is None:
             mod_paths = []
@@ -390,9 +389,9 @@ def load(self, modules, mod_paths=None, purge=False, orig_env=None):
         # purge all loaded modules if desired
         if purge:
             self.purge()
-            # restore original environment if provided
-            if orig_env is not None:
-                restore_env(orig_env)
+            # restore initial environment if provided
+            if init_env is not None:
+                restore_env(init_env)
 
         # make sure $MODULEPATH is set correctly after purging
         self.check_module_path()
@@ -482,7 +481,7 @@ def run_module(self, *args, **kwargs):
         # change to original $LD_LIBRARY_PATH and $LD_PRELOAD before running module command
         environ = os.environ.copy()
         for key in LD_ENV_VAR_KEYS:
-            environ[key] = ORIG_ENVIRON[key]
+            environ[key] = ORIG_OS_ENVIRON.get(key, '')
             self.log.debug("Adjusted %s from '%s' to '%s'" % (key, os.environ.get(key, ''), environ[key]))
 
         # prefix if a particular shell is specified, using shell argument to Popen doesn't work (no output produced (?))
@@ -601,7 +600,7 @@ def modpath_extensions_for(self, mod_names):
         self.log.debug("Determining $MODULEPATH extensions for modules %s" % mod_names)
 
         # copy environment so we can restore it
-        orig_env = os.environ.copy()
+        env = os.environ.copy()
 
         modpath_exts = {}
         for mod_name in mod_names:
@@ -617,8 +616,8 @@ def modpath_extensions_for(self, mod_names):
                 # this is required to obtain the list of $MODULEPATH extensions they make (via 'module show')
                 self.load([mod_name])
 
-        # restore original environment (modules may have been loaded above)
-        restore_env(orig_env)
+        # restore environment (modules may have been loaded above)
+        restore_env(env)
 
         return modpath_exts
 
@@ -654,7 +653,7 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
         @param modpath_exts: list of module path extensions for each of the dependency modules
         """
         # copy environment so we can restore it
-        orig_env = os.environ.copy()
+        env = os.environ.copy()
 
         if path_matches(full_mod_subdir, top_paths):
             self.log.debug("Top of module tree reached with %s (module subdir: %s)" % (mod_name, full_mod_subdir))
@@ -688,7 +687,7 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
                 self.load([dep])
 
         # restore original environment (modules may have been loaded above)
-        restore_env(orig_env)
+        restore_env(env)
 
         path = mods_to_top[:]
         if mods_to_top:

From 7f0154980ce462ac233469b6e5d427e9df61b985 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 24 Mar 2015 10:07:40 +0100
Subject: [PATCH 0782/1356] also copy rotated logs

---
 easybuild/framework/easyblock.py | 29 +++++------------------------
 easybuild/tools/filetools.py     | 31 +++++++++++++++++++++++++++++++
 test/framework/filetools.py      | 28 ++++++++++++++++++++++++++++
 3 files changed, 64 insertions(+), 24 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 1f403bfacc..aa16469e44 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -63,7 +63,7 @@
 from easybuild.tools.environment import restore_env
 from easybuild.tools.filetools import DEFAULT_CHECKSUM
 from easybuild.tools.filetools import adjust_permissions, apply_patch, convert_name, download_file, encode_class_name
-from easybuild.tools.filetools import extract_file, mkdir, read_file, rmtree2
+from easybuild.tools.filetools import extract_file, mkdir, move_logs, read_file, rmtree2
 from easybuild.tools.filetools import write_file, compute_checksum, verify_checksum
 from easybuild.tools.run import run_cmd
 from easybuild.tools.jenkins import write_to_xml
@@ -1928,14 +1928,9 @@ def build_and_install_one(ecdict, orig_environ):
 
         # cleanup logs
         app.close_log()
-        try:
-            mkdir(new_log_dir, parents=True)
-            log_fn = os.path.basename(get_log_filename(app.name, app.version))
-            application_log = os.path.join(new_log_dir, log_fn)
-            shutil.move(app.logfile, application_log)
-            _log.debug("Moved log file %s to %s" % (app.logfile, application_log))
-        except (IOError, OSError), err:
-            print_error("Failed to move log file %s to new log file %s: %s" % (app.logfile, application_log, err))
+        log_fn = os.path.basename(get_log_filename(app.name, app.version))
+        application_log = os.path.join(new_log_dir, log_fn)
+        move_logs(app.logfile, application_log)
 
         try:
             newspec = os.path.join(new_log_dir, "%s-%s.eb" % (app.name, det_full_ec_version(app.cfg)))
@@ -2067,21 +2062,7 @@ def perform_step(step, obj, method, logfile):
 
             # close log and move it
             app.close_log()
-            try:
-                # retain old logs
-                if os.path.exists(applog):
-                    i = 0
-                    old_applog = "%s.%d" % (applog, i)
-                    while os.path.exists(old_applog):
-                        i += 1
-                        old_applog = "%s.%d" % (applog, i)
-                    shutil.move(applog, old_applog)
-                    _log.info("Moved existing log file %s to %s" % (applog, old_applog))
-
-                shutil.move(app.logfile, applog)
-                _log.info("Log file moved to %s" % applog)
-            except IOError, err:
-                print_error("Failed to move log file %s to new log file %s: %s" % (app.logfile, applog, err))
+            move_logs(app.logfile, applog)
 
             if app not in build_stopped:
                 # gather build stats
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 5bcec5bf6a..a34a16fb6e 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -34,6 +34,7 @@
 @author: Ward Poelmans (Ghent University)
 @author: Fotis Georgatos (Uni.Lu, NTUA)
 """
+import glob
 import os
 import re
 import shutil
@@ -875,6 +876,36 @@ def rmtree2(path, n=3):
         _log.info("Path %s successfully removed." % path)
 
 
+def move_logs(from_path, target_path):
+    """Move log file(s)."""
+    mkdir(os.path.dirname(target_path), parents=True)
+    from_path_len = len(from_path)
+    try:
+
+        # there may be multiple log files, due to log rotation
+        app_logs = glob.glob('%s*' % from_path)
+        for app_log in app_logs:
+            # retain possible suffix
+            new_log_path = target_path + app_log[from_path_len:]
+
+            # retain old logs
+            if os.path.exists(new_log_path):
+                i = 0
+                oldlog_backup = "%s_%d" % (new_log_path, i)
+                while os.path.exists(oldlog_backup):
+                    i += 1
+                    oldlog_backup = "%s_%d" % (new_log_path, i)
+                shutil.move(new_log_path, oldlog_backup)
+                _log.info("Moved existing log file %s to %s" % (new_log_path, oldlog_backup))
+
+            # move log to target path
+            shutil.move(app_log, new_log_path)
+            _log.info("Moved log file %s to %s" % (from_path, new_log_path))
+
+    except (IOError, OSError), err:
+        _log.error("Failed to move log file(s) %s* to new log file %s*: %s" % (from_path, target_path, err))
+
+
 def cleanup(logfile, tempdir, testing):
     """Cleanup the specified log file and the tmp directory"""
     if not testing and logfile is not None:
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 4c6d476ef8..9e13752587 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -308,6 +308,34 @@ def test_guess_patch_level(self):
         ]:
             self.assertEqual(ft.guess_patch_level([patched_file], self.test_buildpath), correct_patch_level)
 
+    def test_move_logs(self):
+        """Test move_logs function."""
+        fh, fp = tempfile.mkstemp()
+        os.close(fh)
+        ft.write_file(fp, 'foobar')
+        ft.write_file(fp + '.1', 'moarfoobar')
+        ft.move_logs(fp, os.path.join(self.test_prefix, 'foo.log'))
+
+        self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'foo.log')), 'foobar')
+        self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'foo.log.1')), 'moarfoobar')
+
+        ft.write_file(os.path.join(self.test_prefix, 'bar.log'), 'bar')
+        ft.write_file(os.path.join(self.test_prefix, 'bar.log_1'), 'barbar')
+
+        fh, fp = tempfile.mkstemp()
+        os.close(fh)
+        ft.write_file(fp, 'moarbar')
+        ft.write_file(fp + '.1', 'evenmoarbar')
+        ft.move_logs(fp, os.path.join(self.test_prefix, 'bar.log'))
+
+        logs = ['bar.log', 'bar.log.1', 'bar.log_0', 'bar.log_1', 'foo.log', 'foo.log.1']
+        self.assertEqual(sorted(os.listdir(self.test_prefix)), logs)
+        self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log_0')), 'bar')
+        self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log_1')), 'barbar')
+        self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log')), 'moarbar')
+        self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log.1')), 'evenmoarbar')
+
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(FileToolsTest)

From 5f5b25eaf560318394592b3f96244aa27e358627 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 24 Mar 2015 11:36:45 +0100
Subject: [PATCH 0783/1356] fix remark

---
 easybuild/tools/filetools.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index a34a16fb6e..caa1c122cb 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -876,17 +876,17 @@ def rmtree2(path, n=3):
         _log.info("Path %s successfully removed." % path)
 
 
-def move_logs(from_path, target_path):
+def move_logs(src_logfile, target_logfile):
     """Move log file(s)."""
-    mkdir(os.path.dirname(target_path), parents=True)
-    from_path_len = len(from_path)
+    mkdir(os.path.dirname(target_logfile), parents=True)
+    src_logfile_len = len(src_logfile)
     try:
 
         # there may be multiple log files, due to log rotation
-        app_logs = glob.glob('%s*' % from_path)
+        app_logs = glob.glob('%s*' % src_logfile)
         for app_log in app_logs:
             # retain possible suffix
-            new_log_path = target_path + app_log[from_path_len:]
+            new_log_path = target_logfile + app_log[src_logfile_len:]
 
             # retain old logs
             if os.path.exists(new_log_path):
@@ -900,10 +900,10 @@ def move_logs(from_path, target_path):
 
             # move log to target path
             shutil.move(app_log, new_log_path)
-            _log.info("Moved log file %s to %s" % (from_path, new_log_path))
+            _log.info("Moved log file %s to %s" % (src_logfile, new_log_path))
 
     except (IOError, OSError), err:
-        _log.error("Failed to move log file(s) %s* to new log file %s*: %s" % (from_path, target_path, err))
+        _log.error("Failed to move log file(s) %s* to new log file %s*: %s" % (src_logfile, target_logfile, err))
 
 
 def cleanup(logfile, tempdir, testing):

From 0e5a36f99a7662415355fb0c2debc19aa7405d52 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 24 Mar 2015 12:00:30 +0100
Subject: [PATCH 0784/1356] fix remark w.r.t. cleanup function

---
 easybuild/tools/filetools.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index caa1c122cb..69afd3415c 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -909,11 +909,18 @@ def move_logs(src_logfile, target_logfile):
 def cleanup(logfile, tempdir, testing):
     """Cleanup the specified log file and the tmp directory"""
     if not testing and logfile is not None:
-        os.remove(logfile)
-        print_msg('temporary log file %s has been removed.' % (logfile), log=None, silent=testing)
+        try:
+            for log in glob.glob('%s*' % logfile):
+                os.remove(log)
+        except OSError, err:
+            _log.error("Failed to remove log file(s) %s*: %s" % (logfile, err))
+        print_msg('temporary log file(s) %s* have been removed.' % (logfile), log=None, silent=testing)
 
     if not testing and tempdir is not None:
-        shutil.rmtree(tempdir, ignore_errors=True)
+        try:
+            shutil.rmtree(tempdir, ignore_errors=True)
+        except OSError, err:
+            _log.error("Failed to remove temporary directory %s: %s" % (tempdir, err))
         print_msg('temporary directory %s has been removed.' % (tempdir), log=None, silent=testing)
 
 

From fe2bfc9eb2bcd3df8d56ceb82e55f5c54ca17670 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 24 Mar 2015 16:48:34 +0100
Subject: [PATCH 0785/1356] complain if specified config files are missing

---
 easybuild/tools/options.py | 3 ++-
 test/framework/config.py   | 5 ++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 8a643e2770..206b3a9366 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -79,9 +79,10 @@ class EasyBuildOptions(GeneralOption):
     VERSION = this_is_easybuild()
 
     DEFAULT_LOGLEVEL = 'INFO'
-    DEFAULT_CONFIGFILES = DEFAULT_SYS_CFGFILES + [DEFAULT_USER_CFGFILE]
+    DEFAULT_CONFIGFILES = [p for p in DEFAULT_SYS_CFGFILES + [DEFAULT_USER_CFGFILE] if os.path.exists(p)]
 
     ALLOPTSMANDATORY = False  # allow more than one argument
+    CONFIGFILES_RAISE_MISSING = True  # don't allow non-existing config files to be specified
 
     def __init__(self, *args, **kwargs):
         """Constructor."""
diff --git a/test/framework/config.py b/test/framework/config.py
index e91337f25b..a862e472ce 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -54,6 +54,7 @@ class EasyBuildConfigTest(EnhancedTestCase):
 
     def setUp(self):
         """Prepare for running a config test."""
+        reload(eboptions)
         super(EasyBuildConfigTest, self).setUp()
         self.tmpdir = tempfile.mkdtemp()
 
@@ -397,8 +398,6 @@ def test_XDG_CONFIG_env_vars(self):
             os.path.join(dir1, 'easybuild.d', 'bar.cfg'),
             os.path.join(dir1, 'easybuild.d', 'foo.cfg'),
             os.path.join(dir3, 'easybuild.d', 'foobarbaz.cfg'),
-            # default config file in home dir is last (even if the file is not there)
-            os.path.join(os.path.expanduser('~'), '.config', 'easybuild', 'config.cfg'),
         ]
         reload(eboptions)
         eb_go = eboptions.parse_options(args=[])
@@ -410,7 +409,6 @@ def test_XDG_CONFIG_env_vars(self):
             os.path.join(dir1, 'easybuild.d', 'bar.cfg'),
             os.path.join(dir1, 'easybuild.d', 'foo.cfg'),
             os.path.join(dir3, 'easybuild.d', 'foobarbaz.cfg'),
-            os.path.join(self.test_prefix, 'nosuchdir', 'easybuild', 'config.cfg'),
         ]
         reload(eboptions)
         eb_go = eboptions.parse_options(args=[])
@@ -427,6 +425,7 @@ def test_XDG_CONFIG_env_vars(self):
             del os.environ['XDG_CONFIG_DIRS']
         else:
             os.environ['XDG_CONFIG_DIRS'] = xdg_config_dirs
+        reload(eboptions)
 
 def suite():
     return TestLoader().loadTestsFromTestCase(EasyBuildConfigTest)

From e812a7196900b983d56b1603c42b18355e6a5412 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 24 Mar 2015 16:55:48 +0100
Subject: [PATCH 0786/1356] add test to check for behaviour on missing
 specified cfgfile

---
 easybuild/tools/options.py | 10 +++++++---
 test/framework/options.py  |  6 ++++++
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 206b3a9366..2ad99719ef 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -48,7 +48,8 @@
 from easybuild.framework.easyconfig.templates import template_documentation
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
-from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
+from easybuild.tools import build_log, config, run  # build_log should always stay there, to ensure EasyBuildLog
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
 from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_pretend_installpath
@@ -646,8 +647,11 @@ def parse_options(args=None):
     description = ("Builds software based on easyconfig (or parse a directory).\n"
                    "Provide one or more easyconfigs or directories, use -H or --help more information.")
 
-    eb_go = EasyBuildOptions(usage=usage, description=description, prog='eb', envvar_prefix=CONFIG_ENV_VAR_PREFIX,
-                             go_args=args)
+    try:
+        eb_go = EasyBuildOptions(usage=usage, description=description, prog='eb', envvar_prefix=CONFIG_ENV_VAR_PREFIX,
+                                 go_args=args)
+    except Exception, err:
+        raise EasyBuildError("Failed to parse configuration options: %s" % err)
     return eb_go
 
 
diff --git a/test/framework/options.py b/test/framework/options.py
index 0f381055a0..6e47250ad1 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1484,6 +1484,12 @@ def test_robot(self):
             ec_regex = re.compile(r'^\s\*\s\[[xF ]\]\s%s' % os.path.join(test_ecs_path, ecfile), re.M)
             self.assertTrue(ec_regex.search(outtxt), "Pattern %s found in %s" % (ec_regex.pattern, outtxt))
 
+    def test_missing_cfgfile(self):
+        """Test behaviour when non-existing config file is specified."""
+        args = ['--configfiles=/no/such/cfgfile.foo']
+        error_regex = "parseconfigfiles: configfile .* not found"
+        self.assertErrorRegex(EasyBuildError, error_regex, self.eb_main, args, raise_error=True)
+
 
 def suite():
     """ returns all the testcases in this module """

From b031afe3c58a07ce2f07273a1a4f2517e7456474 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Wed, 25 Mar 2015 21:43:01 -0400
Subject: [PATCH 0787/1356] needed to add this otherwise got an error

---
 easybuild/tools/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 5bcec5bf6a..4f64bd30bc 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -255,7 +255,7 @@ def download_file(filename, url, path):
 
     _log.debug("Trying to download %s from %s to %s", filename, url, path)
 
-    timeout = build_option('download_timeout')
+    timeout = float(build_option('download_timeout'))
     if timeout is None:
         # default to 10sec timeout if none was specified
         # default system timeout (used is nothing is specified) may be infinite (?)

From 12677e2581b3b72ec0e4592138249d82eabfef47 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 26 Mar 2015 09:37:30 +0100
Subject: [PATCH 0788/1356] fix value type for --download-timeout in options.py
 rather than casting a possible None value to a float

---
 easybuild/tools/filetools.py | 2 +-
 easybuild/tools/options.py   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 4f64bd30bc..5bcec5bf6a 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -255,7 +255,7 @@ def download_file(filename, url, path):
 
     _log.debug("Trying to download %s from %s to %s", filename, url, path)
 
-    timeout = float(build_option('download_timeout'))
+    timeout = build_option('download_timeout')
     if timeout is None:
         # default to 10sec timeout if none was specified
         # default system timeout (used is nothing is specified) may be infinite (?)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 8a643e2770..5dc144e522 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -186,7 +186,7 @@ def override_options(self):
             'cleanup-builddir': ("Cleanup build dir after successful installation.", None, 'store_true', True),
             'deprecated': ("Run pretending to be (future) version, to test removal of deprecated code.",
                            None, 'store', None),
-            'download-timeout': ("Timeout for initiating downloads (in seconds)", None, 'store', None),
+            'download-timeout': ("Timeout for initiating downloads (in seconds)", float, 'store', None),
             'easyblock': ("easyblock to use for processing the spec file or dumping the options",
                           None, 'store', None, 'e', {'metavar': 'CLASS'}),
             'experimental': ("Allow experimental code (with behaviour that can be changed/removed at any given time).",

From 2510ad5ce9675b31136c1a706402fe62936a6737 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 26 Mar 2015 09:38:25 +0100
Subject: [PATCH 0789/1356] enhance test_download_file to check type of
 specified download timeout

---
 test/framework/filetools.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 4c6d476ef8..f4be8f9ff5 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -34,7 +34,7 @@
 import stat
 import tempfile
 import urllib2
-from test.framework.utilities import EnhancedTestCase
+from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader, main
 
 import easybuild.tools.filetools as ft
@@ -201,6 +201,18 @@ def test_download_file(self):
         res = ft.download_file(fn, source_url, target_location)
         self.assertEqual(res, target_location, "'download' of local file works after removing broken proxy")
 
+        # make sure specified timeout is parsed correctly (as a float, not a string)
+        opts = init_config(args=['--download-timeout=5.3'])
+        init_config(build_options={'download_timeout': opts.download_timeout})
+        target_location = os.path.join(self.test_prefix, 'jenkins_robots.txt')
+        url = 'https://jenkins1.ugent.be/robots.txt'
+        try:
+            urllib2.urlopen(url)
+            res = ft.download_file(fn, url, target_location)
+            self.assertEqual(res, target_location, "download with specified timeout works")
+        except urllib2.URLError:
+            print "Skipping timeout test in test_download_file (working offline)"
+
     def test_mkdir(self):
         """Test mkdir function."""
         tmpdir = tempfile.mkdtemp()

From 9301deee339edf6e7cd016dd28141941358a8ae8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 26 Mar 2015 14:41:32 +0100
Subject: [PATCH 0790/1356] reset log format after running build_log test

---
 test/framework/build_log.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/test/framework/build_log.py b/test/framework/build_log.py
index 0d89b25a02..cd97e53b32 100644
--- a/test/framework/build_log.py
+++ b/test/framework/build_log.py
@@ -35,7 +35,7 @@
 from unittest import main as unittestmain
 from vsc.utils.fancylogger import getLogger, getRootLoggerName, logToFile, setLogFormat
 
-from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.build_log import LOGGING_FORMAT, EasyBuildError
 from easybuild.tools.filetools import read_file, write_file
 
 
@@ -47,6 +47,11 @@ def raise_easybuilderror(msg, *args, **kwargs):
 class BuildLogTest(EnhancedTestCase):
     """Tests for EasyBuild log infrastructure."""
 
+    def tearDown(self):
+        """Cleanup after test."""
+        # restore default logging format
+        setLogFormat(LOGGING_FORMAT)
+
     def test_easybuilderror(self):
         """Tests for EasyBuildError."""
         fd, tmplog = tempfile.mkstemp()

From afbaee8eca6f8f697aaa9ce620890a25ebb9c772 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 26 Mar 2015 15:04:17 +0100
Subject: [PATCH 0791/1356] replace 'log.error' with 'raise EasyBuildError'

---
 easybuild/framework/easyblock.py              | 125 ++++++++++--------
 easybuild/framework/easyconfig/default.py     |   4 +-
 easybuild/framework/easyconfig/easyconfig.py  |  97 +++++++-------
 .../framework/easyconfig/format/format.py     |  52 ++++----
 easybuild/framework/easyconfig/format/one.py  |  14 +-
 .../easyconfig/format/pyheaderconfigobj.py    |  21 +--
 easybuild/framework/easyconfig/format/two.py  |   5 +-
 .../framework/easyconfig/format/version.py    |  48 +++----
 easybuild/framework/easyconfig/parser.py      |  17 +--
 easybuild/framework/easyconfig/templates.py   |   3 +-
 easybuild/framework/easyconfig/tools.py       |  11 +-
 easybuild/framework/easyconfig/tweak.py       |  33 ++---
 easybuild/framework/extension.py              |   5 +-
 easybuild/framework/extensioneasyblock.py     |   5 +-
 easybuild/main.py                             |   9 +-
 easybuild/scripts/clean_gists.py              |  11 +-
 easybuild/scripts/fix_broken_easyconfigs.py   |   8 +-
 easybuild/scripts/generate_software_list.py   |   4 +-
 easybuild/toolchains/compiler/clang.py        |   4 +-
 easybuild/toolchains/compiler/gcc.py          |   4 +-
 .../toolchains/compiler/inteliccifort.py      |   8 +-
 easybuild/toolchains/fft/fftw.py              |   3 +-
 easybuild/toolchains/fft/intelfftw.py         |  10 +-
 easybuild/toolchains/linalg/acml.py           |   7 +-
 easybuild/toolchains/linalg/intelmkl.py       |  18 +--
 easybuild/tools/config.py                     |  13 +-
 easybuild/tools/convert.py                    |   9 +-
 easybuild/tools/environment.py                |   6 +-
 easybuild/tools/filetools.py                  |  70 +++++-----
 easybuild/tools/github.py                     |  28 ++--
 easybuild/tools/jenkins.py                    |   7 +-
 easybuild/tools/module_generator.py           |   7 +-
 .../module_naming_scheme/hierarchical_mns.py  |  13 +-
 easybuild/tools/module_naming_scheme/mns.py   |   9 +-
 .../tools/module_naming_scheme/toolchain.py   |  13 +-
 easybuild/tools/modules.py                    |  40 +++---
 easybuild/tools/options.py                    |  12 +-
 easybuild/tools/parallelbuild.py              |   4 +-
 easybuild/tools/pbs_job.py                    |  33 +++--
 easybuild/tools/repository/gitrepo.py         |  11 +-
 easybuild/tools/repository/repository.py      |  13 +-
 easybuild/tools/repository/svnrepo.py         |  23 ++--
 easybuild/tools/run.py                        |  32 ++---
 easybuild/tools/systemtools.py                |  27 ++--
 easybuild/tools/testing.py                    |   2 +-
 easybuild/tools/toolchain/compiler.py         |  10 +-
 easybuild/tools/toolchain/linalg.py           |  10 +-
 easybuild/tools/toolchain/mpi.py              |  11 +-
 easybuild/tools/toolchain/options.py          |  10 +-
 easybuild/tools/toolchain/toolchain.py        |  43 +++---
 easybuild/tools/toolchain/utilities.py        |  11 +-
 easybuild/tools/toolchain/variables.py        |   3 +-
 easybuild/tools/variables.py                  |  27 ++--
 .../sandbox/easybuild/easyblocks/toy.py       |   4 +-
 test/framework/toy_build.py                   |   2 +-
 55 files changed, 547 insertions(+), 482 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 1f403bfacc..ddb62e17dc 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -144,7 +144,7 @@ def __init__(self, ec):
         if isinstance(ec, EasyConfig):
             self.cfg = ec
         else:
-            _log.error("Value of incorrect type passed to EasyBlock constructor: %s ('%s')" % (type(ec), ec))
+            raise EasyBuildError("Value of incorrect type passed to EasyBlock constructor: %s ('%s')", type(ec), ec)
 
         # determine install subdirectory, based on module name
         self.install_subdir = None
@@ -217,8 +217,8 @@ def _init_log(self):
         self.log.info(this_is_easybuild())
 
         this_module = inspect.getmodule(self)
-        tup = (self.__class__.__name__, this_module.__name__, this_module.__file__)
-        self.log.info("This is easyblock %s from module %s (%s)" % tup)
+        self.log.info("This is easyblock %s from module %s (%s)",
+                      self.__class__.__name__, this_module.__name__, this_module.__file__)
 
     def close_log(self):
         """
@@ -247,7 +247,7 @@ def get_checksum_for(self, checksums, filename=None, index=None):
         elif checksums is None:
             return None
         else:
-            self.log.error("Invalid type for checksums (%s), should be list, tuple or None." % type(checksums))
+            raise EasyBuildError("Invalid type for checksums (%s), should be list, tuple or None.", type(checksums))
 
     def fetch_sources(self, list_of_sources, checksums=None):
         """
@@ -276,7 +276,7 @@ def fetch_sources(self, list_of_sources, checksums=None):
                     'finalpath': self.builddir,
                 })
             else:
-                self.log.error('No file found for source %s' % source)
+                raise EasyBuildError('No file found for source %s', source)
 
         self.log.info("Added sources: %s" % self.src)
 
@@ -297,8 +297,8 @@ def fetch_patches(self, patch_specs=None, extension=False, checksums=None):
             level = None
             if isinstance(patch_spec, (list, tuple)):
                 if not len(patch_spec) == 2:
-                    self.log.error("Unknown patch specification '%s', only two-element lists/tuples are supported!",
-                                   str(patch_spec))
+                    raise EasyBuildError("Unknown patch specification '%s', only 2-element lists/tuples are supported!",
+                                         str(patch_spec))
                 patch_file = patch_spec[0]
 
                 # this *must* be of typ int, nothing else
@@ -311,7 +311,8 @@ def fetch_patches(self, patch_specs=None, extension=False, checksums=None):
                         copy_file = True
                     suff = patch_spec[1]
                 else:
-                    self.log.error("Wrong patch spec '%s', only int/string are supported as 2nd element" % str(patch_spec))
+                    raise EasyBuildError("Wrong patch spec '%s', only int/string are supported as 2nd element",
+                                         str(patch_spec))
             else:
                 patch_file = patch_spec
 
@@ -336,7 +337,7 @@ def fetch_patches(self, patch_specs=None, extension=False, checksums=None):
                 else:
                     self.patches.append(patchspec)
             else:
-                self.log.error('No file found for patch %s' % patch_spec)
+                raise EasyBuildError('No file found for patch %s', patch_spec)
 
         if extension:
             self.log.info("Fetched extension patches: %s" % patches)
@@ -370,9 +371,9 @@ def fetch_extension_sources(self):
                         ext_options = ext[2]
 
                         if not isinstance(ext_options, dict):
-                            self.log.error("Unexpected type (non-dict) for 3rd element of %s" % ext)
+                            raise EasyBuildError("Unexpected type (non-dict) for 3rd element of %s", ext)
                     elif len(ext) > 3:
-                        self.log.error('Extension specified in unknown format (list/tuple too long)')
+                        raise EasyBuildError('Extension specified in unknown format (list/tuple too long)')
 
                     ext_src = {
                         'name': ext_name,
@@ -401,7 +402,7 @@ def fetch_extension_sources(self):
                                 if verify_checksum(src_fn, fn_checksum):
                                     self.log.info('Checksum for ext source %s verified' % fn)
                                 else:
-                                    self.log.error('Checksum for ext source %s failed' % fn)
+                                    raise EasyBuildError('Checksum for ext source %s failed', fn)
 
                             ext_patches = self.fetch_patches(patch_specs=ext_options.get('patches', []), extension=True)
                             if ext_patches:
@@ -415,20 +416,20 @@ def fetch_extension_sources(self):
                                         if verify_checksum(ext_patch, checksum):
                                             self.log.info('Checksum for extension patch %s verified' % ext_patch)
                                         else:
-                                            self.log.error('Checksum for extension patch %s failed' % ext_patch)
+                                            raise EasyBuildError('Checksum for extension patch %s failed', ext_patch)
                             else:
                                 self.log.debug('No patches found for extension %s.' % ext_name)
 
                             exts_sources.append(ext_src)
 
                         else:
-                            self.log.error("Source for extension %s not found.")
+                            raise EasyBuildError("Source for extension %s not found.")
 
             elif isinstance(ext, basestring):
                 exts_sources.append({'name': ext})
 
             else:
-                self.log.error("Extension specified in unknown format (not a string/list/tuple)")
+                raise EasyBuildError("Extension specified in unknown format (not a string/list/tuple)")
 
         return exts_sources
 
@@ -468,7 +469,7 @@ def obtain_file(self, filename, extension=False, urls=None):
                         return fullpath
 
             except IOError, err:
-                self.log.exception("Downloading file %s from url %s to %s failed: %s" % (filename, url, fullpath, err))
+                raise EasyBuildError("Downloading file %s from url %s to %s failed: %s", filename, url, fullpath, err)
 
         else:
             # try and find file in various locations
@@ -573,7 +574,8 @@ def obtain_file(self, filename, extension=False, urls=None):
                     else:
                         failedpaths.append(fullurl)
 
-                self.log.error("Couldn't find file %s anywhere, and downloading it didn't work either...\nPaths attempted (in order): %s " % (filename, ', '.join(failedpaths)))
+                raise EasyBuildError("Couldn't find file %s anywhere, and downloading it didn't work either... "
+                                     "Paths attempted (in order): %s ", filename, ', '.join(failedpaths))
 
     #
     # GETTER/SETTER UTILITY FUNCTIONS
@@ -652,8 +654,9 @@ def make_builddir(self):
         if not self.build_in_installdir:
             # self.builddir should be already set by gen_builddir()
             if not self.builddir:
-                self.log.error("self.builddir not set, make sure gen_builddir() is called first!")
-            self.log.debug("Creating the build directory %s (cleanup: %s)" % (self.builddir, self.cfg['cleanupoldbuild']))
+                raise EasyBuildError("self.builddir not set, make sure gen_builddir() is called first!")
+            self.log.debug("Creating the build directory %s (cleanup: %s)",
+                           self.builddir, self.cfg['cleanupoldbuild'])
         else:
             self.log.info("Changing build dir to %s" % self.installdir)
             self.builddir = self.installdir
@@ -680,7 +683,7 @@ def gen_installdir(self):
             self.installdir = os.path.abspath(installdir)
             self.log.info("Install dir set to %s" % self.installdir)
         else:
-            self.log.error("Can't set installation directory")
+            raise EasyBuildError("Can't set installation directory")
 
     def make_installdir(self, dontcreate=None):
         """
@@ -707,7 +710,7 @@ def make_dir(self, dir_name, clean, dontcreateinstalldir=False):
                     rmtree2(dir_name)
                     self.log.info("Removed old directory %s" % dir_name)
                 except OSError, err:
-                    self.log.exception("Removal of old directory %s failed: %s" % (dir_name, err))
+                    raise EasyBuildError("Removal of old directory %s failed: %s", dir_name, err)
             else:
                 try:
                     timestamp = time.strftime("%Y%m%d-%H%M%S")
@@ -715,7 +718,7 @@ def make_dir(self, dir_name, clean, dontcreateinstalldir=False):
                     shutil.move(dir_name, backupdir)
                     self.log.info("Moved old directory %s to %s" % (dir_name, backupdir))
                 except OSError, err:
-                    self.log.exception("Moving old directory to backup %s %s failed: %s" % (dir_name, backupdir, err))
+                    raise EasyBuildError("Moving old directory to backup %s %s failed: %s", dir_name, backupdir, err)
 
         if dontcreateinstalldir:
             olddir = dir_name
@@ -858,7 +861,8 @@ def make_module_extra(self):
             if isinstance(value, basestring):
                 value = [value]
             elif not isinstance(value, (tuple, list)):
-                self.log.error("modextrapaths dict value %s (type: %s) is not a list or tuple" % (value, type(value)))
+                raise EasyBuildError("modextrapaths dict value %s (type: %s) is not a list or tuple",
+                                     value, type(value))
             txt += self.module_generator.prepend_paths(key, value)
         if self.cfg['modloadmsg']:
             txt += self.module_generator.msg_on_load(self.cfg['modloadmsg'])
@@ -932,7 +936,7 @@ def make_module_req(self):
             try:
                 os.chdir(self.installdir)
             except OSError, err:
-                self.log.error("Failed to change to %s: %s" % (self.installdir, err))
+                raise EasyBuildError("Failed to change to %s: %s", self.installdir, err)
 
             txt = "\n"
             for key in sorted(requirements):
@@ -943,7 +947,7 @@ def make_module_req(self):
             try:
                 os.chdir(self.orig_workdir)
             except OSError, err:
-                self.log.error("Failed to change back to %s: %s" % (self.orig_workdir, err))
+                raise EasyBuildError("Failed to change back to %s: %s", self.orig_workdir, err)
         else:
             txt = ""
         return txt
@@ -1009,7 +1013,7 @@ def clean_up_fake_module(self, fake_mod_data):
                 modtool.remove_module_path(fake_mod_path)
                 rmtree2(os.path.dirname(fake_mod_path))
             except OSError, err:
-                self.log.error("Failed to clean up fake module dir %s: %s" % (fake_mod_path, err))
+                raise EasyBuildError("Failed to clean up fake module dir %s: %s", fake_mod_path, err)
         elif self.full_mod_name is None:
             self.log.warning("Not unloading module, since self.full_mod_name is not set.")
 
@@ -1042,9 +1046,9 @@ def skip_extensions(self):
         self.cfg.enable_templating = True
 
         if not exts_filter or len(exts_filter) == 0:
-            self.log.error("Skipping of extensions, but no exts_filter set in easyconfig")
+            raise EasyBuildError("Skipping of extensions, but no exts_filter set in easyconfig")
         elif isinstance(exts_filter, basestring) or len(exts_filter) != 2:
-            self.log.error('exts_filter should be a list or tuple of ("command","input")')
+            raise EasyBuildError('exts_filter should be a list or tuple of ("command","input")')
         cmdtmpl = exts_filter[0]
         cmdinputtmpl = exts_filter[1]
         if not self.exts:
@@ -1110,7 +1114,7 @@ def guess_start_dir(self):
             os.chdir(self.cfg['start_dir'])
             self.log.debug("Changed to real build directory %s" % (self.cfg['start_dir']))
         except OSError, err:
-            self.log.exception("Can't change to real build directory %s: %s" % (self.cfg['start_dir'], err))
+            raise EasyBuildError("Can't change to real build directory %s: %s", self.cfg['start_dir'], err)
 
     def handle_iterate_opts(self):
         """Handle options relevant during iterated part of build/install procedure."""
@@ -1164,12 +1168,12 @@ def check_readiness_step(self):
         if not len(self.cfg.dependencies()) == len(self.toolchain.dependencies):
             self.log.debug("dep %s (%s)" % (len(self.cfg.dependencies()), self.cfg.dependencies()))
             self.log.debug("tc.dep %s (%s)" % (len(self.toolchain.dependencies), self.toolchain.dependencies))
-            self.log.error('Not all dependencies have a matching toolchain version')
+            raise EasyBuildError('Not all dependencies have a matching toolchain version')
 
         # check if the application is not loaded at the moment
         (root, env_var) = get_software_root(self.name, with_env_var=True)
         if root:
-            self.log.error("Module is already loaded (%s is set), installation cannot continue." % env_var)
+            raise EasyBuildError("Module is already loaded (%s is set), installation cannot continue.", env_var)
 
         # check if main install needs to be skipped
         # - if a current module can be found, skip is ok
@@ -1189,12 +1193,15 @@ def fetch_step(self, skip_checksums=False):
         # check EasyBuild version
         easybuild_version = self.cfg['easybuild_version']
         if not easybuild_version:
-            self.log.warn("Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version")
+            self.log.warn("Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! "
+                          "Assuming the latest version")
         else:
             if LooseVersion(easybuild_version) < VERSION:
-                self.log.warn("EasyBuild-version %s is older than the currently running one. Proceed with caution!" % easybuild_version)
+                self.log.warn("EasyBuild-version %s is older than the currently running one. Proceed with caution!",
+                              easybuild_version)
             elif LooseVersion(easybuild_version) > VERSION:
-                self.log.error("EasyBuild-version %s is newer than the currently running one. Aborting!" % easybuild_version)
+                raise EasyBuildError("EasyBuild-version %s is newer than the currently running one. Aborting!",
+                                     easybuild_version)
 
         # fetch sources
         if self.cfg['sources']:
@@ -1249,7 +1256,7 @@ def checksum_step(self):
         for fil in self.src + self.patches:
             ok = verify_checksum(fil['path'], fil['checksum'])
             if not ok:
-                self.log.error("Checksum verification for %s using %s failed." % (fil['path'], fil['checksum']))
+                raise EasyBuildError("Checksum verification for %s using %s failed.", fil['path'], fil['checksum'])
             else:
                 self.log.info("Checksum verification for %s using %s passed." % (fil['path'], fil['checksum']))
 
@@ -1263,7 +1270,7 @@ def extract_step(self):
             if srcdir:
                 self.src[self.src.index(src)]['finalpath'] = srcdir
             else:
-                self.log.error("Unpacking source %s failed" % src['name'])
+                raise EasyBuildError("Unpacking source %s failed", src['name'])
 
     def patch_step(self, beginpath=None):
         """
@@ -1281,16 +1288,16 @@ def patch_step(self, beginpath=None):
             # determine whether 'patch' file should be copied rather than applied
             copy_patch = 'copy' in patch and not 'sourcepath' in patch
 
-            tup = (srcind, level, srcpathsuffix, copy)
-            self.log.debug("Source index: %s; patch level: %s; source path suffix: %s; copy patch: %s" % tup)
+            self.log.debug("Source index: %s; patch level: %s; source path suffix: %s; copy patch: %s",
+                           srcind, level, srcpathsuffix, copy)
 
             if beginpath is None:
                 try:
                     beginpath = self.src[srcind]['finalpath']
                     self.log.debug("Determine begin path for patch %s: %s" % (patch['name'], beginpath))
                 except IndexError, err:
-                    tup = (patch['name'], srcind, self.src, err)
-                    self.log.error("Can't apply patch %s to source at index %s of list %s: %s" % tup)
+                    raise EasyBuildError("Can't apply patch %s to source at index %s of list %s: %s",
+                                         patch['name'], srcind, self.src, err)
             else:
                 self.log.debug("Using specified begin path for patch %s: %s" % (patch['name'], beginpath))
 
@@ -1298,7 +1305,7 @@ def patch_step(self, beginpath=None):
             self.log.debug("Applying patch %s in path %s" % (patch, src))
 
             if not apply_patch(patch['path'], src, copy=copy_patch, level=level):
-                self.log.error("Applying patch %s failed" % patch['name'])
+                raise EasyBuildError("Applying patch %s failed", patch['name'])
 
     def prepare_step(self):
         """
@@ -1368,7 +1375,7 @@ def extensions_step(self, fetch=False):
         # we really need a default class
         if not exts_defaultclass:
             self.clean_up_fake_module(fake_mod_data)
-            self.log.error("ERROR: No default extension class set for %s" % self.name)
+            raise EasyBuildError("ERROR: No default extension class set for %s", self.name)
 
         # obtain name and module path for default extention class
         if hasattr(exts_defaultclass, '__iter__'):
@@ -1380,7 +1387,7 @@ def extensions_step(self, fetch=False):
             default_class_modpath = get_module_path(default_class, generic=True)
 
         else:
-            self.log.error("Improper default extension class specification, should be list/tuple or string.")
+            raise EasyBuildError("Improper default extension class specification, should be list/tuple or string.")
 
         # get class instances for all extensions
         for ext in self.exts:
@@ -1413,7 +1420,8 @@ def extensions_step(self, fetch=False):
                     cls = get_class_for(mod_path, class_name)
                     inst = cls(self, ext)
                 except (ImportError, NameError), err:
-                    self.log.error("Failed to load specified class %s for extension %s: %s" % (class_name, ext['name'], err))
+                    raise EasyBuildError("Failed to load specified class %s for extension %s: %s",
+                                         class_name, ext['name'], err)
 
             # fallback attempt: use default class
             if inst is None:
@@ -1421,12 +1429,12 @@ def extensions_step(self, fetch=False):
                     cls = get_class_for(default_class_modpath, default_class)
                     self.log.debug("Obtained class %s for installing extension %s" % (cls, ext['name']))
                     inst = cls(self, ext)
-                    tup = (ext['name'], default_class, default_class_modpath)
-                    self.log.debug("Installing extension %s with default class %s (from %s)" % tup)
+                    self.log.debug("Installing extension %s with default class %s (from %s)",
+                                   ext['name'], default_class, default_class_modpath)
                 except (ImportError, NameError), err:
                     msg = "Also failed to use default class %s from %s for extension %s: %s, giving up" % \
                         (default_class, default_class_modpath, ext['name'], err)
-                    self.log.error(msg)
+                    raise EasyBuildError(msg)
             else:
                 self.log.debug("Installing extension %s with class %s (from %s)" % (ext['name'], class_name, mod_path))
 
@@ -1457,10 +1465,10 @@ def post_install_step(self):
         if self.cfg['postinstallcmds'] is not None:
             # make sure we have a list of commands
             if not isinstance(self.cfg['postinstallcmds'], (list, tuple)):
-                self.log.error("Invalid value for 'postinstallcmds', should be list or tuple of strings.")
+                raise EasyBuildError("Invalid value for 'postinstallcmds', should be list or tuple of strings.")
             for cmd in self.cfg['postinstallcmds']:
                 if not isinstance(cmd, basestring):
-                    self.log.error("Invalid element in 'postinstallcmds', not a string: %s" % cmd)
+                    raise EasyBuildError("Invalid element in 'postinstallcmds', not a string: %s", cmd)
                 run_cmd(cmd, simple=True, log_ok=True, log_all=True)
 
         if self.group is not None:
@@ -1470,7 +1478,7 @@ def post_install_step(self):
                 adjust_permissions(self.installdir, perms, add=False, recursive=True, group_id=self.group[1],
                                    relative=True, ignore_errors=True)
             except EasyBuildError, err:
-                self.log.error("Unable to change group permissions of file(s): %s" % err)
+                raise EasyBuildError("Unable to change group permissions of file(s): %s", err)
             self.log.info("Successfully made software only available for group %s (gid %s)" % self.group)
 
         if read_only_installdir():
@@ -1516,7 +1524,7 @@ def sanity_check_step(self, custom_paths=None, custom_commands=None, extension=F
         lenvals = [len(x) for x in paths.values()]
         req_keys = sorted(path_keys_and_check.keys())
         if not ks == req_keys or sum(valnottypes) > 0 or sum(lenvals) == 0:
-            self.log.error("Incorrect format for sanity_check_paths (should have %s keys, "
+            raise EasyBuildError("Incorrect format for sanity_check_paths (should have %s keys, "
                            "values should be lists (at least one non-empty))." % '/'.join(req_keys))
 
         for key, check_fn in path_keys_and_check.items():
@@ -1524,7 +1532,8 @@ def sanity_check_step(self, custom_paths=None, custom_commands=None, extension=F
                 if isinstance(xs, basestring):
                     xs = (xs,)
                 elif not isinstance(xs, tuple):
-                    self.log.error("Unsupported type '%s' encountered in %s, not a string or tuple" % (key, type(xs)))
+                    raise EasyBuildError("Unsupported type '%s' encountered in %s, not a string or tuple",
+                                         key, type(xs))
                 found = False
                 for name in xs:
                     path = os.path.join(self.installdir, name)
@@ -1599,7 +1608,7 @@ def sanity_check_step(self, custom_paths=None, custom_commands=None, extension=F
 
         # pass or fail
         if self.sanity_check_fail_msgs:
-            self.log.error("Sanity check failed: %s" % ', '.join(self.sanity_check_fail_msgs))
+            raise EasyBuildError("Sanity check failed: %s", ', '.join(self.sanity_check_fail_msgs))
         else:
             self.log.debug("Sanity check passed!")
 
@@ -1626,7 +1635,7 @@ def cleanup_step(self):
                     base = os.path.dirname(base)
 
             except OSError, err:
-                self.log.exception("Cleaning up builddir %s failed: %s" % (self.builddir, err))
+                raise EasyBuildError("Cleaning up builddir %s failed: %s", self.builddir, err)
 
         if not build_option('cleanup_builddir'):
             self.log.info("Keeping builddir %s" % self.builddir)
@@ -1677,13 +1686,13 @@ def test_cases_step(self):
                     if os.path.exists(path):
                         break
                 if not os.path.exists(path):
-                    self.log.error("Test specifies invalid path: %s" % path)
+                    raise EasyBuildError("Test specifies invalid path: %s", path)
 
             try:
                 self.log.debug("Running test %s" % path)
                 run_cmd(path, log_all=True, simple=True)
             except EasyBuildError, err:
-                self.log.exception("Running test %s failed: %s" % (path, err))
+                raise EasyBuildError("Running test %s failed: %s", path, err)
 
     def update_config_template_run_step(self):
         """Update the the easyconfig template dictionary with easyconfig.TEMPLATE_NAMES_EASYBLOCK_RUN_STEP names"""
@@ -1859,8 +1868,8 @@ def build_and_install_one(ecdict, orig_environ):
         app = app_class(ecdict['ec'])
         _log.info("Obtained application instance of for %s (easyblock: %s)" % (name, easyblock))
     except EasyBuildError, err:
-        tup = (name, easyblock, err.msg)
-        print_error("Failed to get application instance for %s (easyblock: %s): %s" % tup, silent=silent)
+        print_error("Failed to get application instance for %s (easyblock: %s): %s" % (name, easyblock, err.msg),
+                    silent=silent)
 
     # application settings
     stop = build_option('stop')
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index feb1bdd5e9..9967b519dc 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -35,6 +35,8 @@
 """
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
+
 
 _log = fancylogger.getLogger('easyconfig.default', fname=False)
 
@@ -180,7 +182,7 @@ def sorted_categories():
 def get_easyconfig_parameter_default(param):
     """Get default value for given easyconfig parameter."""
     if param not in DEFAULT_CONFIG:
-        _log.error("Unkown easyconfig parameter: %s (known: %s)" % (param, sorted(DEFAULT_CONFIG.keys())))
+        raise EasyBuildError("Unkown easyconfig parameter: %s (known: %s)", param, sorted(DEFAULT_CONFIG.keys()))
     else:
         _log.debug("Returning default value for easyconfig parameter %s: %s" % (param, DEFAULT_CONFIG[param][0]))
         return DEFAULT_CONFIG[param][0]
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 7aac218a73..cf5f9e4fbd 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -114,7 +114,7 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
         if path is not None and not os.path.isfile(path):
-            self.log.error("EasyConfig __init__ expected a valid path")
+            raise EasyBuildError("EasyConfig __init__ expected a valid path")
 
         # read easyconfig file contents (or use provided rawtxt), so it can be passed down to avoid multiple re-reads
         self.path = None
@@ -215,7 +215,7 @@ def update(self, key, value):
         elif isinstance(prev_value, list):
             self[key] = prev_value + value
         else:
-            self.log.error("Can't update configuration value for %s, because it's not a string or list." % key)
+            raise EasyBuildError("Can't update configuration value for %s, because it's not a string or list.", key)
 
     def parse(self):
         """
@@ -228,7 +228,8 @@ def parse(self):
             # build a new dictionary with only the expected keys, to pass as named arguments to get_config_dict()
             arg_specs = self.build_specs
         else:
-            self.log.error("Specifications should be specified using a dictionary, got %s" % type(self.build_specs))
+            raise EasyBuildError("Specifications should be specified using a dictionary, got %s",
+                                 type(self.build_specs))
         self.log.debug("Obtained specs dict %s" % arg_specs)
 
         self.log.info("Parsing easyconfig file %s with rawcontent: %s" % (self.path, self.rawtxt))
@@ -241,7 +242,7 @@ def parse(self):
         # this includes both generic mandatory parameters and software-specific parameters defined via extra_options
         missing_mandatory_keys = [key for key in self.mandatory if key not in local_vars]
         if missing_mandatory_keys:
-            self.log.error("mandatory parameters not provided in %s: %s" % (self.path, missing_mandatory_keys))
+            raise EasyBuildError("mandatory parameters not provided in %s: %s", self.path, missing_mandatory_keys)
 
         # provide suggestions for typos
         possible_typos = [(key, difflib.get_close_matches(key.lower(), self._config.keys(), 1, 0.85))
@@ -249,7 +250,7 @@ def parse(self):
 
         typos = [(key, guesses[0]) for (key, guesses) in possible_typos if len(guesses) == 1]
         if typos:
-            self.log.error("You may have some typos in your easyconfig file: %s" %
+            raise EasyBuildError("You may have some typos in your easyconfig file: %s" %
                             ', '.join(["%s -> %s" % typo for typo in typos]))
 
         # we need toolchain to be set when we call _parse_dependency
@@ -263,8 +264,7 @@ def parse(self):
                     self[key] = [self._parse_dependency(dep, hidden=True) for dep in local_vars[key]]
                 else:
                     self[key] = local_vars[key]
-                tup = (key, self[key], type(self[key]))
-                self.log.info("setting config option %s: value %s (type: %s)" % tup)
+                self.log.info("setting config option %s: value %s (type: %s)", key, self[key], type(self[key]))
             elif key in REPLACED_PARAMETERS:
                 _log.nosupport("Easyconfig parameter '%s' is replaced by '%s'" % (key, REPLACED_PARAMETERS[key]), '2.0')
 
@@ -280,8 +280,10 @@ def parse(self):
     def handle_allowed_system_deps(self):
         """Handle allowed system dependencies."""
         for (name, version) in self['allow_system_deps']:
-            env.setvar(get_software_root_env_var_name(name), name)  # root is set to name, not an actual path
-            env.setvar(get_software_version_env_var_name(name), version)  # version is expected to be something that makes sense
+            # root is set to name, not an actual path
+            env.setvar(get_software_root_env_var_name(name), name)
+            # version is expected to be something that makes sense
+            env.setvar(get_software_version_env_var_name(name), version)
 
     def validate(self, check_osdeps=True):
         """
@@ -302,7 +304,7 @@ def validate(self, check_osdeps=True):
 
         self.log.info("Checking skipsteps")
         if not isinstance(self._config['skipsteps'][0], (list, tuple,)):
-            self.log.error('Invalid type for skipsteps. Allowed are list or tuple, got %s (%s)' %
+            raise EasyBuildError('Invalid type for skipsteps. Allowed are list or tuple, got %s (%s)' %
                            (type(self._config['skipsteps'][0]), self._config['skipsteps'][0]))
 
         self.log.info("Checking build option lists")
@@ -317,12 +319,12 @@ def validate_license(self):
         if lic is None:
             # when mandatory, remove this possibility
             if 'software_license' in self.mandatory:
-                self.log.error("License is mandatory, but 'software_license' is undefined")
+                raise EasyBuildError("License is mandatory, but 'software_license' is undefined")
         elif not isinstance(lic, License):
-            self.log.error('License %s has to be a License subclass instance, found classname %s.' %
+            raise EasyBuildError('License %s has to be a License subclass instance, found classname %s.' %
                            (lic, lic.__class__.__name__))
         elif not lic.name in EASYCONFIG_LICENSES_DICT:
-            self.log.error('Invalid license %s (classname: %s).' % (lic.name, lic.__class__.__name__))
+            raise EasyBuildError('Invalid license %s (classname: %s).', lic.name, lic.__class__.__name__)
 
         # TODO, when GROUP_SOURCE and/or GROUP_BINARY is True
         #  check the owner of source / binary (must match 'group' parameter from easyconfig)
@@ -340,13 +342,14 @@ def validate_os_deps(self):
             if isinstance(dep, basestring):
                 dep = (dep,)
             elif not isinstance(dep, tuple):
-                self.log.error("Non-tuple value type for OS dependency specification: %s (type %s)" % (dep, type(dep)))
+                raise EasyBuildError("Non-tuple value type for OS dependency specification: %s (type %s)",
+                                     dep, type(dep))
 
             if not any([check_os_dependency(cand_dep) for cand_dep in dep]):
                 not_found.append(dep)
 
         if not_found:
-            self.log.error("One or more OS dependencies were not found: %s" % not_found)
+            raise EasyBuildError("One or more OS dependencies were not found: %s", not_found)
         else:
             self.log.info("OS dependencies ok: %s" % self['osdependencies'])
 
@@ -365,7 +368,7 @@ def validate_iterate_opts_lists(self):
 
             # anticipate changes in available easyconfig parameters (e.g. makeopts -> buildopts?)
             if self.get(opt, None) is None:
-                self.log.error("%s not available in self.cfg (anymore)?!" % opt)
+                raise EasyBuildError("%s not available in self.cfg (anymore)?!", opt)
 
             # keep track of list, supply first element as first option to handle
             if isinstance(self[opt], (list, tuple)):
@@ -374,7 +377,7 @@ def validate_iterate_opts_lists(self):
         # make sure that options that specify lists have the same length
         list_opt_lengths = [length for (opt, length) in opt_counts if length > 1]
         if len(nub(list_opt_lengths)) > 1:
-            self.log.error("Build option lists for iterated build should have same length: %s" % opt_counts)
+            raise EasyBuildError("Build option lists for iterated build should have same length: %s", opt_counts)
 
         return True
 
@@ -399,8 +402,8 @@ def filter_hidden_deps(self):
                 faulty_deps.append(visible_mod_name)
 
         if faulty_deps:
-            tup = (faulty_deps, dep_mod_names)
-            self.log.error("Hidden dependencies with visible module names %s not in list of dependencies: %s" % tup)
+            raise EasyBuildError("Hidden dependencies with visible module names %s not in list of dependencies: %s",
+                                 faulty_deps, dep_mod_names)
 
     def dependencies(self):
         """
@@ -515,7 +518,7 @@ def _validate(self, attr, values):  # private method
         if values is None:
             values = []
         if self[attr] and self[attr] not in values:
-            self.log.error("%s provided '%s' is not valid: %s" % (attr, self[attr], values))
+            raise EasyBuildError("%s provided '%s' is not valid: %s", attr, self[attr], values)
 
     # private method
     def _parse_dependency(self, dep, hidden=False):
@@ -564,7 +567,7 @@ def _parse_dependency(self, dep, hidden=False):
             dep = list(dep)
             dependency.update(dict(zip(attr, dep)))
         else:
-            self.log.error('Dependency %s of unsupported type: %s.' % (dep, type(dep)))
+            raise EasyBuildError('Dependency %s of unsupported type: %s.', dep, type(dep))
 
         # dependency inherits toolchain, unless it's specified to have a custom toolchain
         tc = copy.deepcopy(self['toolchain'])
@@ -578,14 +581,16 @@ def _parse_dependency(self, dep, hidden=False):
                 if len(tc_spec) == 2:
                     tc = {'name': tc_spec[0], 'version': tc_spec[1]}
                 else:
-                    self.log.error("List/tuple value for toolchain should have two elements (%s)" % str(tc_spec))
+                    raise EasyBuildError("List/tuple value for toolchain should have two elements (%s)", str(tc_spec))
             elif isinstance(tc_spec, dict):
                 if 'name' in tc_spec and 'version' in tc_spec:
                     tc = copy.deepcopy(tc_spec)
                 else:
-                    self.log.error("Found toolchain spec as dict with required 'name'/'version' keys: %s" % tc_spec)
+                    raise EasyBuildError("Found toolchain spec as dict with required 'name'/'version' keys: %s",
+                                         tc_spec)
             else:
-                self.log.error("Unsupported type for toolchain spec encountered: %s => %s" % (tc_spec, type(tc_spec)))
+                raise EasyBuildError("Unsupported type for toolchain spec encountered: %s => %s",
+                                     tc_spec, type(tc_spec))
 
         dependency['toolchain'] = tc
 
@@ -594,10 +599,10 @@ def _parse_dependency(self, dep, hidden=False):
 
         # validations
         if not dependency['name']:
-            self.log.error("Dependency specified without name: %s" % dependency)
+            raise EasyBuildError("Dependency specified without name: %s", dependency)
 
         if not dependency['version']:
-            self.log.error("Dependency specified without version: %s" % dependency)
+            raise EasyBuildError("Dependency specified without version: %s", dependency)
 
         dependency['short_mod_name'] = ActiveMNS().det_short_module_name(dependency)
         dependency['full_mod_name'] = ActiveMNS().det_full_module_name(dependency)
@@ -643,7 +648,7 @@ def __getitem__(self, key):
         if key in self._config:
             value = self._config[key][0]
         else:
-            self.log.error("Use of unknown easyconfig parameter '%s' when getting parameter value" % key)
+            raise EasyBuildError("Use of unknown easyconfig parameter '%s' when getting parameter value", key)
 
         if self.enable_templating:
             if self.template_values is None or len(self.template_values) == 0:
@@ -658,8 +663,8 @@ def __setitem__(self, key, value):
         if key in self._config:
             self._config[key][0] = value
         else:
-            tup = (key, value)
-            self.log.error("Use of unknown easyconfig parameter '%s' when setting parameter value to '%s'" % tup)
+            raise EasyBuildError("Use of unknown easyconfig parameter '%s' when setting parameter value to '%s'",
+                                 key, value)
 
     @handle_deprecated_or_replaced_easyconfig_parameters
     def get(self, key, default=None):
@@ -705,8 +710,8 @@ def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_fa
             # figure out if full path was specified or not
             if es:
                 modulepath = '.'.join(es)
-                tup = (class_name, modulepath)
-                _log.info("Assuming that full easyblock module path was specified (class: %s, modulepath: %s)" % tup)
+                _log.info("Assuming that full easyblock module path was specified (class: %s, modulepath: %s)",
+                          class_name, modulepath)
                 cls = get_class_for(modulepath, class_name)
             else:
                 # if we only get the class name, most likely we're dealing with a generic easyblock
@@ -763,16 +768,17 @@ def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_fa
                         _log.nosupport(depr_msg, '2.0')
                 else:
                     if error_on_failed_import:
-                        _log.error("Failed to import easyblock for %s because of module issue: %s" % (class_name, err))
+                        raise EasyBuildError("Failed to import easyblock for %s because of module issue: %s",
+                                             class_name, err)
                     else:
                         _log.debug("Failed to import easyblock for %s, but ignoring it: %s" % (class_name, err))
 
         if cls is not None:
-            tup = (cls.__name__, easyblock, name)
-            _log.info("Successfully obtained class '%s' for easyblock '%s' (software name '%s')" % tup)
+            _log.info("Successfully obtained class '%s' for easyblock '%s' (software name '%s')",
+                      cls.__name__, easyblock, name)
         else:
-            tup = (easyblock, name, default_fallback)
-            _log.debug("No class found for easyblock '%s' (software name '%s', default fallback: %s" % tup)
+            _log.debug("No class found for easyblock '%s' (software name '%s', default fallback: %s",
+                       easyblock, name, default_fallback)
 
         return cls
 
@@ -780,7 +786,7 @@ def get_easyblock_class(easyblock, name=None, default_fallback=True, error_on_fa
         # simply reraise rather than wrapping it into another error
         raise err
     except Exception, err:
-        _log.error("Failed to obtain class for %s easyblock (not available?): %s" % (easyblock, err))
+        raise EasyBuildError("Failed to obtain class for %s easyblock (not available?): %s", easyblock, err)
 
 
 def get_module_path(name, generic=False, decode=True):
@@ -891,7 +897,7 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False,
             ec = EasyConfig(spec, build_specs=build_specs, validate=validate, hidden=hidden)
         except EasyBuildError, err:
             msg = "Failed to process easyconfig %s:\n%s" % (spec, err.msg)
-            _log.exception(msg)
+            raise EasyBuildError(msg)
 
         name = ec['name']
 
@@ -970,7 +976,7 @@ def robot_find_easyconfig(name, version):
         return _easyconfig_files_cache[key]
     paths = build_option('robot_path')
     if not paths:
-        _log.error("No robot path specified, which is required when looking for easyconfigs (use --robot)")
+        raise EasyBuildError("No robot path specified, which is required when looking for easyconfigs (use --robot)")
     if not isinstance(paths, (list, tuple)):
         paths = [paths]
     # candidate easyconfig paths
@@ -1002,7 +1008,8 @@ def __init__(self, *args, **kwargs):
         if sel_mns in avail_mnss:
             self.mns = avail_mnss[sel_mns]()
         else:
-            self.log.error("Selected module naming scheme %s could not be found in %s" % (sel_mns, avail_mnss.keys()))
+            raise EasyBuildError("Selected module naming scheme %s could not be found in %s",
+                                 sel_mns, avail_mnss.keys())
 
     def requires_full_easyconfig(self, keys):
         """Check whether specified list of easyconfig parameters is sufficient for active module naming scheme."""
@@ -1023,8 +1030,8 @@ def check_ec_type(self, ec):
                     self.log.debug("Full list of parsed easyconfigs: %s" % parsed_ec)
                 ec = parsed_ec[0]['ec']
             else:
-                tup = (ec['name'], det_full_ec_version(ec), ec)
-                self.log.error("Failed to find easyconfig file '%s-%s.eb' when determining module name for: %s" % tup)
+                raise EasyBuildError("Failed to find easyconfig file '%s-%s.eb' when determining module name for: %s",
+                                     ec['name'], det_full_ec_version(ec), ec)
 
         return ec
 
@@ -1047,7 +1054,7 @@ def _det_module_name_with(self, mns_method, ec, force_visible=False):
         mod_name = mns_method(self.check_ec_type(ec))
 
         if not is_valid_module_name(mod_name):
-            self.log.error("%s is not a valid module name" % str(mod_name))
+            raise EasyBuildError("%s is not a valid module name", str(mod_name))
 
         # check whether module name should be hidden or not
         # ec may be either a dict or an EasyConfig instance, 'force_visible' argument overrules
@@ -1076,8 +1083,8 @@ def det_short_module_name(self, ec, force_visible=False):
 
         # sanity check: obtained module name should pass the 'is_short_modname_for' check
         if not self.is_short_modname_for(mod_name, ec['name']):
-            tup = (mod_name, ec['name'])
-            self.log.error("is_short_modname_for('%s', '%s') for active module naming scheme returns False" % tup)
+            raise EasyBuildError("is_short_modname_for('%s', '%s') for active module naming scheme returns False",
+                                 mod_name, ec['name'])
 
         return mod_name
 
diff --git a/easybuild/framework/easyconfig/format/format.py b/easybuild/framework/easyconfig/format/format.py
index d13386386f..13dcaa6ddf 100644
--- a/easybuild/framework/easyconfig/format/format.py
+++ b/easybuild/framework/easyconfig/format/format.py
@@ -37,6 +37,7 @@
 from easybuild.framework.easyconfig.format.version import EasyVersion, OrderedVersionOperators
 from easybuild.framework.easyconfig.format.version import ToolchainVersionOperator, VersionOperator
 from easybuild.framework.easyconfig.format.convert import Dependency
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.configobj import Section
 
 
@@ -59,7 +60,7 @@ def get_format_version(txt):
             maj_min = res.groupdict()
             format_version = EasyVersion(FORMAT_VERSION_TEMPLATE % maj_min)
         except (KeyError, TypeError), err:
-            _log.error("Failed to get version from match %s: %s" % (res.groups(), err))
+            raise EasyBuildError("Failed to get version from match %s: %s", res.groups(), err)
     return format_version
 
 
@@ -242,13 +243,14 @@ def parse_sections(self, toparse, current):
                     new_value = []
                     for dep_name, dep_val in value.items():
                         if isinstance(dep_val, Section):
-                            self.log.error("Unsupported nested section '%s' found in dependencies section" % dep_name)
+                            raise EasyBuildError("Unsupported nested section '%s' found in dependencies section",
+                                                 dep_name)
                         else:
                             # FIXME: parse the dependency specification for version, toolchain, suffix, etc.
                             dep = Dependency(dep_val, name=dep_name)
                             if dep.name() is None or dep.version() is None:
                                 tmpl = "Failed to find name/version in parsed dependency: %s (dict: %s)"
-                                self.log.error(tmpl % (dep, dict(dep)))
+                                raise EasyBuildError(tmpl, dep, dict(dep))
                             new_value.append(dep)
 
                     tmpl = 'Converted dependency section %s to %s, passed it to parent section (or default)'
@@ -268,7 +270,7 @@ def parse_sections(self, toparse, current):
                         else:
                             self.log.debug("Not a %s section marker" % marker_type.__name__)
                     if not new_key:
-                        self.log.error("Unsupported section marker '%s'" % key)
+                        raise EasyBuildError("Unsupported section marker '%s'", key)
 
                     # parse value as a section, recursively
                     new_value = self.parse_sections(value, current.get_nested_dict())
@@ -296,10 +298,10 @@ def parse_sections(self, toparse, current):
                     # remove possible surrounding whitespace (some people add space after comma)
                     new_value = [value_type(x.strip()) for x in value]
                     if False in [x.is_valid() for x in new_value]:
-                        self.log.error("Failed to parse '%s' as list of %s" % (value, value_type.__name__))
+                        raise EasyBuildError("Failed to parse '%s' as list of %s", value, value_type.__name__)
                 else:
-                    tup = (key, value, type(value))
-                    self.log.error('Bug: supported but unknown key %s with non-string value: %s, type %s' % tup)
+                    raise EasyBuildError('Bug: supported but unknown key %s with non-string value: %s, type %s',
+                                         key, value, type(value))
 
                 self.log.debug("Converted value '%s' for key '%s' into new value '%s'" % (value, key, new_value))
                 current[key] = new_value
@@ -334,7 +336,7 @@ def parse(self, configobj):
         self.supported = self.sections.pop(self.SECTION_MARKER_SUPPORTED)
         for key, value in self.supported.items():
             if not key in self.VERSION_OPERATOR_VALUE_TYPES:
-                self.log.error('Unsupported key %s in %s section' % (key, self.SECTION_MARKER_SUPPORTED))
+                raise EasyBuildError('Unsupported key %s in %s section', key, self.SECTION_MARKER_SUPPORTED)
             self.sections['%s' % key] = value
 
         for key, supported_key, fn_name in [('version', 'versions', 'get_version_str'),
@@ -344,7 +346,7 @@ def parse(self, configobj):
                 first = self.supported[supported_key][0]
                 f_val = getattr(first, fn_name)()
                 if f_val is None:
-                    self.log.error("First %s %s can't be used as default (%s returned None)" % (key, first, fn_name))
+                    raise EasyBuildError("First %s %s can't be used as default (%s returned None)", key, first, fn_name)
                 else:
                     self.log.debug('Using first %s (%s) as default %s' % (key, first, f_val))
                     self.default[key] = f_val
@@ -438,8 +440,7 @@ def _squash_netsed_dict(self, key, nested_dict, squashed, sanity, vt_tuple):
             tc_overops.add(key)
 
             if key.test(tcname, tcversion):
-                tup = (tcname, tcversion, key)
-                self.log.debug("Found matching marker for specified toolchain '%s, %s': %s" % tup)
+                self.log.debug("Found matching marker for specified toolchain '%s, %s': %s", tcname, tcversion, key)
                 # TODO remove when unifying add_toolchina with .add()
                 tmp_squashed = self._squash(vt_tuple, nested_dict, sanity)
                 res_sections.update(tmp_squashed.result)
@@ -456,7 +457,7 @@ def _squash_netsed_dict(self, key, nested_dict, squashed, sanity, vt_tuple):
             else:
                 self.log.debug('Found non-matching version marker %s. Ignoring this (nested) section.' % key)
         else:
-            self.log.error("Unhandled section marker '%s' (type '%s')" % (key, type(key)))
+            raise EasyBuildError("Unhandled section marker '%s' (type '%s')", key, type(key))
 
         return res_sections
 
@@ -479,8 +480,8 @@ def _squash_versop(self, key, value, squashed, sanity, vt_tuple):
             tmp_tc_oversops = {}  # temporary, only for conflict checking
             for tcversop in value:
                 tc_overops = tmp_tc_oversops.setdefault(tcversop.tc_name, OrderedVersionOperators())
-                tup = (tcversop, tc_overops, tcname, tcversion)
-                self.log.debug('Add tcversop %s to tc_overops %s tcname %s tcversion %s' % tup)
+                self.log.debug("Add tcversop %s to tc_overops %s tcname %s tcversion %s",
+                               tcversop, tc_overops, tcname, tcversion)
                 tc_overops.add(tcversop)  # test non-conflicting list
                 if tcversop.test(tcname, tcversion):
                     matching_toolchains.append(tcversop)
@@ -507,7 +508,7 @@ def _squash_versop(self, key, value, squashed, sanity, vt_tuple):
                 self.log.debug('No matching versions, removing the whole current key %s' % key)
                 return Squashed()
         else:
-            self.log.error('Unexpected VERSION_OPERATOR_VALUE_TYPES key %s value %s' % (key, value))
+            raise EasyBuildError('Unexpected VERSION_OPERATOR_VALUE_TYPES key %s value %s', key, value)
 
         return None
 
@@ -520,11 +521,11 @@ def get_version_toolchain(self, version=None, tcname=None, tcversion=None):
                 version = self.default['version']
                 self.log.debug("No version specified, using default %s" % version)
             else:
-                self.log.error("No version specified, no default found.")
+                raise EasyBuildError("No version specified, no default found.")
         elif version in versions:
             self.log.debug("Version '%s' is supported in easyconfig." % version)
         else:
-            self.log.error("Version '%s' not supported in easyconfig (only %s)" % (version, versions))
+            raise EasyBuildError("Version '%s' not supported in easyconfig (only %s)", version, versions)
 
         tcnames = [tc.tc_name for tc in self.supported['toolchains']]
         if tcname is None:
@@ -532,11 +533,11 @@ def get_version_toolchain(self, version=None, tcname=None, tcversion=None):
                 tcname = self.default['toolchain']['name']
                 self.log.debug("No toolchain name specified, using default %s" % tcname)
             else:
-                self.log.error("No toolchain name specified, no default found.")
+                raise EasyBuildError("No toolchain name specified, no default found.")
         elif tcname in tcnames:
             self.log.debug("Toolchain '%s' is supported in easyconfig." % tcname)
         else:
-            self.log.error("Toolchain '%s' not supported in easyconfig (only %s)" % (tcname, tcnames))
+            raise EasyBuildError("Toolchain '%s' not supported in easyconfig (only %s)", tcname, tcnames)
 
         tcs = [tc for tc in self.supported['toolchains'] if tc.tc_name == tcname]
         if tcversion is None:
@@ -544,17 +545,16 @@ def get_version_toolchain(self, version=None, tcname=None, tcversion=None):
                 tcversion = self.default['toolchain']['version']
                 self.log.debug("No toolchain version specified, using default %s" % tcversion)
             else:
-                self.log.error("No toolchain version specified, no default found.")
+                raise EasyBuildError("No toolchain version specified, no default found.")
         elif any([tc.test(tcname, tcversion) for tc in tcs]):
             self.log.debug("Toolchain '%s' version '%s' is supported in easyconfig" % (tcname, tcversion))
         else:
-            tup = (tcname, tcversion, tcs)
-            self.log.error("Toolchain '%s' version '%s' not supported in easyconfig (only %s)" % tup)
+            raise EasyBuildError("Toolchain '%s' version '%s' not supported in easyconfig (only %s)",
+                                 tcname, tcversion, tcs)
 
-        tup = (version, tcname, tcversion)
-        self.log.debug('version %s, tcversion %s, tcname %s' % tup)
+        self.log.debug('version %s, tcversion %s, tcname %s', version, tcname, tcversion)
 
-        return tup
+        return (version, tcname, tcversion)
 
     def get_specs_for(self, version=None, tcname=None, tcversion=None):
         """
@@ -578,7 +578,7 @@ def __init__(self):
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
         if not len(self.VERSION) == len(FORMAT_VERSION_TEMPLATE.split('.')):
-            self.log.error('Invalid version number %s (incorrect length)' % self.VERSION)
+            raise EasyBuildError('Invalid version number %s (incorrect length)', self.VERSION)
 
         self.rawtext = None  # text version of the easyconfig
         self.header = None  # easyconfig header (e.g., format version, license, ...)
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 7a613ad0dc..5fca21b5b7 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -39,7 +39,7 @@
 from easybuild.framework.easyconfig.format.format import FORMAT_DEFAULT_VERSION, get_format_version
 from easybuild.framework.easyconfig.format.pyheaderconfigobj import EasyConfigFormatConfigObj
 from easybuild.framework.easyconfig.format.version import EasyVersion
-from easybuild.tools.build_log import print_msg
+from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.filetools import write_file
 
 
@@ -71,14 +71,14 @@ def get_config_dict(self):
         spec_tc_version = spec_tc.get('version', None)
         cfg = self.pyheader_localvars
         if spec_version is not None and not spec_version == cfg['version']:
-            self.log.error('Requested version %s not available, only %s' % (spec_version, cfg['version']))
+            raise EasyBuildError('Requested version %s not available, only %s', spec_version, cfg['version'])
 
         tc_name = cfg['toolchain']['name']
         tc_version = cfg['toolchain']['version']
         if spec_tc_name is not None and not spec_tc_name == tc_name:
-            self.log.error('Requested toolchain name %s not available, only %s' % (spec_tc_name, tc_name))
+            raise EasyBuildError('Requested toolchain name %s not available, only %s', spec_tc_name, tc_name)
         if spec_tc_version is not None and not spec_tc_version == tc_version:
-            self.log.error('Requested toolchain version %s not available, only %s' % (spec_tc_version, tc_version))
+            raise EasyBuildError('Requested toolchain version %s not available, only %s', spec_tc_version, tc_version)
 
         return cfg
 
@@ -102,7 +102,7 @@ def retrieve_blocks_in_spec(spec, only_blocks, silent=False):
     try:
         txt = open(spec).read()
     except IOError, err:
-        _log.error("Failed to read file %s: %s" % (spec, err))
+        raise EasyBuildError("Failed to read file %s: %s", spec, err)
 
     # split into blocks using regex
     pieces = reg_block.split(txt)
@@ -125,7 +125,7 @@ def retrieve_blocks_in_spec(spec, only_blocks, silent=False):
 
             if block_name in [b['name'] for b in blocks]:
                 msg = "Found block %s twice in %s." % (block_name, spec)
-                _log.error(msg)
+                raise EasyBuildError(msg)
 
             block = {'name': block_name, 'contents': block_contents}
 
@@ -157,7 +157,7 @@ def retrieve_blocks_in_spec(spec, only_blocks, silent=False):
             if 'dependencies' in block:
                 for dep in block['dependencies']:
                     if not dep in [b['name'] for b in blocks]:
-                        _log.error("Block %s depends on %s, but block was not found." % (name, dep))
+                        raise EasyBuildError("Block %s depends on %s, but block was not found.", name, dep)
 
                     dep = [b for b in blocks if b['name'] == dep][0]
                     txt += "\n# Dependency block %s" % (dep['name'])
diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index 901efc4966..3159e1a273 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -36,6 +36,7 @@
 from easybuild.framework.easyconfig.format.format import get_format_version, EasyConfigFormat
 from easybuild.framework.easyconfig.licenses import EASYCONFIG_LICENSES_DICT
 from easybuild.framework.easyconfig.templates import TEMPLATE_CONSTANTS
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.configobj import ConfigObj
 from easybuild.tools.systemtools import get_shared_lib_ext
 
@@ -68,7 +69,7 @@ def build_easyconfig_constants_dict():
                 const_dict[cst_key] = cst_val
 
     if len(err) > 0:
-        _log.error("EasyConfig constants sanity check failed: %s" % ("\n".join(err)))
+        raise EasyBuildError("EasyConfig constants sanity check failed: %s", "\n".join(err))
     else:
         return const_dict
 
@@ -128,8 +129,8 @@ def parse(self, txt, strict_section_markers=False):
             last_n = 100
             pre_section_tail = txt[start_section-last_n:start_section]
             sections_head = txt[start_section:start_section+last_n]
-            tup = (start_section, last_n, pre_section_tail, sections_head)
-            self.log.debug('Sections start at index %s, %d-chars context:\n"""%s""""\n<split>\n"""%s..."""' % tup)
+            self.log.debug('Sections start at index %s, %d-chars context:\n"""%s""""\n<split>\n"""%s..."""',
+                           start_section, last_n, pre_section_tail, sections_head)
 
         self.parse_pre_section(txt[:start_section])
         if start_section is not None:
@@ -148,7 +149,7 @@ def parse_pre_section(self, txt):
             format_version = get_format_version(line)
             if format_version is not None:
                 if not format_version == self.VERSION:
-                    self.log.error("Invalid format version %s for current format class" % format_version)
+                    raise EasyBuildError("Invalid format version %s for current format class", format_version)
                 else:
                     self.log.info("Valid format version %s found" % format_version)
                 # version is not part of header
@@ -185,7 +186,7 @@ def parse_pyheader(self, pyheader):
         try:
             exec(pyheader, global_vars, local_vars)
         except SyntaxError, err:
-            self.log.error("SyntaxError in easyconfig pyheader %s: %s" % (pyheader, err))
+            raise EasyBuildError("SyntaxError in easyconfig pyheader %s: %s", pyheader, err)
 
         self.log.debug("pyheader final global_vars %s" % global_vars)
         self.log.debug("pyheader final local_vars %s" % local_vars)
@@ -230,14 +231,14 @@ def _validate_pyheader(self):
         blacklisted parameters are not allowed, mandatory parameters are mandatory unless blacklisted
         """
         if self.pyheader_localvars is None:
-            self.log.error("self.pyheader_localvars must be initialized")
+            raise EasyBuildError("self.pyheader_localvars must be initialized")
         if self.PYHEADER_BLACKLIST is None or self.PYHEADER_MANDATORY is None:
-            self.log.error('Both PYHEADER_BLACKLIST and PYHEADER_MANDATORY must be set')
+            raise EasyBuildError('Both PYHEADER_BLACKLIST and PYHEADER_MANDATORY must be set')
 
         for param in self.PYHEADER_BLACKLIST:
             if param in self.pyheader_localvars:
                 # TODO add to easyconfig unittest (similar to mandatory)
-                self.log.error('blacklisted param %s not allowed in pyheader' % param)
+                raise EasyBuildError('blacklisted param %s not allowed in pyheader', param)
 
         missing = []
         for param in self.PYHEADER_MANDATORY:
@@ -246,13 +247,13 @@ def _validate_pyheader(self):
             if not param in self.pyheader_localvars:
                 missing.append(param)
         if missing:
-            self.log.error('mandatory parameters not provided in pyheader: %s' % ', '.join(missing))
+            raise EasyBuildError('mandatory parameters not provided in pyheader: %s', ', '.join(missing))
 
     def parse_section_block(self, section):
         """Parse the section block by trying to convert it into a ConfigObj instance"""
         try:
             self.configobj = ConfigObj(section.split('\n'))
         except SyntaxError, err:
-            self.log.error('Failed to convert section text %s: %s' % (section, err))
+            raise EasyBuildError('Failed to convert section text %s: %s', section, err)
 
         self.log.debug("Found ConfigObj instance %s" % self.configobj)
diff --git a/easybuild/framework/easyconfig/format/two.py b/easybuild/framework/easyconfig/format/two.py
index 62be586bc4..2c6618cb85 100644
--- a/easybuild/framework/easyconfig/format/two.py
+++ b/easybuild/framework/easyconfig/format/two.py
@@ -37,6 +37,7 @@
 from easybuild.framework.easyconfig.format.pyheaderconfigobj import EasyConfigFormatConfigObj
 from easybuild.framework.easyconfig.format.format import EBConfigObj
 from easybuild.framework.easyconfig.format.version import EasyVersion, ToolchainVersionOperator, VersionOperator
+from easybuild.tools.build_log import EasyBuildError
 
 
 class FormatTwoZero(EasyConfigFormatConfigObj):
@@ -89,10 +90,10 @@ def _check_docstring(self):
             maintainers.append(res['name'])
 
         if self.AUTHOR_REQUIRED and not authors:
-            self.log.error("No author in docstring (regex: '%s')" % self.AUTHOR_DOCSTRING_REGEX.pattern)
+            raise EasyBuildError("No author in docstring (regex: '%s')", self.AUTHOR_DOCSTRING_REGEX.pattern)
 
         if self.MAINTAINER_REQUIRED and not maintainers:
-            self.log.error("No maintainer in docstring (regex: '%s')" % self.MAINTAINER_DOCSTRING_REGEX.pattern)
+            raise EasyBuildError("No maintainer in docstring (regex: '%s')", self.MAINTAINER_DOCSTRING_REGEX.pattern)
 
     def get_config_dict(self):
         """Return the best matching easyconfig dict"""
diff --git a/easybuild/framework/easyconfig/format/version.py b/easybuild/framework/easyconfig/format/version.py
index e04e228afe..7e1891f69a 100644
--- a/easybuild/framework/easyconfig/format/version.py
+++ b/easybuild/framework/easyconfig/format/version.py
@@ -34,6 +34,7 @@
 from distutils.version import LooseVersion
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.utilities import search_toolchain
 
 
@@ -80,7 +81,7 @@ def __init__(self, versop_str=None, error_on_parse_failure=False):
         """
         Initialise VersionOperator instance.
         @param versop_str: intialise with version operator string
-        @param error_on_parse_failure: log.error in case of parse error
+        raise EasyBuildError in case of parse error
         """
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
@@ -100,7 +101,7 @@ def parse_error(self, msg):
         """Special function to deal with parse errors"""
         # TODO major issue what to do in case of misparse. error or not?
         if self.error_on_parse_failure:
-            self.log.error(msg)
+            raise EasyBuildError(msg)
         else:
             self.log.debug(msg)
 
@@ -122,7 +123,7 @@ def set(self, versop_str):
         """
         versop_dict = self.parse_versop_str(versop_str)
         if versop_dict is None:
-            self.log.error("Failed to parse '%s' as a version operator string" % versop_str)
+            raise EasyBuildError("Failed to parse '%s' as a version operator string", versop_str)
         else:
             for k, v in versop_dict.items():
                 setattr(self, k, v)
@@ -136,16 +137,16 @@ def test(self, test_version):
         """
         # checks whether this VersionOperator instance is valid using __bool__ function
         if not self:
-            self.log.error('Not a valid %s. Not initialised yet?' % self.__class__.__name__)
+            raise EasyBuildError('Not a valid %s. Not initialised yet?', self.__class__.__name__)
 
         if isinstance(test_version, basestring):
             test_version = self._convert(test_version)
         elif not isinstance(test_version, EasyVersion):
-            self.log.error("test: argument should be a basestring or EasyVersion (type %s)" % (type(test_version)))
+            raise EasyBuildError("test: argument should be a basestring or EasyVersion (type %s)", type(test_version))
 
         res = self.operator(test_version, self.version)
-        tup = (test_version, self.REVERSE_OPERATOR_MAP[self.operator], self.version, res)
-        self.log.debug("result of testing expression '%s %s %s': %s" % tup)
+        self.log.debug("result of testing expression '%s %s %s': %s",
+                       test_version, self.REVERSE_OPERATOR_MAP[self.operator], self.version, res)
 
         return res
 
@@ -178,7 +179,7 @@ def __eq__(self, versop):
         if versop is None:
             return False
         elif not isinstance(versop, self.__class__):
-            self.log.error("Types don't match in comparison: %s, expected %s" % (type(versop), self.__class__))
+            raise EasyBuildError("Types don't match in comparison: %s, expected %s", type(versop), self.__class__)
         return self.version == versop.version and self.operator == versop.operator and self.suffix == versop.suffix
 
     def __ne__(self, versop):
@@ -270,7 +271,7 @@ def parse_versop_str(self, versop_str, versop_dict=None):
             versop_dict['versop_str'] = versop_str
 
         if not 'versop_str' in versop_dict:
-            self.log.error('Missing versop_str in versop_dict %s' % versop_dict)
+            raise EasyBuildError('Missing versop_str in versop_dict %s', versop_dict)
 
         version = self._convert(versop_dict['version_str'])
         operator = self._convert_operator(versop_dict['operator_str'], version=version)
@@ -311,7 +312,7 @@ def test_overlap_and_conflict(self, versop_other):
         versop_msg = "this versop %s and versop_other %s" % (self, versop_other)
 
         if not isinstance(versop_other, self.__class__):
-            self.log.error('overlap/conflict check needs instance of self %s (got type %s)' %
+            raise EasyBuildError('overlap/conflict check needs instance of self %s (got type %s)' %
                            (self.__class__.__name__, type(versop_other)))
 
         if self == versop_other:
@@ -424,12 +425,12 @@ def _gt_safe(self, version_gt_op, versop_other):
             Suffix are not considered.
         """
         if len(self.ORDERED_OPERATORS) != len(self.OPERATOR_MAP):
-            self.log.error('Inconsistency between ORDERED_OPERATORS and OPERATORS (lists are not of same length)')
+            raise EasyBuildError('Inconsistency between ORDERED_OPERATORS and OPERATORS (lists are not of same length)')
 
         # ensure this function is only used for non-conflicting version operators
         _, conflict = self.test_overlap_and_conflict(versop_other)
         if conflict:
-            self.log.error("Conflicting version operator expressions should not be compared with _gt_safe")
+            raise EasyBuildError("Conflicting version operator expressions should not be compared with _gt_safe")
 
         ordered_operators = [self.OPERATOR_MAP[x] for x in self.ORDERED_OPERATORS]
         if self.version == versop_other.version:
@@ -530,7 +531,7 @@ def parse_versop_str(self, tcversop_str):
         tcversop_dict = super(ToolchainVersionOperator, self).parse_versop_str(None, versop_dict=tcversop_dict)
 
         if tcversop_dict.get('version_str', None) is not None and tcversop_dict.get('operator_str', None) is None:
-            self.log.error("Toolchain version found, but no operator (use ' == '?).")
+            raise EasyBuildError("Toolchain version found, but no operator (use ' == '?).")
 
         self.log.debug("toolchain versop expression '%s' parsed to '%s'" % (tcversop_str, tcversop_dict))
         return tcversop_dict
@@ -552,15 +553,14 @@ def test(self, name, version):
         """
         # checks whether this ToolchainVersionOperator instance is valid using __bool__ function
         if not self:
-            self.log.error('Not a valid %s. Not initialised yet?' % self.__class__.__name__)
+            raise EasyBuildError('Not a valid %s. Not initialised yet?', self.__class__.__name__)
 
         tc_name_res = name == self.tc_name
         if not tc_name_res:
             self.log.debug('Toolchain name %s different from test toolchain name %s' % (self.tc_name, name))
         version_res = super(ToolchainVersionOperator, self).test(version)
         res = tc_name_res and version_res
-        tup = (tc_name_res, version_res, res)
-        self.log.debug("result of testing expression tc_name_res %s version_res %s: %s" % tup)
+        self.log.debug("result of testing expression tc_name_res %s version_res %s: %s", tc_name_res, version_res, res)
 
         return res
 
@@ -622,8 +622,8 @@ def add(self, versop_new, data=None, update=None):
         if isinstance(versop_new, basestring):
             versop_new = VersionOperator(versop_new)
         elif not isinstance(versop_new, VersionOperator):
-            tup = (versop_new, type(versop_new))
-            self.log.error(("add: argument must be a VersionOperator instance or basestring: %s; type %s") % tup)
+            raise EasyBuildError("add: argument must be a VersionOperator instance or basestring: %s; type %s",
+                                 versop_new, type(versop_new))
 
         if versop_new in self.versops:
             self.log.debug("Versop %s already added." % versop_new)
@@ -634,7 +634,7 @@ def add(self, versop_new, data=None, update=None):
                 # conflict
                 msg = 'add: conflict(s) between versop_new %s and existing versions %s'
                 conflict_versops = [(idx, self.versops[idx]) for idx, gt_val in enumerate(gt_test) if gt_val is None]
-                self.log.error(msg % (versop_new, conflict_versops))
+                raise EasyBuildError(msg, versop_new, conflict_versops)
             else:
                 if True in gt_test:
                     # determine first element for which comparison is True
@@ -655,8 +655,8 @@ def _add_data(self, versop_new, data, update):
         if update and versop_new_str in self.datamap:
             self.log.debug("Keeping track of data for %s UPDATE: %s" % (versop_new_str, data))
             if not hasattr(self.datamap[versop_new_str], 'update'):
-                tup = (versop_new_str, type(self.datamap[versop_new_str]))
-                self.log.error("Can't update on datamap key %s type %s" % tup)
+                raise EasyBuildError("Can't update on datamap key %s type %s",
+                                     versop_new_str, type(self.datamap[versop_new_str]))
             self.datamap[versop_new_str].update(data)
         else:
             self.log.debug("Keeping track of data for %s SET: %s" % (versop_new_str, data))
@@ -665,11 +665,11 @@ def _add_data(self, versop_new, data, update):
     def get_data(self, versop):
         """Return the data for versop from datamap"""
         if not isinstance(versop, VersionOperator):
-            tup = (versop, type(versop))
-            self.log.error(("get_data: argument must be a VersionOperator instance: %s; type %s") % tup)
+            raise EasyBuildError(("get_data: argument must be a VersionOperator instance: %s; type %s"),
+                                  versop, type(versop))
 
         versop_str = str(versop)
         if versop_str in self.datamap:
             return self.datamap[versop_str]
         else:
-            self.log.error('No data in datamap for versop %s' % versop)
+            raise EasyBuildError('No data in datamap for versop %s', versop)
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index f47e550403..c73570323d 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -35,6 +35,7 @@
 
 from easybuild.framework.easyconfig.format.format import FORMAT_DEFAULT_VERSION
 from easybuild.framework.easyconfig.format.format import get_format_version, get_format_version_classes
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import read_file, write_file
 
 
@@ -96,7 +97,7 @@ def __init__(self, filename=None, format_version=None, rawcontent=None):
             self._check_filename(filename)
             self.process()
         else:
-            self.log.error("Neither filename nor rawcontent provided to EasyConfigParser")
+            raise EasyBuildError("Neither filename nor rawcontent provided to EasyConfigParser")
 
     def process(self, filename=None):
         """Create an instance"""
@@ -112,9 +113,9 @@ def _check_filename(self, fn):
         self.log.debug("Process filename %s with get function %s, set function %s" % (fn, self.get_fn, self.set_fn))
 
         if self.get_fn is None:
-            self.log.error('Failed to determine get function for filename %s' % fn)
+            raise EasyBuildError('Failed to determine get function for filename %s', fn)
         if self.set_fn is None:
-            self.log.error('Failed to determine set function for filename %s' % fn)
+            raise EasyBuildError('Failed to determine set function for filename %s', fn)
 
     def _read(self, filename=None):
         """Read the easyconfig, dump content in self.rawcontent"""
@@ -124,11 +125,11 @@ def _read(self, filename=None):
         try:
             self.rawcontent = self.get_fn[0](*self.get_fn[1])
         except IOError, err:
-            self.log.error('Failed to obtain content with %s: %s' % (self.get_fn, err))
+            raise EasyBuildError('Failed to obtain content with %s: %s', self.get_fn, err)
 
         if not isinstance(self.rawcontent, basestring):
             msg = 'rawcontent is not basestring: type %s, content %s' % (type(self.rawcontent), self.rawcontent)
-            self.log.error("Unexpected result for raw content: %s" % msg)
+            raise EasyBuildError("Unexpected result for raw content: %s", msg)
 
     def _det_format_version(self):
         """Extract the format version from the raw content"""
@@ -146,10 +147,10 @@ def _get_format_version_class(self):
         if len(found_classes) == 1:
             return found_classes[0]
         elif not found_classes:
-            self.log.error('No format classes found matching version %s' % self.format_version)
+            raise EasyBuildError('No format classes found matching version %s', self.format_version)
         else:
             msg = 'More than one format class found matching version %s in %s' % (self.format_version, found_classes)
-            self.log.error(msg)
+            raise EasyBuildError(msg)
 
     def _set_formatter(self):
         """Obtain instance of the formatter"""
@@ -171,7 +172,7 @@ def write(self, filename=None):
         try:
             self.set_fn[0](*self.set_fn[1])
         except IOError, err:
-            self.log.error('Failed to process content with %s: %s' % (self.set_fn, err))
+            raise EasyBuildError('Failed to process content with %s: %s', self.set_fn, err)
 
     def set_specifications(self, specs):
         """Set specifications."""
diff --git a/easybuild/framework/easyconfig/templates.py b/easybuild/framework/easyconfig/templates.py
index 21762fecf5..046ce3e43f 100644
--- a/easybuild/framework/easyconfig/templates.py
+++ b/easybuild/framework/easyconfig/templates.py
@@ -34,6 +34,7 @@
 from vsc.utils import fancylogger
 from distutils.version import LooseVersion
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.systemtools import get_shared_lib_ext
 
 
@@ -175,7 +176,7 @@ def template_constant_dict(config, ignore=None, skip_lower=True):
                 if softname is not None:
                     template_values['nameletter'] = softname[0]
         else:
-            _log.error("Undefined name %s from TEMPLATE_NAMES_EASYCONFIG" % name)
+            raise EasyBuildError("Undefined name %s from TEMPLATE_NAMES_EASYCONFIG", name)
 
     # step 2: add remaining from config
     for name in TEMPLATE_NAMES_CONFIG:
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index a207b11ea9..1ed42e17c2 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -180,9 +180,8 @@ def dep_graph(*args, **kwargs):
     try:
         _dep_graph(*args, **kwargs)
     except NameError, err:
-        errors = "\n".join(graph_errors)
-        msg = "An optional Python packages required to generate dependency graphs is missing: %s" % errors
-        _log.error("%s\nerr: %s" % (msg, err))
+        raise EasyBuildError("An optional Python packages required to generate dependency graphs is missing: %s, %s",
+                             '\n'.join(graph_errors), err)
 
 
 def get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None):
@@ -314,7 +313,7 @@ def parse_easyconfigs(paths):
         # keep track of whether any files were generated
         generated_ecs |= generated
         if not os.path.exists(path):
-            _log.error("Can't find path %s", path)
+            raise EasyBuildError("Can't find path %s", path)
         try:
             ec_files = find_easyconfigs(path, ignore_dirs=build_option('ignore_dirs'))
             for ec_file in ec_files:
@@ -325,7 +324,7 @@ def parse_easyconfigs(paths):
                 ecs = process_easyconfig(ec_file, **kwargs)
                 easyconfigs.extend(ecs)
         except IOError, err:
-            _log.error("Processing easyconfigs in path %s failed: %s" % (path, err))
+            raise EasyBuildError("Processing easyconfigs in path %s failed: %s", path, err)
 
     return easyconfigs, generated_ecs
 
@@ -335,7 +334,7 @@ def stats_to_str(stats):
     Pretty print build statistics to string.
     """
     if not isinstance(stats, (OrderedDict, dict)):
-        _log.error("Can only pretty print build stats in dictionary form, not of type %s" % type(stats))
+        raise EasyBuildError("Can only pretty print build stats in dictionary form, not of type %s", type(stats))
 
     txt = "{\n"
     pref = "    "
diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index dd14805b85..130af934e5 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -43,6 +43,7 @@
 from vsc.utils.missing import nub
 
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, create_paths, process_easyconfig
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import read_file, write_file
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.robot import resolve_dependencies
@@ -74,7 +75,8 @@ def tweak(easyconfigs, build_specs, targetdir=None):
     # make sure easyconfigs all feature the same toolchain (otherwise we *will* run into trouble)
     toolchains = nub(['%(name)s/%(version)s' % ec['ec']['toolchain'] for ec in easyconfigs])
     if len(toolchains) > 1:
-        _log.error("Multiple toolchains featured in easyconfigs, --try-X not supported in that case: %s" % toolchains)
+        raise EasyBuildError("Multiple toolchains featured in easyconfigs, --try-X not supported in that case: %s",
+                             toolchains)
 
     if 'name' in build_specs or 'version' in build_specs:
         # no recursion if software name/version build specification are included
@@ -143,7 +145,7 @@ def tweak_one(src_fn, target_fn, tweaks, targetdir=None):
         tc_regexp = re.compile(r"^\s*toolchain\s*=\s*(.*)$", re.M)
         res = tc_regexp.search(ectxt)
         if not res:
-            _log.error("No toolchain found in easyconfig file %s?" % src_fn)
+            raise EasyBuildError("No toolchain found in easyconfig file %s?", src_fn)
 
         toolchain = eval(res.group(1))
         for key in ['name', 'version']:
@@ -204,8 +206,8 @@ def __repr__(self):
                 diff = eval(res.group('val')) != val
             except (NameError, SyntaxError):
                 # if eval fails, just fall back to string comparison
-                tup = (res.group('val'), val)
-                _log.debug("eval failed for \"%s\", falling back to string comparison against \"%s\"..." % tup)
+                _log.debug("eval failed for \"%s\", falling back to string comparison against \"%s\"...",
+                           res.group('val'), val)
                 diff = res.group('val') != val
 
             if diff:
@@ -237,7 +239,7 @@ def __repr__(self):
             # get rid of temporary file
             os.remove(tmpfn)
         except OSError, err:
-            _log.error("Failed to determine suiting filename for tweaked easyconfig file: %s" % err)
+            raise EasyBuildError("Failed to determine suiting filename for tweaked easyconfig file: %s", err)
 
         if targetdir is None:
             targetdir = tempfile.gettempdir()
@@ -265,7 +267,7 @@ def pick_version(req_ver, avail_vers):
     """
 
     if not avail_vers:
-        _log.error("Empty list of available versions passed.")
+        raise EasyBuildError("Empty list of available versions passed.")
 
     selected_ver = None
     if req_ver:
@@ -334,7 +336,7 @@ def select_or_generate_ec(fp, paths, specs):
 
     # ensure that at least name is specified
     if not specs.get('name'):
-        _log.error("Supplied 'specs' dictionary doesn't even contain a name of a software package?")
+        raise EasyBuildError("Supplied 'specs' dictionary doesn't even contain a name of a software package?")
     name = specs['name']
     handled_params = ['name']
 
@@ -362,7 +364,8 @@ def select_or_generate_ec(fp, paths, specs):
                 _log.debug("No template found at %s." % templ_file)
 
         if len(ec_files) == 0:
-            _log.error("No easyconfig files found for software %s, and no templates available. I'm all out of ideas." % name)
+            raise EasyBuildError("No easyconfig files found for software %s, and no templates available. "
+                                 "I'm all out of ideas.", name)
 
     ecs_and_files = [(EasyConfig(f, validate=False), f) for f in ec_files]
 
@@ -390,7 +393,7 @@ def unique(l):
         if EASYCONFIG_TEMPLATE in tcnames:
             _log.info("No easyconfig file for specified toolchain, but template is available.")
         else:
-            _log.error("No easyconfig file for %s with toolchain %s, " \
+            raise EasyBuildError("No easyconfig file for %s with toolchain %s, " \
                       "and no template available." % (name, specs['toolchain_name']))
 
     tcname = specs.pop('toolchain_name', None)
@@ -414,7 +417,7 @@ def unique(l):
             else:
                 # if multiple toolchains are available, and none is specified, we quit
                 # we can't just pick one, how would we prefer one over the other?
-                _log.error("No toolchain name specified, and more than one available: %s." % tcnames)
+                raise EasyBuildError("No toolchain name specified, and more than one available: %s.", tcnames)
 
     _log.debug("Filtering easyconfigs based on toolchain name '%s'..." % selected_tcname)
     ecs_and_files = [x for x in ecs_and_files if x[0]['toolchain']['name'] == selected_tcname]
@@ -497,7 +500,7 @@ def unique(l):
             filter_ecs = True
         else:
             # otherwise, we fail, because we don't know how to pick between different fixes
-            _log.error("No %s specified, and can't pick from available %ses %s" % (param,
+            raise EasyBuildError("No %s specified, and can't pick from available %ses %s" % (param,
                                                                                   param,
                                                                                   vals))
 
@@ -515,7 +518,7 @@ def unique(l):
     cnt = len(ecs_and_files)
     if not cnt == 1:
         fs = [x[1] for x in ecs_and_files]
-        _log.error("Failed to select a single easyconfig from available ones, %s left: %s" % (cnt, fs))
+        raise EasyBuildError("Failed to select a single easyconfig from available ones, %s left: %s", cnt, fs)
     else:
         (selected_ec, selected_ec_file) = ecs_and_files[0]
 
@@ -570,11 +573,11 @@ def obtain_ec_for(specs, paths, fp=None):
 
     # ensure that at least name is specified
     if not specs.get('name'):
-        _log.error("Supplied 'specs' dictionary doesn't even contain a name of a software package?")
+        raise EasyBuildError("Supplied 'specs' dictionary doesn't even contain a name of a software package?")
 
     # collect paths to search in
     if not paths:
-        _log.error("No paths to look for easyconfig files, specify a path with --robot.")
+        raise EasyBuildError("No paths to look for easyconfig files, specify a path with --robot.")
 
     # select best easyconfig, or try to generate one that fits the requirements
     res = select_or_generate_ec(fp, paths, specs)
@@ -582,4 +585,4 @@ def obtain_ec_for(specs, paths, fp=None):
     if res:
         return res
     else:
-        _log.error("No easyconfig found for requested software, and also failed to generate one.")
+        raise EasyBuildError("No easyconfig found for requested software, and also failed to generate one.")
diff --git a/easybuild/framework/extension.py b/easybuild/framework/extension.py
index ee240db57c..d8c6f371de 100644
--- a/easybuild/framework/extension.py
+++ b/easybuild/framework/extension.py
@@ -36,6 +36,7 @@
 import copy
 import os
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_path
 from easybuild.tools.run import run_cmd
 
@@ -54,7 +55,7 @@ def __init__(self, mself, ext):
         self.ext = copy.deepcopy(ext)
 
         if not 'name' in self.ext:
-            self.log.error("'name' is missing in supplied class instance 'ext'.")
+            raise EasyBuildError("'name' is missing in supplied class instance 'ext'.")
 
         self.src = self.ext.get('src', None)
         self.patches = self.ext.get('patches', None)
@@ -111,7 +112,7 @@ def sanity_check_step(self):
         try:
             os.chdir(build_path())
         except OSError, err:
-            self.log.error("Failed to change directory: %s" % err)
+            raise EasyBuildError("Failed to change directory: %s", err)
 
         # disabling templating is required here to support legacy string templates like name/version
         self.cfg.enable_templating = False
diff --git a/easybuild/framework/extensioneasyblock.py b/easybuild/framework/extensioneasyblock.py
index 691b283d70..7f9523f3f0 100644
--- a/easybuild/framework/extensioneasyblock.py
+++ b/easybuild/framework/extensioneasyblock.py
@@ -31,6 +31,7 @@
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.framework.extension import Extension
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import apply_patch, extract_file
 from easybuild.tools.utilities import remove_unwanted_chars
 
@@ -97,7 +98,7 @@ def run(self, unpack_src=False):
         if self.patches:
             for patchfile in self.patches:
                 if not apply_patch(patchfile, self.ext_dir):
-                    self.log.error("Applying patch %s failed" % patchfile)
+                    raise EasyBuildError("Applying patch %s failed", patchfile)
 
     def sanity_check_step(self, exts_filter=None, custom_paths=None, custom_commands=None):
         """
@@ -128,7 +129,7 @@ def sanity_check_step(self, exts_filter=None, custom_paths=None, custom_commands
             if self.is_extension:
                 self.log.warning(msg)
             else:
-                self.log.error(msg)
+                raise EasyBuildError(msg)
             return False
         else:
             self.log.info("Sanity check for %s successful!" % self.name)
diff --git a/easybuild/main.py b/easybuild/main.py
index c110727529..0005735c60 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -88,7 +88,7 @@ def find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=
                 _log.warning("Failed to remove generated easyconfig file %s: %s" % (ec_file, err))
 
             # don't use a generated easyconfig unless generation was requested (using a --try-X option)
-            _log.error(("Unable to find an easyconfig for the given specifications: %s; "
+            raise EasyBuildError(("Unable to find an easyconfig for the given specifications: %s; "
                         "to make EasyBuild try to generate a matching easyconfig, "
                         "use the --try-X options ") % build_specs)
 
@@ -132,9 +132,9 @@ def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
 
         if not ec_res['success'] and exit_on_failure:
             if 'traceback' in ec_res:
-                _log.error(ec_res['traceback'])
+                raise EasyBuildError(ec_res['traceback'])
             else:
-                _log.error(test_msg)
+                raise EasyBuildError(test_msg)
 
         res.append((ec, ec_res))
 
@@ -172,7 +172,8 @@ def main(testing_data=(None, None, None)):
 
     # disallow running EasyBuild as root
     if os.getuid() == 0:
-        _log.error("You seem to be running EasyBuild with root privileges which is not wise, so let's end this here.")
+        raise EasyBuildError("You seem to be running EasyBuild with root privileges which is not wise, "
+                             "so let's end this here.")
 
     # log startup info
     eb_cmd_line = eb_go.generate_cmd_line() + eb_go.args
diff --git a/easybuild/scripts/clean_gists.py b/easybuild/scripts/clean_gists.py
index 14e26a6a14..a254d36dff 100755
--- a/easybuild/scripts/clean_gists.py
+++ b/easybuild/scripts/clean_gists.py
@@ -31,6 +31,7 @@
 from vsc.utils import fancylogger
 from vsc.utils.generaloption import simple_option
 from vsc.utils.rest import RestClient
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.github import GITHUB_API_URL, HTTP_STATUS_OK, GITHUB_EASYCONFIGS_REPO
 from easybuild.tools.github import GITHUB_EB_MAIN, fetch_github_token
 from easybuild.tools.options import EasyBuildOptions
@@ -54,7 +55,7 @@ def main():
     log = go.log
 
     if not (go.options.all or go.options.closed_pr or go.options.orphans):
-        log.error("Please tell me what to do?")
+        raise EasyBuildError("Please tell me what to do?")
 
     if go.options.github_user is None:
         eb_go = EasyBuildOptions(envvar_prefix='EASYBUILD', go_args=[])
@@ -64,7 +65,7 @@ def main():
         username = go.options.github_user
 
     if username is None:
-        log.error("Could not find a github username")
+        raise EasyBuildError("Could not find a github username")
     else:
         log.info("Using username = %s", username)
 
@@ -75,7 +76,7 @@ def main():
     status, gists = gh.gists.get(per_page=100)
 
     if status != HTTP_STATUS_OK:
-        log.error("Failed to get a lists of gists for user %s: error code %s, message = %s",
+        raise EasyBuildError("Failed to get a lists of gists for user %s: error code %s, message = %s",
                   username, status, gists)
     else:
         log.info("Found %s gists", len(gists))
@@ -102,7 +103,7 @@ def main():
                 if pr_num not in pr_cache:
                     status, pr = gh.repos[GITHUB_EB_MAIN][GITHUB_EASYCONFIGS_REPO].pulls[pr_num].get()
                     if status != HTTP_STATUS_OK:
-                        log.error("Failed to get pull-request #%s: error code %s, message = %s",
+                        raise EasyBuildError("Failed to get pull-request #%s: error code %s, message = %s",
                                   pr_num, status, pr)
                     pr_cache[pr_num] = pr["state"]
 
@@ -118,7 +119,7 @@ def main():
             status, del_gist = gh.gists[gist["id"]].delete()
 
             if status != HTTP_DELETE_OK:
-                log.error("Unable to remove gist (id=%s): error code %s, message = %s",
+                raise EasyBuildError("Unable to remove gist (id=%s): error code %s, message = %s",
                           gist["id"], status, del_gist)
             else:
                 log.info("Delete gist with id=%s", gist["id"])
diff --git a/easybuild/scripts/fix_broken_easyconfigs.py b/easybuild/scripts/fix_broken_easyconfigs.py
index 0547411188..e8f60cee62 100755
--- a/easybuild/scripts/fix_broken_easyconfigs.py
+++ b/easybuild/scripts/fix_broken_easyconfigs.py
@@ -98,7 +98,7 @@ def process_easyconfig_file(ec_file):
                 os.rename(ec_file, backup_ec_file)
                 log.info("Backed up %s to %s" % (ec_file, backup_ec_file))
             except OSError, err:
-                log.error("Failed to backup %s before rewriting it: %s" % (ec_file, err))
+                raise EasyBuildError("Failed to backup %s before rewriting it: %s", ec_file, err)
 
         write_file(ec_file, fixed_ectxt)
         log.debug("Contents of fixed easyconfig file: %s" % fixed_ectxt)
@@ -124,15 +124,15 @@ def process_easyconfig_file(ec_file):
     try:
         import easybuild.easyblocks.generic.configuremake
     except ImportError, err:
-        log.error("easyblocks are not available in Python search path: %s" % err)
+        raise EasyBuildError("easyblocks are not available in Python search path: %s", err)
 
     for path in go.args:
         if not os.path.exists(path):
-            log.error("Non-existing path %s specified" % path)
+            raise EasyBuildError("Non-existing path %s specified", path)
 
     ec_files = [ec for p in go.args for ec in find_easyconfigs(p)]
     if not ec_files:
-        log.error("No easyconfig files specified")
+        raise EasyBuildError("No easyconfig files specified")
 
     log.info("Processing %d easyconfigs" % len(ec_files))
     for ec_file in ec_files:
diff --git a/easybuild/scripts/generate_software_list.py b/easybuild/scripts/generate_software_list.py
index f7957e2334..d4995d87c6 100644
--- a/easybuild/scripts/generate_software_list.py
+++ b/easybuild/scripts/generate_software_list.py
@@ -33,10 +33,10 @@
 from datetime import date
 from optparse import OptionParser
 
-import easybuild.tools.build_log  # ensure use of EasyBuildLog
 import easybuild.tools.config as config
 import easybuild.tools.options as eboptions
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, get_easyblock_class
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.github import Githubfs
 from vsc.utils import fancylogger
 
@@ -136,7 +136,7 @@
                 configs.append(ec)
                 names.append(ec.name)
         except Exception, err:
-            log.error("faulty easyconfig %s: %s" % (ec_file, err))
+            raise EasyBuildError("faulty easyconfig %s: %s", ec_file, err)
 
 log.info("Found easyconfigs: %s" % [x.name for x in configs])
 # sort by name
diff --git a/easybuild/toolchains/compiler/clang.py b/easybuild/toolchains/compiler/clang.py
index bd5590e463..4192561fff 100644
--- a/easybuild/toolchains/compiler/clang.py
+++ b/easybuild/toolchains/compiler/clang.py
@@ -32,6 +32,7 @@
 """
 
 import easybuild.tools.systemtools as systemtools
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.compiler import Compiler
 
 
@@ -98,6 +99,5 @@ def _set_compiler_vars(self):
         super(Clang, self)._set_compiler_vars()
 
         if self.options.get('32bit', None):
-            self.log.raiseException("_set_compiler_vars: 32bit set, but no support yet for " \
-                                    "32bit Clang in EasyBuild")
+            raise EasyBuildError("_set_compiler_vars: 32bit set, but no support yet for 32bit Clang in EasyBuild")
 
diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py
index 9146f8c773..bdd4fb7001 100644
--- a/easybuild/toolchains/compiler/gcc.py
+++ b/easybuild/toolchains/compiler/gcc.py
@@ -30,6 +30,7 @@
 """
 
 import easybuild.tools.systemtools as systemtools
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.compiler import Compiler
 
 
@@ -83,8 +84,7 @@ def _set_compiler_vars(self):
         super(Gcc, self)._set_compiler_vars()
 
         if self.options.get('32bit', None):
-            self.log.raiseException("_set_compiler_vars: 32bit set, but no support yet for " \
-                                    "32bit GCC in EasyBuild")
+            raise EasyBuildError("_set_compiler_vars: 32bit set, but no support yet for 32bit GCC in EasyBuild")
 
         # to get rid of lots of problems with libgfortranbegin
         # or remove the system gcc-gfortran
diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index 8aa6fd89c5..2e071033a2 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -32,6 +32,7 @@
 from distutils.version import LooseVersion
 
 import easybuild.tools.systemtools as systemtools
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.compiler import Compiler
 
 
@@ -93,14 +94,15 @@ def _set_compiler_vars(self):
         super(IntelIccIfort, self)._set_compiler_vars()
 
         if not ('icc' in self.COMPILER_MODULE_NAME and 'ifort' in self.COMPILER_MODULE_NAME):
-            self.log.raiseException("_set_compiler_vars: missing icc and/or ifort from COMPILER_MODULE_NAME %s" % self.COMPILER_MODULE_NAME)
+            raise EasyBuildError("_set_compiler_vars: missing icc and/or ifort from COMPILER_MODULE_NAME %s",
+                                 self.COMPILER_MODULE_NAME)
 
         icc_root, _ = self.get_software_root(self.COMPILER_MODULE_NAME)
         icc_version, ifort_version = self.get_software_version(self.COMPILER_MODULE_NAME)
 
         if not ifort_version == icc_version:
-            msg = "_set_compiler_vars: mismatch between icc version %s and ifort version %s"
-            self.log.raiseException(msg % (icc_version, ifort_version))
+            raise EasyBuildError("_set_compiler_vars: mismatch between icc version %s and ifort version %s",
+                                 icc_version, ifort_version)
 
         if LooseVersion(icc_version) < LooseVersion('2011'):
             self.LIB_MULTITHREAD.insert(1, "guide")
diff --git a/easybuild/toolchains/fft/fftw.py b/easybuild/toolchains/fft/fftw.py
index 9b901e7e16..1e9a9c3825 100644
--- a/easybuild/toolchains/fft/fftw.py
+++ b/easybuild/toolchains/fft/fftw.py
@@ -31,6 +31,7 @@
 
 from distutils.version import LooseVersion
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.fft import Fft
 
 
@@ -44,7 +45,7 @@ def _set_fftw_variables(self):
         suffix = ''
         version = self.get_software_version(self.FFT_MODULE_NAME)[0]
         if LooseVersion(version) < LooseVersion('2') or LooseVersion(version) >= LooseVersion('4'):
-            self.log.raiseException("_set_fft_variables: FFTW unsupported version %s (major should be 2 or 3)" % version)
+            raise EasyBuildError("_set_fft_variables: FFTW unsupported version %s (major should be 2 or 3)", version)
         elif LooseVersion(version) > LooseVersion('2'):
             suffix = '3'
 
diff --git a/easybuild/toolchains/fft/intelfftw.py b/easybuild/toolchains/fft/intelfftw.py
index ee56497367..94b53c7372 100644
--- a/easybuild/toolchains/fft/intelfftw.py
+++ b/easybuild/toolchains/fft/intelfftw.py
@@ -31,6 +31,7 @@
 import os
 from distutils.version import LooseVersion
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.toolchains.fft.fftw import Fftw
 from easybuild.tools.modules import get_software_root, get_software_version
 
@@ -45,7 +46,7 @@ class IntelFFTW(Fftw):
 
     def _set_fftw_variables(self):
         if not hasattr(self, 'BLAS_LIB_DIR'):
-            self.log.raiseException("_set_fftw_variables: IntelFFT based on IntelMKL (no BLAS_LIB_DIR found)")
+            raise EasyBuildError("_set_fftw_variables: IntelFFT based on IntelMKL (no BLAS_LIB_DIR found)")
 
         imklver = get_software_version(self.FFT_MODULE_NAME[0])
 
@@ -60,7 +61,7 @@ def _set_fftw_variables(self):
             if get_software_root('GCC'):
                 compsuff = '_gnu'
             else:
-                self.log.error("Not using Intel compilers or GCC, don't know compiler suffix for FFTW libraries.")
+                raise EasyBuildError("Not using Intel compilers or GCC, don't know compiler suffix for FFTW libraries.")
 
         fftw_libs = ["fftw3xc%s%s" % (compsuff, picsuff)]
         if self.options['usempi']:
@@ -89,6 +90,5 @@ def _set_fftw_variables(self):
         if all([fftw_lib_exists(lib) for lib in check_fftw_libs]):
             self.FFT_LIB = fftw_libs
         else:
-            tup = (check_fftw_libs, fft_lib_dirs)
-            msg = "Not all FFTW interface libraries %s are found in %s, can't set FFT_LIB." % tup
-            self.log.error(msg)
+            raise EasyBuildError("Not all FFTW interface libraries %s are found in %s, can't set FFT_LIB.",
+                                 check_fftw_libs, fft_lib_dirs)
diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index eb32da15f7..d561bc826f 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -34,6 +34,7 @@
 
 from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP
 from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.linalg import LinAlg
 
 
@@ -60,7 +61,7 @@ class Acml(LinAlg):
     def _set_blas_variables(self):
         """Fix the map a bit"""
         if self.options.get('32bit', None):
-            self.log.raiseException("_set_blas_variables: 32bit ACML not (yet) supported")
+            raise EasyBuildError("_set_blas_variables: 32bit ACML not (yet) supported")
         try:
             for root in self.get_software_root(self.BLAS_MODULE_NAME):
                 subdirs = self.ACML_SUBDIRS_MAP[self.COMPILER_FAMILY]
@@ -69,8 +70,8 @@ def _set_blas_variables(self):
                 incdirs = [os.path.join(x, 'include') for x in subdirs]
                 self.variables.append_exists('CPPFLAGS', root, incdirs, append_all=True)
         except:
-            self.log.raiseException(("_set_blas_variables: ACML set LDFLAGS/CPPFLAGS unknown entry in ACML_SUBDIRS_MAP"
-                                     " with compiler family %s") % self.COMPILER_FAMILY)
+            raise EasyBuildError("_set_blas_variables: ACML set LDFLAGS/CPPFLAGS unknown entry in ACML_SUBDIRS_MAP "
+                                 " with compiler family %s", self.COMPILER_FAMILY)
 
         # version before 5.x still featured the acml_mv library
         ver = self.get_software_version(self.BLAS_MODULE_NAME)[0]
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index 00aa18f44b..6d1886212a 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -38,6 +38,7 @@
 from easybuild.toolchains.mpi.mpich2 import TC_CONSTANT_MPICH2
 from easybuild.toolchains.mpi.mvapich2 import TC_CONSTANT_MVAPICH2
 from easybuild.toolchains.mpi.openmpi import TC_CONSTANT_OPENMPI
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.linalg import LinAlg
 
 
@@ -84,8 +85,8 @@ def _set_blas_variables(self):
                 "interface": interfacemap[self.COMPILER_FAMILY],
             })
         except:
-            self.log.raiseException(("_set_blas_variables: interface unsupported combination"
-                                     " with MPI family %s") % self.COMPILER_FAMILY)
+            raise EasyBuildError("_set_blas_variables: interface unsupported combination with MPI family %s",
+                                 self.COMPILER_FAMILY)
 
         interfacemap_mt = {
             TC_CONSTANT_INTELCOMP: 'intel',
@@ -94,8 +95,8 @@ def _set_blas_variables(self):
         try:
             self.BLAS_LIB_MAP.update({"interface_mt":interfacemap_mt[self.COMPILER_FAMILY]})
         except:
-            self.log.raiseException(("_set_blas_variables: interface_mt unsupported combination "
-                                     "with compiler family %s") % self.COMPILER_FAMILY)
+            raise EasyBuildError("_set_blas_variables: interface_mt unsupported combination with compiler family %s",
+                                 self.COMPILER_FAMILY)
 
 
         if self.options.get('32bit', None):
@@ -117,8 +118,8 @@ def _set_blas_variables(self):
             self.BLAS_INCLUDE_DIR = ['include']
         else:
             if self.options.get('32bit', None):
-                self.log.raiseException(("_set_blas_variables: 32-bit libraries not supported yet "
-                                        "for IMKL v%s (> v10.3)") % found_version)
+                raise EasyBuildError("_set_blas_variables: 32-bit libraries not supported yet for IMKL v%s (> v10.3)",
+                                     found_version)
             else:
                 self.BLAS_LIB_DIR = ['mkl/lib/intel64', 'compiler/lib/intel64' ]
 
@@ -140,8 +141,8 @@ def _set_blacs_variables(self):
         try:
             self.BLACS_LIB_MAP.update({'mpi': mpimap[self.MPI_FAMILY]})
         except:
-            self.log.raiseException(("_set_blacs_variables: mpi unsupported combination with"
-                                     " MPI family %s") % self.MPI_FAMILY)
+            raise EasyBuildError("_set_blacs_variables: mpi unsupported combination with MPI family %s",
+                                 self.MPI_FAMILY)
 
         self.BLACS_LIB_DIR = self.BLAS_LIB_DIR
         self.BLACS_INCLUDE_DIR = self.BLAS_INCLUDE_DIR
@@ -166,4 +167,3 @@ def _set_scalapack_variables(self):
         self.SCALAPACK_INCLUDE_DIR = self.BLAS_INCLUDE_DIR
 
         super(IntelMKL, self)._set_scalapack_variables()
-
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 054b109d26..212adaa44a 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -43,8 +43,8 @@
 from vsc.utils.missing import nub, FrozenDictKnownKeys
 from vsc.utils.patterns import Singleton
 
-import easybuild.tools.build_log  # this import is required to obtain a correct (EasyBuild) logger!
 import easybuild.tools.environment as env
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.environment import read_environment as _read_environment
 from easybuild.tools.run import run_cmd
 
@@ -201,8 +201,7 @@ def get_items_check_required(self):
         """
         missing = [x for x in self.KNOWN_KEYS if not x in self]
         if len(missing) > 0:
-            msg = 'Cannot determine value for configuration variables %s. Please specify it.' % missing
-            self.log.error(msg)
+            raise EasyBuildError("Cannot determine value for configuration variables %s. Please specify it.", missing)
 
         return self.items()
 
@@ -234,7 +233,7 @@ def init(options, config_options_dict):
         tmpdict['sourcepath'] = sourcepath.split(':')
         _log.debug("Converted source path ('%s') to a list of paths: %s" % (sourcepath, tmpdict['sourcepath']))
     elif not isinstance(sourcepath, (tuple, list)):
-        _log.error("Value for sourcepath has invalid type (%s): %s" % (type(sourcepath), sourcepath))
+        raise EasyBuildError("Value for sourcepath has invalid type (%s): %s", type(sourcepath), sourcepath)
 
     # initialize configuration variables (any future calls to ConfigurationVariables() will yield the same instance
     variables = ConfigurationVariables(tmpdict, ignore_unknown_keys=True)
@@ -451,7 +450,7 @@ def set_tmpdir(tmpdir=None, raise_error=False):
             # use tempfile default parent dir
             current_tmpdir = tempfile.mkdtemp(prefix='eb-')
     except OSError, err:
-        _log.error("Failed to create temporary directory (tmpdir: %s): %s" % (tmpdir, err))
+        raise EasyBuildError("Failed to create temporary directory (tmpdir: %s): %s", tmpdir, err)
 
     _log.info("Temporary directory used in this EasyBuild run: %s" % current_tmpdir)
 
@@ -470,7 +469,7 @@ def set_tmpdir(tmpdir=None, raise_error=False):
             msg = "The temporary directory (%s) does not allow to execute files. " % tempfile.gettempdir()
             msg += "This can cause problems in the build process, consider using --tmpdir."
             if raise_error:
-                _log.error(msg)
+                raise EasyBuildError(msg)
             else:
                 _log.warning(msg)
         else:
@@ -478,6 +477,6 @@ def set_tmpdir(tmpdir=None, raise_error=False):
         os.remove(tmptest_file)
 
     except OSError, err:
-        _log.error("Failed to test whether temporary directory allows to execute files: %s" % err)
+        raise EasyBuildError("Failed to test whether temporary directory allows to execute files: %s", err)
 
     return current_tmpdir
diff --git a/easybuild/tools/convert.py b/easybuild/tools/convert.py
index 16a3189417..037595ff29 100644
--- a/easybuild/tools/convert.py
+++ b/easybuild/tools/convert.py
@@ -34,6 +34,9 @@
 from vsc.utils.missing import get_subclasses, nub
 from vsc.utils.wrapper import Wrapper
 
+from easybuild.tools.build_log import EasyBuildError
+
+
 _log = fancylogger.getLogger('tools.convert', fname=False)
 
 
@@ -56,7 +59,7 @@ def __init__(self, obj):
         if isinstance(obj, basestring):
             self.data = self._from_string(obj)
         else:
-            self.log.error('unsupported type %s for %s: %s' % (type(obj), self.__class__.__name__, obj))
+            raise EasyBuildError('unsupported type %s for %s: %s', type(obj), self.__class__.__name__, obj)
         super(Convert, self).__init__(self.data)
 
     def _split_string(self, txt, sep=None, max=0):
@@ -66,7 +69,7 @@ def _split_string(self, txt, sep=None, max=0):
         """
         if sep is None:
             if self.SEPARATOR is None:
-                self.log.error('No SEPARATOR set, also no separator passed')
+                raise EasyBuildError('No SEPARATOR set, also no separator passed')
             else:
                 sep = self.SEPARATOR
         return [x.strip() for x in re.split(r'' + sep, txt, maxsplit=max)]
@@ -221,4 +224,4 @@ def get_convert_class(class_name):
     if len(res) == 1:
         return res[0]
     else:
-        _log.error('More then one Convert subclass found for name %s: %s' % (class_name, res))
+        raise EasyBuildError('More then one Convert subclass found for name %s: %s', class_name, res)
diff --git a/easybuild/tools/environment.py b/easybuild/tools/environment.py
index 45b5b2bc44..c268699083 100644
--- a/easybuild/tools/environment.py
+++ b/easybuild/tools/environment.py
@@ -32,6 +32,8 @@
 from vsc.utils import fancylogger
 from vsc.utils.missing import shell_quote
 
+from easybuild.tools.build_log import EasyBuildError
+
 
 _log = fancylogger.getLogger('environment', fname=False)
 
@@ -53,7 +55,7 @@ def write_changes(filename):
     except IOError, err:
         if script is not None:
             script.close()
-        _log.error("Failed to write to %s: %s" % (filename, err))
+        raise EasyBuildError("Failed to write to %s: %s", filename, err)
     reset_changes()
 
 
@@ -120,7 +122,7 @@ def read_environment(env_vars, strict=False):
         missing = ','.join(["%s / %s" % (k, v) for k, v in env_vars.items() if not k in result])
         msg = 'Following name/variable not found in environment: %s' % missing
         if strict:
-            _log.error(msg)
+            raise EasyBuildError(msg)
         else:
             _log.debug(msg)
 
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 49b05f1191..25754949bb 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -44,7 +44,7 @@
 from vsc.utils import fancylogger
 
 import easybuild.tools.environment as env
-from easybuild.tools.build_log import print_msg  # import build_log must stay, to activate use of EasyBuildLog
+from easybuild.tools.build_log import EasyBuildError, print_msg  # import build_log must stay, to activate use of EasyBuildLog
 from easybuild.tools.config import build_option
 from easybuild.tools import run
 
@@ -147,7 +147,7 @@ def read_file(path, log_error=True):
         if f is not None:
             f.close()
         if log_error:
-            _log.error("Failed to read %s: %s" % (path, err))
+            raise EasyBuildError("Failed to read %s: %s", path, err)
         else:
             return None
 
@@ -168,7 +168,7 @@ def write_file(path, txt, append=False):
         # make sure file handle is always closed
         if f is not None:
             f.close()
-        _log.error("Failed to write to %s: %s" % (path, err))
+        raise EasyBuildError("Failed to write to %s: %s", path, err)
 
 
 def remove_file(path):
@@ -177,7 +177,7 @@ def remove_file(path):
         if os.path.exists(path):
             os.remove(path)
     except OSError, err:
-          _log.error("Failed to remove %s: %s", path, err)
+          raise EasyBuildError("Failed to remove %s: %s", path, err)
 
 
 def extract_file(fn, dest, cmd=None, extra_options=None, overwrite=False):
@@ -186,7 +186,7 @@ def extract_file(fn, dest, cmd=None, extra_options=None, overwrite=False):
     - returns the directory name in case of success
     """
     if not os.path.isfile(fn):
-        _log.error("Can't extract file %s: no such file" % fn)
+        raise EasyBuildError("Can't extract file %s: no such file", fn)
 
     mkdir(dest, parents=True)
 
@@ -198,7 +198,7 @@ def extract_file(fn, dest, cmd=None, extra_options=None, overwrite=False):
         _log.debug("Unpacking %s in directory %s." % (fn, absDest))
         os.chdir(absDest)
     except OSError, err:
-        _log.error("Can't change to directory %s: %s" % (absDest, err))
+        raise EasyBuildError("Can't change to directory %s: %s", absDest, err)
 
     if not cmd:
         cmd = extract_cmd(fn, overwrite=overwrite)
@@ -206,7 +206,7 @@ def extract_file(fn, dest, cmd=None, extra_options=None, overwrite=False):
         # complete command template with filename
         cmd = cmd % fn
     if not cmd:
-        _log.error("Can't extract file %s with unknown filetype" % fn)
+        raise EasyBuildError("Can't extract file %s with unknown filetype", fn)
 
     if extra_options:
         cmd = "%s %s" % (cmd, extra_options)
@@ -232,7 +232,7 @@ def which(cmd):
 def det_common_path_prefix(paths):
     """Determine common path prefix for a given list of paths."""
     if not isinstance(paths, list):
-        _log.error("det_common_path_prefix: argument must be of type list (got %s: %s)" % (type(paths), paths))
+        raise EasyBuildError("det_common_path_prefix: argument must be of type list (got %s: %s)", type(paths), paths)
     elif not paths:
         return None
 
@@ -290,7 +290,7 @@ def download_file(filename, url, path):
             _log.warning("IOError occurred while trying to download %s to %s: %s" % (url, path, err))
             attempt_cnt += 1
         except Exception, err:
-            _log.error("Unexpected error occurred when trying to download %s to %s: %s" % (url, path, err))
+            raise EasyBuildError("Unexpected error occurred when trying to download %s to %s: %s", url, path, err)
 
         if not downloaded and attempt_cnt < max_attempts:
             _log.info("Attempt %d of downloading %s to %s failed, trying again..." % (attempt_cnt, url, path))
@@ -338,7 +338,8 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
     if ignore_dirs is None:
         ignore_dirs = ['.git', '.svn']
     if not isinstance(ignore_dirs, list):
-        _log.error("search_file: ignore_dirs (%s) should be of type list, not %s" % (ignore_dirs, type(ignore_dirs)))
+        raise EasyBuildError("search_file: ignore_dirs (%s) should be of type list, not %s",
+                             ignore_dirs, type(ignore_dirs))
 
     var_lines = []
     hit_lines = []
@@ -386,12 +387,13 @@ def compute_checksum(path, checksum_type=DEFAULT_CHECKSUM):
     @param checksum_type: Type of checksum ('adler32', 'crc32', 'md5' (default), 'sha1', 'size')
     """
     if not checksum_type in CHECKSUM_FUNCTIONS:
-        _log.error("Unknown checksum type (%s), supported types are: %s" % (checksum_type, CHECKSUM_FUNCTIONS.keys()))
+        raise EasyBuildError("Unknown checksum type (%s), supported types are: %s",
+                             checksum_type, CHECKSUM_FUNCTIONS.keys())
 
     try:
         checksum = CHECKSUM_FUNCTIONS[checksum_type](path)
     except IOError, err:
-        _log.error("Failed to read %s: %s" % (path, err))
+        raise EasyBuildError("Failed to read %s: %s", path, err)
     except MemoryError, err:
         _log.warning("A memory error occured when computing the checksum for %s: %s" % (path, err))
         checksum = 'dummy_checksum_due_to_memory_error'
@@ -416,7 +418,7 @@ def calc_block_checksum(path, algorithm):
             algorithm.update(block)
         f.close()
     except IOError, err:
-        _log.error("Failed to read %s: %s" % (path, err))
+        raise EasyBuildError("Failed to read %s: %s", path, err)
 
     return algorithm.hexdigest()
 
@@ -443,7 +445,8 @@ def verify_checksum(path, checksums):
         elif isinstance(checksum, tuple) and len(checksum) == 2:
             typ, checksum = checksum
         else:
-            _log.error("Invalid checksum spec '%s', should be a string (MD5) or 2-tuple (type, value)." % checksum)
+            raise EasyBuildError("Invalid checksum spec '%s', should be a string (MD5) or 2-tuple (type, value).",
+                                 checksum)
 
         actual_checksum = compute_checksum(path, typ)
         _log.debug("Computed %s checksum for %s: %s (correct checksum: %s)" % (typ, path, actual_checksum, checksum))
@@ -482,7 +485,7 @@ def get_local_dirs_purged():
         try:
             os.chdir(new_dir)
         except OSError, err:
-            _log.exception("Changing to dir %s from current dir %s failed: %s" % (new_dir, os.getcwd(), err))
+            raise EasyBuildError("Changing to dir %s from current dir %s failed: %s", new_dir, os.getcwd(), err)
         lst = get_local_dirs_purged()
 
     # make sure it's a directory, and not a (single) file that was in a tarball for example
@@ -548,7 +551,7 @@ def extract_cmd(filepath, overwrite=False):
             cmd_tmpl = "unzip -qq %(filepath)s"
 
     if cmd_tmpl is None:
-        _log.error('Unknown file type for file %s (%s)' % (filepath, exts))
+        raise EasyBuildError('Unknown file type for file %s (%s)', filepath, exts)
 
     return cmd_tmpl % {'filepath': filepath, 'target': target}
 
@@ -564,9 +567,9 @@ def det_patched_files(path=None, txt=None, omit_ab_prefix=False):
             txt = f.read()
             f.close()
         except IOError, err:
-            _log.error("Failed to read patch %s: %s" % (path, err))
+            raise EasyBuildError("Failed to read patch %s: %s", path, err)
     elif txt is None:
-        _log.error("Either a file path or a string representing a patch should be supplied to det_patched_files")
+        raise EasyBuildError("Either a file path or a string representing a patch should be supplied")
 
     patched_files = []
     for match in patched_regex.finditer(txt):
@@ -611,15 +614,15 @@ def apply_patch(patch_file, dest, fn=None, copy=False, level=None):
     """
 
     if not os.path.isfile(patch_file):
-        _log.error("Can't find patch %s: no such file" % patch_file)
+        raise EasyBuildError("Can't find patch %s: no such file", patch_file)
         return
 
     if fn and not os.path.isfile(fn):
-        _log.error("Can't patch file %s: no such file" % fn)
+        raise EasyBuildError("Can't patch file %s: no such file", fn)
         return
 
     if not os.path.isdir(dest):
-        _log.error("Can't patch directory %s: no such directory" % dest)
+        raise EasyBuildError("Can't patch directory %s: no such directory", dest)
         return
 
     # copy missing files
@@ -629,7 +632,7 @@ def apply_patch(patch_file, dest, fn=None, copy=False, level=None):
             _log.debug("Copied patch %s to dir %s" % (patch_file, dest))
             return 'ok'
         except IOError, err:
-            _log.error("Failed to copy %s to dir %s: %s" % (patch_file, dest, err))
+            raise EasyBuildError("Failed to copy %s to dir %s: %s", patch_file, dest, err)
             return
 
     # use absolute paths
@@ -644,14 +647,14 @@ def apply_patch(patch_file, dest, fn=None, copy=False, level=None):
         patched_files = det_patched_files(path=apatch)
 
         if not patched_files:
-            _log.error("Can't guess patchlevel from patch %s: no testfile line found in patch" % apatch)
+            raise EasyBuildError("Can't guess patchlevel from patch %s: no testfile line found in patch", apatch)
             return
 
         patch_level = guess_patch_level(patched_files, adest)
 
         if patch_level is None:  # patch_level can also be 0 (zero), so don't use "not patch_level"
             # no match
-            _log.error("Can't determine patch level for patch %s from directory %s" % (patch_file, adest))
+            raise EasyBuildError("Can't determine patch level for patch %s from directory %s", patch_file, adest)
         else:
             _log.debug("Guessed patch level %d for patch %s" % (patch_level, patch_file))
 
@@ -663,13 +666,13 @@ def apply_patch(patch_file, dest, fn=None, copy=False, level=None):
         os.chdir(adest)
         _log.debug("Changing to directory %s" % adest)
     except OSError, err:
-        _log.error("Can't change to directory %s: %s" % (adest, err))
+        raise EasyBuildError("Can't change to directory %s: %s", adest, err)
         return
 
     patch_cmd = "patch -b -p%d -i %s" % (patch_level, apatch)
     result = run.run_cmd(patch_cmd, simple=True)
     if not result:
-        _log.error("Patching with patch %s failed" % patch_file)
+        raise EasyBuildError("Patching with patch %s failed", patch_file)
         return
 
     return result
@@ -761,14 +764,14 @@ def adjust_permissions(name, permissionBits, add=True, onlyfiles=False, onlydirs
                 failed_paths.append(path)
 
     if failed_paths:
-        _log.error("Failed to chmod/chown several paths: %s (last error: %s)" % (failed_paths, err))
+        raise EasyBuildError("Failed to chmod/chown several paths: %s (last error: %s)", failed_paths, err)
 
     # we ignore some errors, but if there are to many, something is definitely wrong
     fail_ratio = fail_cnt / float(len(allpaths))
     max_fail_ratio = 0.5
     if fail_ratio > max_fail_ratio:
-        _log.error("%.2f%% of permissions/owner operations failed (more than %.2f%%), something must be wrong..." %
-                  (100 * fail_ratio, 100 * max_fail_ratio))
+        raise EasyBuildError("%.2f%% of permissions/owner operations failed (more than %.2f%%), "
+                             "something must be wrong...", 100 * fail_ratio, 100 * max_fail_ratio)
     elif fail_cnt > 0:
         _log.debug("%.2f%% of permissions/owner operations failed, ignoring that..." % (100 * fail_ratio))
 
@@ -813,8 +816,7 @@ def mkdir(path, parents=False, set_gid=None, sticky=None):
 
     # exit early if path already exists
     if not os.path.exists(path):
-        tup = (path, parents, set_gid, sticky)
-        _log.info("Creating directory %s (parents: %s, set_gid: %s, sticky: %s)" % tup)
+        _log.info("Creating directory %s (parents: %s, set_gid: %s, sticky: %s)", path, parents, set_gid, sticky)
         # set_gid and sticky bits are only set on new directories, so we need to determine the existing parent path
         existing_parent_path = os.path.dirname(path)
         try:
@@ -826,7 +828,7 @@ def mkdir(path, parents=False, set_gid=None, sticky=None):
             else:
                 os.mkdir(path)
         except OSError, err:
-            _log.error("Failed to create directory %s: %s" % (path, err))
+            raise EasyBuildError("Failed to create directory %s: %s", path, err)
 
         # set group ID and sticky bits, if desired
         bits = 0
@@ -840,7 +842,7 @@ def mkdir(path, parents=False, set_gid=None, sticky=None):
                 new_path = os.path.join(existing_parent_path, new_subdir.split(os.path.sep)[0])
                 adjust_permissions(new_path, bits, add=True, relative=True, recursive=True, onlydirs=True)
             except OSError, err:
-                _log.error("Failed to set groud ID/sticky bit: %s" % err)
+                raise EasyBuildError("Failed to set groud ID/sticky bit: %s", err)
     else:
         _log.debug("Not creating existing path %s" % path)
 
@@ -868,7 +870,7 @@ def rmtree2(path, n=3):
             _log.debug("Failed to remove path %s with shutil.rmtree at attempt %d: %s" % (path, n, err))
             time.sleep(2)
     if not ok:
-        _log.error("Failed to remove path %s with shutil.rmtree, even after %d attempts." % (path, n))
+        raise EasyBuildError("Failed to remove path %s with shutil.rmtree, even after %d attempts.", path, n)
     else:
         _log.info("Path %s successfully removed." % path)
 
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index c87ee21aa1..cad7be7a8d 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -37,6 +37,8 @@
 from vsc.utils import fancylogger
 from vsc.utils.patterns import Singleton
 
+from easybuild.tools.build_log import EasyBuildError
+
 
 _log = fancylogger.getLogger('github', fname=False)
 
@@ -140,7 +142,7 @@ def listdir(self, path):
             return listing[1]
         else:
             self.log.warning("error: %s" % str(listing))
-            self.log.exception("Invalid response from github (I/O error)")
+            raise EasyBuildError("Invalid response from github (I/O error)")
 
     def walk(self, top=None, topdown=True):
         """
@@ -205,15 +207,15 @@ def download(url, path=None):
                 _, httpmsg = urllib.urlretrieve(url, path)
                 _log.debug("Downloaded %s to %s" % (url, path))
             except IOError, err:
-                _log.error("Failed to download %s to %s: %s" % (url, path, err))
+                raise EasyBuildError("Failed to download %s to %s: %s", url, path, err)
 
             if not httpmsg.type == 'text/plain':
-                _log.error("Unexpected file type for %s: %s" % (path, httpmsg.type))
+                raise EasyBuildError("Unexpected file type for %s: %s", path, httpmsg.type)
         else:
             try:
                 return urllib2.urlopen(url).read()
             except urllib2.URLError, err:
-                _log.error("Failed to open %s for reading: %s" % (url, err))
+                raise EasyBuildError("Failed to open %s for reading: %s", url, err)
 
     # a GitHub token is optional here, but can be used if available in order to be less susceptible to rate limiting
     github_token = fetch_github_token(github_user)
@@ -235,14 +237,14 @@ def download(url, path=None):
         status, pr_data = 0, None
     _log.debug("status: %d, data: %s" % (status, pr_data))
     if not status == HTTP_STATUS_OK:
-        tup = (pr, GITHUB_EB_MAIN, GITHUB_EASYCONFIGS_REPO, status, pr_data)
-        _log.error("Failed to get data for PR #%d from %s/%s (status: %d %s)" % tup)
+        raise EasyBuildError("Failed to get data for PR #%d from %s/%s (status: %d %s)",
+                             pr, GITHUB_EB_MAIN, GITHUB_EASYCONFIGS_REPO, status, pr_data)
 
     # 'clean' on successful (or missing) test, 'unstable' on failed tests
     stable = pr_data['mergeable_state'] == GITHUB_MERGEABLE_STATE_CLEAN
     if not stable:
-        tup = (pr, GITHUB_MERGEABLE_STATE_CLEAN, pr_data['mergeable_state'])
-        _log.warning("Mergeable state for PR #%d is not '%s': %s." % tup)
+        _log.warning("Mergeable state for PR #%d is not '%s': %s.",
+                     pr, GITHUB_MERGEABLE_STATE_CLEAN, pr_data['mergeable_state'])
 
     for key, val in sorted(pr_data.items()):
         _log.debug("\n%s:\n\n%s\n" % (key, val))
@@ -256,7 +258,7 @@ def download(url, path=None):
     # obtain last commit
     # get all commits, increase to (max of) 100 per page
     if pr_data['commits'] > GITHUB_MAX_PER_PAGE:
-        _log.error("PR #%s contains more than %s commits, can't obtain last commit" % (pr, GITHUB_MAX_PER_PAGE))
+        raise EasyBuildError("PR #%s contains more than %s commits, can't obtain last commit", pr, GITHUB_MAX_PER_PAGE)
     status, commits_data = pr_url.commits.get(per_page=GITHUB_MAX_PER_PAGE)
     last_commit = commits_data[-1]
     _log.debug("Commits: %s, last commit: %s" % (commits_data, last_commit['sha']))
@@ -272,7 +274,7 @@ def download(url, path=None):
     all_files = [os.path.basename(x) for x in patched_files]
     tmp_files = os.listdir(path)
     if not sorted(tmp_files) == sorted(all_files):
-        _log.error("Not all patched files were downloaded to %s: %s vs %s" % (path, tmp_files, all_files))
+        raise EasyBuildError("Not all patched files were downloaded to %s: %s vs %s", path, tmp_files, all_files)
 
     ec_files = [os.path.join(path, fn) for fn in tmp_files]
 
@@ -298,7 +300,7 @@ def create_gist(txt, fn, descr=None, github_user=None):
     status, data = g.gists.post(body=body)
 
     if not status == HTTP_STATUS_CREATED:
-        _log.error("Failed to create gist; status %s, data: %s" % (status, data))
+        raise EasyBuildError("Failed to create gist; status %s, data: %s", status, data)
 
     return data['html_url']
 
@@ -309,7 +311,7 @@ def post_comment_in_issue(issue, txt, repo=GITHUB_EASYCONFIGS_REPO, github_user=
         try:
             issue = int(issue)
         except ValueError, err:
-            _log.error("Failed to parse specified pull request number '%s' as an int: %s; " % (issue, err))
+            raise EasyBuildError("Failed to parse specified pull request number '%s' as an int: %s; ", issue, err)
     github_token = fetch_github_token(github_user)
 
     g = RestClient(GITHUB_API_URL, username=github_user, token=github_token)
@@ -317,7 +319,7 @@ def post_comment_in_issue(issue, txt, repo=GITHUB_EASYCONFIGS_REPO, github_user=
 
     status, data = pr_url.comments.post(body={'body': txt})
     if not status == HTTP_STATUS_CREATED:
-        _log.error("Failed to create comment in PR %s#%d; status %s, data: %s" % (repo, issue, status, data))
+        raise EasyBuildError("Failed to create comment in PR %s#%d; status %s, data: %s", repo, issue, status, data)
 
 
 class GithubToken(object):
diff --git a/easybuild/tools/jenkins.py b/easybuild/tools/jenkins.py
index fb9ed78fec..0cc0ee4d1a 100644
--- a/easybuild/tools/jenkins.py
+++ b/easybuild/tools/jenkins.py
@@ -34,6 +34,7 @@
 from datetime import datetime
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.version import FRAMEWORK_VERSION, EASYBLOCKS_VERSION
 
 
@@ -108,7 +109,7 @@ def create_success(name, stats):
         root.writexml(output_file)
         output_file.close()
     except IOError, err:
-        _log.error("Failed to write out XML file %s: %s" % (filename, err))
+        raise EasyBuildError("Failed to write out XML file %s: %s", filename, err)
 
 
 def aggregate_xml_in_dirs(base_dir, output_filename):
@@ -149,7 +150,7 @@ def aggregate_xml_in_dirs(base_dir, output_filename):
             try:
                 dom = xml.parse(xml_file)
             except IOError, err:
-                _log.error("Failed to read/parse XML file %s: %s" % (xml_file, err))
+                raise EasyBuildError("Failed to read/parse XML file %s: %s", xml_file, err)
             # only one should be present, we are just discarding the rest
             testcase = dom.getElementsByTagName("testcase")[0]
             root.firstChild.appendChild(testcase)
@@ -165,6 +166,6 @@ def aggregate_xml_in_dirs(base_dir, output_filename):
         root.writexml(output_file, addindent="\t", newl="\n")
         output_file.close()
     except IOError, err:
-        _log.error("Failed to write out XML file %s: %s" % (output_filename, err))
+        raise EasyBuildError("Failed to write out XML file %s: %s", output_filename, err)
 
     print "Aggregate regtest results written to %s" % output_filename
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 5488329789..046fa975d8 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -39,6 +39,7 @@
 
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS
 from easybuild.tools import config
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import mkdir
 from easybuild.tools.module_naming_scheme.utilities import det_hidden_modname
@@ -95,7 +96,8 @@ def create_symlinks(self):
                     os.remove(class_mod_file)
                 os.symlink(self.filename, class_mod_file)
         except OSError, err:
-            _log.error("Failed to create symlinks from %s to %s: %s" % (self.class_mod_files, self.filename, err))
+            raise EasyBuildError("Failed to create symlinks from %s to %s: %s",
+                                 self.class_mod_files, self.filename, err)
 
     def get_description(self, conflict=True):
         """
@@ -186,7 +188,8 @@ def prepend_paths(self, key, paths, allow_abs=False):
         # make sure only relative paths are passed
         for i in xrange(len(paths)):
             if os.path.isabs(paths[i]) and not allow_abs:
-                _log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % paths[i])
+                raise EasyBuildError("Absolute path %s passed to prepend_paths which only expects relative paths.",
+                                     paths[i])
             elif not os.path.isabs(paths[i]):
                 # prepend $root (= installdir) for relative paths
                 paths[i] = "$root/%s" % paths[i]
diff --git a/easybuild/tools/module_naming_scheme/hierarchical_mns.py b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
index c0f303ad4f..7215d1c01b 100644
--- a/easybuild/tools/module_naming_scheme/hierarchical_mns.py
+++ b/easybuild/tools/module_naming_scheme/hierarchical_mns.py
@@ -33,6 +33,7 @@
 import re
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.module_naming_scheme import ModuleNamingScheme
 from easybuild.tools.module_naming_scheme.toolchain import det_toolchain_compilers, det_toolchain_mpi
 
@@ -102,9 +103,10 @@ def det_toolchain_compilers_name_version(self, tc_comps):
                 tc_comp_ver = tc_comp_ver_tmpl % comp_versions
                 # make sure that icc/ifort versions match
                 if tc_comp_name == 'intel' and comp_versions['icc'] != comp_versions['ifort']:
-                    self.log.error("Bumped into different versions for Intel compilers: %s" % comp_versions)
+                    raise EasyBuildError("Bumped into different versions for Intel compilers: %s", comp_versions)
             else:
-                self.log.error("Unknown set of toolchain compilers, module naming scheme needs work: %s" % comp_names)
+                raise EasyBuildError("Unknown set of toolchain compilers, module naming scheme needs work: %s",
+                                     comp_names)
             res = (tc_comp_name, tc_comp_ver)
         return res
 
@@ -180,10 +182,9 @@ def det_modpath_extensions(self, ec):
 
         elif modclass == MODULECLASS_MPI:
             if tc_comp_info is None:
-                tup = (ec['toolchain'], ec['name'], ec['version'])
-                error_msg = ("No compiler available in toolchain %s used to install MPI library %s v%s, "
-                             "which is required by the active module naming scheme.") % tup
-                self.log.error(error_msg)
+                raise EasyBuildError("No compiler available in toolchain %s used to install MPI library %s v%s, "
+                                     "which is required by the active module naming scheme.",
+                                     ec['toolchain'], ec['name'], ec['version'])
             else:
                 tc_comp_name, tc_comp_ver = tc_comp_info
                 fullver = self.det_full_version(ec)
diff --git a/easybuild/tools/module_naming_scheme/mns.py b/easybuild/tools/module_naming_scheme/mns.py
index 99bd1f1222..29fbb1f3ff 100644
--- a/easybuild/tools/module_naming_scheme/mns.py
+++ b/easybuild/tools/module_naming_scheme/mns.py
@@ -32,6 +32,8 @@
 from vsc.utils import fancylogger
 from vsc.utils.patterns import Singleton
 
+from easybuild.tools.build_log import EasyBuildError
+
 
 class ModuleNamingScheme(object):
     """Abstract class for a module naming scheme implementation."""
@@ -50,7 +52,8 @@ def is_sufficient(self, keys):
         if self.REQUIRED_KEYS is not None:
             return set(keys).issuperset(set(self.REQUIRED_KEYS))
         else:
-            self.log.error("Constant REQUIRED_KEYS is not defined, should specify required easyconfig parameters.")
+            raise EasyBuildError("Constant REQUIRED_KEYS is not defined, "
+                                 "should specify required easyconfig parameters.")
 
     def requires_toolchain_details(self):
         """
@@ -134,7 +137,7 @@ def is_short_modname_for(self, short_modname, name):
         modname_regex = re.compile('^%s/\S+$' % re.escape(name))
         res = bool(modname_regex.match(short_modname))
 
-        tup = (short_modname, name, modname_regex.pattern, res)
-        self.log.debug("Checking whether '%s' is a module name for software with name '%s' via regex %s: %s" % tup)
+        self.log.debug("Checking whether '%s' is a module name for software with name '%s' via regex %s: %s",
+                       short_modname, name, modname_regex.pattern, res)
 
         return res
diff --git a/easybuild/tools/module_naming_scheme/toolchain.py b/easybuild/tools/module_naming_scheme/toolchain.py
index a4f1b419c8..5c63be336a 100644
--- a/easybuild/tools/module_naming_scheme/toolchain.py
+++ b/easybuild/tools/module_naming_scheme/toolchain.py
@@ -30,6 +30,7 @@
 from vsc.utils import fancylogger
 
 from easybuild.framework.easyconfig.easyconfig import process_easyconfig, robot_find_easyconfig
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 
@@ -77,7 +78,7 @@ def det_toolchain_element_details(tc, elem):
         if tc_ec['name'] == elem:
             tc_elem_details = tc_ec
         else:
-            _log.error("No toolchain element '%s' found for toolchain %s: %s" % (elem, tc.as_dict(), tc_ec))
+            raise EasyBuildError("No toolchain element '%s' found for toolchain %s: %s", elem, tc.as_dict(), tc_ec)
     _toolchain_details_cache[key] = tc_elem_details
     _log.debug("Obtained details for '%s' in toolchain '%s', added to cache" % (elem, tc_dict))
     return _toolchain_details_cache[key]
@@ -95,14 +96,15 @@ def det_toolchain_compilers(ec):
         tc_comps = None
     elif not TOOLCHAIN_COMPILER in tc_elems:
         # every toolchain should have at least a compiler
-        _log.error("No compiler found in toolchain %s: %s" % (ec.toolchain.as_dict(), tc_elems))
+        raise EasyBuildError("No compiler found in toolchain %s: %s", ec.toolchain.as_dict(), tc_elems)
     elif tc_elems[TOOLCHAIN_COMPILER]:
         tc_comps = []
         for comp_elem in tc_elems[TOOLCHAIN_COMPILER]:
             tc_comps.append(det_toolchain_element_details(ec.toolchain, comp_elem))
     else:
-        _log.error("Empty list of compilers for %s toolchain definition: %s" % (ec.toolchain.as_dict(), tc_elems))
-    _log.debug("Found compilers %s for toolchain %s (%s)" % (tc_comps, ec.toolchain.name, ec.toolchain.as_dict()))
+        raise EasyBuildError("Empty list of compilers for %s toolchain definition: %s",
+                             ec.toolchain.as_dict(), tc_elems)
+    _log.debug("Found compilers %s for toolchain %s (%s)", tc_comps, ec.toolchain.name, ec.toolchain.as_dict())
 
     return tc_comps
 
@@ -116,7 +118,8 @@ def det_toolchain_mpi(ec):
     tc_elems = ec.toolchain.definition()
     if TOOLCHAIN_MPI in tc_elems:
         if not tc_elems[TOOLCHAIN_MPI]:
-            _log.error("Empty list of MPI libs for %s toolchain definition: %s" % (ec.toolchain.as_dict(), tc_elems))
+            raise EasyBuildError("Empty list of MPI libs for %s toolchain definition: %s",
+                                 ec.toolchain.as_dict(), tc_elems)
         # assumption: only one MPI toolchain element
         tc_mpi = det_toolchain_element_details(ec.toolchain, tc_elems[TOOLCHAIN_MPI][0])
     else:
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index d70bffa424..8396f72963 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -163,7 +163,7 @@ def __init__(self, mod_paths=None, testing=False):
             self.cmd = os.environ[self.COMMAND_ENVIRONMENT]
 
         if self.cmd is None:
-            self.log.error('No command set.')
+            raise EasyBuildError("No command set.")
         else:
             self.log.debug('Using command %s' % self.cmd)
 
@@ -188,7 +188,7 @@ def modules(self):
     def set_and_check_version(self):
         """Get the module version, and check any requirements"""
         if self.VERSION_REGEXP is None:
-            self.log.error('No VERSION_REGEXP defined')
+            raise EasyBuildError("No VERSION_REGEXP defined")
 
         try:
             txt = self.run_module(self.VERSION_OPTION, return_output=True)
@@ -207,16 +207,17 @@ def set_and_check_version(self):
 
                 self.log.info("Converted actual version to '%s'" % self.version)
             else:
-                self.log.error("Failed to determine version from option '%s' output: %s" % (self.VERSION_OPTION, txt))
+                raise EasyBuildError("Failed to determine version from option '%s' output: %s",
+                                     self.VERSION_OPTION, txt)
         except (OSError), err:
-            self.log.error("Failed to check version: %s" % err)
+            raise EasyBuildError("Failed to check version: %s", err)
 
         if self.REQ_VERSION is None:
-            self.log.debug('No version requirement defined.')
+            self.log.debug("No version requirement defined.")
         else:
             if StrictVersion(self.version) < StrictVersion(self.REQ_VERSION):
-                msg = "EasyBuild requires v%s >= v%s (no rc), found v%s"
-                self.log.error(msg % (self.__class__.__name__, self.REQ_VERSION, self.version))
+                raise EasyBuildError("EasyBuild requires v%s >= v%s (no rc), found v%s",
+                                     self.__class__.__name__, self.REQ_VERSION, self.version)
             else:
                 self.log.debug('Version %s matches requirement %s' % (self.version, self.REQ_VERSION))
 
@@ -228,7 +229,7 @@ def check_cmd_avail(self):
             self.log.info("Full path for module command is %s, so using it" % self.cmd)
         else:
             mod_tool = self.__class__.__name__
-            self.log.error("%s modules tool can not be used, '%s' command is not available." % (mod_tool, self.cmd))
+            raise EasyBuildError("%s modules tool can not be used, '%s' command is not available.", mod_tool, self.cmd)
 
     def check_module_function(self, allow_mismatch=False, regex=None):
         """Check whether selected module tool matches 'module' function definition."""
@@ -259,7 +260,7 @@ def check_module_function(self, allow_mismatch=False, regex=None):
                 else:
                     msg += "Or alternatively, use --allow-modules-tool-mismatch to stop treating this as an error. "
                     msg += "Obtained definition of 'module' function: %s" % out
-                    self.log.error(msg)
+                    raise EasyBuildError(msg)
         else:
             # module function may not be defined (weird, but fine)
             self.log.warning("No 'module' function defined, can't check if it matches %s." % mod_details)
@@ -440,9 +441,10 @@ def get_value_from_modulefile(self, mod_name, regex):
             if res:
                 return res.group(1)
             else:
-                self.log.error("Failed to determine value from 'show' (pattern: '%s') in %s" % (regex.pattern, modinfo))
+                raise EasyBuildError("Failed to determine value from 'show' (pattern: '%s') in %s",
+                                     regex.pattern, modinfo)
         else:
-            raise EasyBuildError("Can't get value from a non-existing module %s" % mod_name)
+            raise EasyBuildError("Can't get value from a non-existing module %s", mod_name)
 
     def modulefile_path(self, mod_name):
         """Get the path of the module file for the specified module."""
@@ -490,7 +492,7 @@ def run_module(self, *args, **kwargs):
         if self.COMMAND_SHELL is not None:
             if not isinstance(self.COMMAND_SHELL, (list, tuple)):
                 msg = 'COMMAND_SHELL needs to be list or tuple, now %s (value %s)'
-                self.log.error(msg % (type(self.COMMAND_SHELL), self.COMMAND_SHELL))
+                raise EasyBuildError(msg, type(self.COMMAND_SHELL), self.COMMAND_SHELL)
             cmdlist = self.COMMAND_SHELL + cmdlist
 
         full_cmd = ' '.join(cmdlist + args)
@@ -518,7 +520,7 @@ def run_module(self, *args, **kwargs):
                 exec stdout
             except Exception, err:
                 out = "stdout: %s, stderr: %s" % (stdout, stderr)
-                raise EasyBuildError("Changing environment as dictated by module failed: %s (%s)" % (err, out))
+                raise EasyBuildError("Changing environment as dictated by module failed: %s (%s)", err, out)
 
             # correct LD_LIBRARY_PATH as yielded by the adjustments made
             # make sure we get the order right (reverse lists with [::-1])
@@ -537,7 +539,6 @@ def run_module(self, *args, **kwargs):
 
                 error = output_matchers['error'].search(line)
                 if error:
-                    self.log.error(line)
                     raise EasyBuildError(line)
 
                 modules = output_matchers['available'].finditer(line)
@@ -678,8 +679,8 @@ def path_to_top_of_module_tree(self, top_paths, mod_name, full_mod_subdir, deps,
                 full_mod_subdirs.append(dep_full_mod_subdir)
 
                 mods_to_top.append(dep)
-                tup = (dep, dep_full_mod_subdir, full_modpath_exts)
-                self.log.debug("Found module to top of module tree: %s (subdir: %s, modpath extensions %s)" % tup)
+                self.log.debug("Found module to top of module tree: %s (subdir: %s, modpath extensions %s)",
+                               dep, dep_full_mod_subdir, full_modpath_exts)
 
             if full_modpath_exts:
                 # load module for this dependency, since it may extend $MODULEPATH to make dependencies available
@@ -845,7 +846,7 @@ def update(self):
             (stdout, stderr) = proc.communicate()
 
             if stderr:
-                self.log.error("An error occured when running '%s': %s" % (' '.join(cmd), stderr))
+                raise EasyBuildError("An error occured when running '%s': %s", ' '.join(cmd), stderr)
 
             if self.testing:
                 # don't actually update local cache when testing, just return the cache contents
@@ -861,7 +862,7 @@ def update(self):
                     cache_file.write(stdout)
                     cache_file.close()
                 except (IOError, OSError), err:
-                    self.log.error("Failed to update Lmod spider cache %s: %s" % (cache_fp, err))
+                    raise EasyBuildError("Failed to update Lmod spider cache %s: %s", cache_fp, err)
 
     def prepend_module_path(self, path):
         # Lmod pushes a path to the front on 'module use'
@@ -923,7 +924,8 @@ def get_software_libdir(name, only_one=True, fs=None):
             if len(res) == 1:
                 res = res[0]
             else:
-                _log.error("Multiple library subdirectories found for %s in %s: %s" % (name, root, ', '.join(res)))
+                raise EasyBuildError("Multiple library subdirectories found for %s in %s: %s",
+                                     name, root, ', '.join(res))
         return res
     else:
         # return None if software package root could not be determined
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ebb608c169..83bab4f84a 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -49,6 +49,7 @@
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
 from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_pretend_installpath
@@ -371,7 +372,8 @@ def validate(self):
                 error_cnt += 1
 
         if error_cnt > 0:
-            self.log.error("Found %s problems validating the options, treating warnings above as fatal." % error_cnt)
+            raise EasyBuildError("Found %s problems validating the options, treating warnings above as fatal.",
+                                 error_cnt)
 
     def postprocess(self):
         """Do some postprocessing, in particular print stuff"""
@@ -403,17 +405,17 @@ def postprocess(self):
         # fail early if required dependencies for functionality requiring using GitHub API are not available:
         if self.options.from_pr or self.options.upload_test_report:
             if not HAVE_GITHUB_API:
-                self.log.error("Required support for using GitHub API is not available (see warnings).")
+                raise EasyBuildError("Required support for using GitHub API is not available (see warnings).")
 
         # make sure a GitHub token is available when it's required
         if self.options.upload_test_report:
             if not HAVE_KEYRING:
-                self.log.error("Python 'keyring' module required for obtaining GitHub token is not available.")
+                raise EasyBuildError("Python 'keyring' module required for obtaining GitHub token is not available.")
             if self.options.github_user is None:
-                self.log.error("No GitHub user name provided, required for fetching GitHub token.")
+                raise EasyBuildError("No GitHub user name provided, required for fetching GitHub token.")
             token = fetch_github_token(self.options.github_user)
             if token is None:
-                self.log.error("Failed to obtain required GitHub token for user '%s'" % self.options.github_user)
+                raise EasyBuildError("Failed to obtain required GitHub token for user '%s'", self.options.github_user)
 
         self._postprocess_config()
 
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 136ac83d31..b04495de99 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -68,7 +68,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir=None, p
     # create a single connection, and reuse it
     conn = connect_to_server()
     if conn is None:
-        _log.error("connect_to_server returned %s, can't submit jobs." % (conn))
+        raise EasyBuildError("connect_to_server returned %s, can't submit jobs.", conn)
 
     # determine ppn once, and pass is to each job being created
     # this avoids having to figure out ppn over and over again, every time creating a temp connection to the server
@@ -214,4 +214,4 @@ def prepare_easyconfig(ec):
         easyblock_instance.close_log()
         os.remove(easyblock_instance.logfile)
     except (OSError, EasyBuildError), err:
-        _log.error("An error occured while preparing %s: %s" % (ec, err))
+        raise EasyBuildError("An error occured while preparing %s: %s", ec, err)
diff --git a/easybuild/tools/pbs_job.py b/easybuild/tools/pbs_job.py
index d8eac9e928..28c5ee9c9d 100644
--- a/easybuild/tools/pbs_job.py
+++ b/easybuild/tools/pbs_job.py
@@ -35,6 +35,8 @@
 import time
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
+
 
 _log = fancylogger.getLogger('pbs_job', fname=False)
 
@@ -52,15 +54,13 @@
     KNOWN_HOLD_TYPES = [pbs.USER_HOLD, pbs.OTHER_HOLD, pbs.SYSTEM_HOLD]
 except ImportError:
     _log.debug("Failed to import pbs from pbs_python. Silently ignoring, is only a real issue with --job")
-    pbs_import_failed = ("PBSQuery or pbs modules not available. "
-                         "Please make sure pbs_python is installed and usable.")
+    pbs_import_failed = "PBSQuery or pbs modules not available. Please make sure pbs_python is installed and usable."
 
 
 def connect_to_server(pbs_server=None):
     """Connect to PBS server and return connection."""
     if pbs_import_failed:
-        _log.error(pbs_import_failed)
-        return None
+        raise EasyBuildError(pbs_import_failed)
 
     if not pbs_server:
         pbs_server = pbs.pbs_default()
@@ -70,8 +70,7 @@ def connect_to_server(pbs_server=None):
 def disconnect_from_server(conn):
     """Disconnect a given connection."""
     if pbs_import_failed:
-        _log.error(pbs_import_failed)
-        return None
+        raise EasyBuildError(pbs_import_failed)
 
     pbs.pbs_disconnect(conn)
 
@@ -116,7 +115,7 @@ def __init__(self, script, name, env_vars=None, resources={}, conn=None, ppn=Non
         self.name = name
 
         if pbs_import_failed:
-            self.log.error(pbs_import_failed)
+            raise EasyBuildError(pbs_import_failed)
 
         try:
             self.pbs_server = pbs.pbs_default()
@@ -126,7 +125,7 @@ def __init__(self, script, name, env_vars=None, resources={}, conn=None, ppn=Non
             else:
                 self.pbsconn = pbs.pbs_connect(self.pbs_server)
         except Exception, err:
-            self.log.error("Failed to connect to the default pbs server: %s" % err)
+            raise EasyBuildError("Failed to connect to the default pbs server: %s", err)
 
         # setup the resources requested
 
@@ -242,7 +241,7 @@ def submit(self, with_hold=False):
         jobid = pbs.pbs_submit(self.pbsconn, pbs_attributes, scriptfn, self.queue, NULL)
         is_error, errormsg = pbs.error()
         if is_error or jobid is None:
-            self.log.error("Failed to submit job script %s (job id: %s, error %s)" % (scriptfn, jobid, errormsg))
+            raise EasyBuildError("Failed to submit job script %s (job id: %s, error %s)", scriptfn, jobid, errormsg)
         else:
             self.log.debug("Succesful job submission returned jobid %s" % jobid)
             self.jobid = jobid
@@ -257,13 +256,13 @@ def set_hold(self, hold_type=None):
         # only set hold if it wasn't set before
         if hold_type not in self.holds:
             if hold_type not in KNOWN_HOLD_TYPES:
-                self.log.error("set_hold: unknown hold type: %s (supported: %s)" % (hold_type, KNOWN_HOLD_TYPES))
+                raise EasyBuildError("set_hold: unknown hold type: %s (supported: %s)", hold_type, KNOWN_HOLD_TYPES)
             # set hold, check for errors, and keep track of this hold
             ec = pbs.pbs_holdjob(self.pbsconn, self.jobid, hold_type, NULL)
             is_error, errormsg = pbs.error()
             if is_error or ec:
-                tup = (hold_type, self.jobid, is_error, ec, errormsg)
-                self.log.error("Failed to set hold of type %s on job %s (is_error: %s, exit code: %s, msg: %s)" % tup)
+                raise EasyBuildError("Failed to set hold of type %s on job %s (is_error: %s, exit code: %s, msg: %s)",
+                                     hold_type, self.jobid, is_error, ec, errormsg)
             else:
                 self.holds.append(hold_type)
         else:
@@ -278,14 +277,14 @@ def release_hold(self, hold_type=None):
         # only release hold if it was set
         if hold_type in self.holds:
             if hold_type not in KNOWN_HOLD_TYPES:
-                self.log.error("release_hold: unknown hold type: %s (supported: %s)" % (hold_type, KNOWN_HOLD_TYPES))
+                raise EasyBuildError("release_hold: unknown hold type: %s (supported: %s)", hold_type, KNOWN_HOLD_TYPES)
             # release hold, check for errors, remove from list of holds
             ec = pbs.pbs_rlsjob(self.pbsconn, self.jobid, hold_type, NULL)
             self.log.debug("Released hold of type %s for job %s" % (hold_type, self.jobid))
             is_error, errormsg = pbs.error()
             if is_error or ec:
-                tup = (hold_type, self.jobid, is_error, ec, errormsg)
-                self.log.error("Failed to release hold type %s on job %s (is_error: %s, exit code: %s, msg: %s)" % tup)
+                raise EasyBuildError("Failed to release hold type %s on job %s (is_error: %s, exit code: %s, msg: %s)",
+                                     hold_type, self.jobid, is_error, ec, errormsg)
             else:
                 self.holds.remove(hold_type)
         else:
@@ -371,7 +370,7 @@ def info(self, types=None):
         elif len(jobs) == 1:
             self.log.debug("Request for jobid %s returned one result %s" % (self.jobid, jobs))
         else:
-            self.log.error("Request for jobid %s returned more then one result %s" % (self.jobid, jobs))
+            raise EasyBuildError("Request for jobid %s returned more then one result %s", self.jobid, jobs)
 
         # only expect to have a list with one element
         j = jobs[0]
@@ -386,7 +385,7 @@ def remove(self):
         """Remove the job with id jobid"""
         result = pbs.pbs_deljob(self.pbsconn, self.jobid, '')  # use empty string, not NULL
         if result:
-            self.log.error("Failed to delete job %s: error %s" % (self.jobid, result))
+            raise EasyBuildError("Failed to delete job %s: error %s", self.jobid, result)
         else:
             self.log.debug("Succesfully deleted job %s" % self.jobid)
 
diff --git a/easybuild/tools/repository/gitrepo.py b/easybuild/tools/repository/gitrepo.py
index c70d12efba..956afec522 100644
--- a/easybuild/tools/repository/gitrepo.py
+++ b/easybuild/tools/repository/gitrepo.py
@@ -43,6 +43,7 @@
 import time
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import rmtree2
 from easybuild.tools.repository.filerepo import FileRepository
 
@@ -87,7 +88,7 @@ def setup_repo(self):
         try:
             git.GitCommandError
         except NameError, err:
-            self.log.exception("It seems like GitPython is not available: %s" % err)
+            raise EasyBuildError("It seems like GitPython is not available: %s", err)
 
         self.wc = tempfile.mkdtemp(prefix='git-wc-')
 
@@ -105,7 +106,7 @@ def create_working_copy(self):
             self.log.debug("rep name is %s" % reponame)
         except git.GitCommandError, err:
             # it might already have existed
-            self.log.warning("Git local repo initialization failed, it might already exist: %s" % err)
+            self.log.warning("Git local repo initialization failed, it might already exist: %s", err)
 
         # local repo should now exist, let's connect to it again
         try:
@@ -113,14 +114,14 @@ def create_working_copy(self):
             self.log.debug("connectiong to git repo in %s" % self.wc)
             self.client = git.Git(self.wc)
         except (git.GitCommandError, OSError), err:
-            self.log.error("Could not create a local git repo in wc %s: %s" % (self.wc, err))
+            raise EasyBuildError("Could not create a local git repo in wc %s: %s", self.wc, err)
 
         # try to get the remote data in the local repo
         try:
             res = self.client.pull()
             self.log.debug("pulled succesfully to %s in %s" % (res, self.wc))
         except (git.GitCommandError, OSError), err:
-            self.log.exception("pull in working copy %s went wrong: %s" % (self.wc, err))
+            raise EasyBuildError("pull in working copy %s went wrong: %s", self.wc, err)
 
     def add_easyconfig(self, cfg, name, version, stats, append):
         """
@@ -166,4 +167,4 @@ def cleanup(self):
             self.wc = os.path.dirname(self.wc)
             rmtree2(self.wc)
         except IOError, err:
-            self.log.exception("Can't remove working copy %s: %s" % (self.wc, err))
+            raise EasyBuildError("Can't remove working copy %s: %s", self.wc, err)
diff --git a/easybuild/tools/repository/repository.py b/easybuild/tools/repository/repository.py
index cc588f4191..afb44f7e20 100644
--- a/easybuild/tools/repository/repository.py
+++ b/easybuild/tools/repository/repository.py
@@ -37,6 +37,7 @@
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_subclasses
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.utilities import import_available_modules
 
 _log = fancylogger.getLogger('repository', fname=False)
@@ -126,7 +127,7 @@ def avail_repositories(check_useable=True):
     class_dict = dict([(x.__name__, x) for x in get_subclasses(Repository) if x.USABLE or not check_useable])
 
     if not 'FileRepository' in class_dict:
-        _log.error('avail_repositories: FileRepository missing from list of repositories')
+        raise EasyBuildError("avail_repositories: FileRepository missing from list of repositories")
 
     return class_dict
 
@@ -144,13 +145,13 @@ def init_repository(repository, repository_path):
             elif isinstance(repository_path, (tuple, list)) and len(repository_path) <= 2:
                 inited_repo = repo(*repository_path)
             else:
-                _log.error('repository_path should be a string or list/tuple of maximum 2 elements (current: %s, type %s)' %
-                           (repository_path, type(repository_path)))
+                raise EasyBuildError("repository_path should be a string or list/tuple of maximum 2 elements "
+                                     "(current: %s, type %s)", repository_path, type(repository_path))
         except Exception, err:
-            _log.error('Failed to create a repository instance for %s (class %s) with args %s (msg: %s)' %
-                       (repository, repo.__name__, repository_path, err))
+            raise EasyBuildError("Failed to create a repository instance for %s (class %s) with args %s (msg: %s)",
+                                 repository, repo.__name__, repository_path, err)
     else:
-        _log.error('Unknown typo of repository spec: %s (type %s)' % (repo, type(repo)))
+        raise EasyBuildError("Unknown typo of repository spec: %s (type %s)", repo, type(repo))
 
     inited_repo.init()
     return inited_repo
diff --git a/easybuild/tools/repository/svnrepo.py b/easybuild/tools/repository/svnrepo.py
index 65394deb91..7afc3dd74b 100644
--- a/easybuild/tools/repository/svnrepo.py
+++ b/easybuild/tools/repository/svnrepo.py
@@ -43,6 +43,7 @@
 import time
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import rmtree2
 from easybuild.tools.repository.filerepo import FileRepository
 
@@ -88,8 +89,8 @@ def setup_repo(self):
         try:
             pysvn.ClientError  # IGNORE:E0611 pysvn fails to recognize ClientError is available
         except NameError, err:
-            self.log.exception("pysvn not available (%s). Make sure it is installed " % err +
-                               "properly. Run 'python -c \"import pysvn\"' to test.")
+            raise EasyBuildError("pysvn not available (%s). Make sure it is installed properly. "
+                                 "Run 'python -c \"import pysvn\"' to test.", err)
 
         # try to connect to the repository
         self.log.debug("Try to connect to repository %s" % self.repo)
@@ -97,13 +98,13 @@ def setup_repo(self):
             self.client = pysvn.Client()
             self.client.exception_style = 0
         except ClientError:
-            self.log.exception("Svn Client initialization failed.")
+            raise EasyBuildError("Svn Client initialization failed.")
 
         try:
             if not self.client.is_url(self.repo):
-                self.log.error("Provided repository %s is not a valid svn url" % self.repo)
+                raise EasyBuildError("Provided repository %s is not a valid svn url", self.repo)
         except ClientError:
-            self.log.exception("Can't connect to svn repository %s" % self.repo)
+            raise EasyBuildError("Can't connect to svn repository %s", self.repo)
 
     def create_working_copy(self):
         """
@@ -116,16 +117,16 @@ def create_working_copy(self):
         try:
             self.client.info2(self.repo, recurse=False)
         except ClientError:
-            self.log.exception("Getting info from %s failed." % self.wc)
+            raise EasyBuildError("Getting info from %s failed.", self.wc)
 
         try:
             res = self.client.update(self.wc)
             self.log.debug("Updated to revision %s in %s" % (res, self.wc))
         except ClientError:
-            self.log.exception("Update in wc %s went wrong" % self.wc)
+            raise EasyBuildError("Update in wc %s went wrong", self.wc)
 
         if len(res) == 0:
-            self.log.error("Update returned empy list (working copy: %s)" % (self.wc))
+            raise EasyBuildError("Update returned empy list (working copy: %s)", self.wc)
 
         if res[0].number == -1:
             # revision number of update is -1
@@ -134,7 +135,7 @@ def create_working_copy(self):
                 res = self.client.checkout(self.repo, self.wc)
                 self.log.debug("Checked out revision %s in %s" % (res.number, self.wc))
             except ClientError, err:
-                self.log.exception("Checkout of path / in working copy %s went wrong: %s" % (self.wc, err))
+                raise EasyBuildError("Checkout of path / in working copy %s went wrong: %s", self.wc, err)
 
     def add_easyconfig(self, cfg, name, version, stats, append):
         """
@@ -160,7 +161,7 @@ def commit(self, msg=None):
         try:
             self.client.checkin(self.wc, completemsg, recurse=True)
         except ClientError, err:
-            self.log.exception("Commit from working copy %s (msg: %s) failed: %s" % (self.wc, msg, err))
+            raise EasyBuildError("Commit from working copy %s (msg: %s) failed: %s", self.wc, msg, err)
 
     def cleanup(self):
         """
@@ -169,4 +170,4 @@ def cleanup(self):
         try:
             rmtree2(self.wc)
         except OSError, err:
-            self.log.exception("Can't remove working copy %s: %s" % (self.wc, err))
+            raise EasyBuildError("Can't remove working copy %s: %s", self.wc, err)
diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index 5309db63af..56544bdeff 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -43,7 +43,7 @@
 from vsc.utils import fancylogger
 
 from easybuild.tools.asyncprocess import PIPE, STDOUT, Popen, recv_some, send_all
-import easybuild.tools.build_log  # this import is required to obtain a correct (EasyBuild) logger!
+from easybuild.tools.build_log import EasyBuildError
 
 
 _log = fancylogger.getLogger('run', fname=False)
@@ -88,7 +88,7 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
     Executes a command cmd
     - returns exitcode and stdout+stderr (mixed)
     - no input though stdin
-    - if log_ok or log_all are set -> will log.error if non-zero exit-code
+    - if log_ok or log_all are set -> will raise EasyBuildError if non-zero exit-code
     - if simple is True -> instead of returning a tuple (output, ec) it will just return True or False signifying succes
     - inp is the input given to the command
     - regexp -> Regex used to check the output for errors. If True will use default (see parselogForError)
@@ -119,7 +119,7 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
         p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
                              stdin=subprocess.PIPE, close_fds=True, executable="/bin/bash")
     except OSError, err:
-        _log.error("run_cmd init cmd %s failed:%s" % (cmd, err))
+        raise EasyBuildError("run_cmd init cmd %s failed:%s", cmd, err)
     if inp:
         p.stdin.write(inp)
     p.stdin.close()
@@ -148,7 +148,7 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
     try:
         os.chdir(cwd)
     except OSError, err:
-        _log.error("Failed to return to %s after executing command: %s" % (cwd, err))
+        raise EasyBuildError("Failed to return to %s after executing command: %s", cwd, err)
 
     return parse_cmd_output(cmd, stdouterr, ec, simple, log_all, log_ok, regexp)
 
@@ -200,15 +200,15 @@ def process_QA(q, a_s):
         if regQ.search(q):
             return (a_s, regQ)
         else:
-            _log.error("runqanda: Question %s converted in %s does not match itself" % (q, regQtxt))
+            raise EasyBuildError("runqanda: Question %s converted in %s does not match itself", q, regQtxt)
 
     def check_answers_list(answers):
         """Make sure we have a list of answers (as strings)."""
         if isinstance(answers, basestring):
             answers = [answers]
         elif not isinstance(answers, list):
-            msg = "Invalid type for answer on %s, no string or list: %s (%s)" % (question, type(answers), answers)
-            _log.error(msg)
+            raise EasyBuildError("Invalid type for answer on %s, no string or list: %s (%s)",
+                                 question, type(answers), answers)
         # list is manipulated when answering matching question, so return a copy
         return answers[:]
 
@@ -247,7 +247,7 @@ def check_answers_list(answers):
             _log.debug('run_cmd_qa: Command output will be logged to %s' % runLog.name)
             runLog.write(cmd + "\n\n")
         except IOError, err:
-            _log.error("Opening log file for Q&A failed: %s" % err)
+            raise EasyBuildError("Opening log file for Q&A failed: %s", err)
     else:
         runLog = None
 
@@ -256,7 +256,7 @@ def check_answers_list(answers):
     try:
         p = Popen(cmd, shell=True, stdout=PIPE, stderr=STDOUT, stdin=PIPE, close_fds=True, executable="/bin/bash")
     except OSError, err:
-        _log.error("run_cmd_qa init cmd %s failed:%s" % (cmd, err))
+        raise EasyBuildError("run_cmd_qa init cmd %s failed:%s", cmd, err)
 
     ec = p.poll()
     stdoutErr = ''
@@ -328,8 +328,8 @@ def check_answers_list(answers):
             except OSError, err:
                 _log.debug("run_cmd_qa exception caught when killing child process: %s" % err)
             _log.debug("run_cmd_qa: full stdouterr: %s" % stdoutErr)
-            _log.error("run_cmd_qa: cmd %s : Max nohits %s reached: end of output %s" %
-                       (cmd, maxHitCount, stdoutErr[-500:]))
+            raise EasyBuildError("run_cmd_qa: cmd %s : Max nohits %s reached: end of output %s",
+                                 cmd, maxHitCount, stdoutErr[-500:])
 
         # the sleep below is required to avoid exiting on unknown 'questions' too early (see above)
         time.sleep(1)
@@ -351,7 +351,7 @@ def check_answers_list(answers):
     try:
         os.chdir(cwd)
     except OSError, err:
-        _log.error("Failed to return to %s after executing command: %s" % (cwd, err))
+        raise EasyBuildError("Failed to return to %s after executing command: %s", cwd, err)
 
     return parse_cmd_output(cmd, stdoutErr, ec, simple, log_all, log_ok, regexp)
 
@@ -370,7 +370,7 @@ def parse_cmd_output(cmd, stdouterr, ec, simple, log_all, log_ok, regexp):
         check_ec = True
         use_regexp = True
     else:
-        _log.error("invalid strictness setting: %s" % strictness)
+        raise EasyBuildError("invalid strictness setting: %s", strictness)
 
     # allow for overriding the regexp setting
     if not regexp:
@@ -381,7 +381,7 @@ def parse_cmd_output(cmd, stdouterr, ec, simple, log_all, log_ok, regexp):
     if ec and (log_all or log_ok):
         # We don't want to error if the user doesn't care
         if check_ec:
-            _log.error('cmd "%s" exited with exitcode %s and output:\n%s' % (cmd, ec, stdouterr))
+            raise EasyBuildError('cmd "%s" exited with exitcode %s and output:\n%s', cmd, ec, stdouterr)
         else:
             _log.warn('cmd "%s" exited with exitcode %s and output:\n%s' % (cmd, ec, stdouterr))
     elif not ec:
@@ -394,7 +394,7 @@ def parse_cmd_output(cmd, stdouterr, ec, simple, log_all, log_ok, regexp):
         if len(res) > 0:
             message = "Found %s errors in command output (output: %s)" % (len(res), ", ".join([r[0] for r in res]))
             if use_regexp:
-                _log.error(message)
+                raise EasyBuildError(message)
             else:
                 _log.warn(message)
 
@@ -424,7 +424,7 @@ def parse_log_for_error(txt, regExp=None, stdout=True, msg=None):
     elif type(regExp) == str:
         pass
     else:
-        _log.error("parse_log_for_error no valid regExp used: %s" % regExp)
+        raise EasyBuildError("parse_log_for_error no valid regExp used: %s", regExp)
 
     reg = re.compile(regExp, re.I)
 
diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index f8e6950df5..e3bd6316e9 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -38,6 +38,7 @@
 from vsc.utils import fancylogger
 from vsc.utils.affinity import sched_getaffinity
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import read_file, which
 from easybuild.tools.run import run_cmd
 
@@ -121,8 +122,8 @@ def get_cpu_vendor():
             arch = res.group('vendor')
         if arch in VENDORS:
             vendor = VENDORS[arch]
-            tup = (vendor, vendor_regex.pattern, PROC_CPUINFO_FP)
-            _log.debug("Determined CPU vendor on Linux as being '%s' via regex '%s' in %s" % tup)
+            _log.debug("Determined CPU vendor on Linux as being '%s' via regex '%s' in %s",
+                       vendor, vendor_regex.pattern, PROC_CPUINFO_FP)
 
     elif os_type == DARWIN:
         cmd = "sysctl -n machdep.cpu.vendor"
@@ -157,8 +158,8 @@ def get_cpu_family():
             power_regex = re.compile(r"^cpu\s+:\s*POWER.*", re.M)
             if power_regex.search(cpuinfo_txt):
                 family = POWER
-                tup = (power_regex.pattern, PROC_CPUINFO_FP, family)
-                _log.debug("Determined CPU family using regex '%s' in %s: %s" % tup)
+                _log.debug("Determined CPU family using regex '%s' in %s: %s",
+                           power_regex.pattern, PROC_CPUINFO_FP, family)
 
     if family is None:
         family = UNKNOWN
@@ -182,8 +183,8 @@ def get_cpu_model():
         res = model_regex.search(txt)
         if res is not None:
             model = res.group('model').strip()
-            tup = (model_regex.pattern, PROC_CPUINFO_FP, model)
-            _log.debug("Determined CPU model on Linux using regex '%s' in %s: %s" % tup)
+            _log.debug("Determined CPU model on Linux using regex '%s' in %s: %s",
+                       model_regex.pattern, PROC_CPUINFO_FP, model)
 
     elif os_type == DARWIN:
         cmd = "sysctl -n machdep.cpu.brand_string"
@@ -348,7 +349,7 @@ def get_os_version():
                 if not known_sp:
                     suff = '_UNKNOWN_SP'
             else:
-                _log.error("Don't know how to determine subversions for SLES %s" % os_version)
+                raise EasyBuildError("Don't know how to determine subversions for SLES %s", os_version)
 
         return os_version
     else:
@@ -413,8 +414,8 @@ def get_glibc_version():
             _log.debug("Found glibc version %s" % glibc_version)
             return glibc_version
         else:
-            tup = (glibc_ver_str, glibc_ver_regex.pattern)
-            _log.error("Failed to determine glibc version from '%s' using pattern '%s'." % tup)
+            raise EasyBuildError("Failed to determine glibc version from '%s' using pattern '%s'.",
+                                 glibc_ver_str, glibc_ver_regex.pattern)
     else:
         # no glibc on OS X standard
         _log.debug("No glibc on a non-Linux system, so can't determine version.")
@@ -447,7 +448,7 @@ def use_group(group_name):
     try:
         group_id = grp.getgrnam(group_name).gr_gid
     except KeyError, err:
-        _log.error("Failed to get group ID for '%s', group does not exist (err: %s)" % (group_name, err))
+        raise EasyBuildError("Failed to get group ID for '%s', group does not exist (err: %s)", group_name, err)
 
     group = (group_name, group_id)
     try:
@@ -460,7 +461,7 @@ def use_group(group_name):
             err_msg += "change the primary group before using EasyBuild, using 'newgrp %s'." % group_name
         else:
             err_msg += "current user '%s' is not in group %s (members: %s)" % (user, group, grp_members)
-        _log.error(err_msg)
+        raise EasyBuildError(err_msg)
     _log.info("Using group '%s' (gid: %s)" % group)
 
     return group
@@ -476,7 +477,7 @@ def det_parallelism(par, maxpar):
             try:
                 par = int(par)
             except ValueError, err:
-                _log.error("Specified level of parallelism '%s' is not an integer value: %s" % (par, err))
+                raise EasyBuildError("Specified level of parallelism '%s' is not an integer value: %s", par, err)
     else:
         par = get_avail_core_count()
         # check ulimit -u
@@ -491,7 +492,7 @@ def det_parallelism(par, maxpar):
                 par = par_guess
                 _log.info("Limit parallel builds to %s because max user processes is %s" % (par, out))
         except ValueError, err:
-            _log.exception("Failed to determine max user processes (%s, %s): %s" % (ec, out, err))
+            raise EasyBuildError("Failed to determine max user processes (%s, %s): %s", ec, out, err)
 
     if maxpar is not None and maxpar < par:
         _log.info("Limiting parallellism from %s to %s" % (par, maxpar))
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index 113ec2e747..5c5bc68504 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -96,7 +96,7 @@ def regtest(easyconfig_paths, build_specs=None):
         for path in easyconfig_paths:
             ecfiles += find_easyconfigs(path, ignore_dirs=build_option('ignore_dirs'))
     else:
-        _log.error("No easyconfig paths specified.")
+        raise EasyBuildError("No easyconfig paths specified.")
 
     test_results = []
 
diff --git a/easybuild/tools/toolchain/compiler.py b/easybuild/tools/toolchain/compiler.py
index 06d0860aae..2d519d9794 100644
--- a/easybuild/tools/toolchain/compiler.py
+++ b/easybuild/tools/toolchain/compiler.py
@@ -28,10 +28,8 @@
 @author: Stijn De Weirdt (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
-
-import os
-
 from easybuild.tools import systemtools
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.toolchain.constants import COMPILER_VARIABLES
 from easybuild.tools.toolchain.toolchain import Toolchain
@@ -186,7 +184,7 @@ def _set_compiler_vars(self):
                         # only warn if prefix is set, not all languages may be supported (e.g., no Fortran for CUDA)
                         self.log.warn("_set_compiler_vars: %s compiler variable %s undefined" % (prefix, var))
                     else:
-                        self.log.raiseException("_set_compiler_vars: compiler variable %s undefined" % var)
+                        raise EasyBuildError("_set_compiler_vars: compiler variable %s undefined", var)
 
                 self.variables[pref_var] = value
                 if is32bit:
@@ -273,7 +271,7 @@ def _get_optimal_architecture(self):
             self.options.options_map['optarch'] = optarch
 
         if 'optarch' in self.options.options_map and self.options.options_map.get('optarch', None) is None:
-            self.log.raiseException("_get_optimal_architecture: don't know how to set optarch for %s." % self.arch)
+            raise EasyBuildError("_get_optimal_architecture: don't know how to set optarch for %s", self.arch)
 
     def comp_family(self, prefix=None):
         """
@@ -286,4 +284,4 @@ def comp_family(self, prefix=None):
         if comp_family:
             return comp_family
         else:
-            self.log.raiseException('comp_family: COMPILER_%sFAMILY is undefined.' % infix)
+            raise EasyBuildError("comp_family: COMPILER_%sFAMILY is undefined", infix)
diff --git a/easybuild/tools/toolchain/linalg.py b/easybuild/tools/toolchain/linalg.py
index e5d9b18607..15b091ebba 100644
--- a/easybuild/tools/toolchain/linalg.py
+++ b/easybuild/tools/toolchain/linalg.py
@@ -29,6 +29,7 @@
 @author: Kenneth Hoste (Ghent University)
 """
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.toolchain import Toolchain
 
 
@@ -95,7 +96,7 @@ def set_variables(self):
     def _set_blas_variables(self):
         """Set BLAS related variables"""
         if self.BLAS_LIB is None:
-            self.log.raiseException("_set_blas_variables: BLAS_LIB not set")
+            raise EasyBuildError("_set_blas_variables: BLAS_LIB not set")
 
         self.BLAS_LIB = self.variables.nappend('LIBBLAS', [x % self.BLAS_LIB_MAP for x in self.BLAS_LIB])
         self.variables.add_begin_end_linkerflags(self.BLAS_LIB,
@@ -143,7 +144,7 @@ def _set_lapack_variables(self):
             self.variables.join('LAPACK_INC_DIR', 'BLAS_INC_DIR')
         else:
             if self.LAPACK_LIB is None:
-                self.log.raiseException("_set_lapack_variables: LAPACK_LIB not set")
+                raise EasyBuildError("_set_lapack_variables: LAPACK_LIB not set")
             self.LAPACK_LIB = self.variables.nappend('LIBLAPACK_ONLY', self.LAPACK_LIB)
             self.variables.add_begin_end_linkerflags(self.LAPACK_LIB,
                                                      toggle_startstopgroup=self.LAPACK_LIB_GROUP,
@@ -222,7 +223,7 @@ def _set_scalapack_variables(self):
         """Set ScaLAPACK related variables"""
 
         if self.SCALAPACK_LIB is None:
-            self.log.raiseException("_set_blas_variables: SCALAPACK_LIB not set")
+            raise EasyBuildError("_set_blas_variables: SCALAPACK_LIB not set")
 
         lib_map = {}
         if hasattr(self, 'BLAS_LIB_MAP') and self.BLAS_LIB_MAP is not None:
@@ -268,7 +269,7 @@ def _set_scalapack_variables(self):
             if getattr(self, 'LIB_MULTITHREAD', None) is not None:
                 self.variables.nappend('LIBSCALAPACK_MT', self.LIB_MULTITHREAD)
         else:
-            self.log.raiseException("_set_scalapack_variables: LIBSCALAPACK without SCALAPACK_REQUIRES not implemented")
+            raise EasyBuildError("_set_scalapack_variables: LIBSCALAPACK without SCALAPACK_REQUIRES not implemented")
 
 
         self.variables.join('SCALAPACK_STATIC_LIBS', 'LIBSCALAPACK')
@@ -279,4 +280,3 @@ def _set_scalapack_variables(self):
 
         self._add_dependency_variables(self.SCALAPACK_MODULE_NAME,
                                        ld=self.SCALAPACK_LIB_DIR, cpp=self.SCALAPACK_INCLUDE_DIR)
-
diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index 64038d9849..74da9d5ff6 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -33,6 +33,7 @@
 
 import easybuild.tools.environment as env
 import easybuild.tools.toolchain as toolchain
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import write_file
 from easybuild.tools.toolchain.constants import COMPILER_VARIABLES, MPI_COMPILER_TEMPLATE, SEQ_COMPILER_TEMPLATE
 from easybuild.tools.toolchain.toolchain import Toolchain
@@ -106,7 +107,7 @@ def _set_mpi_compiler_variables(self):
 
             value = getattr(self, 'MPI_COMPILER_%s' % var.upper(), None)
             if value is None:
-                self.log.raiseException("_set_mpi_compiler_variables: mpi compiler variable %s undefined" % var)
+                raise EasyBuildError("_set_mpi_compiler_variables: mpi compiler variable %s undefined", var)
             self.variables.nappend_el(var, value)
 
             # complete compiler variable template to produce e.g. 'mpicc -cc=icc -X -Y' from 'mpicc -cc=%(CC_base)'
@@ -159,7 +160,7 @@ def mpi_family(self):
         if self.MPI_FAMILY:
             return self.MPI_FAMILY
         else:
-            self.log.raiseException("mpi_family: MPI_FAMILY is undefined.")
+            raise EasyBuildError("mpi_family: MPI_FAMILY is undefined.")
 
     # FIXME: deprecate this function, use mympirun instead
     # this requires that either mympirun is packaged together with EasyBuild, or that vsc-tools is a dependency of EasyBuild
@@ -213,7 +214,7 @@ def mpi_cmd_for(self, cmd, nr_ranks):
                     os.remove(fn)
                 write_file(fn, "localhost ifhn=localhost")
             except OSError, err:
-                self.log.error("Failed to create file %s: %s" % (fn, err))
+                raise EasyBuildError("Failed to create file %s: %s", fn, err)
 
             params.update({'mpdbf': "--file=%s" % fn})
 
@@ -224,11 +225,11 @@ def mpi_cmd_for(self, cmd, nr_ranks):
                     os.remove(fn)
                 write_file(fn, "localhost\n" * nr_ranks)
             except OSError, err:
-                self.log.error("Failed to create file %s: %s" % (fn, err))
+                raise EasyBuildError("Failed to create file %s: %s", fn, err)
 
             params.update({'nodesfile': "-machinefile %s" % fn})
 
         if mpi_family in mpi_cmds.keys():
             return mpi_cmds[mpi_family] % params
         else:
-            self.log.error("Don't know how to create an MPI command for MPI library of type '%s'." % mpi_family)
+            raise EasyBuildError("Don't know how to create an MPI command for MPI library of type '%s'.", mpi_family)
diff --git a/easybuild/tools/toolchain/options.py b/easybuild/tools/toolchain/options.py
index f9835b7777..32b162151f 100644
--- a/easybuild/tools/toolchain/options.py
+++ b/easybuild/tools/toolchain/options.py
@@ -37,6 +37,8 @@
 
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
+
 
 class ToolchainOptions(dict):
     def __init__(self):
@@ -62,9 +64,9 @@ def _add_options(self, options):
         self.log.debug("_add_options: adding options %s" % options)
         for name, value in options.items():
             if not isinstance(value, (list, tuple,)) and len(value) == 2:
-                self.log.raiseException("_add_options: option name %s has to be 2 element list (%s)" % (name, value))
+                raise EasyBuildError("_add_options: option name %s has to be 2 element list (%s)", name, value)
             if name in self:
-                self.log.debug("_add_options: redefining previous name %s (previous value %s)" % (name, self.get(name)))
+                self.log.debug("_add_options: redefining previous name %s (previous value %s)", name, self.get(name))
             self.__setitem__(name, value[0])
             self.description.__setitem__(name, value[1])
 
@@ -75,9 +77,9 @@ def _add_options_map(self, options_map):
         for name in options_map.keys():
             if not name in self:
                 if name.startswith('_opt_'):
-                    self.log.debug("_add_options_map: no option with name %s defined, but allowed" % name)
+                    self.log.debug("_add_options_map: no option with name %s defined, but allowed", name)
                 else:
-                    self.log.raiseException("_add_options_map: no option with name %s defined" % name)
+                    raise EasyBuildError("_add_options_map: no option with name %s defined", name)
 
         self.options_map.update(options_map)
 
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 5a5e1d4530..eca2b0ce1b 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -35,6 +35,7 @@
 import re
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, install_path
 from easybuild.tools.environment import setvar
 from easybuild.tools.modules import get_software_root, get_software_version, modules_tool
@@ -81,13 +82,13 @@ def __init__(self, name=None, version=None, mns=None):
         if name is None:
             name = self.NAME
         if name is None:
-            self.log.error("Toolchain init: no name provided")
+            raise EasyBuildError("Toolchain init: no name provided")
         self.name = name
 
         if version is None:
             version = self.VERSION
         if version is None:
-            self.log.error("Toolchain init: no version provided")
+            raise EasyBuildError("Toolchain init: no version provided")
         self.version = version
 
         self.vars = None
@@ -128,7 +129,7 @@ def get_variable(self, name, typ=str):
         elif typ == list:
             return self.variables[name].flatten()
         else:
-            self.log.error("get_variable: Don't know how to create value of type %s." % typ)
+            raise EasyBuildError("get_variable: Don't know how to create value of type %s.", typ)
 
     def set_variables(self):
         """Do nothing? Everything should have been set by others
@@ -187,18 +188,18 @@ def _get_software_root(self, name):
         """Try to get the software root for name"""
         root = get_software_root(name)
         if root is None:
-            self.log.error("get_software_root software root for %s was not found in environment" % name)
+            raise EasyBuildError("get_software_root software root for %s was not found in environment", name)
         else:
-            self.log.debug("get_software_root software root %s for %s was found in environment" % (root, name))
+            self.log.debug("get_software_root software root %s for %s was found in environment", root, name)
         return root
 
     def _get_software_version(self, name):
         """Try to get the software root for name"""
         version = get_software_version(name)
         if version is None:
-            self.log.error("get_software_version software version for %s was not found in environment" % name)
+            raise EasyBuildError("get_software_version software version for %s was not found in environment", name)
         else:
-            self.log.debug("get_software_version software version %s for %s was found in environment" % (version, name))
+            self.log.debug("get_software_version software version %s for %s was found in environment", version, name)
 
         return version
 
@@ -221,7 +222,7 @@ def as_dict(self, name=None, version=None):
     def det_short_module_name(self):
         """Determine module name for this toolchain."""
         if self.mod_short_name is None:
-            self.log.error("Toolchain module name was not set yet (using set_module_info).")
+            raise EasyBuildError("Toolchain module name was not set yet (using set_module_info).")
         return self.mod_short_name
 
     def _toolchain_exists(self):
@@ -234,7 +235,7 @@ def _toolchain_exists(self):
             return True
         else:
             if self.mod_short_name is None:
-                self.log.error("Toolchain module name was not set yet (using set_module_info).")
+                raise EasyBuildError("Toolchain module name was not set yet (using set_module_info).")
             # check whether a matching module exists if self.mod_short_name contains a module name
             return self.modules_tool.exist([self.mod_full_name])[0]
 
@@ -247,7 +248,7 @@ def set_options(self, options):
             else:
                 # used to be warning, but this is a severe error imho
                 known_opts = ','.join(self.options.keys())
-                self.log.error("Undefined toolchain option %s specified (known options: %s)" % (opt, known_opts))
+                raise EasyBuildError("Undefined toolchain option %s specified (known options: %s)", opt, known_opts)
 
     def get_dependency_version(self, dependency):
         """ Generate a version string for a dependency on a module using this toolchain """
@@ -267,7 +268,7 @@ def get_dependency_version(self, dependency):
 
         if 'version' in dependency:
             version = "".join([dependency['version'], toolchain, suffix])
-            self.log.debug("get_dependency_version: version in dependency return %s" % version)
+            self.log.debug("get_dependency_version: version in dependency return %s", version)
             return version
         else:
             toolchain_suffix = "".join([toolchain, suffix])
@@ -275,11 +276,11 @@ def get_dependency_version(self, dependency):
             # Find the most recent (or default) one
             if len(matches) > 0:
                 version = matches[-1][-1]
-                self.log.debug("get_dependency_version: version not in dependency return %s" % version)
+                self.log.debug("get_dependency_version: version not in dependency return %s", version)
                 return
             else:
-                tup = (dependency['name'], toolchain_suffix)
-                self.log.error("No toolchain version for dependency name %s (suffix %s) found" % tup)
+                raise EasyBuildError("No toolchain version for dependency name %s (suffix %s) found",
+                                     dependency['name'], toolchain_suffix)
 
     def add_dependencies(self, dependencies):
         """ Verify if the given dependencies exist and add them """
@@ -289,8 +290,7 @@ def add_dependencies(self, dependencies):
         for dep, dep_mod_name, dep_exists in zip(dependencies, dep_mod_names, deps_exist):
             self.log.debug("add_dependencies: MODULEPATH: %s" % os.environ['MODULEPATH'])
             if not dep_exists:
-                tup = (dep_mod_name, dep)
-                self.log.error("add_dependencies: no module '%s' found for dependency %s" % tup)
+                raise EasyBuildError("add_dependencies: no module '%s' found for dependency %s", dep_mod_name, dep)
             else:
                 self.dependencies.append(dep)
                 self.log.debug('add_dependencies: added toolchain dependency %s' % str(dep))
@@ -328,10 +328,10 @@ def prepare(self, onlymod=None):
         (If string: comma separated list of variables that will be ignored).
         """
         if self.modules_tool is None:
-            self.log.error("No modules tool defined in Toolchain instance.")
+            raise EasyBuildError("No modules tool defined in Toolchain instance.")
 
         if not self._toolchain_exists():
-            self.log.error("No module found for toolchain: %s" % self.mod_short_name)
+            raise EasyBuildError("No module found for toolchain: %s", self.mod_short_name)
 
         if self.name == DUMMY_TOOLCHAIN_NAME:
             if self.version == DUMMY_TOOLCHAIN_VERSION:
@@ -373,8 +373,8 @@ def prepare(self, onlymod=None):
         if all(map(self.is_dep_in_toolchain_module, toolchain_definition)):
             self.log.info("List of toolchain dependency modules and toolchain definition match!")
         else:
-            self.log.error("List of toolchain dependency modules and toolchain definition do not match " \
-                           "(%s vs %s)" % (self.toolchain_dep_mods, toolchain_definition))
+            raise EasyBuildError("List of toolchain dependency modules and toolchain definition do not match "
+                                 "(%s vs %s)", self.toolchain_dep_mods, toolchain_definition)
 
         # Generate the variables to be set
         self.set_variables()
@@ -426,8 +426,7 @@ def _setenv_variables(self, donotset=None):
         donotsetlist = []
         if isinstance(donotset, str):
             # TODO : more legacy code that should be using proper type
-            self.log.error("_setenv_variables: using commas-separated list. should be deprecated.")
-            donotsetlist = donotset.split(',')
+            raise EasyBuildError("_setenv_variables: using commas-separated list. should be deprecated.")
         elif isinstance(donotset, list):
             donotsetlist = donotset
 
diff --git a/easybuild/tools/toolchain/utilities.py b/easybuild/tools/toolchain/utilities.py
index a1ab08074b..73bf78c7c1 100644
--- a/easybuild/tools/toolchain/utilities.py
+++ b/easybuild/tools/toolchain/utilities.py
@@ -40,6 +40,7 @@
 from vsc.utils.missing import get_subclasses, nub
 
 import easybuild.tools.toolchain
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.toolchain.toolchain import Toolchain
 from easybuild.tools.utilities import import_available_modules
 
@@ -83,13 +84,13 @@ def search_toolchain(name):
                     if res:
                         tc_const_name = res.group(1)
                         tc_const_value = getattr(mod_class_mod, elem)
-                        tup = (tc_const_name, tc_const_value, mod_class_mod.__name__, package.__name__)
-                        _log.debug("Found constant %s ('%s') in module %s, adding it to %s" % tup)
+                        _log.debug("Found constant %s ('%s') in module %s, adding it to %s",
+                                   tc_const_name, tc_const_value, mod_class_mod.__name__, package.__name__)
                         if hasattr(package, tc_const_name):
                             cur_value = getattr(package, tc_const_name)
                             if not tc_const_value == cur_value:
-                                tup = (package.__name__, tc_const_name, cur_value, tc_const_value)
-                                _log.error("Constant %s.%s defined as '%s', can't set it to '%s'." % tup)
+                                raise EasyBuildError("Constant %s.%s defined as '%s', can't set it to '%s'.",
+                                                     package.__name__, tc_const_name, cur_value, tc_const_value)
                         else:
                             setattr(package, tc_const_name, tc_const_value)
 
@@ -124,7 +125,7 @@ def get_toolchain(tc, tcopts, mns):
         tc_class, all_tcs = search_toolchain(tc['name'])
         if not tc_class:
             all_tcs_names = ",".join([x.NAME for x in all_tcs])
-            _log.error("Toolchain %s not found, available toolchains: %s" % (tc['name'], all_tcs_names))
+            raise EasyBuildError("Toolchain %s not found, available toolchains: %s", tc['name'], all_tcs_names)
         tc_inst = tc_class(version=tc['version'], mns=mns)
         tc_dict = tc_inst.as_dict()
         _log.debug("Obtained new toolchain instance for %s: %s" % (key, tc_dict))
diff --git a/easybuild/tools/toolchain/variables.py b/easybuild/tools/toolchain/variables.py
index 7b2722e7bf..cdee3ea41b 100644
--- a/easybuild/tools/toolchain/variables.py
+++ b/easybuild/tools/toolchain/variables.py
@@ -29,6 +29,7 @@
 @author: Kenneth Hoste (Ghent University)
 """
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.variables import StrList, AbsPathList
 
 
@@ -141,7 +142,7 @@ def _toggle_map(self, toggle_map, name, descr, idx=None):
                 else:
                     self.insert(idx, toggle_map[name])
             else:
-                self.log.raiseException("%s name %s not found in map %s" % (descr, name, toggle_map))
+                raise EasyBuildError("%s name %s not found in map %s", descr, name, toggle_map)
 
     def toggle_startgroup(self):
         """Append start group"""
diff --git a/easybuild/tools/variables.py b/easybuild/tools/variables.py
index 7b686a8cf4..6d5941c473 100644
--- a/easybuild/tools/variables.py
+++ b/easybuild/tools/variables.py
@@ -29,9 +29,12 @@
 @author: Stijn De Weirdt (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
-from vsc.utils import fancylogger
 import copy
 import os
+from vsc.utils import fancylogger
+
+from easybuild.tools.build_log import EasyBuildError
+
 
 _log = fancylogger.getLogger('variables', fname=False)
 
@@ -62,20 +65,20 @@ def join_map_class(map_classes):
     """Join all class_maps into single class_map"""
     res = {}
     for map_class in map_classes:
-        for k, v in map_class.items():
-            if isinstance(k, (str,)):
-                var_name = k
-                if isinstance(v, (tuple, list)):
+        for key, val in map_class.items():
+            if isinstance(key, (str,)):
+                var_name = key
+                if isinstance(val, (tuple, list)):
                     # second element is documentation
-                    klass = v[0]
+                    klass = val[0]
                 res[var_name] = klass
-            elif type(k) in (type,):
+            elif type(key) in (type,):
                 # k is the class, v a list of tuples (name,doc)
-                klass = k
+                klass = key
                 default = res.setdefault(klass, [])
-                default.extend([tpl[0] for tpl in v])
+                default.extend([tpl[0] for tpl in val])
             else:
-                _log.raiseException("join_map_class: impossible to join key %s value %s" % (k, v))
+                raise EasyBuildError("join_map_class: impossible to join key %s value %s", key, val)
 
     return res
 
@@ -304,7 +307,7 @@ def nextend(self, value=None, **kwargs):
         res = []
         if value is None:
             # TODO ? append_empty ?
-            self.log.raiseException("extend_el with None value unimplemented")
+            raise EasyBuildError("extend_el with None value unimplemented")
         else:
             for el in value:
                 if not self._str_ok(el):
@@ -484,7 +487,7 @@ def join(self, name, *others):
                 for el in self.get(other):
                     self.nappend(name, el)
             else:
-                self.log.raiseException("join: name %s; other %s not found in self." % (name, other))
+                raise EasyBuildError("join: name %s; other %s not found in self.", name, other)
 
     def append(self, name, value):
         """Append value to element name (alias for nappend)"""
diff --git a/test/framework/sandbox/easybuild/easyblocks/toy.py b/test/framework/sandbox/easybuild/easyblocks/toy.py
index 49fcc4b1d4..43d9eebe1c 100644
--- a/test/framework/sandbox/easybuild/easyblocks/toy.py
+++ b/test/framework/sandbox/easybuild/easyblocks/toy.py
@@ -33,10 +33,12 @@
 import shutil
 
 from easybuild.framework.easyblock import EasyBlock
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import mkdir
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.run import run_cmd
 
+
 class EB_toy(EasyBlock):
     """Support for building/installing toy."""
 
@@ -55,7 +57,7 @@ def configure_step(self, name=None):
         # make sure Python system dep is handled correctly when specified
         if self.cfg['allow_system_deps']:
             if get_software_root('Python') != 'Python' or get_software_version('Python') != platform.python_version():
-                self.log.error("Sanity check on allowed Python system dep failed.")
+                raise EasyBlock("Sanity check on allowed Python system dep failed.")
         os.rename('%s.source' % name, '%s.c' % name)
 
     def build_step(self, name=None):
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index abecae9f89..72e5b320d8 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -240,7 +240,7 @@ def test_toy_buggy_easyblock(self):
             'verify': False,
             'verbose': False,
         }
-        err_regex = r"crashed with an error.*Traceback[\S\s]*toy_buggy.py.*build_step[\S\s]*global name 'run_cmd'"
+        err_regex = r"Traceback[\S\s]*toy_buggy.py.*build_step[\S\s]*global name 'run_cmd'"
         self.assertErrorRegex(EasyBuildError, err_regex, self.test_toy_build, **kwargs)
 
     def test_toy_build_formatv2(self):

From aa6f16caba609be49ba9bfc5525ebc854f3196d0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 26 Mar 2015 16:18:15 +0100
Subject: [PATCH 0792/1356] style fixes

---
 easybuild/framework/easyblock.py              | 14 ++++++-------
 easybuild/framework/easyconfig/easyconfig.py  | 21 ++++++++-----------
 .../framework/easyconfig/format/format.py     |  7 +++----
 easybuild/framework/easyconfig/format/one.py  |  3 +--
 .../easyconfig/format/pyheaderconfigobj.py    |  2 +-
 .../framework/easyconfig/format/version.py    | 16 +++++++-------
 easybuild/framework/easyconfig/parser.py      |  6 +++---
 easybuild/framework/easyconfig/tweak.py       |  8 +++----
 easybuild/main.py                             |  6 +++---
 easybuild/scripts/clean_gists.py              |  6 +++---
 easybuild/toolchains/linalg/acml.py           |  2 +-
 easybuild/tools/convert.py                    |  6 +++---
 easybuild/tools/filetools.py                  |  2 +-
 easybuild/tools/modules.py                    |  4 ++--
 easybuild/tools/robot.py                      | 12 +++++------
 15 files changed, 53 insertions(+), 62 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index ddb62e17dc..dc217e49d0 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -423,7 +423,7 @@ def fetch_extension_sources(self):
                             exts_sources.append(ext_src)
 
                         else:
-                            raise EasyBuildError("Source for extension %s not found.")
+                            raise EasyBuildError("Source for extension %s not found.", ext)
 
             elif isinstance(ext, basestring):
                 exts_sources.append({'name': ext})
@@ -655,8 +655,7 @@ def make_builddir(self):
             # self.builddir should be already set by gen_builddir()
             if not self.builddir:
                 raise EasyBuildError("self.builddir not set, make sure gen_builddir() is called first!")
-            self.log.debug("Creating the build directory %s (cleanup: %s)",
-                           self.builddir, self.cfg['cleanupoldbuild'])
+            self.log.debug("Creating the build directory %s (cleanup: %s)", self.builddir, self.cfg['cleanupoldbuild'])
         else:
             self.log.info("Changing build dir to %s" % self.installdir)
             self.builddir = self.installdir
@@ -1432,9 +1431,8 @@ def extensions_step(self, fetch=False):
                     self.log.debug("Installing extension %s with default class %s (from %s)",
                                    ext['name'], default_class, default_class_modpath)
                 except (ImportError, NameError), err:
-                    msg = "Also failed to use default class %s from %s for extension %s: %s, giving up" % \
-                        (default_class, default_class_modpath, ext['name'], err)
-                    raise EasyBuildError(msg)
+                    raise EasyBuildError("Also failed to use default class %s from %s for extension %s: %s, giving up",
+                                         default_class, default_class_modpath, ext['name'], err)
             else:
                 self.log.debug("Installing extension %s with class %s (from %s)" % (ext['name'], class_name, mod_path))
 
@@ -1524,8 +1522,8 @@ def sanity_check_step(self, custom_paths=None, custom_commands=None, extension=F
         lenvals = [len(x) for x in paths.values()]
         req_keys = sorted(path_keys_and_check.keys())
         if not ks == req_keys or sum(valnottypes) > 0 or sum(lenvals) == 0:
-            raise EasyBuildError("Incorrect format for sanity_check_paths (should have %s keys, "
-                           "values should be lists (at least one non-empty))." % '/'.join(req_keys))
+            raise EasyBuildError("Incorrect format for sanity_check_paths (should (only) have %s keys, "
+                                 "values should be lists (at least one non-empty)).", ','.join(req_keys))
 
         for key, check_fn in path_keys_and_check.items():
             for xs in paths[key]:
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index cf5f9e4fbd..dcfc756a0a 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -250,8 +250,8 @@ def parse(self):
 
         typos = [(key, guesses[0]) for (key, guesses) in possible_typos if len(guesses) == 1]
         if typos:
-            raise EasyBuildError("You may have some typos in your easyconfig file: %s" %
-                            ', '.join(["%s -> %s" % typo for typo in typos]))
+            raise EasyBuildError("You may have some typos in your easyconfig file: %s",
+                                 ', '.join(["%s -> %s" % typo for typo in typos]))
 
         # we need toolchain to be set when we call _parse_dependency
         for key in ['toolchain'] + local_vars.keys():
@@ -304,8 +304,8 @@ def validate(self, check_osdeps=True):
 
         self.log.info("Checking skipsteps")
         if not isinstance(self._config['skipsteps'][0], (list, tuple,)):
-            raise EasyBuildError('Invalid type for skipsteps. Allowed are list or tuple, got %s (%s)' %
-                           (type(self._config['skipsteps'][0]), self._config['skipsteps'][0]))
+            raise EasyBuildError('Invalid type for skipsteps. Allowed are list or tuple, got %s (%s)',
+                                 type(self._config['skipsteps'][0]), self._config['skipsteps'][0])
 
         self.log.info("Checking build option lists")
         self.validate_iterate_opts_lists()
@@ -321,8 +321,8 @@ def validate_license(self):
             if 'software_license' in self.mandatory:
                 raise EasyBuildError("License is mandatory, but 'software_license' is undefined")
         elif not isinstance(lic, License):
-            raise EasyBuildError('License %s has to be a License subclass instance, found classname %s.' %
-                           (lic, lic.__class__.__name__))
+            raise EasyBuildError('License %s has to be a License subclass instance, found classname %s.',
+                                 lic, lic.__class__.__name__)
         elif not lic.name in EASYCONFIG_LICENSES_DICT:
             raise EasyBuildError('Invalid license %s (classname: %s).', lic.name, lic.__class__.__name__)
 
@@ -586,11 +586,9 @@ def _parse_dependency(self, dep, hidden=False):
                 if 'name' in tc_spec and 'version' in tc_spec:
                     tc = copy.deepcopy(tc_spec)
                 else:
-                    raise EasyBuildError("Found toolchain spec as dict with required 'name'/'version' keys: %s",
-                                         tc_spec)
+                    raise EasyBuildError("Found toolchain spec as dict with wrong keys (no name/version): %s", tc_spec)
             else:
-                raise EasyBuildError("Unsupported type for toolchain spec encountered: %s => %s",
-                                     tc_spec, type(tc_spec))
+                raise EasyBuildError("Unsupported type for toolchain spec encountered: %s (%s)", tc_spec, type(tc_spec))
 
         dependency['toolchain'] = tc
 
@@ -896,8 +894,7 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False,
         try:
             ec = EasyConfig(spec, build_specs=build_specs, validate=validate, hidden=hidden)
         except EasyBuildError, err:
-            msg = "Failed to process easyconfig %s:\n%s" % (spec, err.msg)
-            raise EasyBuildError(msg)
+            raise EasyBuildError("Failed to process easyconfig %s: %s", spec, err.msg)
 
         name = ec['name']
 
diff --git a/easybuild/framework/easyconfig/format/format.py b/easybuild/framework/easyconfig/format/format.py
index 13dcaa6ddf..01bc6a4268 100644
--- a/easybuild/framework/easyconfig/format/format.py
+++ b/easybuild/framework/easyconfig/format/format.py
@@ -243,14 +243,13 @@ def parse_sections(self, toparse, current):
                     new_value = []
                     for dep_name, dep_val in value.items():
                         if isinstance(dep_val, Section):
-                            raise EasyBuildError("Unsupported nested section '%s' found in dependencies section",
-                                                 dep_name)
+                            raise EasyBuildError("Unsupported nested section '%s' in dependencies section", dep_name)
                         else:
                             # FIXME: parse the dependency specification for version, toolchain, suffix, etc.
                             dep = Dependency(dep_val, name=dep_name)
                             if dep.name() is None or dep.version() is None:
-                                tmpl = "Failed to find name/version in parsed dependency: %s (dict: %s)"
-                                raise EasyBuildError(tmpl, dep, dict(dep))
+                                raise EasyBuildError("Failed to find name/version in parsed dependency: %s (dict: %s)",
+                                                     dep, dict(dep))
                             new_value.append(dep)
 
                     tmpl = 'Converted dependency section %s to %s, passed it to parent section (or default)'
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 5fca21b5b7..da8277b175 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -124,8 +124,7 @@ def retrieve_blocks_in_spec(spec, only_blocks, silent=False):
             block_contents = pieces.pop(0)
 
             if block_name in [b['name'] for b in blocks]:
-                msg = "Found block %s twice in %s." % (block_name, spec)
-                raise EasyBuildError(msg)
+                raise EasyBuildError("Found block %s twice in %s.", block_name, spec)
 
             block = {'name': block_name, 'contents': block_contents}
 
diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index 3159e1a273..78d80be3e4 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -69,7 +69,7 @@ def build_easyconfig_constants_dict():
                 const_dict[cst_key] = cst_val
 
     if len(err) > 0:
-        raise EasyBuildError("EasyConfig constants sanity check failed: %s", "\n".join(err))
+        raise EasyBuildError("EasyConfig constants sanity check failed: %s", '\n'.join(err))
     else:
         return const_dict
 
diff --git a/easybuild/framework/easyconfig/format/version.py b/easybuild/framework/easyconfig/format/version.py
index 7e1891f69a..e4252ce460 100644
--- a/easybuild/framework/easyconfig/format/version.py
+++ b/easybuild/framework/easyconfig/format/version.py
@@ -81,7 +81,7 @@ def __init__(self, versop_str=None, error_on_parse_failure=False):
         """
         Initialise VersionOperator instance.
         @param versop_str: intialise with version operator string
-        raise EasyBuildError in case of parse error
+        @param error_on_parse_failure: raise EasyBuildError in case of parse error
         """
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
@@ -312,8 +312,8 @@ def test_overlap_and_conflict(self, versop_other):
         versop_msg = "this versop %s and versop_other %s" % (self, versop_other)
 
         if not isinstance(versop_other, self.__class__):
-            raise EasyBuildError('overlap/conflict check needs instance of self %s (got type %s)' %
-                           (self.__class__.__name__, type(versop_other)))
+            raise EasyBuildError("overlap/conflict check needs instance of self %s (got type %s)",
+                                 self.__class__.__name__, type(versop_other))
 
         if self == versop_other:
             self.log.debug("%s are equal. Return overlap True, conflict False." % versop_msg)
@@ -425,7 +425,7 @@ def _gt_safe(self, version_gt_op, versop_other):
             Suffix are not considered.
         """
         if len(self.ORDERED_OPERATORS) != len(self.OPERATOR_MAP):
-            raise EasyBuildError('Inconsistency between ORDERED_OPERATORS and OPERATORS (lists are not of same length)')
+            raise EasyBuildError("Inconsistency between ORDERED_OPERATORS and OPERATORS (lists are not of same length)")
 
         # ensure this function is only used for non-conflicting version operators
         _, conflict = self.test_overlap_and_conflict(versop_other)
@@ -632,9 +632,9 @@ def add(self, versop_new, data=None, update=None):
             gt_test = [versop_new > versop for versop in self.versops]
             if None in gt_test:
                 # conflict
-                msg = 'add: conflict(s) between versop_new %s and existing versions %s'
                 conflict_versops = [(idx, self.versops[idx]) for idx, gt_val in enumerate(gt_test) if gt_val is None]
-                raise EasyBuildError(msg, versop_new, conflict_versops)
+                raise EasyBuildError("add: conflict(s) between versop_new %s and existing versions %s",
+                                     versop_new, conflict_versops)
             else:
                 if True in gt_test:
                     # determine first element for which comparison is True
@@ -665,11 +665,11 @@ def _add_data(self, versop_new, data, update):
     def get_data(self, versop):
         """Return the data for versop from datamap"""
         if not isinstance(versop, VersionOperator):
-            raise EasyBuildError(("get_data: argument must be a VersionOperator instance: %s; type %s"),
+            raise EasyBuildError("get_data: argument must be a VersionOperator instance: %s; type %s",
                                   versop, type(versop))
 
         versop_str = str(versop)
         if versop_str in self.datamap:
             return self.datamap[versop_str]
         else:
-            raise EasyBuildError('No data in datamap for versop %s', versop)
+            raise EasyBuildError("No data in datamap for versop %s", versop)
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index c73570323d..3937ad1833 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -149,8 +149,8 @@ def _get_format_version_class(self):
         elif not found_classes:
             raise EasyBuildError('No format classes found matching version %s', self.format_version)
         else:
-            msg = 'More than one format class found matching version %s in %s' % (self.format_version, found_classes)
-            raise EasyBuildError(msg)
+            raise EasyBuildError("More than one format class found matching version %s in %s",
+                                 self.format_version, found_classes)
 
     def _set_formatter(self):
         """Obtain instance of the formatter"""
@@ -172,7 +172,7 @@ def write(self, filename=None):
         try:
             self.set_fn[0](*self.set_fn[1])
         except IOError, err:
-            raise EasyBuildError('Failed to process content with %s: %s', self.set_fn, err)
+            raise EasyBuildError("Failed to process content with %s: %s", self.set_fn, err)
 
     def set_specifications(self, specs):
         """Set specifications."""
diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 130af934e5..552c42471e 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -393,8 +393,8 @@ def unique(l):
         if EASYCONFIG_TEMPLATE in tcnames:
             _log.info("No easyconfig file for specified toolchain, but template is available.")
         else:
-            raise EasyBuildError("No easyconfig file for %s with toolchain %s, " \
-                      "and no template available." % (name, specs['toolchain_name']))
+            raise EasyBuildError("No easyconfig file for %s with toolchain %s, and no template available.",
+                                 name, specs['toolchain_name'])
 
     tcname = specs.pop('toolchain_name', None)
     handled_params.append('toolchain_name')
@@ -500,9 +500,7 @@ def unique(l):
             filter_ecs = True
         else:
             # otherwise, we fail, because we don't know how to pick between different fixes
-            raise EasyBuildError("No %s specified, and can't pick from available %ses %s" % (param,
-                                                                                  param,
-                                                                                  vals))
+            raise EasyBuildError("No %s specified, and can't pick from available ones: %s", param, vals)
 
         if filter_ecs:
             _log.debug("Filtering easyconfigs based on %s '%s'..." % (param, selected_val))
diff --git a/easybuild/main.py b/easybuild/main.py
index 0005735c60..925e377bc2 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -88,9 +88,9 @@ def find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=
                 _log.warning("Failed to remove generated easyconfig file %s: %s" % (ec_file, err))
 
             # don't use a generated easyconfig unless generation was requested (using a --try-X option)
-            raise EasyBuildError(("Unable to find an easyconfig for the given specifications: %s; "
-                        "to make EasyBuild try to generate a matching easyconfig, "
-                        "use the --try-X options ") % build_specs)
+            raise EasyBuildError("Unable to find an easyconfig for the given specifications: %s; "
+                                 "to make EasyBuild try to generate a matching easyconfig, "
+                                 "use the --try-X options ", build_specs)
 
     return [(ec_file, generated)]
 
diff --git a/easybuild/scripts/clean_gists.py b/easybuild/scripts/clean_gists.py
index a254d36dff..ff903b4265 100755
--- a/easybuild/scripts/clean_gists.py
+++ b/easybuild/scripts/clean_gists.py
@@ -77,7 +77,7 @@ def main():
 
     if status != HTTP_STATUS_OK:
         raise EasyBuildError("Failed to get a lists of gists for user %s: error code %s, message = %s",
-                  username, status, gists)
+                             username, status, gists)
     else:
         log.info("Found %s gists", len(gists))
 
@@ -104,7 +104,7 @@ def main():
                     status, pr = gh.repos[GITHUB_EB_MAIN][GITHUB_EASYCONFIGS_REPO].pulls[pr_num].get()
                     if status != HTTP_STATUS_OK:
                         raise EasyBuildError("Failed to get pull-request #%s: error code %s, message = %s",
-                                  pr_num, status, pr)
+                                             pr_num, status, pr)
                     pr_cache[pr_num] = pr["state"]
 
                 if pr_cache[pr_num] == "closed":
@@ -120,7 +120,7 @@ def main():
 
             if status != HTTP_DELETE_OK:
                 raise EasyBuildError("Unable to remove gist (id=%s): error code %s, message = %s",
-                          gist["id"], status, del_gist)
+                                     gist["id"], status, del_gist)
             else:
                 log.info("Delete gist with id=%s", gist["id"])
                 num_deleted += 1
diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index d561bc826f..9594fa428a 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -71,7 +71,7 @@ def _set_blas_variables(self):
                 self.variables.append_exists('CPPFLAGS', root, incdirs, append_all=True)
         except:
             raise EasyBuildError("_set_blas_variables: ACML set LDFLAGS/CPPFLAGS unknown entry in ACML_SUBDIRS_MAP "
-                                 " with compiler family %s", self.COMPILER_FAMILY)
+                                 "with compiler family %s", self.COMPILER_FAMILY)
 
         # version before 5.x still featured the acml_mv library
         ver = self.get_software_version(self.BLAS_MODULE_NAME)[0]
diff --git a/easybuild/tools/convert.py b/easybuild/tools/convert.py
index 037595ff29..b4a2304597 100644
--- a/easybuild/tools/convert.py
+++ b/easybuild/tools/convert.py
@@ -59,7 +59,7 @@ def __init__(self, obj):
         if isinstance(obj, basestring):
             self.data = self._from_string(obj)
         else:
-            raise EasyBuildError('unsupported type %s for %s: %s', type(obj), self.__class__.__name__, obj)
+            raise EasyBuildError("unsupported type %s for %s: %s", type(obj), self.__class__.__name__, obj)
         super(Convert, self).__init__(self.data)
 
     def _split_string(self, txt, sep=None, max=0):
@@ -69,7 +69,7 @@ def _split_string(self, txt, sep=None, max=0):
         """
         if sep is None:
             if self.SEPARATOR is None:
-                raise EasyBuildError('No SEPARATOR set, also no separator passed')
+                raise EasyBuildError("No SEPARATOR set, also no separator passed")
             else:
                 sep = self.SEPARATOR
         return [x.strip() for x in re.split(r'' + sep, txt, maxsplit=max)]
@@ -224,4 +224,4 @@ def get_convert_class(class_name):
     if len(res) == 1:
         return res[0]
     else:
-        raise EasyBuildError('More then one Convert subclass found for name %s: %s', class_name, res)
+        raise EasyBuildError("More than one Convert subclass found for name %s: %s", class_name, res)
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 25754949bb..7e9ef95891 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -44,7 +44,7 @@
 from vsc.utils import fancylogger
 
 import easybuild.tools.environment as env
-from easybuild.tools.build_log import EasyBuildError, print_msg  # import build_log must stay, to activate use of EasyBuildLog
+from easybuild.tools.build_log import EasyBuildError, print_msg  # import build_log must stay, to use of EasyBuildLog
 from easybuild.tools.config import build_option
 from easybuild.tools import run
 
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 8396f72963..a8b0e9fbb7 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -491,8 +491,8 @@ def run_module(self, *args, **kwargs):
         cmdlist = [self.cmd, 'python']
         if self.COMMAND_SHELL is not None:
             if not isinstance(self.COMMAND_SHELL, (list, tuple)):
-                msg = 'COMMAND_SHELL needs to be list or tuple, now %s (value %s)'
-                raise EasyBuildError(msg, type(self.COMMAND_SHELL), self.COMMAND_SHELL)
+                raise EasyBuildError("COMMAND_SHELL needs to be list or tuple, now %s (value %s)",
+                                     type(self.COMMAND_SHELL), self.COMMAND_SHELL)
             cmdlist = self.COMMAND_SHELL + cmdlist
 
         full_cmd = ' '.join(cmdlist + args)
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index c872fbd2ef..d4f3799b81 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -153,8 +153,8 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
         # make sure this stops, we really don't want to get stuck in an infinite loop
         loopcnt += 1
         if loopcnt > maxloopcnt:
-            msg = "Maximum loop cnt %s reached, so quitting (unprocessed: %s, irresolvable: %s)"
-            raise EasyBuildError(msg, maxloopcnt, unprocessed, irresolvable)
+            raise EasyBuildError("Maximum loop cnt %s reached, so quitting (unprocessed: %s, irresolvable: %s)",
+                                 maxloopcnt, unprocessed, irresolvable)
 
         # first try resolving dependencies without using external dependencies
         last_processed_count = -1
@@ -205,8 +205,8 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
                         mods = [spec['ec'].full_mod_name for spec in processed_ecs]
                         dep_mod_name = ActiveMNS().det_full_module_name(cand_dep)
                         if not dep_mod_name in mods:
-                            msg = "easyconfig file %s does not contain module %s (mods: %s)"
-                            raise EasyBuildError(msg, path, dep_mod_name, mods)
+                            raise EasyBuildError("easyconfig file %s does not contain module %s (mods: %s)",
+                                                 path, dep_mod_name, mods)
 
                         for ec in processed_ecs:
                             if not ec in unprocessed + additional:
@@ -229,9 +229,9 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
         irresolvable_mods_eb = [EasyBuildMNS().det_full_module_name(dep) for dep in irresolvable]
         _log.warning("Irresolvable dependencies (EasyBuild module names): %s" % ', '.join(irresolvable_mods_eb))
         irresolvable_mods = [ActiveMNS().det_full_module_name(dep) for dep in irresolvable]
-        raise EasyBuildError('Irresolvable dependencies encountered: %s', ', '.join(irresolvable_mods))
+        raise EasyBuildError("Irresolvable dependencies encountered: %s", ', '.join(irresolvable_mods))
 
-    _log.info("Dependency resolution complete, building as follows:\n%s" % ordered_ecs)
+    _log.info("Dependency resolution complete, building as follows: %s" % ordered_ecs)
     return ordered_ecs
 
 

From 22e28e58b3e3d689ebf698477d7531b0064c1f30 Mon Sep 17 00:00:00 2001
From: Gianluca Santarossa <gianluca.santarossa@gmail.com>
Date: Wed, 11 Feb 2015 15:10:02 +0100
Subject: [PATCH 0793/1356] Added first version of experimental support for
 package_step (based on code by Marc Litherland)

Update easyblock.py

Bug fixes round #1

bugfixing round #2

Bugfixes round #3

Bugfixes round #4

Bugfixes #5. Rewritten map() as list comprehension. Still not available as an optional parameter
---
 easybuild/framework/easyblock.py | 26 ++++++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index f0cf43bb0b..dcaee49fca 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -77,7 +77,6 @@
 from easybuild.tools.utilities import remove_unwanted_chars
 from easybuild.tools.version import this_is_easybuild, VERBOSE_VERSION, VERSION
 
-
 _log = fancylogger.getLogger('easyblock')
 
 
@@ -1444,8 +1443,19 @@ def extensions_step(self, fetch=False):
         self.clean_up_fake_module(fake_mod_data)
 
     def package_step(self):
-        """Package software (e.g. into an RPM)."""
-        pass
+        """Prepare package software (e.g. into an RPM) with fpm."""
+        rpmname = "HPCBIOS.20150211-%s-%s" % (self.name, self.version)
+        os.chdir(os.environ['TMPDIR'])
+        
+        if self.toolchain.name == "dummy":
+            dependencies = []
+        else:
+            dependencies = [ "=".join([ self.toolchain.name, self.toolchain.version ]) ]
+        dependencies.extend([ "=".join([ dep['name'], dep['version'] ]) for dep in self.cfg.dependencies() ])
+        depstring = '--dependency ' + ' --dependency '.join(dependencies)
+
+        cmd = "fpm --workdir $TMPDIR -t rpm --name %s -s dir %s -C %s" % (rpmname, depstring, self.installdir)
+        (out, _) = run_cmd(cmd, log_all=True, simple=False)
 
     def post_install_step(self):
         """
@@ -1787,11 +1797,11 @@ def prepare_step_spec(initial):
         # part 3: post-iteration part
         steps_part3 = [
             ('extensions', 'taking care of extensions', [lambda x: x.extensions_step()], False),
-            ('package', 'packaging', [lambda x: x.package_step()], True),
             ('postproc', 'postprocessing', [lambda x: x.post_install_step()], True),
             ('sanitycheck', 'sanity checking', [lambda x: x.sanity_check_step()], False),
             ('cleanup', 'cleaning up', [lambda x: x.cleanup_step()], False),
             ('module', 'creating module', [lambda x: x.make_module_step()], False),
+            # ('package', 'packaging', [lambda x: x.package_step()], True),
         ]
 
         # full list of steps, included iterated steps
@@ -1803,6 +1813,14 @@ def prepare_step_spec(initial):
                 lambda x: x.test_cases_step(),
             ], False))
 
+        ## CHANGE TRUE TO build_option, and 
+        ## ADD build-pkg to all the configuration dicts
+        ## # if build_option('build-pkg'):
+        if True:
+            steps.append(('package', 'packaging', [lambda x: x.package_step()], True))
+        else:
+            self.log.debug('Skipping package step')
+
         return steps
 
     def run_all_steps(self, run_test_cases):

From 46ad3997d5650ed1a12975236f71ec6aad3ae862 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Sat, 21 Feb 2015 23:02:11 -0500
Subject: [PATCH 0794/1356] adding a new fpm packaging function

---
 easybuild/framework/easyblock.py | 15 +++------
 easybuild/framework/package.py   | 58 ++++++++++++++++++++++++++++++++
 2 files changed, 62 insertions(+), 11 deletions(-)
 create mode 100644 easybuild/framework/package.py

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index dcaee49fca..37e6ef1a6d 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -56,6 +56,7 @@
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP
+from easybuild.framework.package import package_fpm
 from easybuild.tools.build_details import get_build_stats
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
@@ -1444,18 +1445,10 @@ def extensions_step(self, fetch=False):
 
     def package_step(self):
         """Prepare package software (e.g. into an RPM) with fpm."""
-        rpmname = "HPCBIOS.20150211-%s-%s" % (self.name, self.version)
-        os.chdir(os.environ['TMPDIR'])
-        
-        if self.toolchain.name == "dummy":
-            dependencies = []
-        else:
-            dependencies = [ "=".join([ self.toolchain.name, self.toolchain.version ]) ]
-        dependencies.extend([ "=".join([ dep['name'], dep['version'] ]) for dep in self.cfg.dependencies() ])
-        depstring = '--dependency ' + ' --dependency '.join(dependencies)
 
-        cmd = "fpm --workdir $TMPDIR -t rpm --name %s -s dir %s -C %s" % (rpmname, depstring, self.installdir)
-        (out, _) = run_cmd(cmd, log_all=True, simple=False)
+        path_to_module_file = os.path.join(install_path('mod'), build_option('suffix_modules_path'), self.full_mod_name)
+
+        package_fpm(self, path_to_module_file)
 
     def post_install_step(self):
         """
diff --git a/easybuild/framework/package.py b/easybuild/framework/package.py
new file mode 100644
index 0000000000..446a88ba48
--- /dev/null
+++ b/easybuild/framework/package.py
@@ -0,0 +1,58 @@
+# #
+# Copyright 2009-2014 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+
+"""
+A place for packaging functions
+
+"""
+
+import os
+
+def package_fpm(easyblock,modfile_path ):
+    rpmname = "HPCBIOS.20150211-%s-%s" % (easyblock.name, easyblock.version)
+    os.chdir("/tmp")
+
+    if easyblock.toolchain.name == "dummy":
+        dependencies = []
+    else:
+        dependencies = [ "=".join([ easyblock.toolchain.name, easyblock.toolchain.version ]) ]
+    dependencies.extend([ "=".join([ dep['name'], dep['version'] ]) for dep in easyblock.cfg.dependencies() ])
+    depstring = '--depends ' + ' --depends '.join(dependencies)
+    cmdlist=[
+        'fpm',
+        '--workdir', workdir,
+        '--name', pkgname,
+
+    ]
+    cmdlist.extend(' --depends '.join(dependencies))
+    [
+        '-t', flavour, # target
+        '-s', 'dir', # source
+        '-C', easyblock.installdir,
+    ]
+    cmdlist.extend(deplist)
+
+    cmd = "fpm --workdir /tmp --name %s %s -s dir -t rpm -C %s ." % (rpmname, depstring, easyblock.installdir)
+    (out, _) = run_cmd(cmd, log_all=True, simple=False)

From e86ca6a3e46668383944133df21f0ffe68575913 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Mon, 23 Feb 2015 14:55:31 -0500
Subject: [PATCH 0795/1356] trying to teplate out the name and make a command
 list

---
 easybuild/framework/package.py | 23 +++++++++++++++--------
 1 file changed, 15 insertions(+), 8 deletions(-)

diff --git a/easybuild/framework/package.py b/easybuild/framework/package.py
index 446a88ba48..708d23490e 100644
--- a/easybuild/framework/package.py
+++ b/easybuild/framework/package.py
@@ -29,10 +29,19 @@
 """
 
 import os
+from easybuild.tools.run import run_cmd
 
-def package_fpm(easyblock,modfile_path ):
+def package_fpm(easyblock, modfile_path ):
     rpmname = "HPCBIOS.20150211-%s-%s" % (easyblock.name, easyblock.version)
-    os.chdir("/tmp")
+    workdir = "/tmp"
+    os.chdir(workdir)
+
+    pkgtemplate = "HPCBIOS.20150211-%(name)s-%(version)s"
+
+    pkgname=pkgtemplate % {
+        'name' : easyblock.name,
+        'version' : easyblock.version,
+    }
 
     if easyblock.toolchain.name == "dummy":
         dependencies = []
@@ -47,12 +56,10 @@ def package_fpm(easyblock,modfile_path ):
 
     ]
     cmdlist.extend(' --depends '.join(dependencies))
-    [
-        '-t', flavour, # target
+    cmdlist.extend([
+        '-t', 'rpm', # target
         '-s', 'dir', # source
         '-C', easyblock.installdir,
-    ]
-    cmdlist.extend(deplist)
+    ])
 
-    cmd = "fpm --workdir /tmp --name %s %s -s dir -t rpm -C %s ." % (rpmname, depstring, easyblock.installdir)
-    (out, _) = run_cmd(cmd, log_all=True, simple=False)
+    (out, _) = run_cmd(cmdlist, log_all=True, simple=False)

From 8f62f859b94757c76d7096d9ff68cc66860f60d2 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Tue, 3 Mar 2015 09:46:26 -0500
Subject: [PATCH 0796/1356] adding some updates

---
 easybuild/framework/package.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/package.py b/easybuild/framework/package.py
index 708d23490e..658914d1c5 100644
--- a/easybuild/framework/package.py
+++ b/easybuild/framework/package.py
@@ -53,13 +53,13 @@ def package_fpm(easyblock, modfile_path ):
         'fpm',
         '--workdir', workdir,
         '--name', pkgname,
-
-    ]
-    cmdlist.extend(' --depends '.join(dependencies))
-    cmdlist.extend([
         '-t', 'rpm', # target
         '-s', 'dir', # source
         '-C', easyblock.installdir,
+    ]
+    cmdlist.extend([ depstring ])
+    cmdlist.extend([
+        easyblock.installdir,
     ])
 
     (out, _) = run_cmd(cmdlist, log_all=True, simple=False)

From 2a850a7d7000639fe4dabaadec0e2cc37d958fe1 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Tue, 17 Mar 2015 10:02:28 -0400
Subject: [PATCH 0797/1356] update tmp directory generator

---
 easybuild/framework/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/package.py b/easybuild/framework/package.py
index 658914d1c5..ca9ff8fe76 100644
--- a/easybuild/framework/package.py
+++ b/easybuild/framework/package.py
@@ -33,7 +33,7 @@
 
 def package_fpm(easyblock, modfile_path ):
     rpmname = "HPCBIOS.20150211-%s-%s" % (easyblock.name, easyblock.version)
-    workdir = "/tmp"
+    workdir = tempfile.mkdtemp()
     os.chdir(workdir)
 
     pkgtemplate = "HPCBIOS.20150211-%(name)s-%(version)s"

From c2dd5fcbeb3a75dd2dc740a3d4629f70e550aaff Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Tue, 17 Mar 2015 10:11:38 -0400
Subject: [PATCH 0798/1356] cleanup per PR comments from @boegel

---
 easybuild/framework/easyblock.py                    |  3 +--
 .../{framework/package.py => tools/packaging.py}    | 13 ++++++-------
 2 files changed, 7 insertions(+), 9 deletions(-)
 rename easybuild/{framework/package.py => tools/packaging.py} (88%)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 37e6ef1a6d..b792fc471a 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -56,7 +56,7 @@
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP
-from easybuild.framework.package import package_fpm
+from easybuild.tools.packaging import package_fpm
 from easybuild.tools.build_details import get_build_stats
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
@@ -1794,7 +1794,6 @@ def prepare_step_spec(initial):
             ('sanitycheck', 'sanity checking', [lambda x: x.sanity_check_step()], False),
             ('cleanup', 'cleaning up', [lambda x: x.cleanup_step()], False),
             ('module', 'creating module', [lambda x: x.make_module_step()], False),
-            # ('package', 'packaging', [lambda x: x.package_step()], True),
         ]
 
         # full list of steps, included iterated steps
diff --git a/easybuild/framework/package.py b/easybuild/tools/packaging.py
similarity index 88%
rename from easybuild/framework/package.py
rename to easybuild/tools/packaging.py
index ca9ff8fe76..da5811c0ab 100644
--- a/easybuild/framework/package.py
+++ b/easybuild/tools/packaging.py
@@ -34,7 +34,10 @@
 def package_fpm(easyblock, modfile_path ):
     rpmname = "HPCBIOS.20150211-%s-%s" % (easyblock.name, easyblock.version)
     workdir = tempfile.mkdtemp()
-    os.chdir(workdir)
+    try:
+        os.chdir(workdir)
+    except OSError, err:
+        _log.error("Failed to chdir into workdir: %s : %s" % (workdir, err))
 
     pkgtemplate = "HPCBIOS.20150211-%(name)s-%(version)s"
 
@@ -42,11 +45,7 @@ def package_fpm(easyblock, modfile_path ):
         'name' : easyblock.name,
         'version' : easyblock.version,
     }
-
-    if easyblock.toolchain.name == "dummy":
-        dependencies = []
-    else:
-        dependencies = [ "=".join([ easyblock.toolchain.name, easyblock.toolchain.version ]) ]
+    dependencies = []
     dependencies.extend([ "=".join([ dep['name'], dep['version'] ]) for dep in easyblock.cfg.dependencies() ])
     depstring = '--depends ' + ' --depends '.join(dependencies)
     cmdlist=[
@@ -62,4 +61,4 @@ def package_fpm(easyblock, modfile_path ):
         easyblock.installdir,
     ])
 
-    (out, _) = run_cmd(cmdlist, log_all=True, simple=False)
+    (out, _) = run_cmd(cmdlist, log_all=True, simple=True)

From 390ddc73976443afccf99d587b2c1f2f6ec9eaf6 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Tue, 17 Mar 2015 10:17:56 -0400
Subject: [PATCH 0799/1356] adding authors

---
 easybuild/tools/packaging.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index da5811c0ab..07484b5c87 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -26,6 +26,9 @@
 """
 A place for packaging functions
 
+@author: Marc Litherland
+@author: Gianluca Santarossa 
+@author: Robert Schmidt (Ottawa Hospital Research Institute)
 """
 
 import os

From cdeef5191cbccdac5433486a3ceb50cf41ecdd99 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Wed, 18 Mar 2015 21:00:21 -0400
Subject: [PATCH 0800/1356] adding the package_with option

---
 easybuild/framework/easyblock.py | 3 ++-
 easybuild/tools/config.py        | 1 +
 easybuild/tools/options.py       | 1 +
 easybuild/tools/packaging.py     | 1 +
 4 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index b792fc471a..4d73e73d4d 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1808,7 +1808,8 @@ def prepare_step_spec(initial):
         ## CHANGE TRUE TO build_option, and 
         ## ADD build-pkg to all the configuration dicts
         ## # if build_option('build-pkg'):
-        if True:
+        packaging_tool = build_option('package_with')
+        if packaging_tool is not None:
             steps.append(('package', 'packaging', [lambda x: x.package_step()], True))
         else:
             self.log.debug('Skipping package step')
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 054b109d26..fcb4e41322 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -98,6 +98,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'test_report_env_filter',
         'testoutput',
         'umask',
+        'package_with',
     ],
     False: [
         'allow_modules_tool_mismatch',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 5dc144e522..76b51be40c 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -268,6 +268,7 @@ def config_options(self):
                            None, 'store', None),
             'tmp-logdir': ("Log directory where temporary log files are stored", None, 'store', None),
             'tmpdir': ('Directory to use for temporary storage', None, 'store', None),
+            'package-with': ("Define the packaging system to be used", None, 'store', None),
         })
 
         self.log.debug("config_options: descr %s opts %s" % (descr, opts))
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 07484b5c87..c97872ac9c 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -32,6 +32,7 @@
 """
 
 import os
+import tempfile
 from easybuild.tools.run import run_cmd
 
 def package_fpm(easyblock, modfile_path ):

From ddc3855844aea61a42629e7c1b56b2a138da9c23 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Thu, 19 Mar 2015 07:56:32 -0400
Subject: [PATCH 0801/1356] second try to get build_option working

---
 easybuild/framework/easyblock.py | 4 ++--
 easybuild/tools/config.py        | 2 +-
 easybuild/tools/options.py       | 3 ++-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 4d73e73d4d..1bf5a6f728 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1808,11 +1808,11 @@ def prepare_step_spec(initial):
         ## CHANGE TRUE TO build_option, and 
         ## ADD build-pkg to all the configuration dicts
         ## # if build_option('build-pkg'):
-        packaging_tool = build_option('package_with')
+        packaging_tool = build_option('package_tool')
         if packaging_tool is not None:
             steps.append(('package', 'packaging', [lambda x: x.package_step()], True))
         else:
-            self.log.debug('Skipping package step')
+            _log.debug('Skipping package step')
 
         return steps
 
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index fcb4e41322..3848bbab1c 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -91,6 +91,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'modules_footer',
         'only_blocks',
         'optarch',
+        'package_tool',
         'regtest_output_dir',
         'skip',
         'stop',
@@ -98,7 +99,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'test_report_env_filter',
         'testoutput',
         'umask',
-        'package_with',
     ],
     False: [
         'allow_modules_tool_mismatch',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 76b51be40c..de5a51cfd5 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -243,6 +243,8 @@ def config_options(self):
                                None, 'store_or_None', None, {'metavar': "PATH"}),
             'modules-tool': ("Modules tool to use",
                              'choice', 'store', DEFAULT_MODULES_TOOL, sorted(avail_modules_tools().keys())),
+            'package-tool': ("Packaging tool to use",
+                             None, 'store_or_None', None),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
                         "(used prefix for defaults %s)" % DEFAULT_PREFIX),
                        None, 'store', None),
@@ -268,7 +270,6 @@ def config_options(self):
                            None, 'store', None),
             'tmp-logdir': ("Log directory where temporary log files are stored", None, 'store', None),
             'tmpdir': ('Directory to use for temporary storage', None, 'store', None),
-            'package-with': ("Define the packaging system to be used", None, 'store', None),
         })
 
         self.log.debug("config_options: descr %s opts %s" % (descr, opts))

From a6abba7587de82bc9ac90e9b98cace03ebcf78d0 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Thu, 19 Mar 2015 21:15:00 -0400
Subject: [PATCH 0802/1356] moving the build_option to the packaging_step

---
 easybuild/framework/easyblock.py | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 1bf5a6f728..02068e17f0 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1448,7 +1448,12 @@ def package_step(self):
 
         path_to_module_file = os.path.join(install_path('mod'), build_option('suffix_modules_path'), self.full_mod_name)
 
-        package_fpm(self, path_to_module_file)
+        packaging_tool = build_option('package_tool')
+        if packaging_tool is not None:
+            package_fpm(self, path_to_module_file)
+        else:
+            _log.debug('Skipping package step')
+
 
     def post_install_step(self):
         """
@@ -1794,6 +1799,7 @@ def prepare_step_spec(initial):
             ('sanitycheck', 'sanity checking', [lambda x: x.sanity_check_step()], False),
             ('cleanup', 'cleaning up', [lambda x: x.cleanup_step()], False),
             ('module', 'creating module', [lambda x: x.make_module_step()], False),
+            ('package', 'packaging', [lambda x: x.package_step()], True),
         ]
 
         # full list of steps, included iterated steps
@@ -1805,15 +1811,6 @@ def prepare_step_spec(initial):
                 lambda x: x.test_cases_step(),
             ], False))
 
-        ## CHANGE TRUE TO build_option, and 
-        ## ADD build-pkg to all the configuration dicts
-        ## # if build_option('build-pkg'):
-        packaging_tool = build_option('package_tool')
-        if packaging_tool is not None:
-            steps.append(('package', 'packaging', [lambda x: x.package_step()], True))
-        else:
-            _log.debug('Skipping package step')
-
         return steps
 
     def run_all_steps(self, run_test_cases):

From 2dc218a5086deb00f185b5fbd6b0568655d46a73 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Fri, 20 Mar 2015 10:15:10 -0400
Subject: [PATCH 0803/1356] working, but puts the RPM into installdir (under
 package dir)

---
 easybuild/framework/easyblock.py |  6 ++++--
 easybuild/tools/packaging.py     | 20 +++++++++++++++++---
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 02068e17f0..ba1bfe7faa 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1450,10 +1450,12 @@ def package_step(self):
 
         packaging_tool = build_option('package_tool')
         if packaging_tool is not None:
-            package_fpm(self, path_to_module_file)
+            package_dir = package_fpm(self, path_to_module_file)
         else:
             _log.debug('Skipping package step')
 
+        shutil.copytree(package_dir, os.path.join(self.installdir, "package"))
+
 
     def post_install_step(self):
         """
@@ -1930,7 +1932,7 @@ def build_and_install_one(ecdict, orig_environ):
             except EasyBuildError, err:
                 _log.warn("Unable to commit easyconfig to repository: %s", err)
 
-        success = True
+        success = True 
         succ = "successfully"
         summary = "COMPLETED"
 
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index c97872ac9c..082cb868b1 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -27,17 +27,25 @@
 A place for packaging functions
 
 @author: Marc Litherland
-@author: Gianluca Santarossa 
+@author: Gianluca Santarossa (Novartis)
 @author: Robert Schmidt (Ottawa Hospital Research Institute)
+@author: Fotis Georgatos (Uni.Lu, NTUA)
+@author: Kenneth Hoste (Ghent University)
 """
 
 import os
 import tempfile
+from vsc.utils import fancylogger
+
 from easybuild.tools.run import run_cmd
 
+_log = fancylogger.getLogger('tools.packaging')
+
 def package_fpm(easyblock, modfile_path ):
-    rpmname = "HPCBIOS.20150211-%s-%s" % (easyblock.name, easyblock.version)
+    
     workdir = tempfile.mkdtemp()
+    _log.info("Will be writing RPM to %s" % workdir)
+
     try:
         os.chdir(workdir)
     except OSError, err:
@@ -64,5 +72,11 @@ def package_fpm(easyblock, modfile_path ):
     cmdlist.extend([
         easyblock.installdir,
     ])
+    cmdstr = " ".join(cmdlist)
+    _log.debug("The flattened cmdlist looks like" + cmdstr)
+    out = run_cmd(cmdstr, log_all=True, simple=True)
+   
+    _log.info("wrote rpm to %s" % (workdir) )
+
+    return workdir
 
-    (out, _) = run_cmd(cmdlist, log_all=True, simple=True)

From d5e532996664620b0a7c41b237da8c588bab7da8 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Fri, 20 Mar 2015 16:35:37 -0400
Subject: [PATCH 0804/1356] some new options (packagepath and package_template)
 and the code to get it working. Is able to build RPMs, but still somewhat
 broken on teh dependency side

---
 easybuild/framework/easyblock.py | 13 +++++++++----
 easybuild/tools/config.py        | 16 +++++++++++++++-
 easybuild/tools/options.py       |  8 ++++++--
 easybuild/tools/packaging.py     | 14 +++++++++-----
 4 files changed, 39 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index ba1bfe7faa..c7d6c072e8 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -60,7 +60,7 @@
 from easybuild.tools.build_details import get_build_stats
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
-from easybuild.tools.config import install_path, log_path, read_only_installdir, source_paths
+from easybuild.tools.config import install_path, log_path, read_only_installdir, source_paths, package_path
 from easybuild.tools.environment import restore_env
 from easybuild.tools.filetools import DEFAULT_CHECKSUM
 from easybuild.tools.filetools import adjust_permissions, apply_patch, convert_name, download_file, encode_class_name
@@ -1447,15 +1447,20 @@ def package_step(self):
         """Prepare package software (e.g. into an RPM) with fpm."""
 
         path_to_module_file = os.path.join(install_path('mod'), build_option('suffix_modules_path'), self.full_mod_name)
+        packagedir_dest = os.path.abspath(package_path())
 
         packaging_tool = build_option('package_tool')
         if packaging_tool is not None:
-            package_dir = package_fpm(self, path_to_module_file)
+            packagedir_src = package_fpm(self, path_to_module_file)
+   
+            if not os.path.exists(packagedir_dest):
+                mkdir(packagedir_dest)
+        
+            for file in glob.glob(os.path.join(packagedir_src, "*.rpm")):
+                shutil.copy(file, packagedir_dest)
         else:
             _log.debug('Skipping package step')
 
-        shutil.copytree(package_dir, os.path.join(self.installdir, "package"))
-
 
     def post_install_step(self):
         """
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 3848bbab1c..87be90f575 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -58,6 +58,7 @@
 DEFAULT_PATH_SUBDIRS = {
     'buildpath': 'build',
     'installpath': '',
+    'packagepath': 'packages',
     'repositorypath': 'ebfiles_repo',
     'sourcepath': 'sources',
     'subdir_modules': 'modules',
@@ -65,7 +66,7 @@
 }
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
-
+DEFAULT_PACKAGE_TEMPLATE = "easybuild-%(name)s-%(version)s"
 
 # utility function for obtaining default paths
 def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
@@ -182,6 +183,8 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'prefix',
         'buildpath',
         'installpath',
+        'packagepath',
+        'package_template',
         'sourcepath',
         'repository',
         'repositorypath',
@@ -340,6 +343,17 @@ def get_repositorypath():
     """
     return ConfigurationVariables()['repositorypath']
 
+def package_path():
+    """
+    Return the path where built packages are copied to
+    """
+    return ConfigurationVariables()['packagepath']
+
+def package_template():
+    """
+    Returns the package template
+    """
+    return ConfigurationVariables()['package_template']
 
 def get_modules_tool():
     """
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index de5a51cfd5..5457fe8675 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -50,7 +50,7 @@
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
-from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
+from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY, DEFAULT_PACKAGE_TEMPLATE
 from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
@@ -245,6 +245,10 @@ def config_options(self):
                              'choice', 'store', DEFAULT_MODULES_TOOL, sorted(avail_modules_tools().keys())),
             'package-tool': ("Packaging tool to use",
                              None, 'store_or_None', None),
+            'package-template': ("A template string to name the package",
+                             None, 'store', DEFAULT_PACKAGE_TEMPLATE),
+            'packagepath': ("The destination path for the packages built by package-tool",
+                             None, 'store', mk_full_default_path('packagepath')),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
                         "(used prefix for defaults %s)" % DEFAULT_PREFIX),
                        None, 'store', None),
@@ -425,7 +429,7 @@ def _postprocess_config(self):
         if self.options.prefix is not None:
             # prefix applies to all paths, and repository has to be reinitialised to take new repositorypath in account
             # in the legacy-style configuration, repository is initialised in configuration file itself
-            for dest in ['installpath', 'buildpath', 'sourcepath', 'repository', 'repositorypath']:
+            for dest in ['installpath', 'buildpath', 'sourcepath', 'repository', 'repositorypath', 'packagepath']:
                 if not self.options._action_taken.get(dest, False):
                     if dest == 'repository':
                         setattr(self.options, dest, DEFAULT_REPOSITORY)
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 082cb868b1..f120672dea 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -38,6 +38,7 @@
 from vsc.utils import fancylogger
 
 from easybuild.tools.run import run_cmd
+from easybuild.tools.config import install_path, package_template
 
 _log = fancylogger.getLogger('tools.packaging')
 
@@ -51,26 +52,29 @@ def package_fpm(easyblock, modfile_path ):
     except OSError, err:
         _log.error("Failed to chdir into workdir: %s : %s" % (workdir, err))
 
-    pkgtemplate = "HPCBIOS.20150211-%(name)s-%(version)s"
+    pkgtemplate = package_template()
+    #"HPCBIOS.20150211-%(name)s-%(version)s"
 
     pkgname=pkgtemplate % {
         'name' : easyblock.name,
         'version' : easyblock.version,
     }
-    dependencies = []
-    dependencies.extend([ "=".join([ dep['name'], dep['version'] ]) for dep in easyblock.cfg.dependencies() ])
-    depstring = '--depends ' + ' --depends '.join(dependencies)
+
+    depstring = ""    
+    for dep in easyblock.cfg.dependencies():
+        depstring += " --depends %s=%s" % ( dep['name'], dep['version'])
+
     cmdlist=[
         'fpm',
         '--workdir', workdir,
         '--name', pkgname,
         '-t', 'rpm', # target
         '-s', 'dir', # source
-        '-C', easyblock.installdir,
     ]
     cmdlist.extend([ depstring ])
     cmdlist.extend([
         easyblock.installdir,
+        modfile_path
     ])
     cmdstr = " ".join(cmdlist)
     _log.debug("The flattened cmdlist looks like" + cmdstr)

From 1310f4387be6a9119107feac32783ec1d0a89f55 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Fri, 20 Mar 2015 20:46:43 -0400
Subject: [PATCH 0805/1356] adding provides to create the dependencies and
 reordering to put package after extensions

---
 easybuild/framework/easyblock.py | 2 +-
 easybuild/tools/packaging.py     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index c7d6c072e8..5593993112 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1802,11 +1802,11 @@ def prepare_step_spec(initial):
         # part 3: post-iteration part
         steps_part3 = [
             ('extensions', 'taking care of extensions', [lambda x: x.extensions_step()], False),
+            ('package', 'packaging', [lambda x: x.package_step()], True),
             ('postproc', 'postprocessing', [lambda x: x.post_install_step()], True),
             ('sanitycheck', 'sanity checking', [lambda x: x.sanity_check_step()], False),
             ('cleanup', 'cleaning up', [lambda x: x.cleanup_step()], False),
             ('module', 'creating module', [lambda x: x.make_module_step()], False),
-            ('package', 'packaging', [lambda x: x.package_step()], True),
         ]
 
         # full list of steps, included iterated steps
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index f120672dea..7868bacdc5 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -68,6 +68,7 @@ def package_fpm(easyblock, modfile_path ):
         'fpm',
         '--workdir', workdir,
         '--name', pkgname,
+        '--provides', pkgname,
         '-t', 'rpm', # target
         '-s', 'dir', # source
     ]

From a0d84ae8ae8c53e326350be1b4e28502414fbc7e Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Sat, 21 Mar 2015 21:00:28 -0400
Subject: [PATCH 0806/1356] adding a package prefix rather than template by
 option (and it is prefixed to the package name). some debugging on dependency
 issues

---
 easybuild/framework/easyblock.py |  4 ++--
 easybuild/tools/config.py        |  8 ++++----
 easybuild/tools/options.py       |  6 +++---
 easybuild/tools/packaging.py     | 16 ++++++++++------
 4 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 5593993112..890c98ac3f 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1802,11 +1802,11 @@ def prepare_step_spec(initial):
         # part 3: post-iteration part
         steps_part3 = [
             ('extensions', 'taking care of extensions', [lambda x: x.extensions_step()], False),
-            ('package', 'packaging', [lambda x: x.package_step()], True),
             ('postproc', 'postprocessing', [lambda x: x.post_install_step()], True),
             ('sanitycheck', 'sanity checking', [lambda x: x.sanity_check_step()], False),
             ('cleanup', 'cleaning up', [lambda x: x.cleanup_step()], False),
             ('module', 'creating module', [lambda x: x.make_module_step()], False),
+            ('package', 'packaging', [lambda x: x.package_step()], True),
         ]
 
         # full list of steps, included iterated steps
@@ -1937,7 +1937,7 @@ def build_and_install_one(ecdict, orig_environ):
             except EasyBuildError, err:
                 _log.warn("Unable to commit easyconfig to repository: %s", err)
 
-        success = True 
+        success = True
         succ = "successfully"
         summary = "COMPLETED"
 
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 87be90f575..c1dad20186 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -66,7 +66,7 @@
 }
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
-DEFAULT_PACKAGE_TEMPLATE = "easybuild-%(name)s-%(version)s"
+DEFAULT_PACKAGE_PREFIX = "easybuild"
 
 # utility function for obtaining default paths
 def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
@@ -184,7 +184,7 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'buildpath',
         'installpath',
         'packagepath',
-        'package_template',
+        'package_prefix',
         'sourcepath',
         'repository',
         'repositorypath',
@@ -349,11 +349,11 @@ def package_path():
     """
     return ConfigurationVariables()['packagepath']
 
-def package_template():
+def package_prefix():
     """
     Returns the package template
     """
-    return ConfigurationVariables()['package_template']
+    return ConfigurationVariables()['package_prefix']
 
 def get_modules_tool():
     """
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 5457fe8675..b2ab6db75e 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -50,7 +50,7 @@
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
-from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY, DEFAULT_PACKAGE_TEMPLATE
+from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY, DEFAULT_PACKAGE_PREFIX
 from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
@@ -245,8 +245,8 @@ def config_options(self):
                              'choice', 'store', DEFAULT_MODULES_TOOL, sorted(avail_modules_tools().keys())),
             'package-tool': ("Packaging tool to use",
                              None, 'store_or_None', None),
-            'package-template': ("A template string to name the package",
-                             None, 'store', DEFAULT_PACKAGE_TEMPLATE),
+            'package-prefix': ("A template string to name the package",
+                             None, 'store', DEFAULT_PACKAGE_PREFIX),
             'packagepath': ("The destination path for the packages built by package-tool",
                              None, 'store', mk_full_default_path('packagepath')),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 7868bacdc5..7ac0a0d229 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -35,10 +35,12 @@
 
 import os
 import tempfile
+import pprint
+
 from vsc.utils import fancylogger
 
 from easybuild.tools.run import run_cmd
-from easybuild.tools.config import install_path, package_template
+from easybuild.tools.config import install_path, package_prefix
 
 _log = fancylogger.getLogger('tools.packaging')
 
@@ -52,25 +54,27 @@ def package_fpm(easyblock, modfile_path ):
     except OSError, err:
         _log.error("Failed to chdir into workdir: %s : %s" % (workdir, err))
 
-    pkgtemplate = package_template()
+    pkgprefix   = package_prefix()
+    pkgtemplate = "%(prefix)s-%(name)s"
     #"HPCBIOS.20150211-%(name)s-%(version)s"
 
     pkgname=pkgtemplate % {
+        'prefix' : pkgprefix,
         'name' : easyblock.name,
-        'version' : easyblock.version,
     }
-
+    _log.debug("The dependencies to be added to the package are: " + pprint.pformat(easyblock.cfg.dependencies()))
     depstring = ""    
     for dep in easyblock.cfg.dependencies():
-        depstring += " --depends %s=%s" % ( dep['name'], dep['version'])
+        depstring += " --depends '%s-%s = %s-1'" % ( pkgprefix , dep['name'], dep['version'])
 
     cmdlist=[
         'fpm',
         '--workdir', workdir,
         '--name', pkgname,
-        '--provides', pkgname,
+        '--provides', "%s-%s" %(pkgprefix,easyblock.name),
         '-t', 'rpm', # target
         '-s', 'dir', # source
+        '--version', easyblock.version,
     ]
     cmdlist.extend([ depstring ])
     cmdlist.extend([

From 6b41ec881e357cd20623d68d156813ef58e9021e Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Tue, 24 Mar 2015 21:21:25 -0400
Subject: [PATCH 0807/1356] moving the log message outside of the filter block
 for easier debugging

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 7aac218a73..191ee1c743 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -411,9 +411,9 @@ def dependencies(self):
 
         # if filter-deps option is provided we "clean" the list of dependencies for
         # each processed easyconfig to remove the unwanted dependencies
+        self.log.debug("Dependencies BEFORE filtering: %s" % deps)
         filter_deps = build_option('filter_deps')
         if filter_deps:
-            self.log.debug("Dependencies BEFORE filtering: %s" % deps)
             filtered_deps = []
             for dep in deps:
                 if dep['name'] not in filter_deps:

From c98d7310b5b0a709586c7560b563d40b52fe11ff Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Wed, 25 Mar 2015 21:41:24 -0400
Subject: [PATCH 0808/1356] grabbing a full toolchain version

---
 easybuild/tools/packaging.py | 25 +++++++++++++++++++++----
 1 file changed, 21 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 7ac0a0d229..19100c8474 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -41,6 +41,8 @@
 
 from easybuild.tools.run import run_cmd
 from easybuild.tools.config import install_path, package_prefix
+from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
+from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 
 _log = fancylogger.getLogger('tools.packaging')
 
@@ -56,16 +58,31 @@ def package_fpm(easyblock, modfile_path ):
 
     pkgprefix   = package_prefix()
     pkgtemplate = "%(prefix)s-%(name)s"
+    full_ec_version = det_full_ec_version(easyblock.cfg)
     #"HPCBIOS.20150211-%(name)s-%(version)s"
 
     pkgname=pkgtemplate % {
         'prefix' : pkgprefix,
         'name' : easyblock.name,
     }
-    _log.debug("The dependencies to be added to the package are: " + pprint.pformat(easyblock.cfg.dependencies()))
+    
+    # a lot of this logic should probably be put elsewhere, but make_module_dep is the only place I've seen that uses it
+
+    deps = []
+    if easyblock.toolchain.name != DUMMY_TOOLCHAIN_NAME:
+        short_mod_name = easyblock.toolchain.det_short_module_name()
+        _log.debug("The toolchain short module name is: %s" % short_mod_name)
+        toolchain_dict = easyblock.toolchain.as_dict()
+        toolchain_dict["short_mod_name"] = short_mod_name
+        deps.extend([toolchain_dict])
+
+    deps.extend(easyblock.cfg.dependencies())
+ 
+    _log.debug("The dependencies to be added to the package are: " + pprint.pformat([easyblock.toolchain.as_dict()]+easyblock.cfg.dependencies()))
     depstring = ""    
-    for dep in easyblock.cfg.dependencies():
-        depstring += " --depends '%s-%s = %s-1'" % ( pkgprefix , dep['name'], dep['version'])
+    for dep in deps:
+        short_mod_name = dep['short_mod_name'].partition('/')
+        depstring += " --depends '%s-%s = %s-1'" % ( pkgprefix , dep['name'], short_mod_name[2])
 
     cmdlist=[
         'fpm',
@@ -74,7 +91,7 @@ def package_fpm(easyblock, modfile_path ):
         '--provides', "%s-%s" %(pkgprefix,easyblock.name),
         '-t', 'rpm', # target
         '-s', 'dir', # source
-        '--version', easyblock.version,
+        '--version', full_ec_version,
     ]
     cmdlist.extend([ depstring ])
     cmdlist.extend([

From 62ce4bf39236a8b121623d3756f1245e2b42cf11 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Thu, 26 Mar 2015 11:11:20 -0400
Subject: [PATCH 0809/1356] using short mod was bad

---
 easybuild/tools/packaging.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 19100c8474..05235eb5b9 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -70,10 +70,7 @@ def package_fpm(easyblock, modfile_path ):
 
     deps = []
     if easyblock.toolchain.name != DUMMY_TOOLCHAIN_NAME:
-        short_mod_name = easyblock.toolchain.det_short_module_name()
-        _log.debug("The toolchain short module name is: %s" % short_mod_name)
         toolchain_dict = easyblock.toolchain.as_dict()
-        toolchain_dict["short_mod_name"] = short_mod_name
         deps.extend([toolchain_dict])
 
     deps.extend(easyblock.cfg.dependencies())
@@ -81,8 +78,9 @@ def package_fpm(easyblock, modfile_path ):
     _log.debug("The dependencies to be added to the package are: " + pprint.pformat([easyblock.toolchain.as_dict()]+easyblock.cfg.dependencies()))
     depstring = ""    
     for dep in deps:
-        short_mod_name = dep['short_mod_name'].partition('/')
-        depstring += " --depends '%s-%s = %s-1'" % ( pkgprefix , dep['name'], short_mod_name[2])
+        full_dep_version = det_full_ec_version(dep)
+        #by default will only build iteration 1 packages, do we need to enhance this?
+        depstring += " --depends '%s-%s = %s-1'" % ( pkgprefix , dep['name'], full_dep_version)
 
     cmdlist=[
         'fpm',

From 930ce59ffe276def015dd4ba5ec7becacf6d0107 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Thu, 26 Mar 2015 22:05:35 +0100
Subject: [PATCH 0810/1356] Prepare class structure for Tcl and Lua syntax in
 individual checks.

---
 test/framework/module_generator.py | 188 +++++++++++++++++------------
 1 file changed, 109 insertions(+), 79 deletions(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 76b9322018..c33f3789cb 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -77,111 +77,141 @@ def tearDown(self):
 
     def test_descr(self):
         """Test generation of module description (which includes '#%Module' header)."""
-        gzip_txt = "gzip (GNU zip) is a popular data compression program as a replacement for compress "
-        gzip_txt += "- Homepage: http://www.gzip.org/"
-        expected = '\n'.join([
-            "#%Module",
-            "",
-            "proc ModulesHelp { } {",
-            "    puts stderr {   %s" % gzip_txt,
-            "    }",
-            "}",
-            "",
-            "module-whatis {Description: %s}" % gzip_txt,
-            "",
-            "set root    %s" % self.modgen.app.installdir,
-            "",
-            "conflict gzip",
-            "",
-        ]) 
-
-        desc = self.modgen.get_description()
-        self.assertEqual(desc, expected)
+        
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            gzip_txt = "gzip (GNU zip) is a popular data compression program as a replacement for compress "
+            gzip_txt += "- Homepage: http://www.gzip.org/"
+            expected = '\n'.join([
+                "#%Module",
+                "",
+                "proc ModulesHelp { } {",
+                "    puts stderr {   %s" % gzip_txt,
+                "    }",
+                "}",
+                "",
+                "module-whatis {Description: %s}" % gzip_txt,
+                "",
+                "set root    %s" % self.modgen.app.installdir,
+                "",
+                "conflict gzip",
+                "",
+            ])
+
+            desc = self.modgen.get_description()
+            self.assertEqual(desc, expected)
+        else:
+            pass
 
     def test_load(self):
         """Test load part in generated module file."""
-        expected = [
-            "",
-            "if { ![is-loaded mod_name] } {",
-            "    module load mod_name",
-            "}",
-            "",
-        ]
-        self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
-
-        # with recursive unloading: no if is-loaded guard
-        init_config(build_options={'recursive_mod_unload': True})
-        expected = [
-            "",
-            "module load mod_name",
-            "",
-        ]
-        self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
+
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            expected = [
+                "",
+                "if { ![is-loaded mod_name] } {",
+                "    module load mod_name",
+                "}",
+                "",
+            ]
+            self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
+
+            # with recursive unloading: no if is-loaded guard
+            init_config(build_options={'recursive_mod_unload': True})
+            expected = [
+                "",
+                "module load mod_name",
+                "",
+            ]
+            self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
+        else:
+            pass
 
     def test_unload(self):
         """Test unload part in generated module file."""
-        expected = '\n'.join([
-            "",
-            "if { [is-loaded mod_name] } {",
-            "    module unload mod_name",
-            "}",
-            "",
-        ])
-        self.assertEqual(expected, self.modgen.unload_module("mod_name"))
+
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            expected = '\n'.join([
+                "",
+                "if { [is-loaded mod_name] } {",
+                "    module unload mod_name",
+                "}",
+                "",
+            ])
+            self.assertEqual(expected, self.modgen.unload_module("mod_name"))
+        else:
+            pass
 
     def test_prepend_paths(self):
         """Test generating prepend-paths statements."""
         # test prepend_paths
-        expected = ''.join([
-            "prepend-path\tkey\t\t$root/path1\n",
-            "prepend-path\tkey\t\t$root/path2\n",
-        ])
-        self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
 
-        expected = "prepend-path\tbar\t\t$root/foo\n"
-        self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            expected = ''.join([
+                "prepend-path\tkey\t\t$root/path1\n",
+                "prepend-path\tkey\t\t$root/path2\n",
+            ])
+            self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
 
-        self.assertEqual("prepend-path\tkey\t\t/abs/path\n", self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
+            expected = "prepend-path\tbar\t\t$root/foo\n"
+            self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
 
-        self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
-                                              "which only expects relative paths." % self.modgen.app.installdir,
-                              self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])
+            self.assertEqual("prepend-path\tkey\t\t/abs/path\n", self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
+
+            self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
+                                                  "which only expects relative paths." % self.modgen.app.installdir,
+                                  self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])
+        else:
+            pass
 
     def test_use(self):
         """Test generating module use statements."""
-        expected = '\n'.join([
-            "module use /some/path",
-            "module use /foo/bar/baz",
-        ])
-        self.assertEqual(self.modgen.use(["/some/path", "/foo/bar/baz"]), expected)
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            expected = '\n'.join([
+                "module use /some/path",
+                "module use /foo/bar/baz",
+            ])
+            self.assertEqual(self.modgen.use(["/some/path", "/foo/bar/baz"]), expected)
+        else:
+            pass
+
 
     def test_env(self):
         """Test setting of environment variables."""
         # test set_environment
-        self.assertEqual('setenv\tkey\t\t"value"\n', self.modgen.set_environment("key", "value"))
-        self.assertEqual("setenv\tkey\t\t'va\"lue'\n", self.modgen.set_environment("key", 'va"lue'))
-        self.assertEqual('setenv\tkey\t\t"va\'lue"\n', self.modgen.set_environment("key", "va'lue"))
-        self.assertEqual('setenv\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_environment("key", """va"l'ue"""))
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            self.assertEqual('setenv\tkey\t\t"value"\n', self.modgen.set_environment("key", "value"))
+            self.assertEqual("setenv\tkey\t\t'va\"lue'\n", self.modgen.set_environment("key", 'va"lue'))
+            self.assertEqual('setenv\tkey\t\t"va\'lue"\n', self.modgen.set_environment("key", "va'lue"))
+            self.assertEqual('setenv\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_environment("key", """va"l'ue"""))
+        else:
+            pass
     
     def test_alias(self):
         """Test setting of alias in modulefiles."""
-        # test set_alias
-        self.assertEqual('set-alias\tkey\t\t"value"\n', self.modgen.set_alias("key", "value"))
-        self.assertEqual("set-alias\tkey\t\t'va\"lue'\n", self.modgen.set_alias("key", 'va"lue'))
-        self.assertEqual('set-alias\tkey\t\t"va\'lue"\n', self.modgen.set_alias("key", "va'lue"))
-        self.assertEqual('set-alias\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_alias("key", """va"l'ue"""))
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            # test set_alias
+            self.assertEqual('set-alias\tkey\t\t"value"\n', self.modgen.set_alias("key", "value"))
+            self.assertEqual("set-alias\tkey\t\t'va\"lue'\n", self.modgen.set_alias("key", 'va"lue'))
+            self.assertEqual('set-alias\tkey\t\t"va\'lue"\n', self.modgen.set_alias("key", "va'lue"))
+            self.assertEqual('set-alias\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_alias("key", """va"l'ue"""))
+        else:
+            pass
 
     def test_load_msg(self):
         """Test including a load message in the module file."""
-        tcl_load_msg = '\n'.join([
-            '',
-            "if [ module-info mode load ] {",
-            "        puts stderr     \"test \\$test \\$test",
-            "test \\$foo \\$bar\"",
-            "}",
-            '',
-        ])
-        self.assertEqual(tcl_load_msg, self.modgen.msg_on_load('test $test \\$test\ntest $foo \\$bar'))
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            tcl_load_msg = '\n'.join([
+                '',
+                "if [ module-info mode load ] {",
+                "        puts stderr     \"test \\$test \\$test",
+                "test \\$foo \\$bar\"",
+                "}",
+                '',
+            ])
+            self.assertEqual(tcl_load_msg, self.modgen.msg_on_load('test $test \\$test\ntest $foo \\$bar'))
+        else:
+            lua_load_msg = """ """
+
 
     def test_tcl_footer(self):
         """Test including a Tcl footer."""

From 39816f5317a6791a69479d8fe0384482cb93c861 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Thu, 26 Mar 2015 23:26:21 +0100
Subject: [PATCH 0811/1356] Fixed some oversights in Lua code generation. Basic
 tests added. Still some work left.

---
 easybuild/tools/module_generator.py |  8 +--
 test/framework/module_generator.py  | 79 ++++++++++++++++++++++++-----
 2 files changed, 70 insertions(+), 17 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index c2a217525e..b8d0b3ab2c 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -355,7 +355,7 @@ def load_module(self, mod_name):
         else:
             load_statement = [
                 'if ( not isloaded("%(mod_name)s")) then',
-                '  %s' % LOAD_TEMPLATE,
+                '    %s' % LOAD_TEMPLATE,
                 'end',
             ]
         return '\n'.join([""] + load_statement + [""]) % {'mod_name': mod_name}
@@ -366,8 +366,8 @@ def unload_module(self, mod_name):
         """
         return '\n'.join([
             "",
-            "if (isloaded(%(mod_name)s)) then",
-            "    unload(%(mod_name)s)",
+            'if (isloaded("%(mod_name)s")) then,
+            '    unload(%(mod_name)s)',
             "end",
             "",
         ]) % {'mod_name': mod_name}
@@ -434,7 +434,7 @@ def set_alias(self, key, value):
         Generate set-alias statement in modulefile for the given key/value pair.
         """
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
-        return 'setalias(%s,"%s")\n' % (key, quote_str(value))
+        return 'setalias("%s","%s")\n' % (key, quote_str(value))
 
 def avail_module_generators():
     """
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index c33f3789cb..7199c2ac31 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -77,10 +77,11 @@ def tearDown(self):
 
     def test_descr(self):
         """Test generation of module description (which includes '#%Module' header)."""
-        
+
+        gzip_txt = "gzip (GNU zip) is a popular data compression program as a replacement for compress "
+        gzip_txt += "- Homepage: http://www.gzip.org/"
+
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
-            gzip_txt = "gzip (GNU zip) is a popular data compression program as a replacement for compress "
-            gzip_txt += "- Homepage: http://www.gzip.org/"
             expected = '\n'.join([
                 "#%Module",
                 "",
@@ -97,10 +98,25 @@ def test_descr(self):
                 "",
             ])
 
-            desc = self.modgen.get_description()
-            self.assertEqual(desc, expected)
         else:
-            pass
+            expected = [
+                "local pkg = {}",
+                "help = [["
+                "%s"
+                "]]" %s gzip_txt,
+                "whatis([[Name: gzip]])" ,
+                "whatis([[Version: 1.4]])" ,
+                "whatis([[Description: %s]])" % gzip_txt,
+                "whatis([[Homepage: http://www.gzip.org/])",
+                "whatis([[License: N/A ]])",
+                "",
+                "",
+                'pkg.root="%(installdir)s"',
+                "",
+            ]
+
+        desc = self.modgen.get_description()
+        self.assertEqual(desc, expected)
 
     def test_load(self):
         """Test load part in generated module file."""
@@ -124,7 +140,19 @@ def test_load(self):
             ]
             self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
         else:
-            pass
+            expected = '\n'.join([
+                'if ( not isloaded(mod_name)) then',
+                '  load("mod_name")',
+                'end',
+            ])
+            self.assertEqual(expected,self.modgen.load_module("mod_name"))
+
+            init_config(build_options={'recursive_mod_unload': True})
+            expected = '\n'.join([
+                "",
+                'load("mod_name")',
+                "",])
+            self.assertEqual(expected,self.modgen.load_module("mod_name"))
 
     def test_unload(self):
         """Test unload part in generated module file."""
@@ -139,7 +167,14 @@ def test_unload(self):
             ])
             self.assertEqual(expected, self.modgen.unload_module("mod_name"))
         else:
-            pass
+            expected = '\n'.join([
+            "",
+            'if (isloaded("mod_name") then,
+            '    unload("mod_name")",
+            "end",
+            "",
+            ])
+            self.assertEqual(expected, self.modgen.unload_module("mod_name"))
 
     def test_prepend_paths(self):
         """Test generating prepend-paths statements."""
@@ -161,7 +196,20 @@ def test_prepend_paths(self):
                                                   "which only expects relative paths." % self.modgen.app.installdir,
                                   self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])
         else:
-            pass
+            expected = ''.join([
+                'prepend-path("key", pathJoin(pkg.root,"path1"))',
+                'prepend-path("key", pathJoin(pkg.root,"path2"))',
+            ])
+            self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
+
+            expected = 'prepend-path("bar", pathJoin(pkg.root,"foo")\n'
+            self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
+
+            self.assertEqual('prepend-path("key", "/abs/path")', self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
+
+            self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
+                                                  "which only expects relative paths." % self.modgen.app.installdir,
+                                  self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])
 
     def test_use(self):
         """Test generating module use statements."""
@@ -172,7 +220,11 @@ def test_use(self):
             ])
             self.assertEqual(self.modgen.use(["/some/path", "/foo/bar/baz"]), expected)
         else:
-            pass
+            expected = '\n'.join([
+                'use("/some/path")',
+                'use("/foo/bar/baz"),
+            ])
+            self.assertEqual(self.modgen.use(["/some/path", "/foo/bar/baz"]), expected)
 
 
     def test_env(self):
@@ -184,7 +236,8 @@ def test_env(self):
             self.assertEqual('setenv\tkey\t\t"va\'lue"\n', self.modgen.set_environment("key", "va'lue"))
             self.assertEqual('setenv\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_environment("key", """va"l'ue"""))
         else:
-            pass
+            self.assertEqual('setenv("key","value")\n', self.modgen.set_environment("key", "value"))
+
     
     def test_alias(self):
         """Test setting of alias in modulefiles."""
@@ -195,7 +248,7 @@ def test_alias(self):
             self.assertEqual('set-alias\tkey\t\t"va\'lue"\n', self.modgen.set_alias("key", "va'lue"))
             self.assertEqual('set-alias\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_alias("key", """va"l'ue"""))
         else:
-            pass
+            self.assertEqual('set-alias("key","value"\n, self.modgen.set_alias("key", "value"))
 
     def test_load_msg(self):
         """Test including a load message in the module file."""
@@ -210,7 +263,7 @@ def test_load_msg(self):
             ])
             self.assertEqual(tcl_load_msg, self.modgen.msg_on_load('test $test \\$test\ntest $foo \\$bar'))
         else:
-            lua_load_msg = """ """
+            pass
 
 
     def test_tcl_footer(self):

From d2a0d1290f894d48f237ce775257091fe5fe03da Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Thu, 26 Mar 2015 23:29:17 +0100
Subject: [PATCH 0812/1356] Fixed a typo.

---
 easybuild/tools/module_generator.py | 4 ++--
 test/framework/module_generator.py  | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index b8d0b3ab2c..aed58ffb65 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -366,7 +366,7 @@ def unload_module(self, mod_name):
         """
         return '\n'.join([
             "",
-            'if (isloaded("%(mod_name)s")) then,
+            'if (isloaded("%(mod_name)s")) then',
             '    unload(%(mod_name)s)',
             "end",
             "",
@@ -434,7 +434,7 @@ def set_alias(self, key, value):
         Generate set-alias statement in modulefile for the given key/value pair.
         """
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
-        return 'setalias("%s","%s")\n' % (key, quote_str(value))
+        return 'setalias("%s,"%s")\n' % (key, quote_str(value))
 
 def avail_module_generators():
     """
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 7199c2ac31..70add3acd3 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -230,7 +230,7 @@ def test_use(self):
     def test_env(self):
         """Test setting of environment variables."""
         # test set_environment
-        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl():
             self.assertEqual('setenv\tkey\t\t"value"\n', self.modgen.set_environment("key", "value"))
             self.assertEqual("setenv\tkey\t\t'va\"lue'\n", self.modgen.set_environment("key", 'va"lue'))
             self.assertEqual('setenv\tkey\t\t"va\'lue"\n', self.modgen.set_environment("key", "va'lue"))

From 0a6040a3099402b592a921e2f0127d77e8febd17 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Thu, 26 Mar 2015 23:31:35 +0100
Subject: [PATCH 0813/1356] Fixed a typo.

---
 test/framework/module_generator.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 70add3acd3..a893c0fdf0 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -101,9 +101,7 @@ def test_descr(self):
         else:
             expected = [
                 "local pkg = {}",
-                "help = [["
-                "%s"
-                "]]" %s gzip_txt,
+                'help = [["%s""]]' %s gzip_txt,
                 "whatis([[Name: gzip]])" ,
                 "whatis([[Version: 1.4]])" ,
                 "whatis([[Description: %s]])" % gzip_txt,
@@ -198,7 +196,7 @@ def test_prepend_paths(self):
         else:
             expected = ''.join([
                 'prepend-path("key", pathJoin(pkg.root,"path1"))',
-                'prepend-path("key", pathJoin(pkg.root,"path2"))',
+                prepend-path("key", pathJoin(pkg.root,"path2"))',
             ])
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
 

From a64549ebd31699f786e27efbadca75dfb99a439c Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Thu, 26 Mar 2015 23:34:15 +0100
Subject: [PATCH 0814/1356] Fixed a typo.

---
 test/framework/module_generator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index a893c0fdf0..c5dea3f966 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -101,7 +101,7 @@ def test_descr(self):
         else:
             expected = [
                 "local pkg = {}",
-                'help = [["%s""]]' %s gzip_txt,
+                'help = [["%s"]]' %s gzip_txt,
                 "whatis([[Name: gzip]])" ,
                 "whatis([[Version: 1.4]])" ,
                 "whatis([[Description: %s]])" % gzip_txt,

From 5556dad8d02a113dd696a2282f83cebc4f60babb Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Thu, 26 Mar 2015 23:35:15 +0100
Subject: [PATCH 0815/1356] Fixed not needed quotes.

---
 test/framework/module_generator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index c5dea3f966..c5a70c9a40 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -101,7 +101,7 @@ def test_descr(self):
         else:
             expected = [
                 "local pkg = {}",
-                'help = [["%s"]]' %s gzip_txt,
+                'help = [[%s]] %s gzip_txt,
                 "whatis([[Name: gzip]])" ,
                 "whatis([[Version: 1.4]])" ,
                 "whatis([[Description: %s]])" % gzip_txt,

From 1ffb147d13055c88bd4bd7d545f2cb10762edde3 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Fri, 27 Mar 2015 01:04:36 +0100
Subject: [PATCH 0816/1356] Fixed most tests and lua template issues.

---
 easybuild/tools/module_generator.py | 19 ++++++-------
 test/framework/module_generator.py  | 42 ++++++++++++++++-------------
 2 files changed, 31 insertions(+), 30 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index aed58ffb65..67b4995eb3 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -319,14 +319,11 @@ def get_description(self, conflict=True):
 
         lines = [
             "local pkg = {}",
-            "help = [["
-            "%(description)s"
-            "]]",
+            "help = [[%(description)s]]",
             "whatis([[Name: %(name)s]])",
             "whatis([[Version: %(version)s]])",
             "whatis([[Description: %(description)s]])",
-            "whatis([[Homepage: %(homepage)s]])"
-            "whatis([[License: N/A ]])",
+            "whatis([[Homepage: %(homepage)s]])",
             "",
             "",
             'pkg.root="%(installdir)s"',
@@ -351,11 +348,11 @@ def load_module(self, mod_name):
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the depedency "module load" is present,
             # it will get translated to "module unload"
-            load_statement = [LOAD_TEMPLATE]
+            load_statement = [self.LOAD_TEMPLATE]
         else:
             load_statement = [
                 'if ( not isloaded("%(mod_name)s")) then',
-                '    %s' % LOAD_TEMPLATE,
+                '    %s' % self.LOAD_TEMPLATE,
                 'end',
             ]
         return '\n'.join([""] + load_statement + [""]) % {'mod_name': mod_name}
@@ -366,15 +363,15 @@ def unload_module(self, mod_name):
         """
         return '\n'.join([
             "",
-            'if (isloaded("%(mod_name)s")) then',
-            '    unload(%(mod_name)s)',
+            'if (isloaded("%(mod_name)s") then',
+            '    unload("%(mod_name)s")',
             "end",
             "",
         ]) % {'mod_name': mod_name}
 
     def prepend_paths(self, key, paths, allow_abs=False):
         """
-        Generate prepend-path statements for the given list of paths.
+        Generate prepend-path statements for the given list of paths
         """
         template = 'prepend_path(%s,%s)\n'
 
@@ -434,7 +431,7 @@ def set_alias(self, key, value):
         Generate set-alias statement in modulefile for the given key/value pair.
         """
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
-        return 'setalias("%s,"%s")\n' % (key, quote_str(value))
+        return 'setalias("%s",%s)\n' % (key, quote_str(value))
 
 def avail_module_generators():
     """
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index c5a70c9a40..365568f7c1 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -99,19 +99,18 @@ def test_descr(self):
             ])
 
         else:
-            expected = [
+            expected = '\n'.join([
                 "local pkg = {}",
-                'help = [[%s]] %s gzip_txt,
+                'help = [[%s]]' % gzip_txt,
                 "whatis([[Name: gzip]])" ,
                 "whatis([[Version: 1.4]])" ,
                 "whatis([[Description: %s]])" % gzip_txt,
                 "whatis([[Homepage: http://www.gzip.org/])",
-                "whatis([[License: N/A ]])",
                 "",
                 "",
-                'pkg.root="%(installdir)s"',
+                'pkg.root="%s"' %self.modgen.app.installdir,
                 "",
-            ]
+            ])
 
         desc = self.modgen.get_description()
         self.assertEqual(desc, expected)
@@ -139,9 +138,11 @@ def test_load(self):
             self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
         else:
             expected = '\n'.join([
-                'if ( not isloaded(mod_name)) then',
-                '  load("mod_name")',
+                '',
+                'if ( not isloaded("mod_name")) then',
+                '    load("mod_name")',
                 'end',
+                '',
             ])
             self.assertEqual(expected,self.modgen.load_module("mod_name"))
 
@@ -149,7 +150,8 @@ def test_load(self):
             expected = '\n'.join([
                 "",
                 'load("mod_name")',
-                "",])
+                "",
+            ])
             self.assertEqual(expected,self.modgen.load_module("mod_name"))
 
     def test_unload(self):
@@ -167,8 +169,8 @@ def test_unload(self):
         else:
             expected = '\n'.join([
             "",
-            'if (isloaded("mod_name") then,
-            '    unload("mod_name")",
+            'if (isloaded("mod_name") then',
+            '    unload("mod_name")',
             "end",
             "",
             ])
@@ -194,16 +196,17 @@ def test_prepend_paths(self):
                                                   "which only expects relative paths." % self.modgen.app.installdir,
                                   self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])
         else:
-            expected = ''.join([
-                'prepend-path("key", pathJoin(pkg.root,"path1"))',
-                prepend-path("key", pathJoin(pkg.root,"path2"))',
+            expected = '\n'.join([
+                'prepend_path("key", pathJoin(pkg.root,"path1"))',
+                'prepend_path("key", pathJoin(pkg.root,"path2"))',
+                '',
             ])
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
 
-            expected = 'prepend-path("bar", pathJoin(pkg.root,"foo")\n'
+            expected = 'prepend_path("bar", pathJoin(pkg.root,"foo"))\n'
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
 
-            self.assertEqual('prepend-path("key", "/abs/path")', self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
+            self.assertEqual('prepend_path("key", "/abs/path")', self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
 
             self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
                                                   "which only expects relative paths." % self.modgen.app.installdir,
@@ -220,7 +223,8 @@ def test_use(self):
         else:
             expected = '\n'.join([
                 'use("/some/path")',
-                'use("/foo/bar/baz"),
+                'use("/foo/bar/baz")',
+                '',
             ])
             self.assertEqual(self.modgen.use(["/some/path", "/foo/bar/baz"]), expected)
 
@@ -228,13 +232,13 @@ def test_use(self):
     def test_env(self):
         """Test setting of environment variables."""
         # test set_environment
-        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl():
+        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
             self.assertEqual('setenv\tkey\t\t"value"\n', self.modgen.set_environment("key", "value"))
             self.assertEqual("setenv\tkey\t\t'va\"lue'\n", self.modgen.set_environment("key", 'va"lue'))
             self.assertEqual('setenv\tkey\t\t"va\'lue"\n', self.modgen.set_environment("key", "va'lue"))
             self.assertEqual('setenv\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_environment("key", """va"l'ue"""))
         else:
-            self.assertEqual('setenv("key","value")\n', self.modgen.set_environment("key", "value"))
+            self.assertEqual('setenv("key", "value")\n', self.modgen.set_environment("key","value"))
 
     
     def test_alias(self):
@@ -246,7 +250,7 @@ def test_alias(self):
             self.assertEqual('set-alias\tkey\t\t"va\'lue"\n', self.modgen.set_alias("key", "va'lue"))
             self.assertEqual('set-alias\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_alias("key", """va"l'ue"""))
         else:
-            self.assertEqual('set-alias("key","value"\n, self.modgen.set_alias("key", "value"))
+            self.assertEqual('setalias("key","value")\n', self.modgen.set_alias("key", "value"))
 
     def test_load_msg(self):
         """Test including a load message in the module file."""

From c6995bd445052f66d52e08860b8dafd0349f60f0 Mon Sep 17 00:00:00 2001
From: Petar Forai <pfo@pseudoterminal.org>
Date: Fri, 27 Mar 2015 01:06:11 +0100
Subject: [PATCH 0817/1356] Fixed one more test.

---
 test/framework/module_generator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 365568f7c1..1b7fb51d8a 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -105,7 +105,7 @@ def test_descr(self):
                 "whatis([[Name: gzip]])" ,
                 "whatis([[Version: 1.4]])" ,
                 "whatis([[Description: %s]])" % gzip_txt,
-                "whatis([[Homepage: http://www.gzip.org/])",
+                "whatis([[Homepage: http://www.gzip.org/]])",
                 "",
                 "",
                 'pkg.root="%s"' %self.modgen.app.installdir,

From b520a715ac6b1fd556b70cd7287601f3d667f39f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Mar 2015 09:59:52 +0100
Subject: [PATCH 0818/1356] add test to check that log.error and log.exception
 are no longer used

---
 test/framework/general.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/test/framework/general.py b/test/framework/general.py
index d50b854d4d..545e37c062 100644
--- a/test/framework/general.py
+++ b/test/framework/general.py
@@ -28,12 +28,14 @@
 @author: Kenneth hoste (Ghent University)
 """
 import os
+import re
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
 
 import vsc
 
 import easybuild.framework
+from easybuild.tools.filetools import read_file
 
 
 class GeneralTest(EnhancedTestCase):
@@ -50,6 +52,23 @@ def test_vsc_location(self):
         msg = "vsc-base is not provided by EasyBuild framework itself, found location: %s" % vsc_loc
         self.assertFalse(os.path.samefile(framework_loc, vsc_loc), msg)
 
+    def test_error_reporting(self):
+        """Make sure error reporting is done correctly (no more log.error, log.exception)."""
+        # easybuild.framework.__file__ provides location to <prefix>/easybuild/framework/__init__.py
+        easybuild_loc = os.path.dirname(os.path.dirname(os.path.abspath(easybuild.framework.__file__)))
+
+        log_method_regexes = [
+            re.compile("log\.error\("),
+            re.compile("log\.exception\("),
+            re.compile("log\.raiseException\("),
+        ]
+
+        for dirpath, _, filenames in os.walk(easybuild_loc):
+            for filename in [f for f in filenames if f.endswith('.py')]:
+                path = os.path.join(dirpath, filename)
+                txt = read_file(path)
+                for regex in log_method_regexes:
+                    self.assertFalse(regex.search(txt), "No match for '%s' in %s" % (regex.pattern, path))
 
 def suite():
     """ returns all the testcases in this module """

From 4a9e952c90b9f1ce0e76d31fcb1149e231714dc7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Mar 2015 15:42:47 +0100
Subject: [PATCH 0819/1356] trivial style fix

---
 easybuild/tools/filetools.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 7e9ef95891..6bd09297a9 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -191,14 +191,14 @@ def extract_file(fn, dest, cmd=None, extra_options=None, overwrite=False):
     mkdir(dest, parents=True)
 
     # use absolute pathnames from now on
-    absDest = os.path.abspath(dest)
+    abs_dest = os.path.abspath(dest)
 
     # change working directory
     try:
-        _log.debug("Unpacking %s in directory %s." % (fn, absDest))
-        os.chdir(absDest)
+        _log.debug("Unpacking %s in directory %s.", fn, abs_dest)
+        os.chdir(abs_dest)
     except OSError, err:
-        raise EasyBuildError("Can't change to directory %s: %s", absDest, err)
+        raise EasyBuildError("Can't change to directory %s: %s", abs_dest, err)
 
     if not cmd:
         cmd = extract_cmd(fn, overwrite=overwrite)

From 1eb00cdcd98a8bbdc8bdd33416ad093d075b3904 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Mar 2015 16:08:47 +0100
Subject: [PATCH 0820/1356] fix prepend_paths for Lua syntax

---
 easybuild/tools/module_generator.py | 13 ++++++++-----
 test/framework/module_generator.py  |  9 +++++----
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 67b4995eb3..7411858117 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -373,18 +373,21 @@ def prepend_paths(self, key, paths, allow_abs=False):
         """
         Generate prepend-path statements for the given list of paths
         """
-        template = 'prepend_path(%s,%s)\n'
+        template = "prepend_path(%s, %s)\n"
 
         if isinstance(paths, basestring):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
         for i, path in enumerate(paths):
-            if os.path.isabs(path) and not allow_abs:
-                self.log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % path)
-            elif not os.path.isabs(path):
+            if os.path.isabs(path):
+                if allow_abs:
+                    paths[i] = quote_str(path)
+                else:
+                    self.log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % path)
+            else:
                 # use pathJoin(pkg.root, path) for relative paths
-                paths[i]=' pathJoin(pkg.root,"%s")' % path
+                paths[i] = 'pathJoin(pkg.root, "%s")' % path
 
         statements = [template % (quote_str(key), p) for p in paths]
         return ''.join(statements)
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 1b7fb51d8a..67974a92b3 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -197,16 +197,17 @@ def test_prepend_paths(self):
                                   self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])
         else:
             expected = '\n'.join([
-                'prepend_path("key", pathJoin(pkg.root,"path1"))',
-                'prepend_path("key", pathJoin(pkg.root,"path2"))',
+                'prepend_path("key", pathJoin(pkg.root, "path1"))',
+                'prepend_path("key", pathJoin(pkg.root, "path2"))',
                 '',
             ])
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
 
-            expected = 'prepend_path("bar", pathJoin(pkg.root,"foo"))\n'
+            expected = 'prepend_path("bar", pathJoin(pkg.root, "foo"))\n'
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
 
-            self.assertEqual('prepend_path("key", "/abs/path")', self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
+            expected = 'prepend_path("key", "/abs/path")\n'
+            self.assertEqual(expected, self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
 
             self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
                                                   "which only expects relative paths." % self.modgen.app.installdir,

From f2acb53bb2c4f0b90b617624bf14f561f033f2d7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Mar 2015 16:50:29 +0100
Subject: [PATCH 0821/1356] fix typo in easyblock.py

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 77f3a4add6..23db63e7cc 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -847,7 +847,7 @@ def make_module_extra(self):
         environment_name = convert_name(self.name, upper=True)
         
         if self.module_generator.SYNTAX == 'Lua':
-            txt += self.module_generator.self_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, self.installdir)
+            txt += self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, self.installdir)
             devel_path = os.path.join(self.installdir, log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
         elif self.module_generator.SYNTAX == 'Tcl':
             txt += self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, "$root")

From ccf2f41d23fb0a2e3ca87e3f8599aa3572ae0521 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Fri, 27 Mar 2015 11:58:14 -0400
Subject: [PATCH 0822/1356] adding some comments

---
 easybuild/tools/packaging.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 05235eb5b9..420de20e65 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -47,6 +47,9 @@
 _log = fancylogger.getLogger('tools.packaging')
 
 def package_fpm(easyblock, modfile_path ):
+    '''
+    This function will build a package using fpm and return the directory where the packages are
+    '''
     
     workdir = tempfile.mkdtemp()
     _log.info("Will be writing RPM to %s" % workdir)

From 3f93fc7da6a4947ab65fbb83caed7790aa1ff134 Mon Sep 17 00:00:00 2001
From: pescobar <pescobar001@gmail.com>
Date: Fri, 27 Mar 2015 17:33:07 +0100
Subject: [PATCH 0823/1356] modified commit message. First show installed
 software. removed new line. added EB version

---
 easybuild/tools/repository/gitrepo.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/repository/gitrepo.py b/easybuild/tools/repository/gitrepo.py
index c70d12efba..87f02f7835 100644
--- a/easybuild/tools/repository/gitrepo.py
+++ b/easybuild/tools/repository/gitrepo.py
@@ -45,6 +45,7 @@
 
 from easybuild.tools.filetools import rmtree2
 from easybuild.tools.repository.filerepo import FileRepository
+from easybuild.tools.version import VERSION
 
 _log = fancylogger.getLogger('gitrepo', fname=False)
 
@@ -139,10 +140,9 @@ def commit(self, msg=None):
         Commit working copy to git repository
         """
         self.log.debug("committing in git: %s" % msg)
-        completemsg = "EasyBuild-commit from %s (time: %s, user: %s) \n%s" % (socket.gethostname(),
-                                                                              time.strftime("%Y-%m-%d_%H-%M-%S"),
-                                                                              getpass.getuser(),
-                                                                              msg)
+        completemsg = "%s EasyBuild-commit from %s (time: %s, user: %s). Easybuild v%s" % (msg, socket.gethostname(),
+                                                                                           time.strftime("%Y-%m-%d_%H-%M-%S"),
+                                                                                           getpass.getuser(), str(VERSION))
         self.log.debug("git status: %s" % self.client.status())
         try:
             self.client.commit('-am "%s"' % completemsg)

From 82b42a77efd633f0f7550fc4671bbad08c2b4ee7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 27 Mar 2015 20:07:13 +0100
Subject: [PATCH 0824/1356] remove log.error calls after sync with develop

---
 easybuild/tools/filetools.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 51796d14b5..4e635bf9b0 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -905,7 +905,8 @@ def move_logs(src_logfile, target_logfile):
             _log.info("Moved log file %s to %s" % (src_logfile, new_log_path))
 
     except (IOError, OSError), err:
-        _log.error("Failed to move log file(s) %s* to new log file %s*: %s" % (src_logfile, target_logfile, err))
+        raise EasyBuildError("Failed to move log file(s) %s* to new log file %s*: %s" ,
+                             src_logfile, target_logfile, err)
 
 
 def cleanup(logfile, tempdir, testing):
@@ -915,14 +916,14 @@ def cleanup(logfile, tempdir, testing):
             for log in glob.glob('%s*' % logfile):
                 os.remove(log)
         except OSError, err:
-            _log.error("Failed to remove log file(s) %s*: %s" % (logfile, err))
+            raise EasyBuildError("Failed to remove log file(s) %s*: %s", logfile, err)
         print_msg('temporary log file(s) %s* have been removed.' % (logfile), log=None, silent=testing)
 
     if not testing and tempdir is not None:
         try:
             shutil.rmtree(tempdir, ignore_errors=True)
         except OSError, err:
-            _log.error("Failed to remove temporary directory %s: %s" % (tempdir, err))
+            raise EasyBuildError("Failed to remove temporary directory %s: %s", tempdir, err)
         print_msg('temporary directory %s has been removed.' % (tempdir), log=None, silent=testing)
 
 

From 99073fb343558717ffa5dc4ddd5758ad3569430d Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Sat, 28 Mar 2015 22:38:35 -0400
Subject: [PATCH 0825/1356] adding support to specify deb or rpm as a
 package_type and handle a template rather than a prefix

---
 easybuild/framework/easyblock.py |  8 +++++---
 easybuild/tools/config.py        |  9 +++++----
 easybuild/tools/options.py       |  8 +++++---
 easybuild/tools/packaging.py     | 33 ++++++++++++++++++++------------
 4 files changed, 36 insertions(+), 22 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 890c98ac3f..57566dc667 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1450,13 +1450,15 @@ def package_step(self):
         packagedir_dest = os.path.abspath(package_path())
 
         packaging_tool = build_option('package_tool')
-        if packaging_tool is not None:
-            packagedir_src = package_fpm(self, path_to_module_file)
+        if packaging_tool == "fpm":
+            packaging_type = build_option('package_type') if build_option('package_type') else "rpm"
+             
+            packagedir_src = package_fpm(self, path_to_module_file, package_type=packaging_type)
    
             if not os.path.exists(packagedir_dest):
                 mkdir(packagedir_dest)
         
-            for file in glob.glob(os.path.join(packagedir_src, "*.rpm")):
+            for file in glob.glob(os.path.join(packagedir_src, "*.%s" % packaging_type)):
                 shutil.copy(file, packagedir_dest)
         else:
             _log.debug('Skipping package step')
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index c1dad20186..89b104f2cc 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -66,7 +66,7 @@
 }
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
-DEFAULT_PACKAGE_PREFIX = "easybuild"
+DEFAULT_PACKAGE_TEMPLATE = "eb-%(toolchain)s-%(name)s"
 
 # utility function for obtaining default paths
 def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
@@ -93,6 +93,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'only_blocks',
         'optarch',
         'package_tool',
+        'package_type',
         'regtest_output_dir',
         'skip',
         'stop',
@@ -184,7 +185,7 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'buildpath',
         'installpath',
         'packagepath',
-        'package_prefix',
+        'package_template',
         'sourcepath',
         'repository',
         'repositorypath',
@@ -349,11 +350,11 @@ def package_path():
     """
     return ConfigurationVariables()['packagepath']
 
-def package_prefix():
+def package_template():
     """
     Returns the package template
     """
-    return ConfigurationVariables()['package_prefix']
+    return ConfigurationVariables()['package_template']
 
 def get_modules_tool():
     """
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index b2ab6db75e..0f1cf09d45 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -50,7 +50,7 @@
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
-from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY, DEFAULT_PACKAGE_PREFIX
+from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY, DEFAULT_PACKAGE_TEMPLATE
 from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
@@ -245,8 +245,10 @@ def config_options(self):
                              'choice', 'store', DEFAULT_MODULES_TOOL, sorted(avail_modules_tools().keys())),
             'package-tool': ("Packaging tool to use",
                              None, 'store_or_None', None),
-            'package-prefix': ("A template string to name the package",
-                             None, 'store', DEFAULT_PACKAGE_PREFIX),
+            'package-type': ("Packaging type to output to",
+                             None, 'store_or_None', None),
+            'package-template': ("A template string to name the package",
+                             None, 'store', DEFAULT_PACKAGE_TEMPLATE),
             'packagepath': ("The destination path for the packages built by package-tool",
                              None, 'store', mk_full_default_path('packagepath')),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 420de20e65..0ad3aed8d2 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -40,13 +40,13 @@
 from vsc.utils import fancylogger
 
 from easybuild.tools.run import run_cmd
-from easybuild.tools.config import install_path, package_prefix
+from easybuild.tools.config import install_path, package_template
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 
 _log = fancylogger.getLogger('tools.packaging')
 
-def package_fpm(easyblock, modfile_path ):
+def package_fpm(easyblock, modfile_path, package_type="rpm" ):
     '''
     This function will build a package using fpm and return the directory where the packages are
     '''
@@ -59,18 +59,21 @@ def package_fpm(easyblock, modfile_path ):
     except OSError, err:
         _log.error("Failed to chdir into workdir: %s : %s" % (workdir, err))
 
-    pkgprefix   = package_prefix()
-    pkgtemplate = "%(prefix)s-%(name)s"
+    # default package_template is "eb-%(toolchain)s-%(name)s"
+    pkgtemplate = package_template()
     full_ec_version = det_full_ec_version(easyblock.cfg)
-    #"HPCBIOS.20150211-%(name)s-%(version)s"
+    _log.debug("I got a package template that looks like: %s " % pkgtemplate )
 
-    pkgname=pkgtemplate % {
-        'prefix' : pkgprefix,
+    if easyblock.toolchain.name == DUMMY_TOOLCHAIN_NAME:
+        toolchain_name = easyblock.version
+    else:
+        toolchain_name = "%s-%s" % (easyblock.toolchain.name, easyblock.toolchain.version)
+
+    pkgname = pkgtemplate % {
+        'toolchain' : toolchain_name,
         'name' : easyblock.name,
     }
     
-    # a lot of this logic should probably be put elsewhere, but make_module_dep is the only place I've seen that uses it
-
     deps = []
     if easyblock.toolchain.name != DUMMY_TOOLCHAIN_NAME:
         toolchain_dict = easyblock.toolchain.as_dict()
@@ -83,14 +86,20 @@ def package_fpm(easyblock, modfile_path ):
     for dep in deps:
         full_dep_version = det_full_ec_version(dep)
         #by default will only build iteration 1 packages, do we need to enhance this?
-        depstring += " --depends '%s-%s = %s-1'" % ( pkgprefix , dep['name'], full_dep_version)
+        _log.debug("The dep added looks like %s " % dep)
+        dep_pkgname = pkgtemplate % {
+            'name': dep['name'],
+            'toolchain': "%s-%s" % (dep['toolchain']['name'], dep['toolchain']['version']),
+
+        }
+        depstring += " --depends '%s = %s-1'" % ( dep_pkgname,  full_dep_version)
 
     cmdlist=[
         'fpm',
         '--workdir', workdir,
         '--name', pkgname,
-        '--provides', "%s-%s" %(pkgprefix,easyblock.name),
-        '-t', 'rpm', # target
+        '--provides', pkgname,
+        '-t', package_type, # target
         '-s', 'dir', # source
         '--version', full_ec_version,
     ]

From d3e21eb116158631d73c5e0a327b216b27ca8823 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 30 Mar 2015 20:43:36 +0200
Subject: [PATCH 0826/1356] bump required vsc-base version to v2.1.1, cfr.
 https://github.com/hpcugent/vsc-base/pull/163

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 2407249b3c..4fecf38036 100644
--- a/setup.py
+++ b/setup.py
@@ -106,5 +106,5 @@ def find_rel_test():
     provides=["eb"] + easybuild_packages,
     test_suite="test.framework.suite",
     zip_safe=False,
-    install_requires=["vsc-base >= 2.1.0"],
+    install_requires=["vsc-base >= 2.1.1"],
 )

From de09a3522b4e2bcbc9f0a8410ac8626602a809e9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 31 Mar 2015 21:09:13 +0200
Subject: [PATCH 0827/1356] fix origin of raised EasyBuildError in logged error
 message

---
 easybuild/tools/build_log.py | 17 +++++++++++++++--
 test/framework/build_log.py  |  2 +-
 test/framework/options.py    |  7 ++++---
 3 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index b64b5f648e..aeb0b26bc6 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -31,6 +31,7 @@
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
 """
+import inspect
 import os
 import sys
 import tempfile
@@ -63,7 +64,19 @@ class EasyBuildError(LoggedException):
 
     def __init__(self, msg, *args):
         """Constructor: initialise EasyBuildError instance."""
-        msg = msg % args
+        # figure out where error was raised from
+        # current frame: this constructor, one frame above: location where this EasyBuildError was created/raised
+        frameinfo = inspect.getouterframes(inspect.currentframe())[1]
+
+        # determine short location of Python module where error was raised from (starting with 'easybuild/')
+        path_parts = frameinfo[1].split(os.path.sep)
+        relpath = path_parts.pop()
+        while not (relpath.startswith('easybuild/') or relpath.startswith('vsc/')) and path_parts:
+            relpath = os.path.join(path_parts.pop() or os.path.sep, relpath)
+
+        # include location info at the end of the message
+        # for example: "Nope, giving up (at easybuild/tools/somemodule.py:123 in some_function)"
+        msg = "%s (at %s:%s in %s)" % (msg % args, relpath, frameinfo[2], frameinfo[3])
         LoggedException.__init__(self, msg)
         self.msg = msg
 
@@ -133,7 +146,7 @@ def _error_no_raise(self, msg):
         orig_raise_error = self.raiseError
         self.raiseError = False
 
-        self.error(msg)
+        fancylogger.FancyLogger.error(self, msg)
 
         # reinstate previous raiseError setting
         self.raiseError = orig_raise_error
diff --git a/test/framework/build_log.py b/test/framework/build_log.py
index cd97e53b32..e4773e83e6 100644
--- a/test/framework/build_log.py
+++ b/test/framework/build_log.py
@@ -65,7 +65,7 @@ def test_easybuilderror(self):
         self.assertErrorRegex(EasyBuildError, 'BOOM', raise_easybuilderror, 'BOOM')
         logToFile(tmplog, enable=False)
 
-        log_re = re.compile("^%s :: EasyBuild crashed .*: BOOM$" % getRootLoggerName(), re.M)
+        log_re = re.compile("^%s :: BOOM \(at %s:[0-9]+ in [a-z_]+\)$" % (getRootLoggerName(), __file__), re.M)
         logtxt = open(tmplog, 'r').read()
         self.assertTrue(log_re.match(logtxt), "%s matches %s" % (log_re.pattern, logtxt))
 
diff --git a/test/framework/options.py b/test/framework/options.py
index 0f381055a0..038844dac1 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -109,7 +109,7 @@ def test_no_args(self):
 
         outtxt = self.eb_main([])
 
-        error_msg = "ERROR .* Please provide one or multiple easyconfig files,"
+        error_msg = "ERROR Please provide one or multiple easyconfig files,"
         error_msg += " or use software build options to make EasyBuild search for easyconfigs"
         self.assertTrue(re.search(error_msg, outtxt), "Error message when eb is run without arguments")
 
@@ -922,9 +922,10 @@ def test_no_such_software(self):
         outtxt = self.eb_main(args)
 
         # error message when template is not found
-        error_msg1 = "ERROR .* No easyconfig files found for software nosuchsoftware, and no templates available. I'm all out of ideas."
+        error_msg1 = "ERROR No easyconfig files found for software nosuchsoftware, and no templates available. "
+        error_msg1 += "I'm all out of ideas."
         # error message when template is found
-        error_msg2 = "ERROR .* Unable to find an easyconfig for the given specifications"
+        error_msg2 = "ERROR Unable to find an easyconfig for the given specifications"
         msg = "Error message when eb can't find software with specified name (outtxt: %s)" % outtxt
         self.assertTrue(re.search(error_msg1, outtxt) or re.search(error_msg2, outtxt), msg)
 

From 2ae446e5ff8f4bc1fb004183b59738b96f109870 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 31 Mar 2015 21:16:32 +0200
Subject: [PATCH 0828/1356] update comment

---
 easybuild/tools/build_log.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index aeb0b26bc6..f6a30e850e 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -68,7 +68,7 @@ def __init__(self, msg, *args):
         # current frame: this constructor, one frame above: location where this EasyBuildError was created/raised
         frameinfo = inspect.getouterframes(inspect.currentframe())[1]
 
-        # determine short location of Python module where error was raised from (starting with 'easybuild/')
+        # determine short location of Python module where error was raised from (starting with 'easybuild/' or 'vsc/')
         path_parts = frameinfo[1].split(os.path.sep)
         relpath = path_parts.pop()
         while not (relpath.startswith('easybuild/') or relpath.startswith('vsc/')) and path_parts:

From 8540ac88b1e720529ce2149b21781afe4830e22a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 31 Mar 2015 21:29:57 +0200
Subject: [PATCH 0829/1356] replace log.error with raise EasyBuildError

---
 easybuild/tools/module_generator.py | 7 ++++---
 easybuild/tools/options.py          | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 8b596c1895..2d20a62fbc 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -386,7 +386,8 @@ def prepend_paths(self, key, paths, allow_abs=False):
                 if allow_abs:
                     paths[i] = quote_str(path)
                 else:
-                    self.log.error("Absolute path %s passed to prepend_paths which only expects relative paths." % path)
+                    raise EasyBuildError("Absolute path %s passed to prepend_paths which only expects relative paths.",
+                                         path)
             else:
                 # use pathJoin(pkg.root, path) for relative paths
                 paths[i] = 'pathJoin(pkg.root, "%s")' % path
@@ -453,8 +454,8 @@ def module_generator(app, fake=False):
     available_mod_gens = avail_module_generators()
 
     if module_syntax not in available_mod_gens:
-        tup = (module_syntax, available_mod_gens)
-        _log.error("No module generator available for specified syntax '%s' (available: %s)" % tup)
+        raise EasyBuildError("No module generator available for specified syntax '%s' (available: %s)",
+                             module_syntax, available_mod_gens)
 
     module_generator_class = available_mod_gens[module_syntax]
     return module_generator_class(app, fake=fake)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index c2560969b3..43faee2022 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -413,7 +413,7 @@ def postprocess(self):
                 raise EasyBuildError("Required support for using GitHub API is not available (see warnings).")
 
         if self.options.module_syntax == ModuleGeneratorLua.SYNTAX and self.options.modules_tool != Lmod.__name__:
-            self.log.error("Generating Lua module files requires Lmod as modules tool.")
+            raise EasyBuildError("Generating Lua module files requires Lmod as modules tool.")
 
         # make sure a GitHub token is available when it's required
         if self.options.upload_test_report:

From 17c24ddb8a6acd32c49452e9fb3f65cbc695bd45 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Apr 2015 11:41:25 +0200
Subject: [PATCH 0830/1356] extend $MODULEPATH (no 'use' in Lua module files),
 correctly support module footer in Lua syntax, fix msg_on_load for Lua

---
 easybuild/framework/easyblock.py          |  6 ++++--
 easybuild/framework/easyconfig/default.py |  1 +
 easybuild/tools/module_generator.py       | 22 ++++++++++++++++++----
 3 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index fa10e159a3..065b789b69 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -67,7 +67,7 @@
 from easybuild.tools.filetools import write_file, compute_checksum, verify_checksum
 from easybuild.tools.run import run_cmd
 from easybuild.tools.jenkins import write_to_xml
-from easybuild.tools.module_generator import module_generator
+from easybuild.tools.module_generator import ModuleGeneratorLua, ModuleGeneratorTcl, module_generator
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.modules import ROOT_ENV_VAR_NAME_PREFIX, VERSION_ENV_VAR_NAME_PREFIX, DEVEL_ENV_VAR_NAME_PREFIX
 from easybuild.tools.modules import get_software_root, modules_tool
@@ -871,8 +871,10 @@ def make_module_extra(self):
             txt += self.module_generator.prepend_paths(key, value)
         if self.cfg['modloadmsg']:
             txt += self.module_generator.msg_on_load(self.cfg['modloadmsg'])
-        if self.cfg['modtclfooter']:
+        if self.cfg['modtclfooter'] and isinstance(self.module_generator, ModuleGeneratorTcl):
             txt += self.module_generator.add_tcl_footer(self.cfg['modtclfooter'])
+        if self.cfg['modluafooter'] and isinstance(self.module_generator, ModuleGeneratorLua):
+            txt += self.module_generator.add_lua_footer(self.cfg['modluafooter'])
         for (key, value) in self.cfg['modaliases'].items():
             txt += self.module_generator.set_alias(key, value)
 
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index d5e8313081..64cf46be16 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -158,6 +158,7 @@
     'modextrapaths': [{}, "Extra paths to be prepended in module file", MODULES],
     'modextravars': [{}, "Extra environment variables to be added to module file", MODULES],
     'modloadmsg': [{}, "Message that should be printed when generated module is loaded", MODULES],
+    'modluafooter': ["", "Footer to include in generated module file (Lua syntax)", MODULES],
     'modtclfooter': ["", "Footer to include in generated module file (Tcl syntax)", MODULES],
     'modaliases': [{}, "Aliases to be defined in module file", MODULES],
     'moduleclass': ['base', 'Module class to be used for this software', MODULES],
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 2d20a62fbc..017e4ef9b9 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -281,6 +281,11 @@ def add_tcl_footer(self, tcltxt):
         """
         return tcltxt
 
+    def add_lua_footer(self, luatxt):
+        """
+        Appending Tcl code in Lua files doesn't make sense."""
+        raise EasyBuildError("Appending Lua footer to module file in Tcl syntax doesn't work: %s", luatxt)
+
     def set_alias(self, key, value):
         """
         Generate set-alias statement in modulefile for the given key/value pair.
@@ -400,7 +405,7 @@ def use(self, paths):
         Generate module use statements for given list of module paths.
         @param paths: list of module path extensions to generate use statements for
         """
-        return '\n'.join(['use("%s")' % p for p in paths] + [''])
+        return '\n'.join(['prepend_path("MODULEPATH", "%s")' % p for p in paths] + [''])
 
     def set_environment(self, key, value):
         """
@@ -421,12 +426,21 @@ def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.
         """
-        pass
+        msg = re.sub(r'((?<!\\)[%s])'% ''.join(self.CHARS_TO_ESCAPE), r'\\\1', msg)
+        return '\n'.join([
+            "",
+            'if (mode() == "load") then',
+            '    io.stderr:write("%s\n")' % msg,
+            "end",
+            "",
+        ])
 
     def add_tcl_footer(self, tcltxt):
-        raise NotImplementedError
+        """
+        Appending Tcl code in Lua files doesn't make sense."""
+        raise EasyBuildError("Appending Tcl footer to module file in Lua syntax doesn't work: %s", tcltxt)
 
-    def add_lua_footer(self,luatxt):
+    def add_lua_footer(self, luatxt):
         """
         Append whatever Lua code you want to your modulefile
         """

From 7fe647d19a4647fb51b3f7c389880cce92ef2644 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Apr 2015 11:48:12 +0200
Subject: [PATCH 0831/1356] fix tests that are broken when using Lua module
 syntax

---
 test/framework/easyblock.py |  83 ++++++++++++++++++++++-------
 test/framework/options.py   |  31 ++++++++---
 test/framework/toy_build.py | 102 ++++++++++++++++++++++++++++++------
 3 files changed, 173 insertions(+), 43 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index d1153186b6..17c06287f5 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -43,6 +43,7 @@
 from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
 from easybuild.tools import config
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import get_module_syntax
 from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.modules import modules_tool
 
@@ -192,11 +193,20 @@ def test_make_module_req(self):
 
         guess = eb.make_module_req()
 
-        self.assertTrue(re.search("^prepend-path\s+CLASSPATH\s+\$root/bla.jar$", guess, re.M))
-        self.assertTrue(re.search("^prepend-path\s+CLASSPATH\s+\$root/foo.jar$", guess, re.M))
-        self.assertTrue(re.search("^prepend-path\s+MANPATH\s+\$root/share/man$", guess, re.M))
-        self.assertTrue(re.search("^prepend-path\s+PATH\s+\$root/bin$", guess, re.M))
-        self.assertFalse(re.search("^prepend-path\s+CPATH\s+.*$", guess, re.M))
+        if get_module_syntax() == 'Tcl':
+            self.assertTrue(re.search("^prepend-path\s+CLASSPATH\s+\$root/bla.jar$", guess, re.M))
+            self.assertTrue(re.search("^prepend-path\s+CLASSPATH\s+\$root/foo.jar$", guess, re.M))
+            self.assertTrue(re.search("^prepend-path\s+MANPATH\s+\$root/share/man$", guess, re.M))
+            self.assertTrue(re.search("^prepend-path\s+PATH\s+\$root/bin$", guess, re.M))
+            self.assertFalse(re.search("^prepend-path\s+CPATH\s+.*$", guess, re.M))
+        elif get_module_syntax() == 'Lua':
+            self.assertTrue(re.search('^prepend_path\("CLASSPATH", pathJoin\(pkg.root, "bla.jar"\)\)$', guess, re.M))
+            self.assertTrue(re.search('^prepend_path\("CLASSPATH", pathJoin\(pkg.root, "foo.jar"\)\)$', guess, re.M))
+            self.assertTrue(re.search('^prepend_path\("MANPATH", pathJoin\(pkg.root, "share/man"\)\)$', guess, re.M))
+            self.assertTrue(re.search('^prepend_path\("PATH", pathJoin\(pkg.root, "bin"\)\)$', guess, re.M))
+            self.assertFalse(re.search('^prepend_path\("CPATH", .*\)$', guess, re.M))
+        else:
+            self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
 
         # cleanup
         eb.close_log()
@@ -300,29 +310,63 @@ def test_make_module_step(self):
         eb.check_readiness_step()
 
         modpath = os.path.join(eb.make_module_step(), name, version)
+        if get_module_syntax() == 'Lua':
+            modpath += '.lua'
         self.assertTrue(os.path.exists(modpath), "%s exists" % modpath)
 
         # verify contents of module
-        f = open(modpath, 'r')
-        txt = f.read()
-        f.close()
-        self.assertTrue(re.search("^#%Module", txt.split('\n')[0]))
-        self.assertTrue(re.search("^conflict\s+%s$" % name, txt, re.M))
-        self.assertTrue(re.search("^set\s+root\s+%s$" % eb.installdir, txt, re.M))
-        ebroot_regex = re.compile('^setenv\s+EBROOT%s\s+".root"\s*$' % name.upper(), re.M)
-        self.assertTrue(ebroot_regex.search(txt), "%s in %s" % (ebroot_regex.pattern, txt))
-        self.assertTrue(re.search('^setenv\s+EBVERSION%s\s+"%s"$' % (name.upper(), version), txt, re.M))
+        txt = read_file(modpath)
+        if get_module_syntax() == 'Tcl':
+            self.assertTrue(re.search(r"^#%Module", txt.split('\n')[0]))
+            self.assertTrue(re.search(r"^conflict\s+%s$" % name, txt, re.M))
+
+            self.assertTrue(re.search(r"^set\s+root\s+%s$" % eb.installdir, txt, re.M))
+            ebroot_regex = re.compile(r'^setenv\s+EBROOT%s\s+".root"\s*$' % name.upper(), re.M)
+            self.assertTrue(ebroot_regex.search(txt), "%s in %s" % (ebroot_regex.pattern, txt))
+            self.assertTrue(re.search(r'^setenv\s+EBVERSION%s\s+"%s"$' % (name.upper(), version), txt, re.M))
+
+        elif get_module_syntax() == 'Lua':
+            ebroot_regex = re.compile(r'^setenv\("EBROOT%s", ".*%s.*"\)$' % (name.upper(), eb.installdir), re.M)
+            self.assertTrue(ebroot_regex.search(txt), "%s in %s" % (ebroot_regex.pattern, txt))
+            self.assertTrue(re.search(r'^setenv\("EBVERSION%s", "%s"\)$' % (name.upper(), version), txt, re.M))
+
+        else:
+            self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
+
         for (key, val) in modextravars.items():
-            regex = re.compile('^setenv\s+%s\s+"%s"$' % (key, val), re.M)
+            if get_module_syntax() == 'Tcl':
+                regex = re.compile(r'^setenv\s+%s\s+"%s"$' % (key, val), re.M)
+            elif get_module_syntax() == 'Lua':
+                regex = re.compile(r'^setenv\("%s", "%s"\)$' % (key, val), re.M)
+            else:
+                self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
             self.assertTrue(regex.search(txt), "Pattern %s found in %s" % (regex.pattern, txt))
+
         for (key, val) in modextrapaths.items():
-            regex = re.compile('^prepend-path\s+%s\s+\$root/%s$' % (key, val), re.M)
+            if get_module_syntax() == 'Tcl':
+                regex = re.compile(r'^prepend-path\s+%s\s+\$root/%s$' % (key, val), re.M)
+            elif get_module_syntax() == 'Lua':
+                regex = re.compile(r'^prepend_path\("%s", pathJoin\(pkg.root, "%s"\)\)$' % (key, val), re.M)
+            else:
+                self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
             self.assertTrue(regex.search(txt), "Pattern %s found in %s" % (regex.pattern, txt))
+
         for (name, ver) in deps:
-            regex = re.compile('^\s*module load %s\s*$' % os.path.join(name, ver), re.M)
+            if get_module_syntax() == 'Tcl':
+                regex = re.compile(r'^\s*module load %s\s*$' % os.path.join(name, ver), re.M)
+            elif get_module_syntax() == 'Lua':
+                regex = re.compile(r'^\s*load\("%s"\)$' % os.path.join(name, ver), re.M)
+            else:
+                self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
             self.assertTrue(regex.search(txt), "Pattern %s found in %s" % (regex.pattern, txt))
+
         for (name, ver) in hiddendeps:
-            regex = re.compile('^\s*module load %s/.%s\s*$' % (name, ver), re.M)
+            if get_module_syntax() == 'Tcl':
+                regex = re.compile(r'^\s*module load %s/.%s\s*$' % (name, ver), re.M)
+            elif get_module_syntax() == 'Lua':
+                regex = re.compile(r'^\s*load\("%s/.%s"\)$' % (name, ver), re.M)
+            else:
+                self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
             self.assertTrue(regex.search(txt), "Pattern %s found in %s" % (regex.pattern, txt))
 
     def test_gen_dirs(self):
@@ -546,6 +590,9 @@ def test_exclude_path_to_top_of_module_tree(self):
 
         impi_modfile_path = os.path.join('Compiler', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049')
         imkl_modfile_path = os.path.join('MPI', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
+        if get_module_syntax() == 'Lua':
+            impi_modfile_path += '.lua'
+            imkl_modfile_path += '.lua'
 
         # example: for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included
         # not for the toolchain or any of the toolchain components,
diff --git a/test/framework/options.py b/test/framework/options.py
index 0f381055a0..efce8a9059 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -42,6 +42,7 @@
 from easybuild.framework.easyconfig import BUILD, CUSTOM, DEPENDENCIES, EXTENSIONS, FILEMANAGEMENT, LICENSE
 from easybuild.framework.easyconfig import MANDATORY, MODULES, OTHER, TOOLCHAIN
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import get_module_syntax
 from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.github import fetch_github_token
@@ -932,15 +933,22 @@ def test_footer(self):
         """Test specifying a module footer."""
 
         # create file containing modules footer
-        module_footer_txt = '\n'.join([
-            "# test footer",
-            "setenv SITE_SPECIFIC_ENV_VAR foobar",
-        ])
+        if get_module_syntax() == 'Tcl':
+            module_footer_txt = '\n'.join([
+                "# test footer",
+                "setenv SITE_SPECIFIC_ENV_VAR foobar",
+            ])
+        elif get_module_syntax() == 'Lua':
+            module_footer_txt = '\n'.join([
+                "-- test footer",
+                'setenv("SITE_SPECIFIC_ENV_VAR", "foobar")',
+            ])
+        else:
+            self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
+
         fd, modules_footer = tempfile.mkstemp(prefix='modules-footer-')
         os.close(fd)
-        f = open(modules_footer, 'w')
-        f.write(module_footer_txt)
-        f.close()
+        write_file(modules_footer, module_footer_txt)
 
         # use toy-0.0.eb easyconfig file that comes with the tests
         eb_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
@@ -958,8 +966,10 @@ def test_footer(self):
         self.eb_main(args, do_build=True)
 
         toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0')
+        if get_module_syntax() == 'Lua':
+            toy_module += '.lua'
         toy_module_txt = read_file(toy_module)
-        footer_regex = re.compile(r'%s$' % module_footer_txt, re.M)
+        footer_regex = re.compile(r'%s$' % module_footer_txt.replace('(', '\\(').replace(')', '\\)'), re.M)
         msg = "modules footer '%s' is present in '%s'" % (module_footer_txt, toy_module_txt)
         self.assertTrue(footer_regex.search(toy_module_txt), msg)
 
@@ -985,6 +995,8 @@ def test_recursive_module_unload(self):
         self.eb_main(args, do_build=True, verbose=True)
 
         toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0-deps')
+        if get_module_syntax() == 'Lua':
+            toy_module += '.lua'
         toy_module_txt = read_file(toy_module)
         is_loaded_regex = re.compile(r"if { !\[is-loaded gompi/1.3.12\] }", re.M)
         self.assertFalse(is_loaded_regex.search(toy_module_txt), "Recursive unloading is used: %s" % toy_module_txt)
@@ -1169,6 +1181,7 @@ def test_allow_modules_tool_mismatch(self):
         args = [
             ec_file,
             '--modules-tool=MockModulesTool',
+            '--module-syntax=Tcl',  # Lua would require Lmod
         ]
         self.eb_main(args, do_build=True)
         outtxt = read_file(self.logfile)
@@ -1180,6 +1193,7 @@ def test_allow_modules_tool_mismatch(self):
         args = [
             ec_file,
             '--modules-tool=MockModulesTool',
+            '--module-syntax=Tcl',  # Lua would require Lmod
             '--allow-modules-tool-mismatch',
         ]
         self.eb_main(args, do_build=True)
@@ -1192,6 +1206,7 @@ def test_allow_modules_tool_mismatch(self):
         args = [
             ec_file,
             '--modules-tool=MockModulesTool',
+            '--module-syntax=Tcl',  # Lua would require Lmod
             '--debug',
         ]
         self.eb_main(args, do_build=True)
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 72e5b320d8..ebf18b8ab1 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -43,6 +43,7 @@
 import easybuild.tools.module_naming_scheme  # required to dynamically load test module naming scheme(s)
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import get_module_syntax
 from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.modules import modules_tool
 
@@ -79,10 +80,14 @@ def check_toy(self, installpath, outtxt, version='0.0', versionprefix='', versio
         # if the module exists, it should be fine
         toy_module = os.path.join(installpath, 'modules', 'all', 'toy', full_version)
         msg = "module for toy build toy/%s found (path %s)" % (full_version, toy_module)
+        if get_module_syntax() == 'Lua':
+            toy_module += '.lua'
         self.assertTrue(os.path.exists(toy_module), msg)
 
         # module file is symlinked according to moduleclass
         toy_module_symlink = os.path.join(installpath, 'modules', 'tools', 'toy', full_version)
+        if get_module_syntax() == 'Lua':
+            toy_module_symlink += '.lua'
         self.assertTrue(os.path.islink(toy_module_symlink))
         self.assertTrue(os.path.exists(toy_module_symlink))
 
@@ -207,7 +212,8 @@ def test_toy_tweaked(self):
             "modextrapaths = {'SOMEPATH': ['foo/bar', 'baz']}",
             "modextravars = {'FOO': 'bar'}",
             "modloadmsg =  'THANKS FOR LOADING ME, I AM %(name)s v%(version)s'",
-            "modtclfooter = 'puts stderr \"oh hai!\"'",
+            "modtclfooter = 'puts stderr \"oh hai!\"'",  # ignored when module syntax is Lua
+            "modluafooter = 'io.stderr:write(\"oh hai!\")'"  # ignored when module syntax is Tcl
         ])
         write_file(ec_file, ec_extra, append=True)
 
@@ -222,13 +228,25 @@ def test_toy_tweaked(self):
         outtxt = self.eb_main(args, do_build=True, verbose=True, raise_error=True)
         self.check_toy(self.test_installpath, outtxt, versionsuffix='-tweaked')
         toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0-tweaked')
+        if get_module_syntax() == 'Lua':
+            toy_module += '.lua'
         toy_module_txt = read_file(toy_module)
 
-        self.assertTrue(re.search('setenv\s*FOO\s*"bar"', toy_module_txt))
-        self.assertTrue(re.search('prepend-path\s*SOMEPATH\s*\$root/foo/bar', toy_module_txt))
-        self.assertTrue(re.search('prepend-path\s*SOMEPATH\s*\$root/baz', toy_module_txt))
-        self.assertTrue(re.search('module-info mode load.*\n\s*puts stderr\s*.*I AM toy v0.0', toy_module_txt))
-        self.assertTrue(re.search('puts stderr "oh hai!"', toy_module_txt))
+        if get_module_syntax() == 'Tcl':
+            self.assertTrue(re.search(r'setenv\s*FOO\s*"bar"', toy_module_txt))
+            self.assertTrue(re.search(r'prepend-path\s*SOMEPATH\s*\$root/foo/bar', toy_module_txt))
+            self.assertTrue(re.search(r'prepend-path\s*SOMEPATH\s*\$root/baz', toy_module_txt))
+            self.assertTrue(re.search(r'module-info mode load.*\n\s*puts stderr\s*.*I AM toy v0.0', toy_module_txt))
+            self.assertTrue(re.search(r'puts stderr "oh hai!"', toy_module_txt))
+        elif get_module_syntax() == 'Lua':
+            self.assertTrue(re.search(r'setenv\("FOO", "bar"\)', toy_module_txt))
+            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(pkg.root, "foo/bar"\)\)', toy_module_txt))
+            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(pkg.root, "baz"\)\)', toy_module_txt))
+            self.assertTrue(re.search(r'if \(mode\(\) == "load"\) then\n\s*io.stderr:write\(".*I AM toy v0.0\n"\)',
+                                      toy_module_txt))
+            self.assertTrue(re.search(r'io.stderr:write\("oh hai!"\)', toy_module_txt))
+        else:
+            self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
 
     def test_toy_buggy_easyblock(self):
         """Test build using a buggy/broken easyblock, make sure a traceback is reported."""
@@ -442,8 +460,12 @@ def test_toy_permissions(self):
                     (('modules', ), dir_perms),
                     (('modules', 'all'), dir_perms),
                     (('modules', 'all', 'toy'), dir_perms),
-                    (('modules', 'all', 'toy', '0.0'), fil_perms),
                 ])
+                if get_module_syntax() == 'Tcl':
+                    paths_perms.append((('modules', 'all', 'toy', '0.0'), fil_perms))
+                elif get_module_syntax() == 'Lua':
+                    paths_perms.append((('modules', 'all', 'toy', '0.0.lua'), fil_perms))
+
             for path, correct_perms in paths_perms:
                 fullpath = glob.glob(os.path.join(self.test_installpath, *path))[0]
                 perms = os.stat(fullpath).st_mode & 0777
@@ -532,16 +554,25 @@ def test_toy_hierarchical(self):
 
         # make sure module file is installed in correct path
         toy_module_path = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4', 'toy', '0.0')
+        if get_module_syntax() == 'Lua':
+            toy_module_path += '.lua'
         self.assertTrue(os.path.exists(toy_module_path))
 
         # check that toolchain load is expanded to loads for toolchain dependencies,
         # except for the ones that extend $MODULEPATH to make the toy module available
+        if get_module_syntax() == 'Tcl':
+            load_regex_template = "load %s"
+        elif get_module_syntax() == 'Lua':
+            load_regex_template = r'load\("%s/.*"\)'
+        else:
+            self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
+
         modtxt = read_file(toy_module_path)
         for dep in ['goolf', 'GCC', 'OpenMPI']:
-            load_regex = re.compile("load %s" % dep)
+            load_regex = re.compile(load_regex_template % dep)
             self.assertFalse(load_regex.search(modtxt), "Pattern '%s' not found in %s" % (load_regex.pattern, modtxt))
         for dep in ['OpenBLAS', 'FFTW', 'ScaLAPACK']:
-            load_regex = re.compile("load %s" % dep)
+            load_regex = re.compile(load_regex_template % dep)
             self.assertTrue(load_regex.search(modtxt), "Pattern '%s' found in %s" % (load_regex.pattern, modtxt))
 
         os.remove(toy_module_path)
@@ -554,6 +585,8 @@ def test_toy_hierarchical(self):
 
         # make sure module file is installed in correct path
         toy_module_path = os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'toy', '0.0')
+        if get_module_syntax() == 'Lua':
+            toy_module_path += '.lua'
         self.assertTrue(os.path.exists(toy_module_path))
 
         # no dependencies or toolchain => no module load statements in module file
@@ -570,12 +603,21 @@ def test_toy_hierarchical(self):
 
         # make sure module file is installed in correct path
         toy_module_path = os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'toy', '0.0')
+        if get_module_syntax() == 'Lua':
+            toy_module_path += '.lua'
         self.assertTrue(os.path.exists(toy_module_path))
 
         # 'module use' statements to extend $MODULEPATH are present
         modtxt = read_file(toy_module_path)
         modpath_extension = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'toy', '0.0')
-        self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        if get_module_syntax() == 'Tcl':
+            self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        elif get_module_syntax() == 'Lua':
+            fullmodpath_extension = os.path.join(self.test_installpath, modpath_extension)
+            regex = re.compile(r'^prepend_path\("MODULEPATH", "%s"\)' % fullmodpath_extension, re.M)
+            self.assertTrue(regex.search(modtxt), "Pattern '%s' found in %s" % (regex.pattern, modtxt))
+        else:
+            self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
         os.remove(toy_module_path)
 
         # ... unless they shouldn't be
@@ -583,7 +625,14 @@ def test_toy_hierarchical(self):
         self.eb_main(args + extra_args, logfile=self.dummylogfn, do_build=True, verbose=True, raise_error=True)
         modtxt = read_file(toy_module_path)
         modpath_extension = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'toy', '0.0')
-        self.assertFalse(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        if get_module_syntax() == 'Tcl':
+            self.assertFalse(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        elif get_module_syntax() == 'Lua':
+            fullmodpath_extension = os.path.join(self.test_installpath, modpath_extension)
+            regex = re.compile(r'^prepend_path\("MODULEPATH", "%s"\)' % fullmodpath_extension, re.M)
+            self.assertFalse(regex.search(modtxt), "Pattern '%s' found in %s" % (regex.pattern, modtxt))
+        else:
+            self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
         os.remove(toy_module_path)
 
         # test module path with dummy/dummy build
@@ -594,6 +643,8 @@ def test_toy_hierarchical(self):
 
         # make sure module file is installed in correct path
         toy_module_path = os.path.join(mod_prefix, 'Core', 'toy', '0.0')
+        if get_module_syntax() == 'Lua':
+            toy_module_path += '.lua'
         self.assertTrue(os.path.exists(toy_module_path))
 
         # no dependencies or toolchain => no module load statements in module file
@@ -610,12 +661,21 @@ def test_toy_hierarchical(self):
 
         # make sure module file is installed in correct path
         toy_module_path = os.path.join(mod_prefix, 'Core', 'toy', '0.0')
+        if get_module_syntax() == 'Lua':
+            toy_module_path += '.lua'
         self.assertTrue(os.path.exists(toy_module_path))
 
         # no dependencies or toolchain => no module load statements in module file
         modtxt = read_file(toy_module_path)
         modpath_extension = os.path.join(mod_prefix, 'Compiler', 'toy', '0.0')
-        self.assertTrue(re.search(r"^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        if get_module_syntax() == 'Tcl':
+            self.assertTrue(re.search("^module\s*use\s*%s" % modpath_extension, modtxt, re.M))
+        elif get_module_syntax() == 'Lua':
+            fullmodpath_extension = os.path.join(self.test_installpath, modpath_extension)
+            regex = re.compile(r'^prepend_path\("MODULEPATH", "%s"\)' % fullmodpath_extension, re.M)
+            self.assertTrue(regex.search(modtxt), "Pattern '%s' found in %s" % (regex.pattern, modtxt))
+        else:
+            self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
         os.remove(toy_module_path)
 
         # building a toolchain module should also work
@@ -623,6 +683,8 @@ def test_toy_hierarchical(self):
         modules_tool().purge()
         self.eb_main(args, logfile=self.dummylogfn, do_build=True, verbose=True, raise_error=False)
         gompi_module_path = os.path.join(mod_prefix, 'Core', 'gompi', '1.4.10')
+        if get_module_syntax() == 'Lua':
+            gompi_module_path += '.lua'
         self.assertTrue(os.path.exists(gompi_module_path))
 
     def test_toy_advanced(self):
@@ -638,6 +700,8 @@ def test_toy_hidden(self):
         self.test_toy_build(ec_file=ec_file, extra_args=['--hidden'], verify=False)
         # module file is hidden
         toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '.0.0')
+        if get_module_syntax() == 'Lua':
+            toy_module += '.lua'
         self.assertTrue(os.path.exists(toy_module), 'Found hidden module %s' % toy_module)
         # installed software is not hidden
         toybin = os.path.join(self.test_installpath, 'software', 'toy', '0.0', 'bin', 'toy')
@@ -667,11 +731,15 @@ def test_module_filepath_tweaking(self):
         ]
         self.eb_main(args, do_build=True, verbose=True)
         mod_file_prefix = os.path.join(self.test_installpath, 'modules')
-        self.assertTrue(os.path.exists(os.path.join(mod_file_prefix, 'foobarbaz', 'toy', '0.0')))
-        self.assertTrue(os.path.exists(os.path.join(mod_file_prefix, 'TOOLS', 'toy', '0.0')))
-        self.assertTrue(os.path.islink(os.path.join(mod_file_prefix, 'TOOLS', 'toy', '0.0')))
-        self.assertTrue(os.path.exists(os.path.join(mod_file_prefix, 't', 'toy', '0.0')))
-        self.assertTrue(os.path.islink(os.path.join(mod_file_prefix, 't', 'toy', '0.0')))
+        mod_file_suffix = ''
+        if get_module_syntax() == 'Lua':
+            mod_file_suffix += '.lua'
+
+        self.assertTrue(os.path.exists(os.path.join(mod_file_prefix, 'foobarbaz', 'toy', '0.0' + mod_file_suffix)))
+        self.assertTrue(os.path.exists(os.path.join(mod_file_prefix, 'TOOLS', 'toy', '0.0' + mod_file_suffix)))
+        self.assertTrue(os.path.islink(os.path.join(mod_file_prefix, 'TOOLS', 'toy', '0.0' + mod_file_suffix)))
+        self.assertTrue(os.path.exists(os.path.join(mod_file_prefix, 't', 'toy', '0.0' + mod_file_suffix)))
+        self.assertTrue(os.path.islink(os.path.join(mod_file_prefix, 't', 'toy', '0.0' + mod_file_suffix)))
 
     def test_toy_archived_easyconfig(self):
         """Test archived easyconfig for a succesful build."""

From c41b70846e991e8ea72f8b7f09373cf1cbde8d63 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Apr 2015 12:57:24 +0200
Subject: [PATCH 0832/1356] fix msg_on_load for Lua, fix test that checks for
 'use' statements in Lua

---
 easybuild/tools/module_generator.py | 2 +-
 test/framework/module_generator.py  | 4 ++--
 test/framework/toy_build.py         | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 017e4ef9b9..e292e33e2c 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -430,7 +430,7 @@ def msg_on_load(self, msg):
         return '\n'.join([
             "",
             'if (mode() == "load") then',
-            '    io.stderr:write("%s\n")' % msg,
+            '    io.stderr:write("%s")' % msg,
             "end",
             "",
         ])
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 67974a92b3..8f155a0c70 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -223,8 +223,8 @@ def test_use(self):
             self.assertEqual(self.modgen.use(["/some/path", "/foo/bar/baz"]), expected)
         else:
             expected = '\n'.join([
-                'use("/some/path")',
-                'use("/foo/bar/baz")',
+                'prepend_path("MODULEPATH", "/some/path")',
+                'prepend_path("MODULEPATH", "/foo/bar/baz")',
                 '',
             ])
             self.assertEqual(self.modgen.use(["/some/path", "/foo/bar/baz"]), expected)
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index ebf18b8ab1..4e9cfd7ea7 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -242,7 +242,7 @@ def test_toy_tweaked(self):
             self.assertTrue(re.search(r'setenv\("FOO", "bar"\)', toy_module_txt))
             self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(pkg.root, "foo/bar"\)\)', toy_module_txt))
             self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(pkg.root, "baz"\)\)', toy_module_txt))
-            self.assertTrue(re.search(r'if \(mode\(\) == "load"\) then\n\s*io.stderr:write\(".*I AM toy v0.0\n"\)',
+            self.assertTrue(re.search(r'if \(mode\(\) == "load"\) then\n\s*io.stderr:write\(".*I AM toy v0.0"\)',
                                       toy_module_txt))
             self.assertTrue(re.search(r'io.stderr:write\("oh hai!"\)', toy_module_txt))
         else:

From c3d0d10a71d1e38f1041344db6b713627ebabdb7 Mon Sep 17 00:00:00 2001
From: Pablo Escobar <pescobar001@gmail.com>
Date: Wed, 1 Apr 2015 14:52:33 +0200
Subject: [PATCH 0833/1356] added command line option

---
 easybuild/tools/config.py  | 1 +
 easybuild/tools/options.py | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 054b109d26..90f54c8be8 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -84,6 +84,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'dump_test_report',
         'easyblock',
         'filter_deps',
+        'hide_deps',
         'from_pr',
         'github_user',
         'group',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ebb608c169..b3d1ab6510 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -195,6 +195,9 @@ def override_options(self):
             'filter-deps': ("Comma separated list of dependencies that you DON'T want to install with EasyBuild, "
                             "because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses)",
                             str, 'extend', None),
+            'hide-deps': ("Comma separated list of dependencies that you want automatically hidden, "
+                            "(e.g. --hide-deps=zlib,ncurses)",
+                            str, 'extend', None),
             'oldstyleconfig':   ("Look for and use the oldstyle configuration file.",
                                  None, 'store_true', True),
             'optarch': ("Set architecture optimization, overriding native architecture optimizations",

From 5a9a8d84bce0833151c111e87acbe44773601aa8 Mon Sep 17 00:00:00 2001
From: Pablo Escobar <pescobar001@gmail.com>
Date: Wed, 1 Apr 2015 14:55:44 +0200
Subject: [PATCH 0834/1356] filter hidden deps

---
 easybuild/framework/easyconfig/easyconfig.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 7aac218a73..ea5567c1dc 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -566,6 +566,10 @@ def _parse_dependency(self, dep, hidden=False):
         else:
             self.log.error('Dependency %s of unsupported type: %s.' % (dep, type(dep)))
 
+        # check whether this dependency should be hidden according to --hide-deps
+        if build_option('hide_deps'):
+            dependency['hidden'] |= dependency['name'] in build_option('hide_deps')
+
         # dependency inherits toolchain, unless it's specified to have a custom toolchain
         tc = copy.deepcopy(self['toolchain'])
         tc_spec = dependency['toolchain']

From d46e967de7ac4095b57506e0787958589ac7ca93 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Apr 2015 20:55:50 +0200
Subject: [PATCH 0835/1356] style changes, add use of 'conflict' statement in
 Lua module files

---
 easybuild/framework/easyblock.py    |  97 +++++++-----
 easybuild/tools/module_generator.py | 229 ++++++++++++----------------
 easybuild/tools/modules.py          |   2 -
 test/framework/easyblock.py         |   2 +-
 test/framework/module_generator.py  |  79 +++++-----
 test/framework/toy_build.py         |   2 +-
 6 files changed, 187 insertions(+), 224 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 065b789b69..10b175179a 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -747,16 +747,16 @@ def make_devel_module(self, create_in_builddir=False):
         # load fake module
         fake_mod_data = self.load_fake_module(purge=True)
 
-        header = self.module_generator.module_header()
+        header = self.module_generator.MODULE_HEADER
 
-        env_txt = ""
+        env_lines = []
         for (key, val) in env.get_changes().items():
             # check if non-empty string
             # TODO: add unset for empty vars?
             if val.strip():
-                env_txt += self.module_generator.set_environment(key, val)
+                env_lines.append(self.module_generator.set_environment(key, val))
 
-        load_txt = ""
+        load_lines = []
         # capture all the EBDEVEL vars
         # these should be all the dependencies and we should load them
         for key in os.environ:
@@ -766,7 +766,7 @@ def make_devel_module(self, create_in_builddir=False):
                     path = os.environ[key]
                     if os.path.isfile(path):
                         mod_name = path.rsplit(os.path.sep, 1)[-1]
-                        load_txt += self.module_generator.load_module(mod_name)
+                        load_lines.append(self.module_generator.load_module(mod_name))
             elif key.startswith('SOFTDEVEL'):
                 self.log.nosupport("Environment variable SOFTDEVEL* being relied on", '2.0')
 
@@ -779,7 +779,8 @@ def make_devel_module(self, create_in_builddir=False):
         filename = os.path.join(output_dir, ActiveMNS().det_devel_module_filename(self.cfg))
         self.log.debug("Writing devel module to %s" % filename)
 
-        write_file(filename, header + load_txt + env_txt)
+        txt = '\n'.join([header] + load_lines + env_lines)
+        write_file(filename, txt)
 
         # cleanup: unload fake module, remove fake module dir
         self.clean_up_fake_module(fake_mod_data)
@@ -843,42 +844,54 @@ def make_module_extra(self):
         """
         Sets optional variables (EBROOT, MPI tuning variables).
         """
-        txt = "\n"
+        lines = ['']
 
         # EBROOT + EBVERSION + EBDEVEL
-        environment_name = convert_name(self.name, upper=True)
-        
-        if self.module_generator.SYNTAX == 'Lua':
-            txt += self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, self.installdir)
-            devel_path = os.path.join(self.installdir, log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
-        elif self.module_generator.SYNTAX == 'Tcl':
-            txt += self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + environment_name, "$root")
-            devel_path = os.path.join("$root", log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
-        else: 
-            raise NotImplementedError
-        txt += self.module_generator.set_environment(VERSION_ENV_VAR_NAME_PREFIX + environment_name, self.version)
-        txt += self.module_generator.set_environment(DEVEL_ENV_VAR_NAME_PREFIX + environment_name, devel_path)
-
-        txt += "\n"
+        env_name = convert_name(self.name, upper=True)
+
+        lines.append(self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + env_name, self.installdir))
+        lines.append(self.module_generator.set_environment(VERSION_ENV_VAR_NAME_PREFIX + env_name, self.version))
+
+        devel_path = os.path.join(self.installdir, log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
+        lines.append(self.module_generator.set_environment(DEVEL_ENV_VAR_NAME_PREFIX + env_name, devel_path))
+
+        lines.append('')
         for (key, value) in self.cfg['modextravars'].items():
-            txt += self.module_generator.set_environment(key, value)
+            lines.append(self.module_generator.set_environment(key, value))
+
         for (key, value) in self.cfg['modextrapaths'].items():
             if isinstance(value, basestring):
                 value = [value]
             elif not isinstance(value, (tuple, list)):
                 raise EasyBuildError("modextrapaths dict value %s (type: %s) is not a list or tuple",
                                      value, type(value))
-            txt += self.module_generator.prepend_paths(key, value)
+            lines.append(self.module_generator.prepend_paths(key, value))
+
         if self.cfg['modloadmsg']:
-            txt += self.module_generator.msg_on_load(self.cfg['modloadmsg'])
-        if self.cfg['modtclfooter'] and isinstance(self.module_generator, ModuleGeneratorTcl):
-            txt += self.module_generator.add_tcl_footer(self.cfg['modtclfooter'])
-        if self.cfg['modluafooter'] and isinstance(self.module_generator, ModuleGeneratorLua):
-            txt += self.module_generator.add_lua_footer(self.cfg['modluafooter'])
+            lines.append(self.module_generator.msg_on_load(self.cfg['modloadmsg']))
+
+        if self.cfg['modtclfooter']:
+            if isinstance(self.module_generator, ModuleGeneratorTcl):
+                self.log.debug("Including Tcl footer in module: %s", self.cfg['modtclfooter'])
+                lines.append(self.cfg['modtclfooter'])
+            else:
+                self.log.warning("Not including footer in Tcl syntax in non-Tcl module file: %s",
+                                 self.cfg['modtclfooter'])
+
+        if self.cfg['modluafooter']:
+            if isinstance(self.module_generator, ModuleGeneratorLua):
+                self.log.debug("Including Lua footer in module: %s", self.cfg['modluafooter'])
+                lines.append(self.cfg['modluafooter'])
+            else:
+                self.log.warning("Not including footer in Lua syntax in non-Lua module file: %s",
+                                 self.cfg['modluafooter'])
+
         for (key, value) in self.cfg['modaliases'].items():
-            txt += self.module_generator.set_alias(key, value)
+            lines.append(self.module_generator.set_alias(key, value))
 
-        self.log.debug("make_module_extra added this: %s" % txt)
+        lines.append('')
+        txt = '\n'.join(lines)
+        self.log.debug("make_module_extra added this: %s", txt)
 
         return txt
 
@@ -887,32 +900,32 @@ def make_module_extra_extensions(self):
         Sets optional variables for extensions.
         """
         # add stuff specific to individual extensions
-        txt = self.module_extra_extensions
+        lines = [self.module_extra_extensions]
 
         # set environment variable that specifies list of extensions
         if self.exts_all:
             exts_list = ','.join(['%s-%s' % (ext['name'], ext.get('version', '')) for ext in self.exts_all])
             env_var_name = convert_name(self.name, upper=True)
-            txt += self.module_generator.set_environment('EBEXTSLIST%s' % env_var_name, exts_list)
+            lines.append(self.module_generator.set_environment('EBEXTSLIST%s' % env_var_name, exts_list))
 
-        return txt
+        return '\n'.join(lines)
 
     def make_module_footer(self):
         """
         Insert a footer section in the modulefile, primarily meant for contextual information
         """
-        txt = '\n' + self.module_generator.comment("Built with EasyBuild version %s" % VERBOSE_VERSION)
+        footer = [self.module_generator.comment("Built with EasyBuild version %s" % VERBOSE_VERSION)]
 
         # add extra stuff for extensions (if any)
         if self.cfg['exts_list']:
-            txt += self.make_module_extra_extensions()
+            footer.append(self.make_module_extra_extensions())
 
         # include modules footer if one is specified
         if self.modules_footer is not None:
             self.log.debug("Including specified footer into module: '%s'" % self.modules_footer)
-            txt += self.modules_footer
+            footer.append(self.modules_footer)
 
-        return txt
+        return '\n'.join(footer)
 
     def make_module_extend_modpath(self):
         """
@@ -939,25 +952,25 @@ def make_module_req(self):
         """
         requirements = self.make_module_req_guess()
 
+        lines = []
         if os.path.exists(self.installdir):
             try:
                 os.chdir(self.installdir)
             except OSError, err:
                 raise EasyBuildError("Failed to change to %s: %s", self.installdir, err)
 
-            txt = "\n"
+            lines.append('')
             for key in sorted(requirements):
                 for path in requirements[key]:
                     paths = sorted(glob.glob(path))
                     if paths:
-                        txt += self.module_generator.prepend_paths(key, paths)
+                        lines.append(self.module_generator.prepend_paths(key, paths))
             try:
                 os.chdir(self.orig_workdir)
             except OSError, err:
                 raise EasyBuildError("Failed to change back to %s: %s", self.orig_workdir, err)
-        else:
-            txt = ""
-        return txt
+
+        return '\n'.join(lines)
 
     def make_module_req_guess(self):
         """
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index e292e33e2c..fb04f5aaff 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -57,7 +57,9 @@ class ModuleGenerator(object):
 
     # chars we want to escape in the generated modulefiles
     CHARS_TO_ESCAPE = None
+
     MODULE_FILE_EXTENSION = None
+    MODULE_HEADER = None
 
     def __init__(self, application, fake=False):
         """ModuleGenerator constructor."""
@@ -67,6 +69,7 @@ def __init__(self, application, fake=False):
         self.filename = None
         self.class_mod_file = None
         self.module_path = None
+        self.class_mod_files = None
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
     def prepare(self, mod_symlink_paths):
@@ -74,7 +77,7 @@ def prepare(self, mod_symlink_paths):
         Creates the absolute filename for the module.
         """
         mod_path_suffix = build_option('suffix_modules_path')
-        full_mod_name = '%s%s' % (self.app.full_mod_name, self.MODULE_FILE_EXTENSION)
+        full_mod_name = self.app.full_mod_name + self.MODULE_FILE_EXTENSION
         # module file goes in general moduleclass category
         self.filename = os.path.join(self.module_path, mod_path_suffix, full_mod_name)
         # make symlink in moduleclass category
@@ -103,12 +106,12 @@ def create_symlinks(self):
                                  self.class_mod_files, self.filename, err)
 
     def is_fake(self):
-        """Return whether this ModuleGeneratorTcl instance generates fake modules or not."""
+        """Return whether this ModuleGenerator instance generates fake modules or not."""
         return self.fake
 
     def set_fake(self, fake):
-        """Determine whether this ModuleGeneratorTcl instance should generate fake modules."""
-        self.log.debug("Updating fake for this ModuleGeneratorTcl instance to %s (was %s)" % (fake, self.fake))
+        """Determine whether this ModuleGenerator instance should generate fake modules."""
+        self.log.debug("Updating fake for this ModuleGenerator instance to %s (was %s)" % (fake, self.fake))
         self.fake = fake
         # fake mode: set installpath to temporary dir
         if self.fake:
@@ -118,12 +121,12 @@ def set_fake(self, fake):
         else:
             self.module_path = install_path('mod')
 
-    def module_header(self):
-        """Return module header string."""
+    def comment(self, str):
+        """Return given string formatted as a comment."""
         raise NotImplementedError
 
-    def comment(self, msg):
-        """Return string containing given message as a comment."""
+    def conditional_statement(self, condition, body, negative=False):
+        """Return formatted conditional statement, with given condition and body."""
         raise NotImplementedError
 
 
@@ -131,20 +134,28 @@ class ModuleGeneratorTcl(ModuleGenerator):
     """
     Class for generating Tcl module files.
     """
-    MODULE_FILE_EXTENSION = ''  # no suffix for Tcl module files
     SYNTAX = 'Tcl'
-    CHARS_TO_ESCAPE = ["$"]
+    MODULE_FILE_EXTENSION = ''  # no suffix for Tcl module files
+    MODULE_HEADER = '#%Module'
+    CHARS_TO_ESCAPE = ['$']
 
     LOAD_REGEX = r"^\s*module\s+load\s+(\S+)"
     LOAD_TEMPLATE = "module load %(mod_name)s"
 
-    def module_header(self):
-        """Return module header string."""
-        return "#%Module\n"
-
     def comment(self, msg):
         """Return string containing given message as a comment."""
-        return "# %s\n" % msg
+        return "# %s" % msg
+
+    def conditional_statement(self, condition, body, negative=False):
+        """Return formatted conditional statement, with given condition and body."""
+        if negative:
+            lines = ["if { ![ %s ] } {" % condition]
+        else:
+            lines = ["if { [ %s ] } {" % condition]
+
+        lines.append('    ' + body)
+        lines.append('}')
+        return '\n'.join(lines)
 
     def get_description(self, conflict=True):
         """
@@ -153,27 +164,20 @@ def get_description(self, conflict=True):
         description = "%s - Homepage: %s" % (self.app.cfg['description'], self.app.cfg['homepage'])
 
         lines = [
-            "",
+            '',
             "proc ModulesHelp { } {",
-            "    puts stderr {   %(description)s",
+            "    puts stderr { %(description)s",
             "    }",
-            "}",
-            "",
+            '}',
+            '',
             "module-whatis {Description: %(description)s}",
-            "",
-            "set root    %(installdir)s",
-            "",
+            '',
+            "set root %(installdir)s",
         ]
 
         if self.app.cfg['moduleloadnoconflict']:
-            lines.extend([
-                "if { ![is-loaded %(name)s/%(version)s] } {",
-                "    if { [is-loaded %(name)s] } {",
-                "        module unload %(name)s",
-                "    }",
-                "}",
-                "",
-            ])
+            cond_unload = self.conditional_statement("is-loaded %(name)s", "module unload %(name)s")
+            lines.append(self.conditional_statement("is-loaded %(name)s/%(version)s", cond_unload, negative=True))
 
         elif conflict:
             # conflict on 'name' part of module name (excluding version part at the end)
@@ -181,10 +185,9 @@ def get_description(self, conflict=True):
             # - 'conflict GCC' for 'GCC/4.8.3'
             # - 'conflict Core/GCC' for 'Core/GCC/4.8.2'
             # - 'conflict Compiler/GCC/4.8.2/OpenMPI' for 'Compiler/GCC/4.8.2/OpenMPI/1.6.4'
-            lines.append("conflict %s\n" % os.path.dirname(self.app.short_mod_name))
+            lines.extend(['', "conflict %s" % os.path.dirname(self.app.short_mod_name)])
 
-        txt = self.module_header()
-        txt += '\n'.join(lines) % {
+        txt = self.MODULE_HEADER + '\n'.join([''] + lines + ['']) % {
             'name': self.app.name,
             'version': self.app.version,
             'description': description,
@@ -203,30 +206,21 @@ def load_module(self, mod_name):
             # it will get translated to "module unload"
             load_statement = ["module load %(mod_name)s"]
         else:
-            load_statement = [
-                "if { ![is-loaded %(mod_name)s] } {",
-                "    %s" % self.LOAD_TEMPLATE,
-                "}",
-            ]
-        return '\n'.join([""] + load_statement + [""]) % {'mod_name': mod_name}
+            load_statement = [self.conditional_statement("is-loaded %(mod_name)s", self.LOAD_TEMPLATE, negative=True)]
+        return '\n'.join([''] + load_statement + ['']) % {'mod_name': mod_name}
 
     def unload_module(self, mod_name):
         """
         Generate unload statements for module.
         """
-        return '\n'.join([
-            "",
-            "if { [is-loaded %(mod_name)s] } {",
-            "    module unload %(mod_name)s",
-            "}",
-            "",
-        ]) % {'mod_name': mod_name}
+        cond_unload = self.conditional_statement("is-loaded %(mod)s", "module unload %(mod)s") % {'mod': mod_name}
+        return '\n'.join(['', cond_unload, ''])
 
     def prepend_paths(self, key, paths, allow_abs=False):
         """
         Generate prepend-path statements for the given list of paths.
         """
-        template = "prepend-path\t%s\t\t%s\n"
+        template = "prepend-path\t%s\t\t%s"
 
         if isinstance(paths, basestring):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
@@ -238,12 +232,10 @@ def prepend_paths(self, key, paths, allow_abs=False):
                                      path)
             elif not os.path.isabs(path):
                 # prepend $root (= installdir) for relative paths
-                paths[i]="$root/%s" % path
-
+                paths[i] = os.path.join('$root', path)
 
         statements = [template % (key, p) for p in paths]
-        return ''.join(statements)
-
+        return '\n'.join(statements)
 
     def use(self, paths):
         """
@@ -259,63 +251,59 @@ def set_environment(self, key, value):
         Generate setenv statement for the given key/value pair.
         """
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
-        return 'setenv\t%s\t\t%s\n' % (key, quote_str(value))
-    
+        return 'setenv\t%s\t\t%s' % (key, quote_str(value))
+
     def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.
         """
         # escape any (non-escaped) characters with special meaning by prefixing them with a backslash
         msg = re.sub(r'((?<!\\)[%s])'% ''.join(self.CHARS_TO_ESCAPE), r'\\\1', msg)
-        return '\n'.join([
-            "",
-            "if [ module-info mode load ] {",
-            '        puts stderr     "%s"' % msg,
-            "}",
-            "",
-        ])
-    
-    def add_tcl_footer(self, tcltxt):
-        """
-        Append whatever Tcl code you want to your modulefile
-        """
-        return tcltxt
-
-    def add_lua_footer(self, luatxt):
-        """
-        Appending Tcl code in Lua files doesn't make sense."""
-        raise EasyBuildError("Appending Lua footer to module file in Tcl syntax doesn't work: %s", luatxt)
+        print_cmd = "puts stderr %s" % quote_str(msg)
+        return '\n'.join(['', self.conditional_statement("module-info mode load", print_cmd), ''])
 
     def set_alias(self, key, value):
         """
         Generate set-alias statement in modulefile for the given key/value pair.
         """
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
-        return 'set-alias\t%s\t\t%s\n' % (key, quote_str(value))
+        return 'set-alias\t%s\t\t%s' % (key, quote_str(value))
 
 
 class ModuleGeneratorLua(ModuleGenerator):
     """
     Class for generating Lua module files.
     """
-    MODULE_FILE_EXTENSION = '.lua'
     SYNTAX = 'Lua'
-    CHARS_TO_ESCAPE = ["%"]
+    MODULE_FILE_EXTENSION = '.lua'
+    MODULE_HEADER = ''  # no header in Lua module files
+    CHARS_TO_ESCAPE = []
 
     LOAD_REGEX = r'^\s*load\("(\S+)"'
     LOAD_TEMPLATE = 'load("%(mod_name)s")'
 
+    PATH_JOIN_TEMPLATE = 'pathJoin(pkg.root, "%s")'
+    PREPEND_PATH_TEMPLATE = 'prepend_path("%s", %s)'
+
     def __init__(self, *args, **kwargs):
         """ModuleGeneratorLua constructor."""
         super(ModuleGeneratorLua, self).__init__(*args, **kwargs)
 
-    def module_header(self):
-        """Return module header string."""
-        return ''
-
     def comment(self, msg):
         """Return string containing given message as a comment."""
-        return " -- %s\n" % msg
+        return " -- %s" % msg
+
+    def conditional_statement(self, condition, body, negative=False):
+        """Return formatted conditional statement, with given condition and body."""
+        if negative:
+            lines = ["if not %s then" % condition]
+        else:
+            lines = ["if %s then" % condition]
+
+        for line in body.split('\n'):
+            lines.append('    ' + line)
+        lines.append('end')
+        return '\n'.join(lines)
 
     def get_description(self, conflict=True):
         """
@@ -331,13 +319,18 @@ def get_description(self, conflict=True):
             "whatis([[Version: %(version)s]])",
             "whatis([[Description: %(description)s]])",
             "whatis([[Homepage: %(homepage)s]])",
-            "",
-            "",
-            'pkg.root="%(installdir)s"',
-            "",
-            ]
+            '',
+            'pkg.root = "%(installdir)s"',
+        ]
+
+        if self.app.cfg['moduleloadnoconflict']:
+            self.log.info("Nothing to do to ensure no conflicts can occur on load when using Lua modules files/Lmod")
 
-        txt = '\n'.join(lines) % {
+        elif conflict:
+            # conflict on 'name' part of module name (excluding version part at the end)
+            lines.extend(['', 'conflict("%s")' % os.path.dirname(self.app.short_mod_name)])
+
+        txt = '\n'.join(lines + ['']) % {
             'name': self.app.name,
             'version': self.app.version,
             'description': description,
@@ -357,33 +350,23 @@ def load_module(self, mod_name):
             # it will get translated to "module unload"
             load_statement = [self.LOAD_TEMPLATE]
         else:
-            load_statement = [
-                'if ( not isloaded("%(mod_name)s")) then',
-                '    %s' % self.LOAD_TEMPLATE,
-                'end',
-            ]
-        return '\n'.join([""] + load_statement + [""]) % {'mod_name': mod_name}
+            load_statement = [self.conditional_statement('isloaded("%(mod_name)s")', self.LOAD_TEMPLATE, negative=True)]
+
+        return '\n'.join([''] + load_statement + ['']) % {'mod_name': mod_name}
 
     def unload_module(self, mod_name):
         """
         Generate unload statements for module.
         """
-        return '\n'.join([
-            "",
-            'if (isloaded("%(mod_name)s") then',
-            '    unload("%(mod_name)s")',
-            "end",
-            "",
-        ]) % {'mod_name': mod_name}
+        cond_unload = self.conditional_statement('isloaded("%(mod)s")', 'unload("%(mod)s")') % {'mod': mod_name}
+        return '\n'.join(['', cond_unload, ''])
 
     def prepend_paths(self, key, paths, allow_abs=False):
         """
         Generate prepend-path statements for the given list of paths
         """
-        template = "prepend_path(%s, %s)\n"
-
         if isinstance(paths, basestring):
-            self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
+            self.log.debug("Wrapping %s into a list before using it to prepend path %s", paths, key)
             paths = [paths]
 
         for i, path in enumerate(paths):
@@ -394,18 +377,18 @@ def prepend_paths(self, key, paths, allow_abs=False):
                     raise EasyBuildError("Absolute path %s passed to prepend_paths which only expects relative paths.",
                                          path)
             else:
-                # use pathJoin(pkg.root, path) for relative paths
-                paths[i] = 'pathJoin(pkg.root, "%s")' % path
+                # use pathJoin for relative paths
+                paths[i] = self.PATH_JOIN_TEMPLATE % path
 
-        statements = [template % (quote_str(key), p) for p in paths]
-        return ''.join(statements)
+        statements = [self.PREPEND_PATH_TEMPLATE % (key, p) for p in paths]
+        return '\n'.join(statements)
 
     def use(self, paths):
         """
         Generate module use statements for given list of module paths.
         @param paths: list of module path extensions to generate use statements for
         """
-        return '\n'.join(['prepend_path("MODULEPATH", "%s")' % p for p in paths] + [''])
+        return '\n'.join([self.PREPEND_PATH_TEMPLATE % ('MODULEPATH', quote_str(p)) for p in paths] + [''])
 
     def set_environment(self, key, value):
         """
@@ -414,44 +397,22 @@ def set_environment(self, key, value):
         # setting of $EBDEVELFOO modulefile path in Tcl case uses string
         # interpolation available in Tcl, but not in Lua. Ie
         # setenv("FOO","pkg.root/somevar") where pkg.root and somevar are
-        # variables cant be used. 
-        return 'setenv("%s", %s)\n' % (key, quote_str(value))
-
-    def set_environment_unquoted(self, key, unquotedvalue):
-        """ Generate an unquoted setenv statement for the given key/value pair.
-        """
-        return 'setenv("%s",%s)\n' % (key, unquotedvalue)
+        # variables cant be used.
+        return 'setenv("%s", %s)' % (key, quote_str(value))
 
     def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.
         """
-        msg = re.sub(r'((?<!\\)[%s])'% ''.join(self.CHARS_TO_ESCAPE), r'\\\1', msg)
-        return '\n'.join([
-            "",
-            'if (mode() == "load") then',
-            '    io.stderr:write("%s")' % msg,
-            "end",
-            "",
-        ])
-
-    def add_tcl_footer(self, tcltxt):
-        """
-        Appending Tcl code in Lua files doesn't make sense."""
-        raise EasyBuildError("Appending Tcl footer to module file in Lua syntax doesn't work: %s", tcltxt)
-
-    def add_lua_footer(self, luatxt):
-        """
-        Append whatever Lua code you want to your modulefile
-        """
-        return luatxt
+        return '\n'.join(['', self.conditional_statement('mode() == "load"', 'io.stderr:write("%s")' % msg), ''])
 
     def set_alias(self, key, value):
         """
         Generate set-alias statement in modulefile for the given key/value pair.
         """
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
-        return 'setalias("%s",%s)\n' % (key, quote_str(value))
+        return 'setalias("%s", %s)' % (key, quote_str(value))
+
 
 def avail_module_generators():
     """
@@ -479,7 +440,7 @@ def module_load_regex(modfilepath):
     """
     Return the correct (compiled) regex to extract dependencies, depending on the module file type (Lua vs Tcl)
     """
-    if modfilepath.endswith('.lua'):
+    if modfilepath.endswith(ModuleGeneratorLua.MODULE_FILE_EXTENSION):
         regex = ModuleGeneratorLua.LOAD_REGEX
     else:
         regex = ModuleGeneratorTcl.LOAD_REGEX
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index c1ba1c9830..415c1a6b77 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -174,8 +174,6 @@ def __init__(self, mod_paths=None, testing=False):
         self.check_module_function(allow_mismatch=build_option('allow_modules_tool_mismatch'))
         self.set_and_check_version()
 
-        self.det_load_regex = None
-
     def buildstats(self):
         """Return tuple with data to be included in buildstats"""
         return (self.__class__.__name__, self.cmd, self.version)
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 17c06287f5..d768120797 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -321,7 +321,7 @@ def test_make_module_step(self):
             self.assertTrue(re.search(r"^conflict\s+%s$" % name, txt, re.M))
 
             self.assertTrue(re.search(r"^set\s+root\s+%s$" % eb.installdir, txt, re.M))
-            ebroot_regex = re.compile(r'^setenv\s+EBROOT%s\s+".root"\s*$' % name.upper(), re.M)
+            ebroot_regex = re.compile(r'^setenv\s+EBROOT%s\s+"%s"\s*$' % (name.upper(), eb.installdir), re.M)
             self.assertTrue(ebroot_regex.search(txt), "%s in %s" % (ebroot_regex.pattern, txt))
             self.assertTrue(re.search(r'^setenv\s+EBVERSION%s\s+"%s"$' % (name.upper(), version), txt, re.M))
 
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 8f155a0c70..0bb0889d20 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -86,16 +86,16 @@ def test_descr(self):
                 "#%Module",
                 "",
                 "proc ModulesHelp { } {",
-                "    puts stderr {   %s" % gzip_txt,
+                "    puts stderr { %s" % gzip_txt,
                 "    }",
                 "}",
-                "",
+                '',
                 "module-whatis {Description: %s}" % gzip_txt,
-                "",
-                "set root    %s" % self.modgen.app.installdir,
-                "",
+                '',
+                "set root %s" % self.modgen.app.installdir,
+                '',
                 "conflict gzip",
-                "",
+                '',
             ])
 
         else:
@@ -106,10 +106,11 @@ def test_descr(self):
                 "whatis([[Version: 1.4]])" ,
                 "whatis([[Description: %s]])" % gzip_txt,
                 "whatis([[Homepage: http://www.gzip.org/]])",
-                "",
-                "",
-                'pkg.root="%s"' %self.modgen.app.installdir,
-                "",
+                '',
+                'pkg.root = "%s"' %self.modgen.app.installdir,
+                '',
+                'conflict("gzip")',
+                '',
             ])
 
         desc = self.modgen.get_description()
@@ -121,7 +122,7 @@ def test_load(self):
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
             expected = [
                 "",
-                "if { ![is-loaded mod_name] } {",
+                "if { ![ is-loaded mod_name ] } {",
                 "    module load mod_name",
                 "}",
                 "",
@@ -139,7 +140,7 @@ def test_load(self):
         else:
             expected = '\n'.join([
                 '',
-                'if ( not isloaded("mod_name")) then',
+                'if not isloaded("mod_name") then',
                 '    load("mod_name")',
                 'end',
                 '',
@@ -160,7 +161,7 @@ def test_unload(self):
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
             expected = '\n'.join([
                 "",
-                "if { [is-loaded mod_name] } {",
+                "if { [ is-loaded mod_name ] } {",
                 "    module unload mod_name",
                 "}",
                 "",
@@ -169,7 +170,7 @@ def test_unload(self):
         else:
             expected = '\n'.join([
             "",
-            'if (isloaded("mod_name") then',
+            'if isloaded("mod_name") then',
             '    unload("mod_name")',
             "end",
             "",
@@ -181,16 +182,17 @@ def test_prepend_paths(self):
         # test prepend_paths
 
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
-            expected = ''.join([
-                "prepend-path\tkey\t\t$root/path1\n",
-                "prepend-path\tkey\t\t$root/path2\n",
+            expected = '\n'.join([
+                "prepend-path\tkey\t\t$root/path1",
+                "prepend-path\tkey\t\t$root/path2",
             ])
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
 
-            expected = "prepend-path\tbar\t\t$root/foo\n"
+            expected = "prepend-path\tbar\t\t$root/foo"
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
 
-            self.assertEqual("prepend-path\tkey\t\t/abs/path\n", self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
+            res = self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True)
+            self.assertEqual("prepend-path\tkey\t\t/abs/path", res)
 
             self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
                                                   "which only expects relative paths." % self.modgen.app.installdir,
@@ -199,14 +201,13 @@ def test_prepend_paths(self):
             expected = '\n'.join([
                 'prepend_path("key", pathJoin(pkg.root, "path1"))',
                 'prepend_path("key", pathJoin(pkg.root, "path2"))',
-                '',
             ])
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
 
-            expected = 'prepend_path("bar", pathJoin(pkg.root, "foo"))\n'
+            expected = 'prepend_path("bar", pathJoin(pkg.root, "foo"))'
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
 
-            expected = 'prepend_path("key", "/abs/path")\n'
+            expected = 'prepend_path("key", "/abs/path")'
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
 
             self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
@@ -234,32 +235,31 @@ def test_env(self):
         """Test setting of environment variables."""
         # test set_environment
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
-            self.assertEqual('setenv\tkey\t\t"value"\n', self.modgen.set_environment("key", "value"))
-            self.assertEqual("setenv\tkey\t\t'va\"lue'\n", self.modgen.set_environment("key", 'va"lue'))
-            self.assertEqual('setenv\tkey\t\t"va\'lue"\n', self.modgen.set_environment("key", "va'lue"))
-            self.assertEqual('setenv\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_environment("key", """va"l'ue"""))
+            self.assertEqual('setenv\tkey\t\t"value"', self.modgen.set_environment("key", "value"))
+            self.assertEqual("setenv\tkey\t\t'va\"lue'", self.modgen.set_environment("key", 'va"lue'))
+            self.assertEqual('setenv\tkey\t\t"va\'lue"', self.modgen.set_environment("key", "va'lue"))
+            self.assertEqual('setenv\tkey\t\t"""va"l\'ue"""', self.modgen.set_environment("key", """va"l'ue"""))
         else:
-            self.assertEqual('setenv("key", "value")\n', self.modgen.set_environment("key","value"))
+            self.assertEqual('setenv("key", "value")', self.modgen.set_environment("key", "value"))
 
-    
     def test_alias(self):
         """Test setting of alias in modulefiles."""
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
             # test set_alias
-            self.assertEqual('set-alias\tkey\t\t"value"\n', self.modgen.set_alias("key", "value"))
-            self.assertEqual("set-alias\tkey\t\t'va\"lue'\n", self.modgen.set_alias("key", 'va"lue'))
-            self.assertEqual('set-alias\tkey\t\t"va\'lue"\n', self.modgen.set_alias("key", "va'lue"))
-            self.assertEqual('set-alias\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_alias("key", """va"l'ue"""))
+            self.assertEqual('set-alias\tkey\t\t"value"', self.modgen.set_alias("key", "value"))
+            self.assertEqual("set-alias\tkey\t\t'va\"lue'", self.modgen.set_alias("key", 'va"lue'))
+            self.assertEqual('set-alias\tkey\t\t"va\'lue"', self.modgen.set_alias("key", "va'lue"))
+            self.assertEqual('set-alias\tkey\t\t"""va"l\'ue"""', self.modgen.set_alias("key", """va"l'ue"""))
         else:
-            self.assertEqual('setalias("key","value")\n', self.modgen.set_alias("key", "value"))
+            self.assertEqual('setalias("key", "value")', self.modgen.set_alias("key", "value"))
 
     def test_load_msg(self):
         """Test including a load message in the module file."""
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
             tcl_load_msg = '\n'.join([
                 '',
-                "if [ module-info mode load ] {",
-                "        puts stderr     \"test \\$test \\$test",
+                "if { [ module-info mode load ] } {",
+                "    puts stderr \"test \\$test \\$test",
                 "test \\$foo \\$bar\"",
                 "}",
                 '',
@@ -268,15 +268,6 @@ def test_load_msg(self):
         else:
             pass
 
-
-    def test_tcl_footer(self):
-        """Test including a Tcl footer."""
-        if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
-            tcltxt = 'puts stderr "foo"'
-            self.assertEqual(tcltxt, self.modgen.add_tcl_footer(tcltxt))
-        else:
-            pass
-
     def test_module_naming_scheme(self):
         """Test using default module naming scheme."""
         all_stops = [x[0] for x in EasyBlock.get_steps()]
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 4e9cfd7ea7..603e5d9a36 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -242,7 +242,7 @@ def test_toy_tweaked(self):
             self.assertTrue(re.search(r'setenv\("FOO", "bar"\)', toy_module_txt))
             self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(pkg.root, "foo/bar"\)\)', toy_module_txt))
             self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(pkg.root, "baz"\)\)', toy_module_txt))
-            self.assertTrue(re.search(r'if \(mode\(\) == "load"\) then\n\s*io.stderr:write\(".*I AM toy v0.0"\)',
+            self.assertTrue(re.search(r'if mode\(\) == "load" then\n\s*io.stderr:write\(".*I AM toy v0.0"\)',
                                       toy_module_txt))
             self.assertTrue(re.search(r'io.stderr:write\("oh hai!"\)', toy_module_txt))
         else:

From 91ae79170204d22ad3a5adae9365450b5549e8ef Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Apr 2015 21:49:48 +0200
Subject: [PATCH 0836/1356] pkg.root => root, use it for $EBROOT, $EBDEVEL too

---
 easybuild/framework/easyblock.py    |  7 +++--
 easybuild/tools/module_generator.py | 45 +++++++++++++++++++----------
 test/framework/easyblock.py         | 26 ++++++++---------
 test/framework/module_generator.py  | 24 +++++++--------
 test/framework/toy_build.py         |  8 +++--
 5 files changed, 63 insertions(+), 47 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 10b175179a..8493babab6 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -849,11 +849,12 @@ def make_module_extra(self):
         # EBROOT + EBVERSION + EBDEVEL
         env_name = convert_name(self.name, upper=True)
 
-        lines.append(self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + env_name, self.installdir))
+        lines.append(self.module_generator.set_environment(ROOT_ENV_VAR_NAME_PREFIX + env_name, '', relpath=True))
         lines.append(self.module_generator.set_environment(VERSION_ENV_VAR_NAME_PREFIX + env_name, self.version))
 
-        devel_path = os.path.join(self.installdir, log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
-        lines.append(self.module_generator.set_environment(DEVEL_ENV_VAR_NAME_PREFIX + env_name, devel_path))
+        devel_path = os.path.join(log_path(), ActiveMNS().det_devel_module_filename(self.cfg))
+        devel_path_envvar = DEVEL_ENV_VAR_NAME_PREFIX + env_name
+        lines.append(self.module_generator.set_environment(devel_path_envvar, devel_path, relpath=True))
 
         lines.append('')
         for (key, value) in self.cfg['modextravars'].items():
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index fb04f5aaff..0c46d916e1 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -231,8 +231,11 @@ def prepend_paths(self, key, paths, allow_abs=False):
                 raise EasyBuildError("Absolute path %s passed to prepend_paths which only expects relative paths.",
                                      path)
             elif not os.path.isabs(path):
-                # prepend $root (= installdir) for relative paths
-                paths[i] = os.path.join('$root', path)
+                # prepend $root (= installdir) for (non-empty) relative paths
+                if path:
+                    paths[i] = os.path.join('$root', path)
+                else:
+                    paths[i] = '$root'
 
         statements = [template % (key, p) for p in paths]
         return '\n'.join(statements)
@@ -246,12 +249,19 @@ def use(self, paths):
             use_statements.append("module use %s" % path)
         return '\n'.join(use_statements)
 
-    def set_environment(self, key, value):
+    def set_environment(self, key, value, relpath=False):
         """
         Generate setenv statement for the given key/value pair.
         """
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
-        return 'setenv\t%s\t\t%s' % (key, quote_str(value))
+        if relpath:
+            if value:
+                val = quote_str(os.path.join('$root', value))
+            else:
+                val = '"$root"'
+        else:
+            val = quote_str(value)
+        return 'setenv\t%s\t\t%s' % (key, val)
 
     def msg_on_load(self, msg):
         """
@@ -282,7 +292,7 @@ class ModuleGeneratorLua(ModuleGenerator):
     LOAD_REGEX = r'^\s*load\("(\S+)"'
     LOAD_TEMPLATE = 'load("%(mod_name)s")'
 
-    PATH_JOIN_TEMPLATE = 'pathJoin(pkg.root, "%s")'
+    PATH_JOIN_TEMPLATE = 'pathJoin(root, "%s")'
     PREPEND_PATH_TEMPLATE = 'prepend_path("%s", %s)'
 
     def __init__(self, *args, **kwargs):
@@ -313,14 +323,13 @@ def get_description(self, conflict=True):
         description = "%s - Homepage: %s" % (self.app.cfg['description'], self.app.cfg['homepage'])
 
         lines = [
-            "local pkg = {}",
             "help = [[%(description)s]]",
             "whatis([[Name: %(name)s]])",
             "whatis([[Version: %(version)s]])",
             "whatis([[Description: %(description)s]])",
             "whatis([[Homepage: %(homepage)s]])",
             '',
-            'pkg.root = "%(installdir)s"',
+            'local root = "%(installdir)s"',
         ]
 
         if self.app.cfg['moduleloadnoconflict']:
@@ -377,8 +386,11 @@ def prepend_paths(self, key, paths, allow_abs=False):
                     raise EasyBuildError("Absolute path %s passed to prepend_paths which only expects relative paths.",
                                          path)
             else:
-                # use pathJoin for relative paths
-                paths[i] = self.PATH_JOIN_TEMPLATE % path
+                # use pathJoin for (non-empty) relative paths
+                if path:
+                    paths[i] = self.PATH_JOIN_TEMPLATE % path
+                else:
+                    paths[i] = 'root'
 
         statements = [self.PREPEND_PATH_TEMPLATE % (key, p) for p in paths]
         return '\n'.join(statements)
@@ -390,15 +402,18 @@ def use(self, paths):
         """
         return '\n'.join([self.PREPEND_PATH_TEMPLATE % ('MODULEPATH', quote_str(p)) for p in paths] + [''])
 
-    def set_environment(self, key, value):
+    def set_environment(self, key, value, relpath=False):
         """
         Generate a quoted setenv statement for the given key/value pair.
         """
-        # setting of $EBDEVELFOO modulefile path in Tcl case uses string
-        # interpolation available in Tcl, but not in Lua. Ie
-        # setenv("FOO","pkg.root/somevar") where pkg.root and somevar are
-        # variables cant be used.
-        return 'setenv("%s", %s)' % (key, quote_str(value))
+        if relpath:
+            if value:
+                val = self.PATH_JOIN_TEMPLATE % value
+            else:
+                val = 'root'
+        else:
+            val = quote_str(value)
+        return 'setenv("%s", %s)' % (key, val)
 
     def msg_on_load(self, msg):
         """
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index d768120797..b9c8181d01 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -194,17 +194,17 @@ def test_make_module_req(self):
         guess = eb.make_module_req()
 
         if get_module_syntax() == 'Tcl':
-            self.assertTrue(re.search("^prepend-path\s+CLASSPATH\s+\$root/bla.jar$", guess, re.M))
-            self.assertTrue(re.search("^prepend-path\s+CLASSPATH\s+\$root/foo.jar$", guess, re.M))
-            self.assertTrue(re.search("^prepend-path\s+MANPATH\s+\$root/share/man$", guess, re.M))
-            self.assertTrue(re.search("^prepend-path\s+PATH\s+\$root/bin$", guess, re.M))
-            self.assertFalse(re.search("^prepend-path\s+CPATH\s+.*$", guess, re.M))
+            self.assertTrue(re.search(r"^prepend-path\s+CLASSPATH\s+\$root/bla.jar$", guess, re.M))
+            self.assertTrue(re.search(r"^prepend-path\s+CLASSPATH\s+\$root/foo.jar$", guess, re.M))
+            self.assertTrue(re.search(r"^prepend-path\s+MANPATH\s+\$root/share/man$", guess, re.M))
+            self.assertTrue(re.search(r"^prepend-path\s+PATH\s+\$root/bin$", guess, re.M))
+            self.assertFalse(re.search(r"^prepend-path\s+CPATH\s+.*$", guess, re.M))
         elif get_module_syntax() == 'Lua':
-            self.assertTrue(re.search('^prepend_path\("CLASSPATH", pathJoin\(pkg.root, "bla.jar"\)\)$', guess, re.M))
-            self.assertTrue(re.search('^prepend_path\("CLASSPATH", pathJoin\(pkg.root, "foo.jar"\)\)$', guess, re.M))
-            self.assertTrue(re.search('^prepend_path\("MANPATH", pathJoin\(pkg.root, "share/man"\)\)$', guess, re.M))
-            self.assertTrue(re.search('^prepend_path\("PATH", pathJoin\(pkg.root, "bin"\)\)$', guess, re.M))
-            self.assertFalse(re.search('^prepend_path\("CPATH", .*\)$', guess, re.M))
+            self.assertTrue(re.search(r'^prepend_path\("CLASSPATH", pathJoin\(root, "bla.jar"\)\)$', guess, re.M))
+            self.assertTrue(re.search(r'^prepend_path\("CLASSPATH", pathJoin\(root, "foo.jar"\)\)$', guess, re.M))
+            self.assertTrue(re.search(r'^prepend_path\("MANPATH", pathJoin\(root, "share/man"\)\)$', guess, re.M))
+            self.assertTrue(re.search(r'^prepend_path\("PATH", pathJoin\(root, "bin"\)\)$', guess, re.M))
+            self.assertFalse(re.search(r'^prepend_path\("CPATH", .*\)$', guess, re.M))
         else:
             self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
 
@@ -321,12 +321,12 @@ def test_make_module_step(self):
             self.assertTrue(re.search(r"^conflict\s+%s$" % name, txt, re.M))
 
             self.assertTrue(re.search(r"^set\s+root\s+%s$" % eb.installdir, txt, re.M))
-            ebroot_regex = re.compile(r'^setenv\s+EBROOT%s\s+"%s"\s*$' % (name.upper(), eb.installdir), re.M)
+            ebroot_regex = re.compile(r'^setenv\s+EBROOT%s\s+"\$root"\s*$' % name.upper(), re.M)
             self.assertTrue(ebroot_regex.search(txt), "%s in %s" % (ebroot_regex.pattern, txt))
             self.assertTrue(re.search(r'^setenv\s+EBVERSION%s\s+"%s"$' % (name.upper(), version), txt, re.M))
 
         elif get_module_syntax() == 'Lua':
-            ebroot_regex = re.compile(r'^setenv\("EBROOT%s", ".*%s.*"\)$' % (name.upper(), eb.installdir), re.M)
+            ebroot_regex = re.compile(r'^setenv\("EBROOT%s", root\)$' % name.upper(), re.M)
             self.assertTrue(ebroot_regex.search(txt), "%s in %s" % (ebroot_regex.pattern, txt))
             self.assertTrue(re.search(r'^setenv\("EBVERSION%s", "%s"\)$' % (name.upper(), version), txt, re.M))
 
@@ -346,7 +346,7 @@ def test_make_module_step(self):
             if get_module_syntax() == 'Tcl':
                 regex = re.compile(r'^prepend-path\s+%s\s+\$root/%s$' % (key, val), re.M)
             elif get_module_syntax() == 'Lua':
-                regex = re.compile(r'^prepend_path\("%s", pathJoin\(pkg.root, "%s"\)\)$' % (key, val), re.M)
+                regex = re.compile(r'^prepend_path\("%s", pathJoin\(root, "%s"\)\)$' % (key, val), re.M)
             else:
                 self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
             self.assertTrue(regex.search(txt), "Pattern %s found in %s" % (regex.pattern, txt))
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 0bb0889d20..01c9ada606 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -100,14 +100,13 @@ def test_descr(self):
 
         else:
             expected = '\n'.join([
-                "local pkg = {}",
                 'help = [[%s]]' % gzip_txt,
                 "whatis([[Name: gzip]])" ,
                 "whatis([[Version: 1.4]])" ,
                 "whatis([[Description: %s]])" % gzip_txt,
                 "whatis([[Homepage: http://www.gzip.org/]])",
                 '',
-                'pkg.root = "%s"' %self.modgen.app.installdir,
+                'local root = "%s"' % self.modgen.app.installdir,
                 '',
                 'conflict("gzip")',
                 '',
@@ -185,8 +184,9 @@ def test_prepend_paths(self):
             expected = '\n'.join([
                 "prepend-path\tkey\t\t$root/path1",
                 "prepend-path\tkey\t\t$root/path2",
+                "prepend-path\tkey\t\t$root",
             ])
-            self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
+            self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2", '']))
 
             expected = "prepend-path\tbar\t\t$root/foo"
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
@@ -194,25 +194,23 @@ def test_prepend_paths(self):
             res = self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True)
             self.assertEqual("prepend-path\tkey\t\t/abs/path", res)
 
-            self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
-                                                  "which only expects relative paths." % self.modgen.app.installdir,
-                                  self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])
         else:
             expected = '\n'.join([
-                'prepend_path("key", pathJoin(pkg.root, "path1"))',
-                'prepend_path("key", pathJoin(pkg.root, "path2"))',
+                'prepend_path("key", pathJoin(root, "path1"))',
+                'prepend_path("key", pathJoin(root, "path2"))',
+                'prepend_path("key", root)',
             ])
-            self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2"]))
+            self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2", '']))
 
-            expected = 'prepend_path("bar", pathJoin(pkg.root, "foo"))'
+            expected = 'prepend_path("bar", pathJoin(root, "foo"))'
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
 
             expected = 'prepend_path("key", "/abs/path")'
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
 
-            self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
-                                                  "which only expects relative paths." % self.modgen.app.installdir,
-                                  self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])
+        self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
+                                              "which only expects relative paths." % self.modgen.app.installdir,
+                              self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])
 
     def test_use(self):
         """Test generating module use statements."""
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 603e5d9a36..efa425cf56 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -209,7 +209,7 @@ def test_toy_tweaked(self):
         # tweak easyconfig by appending to it
         ec_extra = '\n'.join([
             "versionsuffix = '-tweaked'",
-            "modextrapaths = {'SOMEPATH': ['foo/bar', 'baz']}",
+            "modextrapaths = {'SOMEPATH': ['foo/bar', 'baz', '']}",
             "modextravars = {'FOO': 'bar'}",
             "modloadmsg =  'THANKS FOR LOADING ME, I AM %(name)s v%(version)s'",
             "modtclfooter = 'puts stderr \"oh hai!\"'",  # ignored when module syntax is Lua
@@ -236,12 +236,14 @@ def test_toy_tweaked(self):
             self.assertTrue(re.search(r'setenv\s*FOO\s*"bar"', toy_module_txt))
             self.assertTrue(re.search(r'prepend-path\s*SOMEPATH\s*\$root/foo/bar', toy_module_txt))
             self.assertTrue(re.search(r'prepend-path\s*SOMEPATH\s*\$root/baz', toy_module_txt))
+            self.assertTrue(re.search(r'prepend-path\s*SOMEPATH\s*\$root', toy_module_txt))
             self.assertTrue(re.search(r'module-info mode load.*\n\s*puts stderr\s*.*I AM toy v0.0', toy_module_txt))
             self.assertTrue(re.search(r'puts stderr "oh hai!"', toy_module_txt))
         elif get_module_syntax() == 'Lua':
             self.assertTrue(re.search(r'setenv\("FOO", "bar"\)', toy_module_txt))
-            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(pkg.root, "foo/bar"\)\)', toy_module_txt))
-            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(pkg.root, "baz"\)\)', toy_module_txt))
+            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(root, "foo/bar"\)\)', toy_module_txt))
+            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(root, "baz"\)\)', toy_module_txt))
+            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", root\)', toy_module_txt))
             self.assertTrue(re.search(r'if mode\(\) == "load" then\n\s*io.stderr:write\(".*I AM toy v0.0"\)',
                                       toy_module_txt))
             self.assertTrue(re.search(r'io.stderr:write\("oh hai!"\)', toy_module_txt))

From f2f0d8b8c90c44aa42628cf1edb50d18e8b8a21e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Apr 2015 12:33:37 +0200
Subject: [PATCH 0837/1356] add unit test for --hide-deps

---
 easybuild/tools/options.py |  5 ++---
 test/framework/options.py  | 41 ++++++++++++++++++++++++++++++++++++--
 2 files changed, 41 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index b3d1ab6510..d9f5a9ce57 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -194,10 +194,9 @@ def override_options(self):
             'ignore-osdeps': ("Ignore any listed OS dependencies", None, 'store_true', False),
             'filter-deps': ("Comma separated list of dependencies that you DON'T want to install with EasyBuild, "
                             "because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses)",
-                            str, 'extend', None),
+                            'strlist', 'extend', None),
             'hide-deps': ("Comma separated list of dependencies that you want automatically hidden, "
-                            "(e.g. --hide-deps=zlib,ncurses)",
-                            str, 'extend', None),
+                          "(e.g. --hide-deps=zlib,ncurses)", 'strlist', 'extend', None),
             'oldstyleconfig':   ("Look for and use the oldstyle configuration file.",
                                  None, 'store_true', True),
             'optarch': ("Set architecture optimization, overriding native architecture optimizations",
diff --git a/test/framework/options.py b/test/framework/options.py
index 0f381055a0..74787b2b4b 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1376,7 +1376,44 @@ def test_filter_deps(self):
         self.assertFalse(re.search('module: FFTW/3.3.3-gompi', outtxt))
         self.assertFalse(re.search('module: ScaLAPACK/2.0.2-gompi', outtxt))
         self.assertFalse(re.search('module: zlib', outtxt))
-    
+
+    def test_hide_deps(self):
+        """Test use of --hide-deps."""
+        test_dir = os.path.dirname(os.path.abspath(__file__))
+        ec_file = os.path.join(test_dir, 'easyconfigs', 'goolf-1.4.10.eb')
+        os.environ['MODULEPATH'] = os.path.join(test_dir, 'modules')
+        args = [
+            ec_file,
+            '--buildpath=%s' % self.test_buildpath,
+            '--installpath=%s' % self.test_installpath,
+            '--robot=%s' % os.path.join(test_dir, 'easyconfigs'),
+            '--dry-run',
+        ]
+        outtxt = self.eb_main(args, do_build=True, verbose=True, raise_error=True)
+        self.assertTrue(re.search('module: GCC/4.7.2', outtxt))
+        self.assertTrue(re.search('module: OpenMPI/1.6.4-GCC-4.7.2', outtxt))
+        self.assertTrue(re.search('module: OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2', outtxt))
+        self.assertTrue(re.search('module: FFTW/3.3.3-gompi', outtxt))
+        self.assertTrue(re.search('module: ScaLAPACK/2.0.2-gompi', outtxt))
+        # zlib is not a dep at all
+        self.assertFalse(re.search('module: zlib', outtxt))
+
+        # clear log file
+        open(self.logfile, 'w').write('')
+
+        # filter deps (including a non-existing dep, i.e. zlib)
+        args.append('--hide-deps=FFTW,ScaLAPACK,zlib')
+        outtxt = self.eb_main(args, do_build=True, verbose=True, raise_error=True)
+        self.assertTrue(re.search('module: GCC/4.7.2', outtxt))
+        self.assertTrue(re.search('module: OpenMPI/1.6.4-GCC-4.7.2', outtxt))
+        self.assertTrue(re.search('module: OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2', outtxt))
+        self.assertFalse(re.search(r'module: FFTW/3\.3\.3-gompi', outtxt))
+        self.assertTrue(re.search(r'module: FFTW/\.3\.3\.3-gompi', outtxt))
+        self.assertFalse(re.search(r'module: ScaLAPACK/2\.0\.2-gompi', outtxt))
+        self.assertTrue(re.search(r'module: ScaLAPACK/\.2\.0\.2-gompi', outtxt))
+        # zlib is not a dep at all
+        self.assertFalse(re.search(r'module: zlib', outtxt))
+
     def test_test_report_env_filter(self):
         """Test use of --test-report-env-filter."""
 
@@ -1442,7 +1479,7 @@ def test_robot(self):
             eb_file,
             '--robot-paths=%s' % test_ecs_path,
         ]
-        error_regex ='no module .* found for dependency'
+        error_regex = 'no module .* found for dependency'
         self.assertErrorRegex(EasyBuildError, error_regex, self.eb_main, args, raise_error=True, do_build=True)
 
         # enable robot, but without passing path required to resolve toy dependency => FAIL

From 6ff8596da8ed0582cc8d0944089011df64a73c80 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Apr 2015 13:03:58 +0200
Subject: [PATCH 0838/1356] clean up git commit log msg, enhance logging and
 unit test

---
 easybuild/tools/repository/gitrepo.py | 24 ++++++++++++------------
 test/framework/repository.py          |  6 ++++++
 2 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/easybuild/tools/repository/gitrepo.py b/easybuild/tools/repository/gitrepo.py
index 87f02f7835..34b012d4e5 100644
--- a/easybuild/tools/repository/gitrepo.py
+++ b/easybuild/tools/repository/gitrepo.py
@@ -139,24 +139,24 @@ def commit(self, msg=None):
         """
         Commit working copy to git repository
         """
-        self.log.debug("committing in git: %s" % msg)
-        completemsg = "%s EasyBuild-commit from %s (time: %s, user: %s). Easybuild v%s" % (msg, socket.gethostname(),
-                                                                                           time.strftime("%Y-%m-%d_%H-%M-%S"),
-                                                                                           getpass.getuser(), str(VERSION))
+        host = socket.gethostname()
+        timestamp = time.strftime("%Y-%m-%d_%H-%M-%S")
+        user = getpass.getuser()
+        completemsg = "%s with EasyBuild v%s @ %s (time: %s, user: %s)" % (msg, VERSION, host, timestamp, user)
+        self.log.debug("committing in git with message: %s" % msg)
+
         self.log.debug("git status: %s" % self.client.status())
         try:
-            self.client.commit('-am "%s"' % completemsg)
-            self.log.debug("succesfull commit")
+            self.client.commit('-am %s' % completemsg)
+            self.log.debug("succesfull commit: %s", self.client.log('HEAD^!'))
         except GitCommandError, err:
-            self.log.warning("Commit from working copy %s (msg: %s) failed, empty commit?\n%s" % (self.wc, msg, err))
+            self.log.warning("Commit from working copy %s failed, empty commit? (msg: %s): %s", self.wc, msg, err)
         try:
             info = self.client.push()
-            self.log.debug("push info: %s " % info)
+            self.log.debug("push info: %s ", info)
         except GitCommandError, err:
-            self.log.warning("Push from working copy %s to remote %s (msg: %s) failed: %s" % (self.wc,
-                                                                                              self.repo,
-                                                                                              msg,
-                                                                                              err))
+            self.log.warning("Push from working copy %s to remote %s failed (msg: %s): %s",
+                             self.wc, self.repo, msg, err)
 
     def cleanup(self):
         """
diff --git a/test/framework/repository.py b/test/framework/repository.py
index 405a7125b8..5622e49f65 100644
--- a/test/framework/repository.py
+++ b/test/framework/repository.py
@@ -40,6 +40,7 @@
 from easybuild.tools.repository.svnrepo import SvnRepository
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.run import run_cmd
+from easybuild.tools.version import VERSION
 
 
 class RepositoryTest(EnhancedTestCase):
@@ -97,6 +98,11 @@ def test_gitrepo(self):
             repo.init()
             toy_ec_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
             repo.add_easyconfig(toy_ec_file, 'test', '1.0', {}, False)
+            repo.commit("toy/0.0")
+
+            log_regex = re.compile(r"toy/0.0 with EasyBuild v%s @ .* \(time: .*, user: .*\)" % VERSION, re.M)
+            logmsg = repo.client.log('HEAD^!')
+            self.assertTrue(log_regex.search(logmsg), "Pattern '%s' found in %s" % (log_regex.pattern, logmsg))
 
             shutil.rmtree(repo.wc)
             shutil.rmtree(tmpdir)

From 6d975275db5282a04452cc7993c6c395d65138f3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Apr 2015 13:25:29 +0200
Subject: [PATCH 0839/1356] fix remark

---
 easybuild/tools/options.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 49abe37a69..6ade5060fa 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -80,7 +80,9 @@ class EasyBuildOptions(GeneralOption):
     VERSION = this_is_easybuild()
 
     DEFAULT_LOGLEVEL = 'INFO'
-    DEFAULT_CONFIGFILES = [p for p in DEFAULT_SYS_CFGFILES + [DEFAULT_USER_CFGFILE] if os.path.exists(p)]
+    DEFAULT_CONFIGFILES = DEFAULT_SYS_CFGFILES[:]
+    if os.path.exists(DEFAULT_USER_CFGFILE):
+        DEFAULT_CONFIGFILES.append(DEFAULT_USER_CFGFILE)
 
     ALLOPTSMANDATORY = False  # allow more than one argument
     CONFIGFILES_RAISE_MISSING = True  # don't allow non-existing config files to be specified

From 16564b996992467d350f9254b648307d2309aab7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Apr 2015 14:29:49 +0200
Subject: [PATCH 0840/1356] require vsc-base 2.2.0 (see
 https://github.com/hpcugent/vsc-base/pull/162)

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 4fecf38036..6335ba4f77 100644
--- a/setup.py
+++ b/setup.py
@@ -106,5 +106,5 @@ def find_rel_test():
     provides=["eb"] + easybuild_packages,
     test_suite="test.framework.suite",
     zip_safe=False,
-    install_requires=["vsc-base >= 2.1.1"],
+    install_requires=["vsc-base >= 2.2.0"],
 )

From 13358e5d7e5d3cc3584f5a6b2f9171e48c927cab Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Apr 2015 15:22:49 +0200
Subject: [PATCH 0841/1356] add support for appending/prepending to
 --robot-paths to avoid destroying the default

---
 easybuild/tools/options.py |  2 +-
 test/framework/config.py   | 90 ++++++++++++++++++++++++++++++++++++++
 test/framework/options.py  |  4 +-
 3 files changed, 93 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index e707031d75..374977cebd 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -125,7 +125,7 @@ def basic_options(self):
             'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
                       'pathlist', 'store_or_None', [], 'r', {'metavar': 'PATH[%sPATH]' % os.pathsep}),
             'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
-                            'pathlist', 'store', self.default_robot_paths, {'metavar': 'PATH[%sPATH]' % os.pathsep}),
+                            'pathlist', 'add_flex', self.default_robot_paths, {'metavar': 'PATH[%sPATH]' % os.pathsep}),
             'skip': ("Skip existing software (useful for installing additional packages)",
                      None, 'store_true', False, 'k'),
             'stop': ("Stop the installation after certain step", 'choice', 'store_or_None', 'source', 's', all_stops),
diff --git a/test/framework/config.py b/test/framework/config.py
index e91337f25b..30a2eb5da8 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -428,6 +428,96 @@ def test_XDG_CONFIG_env_vars(self):
         else:
             os.environ['XDG_CONFIG_DIRS'] = xdg_config_dirs
 
+    def test_flex_robot_paths(self):
+        """Test prepend/appending to default robot search path via --robot-paths."""
+        # unset $EASYBUILD_ROBOT_PATHS that was defined in setUp
+        del os.environ['EASYBUILD_ROBOT_PATHS']
+
+        # copy test easyconfigs to easybuild/easyconfigs subdirectory of temp directory
+        # to check whether easyconfigs install path is auto-included in robot path
+        tmpdir = tempfile.mkdtemp(prefix='easybuild-easyconfigs-pkg-install-path')
+        mkdir(os.path.join(tmpdir, 'easybuild'), parents=True)
+        test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        tmp_ecs_dir = os.path.join(tmpdir, 'easybuild', 'easyconfigs')
+        shutil.copytree(test_ecs_path, tmp_ecs_dir)
+
+        # prepend path to test easyconfigs into Python search path, so it gets picked up as --robot-paths default
+        orig_sys_path = sys.path[:]
+        sys.path = [tmpdir] + [p for p in sys.path if not os.path.exists(os.path.join(p, 'easybuild', 'easyconfigs'))]
+
+        # default: only pick up installed easyconfigs via sys.path
+        eb_go = eboptions.parse_options(args=[])
+        self.assertEqual(eb_go.options.robot_paths, [tmp_ecs_dir])
+
+        # prepend to default robot path
+        eb_go = eboptions.parse_options(args=['--robot-paths=/foo:'])
+        self.assertEqual(eb_go.options.robot_paths, ['/foo', tmp_ecs_dir])
+        eb_go = eboptions.parse_options(args=['--robot-paths=/foo:/bar/baz/:'])
+        self.assertEqual(eb_go.options.robot_paths, ['/foo', '/bar/baz/', tmp_ecs_dir])
+
+        # append to default robot path
+        eb_go = eboptions.parse_options(args=['--robot-paths=:/bar/baz'])
+        self.assertEqual(eb_go.options.robot_paths, [tmp_ecs_dir, '/bar/baz'])
+        # append to default robot path
+        eb_go = eboptions.parse_options(args=['--robot-paths=:/bar/baz:/foo'])
+        self.assertEqual(eb_go.options.robot_paths, [tmp_ecs_dir, '/bar/baz', '/foo'])
+
+        # prepend and append to default robot path
+        eb_go = eboptions.parse_options(args=['--robot-paths=/foo/bar::/baz'])
+        self.assertEqual(eb_go.options.robot_paths, ['/foo/bar', tmp_ecs_dir, '/baz'])
+        eb_go = eboptions.parse_options(args=['--robot-paths=/foo/bar::/baz:/trala'])
+        self.assertEqual(eb_go.options.robot_paths, ['/foo/bar', tmp_ecs_dir, '/baz', '/trala'])
+        eb_go = eboptions.parse_options(args=['--robot-paths=/foo/bar:/trala::/baz'])
+        self.assertEqual(eb_go.options.robot_paths, ['/foo/bar', '/trala', tmp_ecs_dir, '/baz'])
+
+        # also via $EASYBUILD_ROBOT_PATHS
+        os.environ['EASYBUILD_ROBOT_PATHS'] = '/foo::/bar/baz'
+        eb_go = eboptions.parse_options(args=[])
+        self.assertEqual(eb_go.options.robot_paths, ['/foo', tmp_ecs_dir, '/bar/baz'])
+
+        # combining $EASYBUILD_ROBOT_PATHS and --robot-paths: all paths are retained in the order to be expected
+        os.environ['EASYBUILD_ROBOT_PATHS'] = '/foo::/bar/baz'
+        eb_go = eboptions.parse_options(args=['--robot-paths=/one::/last'])
+        self.assertEqual(eb_go.options.robot_paths, ['/one', '/foo', tmp_ecs_dir, '/bar/baz', '/last'])
+
+        del os.environ['EASYBUILD_ROBOT_PATHS']
+
+        # also works with a cfgfile in the mix
+        config_file = os.path.join(self.tmpdir, 'testconfig.cfg')
+        cfgtxt = '\n'.join([
+            '[config]',
+            'robot-paths=/cfgfirst::/cfglast',
+        ])
+        write_file(config_file, cfgtxt)
+        eb_go = eboptions.parse_options(args=['--configfiles=%s' % config_file])
+        self.assertEqual(eb_go.options.robot_paths, ['/cfgfirst', tmp_ecs_dir, '/cfglast'])
+
+        # cfgfile entry is lost when env var and/or cmdline options are used
+        os.environ['EASYBUILD_ROBOT_PATHS'] = '/envfirst::/envend'
+        eb_go = eboptions.parse_options(args=['--configfiles=%s' % config_file])
+        self.assertEqual(eb_go.options.robot_paths, ['/envfirst', tmp_ecs_dir, '/envend'])
+
+        del os.environ['EASYBUILD_ROBOT_PATHS']
+        eb_go = eboptions.parse_options(args=['--robot-paths=/veryfirst:', '--configfiles=%s' % config_file])
+        self.assertEqual(eb_go.options.robot_paths, ['/veryfirst', tmp_ecs_dir])
+
+        os.environ['EASYBUILD_ROBOT_PATHS'] = ':/envend'
+        eb_go = eboptions.parse_options(args=['--robot-paths=/veryfirst:', '--configfiles=%s' % config_file])
+        self.assertEqual(eb_go.options.robot_paths, ['/veryfirst', tmp_ecs_dir, '/envend'])
+
+        del os.environ['EASYBUILD_ROBOT_PATHS']
+
+        # override default robot path
+        eb_go = eboptions.parse_options(args=['--robot-paths=/foo:/bar/baz'])
+        self.assertEqual(eb_go.options.robot_paths, ['/foo', '/bar/baz'])
+
+        # --robot paths still get preference
+        eb_go = eboptions.parse_options(args=['--robot-paths=/foo/bar::/baz', '--robot=/first'])
+        self.assertEqual(eb_go.options.robot_paths, ['/first', '/foo/bar', tmp_ecs_dir, '/baz'])
+
+        sys.path[:] = orig_sys_path
+
+
 def suite():
     return TestLoader().loadTestsFromTestCase(EasyBuildConfigTest)
 
diff --git a/test/framework/options.py b/test/framework/options.py
index 0f381055a0..0f062e6b85 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -298,7 +298,8 @@ def check_args(job_args, passed_args=None):
         check_args(['--debug', '--stop=configure', '--try-software-name=foo'])
         check_args(['--debug', '--robot-paths=/tmp/foo:/tmp/bar'])
         # --robot has preference over --robot-paths, --robot is not passed down
-        check_args(['--debug', '--robot-paths=/tmp/foo', '--robot=/tmp/bar'], passed_args=['--debug', '--robot-paths=/tmp/bar:/tmp/foo'])
+        check_args(['--debug', '--robot-paths=/tmp/foo', '--robot=/tmp/bar'],
+                   passed_args=['--debug', '--robot-paths=/tmp/bar:/tmp/foo'])
 
     # 'zzz' prefix in the test name is intentional to make this test run last,
     # since it fiddles with the logging infrastructure which may break things
@@ -1484,7 +1485,6 @@ def test_robot(self):
             ec_regex = re.compile(r'^\s\*\s\[[xF ]\]\s%s' % os.path.join(test_ecs_path, ecfile), re.M)
             self.assertTrue(ec_regex.search(outtxt), "Pattern %s found in %s" % (ec_regex.pattern, outtxt))
 
-
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(CommandLineOptionsTest)

From 3c3b26f207fa62e3855e8e1d97e7a3325c0811c3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Apr 2015 14:29:49 +0200
Subject: [PATCH 0842/1356] require vsc-base 2.2.0 (see
 https://github.com/hpcugent/vsc-base/pull/162)

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 4fecf38036..6335ba4f77 100644
--- a/setup.py
+++ b/setup.py
@@ -106,5 +106,5 @@ def find_rel_test():
     provides=["eb"] + easybuild_packages,
     test_suite="test.framework.suite",
     zip_safe=False,
-    install_requires=["vsc-base >= 2.1.1"],
+    install_requires=["vsc-base >= 2.2.0"],
 )

From 0f4953b6504f2e88de261ece6b6327a2c12cf7a2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Apr 2015 15:33:57 +0200
Subject: [PATCH 0843/1356] enable detection of use of unknown
 $EASYBUILD-prefixed env vars

---
 easybuild/tools/options.py | 2 +-
 test/framework/config.py   | 8 ++++++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index e707031d75..1d60c28ca0 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -648,7 +648,7 @@ def parse_options(args=None):
                    "Provide one or more easyconfigs or directories, use -H or --help more information.")
 
     eb_go = EasyBuildOptions(usage=usage, description=description, prog='eb', envvar_prefix=CONFIG_ENV_VAR_PREFIX,
-                             go_args=args)
+                             go_args=args, error_env_options=True)
     return eb_go
 
 
diff --git a/test/framework/config.py b/test/framework/config.py
index e91337f25b..35d923470e 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -168,6 +168,14 @@ def test_generaloption_config(self):
         del os.environ['EASYBUILD_PREFIX']
         del os.environ['EASYBUILD_SUBDIR_SOFTWARE']
 
+    def test_error_env_var_typo(self):
+        """Test error reporting on use of known $EASYBUILD-prefixed env vars."""
+        os.environ['EASYBUILD_THERESNOSUCHCONFIGURATIONOPTION'] = 'whatever'
+
+        init_config()
+
+        del os.environ['EASYBUILD_THERESNOSUCHCONFIGURATIONOPTION']
+
     def test_generaloption_config_file(self):
         """Test use of new-style configuration file."""
         self.purge_environment()

From 06f0e91c8d3bae83a81f085ac99e7608c5836653 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Apr 2015 16:00:51 +0200
Subject: [PATCH 0844/1356] use new raise_easybuilderror function to report
 detection of use of unknown $EASYBUILD env vars

---
 easybuild/tools/build_log.py |  5 +++++
 easybuild/tools/options.py   |  4 ++--
 test/framework/config.py     | 16 ++++++++++++----
 3 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index b64b5f648e..fcea59db41 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -72,6 +72,11 @@ def __str__(self):
         return repr(self.msg)
 
 
+def raise_easybuilderror(msg, *args):
+    """Raise EasyBuildError with given message, formatted by provided string arguments."""
+    raise EasyBuildError(msg, *args)
+
+
 class EasyBuildLog(fancylogger.FancyLogger):
     """
     The EasyBuild logger, with its own error and exception functions.
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 1d60c28ca0..a4ccb046d6 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -49,7 +49,7 @@
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
 from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
-from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.build_log import EasyBuildError, raise_easybuilderror
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES
 from easybuild.tools.config import DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_pretend_installpath
@@ -648,7 +648,7 @@ def parse_options(args=None):
                    "Provide one or more easyconfigs or directories, use -H or --help more information.")
 
     eb_go = EasyBuildOptions(usage=usage, description=description, prog='eb', envvar_prefix=CONFIG_ENV_VAR_PREFIX,
-                             go_args=args, error_env_options=True)
+                             go_args=args, error_env_options=True, error_env_option_method=raise_easybuilderror)
     return eb_go
 
 
diff --git a/test/framework/config.py b/test/framework/config.py
index 35d923470e..a291ca7071 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -38,13 +38,13 @@
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 
 import easybuild.tools.options as eboptions
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_path, source_paths, install_path, get_repositorypath
 from easybuild.tools.config import set_tmpdir, BuildOptions, ConfigurationVariables
-from easybuild.tools.config import get_build_log_path, DEFAULT_PATH_SUBDIRS, init_build_options, build_option
+from easybuild.tools.config import get_build_log_path, DEFAULT_PATH_SUBDIRS, init_build_options
 from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import mkdir, write_file
-from easybuild.tools.repository.filerepo import FileRepository
-from easybuild.tools.repository.repository import init_repository
+from easybuild.tools.options import CONFIG_ENV_VAR_PREFIX
 
 
 class EasyBuildConfigTest(EnhancedTestCase):
@@ -170,11 +170,19 @@ def test_generaloption_config(self):
 
     def test_error_env_var_typo(self):
         """Test error reporting on use of known $EASYBUILD-prefixed env vars."""
+        # all is well
+        init_config()
+
+        os.environ['EASYBUILD_FOO'] = 'foo'
         os.environ['EASYBUILD_THERESNOSUCHCONFIGURATIONOPTION'] = 'whatever'
 
-        init_config()
+        error = r"Found 2 environment variable\(s\) that are prefixed with %s " % CONFIG_ENV_VAR_PREFIX
+        error += "but do not match valid option\(s\): "
+        error += ','.join(['EASYBUILD_FOO', 'EASYBUILD_THERESNOSUCHCONFIGURATIONOPTION'])
+        self.assertErrorRegex(EasyBuildError, error, init_config)
 
         del os.environ['EASYBUILD_THERESNOSUCHCONFIGURATIONOPTION']
+        del os.environ['EASYBUILD_FOO']
 
     def test_generaloption_config_file(self):
         """Test use of new-style configuration file."""

From 1511e213d9187fa4f7c366f11d5e099e2dfcf378 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Thu, 2 Apr 2015 20:34:54 -0400
Subject: [PATCH 0845/1356] Adding a better default

---
 easybuild/tools/config.py    |  2 +-
 easybuild/tools/packaging.py | 12 +++++-------
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 89b104f2cc..4eeb06a66d 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -66,7 +66,7 @@
 }
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
-DEFAULT_PACKAGE_TEMPLATE = "eb-%(toolchain)s-%(name)s"
+DEFAULT_PACKAGE_TEMPLATE = "eb-%(name)s-%(version)s-%(toolchain)s"
 
 # utility function for obtaining default paths
 def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 0ad3aed8d2..cc729e709c 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -64,13 +64,11 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
     full_ec_version = det_full_ec_version(easyblock.cfg)
     _log.debug("I got a package template that looks like: %s " % pkgtemplate )
 
-    if easyblock.toolchain.name == DUMMY_TOOLCHAIN_NAME:
-        toolchain_name = easyblock.version
-    else:
-        toolchain_name = "%s-%s" % (easyblock.toolchain.name, easyblock.toolchain.version)
+    toolchain_name = "%s-%s" % (easyblock.toolchain.name, easyblock.toolchain.version)
 
     pkgname = pkgtemplate % {
         'toolchain' : toolchain_name,
+        'version': '-'.join([x for x in [easyblock.cfg.get('versionprefix', ''), easyblock.cfg['version'], easyblock.cfg['versionsuffix']] if x]),
         'name' : easyblock.name,
     }
     
@@ -89,10 +87,10 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
         _log.debug("The dep added looks like %s " % dep)
         dep_pkgname = pkgtemplate % {
             'name': dep['name'],
+            'version': '-'.join([x for x in [dep.get('versionprefix',''), dep['version'], dep['versionsuffix']] if x]),
             'toolchain': "%s-%s" % (dep['toolchain']['name'], dep['toolchain']['version']),
-
         }
-        depstring += " --depends '%s = %s-1'" % ( dep_pkgname,  full_dep_version)
+        depstring += " --depends '%s'" % ( dep_pkgname)
 
     cmdlist=[
         'fpm',
@@ -101,7 +99,7 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
         '--provides', pkgname,
         '-t', package_type, # target
         '-s', 'dir', # source
-        '--version', full_ec_version,
+        '--version', "eb",
     ]
     cmdlist.extend([ depstring ])
     cmdlist.extend([

From 873e093eb0f84c8bcd2491d3aff0fc8edc069362 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Apr 2015 11:41:15 +0200
Subject: [PATCH 0846/1356] restore newlines at the end of
 setenv/prepend-path/set-alias statements

---
 easybuild/framework/easyblock.py    |  40 +++++------
 easybuild/tools/module_generator.py |  52 +++++++-------
 test/framework/module_generator.py  |  84 +++++++++++-----------
 test/framework/toy_build.py         | 104 ++++++++++++++++++++++++----
 4 files changed, 178 insertions(+), 102 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 8493babab6..7697697f82 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -748,13 +748,8 @@ def make_devel_module(self, create_in_builddir=False):
         fake_mod_data = self.load_fake_module(purge=True)
 
         header = self.module_generator.MODULE_HEADER
-
-        env_lines = []
-        for (key, val) in env.get_changes().items():
-            # check if non-empty string
-            # TODO: add unset for empty vars?
-            if val.strip():
-                env_lines.append(self.module_generator.set_environment(key, val))
+        if header:
+            header += '\n'
 
         load_lines = []
         # capture all the EBDEVEL vars
@@ -770,6 +765,13 @@ def make_devel_module(self, create_in_builddir=False):
             elif key.startswith('SOFTDEVEL'):
                 self.log.nosupport("Environment variable SOFTDEVEL* being relied on", '2.0')
 
+        env_lines = []
+        for (key, val) in env.get_changes().items():
+            # check if non-empty string
+            # TODO: add unset for empty vars?
+            if val.strip():
+                env_lines.append(self.module_generator.set_environment(key, val))
+
         if create_in_builddir:
             output_dir = self.builddir
         else:
@@ -779,7 +781,7 @@ def make_devel_module(self, create_in_builddir=False):
         filename = os.path.join(output_dir, ActiveMNS().det_devel_module_filename(self.cfg))
         self.log.debug("Writing devel module to %s" % filename)
 
-        txt = '\n'.join([header] + load_lines + env_lines)
+        txt = ''.join([header] + load_lines + env_lines)
         write_file(filename, txt)
 
         # cleanup: unload fake module, remove fake module dir
@@ -856,7 +858,7 @@ def make_module_extra(self):
         devel_path_envvar = DEVEL_ENV_VAR_NAME_PREFIX + env_name
         lines.append(self.module_generator.set_environment(devel_path_envvar, devel_path, relpath=True))
 
-        lines.append('')
+        lines.append('\n')
         for (key, value) in self.cfg['modextravars'].items():
             lines.append(self.module_generator.set_environment(key, value))
 
@@ -874,7 +876,7 @@ def make_module_extra(self):
         if self.cfg['modtclfooter']:
             if isinstance(self.module_generator, ModuleGeneratorTcl):
                 self.log.debug("Including Tcl footer in module: %s", self.cfg['modtclfooter'])
-                lines.append(self.cfg['modtclfooter'])
+                lines.extend([self.cfg['modtclfooter'], '\n'])
             else:
                 self.log.warning("Not including footer in Tcl syntax in non-Tcl module file: %s",
                                  self.cfg['modtclfooter'])
@@ -882,7 +884,7 @@ def make_module_extra(self):
         if self.cfg['modluafooter']:
             if isinstance(self.module_generator, ModuleGeneratorLua):
                 self.log.debug("Including Lua footer in module: %s", self.cfg['modluafooter'])
-                lines.append(self.cfg['modluafooter'])
+                lines.extend([self.cfg['modluafooter'], '\n'])
             else:
                 self.log.warning("Not including footer in Lua syntax in non-Lua module file: %s",
                                  self.cfg['modluafooter'])
@@ -890,8 +892,7 @@ def make_module_extra(self):
         for (key, value) in self.cfg['modaliases'].items():
             lines.append(self.module_generator.set_alias(key, value))
 
-        lines.append('')
-        txt = '\n'.join(lines)
+        txt = ''.join(lines)
         self.log.debug("make_module_extra added this: %s", txt)
 
         return txt
@@ -909,7 +910,7 @@ def make_module_extra_extensions(self):
             env_var_name = convert_name(self.name, upper=True)
             lines.append(self.module_generator.set_environment('EBEXTSLIST%s' % env_var_name, exts_list))
 
-        return '\n'.join(lines)
+        return ''.join(lines)
 
     def make_module_footer(self):
         """
@@ -926,7 +927,7 @@ def make_module_footer(self):
             self.log.debug("Including specified footer into module: '%s'" % self.modules_footer)
             footer.append(self.modules_footer)
 
-        return '\n'.join(footer)
+        return ''.join(footer)
 
     def make_module_extend_modpath(self):
         """
@@ -960,7 +961,7 @@ def make_module_req(self):
             except OSError, err:
                 raise EasyBuildError("Failed to change to %s: %s", self.installdir, err)
 
-            lines.append('')
+            lines.append('\n')
             for key in sorted(requirements):
                 for path in requirements[key]:
                     paths = sorted(glob.glob(path))
@@ -971,7 +972,7 @@ def make_module_req(self):
             except OSError, err:
                 raise EasyBuildError("Failed to change back to %s: %s", self.orig_workdir, err)
 
-        return '\n'.join(lines)
+        return ''.join(lines)
 
     def make_module_req_guess(self):
         """
@@ -1671,8 +1672,7 @@ def make_module_step(self, fake=False):
         mod_symlink_paths = ActiveMNS().det_module_symlink_paths(self.cfg)
         modpath = self.module_generator.prepare(mod_symlink_paths)
 
-        txt = ''
-        txt += self.make_module_description()
+        txt = self.make_module_description()
         txt += self.make_module_dep()
         txt += self.make_module_extend_modpath()
         txt += self.make_module_req()
@@ -1681,7 +1681,7 @@ def make_module_step(self, fake=False):
 
         write_file(self.module_generator.filename, txt)
 
-        self.log.info("Module file %s written" % self.module_generator.filename)
+        self.log.info("Module file %s written: %s", self.module_generator.filename, txt)
 
          # only update after generating final module file
         if not fake:
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 0c46d916e1..1332f3f3e5 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -144,7 +144,7 @@ class ModuleGeneratorTcl(ModuleGenerator):
 
     def comment(self, msg):
         """Return string containing given message as a comment."""
-        return "# %s" % msg
+        return "# %s\n" % msg
 
     def conditional_statement(self, condition, body, negative=False):
         """Return formatted conditional statement, with given condition and body."""
@@ -154,7 +154,7 @@ def conditional_statement(self, condition, body, negative=False):
             lines = ["if { [ %s ] } {" % condition]
 
         lines.append('    ' + body)
-        lines.append('}')
+        lines.extend(['}', ''])
         return '\n'.join(lines)
 
     def get_description(self, conflict=True):
@@ -164,7 +164,7 @@ def get_description(self, conflict=True):
         description = "%s - Homepage: %s" % (self.app.cfg['description'], self.app.cfg['homepage'])
 
         lines = [
-            '',
+            self.MODULE_HEADER.replace('%', '%%'),
             "proc ModulesHelp { } {",
             "    puts stderr { %(description)s",
             "    }",
@@ -177,7 +177,7 @@ def get_description(self, conflict=True):
 
         if self.app.cfg['moduleloadnoconflict']:
             cond_unload = self.conditional_statement("is-loaded %(name)s", "module unload %(name)s")
-            lines.append(self.conditional_statement("is-loaded %(name)s/%(version)s", cond_unload, negative=True))
+            lines.extend(['', self.conditional_statement("is-loaded %(name)s/%(version)s", cond_unload, negative=True)])
 
         elif conflict:
             # conflict on 'name' part of module name (excluding version part at the end)
@@ -187,7 +187,7 @@ def get_description(self, conflict=True):
             # - 'conflict Compiler/GCC/4.8.2/OpenMPI' for 'Compiler/GCC/4.8.2/OpenMPI/1.6.4'
             lines.extend(['', "conflict %s" % os.path.dirname(self.app.short_mod_name)])
 
-        txt = self.MODULE_HEADER + '\n'.join([''] + lines + ['']) % {
+        txt = '\n'.join(lines + ['']) % {
             'name': self.app.name,
             'version': self.app.version,
             'description': description,
@@ -204,23 +204,23 @@ def load_module(self, mod_name):
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the depedency "module load" is present,
             # it will get translated to "module unload"
-            load_statement = ["module load %(mod_name)s"]
+            load_statement = [self.LOAD_TEMPLATE, '']
         else:
             load_statement = [self.conditional_statement("is-loaded %(mod_name)s", self.LOAD_TEMPLATE, negative=True)]
-        return '\n'.join([''] + load_statement + ['']) % {'mod_name': mod_name}
+        return '\n'.join([''] + load_statement) % {'mod_name': mod_name}
 
     def unload_module(self, mod_name):
         """
         Generate unload statements for module.
         """
         cond_unload = self.conditional_statement("is-loaded %(mod)s", "module unload %(mod)s") % {'mod': mod_name}
-        return '\n'.join(['', cond_unload, ''])
+        return '\n'.join(['', cond_unload])
 
     def prepend_paths(self, key, paths, allow_abs=False):
         """
         Generate prepend-path statements for the given list of paths.
         """
-        template = "prepend-path\t%s\t\t%s"
+        template = "prepend-path\t%s\t\t%s\n"
 
         if isinstance(paths, basestring):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
@@ -238,7 +238,7 @@ def prepend_paths(self, key, paths, allow_abs=False):
                     paths[i] = '$root'
 
         statements = [template % (key, p) for p in paths]
-        return '\n'.join(statements)
+        return ''.join(statements)
 
     def use(self, paths):
         """
@@ -246,8 +246,8 @@ def use(self, paths):
         """
         use_statements = []
         for path in paths:
-            use_statements.append("module use %s" % path)
-        return '\n'.join(use_statements)
+            use_statements.append("module use %s\n" % path)
+        return ''.join(use_statements)
 
     def set_environment(self, key, value, relpath=False):
         """
@@ -261,7 +261,7 @@ def set_environment(self, key, value, relpath=False):
                 val = '"$root"'
         else:
             val = quote_str(value)
-        return 'setenv\t%s\t\t%s' % (key, val)
+        return 'setenv\t%s\t\t%s\n' % (key, val)
 
     def msg_on_load(self, msg):
         """
@@ -270,14 +270,14 @@ def msg_on_load(self, msg):
         # escape any (non-escaped) characters with special meaning by prefixing them with a backslash
         msg = re.sub(r'((?<!\\)[%s])'% ''.join(self.CHARS_TO_ESCAPE), r'\\\1', msg)
         print_cmd = "puts stderr %s" % quote_str(msg)
-        return '\n'.join(['', self.conditional_statement("module-info mode load", print_cmd), ''])
+        return '\n'.join(['', self.conditional_statement("module-info mode load", print_cmd)])
 
     def set_alias(self, key, value):
         """
         Generate set-alias statement in modulefile for the given key/value pair.
         """
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
-        return 'set-alias\t%s\t\t%s' % (key, quote_str(value))
+        return 'set-alias\t%s\t\t%s\n' % (key, quote_str(value))
 
 
 class ModuleGeneratorLua(ModuleGenerator):
@@ -293,7 +293,7 @@ class ModuleGeneratorLua(ModuleGenerator):
     LOAD_TEMPLATE = 'load("%(mod_name)s")'
 
     PATH_JOIN_TEMPLATE = 'pathJoin(root, "%s")'
-    PREPEND_PATH_TEMPLATE = 'prepend_path("%s", %s)'
+    PREPEND_PATH_TEMPLATE = 'prepend_path("%s", %s)\n'
 
     def __init__(self, *args, **kwargs):
         """ModuleGeneratorLua constructor."""
@@ -301,7 +301,7 @@ def __init__(self, *args, **kwargs):
 
     def comment(self, msg):
         """Return string containing given message as a comment."""
-        return " -- %s" % msg
+        return "-- %s\n" % msg
 
     def conditional_statement(self, condition, body, negative=False):
         """Return formatted conditional statement, with given condition and body."""
@@ -312,7 +312,7 @@ def conditional_statement(self, condition, body, negative=False):
 
         for line in body.split('\n'):
             lines.append('    ' + line)
-        lines.append('end')
+        lines.extend(['end', ''])
         return '\n'.join(lines)
 
     def get_description(self, conflict=True):
@@ -357,18 +357,18 @@ def load_module(self, mod_name):
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the depedency "module load" is present,
             # it will get translated to "module unload"
-            load_statement = [self.LOAD_TEMPLATE]
+            load_statement = [self.LOAD_TEMPLATE, '']
         else:
             load_statement = [self.conditional_statement('isloaded("%(mod_name)s")', self.LOAD_TEMPLATE, negative=True)]
 
-        return '\n'.join([''] + load_statement + ['']) % {'mod_name': mod_name}
+        return '\n'.join([''] + load_statement) % {'mod_name': mod_name}
 
     def unload_module(self, mod_name):
         """
         Generate unload statements for module.
         """
         cond_unload = self.conditional_statement('isloaded("%(mod)s")', 'unload("%(mod)s")') % {'mod': mod_name}
-        return '\n'.join(['', cond_unload, ''])
+        return '\n'.join(['', cond_unload])
 
     def prepend_paths(self, key, paths, allow_abs=False):
         """
@@ -393,14 +393,14 @@ def prepend_paths(self, key, paths, allow_abs=False):
                     paths[i] = 'root'
 
         statements = [self.PREPEND_PATH_TEMPLATE % (key, p) for p in paths]
-        return '\n'.join(statements)
+        return ''.join(statements)
 
     def use(self, paths):
         """
         Generate module use statements for given list of module paths.
         @param paths: list of module path extensions to generate use statements for
         """
-        return '\n'.join([self.PREPEND_PATH_TEMPLATE % ('MODULEPATH', quote_str(p)) for p in paths] + [''])
+        return ''.join([self.PREPEND_PATH_TEMPLATE % ('MODULEPATH', quote_str(p)) for p in paths])
 
     def set_environment(self, key, value, relpath=False):
         """
@@ -413,20 +413,20 @@ def set_environment(self, key, value, relpath=False):
                 val = 'root'
         else:
             val = quote_str(value)
-        return 'setenv("%s", %s)' % (key, val)
+        return 'setenv("%s", %s)\n' % (key, val)
 
     def msg_on_load(self, msg):
         """
         Add a message that should be printed when loading the module.
         """
-        return '\n'.join(['', self.conditional_statement('mode() == "load"', 'io.stderr:write("%s")' % msg), ''])
+        return '\n'.join(['', self.conditional_statement('mode() == "load"', 'io.stderr:write("%s")' % msg)])
 
     def set_alias(self, key, value):
         """
         Generate set-alias statement in modulefile for the given key/value pair.
         """
         # quotes are needed, to ensure smooth working of EBDEVEL* modulefiles
-        return 'setalias("%s", %s)' % (key, quote_str(value))
+        return 'setalias("%s", %s)\n' % (key, quote_str(value))
 
 
 def avail_module_generators():
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 01c9ada606..99c031b928 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -84,7 +84,6 @@ def test_descr(self):
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
             expected = '\n'.join([
                 "#%Module",
-                "",
                 "proc ModulesHelp { } {",
                 "    puts stderr { %s" % gzip_txt,
                 "    }",
@@ -120,20 +119,20 @@ def test_load(self):
 
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
             expected = [
-                "",
+                '',
                 "if { ![ is-loaded mod_name ] } {",
                 "    module load mod_name",
                 "}",
-                "",
+                '',
             ]
             self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
 
             # with recursive unloading: no if is-loaded guard
             init_config(build_options={'recursive_mod_unload': True})
             expected = [
-                "",
+                '',
                 "module load mod_name",
-                "",
+                '',
             ]
             self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
         else:
@@ -148,9 +147,9 @@ def test_load(self):
 
             init_config(build_options={'recursive_mod_unload': True})
             expected = '\n'.join([
-                "",
+                '',
                 'load("mod_name")',
-                "",
+                '',
             ])
             self.assertEqual(expected,self.modgen.load_module("mod_name"))
 
@@ -159,20 +158,20 @@ def test_unload(self):
 
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
             expected = '\n'.join([
-                "",
+                '',
                 "if { [ is-loaded mod_name ] } {",
                 "    module unload mod_name",
                 "}",
-                "",
+                '',
             ])
             self.assertEqual(expected, self.modgen.unload_module("mod_name"))
         else:
             expected = '\n'.join([
-            "",
-            'if isloaded("mod_name") then',
-            '    unload("mod_name")',
-            "end",
-            "",
+                '',
+                'if isloaded("mod_name") then',
+                '    unload("mod_name")',
+                "end",
+                '',
             ])
             self.assertEqual(expected, self.modgen.unload_module("mod_name"))
 
@@ -181,31 +180,31 @@ def test_prepend_paths(self):
         # test prepend_paths
 
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
-            expected = '\n'.join([
-                "prepend-path\tkey\t\t$root/path1",
-                "prepend-path\tkey\t\t$root/path2",
-                "prepend-path\tkey\t\t$root",
+            expected = ''.join([
+                "prepend-path\tkey\t\t$root/path1\n",
+                "prepend-path\tkey\t\t$root/path2\n",
+                "prepend-path\tkey\t\t$root\n",
             ])
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2", '']))
 
-            expected = "prepend-path\tbar\t\t$root/foo"
+            expected = "prepend-path\tbar\t\t$root/foo\n"
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
 
             res = self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True)
-            self.assertEqual("prepend-path\tkey\t\t/abs/path", res)
+            self.assertEqual("prepend-path\tkey\t\t/abs/path\n", res)
 
         else:
-            expected = '\n'.join([
-                'prepend_path("key", pathJoin(root, "path1"))',
-                'prepend_path("key", pathJoin(root, "path2"))',
-                'prepend_path("key", root)',
+            expected = ''.join([
+                'prepend_path("key", pathJoin(root, "path1"))\n',
+                'prepend_path("key", pathJoin(root, "path2"))\n',
+                'prepend_path("key", root)\n',
             ])
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2", '']))
 
-            expected = 'prepend_path("bar", pathJoin(root, "foo"))'
+            expected = 'prepend_path("bar", pathJoin(root, "foo"))\n'
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
 
-            expected = 'prepend_path("key", "/abs/path")'
+            expected = 'prepend_path("key", "/abs/path")\n'
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
 
         self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
@@ -215,16 +214,15 @@ def test_prepend_paths(self):
     def test_use(self):
         """Test generating module use statements."""
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
-            expected = '\n'.join([
-                "module use /some/path",
-                "module use /foo/bar/baz",
+            expected = ''.join([
+                "module use /some/path\n",
+                "module use /foo/bar/baz\n",
             ])
             self.assertEqual(self.modgen.use(["/some/path", "/foo/bar/baz"]), expected)
         else:
-            expected = '\n'.join([
-                'prepend_path("MODULEPATH", "/some/path")',
-                'prepend_path("MODULEPATH", "/foo/bar/baz")',
-                '',
+            expected = ''.join([
+                'prepend_path("MODULEPATH", "/some/path")\n',
+                'prepend_path("MODULEPATH", "/foo/bar/baz")\n',
             ])
             self.assertEqual(self.modgen.use(["/some/path", "/foo/bar/baz"]), expected)
 
@@ -233,23 +231,23 @@ def test_env(self):
         """Test setting of environment variables."""
         # test set_environment
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
-            self.assertEqual('setenv\tkey\t\t"value"', self.modgen.set_environment("key", "value"))
-            self.assertEqual("setenv\tkey\t\t'va\"lue'", self.modgen.set_environment("key", 'va"lue'))
-            self.assertEqual('setenv\tkey\t\t"va\'lue"', self.modgen.set_environment("key", "va'lue"))
-            self.assertEqual('setenv\tkey\t\t"""va"l\'ue"""', self.modgen.set_environment("key", """va"l'ue"""))
+            self.assertEqual('setenv\tkey\t\t"value"\n', self.modgen.set_environment("key", "value"))
+            self.assertEqual("setenv\tkey\t\t'va\"lue'\n", self.modgen.set_environment("key", 'va"lue'))
+            self.assertEqual('setenv\tkey\t\t"va\'lue"\n', self.modgen.set_environment("key", "va'lue"))
+            self.assertEqual('setenv\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_environment("key", """va"l'ue"""))
         else:
-            self.assertEqual('setenv("key", "value")', self.modgen.set_environment("key", "value"))
+            self.assertEqual('setenv("key", "value")\n', self.modgen.set_environment("key", "value"))
 
     def test_alias(self):
         """Test setting of alias in modulefiles."""
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
             # test set_alias
-            self.assertEqual('set-alias\tkey\t\t"value"', self.modgen.set_alias("key", "value"))
-            self.assertEqual("set-alias\tkey\t\t'va\"lue'", self.modgen.set_alias("key", 'va"lue'))
-            self.assertEqual('set-alias\tkey\t\t"va\'lue"', self.modgen.set_alias("key", "va'lue"))
-            self.assertEqual('set-alias\tkey\t\t"""va"l\'ue"""', self.modgen.set_alias("key", """va"l'ue"""))
+            self.assertEqual('set-alias\tkey\t\t"value"\n', self.modgen.set_alias("key", "value"))
+            self.assertEqual("set-alias\tkey\t\t'va\"lue'\n", self.modgen.set_alias("key", 'va"lue'))
+            self.assertEqual('set-alias\tkey\t\t"va\'lue"\n', self.modgen.set_alias("key", "va'lue"))
+            self.assertEqual('set-alias\tkey\t\t"""va"l\'ue"""\n', self.modgen.set_alias("key", """va"l'ue"""))
         else:
-            self.assertEqual('setalias("key", "value")', self.modgen.set_alias("key", "value"))
+            self.assertEqual('setalias("key", "value")\n', self.modgen.set_alias("key", "value"))
 
     def test_load_msg(self):
         """Test including a load message in the module file."""
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index efa425cf56..ec34fc1e23 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -233,20 +233,20 @@ def test_toy_tweaked(self):
         toy_module_txt = read_file(toy_module)
 
         if get_module_syntax() == 'Tcl':
-            self.assertTrue(re.search(r'setenv\s*FOO\s*"bar"', toy_module_txt))
-            self.assertTrue(re.search(r'prepend-path\s*SOMEPATH\s*\$root/foo/bar', toy_module_txt))
-            self.assertTrue(re.search(r'prepend-path\s*SOMEPATH\s*\$root/baz', toy_module_txt))
-            self.assertTrue(re.search(r'prepend-path\s*SOMEPATH\s*\$root', toy_module_txt))
-            self.assertTrue(re.search(r'module-info mode load.*\n\s*puts stderr\s*.*I AM toy v0.0', toy_module_txt))
-            self.assertTrue(re.search(r'puts stderr "oh hai!"', toy_module_txt))
+            self.assertTrue(re.search(r'^setenv\s*FOO\s*"bar"$', toy_module_txt, re.M))
+            self.assertTrue(re.search(r'^prepend-path\s*SOMEPATH\s*\$root/foo/bar$', toy_module_txt, re.M))
+            self.assertTrue(re.search(r'^prepend-path\s*SOMEPATH\s*\$root/baz$', toy_module_txt, re.M))
+            self.assertTrue(re.search(r'^prepend-path\s*SOMEPATH\s*\$root$', toy_module_txt, re.M))
+            self.assertTrue(re.search(r'module-info mode load.*\n\s*puts stderr\s*.*I AM toy v0.0"$', toy_module_txt, re.M))
+            self.assertTrue(re.search(r'^puts stderr "oh hai!"$', toy_module_txt, re.M))
         elif get_module_syntax() == 'Lua':
-            self.assertTrue(re.search(r'setenv\("FOO", "bar"\)', toy_module_txt))
-            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(root, "foo/bar"\)\)', toy_module_txt))
-            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", pathJoin\(root, "baz"\)\)', toy_module_txt))
-            self.assertTrue(re.search(r'prepend_path\("SOMEPATH", root\)', toy_module_txt))
-            self.assertTrue(re.search(r'if mode\(\) == "load" then\n\s*io.stderr:write\(".*I AM toy v0.0"\)',
-                                      toy_module_txt))
-            self.assertTrue(re.search(r'io.stderr:write\("oh hai!"\)', toy_module_txt))
+            self.assertTrue(re.search(r'^setenv\("FOO", "bar"\)', toy_module_txt, re.M))
+            self.assertTrue(re.search(r'^prepend_path\("SOMEPATH", pathJoin\(root, "foo/bar"\)\)$', toy_module_txt, re.M))
+            self.assertTrue(re.search(r'^prepend_path\("SOMEPATH", pathJoin\(root, "baz"\)\)$', toy_module_txt, re.M))
+            self.assertTrue(re.search(r'^prepend_path\("SOMEPATH", root\)$', toy_module_txt, re.M))
+            self.assertTrue(re.search(r'^if mode\(\) == "load" then\n\s*io.stderr:write\(".*I AM toy v0.0"\)$',
+                                      toy_module_txt, re.M))
+            self.assertTrue(re.search(r'^io.stderr:write\("oh hai!"\)$', toy_module_txt, re.M))
         else:
             self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
 
@@ -758,6 +758,84 @@ def test_toy_archived_easyconfig(self):
         self.assertEqual(ec.name, 'toy')
         self.assertEqual(ec.version, '0.0')
 
+    def test_toy_module_fulltxt(self):
+        """Strict text comparison of generated module file."""
+        self.test_toy_tweaked()
+
+        toy_module = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0-tweaked')
+        if get_module_syntax() == 'Lua':
+            toy_module += '.lua'
+        toy_mod_txt = read_file(toy_module)
+
+        if get_module_syntax() == 'Lua':
+            mod_txt_regex_pattern = '\n'.join([
+                r'help = \[\[Toy C program. - Homepage: http://hpcugent.github.com/easybuild\]\]',
+                r'whatis\(\[\[Name: toy\]\]\)',
+                r'whatis\(\[\[Version: 0.0\]\]\)',
+                r'whatis\(\[\[Description: Toy C program. - Homepage: http://hpcugent.github.com/easybuild\]\]\)',
+                r'whatis\(\[\[Homepage: http://hpcugent.github.com/easybuild\]\]\)',
+                r'',
+                r'local root = "%s/software/toy/0.0-tweaked"' % self.test_installpath,
+                r'',
+                r'conflict\("toy"\)',
+                r'',
+                r'prepend_path\("LD_LIBRARY_PATH", pathJoin\(root, "lib"\)\)',
+                r'prepend_path\("LIBRARY_PATH", pathJoin\(root, "lib"\)\)',
+                r'prepend_path\("PATH", pathJoin\(root, "bin"\)\)',
+                r'setenv\("EBROOTTOY", root\)',
+                r'setenv\("EBVERSIONTOY", "0.0"\)',
+                r'setenv\("EBDEVELTOY", pathJoin\(root, "easybuild/toy-0.0-tweaked-easybuild-devel"\)\)',
+                r'',
+                r'setenv\("FOO", "bar"\)',
+                r'prepend_path\("SOMEPATH", pathJoin\(root, "foo/bar"\)\)',
+                r'prepend_path\("SOMEPATH", pathJoin\(root, "baz"\)\)',
+                r'prepend_path\("SOMEPATH", root\)',
+                r'',
+                r'if mode\(\) == "load" then',
+                r'    io.stderr:write\("THANKS FOR LOADING ME, I AM toy v0.0"\)',
+                r'end',
+                r'io.stderr:write\("oh hai\!"\)',
+                r'-- Built with EasyBuild version .*$',
+            ])
+        elif get_module_syntax() == 'Tcl':
+            mod_txt_regex_pattern = '\n'.join([
+                r'^#%Module',
+                r'proc ModulesHelp { } {',
+                r'    puts stderr { Toy C program. - Homepage: http://hpcugent.github.com/easybuild',
+                r'    }',
+                r'}',
+                r'',
+                r'module-whatis {Description: Toy C program. - Homepage: http://hpcugent.github.com/easybuild}',
+                r'',
+                r'set root %s/software/toy/0.0-tweaked' % self.test_installpath,
+                r'',
+                r'conflict toy',
+                r'',
+                r'prepend-path	LD_LIBRARY_PATH		\$root/lib',
+                r'prepend-path	LIBRARY_PATH		\$root/lib',
+                r'prepend-path	PATH		\$root/bin',
+                r'setenv	EBROOTTOY		"\$root"',
+                r'setenv	EBVERSIONTOY		"0.0"',
+                r'setenv	EBDEVELTOY		"\$root/easybuild/toy-0.0-tweaked-easybuild-devel"',
+                r'',
+                r'setenv	FOO		"bar"',
+                r'prepend-path	SOMEPATH		\$root/foo/bar',
+                r'prepend-path	SOMEPATH		\$root/baz',
+                r'prepend-path	SOMEPATH		\$root',
+                r'',
+                r'if { \[ module-info mode load \] } {',
+                r'    puts stderr "THANKS FOR LOADING ME, I AM toy v0.0"',
+                r'}',
+                r'puts stderr "oh hai\!"',
+                r'# Built with EasyBuild version .*$',
+            ])
+        else:
+            self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
+
+        mod_txt_regex = re.compile(mod_txt_regex_pattern)
+        msg = "Pattern '%s' matches with: %s" % (mod_txt_regex.pattern, toy_mod_txt)
+        self.assertTrue(mod_txt_regex.match(toy_mod_txt), msg)
+
 def suite():
     """ return all the tests in this file """
     return TestLoader().loadTestsFromTestCase(ToyBuildTest)

From 87734bfed3790e4d47848f17def5309cd2c374f4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Apr 2015 14:52:35 +0200
Subject: [PATCH 0847/1356] fix remarks

---
 easybuild/tools/modules.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 1cd2e4d7c7..287def9033 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -478,11 +478,12 @@ def run_module(self, *args, **kwargs):
 
         self.log.debug('Current MODULEPATH: %s' % os.environ.get('MODULEPATH', ''))
 
-        # change to original $LD_LIBRARY_PATH and $LD_PRELOAD before running module command
+        # restore selected original environment variables before running module command
         environ = os.environ.copy()
         for key in LD_ENV_VAR_KEYS:
             environ[key] = ORIG_OS_ENVIRON.get(key, '')
-            self.log.debug("Adjusted %s from '%s' to '%s'" % (key, os.environ.get(key, ''), environ[key]))
+            self.log.debug("Changing %s from '%s' to '%s' in environment for module command",
+                           key, os.environ.get(key, ''), environ[key])
 
         # prefix if a particular shell is specified, using shell argument to Popen doesn't work (no output produced (?))
         cmdlist = [self.cmd, 'python']
@@ -503,11 +504,11 @@ def run_module(self, *args, **kwargs):
         if kwargs.get('return_output', False):
             return stdout + stderr
         else:
-            # the module command was run with an outdated $LD_LIBRARY_PATH and $LD_PRELOAD,
+            # the module command was run with an outdated selected environment variables (see LD_ENV_VAR_KEYS list)
             # which will be adjusted on loading a module;
             # this needs to be taken into account when updating the environment via produced output, see below
 
-            # keep track of current $LD_LIBRARY_PATH/$LD_PRELOAD, so we can correct the adjusted values below
+            # keep track of current values of select env vars, so we can correct the adjusted values below
             prev_ld_values = dict([(key, os.environ.get(key, '').split(os.pathsep)[::-1]) for key in LD_ENV_VAR_KEYS])
 
             # Change the environment
@@ -520,11 +521,11 @@ def run_module(self, *args, **kwargs):
                 out = "stdout: %s, stderr: %s" % (stdout, stderr)
                 raise EasyBuildError("Changing environment as dictated by module failed: %s (%s)", err, out)
 
-            # correct $LD_LIBRARY_PATH and $LD_PRELOAD as yielded by the adjustments made
+            # correct values of selected environment variables as yielded by the adjustments made
             # make sure we get the order right (reverse lists with [::-1])
             for key in LD_ENV_VAR_KEYS:
                 curr_ld_val = os.environ.get(key, '').split(os.pathsep)
-                new_ld_val = [x for x in nub(prev_ld_values[key] + curr_ld_val[::-1]) if len(x)][::-1]
+                new_ld_val = [x for x in nub(prev_ld_values[key] + curr_ld_val[::-1]) if x][::-1]
 
                 self.log.debug("Correcting paths in $%s from %s to %s" % (key, curr_ld_val, new_ld_val))
                 self.set_path_env_var(key, new_ld_val)
@@ -708,7 +709,7 @@ class EnvironmentModulesTcl(EnvironmentModulesC):
     VERSION_REGEXP = r'^Modules\s+Release\s+Tcl\s+(?P<version>\d\S*)\s'
 
     def set_path_env_var(self, key, paths):
-        """Set $LD_X environment variable to the given list of paths."""
+        """Set environment variable with given name to the given list of paths."""
         super(EnvironmentModulesTcl, self).set_path_env_var(paths)
         # for Tcl environment modules, we need to make sure the _modshare env var is kept in sync
         os.environ['%s_modshare' % key] = ':1:'.join(paths)

From 33a8e65fcc9c9bed73e16d7db7bd5f4fb8217405 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Apr 2015 16:33:02 +0200
Subject: [PATCH 0848/1356] stop using log.error in multidiff.py

---
 easybuild/tools/multidiff.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/multidiff.py b/easybuild/tools/multidiff.py
index 8d92f3cbb8..e145d6bb39 100644
--- a/easybuild/tools/multidiff.py
+++ b/easybuild/tools/multidiff.py
@@ -34,6 +34,7 @@
 import os
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import read_file
 from easybuild.tools.utilities import det_terminal_size
 
@@ -92,7 +93,7 @@ def parse_line(self, line_no, diff_line, meta, squigly_line):
         # register (diff_line, meta, squigly_line) tuple for specified line number and determined key
         key = diff_line[0]
         if not key in [MINUS, PLUS]:
-            _log.error("diff line starts with unexpected character: %s" % diff_line)
+            raise EasyBuildError("diff line starts with unexpected character: %s", diff_line)
         line_key_tuples = self.diff_info.setdefault(line_no, {}).setdefault(key, [])
         line_key_tuples.append((diff_line, meta, squigly_line))
 

From fdc5a65936a062dc433722e3ef97a0f961c8904a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Apr 2015 17:27:38 +0200
Subject: [PATCH 0849/1356] fix set_path_env_var arguments in super call in
 EnvironmentModulesTcl

---
 easybuild/tools/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 287def9033..433559e8e3 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -710,7 +710,7 @@ class EnvironmentModulesTcl(EnvironmentModulesC):
 
     def set_path_env_var(self, key, paths):
         """Set environment variable with given name to the given list of paths."""
-        super(EnvironmentModulesTcl, self).set_path_env_var(paths)
+        super(EnvironmentModulesTcl, self).set_path_env_var(key, paths)
         # for Tcl environment modules, we need to make sure the _modshare env var is kept in sync
         os.environ['%s_modshare' % key] = ':1:'.join(paths)
 

From 270ac5e8a328f07ca66cb480d9bdf9eb7e2169eb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 5 Apr 2015 14:43:11 +0200
Subject: [PATCH 0850/1356] add --installpath-modules and
 --installpath-software configuration options

---
 easybuild/tools/config.py  | 13 +++++++++++--
 easybuild/tools/options.py |  2 ++
 test/framework/config.py   | 12 +++++++++++-
 3 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 207e75bba0..a1e1968a25 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -181,6 +181,8 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'buildpath',
         'config',
         'installpath',
+        'installpath_modules',
+        'installpath_software',
         'logfile_format',
         'moduleclasses',
         'module_naming_scheme',
@@ -323,8 +325,15 @@ def install_path(typ=None):
         typ = 'modules'
 
     variables = ConfigurationVariables()
-    suffix = variables['subdir_%s' % typ]
-    return os.path.join(variables['installpath'], suffix)
+
+    res = None
+    if variables.get('installpath_%s' % typ, None) is None:
+        suffix = variables['subdir_%s' % typ]
+        res = os.path.join(variables['installpath'], suffix)
+    else:
+        res = variables['installpath_%s' % typ]
+
+    return res
 
 
 def get_repository():
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ef61781dcb..54ed542a1d 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -236,6 +236,8 @@ def config_options(self):
                             'strlist', 'store', ['.git', '.svn']),
             'installpath': ("Install path for software and modules",
                             None, 'store', mk_full_default_path('installpath')),
+            'installpath-modules': ("Install path for modules", None, 'store', None),
+            'installpath-software': ("Install path for software", None, 'store', None),
             # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
diff --git a/test/framework/config.py b/test/framework/config.py
index e91337f25b..8257d2d922 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -159,11 +159,14 @@ def test_generaloption_config(self):
 
         os.environ['EASYBUILD_PREFIX'] = prefix
         os.environ['EASYBUILD_SUBDIR_SOFTWARE'] = subdir_software
+        installpath_modules = tempfile.mkdtemp(prefix='installpath-modules')
+        os.environ['EASYBUILD_INSTALLPATH_MODULES'] = installpath_modules
 
         options = init_config(args=args)
 
         self.assertEqual(build_path(), os.path.join(prefix, 'build'))
         self.assertEqual(install_path(), os.path.join(install, subdir_software))
+        self.assertEqual(install_path('mod'), installpath_modules)
 
         del os.environ['EASYBUILD_PREFIX']
         del os.environ['EASYBUILD_SUBDIR_SOFTWARE']
@@ -187,16 +190,19 @@ def test_generaloption_config_file(self):
         ])
         write_file(config_file, cfgtxt)
 
+        installpath_software = tempfile.mkdtemp(prefix='installpath-software')
         args = [
             '--configfiles', config_file,
             '--debug',
             '--buildpath', testpath1,
+            '--installpath-software', installpath_software,
         ]
         options = init_config(args=args)
 
         self.assertEqual(build_path(), testpath1)  # via command line
         self.assertEqual(source_paths(), [os.path.join(os.getenv('HOME'), '.local', 'easybuild', 'sources')])  # default
-        self.assertEqual(install_path(), os.path.join(testpath2, 'software'))  # via config file
+        self.assertEqual(install_path(), installpath_software)  # via cmdline arg
+        self.assertEqual(install_path('mod'), os.path.join(testpath2, 'modules'))  # via config file
 
         # copy test easyconfigs to easybuild/easyconfigs subdirectory of temp directory
         # to check whether easyconfigs install path is auto-included in robot path
@@ -210,12 +216,14 @@ def test_generaloption_config_file(self):
         sys.path.insert(0, tmpdir)  # prepend to give it preference over possible other installed easyconfigs pkgs
 
         # test with config file passed via environment variable
+        installpath_modules = tempfile.mkdtemp(prefix='installpath-modules')
         cfgtxt = '\n'.join([
             '[config]',
             'buildpath = %s' % testpath1,
             'sourcepath = %(DEFAULT_REPOSITORYPATH)s',
             'repositorypath = %(DEFAULT_REPOSITORYPATH)s,somesubdir',
             'robot-paths=/tmp/foo:%(sourcepath)s:%(DEFAULT_ROBOT_PATHS)s',
+            'installpath-modules=%s' % installpath_modules,
         ])
         write_file(config_file, cfgtxt)
 
@@ -228,6 +236,7 @@ def test_generaloption_config_file(self):
 
         topdir = os.path.join(os.getenv('HOME'), '.local', 'easybuild')
         self.assertEqual(install_path(), os.path.join(topdir, 'software'))  # default
+        self.assertEqual(install_path('mod'), installpath_modules),  # via config file
         self.assertEqual(source_paths(), [testpath2])  # via command line
         self.assertEqual(build_path(), testpath1)  # via config file
         self.assertEqual(get_repositorypath(), [os.path.join(topdir, 'ebfiles_repo'), 'somesubdir'])  # via config file
@@ -248,6 +257,7 @@ def test_generaloption_config_file(self):
 
         self.assertEqual(source_paths(), [testpath2])  # via environment variable $EASYBUILD_SOURCEPATHS
         self.assertEqual(install_path(), os.path.join(testpath3, 'software'))  # via command line
+        self.assertEqual(install_path('mod'), installpath_modules),  # via config file
         self.assertEqual(build_path(), testpath1)  # via config file
 
         del os.environ['EASYBUILD_CONFIGFILES']

From 916c2d054cba1119732abb7a5bab79e07e5030ec Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 5 Apr 2015 15:04:31 +0200
Subject: [PATCH 0851/1356] make sure subdir configuration options are being
 passed relative paths

---
 easybuild/tools/options.py | 30 +++++++++++++++++++++---------
 test/framework/config.py   | 10 +++++++++-
 2 files changed, 30 insertions(+), 10 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 54ed542a1d..fb9c4db892 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -366,23 +366,35 @@ def unittest_options(self):
 
     def validate(self):
         """Additional validation of options"""
-        error_cnt = 0
+        error_msgs = []
 
         for opt in ['software', 'try-software', 'toolchain', 'try-toolchain']:
             val = getattr(self.options, opt.replace('-', '_'))
             if val and len(val) != 2:
-                self.log.warning('--%s requires NAME,VERSION (given %s)' % (opt, ','.join(val)))
-                error_cnt += 1
+                msg = "--%s requires NAME,VERSION (given %s)" % (opt, ','.join(val))
+                self.log.warning(msg)
+                error_msgs.append(msg)
 
         if self.options.umask:
             umask_regex = re.compile('^[0-7]{3}$')
             if not umask_regex.match(self.options.umask):
-                self.log.warning("--umask value should be 3 digits (0-7) (regex pattern '%s')" % umask_regex.pattern)
-                error_cnt += 1
-
-        if error_cnt > 0:
-            raise EasyBuildError("Found %s problems validating the options, treating warnings above as fatal.",
-                                 error_cnt)
+                msg = "--umask value should be 3 digits (0-7) (regex pattern '%s')" % umask_regex.pattern
+                self.log.warning(msg)
+                error_msgs.append(msg)
+
+        # subdir options must be relative
+        for typ in ['modules', 'software']:
+            subdir_opt = 'subdir_%s' % typ
+            val = getattr(self.options, subdir_opt)
+            if os.path.isabs(getattr(self.options, subdir_opt)):
+                msg = "Configuration option '%s' must specify a *relative* path (use 'installpath-%s' instead?): '%s'"
+                msg = msg % (subdir_opt, typ, val)
+                self.log.warning(msg)
+                error_msgs.append(msg)
+
+        if error_msgs:
+            raise EasyBuildError("Found problems validating the options, treating warnings in log file as fatal: %s",
+                                 '\n'.join(error_msgs))
 
     def postprocess(self):
         """Do some postprocessing, in particular print stuff"""
diff --git a/test/framework/config.py b/test/framework/config.py
index 8257d2d922..00f7c37c79 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -38,6 +38,7 @@
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 
 import easybuild.tools.options as eboptions
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_path, source_paths, install_path, get_repositorypath
 from easybuild.tools.config import set_tmpdir, BuildOptions, ConfigurationVariables
 from easybuild.tools.config import get_build_log_path, DEFAULT_PATH_SUBDIRS, init_build_options, build_option
@@ -137,12 +138,13 @@ def test_generaloption_config(self):
             '--prefix', prefix,
             '--installpath', install,
             '--repositorypath', repopath,
+            '--subdir-software', 'APPS',
         ]
 
         options = init_config(args=args)
 
         self.assertEqual(build_path(), os.path.join(prefix, 'build'))
-        self.assertEqual(install_path(), os.path.join(install, 'software'))
+        self.assertEqual(install_path(), os.path.join(install, 'APPS'))
         self.assertEqual(install_path(typ='mod'), os.path.join(install, 'modules'))
 
         self.assertEqual(options.installpath, install)
@@ -168,6 +170,12 @@ def test_generaloption_config(self):
         self.assertEqual(install_path(), os.path.join(install, subdir_software))
         self.assertEqual(install_path('mod'), installpath_modules)
 
+        # subdir options *must* be relative (to --installpath)
+        installpath_software = tempfile.mkdtemp(prefix='installpath-software')
+        os.environ['EASYBUILD_SUBDIR_SOFTWARE'] = installpath_software
+        error_regex = r"Found problems validating the options.*'subdir_software' must specify a \*relative\* path"
+        self.assertErrorRegex(EasyBuildError, error_regex, init_config)
+
         del os.environ['EASYBUILD_PREFIX']
         del os.environ['EASYBUILD_SUBDIR_SOFTWARE']
 

From 3b26b1e2869f85d99df933fa7537f7e64a8e6a52 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 5 Apr 2015 23:08:30 +0200
Subject: [PATCH 0852/1356] fleshed out code to determine location info in
 EasyBuildError to LoggedException in vsc-base

---
 easybuild/tools/build_log.py | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index f6a30e850e..b336495252 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -58,25 +58,17 @@ class EasyBuildError(LoggedException):
     """
     EasyBuildError is thrown when EasyBuild runs into something horribly wrong.
     """
+    LOC_INFO_TOP_PKG_NAMES = ['easybuild', 'vsc']
+    LOC_INFO_LEVEL = 1
+
     # use custom error logging method, to make sure EasyBuildError isn't being raised again to avoid infinite recursion
     # only required because 'error' log method raises (should no longer be needed in EB v3.x)
     LOGGING_METHOD_NAME = '_error_no_raise'
 
     def __init__(self, msg, *args):
         """Constructor: initialise EasyBuildError instance."""
-        # figure out where error was raised from
-        # current frame: this constructor, one frame above: location where this EasyBuildError was created/raised
-        frameinfo = inspect.getouterframes(inspect.currentframe())[1]
-
-        # determine short location of Python module where error was raised from (starting with 'easybuild/' or 'vsc/')
-        path_parts = frameinfo[1].split(os.path.sep)
-        relpath = path_parts.pop()
-        while not (relpath.startswith('easybuild/') or relpath.startswith('vsc/')) and path_parts:
-            relpath = os.path.join(path_parts.pop() or os.path.sep, relpath)
-
-        # include location info at the end of the message
-        # for example: "Nope, giving up (at easybuild/tools/somemodule.py:123 in some_function)"
-        msg = "%s (at %s:%s in %s)" % (msg % args, relpath, frameinfo[2], frameinfo[3])
+        if args:
+            msg = msg % args
         LoggedException.__init__(self, msg)
         self.msg = msg
 

From b39c586cd26f569a70658fb7b128e402f42870ae Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 5 Apr 2015 23:11:09 +0200
Subject: [PATCH 0853/1356] remove unused import

---
 easybuild/tools/build_log.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index b336495252..b663dbe30e 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -31,7 +31,6 @@
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
 """
-import inspect
 import os
 import sys
 import tempfile

From f5e742300cb92928f74706139d3644070bd0a9ab Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 5 Apr 2015 23:14:23 +0200
Subject: [PATCH 0854/1356] bump required vsc-base version

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 4fecf38036..6335ba4f77 100644
--- a/setup.py
+++ b/setup.py
@@ -106,5 +106,5 @@ def find_rel_test():
     provides=["eb"] + easybuild_packages,
     test_suite="test.framework.suite",
     zip_safe=False,
-    install_requires=["vsc-base >= 2.1.1"],
+    install_requires=["vsc-base >= 2.2.0"],
 )

From 904e063fe7ac257829ce5b78670d4c9d95c4a038 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Apr 2015 11:25:50 +0200
Subject: [PATCH 0855/1356] fix remarks, add dedicated unit test for
 install_path function

---
 easybuild/tools/config.py  | 17 ++++++++++++-----
 easybuild/tools/options.py | 12 +++++-------
 test/framework/config.py   | 34 ++++++++++++++++++++++++++++++++++
 3 files changed, 51 insertions(+), 12 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index a1e1968a25..92033c2cd5 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -324,14 +324,21 @@ def install_path(typ=None):
     elif typ == 'mod':
         typ = 'modules'
 
+    known_types = ['modules', 'software']
+    if typ not in known_types:
+        raise EasyBuildError("Unknown type specified in install_path(): %s (known: %s)", typ, ', '.join(known_types))
+
     variables = ConfigurationVariables()
 
-    res = None
-    if variables.get('installpath_%s' % typ, None) is None:
-        suffix = variables['subdir_%s' % typ]
-        res = os.path.join(variables['installpath'], suffix)
+    key = 'installpath_%s' % typ
+    res = variables[key]
+    if res is None:
+        key = 'subdir_%s' % typ
+        subdir = variables[key]
+        res = os.path.join(variables['installpath'], subdir)
+        _log.debug("%s install path as specified by 'installpath' and '%s': %s", typ, key, res)
     else:
-        res = variables['installpath_%s' % typ]
+        _log.debug("%s install path as specified by '%s': %s", typ, key, res)
 
     return res
 
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index fb9c4db892..736fd0d856 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -236,8 +236,10 @@ def config_options(self):
                             'strlist', 'store', ['.git', '.svn']),
             'installpath': ("Install path for software and modules",
                             None, 'store', mk_full_default_path('installpath')),
-            'installpath-modules': ("Install path for modules", None, 'store', None),
-            'installpath-software': ("Install path for software", None, 'store', None),
+            'installpath-modules': ("Install path for modules (if None, combine --installpath and --subdir-modules)",
+                                    None, 'store', None),
+            'installpath-software': ("Install path for software (if None, combine --installpath and --subdir-software)",
+                                     None, 'store', None),
             # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
@@ -372,14 +374,12 @@ def validate(self):
             val = getattr(self.options, opt.replace('-', '_'))
             if val and len(val) != 2:
                 msg = "--%s requires NAME,VERSION (given %s)" % (opt, ','.join(val))
-                self.log.warning(msg)
                 error_msgs.append(msg)
 
         if self.options.umask:
             umask_regex = re.compile('^[0-7]{3}$')
             if not umask_regex.match(self.options.umask):
                 msg = "--umask value should be 3 digits (0-7) (regex pattern '%s')" % umask_regex.pattern
-                self.log.warning(msg)
                 error_msgs.append(msg)
 
         # subdir options must be relative
@@ -389,12 +389,10 @@ def validate(self):
             if os.path.isabs(getattr(self.options, subdir_opt)):
                 msg = "Configuration option '%s' must specify a *relative* path (use 'installpath-%s' instead?): '%s'"
                 msg = msg % (subdir_opt, typ, val)
-                self.log.warning(msg)
                 error_msgs.append(msg)
 
         if error_msgs:
-            raise EasyBuildError("Found problems validating the options, treating warnings in log file as fatal: %s",
-                                 '\n'.join(error_msgs))
+            raise EasyBuildError("Found problems validating the options: %s", '\n'.join(error_msgs))
 
     def postprocess(self):
         """Do some postprocessing, in particular print stuff"""
diff --git a/test/framework/config.py b/test/framework/config.py
index 00f7c37c79..dea4014bdf 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -179,6 +179,40 @@ def test_generaloption_config(self):
         del os.environ['EASYBUILD_PREFIX']
         del os.environ['EASYBUILD_SUBDIR_SOFTWARE']
 
+    def test_install_path(self):
+        """Test install_path function."""
+        # defaults
+        self.assertEqual(install_path(), os.path.join(self.test_installpath, 'software'))
+        self.assertEqual(install_path('software'), os.path.join(self.test_installpath, 'software'))
+        self.assertEqual(install_path(typ='mod'), os.path.join(self.test_installpath, 'modules'))
+        self.assertEqual(install_path('modules'), os.path.join(self.test_installpath, 'modules'))
+
+        self.assertErrorRegex(EasyBuildError, "Unknown type specified", install_path, typ='foo')
+
+        args = [
+            '--subdir-software', 'SOFT',
+            '--installpath', '/foo',
+        ]
+        os.environ['EASYBUILD_SUBDIR_MODULES'] = 'MOD'
+        init_config(args=args)
+        self.assertEqual(install_path(), os.path.join('/foo', 'SOFT'))
+        self.assertEqual(install_path(typ='mod'), os.path.join('/foo', 'MOD'))
+        del os.environ['EASYBUILD_SUBDIR_MODULES']
+
+        args = [
+            '--installpath', '/prefix',
+            '--installpath-modules', '/foo',
+        ]
+        os.environ['EASYBUILD_INSTALLPATH_SOFTWARE'] = '/bar/baz'
+        init_config(args=args)
+        self.assertEqual(install_path(), os.path.join('/bar', 'baz'))
+        self.assertEqual(install_path(typ='mod'), '/foo')
+
+        del os.environ['EASYBUILD_INSTALLPATH_SOFTWARE']
+        init_config(args=args)
+        self.assertEqual(install_path(), os.path.join('/prefix', 'software'))
+        self.assertEqual(install_path(typ='mod'), '/foo')
+
     def test_generaloption_config_file(self):
         """Test use of new-style configuration file."""
         self.purge_environment()

From 41218816702de3d3b01e0d179769285c6262f0db Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Apr 2015 11:27:12 +0200
Subject: [PATCH 0856/1356] minor cleanup in install_path

---
 easybuild/tools/config.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 92033c2cd5..7b398be0aa 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -334,8 +334,7 @@ def install_path(typ=None):
     res = variables[key]
     if res is None:
         key = 'subdir_%s' % typ
-        subdir = variables[key]
-        res = os.path.join(variables['installpath'], subdir)
+        res = os.path.join(variables['installpath'], variables[key])
         _log.debug("%s install path as specified by 'installpath' and '%s': %s", typ, key, res)
     else:
         _log.debug("%s install path as specified by '%s': %s", typ, key, res)

From 3cdc6508912858855448ca9ebc846b9cc15eaf19 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Apr 2015 17:13:10 +0200
Subject: [PATCH 0857/1356] avoid reusing same values in --robot-paths test

---
 test/framework/config.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index 30a2eb5da8..5ae5dea935 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -476,9 +476,9 @@ def test_flex_robot_paths(self):
         self.assertEqual(eb_go.options.robot_paths, ['/foo', tmp_ecs_dir, '/bar/baz'])
 
         # combining $EASYBUILD_ROBOT_PATHS and --robot-paths: all paths are retained in the order to be expected
-        os.environ['EASYBUILD_ROBOT_PATHS'] = '/foo::/bar/baz'
+        os.environ['EASYBUILD_ROBOT_PATHS'] = '/foobar::/barbar/baz/baz'
         eb_go = eboptions.parse_options(args=['--robot-paths=/one::/last'])
-        self.assertEqual(eb_go.options.robot_paths, ['/one', '/foo', tmp_ecs_dir, '/bar/baz', '/last'])
+        self.assertEqual(eb_go.options.robot_paths, ['/one', '/foobar', tmp_ecs_dir, '/barbar/baz/baz', '/last'])
 
         del os.environ['EASYBUILD_ROBOT_PATHS']
 

From 8d0498c08db6c7f245880735183d39d0599440ab Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Apr 2015 20:56:55 +0200
Subject: [PATCH 0858/1356] add --show-default-configfiles + dedicated unit
 test for it

---
 easybuild/tools/options.py |  38 +++++++++++--
 test/framework/options.py  | 114 +++++++++++++++++++++++++++++++++++++
 2 files changed, 146 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 6ade5060fa..b8889415bb 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -258,8 +258,6 @@ def config_options(self):
                                 "(is passed as list of arguments to create the repository instance). "
                                 "For more info, use --avail-repositories."),
                                'strlist', 'store', self.default_repositorypath),
-            'show-default-moduleclasses': ("Show default module classes with description",
-                                           None, 'store_true', False),
             'sourcepath': ("Path(s) to where sources should be downloaded (string, colon-separated)",
                            None, 'store', mk_full_default_path('sourcepath')),
             'subdir-modules': ("Installpath subdir for modules", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_modules']),
@@ -304,6 +302,9 @@ def informative_options(self):
                        None, 'store', None, {'metavar': 'STR'}),
             'search-short': ("Search for easyconfig files in the robot directory, print short paths",
                              None, 'store', None, 'S', {'metavar': 'STR'}),
+            'show-default-configfiles': ("Show list of default config files", None, 'store_true', False),
+            'show-default-moduleclasses': ("Show default module classes with description",
+                                           None, 'store_true', False),
         })
 
         self.log.debug("informative_options: descr %s opts %s" % (descr, opts))
@@ -402,6 +403,7 @@ def postprocess(self):
                 self.options.avail_easyconfig_constants, self.options.avail_easyconfig_licenses,
                 self.options.avail_repositories, self.options.show_default_moduleclasses,
                 self.options.avail_modules_tools, self.options.avail_module_naming_schemes,
+                self.options.show_default_configfiles,
                 ]):
             build_easyconfig_constants_dict()  # runs the easyconfig constants sanity check
             self._postprocess_list_avail()
@@ -494,6 +496,10 @@ def _postprocess_list_avail(self):
         if self.options.avail_module_naming_schemes:
             msg += self.avail_list('module naming schemes', avail_module_naming_schemes())
 
+        # dump default list of config files that are considered
+        if self.options.show_default_configfiles:
+            msg += self.show_default_configfiles()
+
         # dump default moduleclasses with description
         if self.options.show_default_moduleclasses:
             msg += self.show_default_moduleclasses()
@@ -629,14 +635,34 @@ def avail_list(self, name, items):
         """Show list of available values passed by argument."""
         return "List of supported %s:\n\t%s" % (name, '\n\t'.join(items))
 
+    def show_default_configfiles(self):
+        """Show list of default config files."""
+        xdg_config_home = os.environ.get('XDG_CONFIG_HOME', '(not set)')
+        xdg_config_dirs = os.environ.get('XDG_CONFIG_DIRS', '(not set)')
+        system_cfg_glob_paths = os.path.join('{' + ', '.join(XDG_CONFIG_DIRS) + '}', 'easybuild.d', '*.cfg')
+        found_cfgfile_cnt = len(self.DEFAULT_CONFIGFILES)
+        found_cfgfile_list = ', '.join(self.DEFAULT_CONFIGFILES) or '(none)'
+        lines = [
+            "Default list of configuration files:",
+            '',
+            "[with $XDG_CONFIG_HOME: %s, $XDG_CONFIG_DIRS: %s]" % (xdg_config_home, xdg_config_dirs),
+            '',
+            "* user-level: %s" % os.path.join('${XDG_CONFIG_HOME:-$HOME/.config}', 'easybuild', 'config.cfg'),
+            "  -> %s => %s" % (DEFAULT_USER_CFGFILE, ('not found', 'found')[os.path.exists(DEFAULT_USER_CFGFILE)]),
+            "* system-level: %s" % os.path.join('${XDG_CONFIG_DIRS:-/etc}', 'easybuild.d', '*.cfg'),
+            "  -> %s => %s" % (system_cfg_glob_paths, ', '.join(DEFAULT_SYS_CFGFILES) or "(no matches)"),
+            '',
+            "Default list of existing configuration files (%d): %s" % (found_cfgfile_cnt, found_cfgfile_list),
+        ]
+        return '\n'.join(lines)
+
     def show_default_moduleclasses(self):
         """Show list of default moduleclasses and description."""
-        txt = ["Default available moduleclasses"]
-        indent = " " * 2
+        lines = ["Default available module classes:", '']
         maxlen = max([len(x[0]) for x in DEFAULT_MODULECLASSES]) + 1  # at least 1 space
         for name, descr in DEFAULT_MODULECLASSES:
-            txt.append("%s%s:%s%s" % (indent, name, (" " * (maxlen - len(name))), descr))
-        return "\n".join(txt)
+            lines.append("\t%s:%s%s" % (name, (" " * (maxlen - len(name))), descr))
+        return '\n'.join(lines)
 
 
 def parse_options(args=None):
diff --git a/test/framework/options.py b/test/framework/options.py
index 6e47250ad1..2caa7ed962 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -39,9 +39,11 @@
 from urllib2 import URLError
 
 import easybuild.tools.build_log
+import easybuild.tools.options
 from easybuild.framework.easyconfig import BUILD, CUSTOM, DEPENDENCIES, EXTENSIONS, FILEMANAGEMENT, LICENSE
 from easybuild.framework.easyconfig import MANDATORY, MODULES, OTHER, TOOLCHAIN
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import DEFAULT_MODULECLASSES
 from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.github import fetch_github_token
@@ -1490,6 +1492,118 @@ def test_missing_cfgfile(self):
         error_regex = "parseconfigfiles: configfile .* not found"
         self.assertErrorRegex(EasyBuildError, error_regex, self.eb_main, args, raise_error=True)
 
+    def test_show_default_moduleclasses(self):
+        """Test --show-default-moduleclasses."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        args = [
+            '--unittest-file=%s' % self.logfile,
+            '--show-default-moduleclasses',
+        ]
+        write_file(self.logfile, '')
+        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
+
+        lst = ["\t%s:[ ]*%s" % (c, d.replace('(', '\\(').replace(')', '\\)')) for (c, d) in DEFAULT_MODULECLASSES]
+        regex = re.compile("Default available module classes:\n\n" + '\n'.join(lst), re.M)
+
+        self.assertTrue(regex.search(outtxt), "Pattern '%s' found in %s" % (regex.pattern, outtxt))
+
+    def test_show_default_configfiles(self):
+        """Test --show-default-configfiles."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        home = os.environ['HOME']
+        for envvar in ['XDG_CONFIG_DIRS', 'XDG_CONFIG_HOME']:
+            if envvar in os.environ:
+                del os.environ[envvar]
+
+        args = [
+            '--unittest-file=%s' % self.logfile,
+            '--show-default-configfiles',
+        ]
+
+        cfgtxt = '\n'.join([
+            '[config]',
+            'prefix = %s' % self.test_prefix,
+        ])
+
+        expected_tmpl = '\n'.join([
+            "Default list of configuration files:",
+            '',
+            "[with $XDG_CONFIG_HOME: %s, $XDG_CONFIG_DIRS: %s]",
+            '',
+            "* user-level: ${XDG_CONFIG_HOME:-$HOME/.config}/easybuild/config.cfg",
+            "  -> %s",
+            "* system-level: ${XDG_CONFIG_DIRS:-/etc}/easybuild.d/*.cfg",
+            "  -> %s/easybuild.d/*.cfg => ",
+        ])
+
+        write_file(self.logfile, '')
+        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
+
+        homecfgfile = os.path.join(os.environ['HOME'], '.config', 'easybuild', 'config.cfg')
+        homecfgfile_str = homecfgfile
+        if os.path.exists(homecfgfile):
+            homecfgfile_str += " => found"
+        else:
+            homecfgfile_str += " => not found"
+        expected = expected_tmpl % ('(not set)', '(not set)', homecfgfile_str, '{/etc}')
+        self.assertTrue(expected in outtxt)
+
+        # to predict the full output, we need to take control over $HOME and $XDG_CONFIG_DIRS
+        os.environ['HOME'] = self.test_prefix
+        xdg_config_dirs = os.path.join(self.test_prefix, 'etc')
+        os.environ['XDG_CONFIG_DIRS'] = xdg_config_dirs
+
+        expected_tmpl += '\n'.join([
+            "%s",
+            '',
+            "Default list of existing configuration files (%d): %s",
+        ])
+
+        # put dummy cfgfile in place in $HOME (to predict last line of output which only lists *existing* files)
+        mkdir(os.path.join(self.test_prefix, '.config', 'easybuild'), parents=True)
+        homecfgfile = os.path.join(self.test_prefix, '.config', 'easybuild', 'config.cfg')
+        write_file(homecfgfile, cfgtxt)
+
+        reload(easybuild.tools.options)
+        write_file(self.logfile, '')
+        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
+        expected = expected_tmpl % ('(not set)', xdg_config_dirs, "%s => found" % homecfgfile, '{%s}' % xdg_config_dirs,
+                                    '(no matches)', 1, homecfgfile)
+        self.assertTrue(expected in outtxt)
+
+        xdg_config_home = os.path.join(self.test_prefix, 'home')
+        os.environ['XDG_CONFIG_HOME'] = xdg_config_home
+        xdg_config_dirs = [os.path.join(self.test_prefix, 'etc'), os.path.join(self.test_prefix, 'moaretc')]
+        os.environ['XDG_CONFIG_DIRS'] = os.pathsep.join(xdg_config_dirs)
+
+        # put various dummy cfgfiles in place
+        cfgfiles = [
+            os.path.join(self.test_prefix, 'etc', 'easybuild.d', 'config.cfg'),
+            os.path.join(self.test_prefix, 'moaretc', 'easybuild.d', 'bar.cfg'),
+            os.path.join(self.test_prefix, 'moaretc', 'easybuild.d', 'foo.cfg'),
+            os.path.join(xdg_config_home, 'easybuild', 'config.cfg'),
+        ]
+        for cfgfile in cfgfiles:
+            mkdir(os.path.dirname(cfgfile), parents=True)
+            write_file(cfgfile, cfgtxt)
+        reload(easybuild.tools.options)
+
+        write_file(self.logfile, '')
+        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
+        expected = expected_tmpl % (xdg_config_home, os.pathsep.join(xdg_config_dirs),
+                                    "%s => found" % os.path.join(xdg_config_home, 'easybuild', 'config.cfg'),
+                                    '{' + ', '.join(xdg_config_dirs) + '}',
+                                    ', '.join(cfgfiles[:-1]), 4, ', '.join(cfgfiles))
+        self.assertTrue(expected in outtxt)
+
+        del os.environ['XDG_CONFIG_DIRS']
+        del os.environ['XDG_CONFIG_HOME']
+        os.environ['HOME'] = home
+        reload(easybuild.tools.options)
 
 def suite():
     """ returns all the testcases in this module """

From 6ce5b9008ca0c10beaf5b0bb764c8fef08e05443 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 8 Apr 2015 08:30:00 +0200
Subject: [PATCH 0859/1356] make test_XDG_CONFIG_env_vars unit test robust
 against existing user config file in default location

---
 test/framework/config.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index 8dab1f9218..56659ed619 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -453,7 +453,8 @@ def test_XDG_CONFIG_env_vars(self):
         ]
         reload(eboptions)
         eb_go = eboptions.parse_options(args=[])
-        self.assertEqual(eb_go.options.configfiles, cfg_files)
+        # note: there may be a config file in $HOME too, so don't use a strict comparison
+        self.assertEqual(cfg_files, eb_go.options.configfiles[:3])
 
         # $XDG_CONFIG_HOME set to non-existing directory, multiple directories listed in $XDG_CONFIG_DIRS
         os.environ['XDG_CONFIG_HOME'] = os.path.join(self.test_prefix, 'nosuchdir')

From 12a47d7eea482f072a14e4af6ae8b1c672d39f62 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 8 Apr 2015 11:23:19 +0200
Subject: [PATCH 0860/1356] use dedicated tmpdir subdir for each test

---
 test/framework/utilities.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 4ddbc3bf34..5b9a221610 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -46,7 +46,7 @@
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.main import main
 from easybuild.tools import config
-from easybuild.tools.config import module_classes
+from easybuild.tools.config import module_classes, set_tmpdir
 from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import mkdir, read_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
@@ -81,12 +81,15 @@ class EnhancedTestCase(_EnhancedTestCase):
 
     def setUp(self):
         """Set up testcase."""
+        self.orig_tmpdir = tempfile.gettempdir()
+        # use a subdirectory for this test (which we can clean up easily after the test completes)
+        self.test_prefix = set_tmpdir()
+
         super(EnhancedTestCase, self).setUp()
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
         fd, self.logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')
         os.close(fd)
         self.cwd = os.getcwd()
-        self.test_prefix = tempfile.mkdtemp()
 
         # keep track of original environment to restore
         self.orig_environ = copy.deepcopy(os.environ)
@@ -158,6 +161,13 @@ def tearDown(self):
             except OSError, err:
                 pass
 
+        # restore original 'parent' tmpdir
+        for var in ['TMPDIR', 'TEMP', 'TMP']:
+            os.environ[var] = self.orig_tmpdir
+
+        # reset to make sure tempfile picks up new temporary directory to use
+        tempfile.tempdir = None
+
         for path in ['buildpath', 'installpath', 'sourcepath']:
             if self.orig_paths[path] is not None:
                 os.environ['EASYBUILD_%s' % path.upper()] = self.orig_paths[path]

From 3d2c4ea8b0f4b5aebaae93f85098f17446f290f1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 8 Apr 2015 12:15:07 +0200
Subject: [PATCH 0861/1356] deal with broken tearDowns, fix broken filetools
 tests after fiddling with self.test_prefix

---
 test/framework/easyblock.py        | 10 ----------
 test/framework/filetools.py        |  6 ++++--
 test/framework/module_generator.py |  6 ------
 3 files changed, 4 insertions(+), 18 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index b9c8181d01..98fb54d10f 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -62,7 +62,6 @@ def setUp(self):
         fd, self.eb_file = tempfile.mkstemp(prefix='easyblock_test_file_', suffix='.eb')
         os.close(fd)
 
-        self.orig_tmp_logdir = os.environ.get('EASYBUILD_TMP_LOGDIR', None)
         self.test_tmp_logdir = tempfile.mkdtemp()
         os.environ['EASYBUILD_TMP_LOGDIR'] = self.test_tmp_logdir
 
@@ -636,15 +635,6 @@ def test_patch_step(self):
         eb.extract_step()
         eb.patch_step()
 
-    def tearDown(self):
-        """ make sure to remove the temporary file """
-        super(EasyBlockTest, self).tearDown()
-
-        os.remove(self.eb_file)
-        if self.orig_tmp_logdir is not None:
-            os.environ['EASYBUILD_TMP_LOGDIR'] = self.orig_tmp_logdir
-            shutil.rmtree(self.test_tmp_logdir, True)
-
 
 def suite():
     """ return all the tests in this file """
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 3c35863192..a6545454f6 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -340,8 +340,10 @@ def test_move_logs(self):
         ft.write_file(fp + '.1', 'evenmoarbar')
         ft.move_logs(fp, os.path.join(self.test_prefix, 'bar.log'))
 
-        logs = ['bar.log', 'bar.log.1', 'bar.log_0', 'bar.log_1', 'foo.log', 'foo.log.1']
-        self.assertEqual(sorted(os.listdir(self.test_prefix)), logs)
+        logs = ['bar.log', 'bar.log.1', 'bar.log_0', 'bar.log_1',
+                os.path.basename(self.logfile),
+                'foo.log', 'foo.log.1']
+        self.assertEqual(sorted([f for f in os.listdir(self.test_prefix) if not f.startswith('tmp')]), logs)
         self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log_0')), 'bar')
         self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log_1')), 'barbar')
         self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log')), 'moarbar')
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 99c031b928..f898bf913f 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -69,12 +69,6 @@ def setUp(self):
         
         self.orig_module_naming_scheme = config.get_module_naming_scheme()
 
-    def tearDown(self):
-        """Test cleanup."""
-        super(ModuleGeneratorTest, self).tearDown()
-        os.remove(self.eb.logfile)
-        shutil.rmtree(self.modgen.app.installdir)
-
     def test_descr(self):
         """Test generation of module description (which includes '#%Module' header)."""
 

From 2dbd09dd949dbf788baced41f815bbb30d461168 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 8 Apr 2015 13:19:23 +0200
Subject: [PATCH 0862/1356] read correct log file in eb_main

---
 test/framework/utilities.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 5b9a221610..b63499f472 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -216,9 +216,9 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
             raise myerr
 
         if return_error:
-            return read_file(self.logfile), myerr
+            return read_file(logfile), myerr
         else:
-            return read_file(self.logfile)
+            return read_file(logfile)
 
     def setup_hierarchical_modules(self):
         """Setup hierarchical modules to run tests on."""

From b182fbbbb1940c63e29ce7c37ba6121a8912f77e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 8 Apr 2015 22:27:40 +0200
Subject: [PATCH 0863/1356] don't hardcode root logge name

---
 test/framework/build_log.py | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/test/framework/build_log.py b/test/framework/build_log.py
index cd97e53b32..a12f3db688 100644
--- a/test/framework/build_log.py
+++ b/test/framework/build_log.py
@@ -99,12 +99,14 @@ def test_easybuildlog(self):
         logToFile(tmplog, enable=False)
         logtxt = read_file(tmplog)
 
+        root = getRootLoggerName()
+
         expected_logtxt = '\n'.join([
-            r"runpy.test_easybuildlog \[DEBUG\] :: 123 debug",
-            r"runpy.test_easybuildlog \[INFO\] :: foobar info",
-            r"runpy.test_easybuildlog \[WARNING\] :: justawarning",
-            r"runpy.test_easybuildlog \[ERROR\] :: EasyBuild crashed with an error \(at .* in .*\): kaput",
-            r"runpy.test_easybuildlog \[ERROR\] :: .*EasyBuild encountered an exception \(at .* in .*\): oops",
+            r"%s.test_easybuildlog \[DEBUG\] :: 123 debug" % root,
+            r"%s.test_easybuildlog \[INFO\] :: foobar info" % root,
+            r"%s.test_easybuildlog \[WARNING\] :: justawarning" % root,
+            r"%s.test_easybuildlog \[ERROR\] :: EasyBuild crashed with an error \(at .* in .*\): kaput" % root,
+            r"%s.test_easybuildlog \[ERROR\] :: .*EasyBuild encountered an exception \(at .* in .*\): oops" % root,
             '',
         ])
         logtxt_regex = re.compile(r'^%s' % expected_logtxt, re.M)
@@ -125,10 +127,10 @@ def test_easybuildlog(self):
         logToFile(tmplog, enable=False)
         logtxt = read_file(tmplog)
         expected_logtxt = '\n'.join([
-            r"runpy.test_easybuildlog \[WARNING\] :: bleh",
-            r"runpy.test_easybuildlog \[INFO\] :: 4\+2 = 42",
-            r"runpy.test_easybuildlog \[DEBUG\] :: this is just a test",
-            r"runpy.test_easybuildlog \[ERROR\] :: EasyBuild crashed with an error \(at .* in .*\): foo baz baz",
+            r"%s.test_easybuildlog \[WARNING\] :: bleh" % root,
+            r"%s.test_easybuildlog \[INFO\] :: 4\+2 = 42" % root,
+            r"%s.test_easybuildlog \[DEBUG\] :: this is just a test" % root,
+            r"%s.test_easybuildlog \[ERROR\] :: EasyBuild crashed with an error \(at .* in .*\): foo baz baz" % root,
             '',
         ])
         logtxt_regex = re.compile(r'^%s' % expected_logtxt, re.M)

From 14577b0acd7d50ab6017cff772f36d8782ce3d17 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 8 Apr 2015 22:27:58 +0200
Subject: [PATCH 0864/1356] read correct logfile in options unit tests

---
 test/framework/options.py | 77 +++++++++++++++++++++++----------------
 1 file changed, 46 insertions(+), 31 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index fd953416c3..e1a14ec963 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -372,6 +372,7 @@ def run_test(custom=None, extra_params=[], fmt=None):
                     args.extend(['-e', custom])
 
                 outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
+                logtxt = read_file(self.logfile)
 
                 # check whether all parameter types are listed
                 par_types = [BUILD, DEPENDENCIES, EXTENSIONS, FILEMANAGEMENT,
@@ -382,18 +383,18 @@ def run_test(custom=None, extra_params=[], fmt=None):
                 for param_type in [x[1] for x in par_types]:
                     # regex for parameter group title, matches both txt and rst formats
                     regex = re.compile("%s.*\n%s" % (param_type, '-' * len(param_type)), re.I)
-                    tup = (param_type, avail_arg, args, outtxt)
+                    tup = (param_type, avail_arg, args, logtxt)
                     msg = "Parameter type %s is featured in output of eb %s (args: %s): %s" % tup
-                    self.assertTrue(regex.search(outtxt), msg)
+                    self.assertTrue(regex.search(logtxt), msg)
 
                 # check a couple of easyconfig parameters
                 for param in ["name", "version", "toolchain", "versionsuffix", "buildopts", "sources", "start_dir",
                               "dependencies", "group", "exts_list", "moduleclass", "buildstats"] + extra_params:
                     # regex for parameter name (with optional '*') & description, matches both txt and rst formats
                     regex = re.compile("^[`]*%s(?:\*)?[`]*\s+\w+" % param, re.M)
-                    tup = (param, avail_arg, args, regex.pattern, outtxt)
+                    tup = (param, avail_arg, args, regex.pattern, logtxt)
                     msg = "Parameter %s is listed with help in output of eb %s (args: %s, regex: %s): %s" % tup
-                    self.assertTrue(regex.search(outtxt), msg)
+                    self.assertTrue(regex.search(logtxt), msg)
 
                 modify_env(os.environ, self.orig_environ)
                 tempfile.tempdir = None
@@ -422,7 +423,8 @@ def test__list_toolchains(self):
         outtxt = self.eb_main(args, logfile=dummylogfn)
 
         info_msg = r"INFO List of known toolchains \(toolchainname: module\[,module\.\.\.\]\):"
-        self.assertTrue(re.search(info_msg, outtxt), "Info message with list of known compiler toolchains")
+        logtxt = read_file(self.logfile)
+        self.assertTrue(re.search(info_msg, logtxt), "Info message with list of known compiler toolchains")
         # toolchain elements should be in alphabetical order
         tcs = {
             'dummy': [],
@@ -430,7 +432,7 @@ def test__list_toolchains(self):
             'ictce': ['icc', 'ifort', 'imkl', 'impi'],
         }
         for tc, tcelems in tcs.items():
-            res = re.findall("^\s*%s: .*" % tc, outtxt, re.M)
+            res = re.findall("^\s*%s: .*" % tc, logtxt, re.M)
             self.assertTrue(res, "Toolchain %s is included in list of known compiler toolchains" % tc)
             # every toolchain should only be mentioned once
             n = len(res)
@@ -457,12 +459,13 @@ def test_avail_lists(self):
                     '--unittest-file=%s' % self.logfile,
                    ]
             outtxt = self.eb_main(args, logfile=dummylogfn)
+            logtxt = read_file(self.logfile)
 
             words = name.replace('-', ' ')
             info_msg = r"INFO List of supported %s:" % words
-            self.assertTrue(re.search(info_msg, outtxt), "Info message with list of available %s" % words)
+            self.assertTrue(re.search(info_msg, logtxt), "Info message with list of available %s" % words)
             for item in items:
-                res = re.findall("^\s*%s" % item, outtxt, re.M)
+                res = re.findall("^\s*%s" % item, logtxt, re.M)
                 self.assertTrue(res, "%s is included in list of available %s" % (item, words))
                 # every item should only be mentioned once
                 n = len(res)
@@ -495,13 +498,14 @@ def test_avail_cfgfile_constants(self):
             '--unittest-file=%s' % self.logfile,
         ]
         outtxt = self.eb_main(args, logfile=dummylogfn)
+        logtxt = read_file(self.logfile)
         cfgfile_constants = {
             'DEFAULT_ROBOT_PATHS': os.path.join(tmpdir, 'easybuild', 'easyconfigs'),
         }
         for cst_name, cst_value in cfgfile_constants.items():
-            cst_regex = re.compile("^\*\s%s:\s.*\s\[value: .*%s.*\]" % (cst_name, cst_value), re.M)
-            tup = (cst_regex.pattern, outtxt)
-            self.assertTrue(cst_regex.search(outtxt), "Pattern '%s' in --avail-cfgfile_constants output: %s" % tup)
+            cst_regex = re.compile(r"^\*\s%s:\s.*\s\[value: .*%s.*\]" % (cst_name, cst_value), re.M)
+            tup = (cst_regex.pattern, logtxt)
+            self.assertTrue(cst_regex.search(logtxt), "Pattern '%s' in --avail-cfgfile_constants output: %s" % tup)
 
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
@@ -536,6 +540,7 @@ def test_list_easyblocks(self):
                     '--unittest-file=%s' % self.logfile,
                    ]
             outtxt = self.eb_main(args, logfile=dummylogfn)
+            logtxt = read_file(self.logfile)
 
             for pat in [
                         r"EasyBlock\n",
@@ -543,7 +548,8 @@ def test_list_easyblocks(self):
                         r"|--\s+bar\n",
                        ]:
 
-                self.assertTrue(re.search(pat, outtxt), "Pattern '%s' is found in output of --list-easyblocks: %s" % (pat, outtxt))
+                msg = "Pattern '%s' is found in output of --list-easyblocks: %s" % (pat, logtxt)
+                self.assertTrue(re.search(pat, logtxt), msg)
 
             modify_env(os.environ, self.orig_environ)
             tempfile.tempdir = None
@@ -557,6 +563,7 @@ def test_list_easyblocks(self):
                 '--unittest-file=%s' % self.logfile,
                ]
         outtxt = self.eb_main(args, logfile=dummylogfn)
+        logtxt = read_file(self.logfile)
 
         for pat in [
                     r"EasyBlock\s+\(easybuild.framework.easyblock\)\n",
@@ -564,7 +571,8 @@ def test_list_easyblocks(self):
                     r"|--\s+bar\s+\(easybuild.easyblocks.generic.bar\)\n",
                    ]:
 
-            self.assertTrue(re.search(pat, outtxt), "Pattern '%s' is found in output of --list-easyblocks: %s" % (pat, outtxt))
+            msg = "Pattern '%s' is found in output of --list-easyblocks: %s" % (pat, logtxt)
+            self.assertTrue(re.search(pat, logtxt), msg)
 
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
@@ -580,12 +588,13 @@ def test_search(self):
             '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
             '--unittest-file=%s' % self.logfile,
         ]
-        outtxt = self.eb_main(args, logfile=dummylogfn)
+        self.eb_main(args, logfile=dummylogfn)
+        logtxt = read_file(self.logfile)
 
         info_msg = r"Searching \(case-insensitive\) for 'gzip' in"
-        self.assertTrue(re.search(info_msg, outtxt), "Info message when searching for easyconfigs in '%s'" % outtxt)
+        self.assertTrue(re.search(info_msg, logtxt), "Info message when searching for easyconfigs in '%s'" % logtxt)
         for ec in ["gzip-1.4.eb", "gzip-1.4-GCC-4.6.3.eb"]:
-            self.assertTrue(re.search(" \* \S*%s$" % ec, outtxt, re.M), "Found easyconfig %s in '%s'" % (ec, outtxt))
+            self.assertTrue(re.search(r" \* \S*%s$" % ec, logtxt, re.M), "Found easyconfig %s in '%s'" % (ec, logtxt))
 
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
@@ -599,13 +608,14 @@ def test_search(self):
                 os.path.join(os.path.dirname(__file__), 'easyconfigs'),
                 '--unittest-file=%s' % self.logfile,
             ]
-            outtxt = self.eb_main(args, logfile=dummylogfn, raise_error=True, verbose=True)
+            self.eb_main(args, logfile=dummylogfn, raise_error=True, verbose=True)
+            logtxt = read_file(self.logfile)
 
             info_msg = r"Searching \(case-insensitive\) for 'toy-0.0' in"
-            self.assertTrue(re.search(info_msg, outtxt), "Info message when searching for easyconfigs in '%s'" % outtxt)
-            self.assertTrue(re.search('INFO CFGS\d+=', outtxt), "CFGS line message found in '%s'" % outtxt)
+            self.assertTrue(re.search(info_msg, logtxt), "Info message when searching for easyconfigs in '%s'" % logtxt)
+            self.assertTrue(re.search('INFO CFGS\d+=', logtxt), "CFGS line message found in '%s'" % logtxt)
             for ec in ["toy-0.0.eb", "toy-0.0-multiple.eb"]:
-                self.assertTrue(re.search(" \* \$CFGS\d+/*%s" % ec, outtxt), "Found easyconfig %s in '%s'" % (ec, outtxt))
+                self.assertTrue(re.search(" \* \$CFGS\d+/*%s" % ec, logtxt), "Found easyconfig %s in '%s'" % (ec, logtxt))
 
             if os.path.exists(dummylogfn):
                 os.remove(dummylogfn)
@@ -621,17 +631,18 @@ def test_dry_run(self):
             '--unittest-file=%s' % self.logfile,
             '--robot-paths=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
         ]
-        outtxt = self.eb_main(args, logfile=dummylogfn)
+        self.eb_main(args, logfile=dummylogfn)
+        logtxt = read_file(self.logfile)
 
         info_msg = r"Dry run: printing build status of easyconfigs and dependencies"
-        self.assertTrue(re.search(info_msg, outtxt, re.M), "Info message dry running in '%s'" % outtxt)
+        self.assertTrue(re.search(info_msg, logtxt, re.M), "Info message dry running in '%s'" % logtxt)
         ecs_mods = [
             ("gzip-1.4-GCC-4.6.3.eb", "gzip/1.4-GCC-4.6.3", ' '),
             ("GCC-4.6.3.eb", "GCC/4.6.3", 'x'),
         ]
         for ec, mod, mark in ecs_mods:
             regex = re.compile(r" \* \[%s\] \S+%s \(module: %s\)" % (mark, ec, mod), re.M)
-            self.assertTrue(regex.search(outtxt), "Found match for pattern %s in '%s'" % (regex.pattern, outtxt))
+            self.assertTrue(regex.search(logtxt), "Found match for pattern %s in '%s'" % (regex.pattern, logtxt))
 
     def test_dry_run_short(self):
         """Test dry run (short format)."""
@@ -1553,12 +1564,13 @@ def test_show_default_moduleclasses(self):
             '--show-default-moduleclasses',
         ]
         write_file(self.logfile, '')
-        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
+        self.eb_main(args, logfile=dummylogfn, verbose=True)
+        logtxt = read_file(self.logfile)
 
         lst = ["\t%s:[ ]*%s" % (c, d.replace('(', '\\(').replace(')', '\\)')) for (c, d) in DEFAULT_MODULECLASSES]
         regex = re.compile("Default available module classes:\n\n" + '\n'.join(lst), re.M)
 
-        self.assertTrue(regex.search(outtxt), "Pattern '%s' found in %s" % (regex.pattern, outtxt))
+        self.assertTrue(regex.search(logtxt), "Pattern '%s' found in %s" % (regex.pattern, logtxt))
 
     def test_show_default_configfiles(self):
         """Test --show-default-configfiles."""
@@ -1592,7 +1604,8 @@ def test_show_default_configfiles(self):
         ])
 
         write_file(self.logfile, '')
-        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
+        self.eb_main(args, logfile=dummylogfn, verbose=True)
+        logtxt = read_file(self.logfile)
 
         homecfgfile = os.path.join(os.environ['HOME'], '.config', 'easybuild', 'config.cfg')
         homecfgfile_str = homecfgfile
@@ -1601,7 +1614,7 @@ def test_show_default_configfiles(self):
         else:
             homecfgfile_str += " => not found"
         expected = expected_tmpl % ('(not set)', '(not set)', homecfgfile_str, '{/etc}')
-        self.assertTrue(expected in outtxt)
+        self.assertTrue(expected in logtxt)
 
         # to predict the full output, we need to take control over $HOME and $XDG_CONFIG_DIRS
         os.environ['HOME'] = self.test_prefix
@@ -1621,10 +1634,11 @@ def test_show_default_configfiles(self):
 
         reload(easybuild.tools.options)
         write_file(self.logfile, '')
-        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
+        self.eb_main(args, logfile=dummylogfn, verbose=True)
+        logtxt = read_file(self.logfile)
         expected = expected_tmpl % ('(not set)', xdg_config_dirs, "%s => found" % homecfgfile, '{%s}' % xdg_config_dirs,
                                     '(no matches)', 1, homecfgfile)
-        self.assertTrue(expected in outtxt)
+        self.assertTrue(expected in logtxt)
 
         xdg_config_home = os.path.join(self.test_prefix, 'home')
         os.environ['XDG_CONFIG_HOME'] = xdg_config_home
@@ -1644,12 +1658,13 @@ def test_show_default_configfiles(self):
         reload(easybuild.tools.options)
 
         write_file(self.logfile, '')
-        outtxt = self.eb_main(args, logfile=dummylogfn, verbose=True)
+        self.eb_main(args, logfile=dummylogfn, verbose=True)
+        logtxt = read_file(self.logfile)
         expected = expected_tmpl % (xdg_config_home, os.pathsep.join(xdg_config_dirs),
                                     "%s => found" % os.path.join(xdg_config_home, 'easybuild', 'config.cfg'),
                                     '{' + ', '.join(xdg_config_dirs) + '}',
                                     ', '.join(cfgfiles[:-1]), 4, ', '.join(cfgfiles))
-        self.assertTrue(expected in outtxt)
+        self.assertTrue(expected in logtxt)
 
         del os.environ['XDG_CONFIG_DIRS']
         del os.environ['XDG_CONFIG_HOME']

From 9b71c57fa31cfe492708a87c5bf655a36414d7b1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 9 Apr 2015 08:28:37 +0200
Subject: [PATCH 0865/1356] properly close log file after clearing it in
 eb_main

---
 test/framework/utilities.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index b63499f472..d831aaeefd 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -81,11 +81,12 @@ class EnhancedTestCase(_EnhancedTestCase):
 
     def setUp(self):
         """Set up testcase."""
+        super(EnhancedTestCase, self).setUp()
+
         self.orig_tmpdir = tempfile.gettempdir()
         # use a subdirectory for this test (which we can clean up easily after the test completes)
         self.test_prefix = set_tmpdir()
 
-        super(EnhancedTestCase, self).setUp()
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
         fd, self.logfile = tempfile.mkstemp(suffix='.log', prefix='eb-test-')
         os.close(fd)
@@ -196,7 +197,9 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
         if logfile is None:
             logfile = self.logfile
         # clear log file
-        open(logfile, 'w').write('')
+        f = open(logfile, 'w')
+        f.write('')
+        f.close()
 
         try:
             main((args, logfile, do_build))

From 6dfdebb9bc0a70f731cb35f74b470bb7521c929d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 9 Apr 2015 12:21:03 +0200
Subject: [PATCH 0866/1356] don't specify log location in build_log test

---
 test/framework/build_log.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/build_log.py b/test/framework/build_log.py
index 880a329fab..814308ba87 100644
--- a/test/framework/build_log.py
+++ b/test/framework/build_log.py
@@ -65,7 +65,7 @@ def test_easybuilderror(self):
         self.assertErrorRegex(EasyBuildError, 'BOOM', raise_easybuilderror, 'BOOM')
         logToFile(tmplog, enable=False)
 
-        log_re = re.compile("^%s :: BOOM \(at %s:[0-9]+ in [a-z_]+\)$" % (getRootLoggerName(), __file__), re.M)
+        log_re = re.compile("^%s :: BOOM \(at .*:[0-9]+ in [a-z_]+\)$" % getRootLoggerName(), re.M)
         logtxt = open(tmplog, 'r').read()
         self.assertTrue(log_re.match(logtxt), "%s matches %s" % (log_re.pattern, logtxt))
 

From 1e0f65c3755ce6ae86dd6d59482450dac81f4094 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 9 Apr 2015 13:05:07 +0200
Subject: [PATCH 0867/1356] restore env right after running main(), clean up
 options tests

---
 test/framework/options.py   | 38 ++++++-------------------------------
 test/framework/utilities.py | 17 ++++++++++++++---
 2 files changed, 20 insertions(+), 35 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 4126594a99..4e96f39ad0 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -128,9 +128,6 @@ def test_debug(self):
                 res = re.search(' %s ' % log_msg_type, outtxt)
                 self.assertTrue(res, "%s log messages are included when using %s: %s" % (log_msg_type, debug_arg, outtxt))
 
-            modify_env(os.environ, self.orig_environ)
-            tempfile.tempdir = None
-
     def test_info(self):
         """Test enabling info logging."""
 
@@ -149,12 +146,8 @@ def test_info(self):
                 res = re.search(' %s ' % log_msg_type, outtxt)
                 self.assertTrue(not res, "%s log messages are *not* included when using %s" % (log_msg_type, info_arg))
 
-            modify_env(os.environ, self.orig_environ)
-            tempfile.tempdir = None
-
     def test_quiet(self):
         """Test enabling quiet logging (errors only)."""
-
         for quiet_arg in ['--quiet']:
             args = [
                     'nosuchfile.eb',
@@ -164,14 +157,13 @@ def test_quiet(self):
 
             for log_msg_type in ['ERROR']:
                 res = re.search(' %s ' % log_msg_type, outtxt)
-                self.assertTrue(res, "%s log messages are included when using %s (outtxt: %s)" % (log_msg_type, quiet_arg, outtxt))
+                msg = "%s log messages are included when using %s (outtxt: %s)" % (log_msg_type, quiet_arg, outtxt)
+                self.assertTrue(res, msg)
 
             for log_msg_type in ['DEBUG', 'INFO']:
                 res = re.search(' %s ' % log_msg_type, outtxt)
-                self.assertTrue(not res, "%s log messages are *not* included when using %s (outtxt: %s)" % (log_msg_type, quiet_arg, outtxt))
-
-            modify_env(os.environ, self.orig_environ)
-            tempfile.tempdir = None
+                msg = "%s log messages are *not* included when using %s (outtxt: %s)" % (log_msg_type, quiet_arg, outtxt)
+                self.assertTrue(not res, msg)
 
     def test_force(self):
         """Test forcing installation even if the module is already available."""
@@ -191,10 +183,8 @@ def test_force(self):
         already_msg = "GCC/4.6.3 is already installed"
         self.assertTrue(re.search(already_msg, outtxt), "Already installed message without --force, outtxt: %s" % outtxt)
 
-        # clear log file, clean up environment
+        # clear log file
         write_file(self.logfile, '')
-        modify_env(os.environ, self.orig_environ)
-        tempfile.tempdir = None
 
         # check that --force works
         args = [
@@ -236,10 +226,8 @@ def test_skip(self):
         os.chdir(self.cwd)
         modules_tool().purge()
         # reinitialize modules tool with original $MODULEPATH, to avoid problems with future tests
-        modify_env(os.environ, self.orig_environ)
         os.environ['MODULEPATH'] = ''
         modules_tool()
-        tempfile.tempdir = None
 
         # check log message with --skip for non-existing module
         args = [
@@ -292,9 +280,6 @@ def check_args(job_args, passed_args=None):
             assertmsg = "Info log msg with job command template for --job (job_msg: %s, outtxt: %s)" % (job_msg, outtxt)
             self.assertTrue(re.search(job_msg, outtxt), assertmsg)
 
-            modify_env(os.environ, self.orig_environ)
-            tempfile.tempdir = None
-
         # options passed are reordered, so order here matters to make tests pass
         check_args(['--debug'])
         check_args(['--debug', '--stop=configure', '--try-software-name=foo'])
@@ -337,8 +322,6 @@ def test_zzz_logtostdout(self):
 
             # cleanup
             os.remove(fn)
-            modify_env(os.environ, self.orig_environ)
-            tempfile.tempdir = None
 
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
@@ -396,9 +379,6 @@ def run_test(custom=None, extra_params=[], fmt=None):
                     msg = "Parameter %s is listed with help in output of eb %s (args: %s, regex: %s): %s" % tup
                     self.assertTrue(regex.search(logtxt), msg)
 
-                modify_env(os.environ, self.orig_environ)
-                tempfile.tempdir = None
-
             if os.path.exists(dummylogfn):
                 os.remove(dummylogfn)
 
@@ -471,9 +451,6 @@ def test_avail_lists(self):
                 n = len(res)
                 self.assertEqual(n, 1, "%s is only mentioned once (count: %d)" % (item, n))
 
-            modify_env(os.environ, self.orig_environ)
-            tempfile.tempdir = None
-
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
@@ -551,9 +528,6 @@ def test_list_easyblocks(self):
                 msg = "Pattern '%s' is found in output of --list-easyblocks: %s" % (pat, logtxt)
                 self.assertTrue(re.search(pat, logtxt), msg)
 
-            modify_env(os.environ, self.orig_environ)
-            tempfile.tempdir = None
-
         # clear log
         write_file(self.logfile, '')
 
@@ -1032,7 +1006,7 @@ def test_tmpdir(self):
             '--debug',
             '--tmpdir=%s' % tmpdir,
         ]
-        outtxt = self.eb_main(args, do_build=True)
+        outtxt = self.eb_main(args, do_build=True, reset_env=False)
 
         tmpdir_msg = r"Using %s\S+ as temporary directory" % os.path.join(tmpdir, 'eb-')
         found = re.search(tmpdir_msg, outtxt, re.M)
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index d831aaeefd..7d18614830 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -189,7 +189,8 @@ def reset_modulepath(self, modpaths):
         for modpath in modpaths:
             modtool.add_module_path(modpath)
 
-    def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbose=False, raise_error=False):
+    def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbose=False, raise_error=False,
+                reset_env=True):
         """Helper method to call EasyBuild main function."""
         cleanup()
 
@@ -201,6 +202,8 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
         f.write('')
         f.close()
 
+        env_before = copy.deepcopy(os.environ)
+
         try:
             main((args, logfile, do_build))
         except SystemExit:
@@ -210,18 +213,26 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
             if verbose:
                 print "err: %s" % err
 
+        logtxt = read_file(logfile)
+
         os.chdir(self.cwd)
 
         # make sure config is reinitialized
         init_config()
 
+        # restore environment to what it was before running main,
+        # changes may have been made by eb_main (e.g. $TMPDIR & co)
+        if reset_env:
+            modify_env(os.environ, env_before)
+            tempfile.tempdir = None
+
         if myerr and raise_error:
             raise myerr
 
         if return_error:
-            return read_file(logfile), myerr
+            return logtxt, myerr
         else:
-            return read_file(logfile)
+            return logtxt
 
     def setup_hierarchical_modules(self):
         """Setup hierarchical modules to run tests on."""

From f86e5e46786e76c767acd55152bacdc8fffdedd1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 9 Apr 2015 18:18:57 +0200
Subject: [PATCH 0868/1356] fix vsc-base dep version

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 6335ba4f77..9ec31123b2 100644
--- a/setup.py
+++ b/setup.py
@@ -106,5 +106,5 @@ def find_rel_test():
     provides=["eb"] + easybuild_packages,
     test_suite="test.framework.suite",
     zip_safe=False,
-    install_requires=["vsc-base >= 2.2.0"],
+    install_requires=["vsc-base >= 2.1.3"],
 )

From fdcde9728370a951d6294cdb4f5998b1ea6de32d Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Wed, 15 Apr 2015 01:07:01 +0300
Subject: [PATCH 0869/1356] Fixed error in GNU wrapper to really use GCC
 instead of IntelIccIfort's CC and friends.

---
 easybuild/toolchains/compiler/craypewrappers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 9a08806258..2ee8a25b99 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -151,7 +151,7 @@ def _set_compiler_vars(self):
             comp_attrs = ['UNIQUE_OPTS', 'UNIQUE_OPTION_MAP', 'CC', 'CXX', 'C_UNIQUE_FLAGS',
                           'F77', 'F90', 'F_UNIQUE_FLAGS']
             for attr_name in ['COMPILER_%s' % a for a in comp_attrs]:
-                setattr(self, attr_name, getattr(IntelIccIfort, attr_name))
+                setattr(self, attr_name, getattr(Gcc, attr_name))
 
         super(CrayPEWrapperGNU,self)._set_compiler_vars()
 

From 081a926c483f3733e5c45553dd3922db19fd0a6c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Apr 2015 17:15:15 +0200
Subject: [PATCH 0870/1356] replace log.error with raise EasyBuildError

---
 easybuild/toolchains/compiler/craypewrappers.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 2ee8a25b99..2dd5af6149 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -39,7 +39,7 @@
 @author: Petar Forai (IMP/IMBA, Austria)
 @author: Kenneth Hoste (Ghent University)
 """
-
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.toolchain.compiler import Compiler
 from easybuild.toolchains.compiler.gcc import Gcc
@@ -106,7 +106,7 @@ def _set_optimal_architecture(self):
         """Load craype module specified via 'optarch' build option."""
         optarch = build_option('optarch')
         if optarch is None:
-            self.log.error("Don't know which 'craype' module to load, 'optarch' build option is unspecified.")
+            raise EasyBuildError("Don't know which 'craype' module to load, 'optarch' build option is unspecified.")
         else:
             self.modules_tool.load([self.CRAYPE_MODULE_NAME_TEMPLATE % {'optarch': optarch}])
 

From a8654a894570ed36280477ffc0ecdf3802937d40 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Apr 2015 18:04:28 +0200
Subject: [PATCH 0871/1356] reload tools.options after unsetting $XDG* env vars
 in test

---
 test/framework/options.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 4e96f39ad0..6122d6a503 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1556,6 +1556,7 @@ def test_show_default_configfiles(self):
         for envvar in ['XDG_CONFIG_DIRS', 'XDG_CONFIG_HOME']:
             if envvar in os.environ:
                 del os.environ[envvar]
+        reload(easybuild.tools.options)
 
         args = [
             '--unittest-file=%s' % self.logfile,

From 4e0d305d9db7c8f0ea33ac730fc588a350944333 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Apr 2015 18:09:24 +0200
Subject: [PATCH 0872/1356] make sure both vsc-base and easybuild-framework are
 included in $PYTHONPATH in scripts tests

---
 test/framework/scripts.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 3b78519baa..f406640da0 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -34,6 +34,9 @@
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
 
+import vsc
+
+import easybuild.framework
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools.filetools import read_file, write_file
 from easybuild.tools.run import run_cmd
@@ -42,6 +45,16 @@
 class ScriptsTest(EnhancedTestCase):
     """ Testcase for run module """
 
+    def setUp(self):
+        """Test setup."""
+        super(ScriptsTest, self).setUp()
+
+        # make sure both vsc-base and easybuild-framework are included in $PYTHONPATH (so scripts can pick it up)
+        vsc_loc = os.path.dirname(os.path.dirname(os.path.abspath(vsc.__file__)))
+        framework_loc = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(easybuild.framework.__file__))))
+        pythonpath = os.environ.get('PYTHONPATH', '')
+        os.environ['PYTHONPATH'] = os.pathsep.join([vsc_loc, framework_loc, pythonpath])
+
     def test_generate_software_list(self):
         """Test for generate_software_list.py script."""
 

From 6ca5e1f7398fbe230ecb10134e1452d445b17f5f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 19 Apr 2015 22:14:25 +0200
Subject: [PATCH 0873/1356] update Cray toolchain support for make HPL build
 work

---
 .../toolchains/compiler/craypewrappers.py     | 160 +++++++++++++++---
 1 file changed, 133 insertions(+), 27 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index 2dd5af6149..f7de1ec89b 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -39,17 +39,24 @@
 @author: Petar Forai (IMP/IMBA, Austria)
 @author: Kenneth Hoste (Ghent University)
 """
+import os
+
+from easybuild.toolchains.compiler.gcc import Gcc
+from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.toolchains.fft.fftw import Fftw
+from easybuild.toolchains.mpi.mpich import TC_CONSTANT_MPI_TYPE_MPICH
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.toolchain.compiler import Compiler
-from easybuild.toolchains.compiler.gcc import Gcc
-from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.tools.toolchain.constants import COMPILER_VARIABLES, MPI_COMPILER_TEMPLATE, SEQ_COMPILER_TEMPLATE
+from easybuild.tools.toolchain.linalg import LinAlg
+from easybuild.tools.toolchain.mpi import Mpi
 
 
 TC_CONSTANT_CRAYPEWRAPPER = "CRAYPEWRAPPER"
 
 
-class CrayPEWrapper(Compiler):
+class CrayPEWrapper(Compiler, Mpi, LinAlg, Fftw):
     """Generic support for using Cray compiler wrappers"""
 
     # no toolchain components, so no modules to list here (empty toolchain definition w.r.t. components)
@@ -80,10 +87,41 @@ class CrayPEWrapper(Compiler):
     COMPILER_F77 = 'ftn'
     COMPILER_F90 = 'ftn'
 
-    # FIXME (kehoste) hmmmm, really? then how do you control optimisation, precision when using the Cray wrappers?
-    COMPILER_FLAGS = []  # we dont have this for the wrappers
-    COMPILER_OPT_FLAGS = []  # or those
-    COMPILER_PREC_FLAGS = []  # and those for sure not !
+    # MPI support
+    # no separate module, Cray compiler drivers always provide MPI support
+    MPI_MODULE_NAME = []
+    MPI_FAMILY = TC_CONSTANT_CRAYPEWRAPPER
+    MPI_TYPE = TC_CONSTANT_MPI_TYPE_MPICH
+
+    MPI_COMPILER_MPICC = COMPILER_CC
+    MPI_COMPILER_MPICXX = COMPILER_CXX
+    MPI_COMPILER_MPIF77 = COMPILER_F77
+    MPI_COMPILER_MPIF90 = COMPILER_F90
+
+    MPI_SHARED_OPTION_MAP = {
+        '_opt_MPICC': '',
+        '_opt_MPICXX': '',
+        '_opt_MPIF77': '',
+        '_opt_MPIF90': '',
+    }
+
+    # BLAS/LAPACK support
+    # via cray-libsci module, which gets loaded via the PrgEnv module
+    # see https://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/
+    BLAS_MODULE_NAME = ['cray-libsci']
+    # specific library depends on PrgEnv flavor
+    # FIXME: make this (always) empty list?
+    BLAS_LIB = None
+    BLAS_LIB_MT = None
+
+    LAPACK_MODULE_NAME = ['cray-libsci']
+    LAPACK_IS_BLAS = True
+
+    BLACS_MODULE_NAME = []
+    SCALAPACK_MODULE_NAME = []
+
+    # FFT support, via Cray-provided fftw module
+    FFT_MODULE_NAME = ['fftw']
 
     # template and name suffix for PrgEnv module that matches this toolchain
     # e.g. 'gnu' => 'PrgEnv-gnu/<version>'
@@ -93,7 +131,7 @@ class CrayPEWrapper(Compiler):
     # template for craype module (determines code generator backend of Cray compiler wrappers)
     CRAYPE_MODULE_NAME_TEMPLATE = 'craype-%(optarch)s'
 
-    def _pre_preprare(self):
+    def _pre_prepare(self):
         """Load PrgEnv module."""
         prgenv_mod_name = self.PRGENV_MODULE_NAME_TEMPLATE % {
             'suffix': self.PRGENV_MODULE_NAME_SUFFIX,
@@ -110,30 +148,86 @@ def _set_optimal_architecture(self):
         else:
             self.modules_tool.load([self.CRAYPE_MODULE_NAME_TEMPLATE % {'optarch': optarch}])
 
-    # FIXME: (kehoste) is it really needed to customise this?
-    # this looks like a workaround for setting the COMPILER_*_FLAGS lists empty?
     def _set_compiler_flags(self):
-        """Collect the flags set, and add them as variables too"""
-
-        flags = [self.options.option(x) for x in self.COMPILER_FLAGS if self.options.get(x, False)]
-        cflags = [self.options.option(x) for x in self.COMPILER_C_FLAGS + self.COMPILER_C_UNIQUE_FLAGS \
-                  if self.options.get(x, False)]
-        fflags = [self.options.option(x) for x in self.COMPILER_F_FLAGS + self.COMPILER_F_UNIQUE_FLAGS \
-                  if self.options.get(x, False)]
-
+        """Set compiler flag variables empty."""
+        # FIXME: actually define these to be *empty*
+        self.variables.nappend('CFLAGS', 'L.')
+        self.variables.nappend('CXXFLAGS', 'L.')
+        self.variables.nappend('FFLAGS', 'L.')
+        self.variables.nappend('F90FLAGS', 'L.')
+
+    def _set_mpi_compiler_variables(self):
+        """Set the MPI compiler variables"""
+        for var_tuple in COMPILER_VARIABLES:
+            c_var = var_tuple[0]  # [1] is the description
+            var = MPI_COMPILER_TEMPLATE % {'c_var':c_var}
+
+            value = getattr(self, 'MPI_COMPILER_%s' % var.upper(), None)
+            if value is None:
+                raise EasyBuildError("_set_mpi_compiler_variables: mpi compiler variable %s undefined", var)
+            self.variables.nappend_el(var, value)
+
+            if self.options.get('usempi', None):
+                var_seq = SEQ_COMPILER_TEMPLATE % {'c_var': c_var}
+                seq_comp = self.variables[c_var]
+                self.log.debug('_set_mpi_compiler_variables: usempi set: defining %s as %s', var_seq, seq_comp)
+                self.variables[var_seq] = seq_comp
+
+        if self.options.get('cciscxx', None):
+            self.log.debug("_set_mpi_compiler_variables: cciscxx set: switching MPICXX %s for MPICC value %s" %
+                           (self.variables['MPICXX'], self.variables['MPICC']))
+            self.variables['MPICXX'] = self.variables['MPICC']
+
+    def _get_software_root(self, name):
+        """Get install prefix for specified software name; special treatment for Cray modules."""
+        if name == 'cray-libsci':
+            # Cray-provided LibSci module
+            env_var = 'CRAY_LIBSCI_PREFIX_DIR'
+            root = os.getenv(env_var, None)
+            if root is None:
+                raise EasyBuildError("Failed to determine install prefix for %s via $%s", name, env_var)
+            else:
+                self.log.debug("Obtained install prefix for %s via $%s: %s", name, env_var, root)
+        elif name == 'fftw':
+            # Cray-provided fftw module
+            env_var = 'FFTW_INC'
+            incdir = os.getenv(env_var, None)
+            if incdir is None:
+                raise EasyBuildError("Failed to determine install prefix for %s via $%s", name, env_var)
+            else:
+                root = os.path.dirname(incdir)
+                self.log.debug("Obtained install prefix for %s via $%s: %s", name, env_var, root)
+        else:
+            root = super(CrayPEWrapper, self)._get_software_root(name)
+
+        return root
+
+    def _get_software_version(self, name):
+        """Get version for specified software name; special treatment for Cray modules."""
+        if name == 'fftw':
+            # Cray-provided fftw module
+            env_var = 'FFTW_VERSION'
+            ver = os.getenv(env_var, None)
+            if ver is None:
+                raise EasyBuildError("Failed to determine version for %s via $%s", name, env_var)
+            else:
+                self.log.debug("Obtained version for %s via $%s: %s", name, env_var, ver)
+        else:
+            ver = super(CrayPEWrapper, self)._get_software_version(name)
 
-        # precflags last
-        self.variables.nappend('CFLAGS', flags)
-        self.variables.nappend('CFLAGS', cflags)
+        return ver
 
-        self.variables.nappend('CXXFLAGS', flags)
-        self.variables.nappend('CXXFLAGS', cflags)
+    def _set_blacs_variables(self):
+        """Skip setting BLACS related variables"""
+        pass
 
-        self.variables.nappend('FFLAGS', flags)
-        self.variables.nappend('FFLAGS', fflags)
+    def _set_scalapack_variables(self):
+        """Skip setting ScaLAPACK related variables"""
+        pass
 
-        self.variables.nappend('F90FLAGS', flags)
-        self.variables.nappend('F90FLAGS', fflags)
+    def definition(self):
+        """Empty toolchain definition (no modules listed as toolchain dependencies)."""
+        return {}
 
 
 # Gcc's base is Compiler
@@ -141,6 +235,10 @@ class CrayPEWrapperGNU(CrayPEWrapper):
     """Support for using the Cray GNU compiler wrappers."""
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_GNU'
 
+    # FIXME: make this empty list?
+    BLAS_LIB = ['sci_gnu_mpi']
+    BLAS_LIB_MT = ['sci_gnu_mpi_mp']
+
     PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
 
     def _set_compiler_vars(self):
@@ -160,6 +258,10 @@ class CrayPEWrapperIntel(CrayPEWrapper):
     """Support for using the Cray Intel compiler wrappers."""
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_INTEL'
 
+    # FIXME: make this empty list?
+    BLAS_LIB = ['sci_intel_mpi']
+    BLAS_LIB_MT = ['sci_intel_mpi_mp']
+
     PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
 
     def _set_compiler_flags(self):
@@ -179,4 +281,8 @@ class CrayPEWrapperCray(CrayPEWrapper):
     """Support for using the Cray CCE compiler wrappers."""
     TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_CRAY'
 
+    # FIXME: make this empty list?
+    BLAS_LIB = ['sci_cray_mpi']
+    BLAS_LIB_MT = ['sci_cray_mpi_mp']
+
     PRGENV_MODULE_NAME_SUFFIX = 'cray'  # PrgEnv-cray

From bdc29a34dc17192c052bd44accf9f3167c670c3e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 20 Apr 2015 22:54:34 +0200
Subject: [PATCH 0874/1356] play around with compiler flags and toolchain
 options, to make HPL+zlib+Szip work

---
 .../toolchains/compiler/craypewrappers.py     | 32 +++++++++++++------
 1 file changed, 23 insertions(+), 9 deletions(-)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craypewrappers.py
index f7de1ec89b..7ce3079842 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craypewrappers.py
@@ -66,19 +66,33 @@ class CrayPEWrapper(Compiler, Mpi, LinAlg, Fftw):
 
     COMPILER_UNIQUE_OPTS = {
         # FIXME: (kehoste) how is this different from the existing 'shared' toolchain option? just map 'shared' to '-dynamic'? (already done)
-        'dynamic': (True, "Generate dynamically linked executables and libraries."),
+        'dynamic': (False, "Generate dynamically linked executable"),
         'mpich-mt': (False, "Directs the driver to link in an alternate version of the Cray-MPICH library which \
                              provides fine-grained multi-threading support to applications that perform \
                              MPI operations within threaded regions."),
         'usewrappedcompiler': (False, "Use the embedded compiler instead of the wrapper"),
+        'verbose': (True, "Verbose output"),
+        'optarch': (False, "Enable architecture optimizations"),
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-        'pic': 'shared',
-        'shared': 'dynamic',
+        #'pic': 'shared',  # FIXME (use compiler-specific setting?)
+        'shared': 'shared',
+        'dynamic': 'dynamic',
         'static': 'static',
         'verbose': 'craype-verbose',
         'mpich-mt': 'craympich-mt',
+        # no optimization flags
+        'noopt': [],
+        'lowopt': [],
+        'defaultopt': [],
+        'opt': [],
+        # no precision flags
+        'strict': [],
+        'precise': [],
+        'defaultprec': [],
+        'loose': [],
+        'veryloose': [],
     }
 
     COMPILER_CC = 'cc'
@@ -148,13 +162,13 @@ def _set_optimal_architecture(self):
         else:
             self.modules_tool.load([self.CRAYPE_MODULE_NAME_TEMPLATE % {'optarch': optarch}])
 
+        # no compiler flag when optarch toolchain option is enabled
+        self.options.options_map['optarch'] = ''
+
     def _set_compiler_flags(self):
-        """Set compiler flag variables empty."""
-        # FIXME: actually define these to be *empty*
-        self.variables.nappend('CFLAGS', 'L.')
-        self.variables.nappend('CXXFLAGS', 'L.')
-        self.variables.nappend('FFLAGS', 'L.')
-        self.variables.nappend('F90FLAGS', 'L.')
+        """Set compiler flags."""
+        self.COMPILER_FLAGS.extend(['dynamic'])
+        super(CrayPEWrapper, self)._set_compiler_flags()
 
     def _set_mpi_compiler_variables(self):
         """Set the MPI compiler variables"""

From bdebab6fc5d9abe7372fd45917ea68ceed1295e6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 13:36:51 +0200
Subject: [PATCH 0875/1356] remove system_modules parameter/option

---
 easybuild/framework/easyblock.py          | 10 ++-------
 easybuild/framework/easyconfig/default.py |  1 -
 easybuild/tools/config.py                 |  1 -
 easybuild/tools/options.py                |  1 -
 test/framework/modules.py                 | 25 -----------------------
 5 files changed, 2 insertions(+), 36 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 35670ced1d..c1e7542d27 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1329,19 +1329,13 @@ def prepare_step(self):
         """
         Pre-configure step. Set's up the builddir just before starting configure
         """
+        # clean environment, undefine any unwanted environment variables that may be harmful
         self.cfg['unwanted_env_vars'] = env.unset_env_vars(self.cfg['unwanted_env_vars'])
 
-        # load system modules first, before loading toolchain and dependencies
-        system_modules = build_option('system_modules')
-        if system_modules is None:
-            system_modules = []
-
-        self.log.info("Loading specified system modules: %s + %s", system_modules, self.cfg['system_modules'])
-        self.modules_tool.load(system_modules + self.cfg['system_modules'])
-
         # prepare toolchain: load toolchain module and dependencies, set up build environment
         self.toolchain.prepare(self.cfg['onlytcmod'])
 
+        # guess directory to start configure/build/install process in, and move there
         self.guess_start_dir()
 
     def configure_step(self):
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index c5bdc026e2..64cf46be16 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -139,7 +139,6 @@
     'dependencies': [[], "List of dependencies", DEPENDENCIES],
     'hiddendependencies': [[], "List of dependencies available as hidden modules", DEPENDENCIES],
     'osdependencies': [[], "OS dependencies that should be present on the system", DEPENDENCIES],
-    'system_modules': [[], "System module dependencies that should be present on the system", DEPENDENCIES],
 
     # LICENSE easyconfig parameters
     'group': [None, "Name of the user group for which the software should be available", LICENSE],
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 6563280421..7b398be0aa 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -96,7 +96,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'skip',
         'stop',
         'suffix_modules_path',
-        'system_modules',
         'test_report_env_filter',
         'testoutput',
         'umask',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 0dd67c0666..9add9d423a 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -214,7 +214,6 @@ def override_options(self):
             'set-gid-bit': ("Set group ID bit on newly created directories", None, 'store_true', False),
             'sticky-bit': ("Set sticky bit on newly created directories", None, 'store_true', False),
             'skip-test-cases': ("Skip running test cases", None, 'store_true', False, 't'),
-            'system-modules': ("System modules to load", 'strlist', 'store', None),
             'umask': ("umask to use (e.g. '022'); non-user write permissions on install directories are removed",
                       None, 'store', None),
             'update-modules-tool-cache': ("Update modules tool cache file(s) after generating module file",
diff --git a/test/framework/modules.py b/test/framework/modules.py
index 2b8ea94fbf..487cbb8ccb 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -322,31 +322,6 @@ def test_path_to_top_of_module_tree_categorized_hmns(self):
         path = modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
         self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
 
-    def test_system_modules(self):
-        """Test use of system modules."""
-        ectxt = read_file(os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb'))
-        toy_ec = os.path.join(self.test_prefix, 'toy-0.0-system-modules.eb')
-
-        # just specify some of the test modules we ship, doesn't matter where they come from
-        ectxt += "\nsystem_modules = ['GCC/4.6.4', 'ifort/2011.13.367']"
-        ectxt += "\nstart_dir = '%s'" % self.test_prefix  # require to be able to call prepare_step() method
-        write_file(toy_ec, ectxt)
-
-        opts = init_config(args=["--system-modules=CUDA/5.0.35-1,toy/0.0"])
-        self.assertEqual(opts.system_modules, ['CUDA/5.0.35-1', 'toy/0.0'])
-
-        build_options = {
-            'system_modules': opts.system_modules,
-            'valid_module_classes': config.module_classes(),
-        }
-        init_config(build_options=build_options)
-
-        ec = EasyConfig(toy_ec)
-        eb = EasyBlock(ec)
-
-        eb.prepare_step()
-        expected_modules = ['CUDA/5.0.35-1', 'toy/0.0', 'GCC/4.6.4', 'ifort/2011.13.367']
-        self.assertEqual(expected_modules, [x['mod_name'] for x in eb.modules_tool.list()])
 
 def suite():
     """ returns all the testcases in this module """

From 0f15d9f6595c9d7ada4fddaefe43e65e55c4d42f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 14:45:55 +0200
Subject: [PATCH 0876/1356] add support for marking dependencies as external
 modules

---
 easybuild/framework/easyconfig/constants.py  |  4 ++
 easybuild/framework/easyconfig/easyconfig.py | 42 +++++++++++++-----
 easybuild/framework/easyconfig/tools.py      | 14 +++++-
 easybuild/tools/robot.py                     |  8 ++++
 test/framework/easyconfig.py                 | 31 ++++++++++++++
 test/framework/toy_build.py                  | 45 ++++++++++++++++++++
 6 files changed, 131 insertions(+), 13 deletions(-)

diff --git a/easybuild/framework/easyconfig/constants.py b/easybuild/framework/easyconfig/constants.py
index 5cdb3168b4..501db4dcca 100644
--- a/easybuild/framework/easyconfig/constants.py
+++ b/easybuild/framework/easyconfig/constants.py
@@ -37,8 +37,12 @@
 
 _log = fancylogger.getLogger('easyconfig.constants', fname=False)
 
+
+EXTERNAL_MODULE_MARKER = 'EXTERNAL_MODULE'
+
 # constants that can be used in easyconfig
 EASYCONFIG_CONSTANTS = {
+    'EXTERNAL_MODULE': (EXTERNAL_MODULE_MARKER, "External module marker"),
     'SYS_PYTHON_VERSION': (platform.python_version(), "System Python version (platform.python_version())"),
     'OS_TYPE': (get_os_type(), "System type (e.g. 'Linux' or 'Darwin')"),
     'OS_NAME': (get_os_name(), "System name (e.g. 'fedora' or 'RHEL')"),
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 71269bccd5..cf1c756d10 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -56,6 +56,7 @@
 from easybuild.tools.toolchain.utilities import get_toolchain
 from easybuild.tools.utilities import remove_unwanted_chars
 from easybuild.framework.easyconfig import MANDATORY
+from easybuild.framework.easyconfig.constants import EXTERNAL_MODULE_MARKER
 from easybuild.framework.easyconfig.default import DEFAULT_CONFIG
 from easybuild.framework.easyconfig.format.convert import Dependency
 from easybuild.framework.easyconfig.format.one import retrieve_blocks_in_spec
@@ -530,29 +531,34 @@ def _parse_dependency(self, dep, hidden=False):
         of these attributes, 'name' and 'version' are mandatory
 
         output dict contains these attributes:
-        ['name', 'version', 'versionsuffix', 'dummy', 'toolchain', 'short_mod_name', 'full_mod_name', 'hidden']
+        ['name', 'version', 'versionsuffix', 'dummy', 'toolchain', 'short_mod_name', 'full_mod_name', 'hidden',
+         'external_module']
 
         @param hidden: indicate whether corresponding module file should be installed hidden ('.'-prefixed)
         """
         # convert tuple to string otherwise python might complain about the formatting
         self.log.debug("Parsing %s as a dependency" % str(dep))
 
+        dummy_toolchain = {'name': DUMMY_TOOLCHAIN_NAME, 'version': DUMMY_TOOLCHAIN_VERSION}
+
         attr = ['name', 'version', 'versionsuffix', 'toolchain']
         dependency = {
             'dummy': False,
             'full_mod_name': None,  # full module name
             'short_mod_name': None,  # short module name
-            'name': '',  # software name
+            'name': None,  # software name
             'toolchain': None,
-            'version': '',
+            'version': None,
             'versionsuffix': '',
             'hidden': hidden,
+            'external_module': False
         }
         if isinstance(dep, dict):
             dependency.update(dep)
             # make sure 'dummy' key is handled appropriately
             if 'dummy' in dep and not 'toolchain' in dep:
                 dependency['toolchain'] = dep['dummy']
+
         elif isinstance(dep, Dependency):
             dependency['name'] = dep.name()
             dependency['version'] = dep.version()
@@ -562,12 +568,25 @@ def _parse_dependency(self, dep, hidden=False):
             toolchain = dep.toolchain()
             if toolchain is not None:
                 dependency['toolchain'] = toolchain
+
         elif isinstance(dep, (list, tuple)):
-            # try and convert to list
-            dep = list(dep)
-            dependency.update(dict(zip(attr, dep)))
+            if dep and dep[-1] == EXTERNAL_MODULE_MARKER:
+                if len(dep) == 2:
+                    dependency['external_module'] = True
+                    dependency['short_mod_name'] = dep[0]
+                    dependency['full_mod_name'] = dep[0]
+                else:
+                    raise EasyBuildError("Incorrect external dependency specification: %s", dep)
+            else:
+                # non-external dependency: tuple (or list) that specifies name/version(/versionsuffix(/toolchain))
+                dependency.update(dict(zip(attr, dep)))
+
         else:
-            raise EasyBuildError('Dependency %s of unsupported type: %s.', dep, type(dep))
+            raise EasyBuildError("Dependency %s of unsupported type: %s", dep, type(dep))
+
+        if dependency['external_module']:
+            self.log.debug("Returning parsed external dependency: %s", dependency)
+            return dependency
 
         # check whether this dependency should be hidden according to --hide-deps
         if build_option('hide_deps'):
@@ -579,7 +598,7 @@ def _parse_dependency(self, dep, hidden=False):
         if tc_spec is not None:
             # (true) boolean value simply indicates that a dummy toolchain is used
             if isinstance(tc_spec, bool) and tc_spec:
-                tc = {'name': DUMMY_TOOLCHAIN_NAME, 'version': DUMMY_TOOLCHAIN_VERSION}
+                tc = dummy_toolchain
             # two-element list/tuple value indicates custom toolchain specification
             elif isinstance(tc_spec, (list, tuple,)):
                 if len(tc_spec) == 2:
@@ -594,18 +613,20 @@ def _parse_dependency(self, dep, hidden=False):
             else:
                 raise EasyBuildError("Unsupported type for toolchain spec encountered: %s (%s)", tc_spec, type(tc_spec))
 
+        self.log.debug("Derived toolchain to use for dependency %s, based on toolchain spec %s: %s", dep, tc_spec, tc)
         dependency['toolchain'] = tc
 
         # make sure 'dummy' value is set correctly
         dependency['dummy'] = dependency['toolchain']['name'] == DUMMY_TOOLCHAIN_NAME
 
         # validations
-        if not dependency['name']:
+        if dependency['name'] is None:
             raise EasyBuildError("Dependency specified without name: %s", dependency)
 
-        if not dependency['version']:
+        if dependency['version'] is None:
             raise EasyBuildError("Dependency specified without version: %s", dependency)
 
+        # set module names
         dependency['short_mod_name'] = ActiveMNS().det_short_module_name(dependency)
         dependency['full_mod_name'] = ActiveMNS().det_full_module_name(dependency)
 
@@ -1086,7 +1107,6 @@ def det_short_module_name(self, ec, force_visible=False):
         if not self.is_short_modname_for(mod_name, ec['name']):
             raise EasyBuildError("is_short_modname_for('%s', '%s') for active module naming scheme returns False",
                                  mod_name, ec['name'])
-
         return mod_name
 
     def det_module_subdir(self, ec):
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 1ed42e17c2..5405f5ed1c 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -111,13 +111,23 @@ def find_resolved_modules(unprocessed, avail_modules, retain_all_deps=False):
         new_ec = ec.copy()
         deps = []
         for dep in new_ec['dependencies']:
-            full_mod_name = ActiveMNS().det_full_module_name(dep)
+            full_mod_name = dep.get('full_mod_name', None)
+            if full_mod_name is None:
+                full_mod_name = ActiveMNS().det_full_module_name(dep)
+
             dep_resolved = full_mod_name in new_avail_modules
             if not retain_all_deps:
                 # hidden modules need special care, since they may not be included in list of available modules
                 dep_resolved |= dep['hidden'] and modtool.exist([full_mod_name])[0]
+
             if not dep_resolved:
-                deps.append(dep)
+                # treat external modules as resolved when retain_all_deps is enabled (e.g., under --dry-run)
+                if retain_all_deps and dep['external_module']:
+                    _log.debug("Treating dependency marked as external dependency as resolved: %s", dep)
+                else:
+                    # no module available (yet) => retain dependency as one to be resolved
+                    deps.append(dep)
+
         new_ec['dependencies'] = deps
 
         if len(new_ec['dependencies']) == 0:
diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index d4f3799b81..bb8cd15271 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -166,6 +166,13 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
                 if not ec['full_mod_name'] in [x['full_mod_name'] for x in ordered_ecs]:
                     ordered_ecs.append(ec)
 
+        # dependencies marked as external modules should be resolved via available modules at this point
+        missing_external_modules = [d['full_mod_name'] for ec in unprocessed for d in ec['dependencies']
+                                    if d['external_module']]
+        if missing_external_modules:
+            raise EasyBuildError("Missing modules for one or more dependencies marked as external modules: %s",
+                                 missing_external_modules)
+
         # robot: look for existing dependencies, add them
         if robot and unprocessed:
 
@@ -218,6 +225,7 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
 
             # add additional (new) easyconfigs to list of stuff to process
             unprocessed.extend(additional)
+            _log.debug("Unprocessed dependencies: %s", unprocessed)
 
         elif not robot:
             # no use in continuing if robot is not enabled, dependencies won't be resolved anyway
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index a00524bbcf..34c365110e 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -42,6 +42,7 @@
 import easybuild.tools.build_log
 import easybuild.framework.easyconfig as easyconfig
 from easybuild.framework.easyblock import EasyBlock
+from easybuild.framework.easyconfig.constants import EXTERNAL_MODULE_MARKER
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.framework.easyconfig.easyconfig import create_paths
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
@@ -212,6 +213,9 @@ def test_dependency(self):
         self.assertErrorRegex(EasyBuildError, "Dependency foo of unsupported type", eb._parse_dependency, "foo")
         self.assertErrorRegex(EasyBuildError, "without name", eb._parse_dependency, ())
         self.assertErrorRegex(EasyBuildError, "without version", eb._parse_dependency, {'name': 'test'})
+        err_msg = "Incorrect external dependency specification"
+        self.assertErrorRegex(EasyBuildError, err_msg, eb._parse_dependency, (EXTERNAL_MODULE_MARKER,))
+        self.assertErrorRegex(EasyBuildError, err_msg, eb._parse_dependency, ('foo', '1.2.3', EXTERNAL_MODULE_MARKER))
 
     def test_extra_options(self):
         """ extra_options should allow other variables to be stored """
@@ -574,6 +578,7 @@ def test_obtain_easyconfig(self):
                 'short_mod_name': 'foo/1.2.3-GCC-4.4.5',
                 'full_mod_name': 'foo/1.2.3-GCC-4.4.5',
                 'hidden': False,
+                'external_module': False,
             },
             {
                 'name': 'bar',
@@ -584,6 +589,7 @@ def test_obtain_easyconfig(self):
                 'short_mod_name': 'bar/666-gompi-1.4.10-bleh',
                 'full_mod_name': 'bar/666-gompi-1.4.10-bleh',
                 'hidden': False,
+                'external_module': False,
             },
             {
                 'name': 'test',
@@ -594,6 +600,7 @@ def test_obtain_easyconfig(self):
                 'short_mod_name': 'test/.3.2.1-GCC-4.4.5',
                 'full_mod_name': 'test/.3.2.1-GCC-4.4.5',
                 'hidden': True,
+                'external_module': False,
             },
         ]
 
@@ -1030,6 +1037,29 @@ def set_ec_key(key):
             ec[key] = 'foobar'
         self.assertErrorRegex(EasyBuildError, error_regex, set_ec_key, 'therenosucheasyconfigparameterlikethis')
 
+    def test_external_dependencies(self):
+        """Test specifying external (build) dependencies."""
+        ectxt = read_file(os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0-deps.eb'))
+        toy_ec = os.path.join(self.test_prefix, 'toy-0.0-external-deps.eb')
+
+        # just specify some of the test modules we ship, doesn't matter where they come from
+        ectxt += "\ndependencies += [('foobar/1.2.3', EXTERNAL_MODULE)]"
+        ectxt += "\nbuilddependencies = [('somebuilddep/0.1', EXTERNAL_MODULE)]"
+        write_file(toy_ec, ectxt)
+
+        ec = EasyConfig(toy_ec)
+
+        builddeps = ec.builddependencies()
+        self.assertEqual(len(builddeps), 1)
+        self.assertEqual(builddeps[0]['short_mod_name'], 'somebuilddep/0.1')
+        self.assertEqual(builddeps[0]['full_mod_name'], 'somebuilddep/0.1')
+        self.assertEqual(builddeps[0]['external_module'], True)
+
+        deps = ec.dependencies()
+        self.assertEqual(len(deps), 3)
+        self.assertEqual([d['short_mod_name'] for d in deps], ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1'])
+        self.assertEqual([d['full_mod_name'] for d in deps], ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1'])
+        self.assertEqual([d['external_module'] for d in deps], [False, True, True])
 
     def test_update(self):
         """Test use of update() method for EasyConfig instances."""
@@ -1052,6 +1082,7 @@ def test_update(self):
         ec.update('patches', ['foo.patch', 'bar.patch'])
         self.assertEqual(ec['patches'], ['toy-0.0_typo.patch', 'foo.patch', 'bar.patch'])
 
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(EasyConfigTest)
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index ec34fc1e23..ce14cda823 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -836,6 +836,51 @@ def test_toy_module_fulltxt(self):
         msg = "Pattern '%s' matches with: %s" % (mod_txt_regex.pattern, toy_mod_txt)
         self.assertTrue(mod_txt_regex.match(toy_mod_txt), msg)
 
+    def test_external_dependencies(self):
+        """Test specifying external (build) dependencies."""
+        ectxt = read_file(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0-deps.eb'))
+        toy_ec = os.path.join(self.test_prefix, 'toy-0.0-external-deps.eb')
+
+        # just specify some of the test modules we ship, doesn't matter where they come from
+        extraectxt = "\ndependencies += [('foobar/1.2.3', EXTERNAL_MODULE)]"
+        extraectxt += "\nbuilddependencies = [('somebuilddep/0.1', EXTERNAL_MODULE)]"
+        extraectxt += "\nversionsuffix = '-external-deps'"
+        write_file(toy_ec, ectxt + extraectxt)
+
+        # install dummy modules
+        modulepath = os.path.join(self.test_prefix, 'modules')
+        for mod in ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1']:
+            mkdir(os.path.join(modulepath, os.path.dirname(mod)), parents=True)
+            write_file(os.path.join(modulepath, mod), "#%Module")
+
+        self.reset_modulepath([modulepath])
+        self.test_toy_build(ec_file=toy_ec, versionsuffix='-external-deps', verbose=True)
+
+        modules_tool().load(['toy/0.0-external-deps'])
+        # note build dependency is not loaded
+        mods = ['ictce/4.1.13', 'foobar/1.2.3', 'toy/0.0-external-deps']
+        self.assertEqual([x['mod_name'] for x in modules_tool().list()], mods)
+
+        # check behaviour when a non-existing external (build) dependency is included
+        err_msg = "Missing modules for one or more dependencies marked as external modules:"
+
+        extraectxt = "\nbuilddependencies = [('nosuchbuilddep/0.0.0', EXTERNAL_MODULE)]"
+        extraectxt += "\nversionsuffix = '-external-deps-broken1'"
+        write_file(toy_ec, ectxt + extraectxt)
+        self.assertErrorRegex(EasyBuildError, err_msg, self.test_toy_build, ec_file=toy_ec,
+                              raise_error=True, verbose=False)
+
+        extraectxt = "\ndependencies += [('nosuchmodule/1.2.3', EXTERNAL_MODULE)]"
+        extraectxt += "\nversionsuffix = '-external-deps-broken2'"
+        write_file(toy_ec, ectxt + extraectxt)
+        self.assertErrorRegex(EasyBuildError, err_msg, self.test_toy_build, ec_file=toy_ec,
+                              raise_error=True, verbose=False)
+
+        # --dry-run still works when external modules are missing; external modules are treated as if they were there
+        outtxt = self.test_toy_build(ec_file=toy_ec, verbose=True, extra_args=['--dry-run'], verify=False)
+        self.assertTrue(re.search(r"^ \* \[ \] .* \(module: toy/0.0-external-deps-broken2\)", outtxt, re.M))
+
+
 def suite():
     """ return all the tests in this file """
     return TestLoader().loadTestsFromTestCase(ToyBuildTest)

From 897e0befbca6439f272af6694d69cb94e3ccb3e0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 15:14:30 +0200
Subject: [PATCH 0877/1356] broken KeyError issue

---
 easybuild/tools/robot.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/robot.py b/easybuild/tools/robot.py
index bb8cd15271..9b82878931 100644
--- a/easybuild/tools/robot.py
+++ b/easybuild/tools/robot.py
@@ -168,7 +168,7 @@ def resolve_dependencies(unprocessed, build_specs=None, retain_all_deps=False):
 
         # dependencies marked as external modules should be resolved via available modules at this point
         missing_external_modules = [d['full_mod_name'] for ec in unprocessed for d in ec['dependencies']
-                                    if d['external_module']]
+                                    if d.get('external_module', False)]
         if missing_external_modules:
             raise EasyBuildError("Missing modules for one or more dependencies marked as external modules: %s",
                                  missing_external_modules)

From 205e3cf1f10c4ef26d394c3a228dc264da4997a0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 15:48:45 +0200
Subject: [PATCH 0878/1356] fix remark and remaining KeyError issue

---
 easybuild/framework/easyconfig/tools.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 5405f5ed1c..9fd1bd3711 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -121,8 +121,9 @@ def find_resolved_modules(unprocessed, avail_modules, retain_all_deps=False):
                 dep_resolved |= dep['hidden'] and modtool.exist([full_mod_name])[0]
 
             if not dep_resolved:
-                # treat external modules as resolved when retain_all_deps is enabled (e.g., under --dry-run)
-                if retain_all_deps and dep['external_module']:
+                # treat external modules as resolved when retain_all_deps is enabled (e.g., under --dry-run),
+                # since no corresponding easyconfig can be found for them
+                if retain_all_deps and dep.get('external_module', False):
                     _log.debug("Treating dependency marked as external dependency as resolved: %s", dep)
                 else:
                     # no module available (yet) => retain dependency as one to be resolved

From 23ed6c58ee9d50fddec072481f129350a8d61b5e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 15:58:32 +0200
Subject: [PATCH 0879/1356] fix test cases w.r.t. flex aspect of --robot-paths

---
 test/framework/config.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/framework/config.py b/test/framework/config.py
index f039dddd0f..669ec96e4e 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -527,10 +527,10 @@ def test_flex_robot_paths(self):
         eb_go = eboptions.parse_options(args=[])
         self.assertEqual(eb_go.options.robot_paths, ['/foo', tmp_ecs_dir, '/bar/baz'])
 
-        # combining $EASYBUILD_ROBOT_PATHS and --robot-paths: all paths are retained in the order to be expected
+        # --robot-paths overrides $EASYBUILD_ROBOT_PATHS
         os.environ['EASYBUILD_ROBOT_PATHS'] = '/foobar::/barbar/baz/baz'
         eb_go = eboptions.parse_options(args=['--robot-paths=/one::/last'])
-        self.assertEqual(eb_go.options.robot_paths, ['/one', '/foobar', tmp_ecs_dir, '/barbar/baz/baz', '/last'])
+        self.assertEqual(eb_go.options.robot_paths, ['/one', tmp_ecs_dir, '/last'])
 
         del os.environ['EASYBUILD_ROBOT_PATHS']
 
@@ -555,7 +555,7 @@ def test_flex_robot_paths(self):
 
         os.environ['EASYBUILD_ROBOT_PATHS'] = ':/envend'
         eb_go = eboptions.parse_options(args=['--robot-paths=/veryfirst:', '--configfiles=%s' % config_file])
-        self.assertEqual(eb_go.options.robot_paths, ['/veryfirst', tmp_ecs_dir, '/envend'])
+        self.assertEqual(eb_go.options.robot_paths, ['/veryfirst', tmp_ecs_dir])
 
         del os.environ['EASYBUILD_ROBOT_PATHS']
 
@@ -563,7 +563,7 @@ def test_flex_robot_paths(self):
         eb_go = eboptions.parse_options(args=['--robot-paths=/foo:/bar/baz'])
         self.assertEqual(eb_go.options.robot_paths, ['/foo', '/bar/baz'])
 
-        # --robot paths still get preference
+        # paths specified via --robot still get preference
         eb_go = eboptions.parse_options(args=['--robot-paths=/foo/bar::/baz', '--robot=/first'])
         self.assertEqual(eb_go.options.robot_paths, ['/first', '/foo/bar', tmp_ecs_dir, '/baz'])
 

From 59f36bfd00de1d2a82a350b8e917726961131f54 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 15:58:48 +0200
Subject: [PATCH 0880/1356] fix indendation issue in options unit test module

---
 test/framework/options.py | 220 +++++++++++++++++++-------------------
 1 file changed, 110 insertions(+), 110 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index f4ca215a0f..38028a2a4a 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1524,129 +1524,129 @@ def test_robot(self):
             ec_regex = re.compile(r'^\s\*\s\[[xF ]\]\s%s' % os.path.join(test_ecs_path, ecfile), re.M)
             self.assertTrue(ec_regex.search(outtxt), "Pattern %s found in %s" % (ec_regex.pattern, outtxt))
 
-        def test_missing_cfgfile(self):
-            """Test behaviour when non-existing config file is specified."""
-            args = ['--configfiles=/no/such/cfgfile.foo']
-            error_regex = "parseconfigfiles: configfile .* not found"
-            self.assertErrorRegex(EasyBuildError, error_regex, self.eb_main, args, raise_error=True)
-
-        def test_show_default_moduleclasses(self):
-            """Test --show-default-moduleclasses."""
-            fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
-            os.close(fd)
+    def test_missing_cfgfile(self):
+        """Test behaviour when non-existing config file is specified."""
+        args = ['--configfiles=/no/such/cfgfile.foo']
+        error_regex = "parseconfigfiles: configfile .* not found"
+        self.assertErrorRegex(EasyBuildError, error_regex, self.eb_main, args, raise_error=True)
+
+    def test_show_default_moduleclasses(self):
+        """Test --show-default-moduleclasses."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
 
-            args = [
-                '--unittest-file=%s' % self.logfile,
-                '--show-default-moduleclasses',
-            ]
-            write_file(self.logfile, '')
-            self.eb_main(args, logfile=dummylogfn, verbose=True)
-            logtxt = read_file(self.logfile)
+        args = [
+            '--unittest-file=%s' % self.logfile,
+            '--show-default-moduleclasses',
+        ]
+        write_file(self.logfile, '')
+        self.eb_main(args, logfile=dummylogfn, verbose=True)
+        logtxt = read_file(self.logfile)
 
-            lst = ["\t%s:[ ]*%s" % (c, d.replace('(', '\\(').replace(')', '\\)')) for (c, d) in DEFAULT_MODULECLASSES]
-            regex = re.compile("Default available module classes:\n\n" + '\n'.join(lst), re.M)
+        lst = ["\t%s:[ ]*%s" % (c, d.replace('(', '\\(').replace(')', '\\)')) for (c, d) in DEFAULT_MODULECLASSES]
+        regex = re.compile("Default available module classes:\n\n" + '\n'.join(lst), re.M)
 
-            self.assertTrue(regex.search(logtxt), "Pattern '%s' found in %s" % (regex.pattern, logtxt))
+        self.assertTrue(regex.search(logtxt), "Pattern '%s' found in %s" % (regex.pattern, logtxt))
 
-        def test_show_default_configfiles(self):
-            """Test --show-default-configfiles."""
-            fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
-            os.close(fd)
+    def test_show_default_configfiles(self):
+        """Test --show-default-configfiles."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
 
-            home = os.environ['HOME']
-            for envvar in ['XDG_CONFIG_DIRS', 'XDG_CONFIG_HOME']:
-                if envvar in os.environ:
-                    del os.environ[envvar]
-            reload(easybuild.tools.options)
+        home = os.environ['HOME']
+        for envvar in ['XDG_CONFIG_DIRS', 'XDG_CONFIG_HOME']:
+            if envvar in os.environ:
+                del os.environ[envvar]
+        reload(easybuild.tools.options)
 
-            args = [
-                '--unittest-file=%s' % self.logfile,
-                '--show-default-configfiles',
-            ]
+        args = [
+            '--unittest-file=%s' % self.logfile,
+            '--show-default-configfiles',
+        ]
 
-            cfgtxt = '\n'.join([
-                '[config]',
-                'prefix = %s' % self.test_prefix,
-            ])
+        cfgtxt = '\n'.join([
+            '[config]',
+            'prefix = %s' % self.test_prefix,
+        ])
 
-            expected_tmpl = '\n'.join([
-                "Default list of configuration files:",
-                '',
-                "[with $XDG_CONFIG_HOME: %s, $XDG_CONFIG_DIRS: %s]",
-                '',
-                "* user-level: ${XDG_CONFIG_HOME:-$HOME/.config}/easybuild/config.cfg",
-                "  -> %s",
-                "* system-level: ${XDG_CONFIG_DIRS:-/etc}/easybuild.d/*.cfg",
-                "  -> %s/easybuild.d/*.cfg => ",
-            ])
+        expected_tmpl = '\n'.join([
+            "Default list of configuration files:",
+            '',
+            "[with $XDG_CONFIG_HOME: %s, $XDG_CONFIG_DIRS: %s]",
+            '',
+            "* user-level: ${XDG_CONFIG_HOME:-$HOME/.config}/easybuild/config.cfg",
+            "  -> %s",
+            "* system-level: ${XDG_CONFIG_DIRS:-/etc}/easybuild.d/*.cfg",
+            "  -> %s/easybuild.d/*.cfg => ",
+        ])
 
-            write_file(self.logfile, '')
-            self.eb_main(args, logfile=dummylogfn, verbose=True)
-            logtxt = read_file(self.logfile)
+        write_file(self.logfile, '')
+        self.eb_main(args, logfile=dummylogfn, verbose=True)
+        logtxt = read_file(self.logfile)
 
-            homecfgfile = os.path.join(os.environ['HOME'], '.config', 'easybuild', 'config.cfg')
-            homecfgfile_str = homecfgfile
-            if os.path.exists(homecfgfile):
-                homecfgfile_str += " => found"
-            else:
-                homecfgfile_str += " => not found"
-            expected = expected_tmpl % ('(not set)', '(not set)', homecfgfile_str, '{/etc}')
-            self.assertTrue(expected in logtxt)
-
-            # to predict the full output, we need to take control over $HOME and $XDG_CONFIG_DIRS
-            os.environ['HOME'] = self.test_prefix
-            xdg_config_dirs = os.path.join(self.test_prefix, 'etc')
-            os.environ['XDG_CONFIG_DIRS'] = xdg_config_dirs
-
-            expected_tmpl += '\n'.join([
-                "%s",
-                '',
-                "Default list of existing configuration files (%d): %s",
-            ])
+        homecfgfile = os.path.join(os.environ['HOME'], '.config', 'easybuild', 'config.cfg')
+        homecfgfile_str = homecfgfile
+        if os.path.exists(homecfgfile):
+            homecfgfile_str += " => found"
+        else:
+            homecfgfile_str += " => not found"
+        expected = expected_tmpl % ('(not set)', '(not set)', homecfgfile_str, '{/etc}')
+        self.assertTrue(expected in logtxt)
+
+        # to predict the full output, we need to take control over $HOME and $XDG_CONFIG_DIRS
+        os.environ['HOME'] = self.test_prefix
+        xdg_config_dirs = os.path.join(self.test_prefix, 'etc')
+        os.environ['XDG_CONFIG_DIRS'] = xdg_config_dirs
+
+        expected_tmpl += '\n'.join([
+            "%s",
+            '',
+            "Default list of existing configuration files (%d): %s",
+        ])
 
-            # put dummy cfgfile in place in $HOME (to predict last line of output which only lists *existing* files)
-            mkdir(os.path.join(self.test_prefix, '.config', 'easybuild'), parents=True)
-            homecfgfile = os.path.join(self.test_prefix, '.config', 'easybuild', 'config.cfg')
-            write_file(homecfgfile, cfgtxt)
+        # put dummy cfgfile in place in $HOME (to predict last line of output which only lists *existing* files)
+        mkdir(os.path.join(self.test_prefix, '.config', 'easybuild'), parents=True)
+        homecfgfile = os.path.join(self.test_prefix, '.config', 'easybuild', 'config.cfg')
+        write_file(homecfgfile, cfgtxt)
 
-            reload(easybuild.tools.options)
-            write_file(self.logfile, '')
-            self.eb_main(args, logfile=dummylogfn, verbose=True)
-            logtxt = read_file(self.logfile)
-            expected = expected_tmpl % ('(not set)', xdg_config_dirs, "%s => found" % homecfgfile, '{%s}' % xdg_config_dirs,
-                                        '(no matches)', 1, homecfgfile)
-            self.assertTrue(expected in logtxt)
-
-            xdg_config_home = os.path.join(self.test_prefix, 'home')
-            os.environ['XDG_CONFIG_HOME'] = xdg_config_home
-            xdg_config_dirs = [os.path.join(self.test_prefix, 'etc'), os.path.join(self.test_prefix, 'moaretc')]
-            os.environ['XDG_CONFIG_DIRS'] = os.pathsep.join(xdg_config_dirs)
-
-            # put various dummy cfgfiles in place
-            cfgfiles = [
-                os.path.join(self.test_prefix, 'etc', 'easybuild.d', 'config.cfg'),
-                os.path.join(self.test_prefix, 'moaretc', 'easybuild.d', 'bar.cfg'),
-                os.path.join(self.test_prefix, 'moaretc', 'easybuild.d', 'foo.cfg'),
-                os.path.join(xdg_config_home, 'easybuild', 'config.cfg'),
-            ]
-            for cfgfile in cfgfiles:
-                mkdir(os.path.dirname(cfgfile), parents=True)
-                write_file(cfgfile, cfgtxt)
-            reload(easybuild.tools.options)
+        reload(easybuild.tools.options)
+        write_file(self.logfile, '')
+        self.eb_main(args, logfile=dummylogfn, verbose=True)
+        logtxt = read_file(self.logfile)
+        expected = expected_tmpl % ('(not set)', xdg_config_dirs, "%s => found" % homecfgfile, '{%s}' % xdg_config_dirs,
+                                    '(no matches)', 1, homecfgfile)
+        self.assertTrue(expected in logtxt)
+
+        xdg_config_home = os.path.join(self.test_prefix, 'home')
+        os.environ['XDG_CONFIG_HOME'] = xdg_config_home
+        xdg_config_dirs = [os.path.join(self.test_prefix, 'etc'), os.path.join(self.test_prefix, 'moaretc')]
+        os.environ['XDG_CONFIG_DIRS'] = os.pathsep.join(xdg_config_dirs)
+
+        # put various dummy cfgfiles in place
+        cfgfiles = [
+            os.path.join(self.test_prefix, 'etc', 'easybuild.d', 'config.cfg'),
+            os.path.join(self.test_prefix, 'moaretc', 'easybuild.d', 'bar.cfg'),
+            os.path.join(self.test_prefix, 'moaretc', 'easybuild.d', 'foo.cfg'),
+            os.path.join(xdg_config_home, 'easybuild', 'config.cfg'),
+        ]
+        for cfgfile in cfgfiles:
+            mkdir(os.path.dirname(cfgfile), parents=True)
+            write_file(cfgfile, cfgtxt)
+        reload(easybuild.tools.options)
 
-            write_file(self.logfile, '')
-            self.eb_main(args, logfile=dummylogfn, verbose=True)
-            logtxt = read_file(self.logfile)
-            expected = expected_tmpl % (xdg_config_home, os.pathsep.join(xdg_config_dirs),
-                                        "%s => found" % os.path.join(xdg_config_home, 'easybuild', 'config.cfg'),
-                                        '{' + ', '.join(xdg_config_dirs) + '}',
-                                        ', '.join(cfgfiles[:-1]), 4, ', '.join(cfgfiles))
-            self.assertTrue(expected in logtxt)
-
-            del os.environ['XDG_CONFIG_DIRS']
-            del os.environ['XDG_CONFIG_HOME']
-            os.environ['HOME'] = home
-            reload(easybuild.tools.options)
+        write_file(self.logfile, '')
+        self.eb_main(args, logfile=dummylogfn, verbose=True)
+        logtxt = read_file(self.logfile)
+        expected = expected_tmpl % (xdg_config_home, os.pathsep.join(xdg_config_dirs),
+                                    "%s => found" % os.path.join(xdg_config_home, 'easybuild', 'config.cfg'),
+                                    '{' + ', '.join(xdg_config_dirs) + '}',
+                                    ', '.join(cfgfiles[:-1]), 4, ', '.join(cfgfiles))
+        self.assertTrue(expected in logtxt)
+
+        del os.environ['XDG_CONFIG_DIRS']
+        del os.environ['XDG_CONFIG_HOME']
+        os.environ['HOME'] = home
+        reload(easybuild.tools.options)
 
 
 def suite():

From 3586bbc3f66839e35cb9b1ea60473e0d22db6deb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 16:37:09 +0200
Subject: [PATCH 0881/1356] fix dep_graph w.r.t. external modules

---
 easybuild/framework/easyconfig/easyconfig.py |  4 +---
 easybuild/framework/easyconfig/tools.py      | 15 +++++++++++----
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index cf1c756d10..bd161ab708 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -539,8 +539,6 @@ def _parse_dependency(self, dep, hidden=False):
         # convert tuple to string otherwise python might complain about the formatting
         self.log.debug("Parsing %s as a dependency" % str(dep))
 
-        dummy_toolchain = {'name': DUMMY_TOOLCHAIN_NAME, 'version': DUMMY_TOOLCHAIN_VERSION}
-
         attr = ['name', 'version', 'versionsuffix', 'toolchain']
         dependency = {
             'dummy': False,
@@ -598,7 +596,7 @@ def _parse_dependency(self, dep, hidden=False):
         if tc_spec is not None:
             # (true) boolean value simply indicates that a dummy toolchain is used
             if isinstance(tc_spec, bool) and tc_spec:
-                tc = dummy_toolchain
+                tc = {'name': DUMMY_TOOLCHAIN_NAME, 'version': DUMMY_TOOLCHAIN_VERSION}
             # two-element list/tuple value indicates custom toolchain specification
             elif isinstance(tc_spec, (list, tuple,)):
                 if len(tc_spec) == 2:
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 9fd1bd3711..ed7b118571 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -155,19 +155,26 @@ def _dep_graph(fn, specs, silent=False):
     omit_versions = len(names) == len(specs)
 
     def mk_node_name(spec):
-        if omit_versions:
-            return spec['name']
+        if spec.get('external_module', False):
+            node_name = "%s (EXT)" % spec['full_mod_name']
+        elif omit_versions:
+            node_name = spec['name']
         else:
-            return ActiveMNS().det_full_module_name(spec)
+            node_name = ActiveMNS().det_full_module_name(spec)
+
+        return node_name
 
     # enhance list of specs
+    all_nodes = set()
     for spec in specs:
         spec['module'] = mk_node_name(spec['ec'])
+        all_nodes.add(spec['module'])
         spec['unresolved_deps'] = [mk_node_name(s) for s in spec['unresolved_deps']]
+        all_nodes.update(spec['unresolved_deps'])
 
     # build directed graph
     dgr = digraph()
-    dgr.add_nodes([spec['module'] for spec in specs])
+    dgr.add_nodes(all_nodes)
     for spec in specs:
         for dep in spec['unresolved_deps']:
             dgr.add_edge((spec['module'], dep))

From 066c8aed69a1f47fcb794916289cacac97f0f4d0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 21:10:58 +0200
Subject: [PATCH 0882/1356] fix dealing with empty variables in Variables.join
 method

---
 easybuild/tools/variables.py |  4 ++++
 test/framework/variables.py  | 10 ++++++++++
 2 files changed, 14 insertions(+)

diff --git a/easybuild/tools/variables.py b/easybuild/tools/variables.py
index 6d5941c473..a480f58eb3 100644
--- a/easybuild/tools/variables.py
+++ b/easybuild/tools/variables.py
@@ -481,6 +481,10 @@ def join(self, name, *others):
                 else it is nappend-ed
         """
         self.log.debug("join name %s others %s" % (name, others))
+
+        # make sure name is defined, even if 'others' list is empty
+        self[name] = []
+
         for other in others:
             if other in self:
                 self.log.debug("join other %s in self: other %s" % (other, self.get(other).__repr__()))
diff --git a/test/framework/variables.py b/test/framework/variables.py
index 9f92769275..c377b507b6 100644
--- a/test/framework/variables.py
+++ b/test/framework/variables.py
@@ -78,6 +78,16 @@ class TestVariables(Variables):
         cmd = CommandFlagList(["gcc", "bar", "baz"])
         self.assertEqual(str(cmd), "gcc -bar -baz")
 
+    def test_empty_variables(self):
+        """Test playing around with empty variables."""
+        v = Variables()
+        v.nappend('FOO', [])
+        self.assertEqual(v['FOO'], [])
+        v.join('BAR', 'FOO')
+        self.assertEqual(v['BAR'], [])
+        v.join('FOOBAR', 'BAR')
+        self.assertEqual(v['FOOBAR'], [])
+
 def suite():
     """ return all the tests"""
     return TestLoader().loadTestsFromTestCase(VariablesTest)

From 69f6f9104a9fddd86fbcc53cbbe53f1d9ef62382 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 20:10:14 +0200
Subject: [PATCH 0883/1356] drop 'wrapper' lingo

---
 .../compiler/{craypewrappers.py => craype.py} | 36 +++++++++----------
 easybuild/toolchains/craycce.py               |  4 +--
 easybuild/toolchains/craygnu.py               |  4 +--
 easybuild/toolchains/crayintel.py             |  4 +--
 4 files changed, 23 insertions(+), 25 deletions(-)
 rename easybuild/toolchains/compiler/{craypewrappers.py => craype.py} (91%)

diff --git a/easybuild/toolchains/compiler/craypewrappers.py b/easybuild/toolchains/compiler/craype.py
similarity index 91%
rename from easybuild/toolchains/compiler/craypewrappers.py
rename to easybuild/toolchains/compiler/craype.py
index 7ce3079842..25dc10b68f 100644
--- a/easybuild/toolchains/compiler/craypewrappers.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -23,19 +23,17 @@
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
 """
-Support for the Cray Programming Environment Wrappers (aka cc, CC, ftn).
-The Cray compiler wrappers are actually way more than just a compiler drivers.
+Support for the Cray Programming Environment (craype) compiler drivers (aka cc, CC, ftn).
 
 The basic concept is that the compiler driver knows how to invoke the true underlying
 compiler with the compiler's specific options tuned to Cray systems.
 
 That means that certain defaults are set that are specific to Cray's computers.
 
-The compiler wrappers are quite similar to EB toolchains as they include
+The compiler drivers are quite similar to EB toolchains as they include
 linker and compiler directives to use the Cray libraries for their MPI (and network drivers)
 Cray's LibSci (BLAS/LAPACK et al), FFT library, etc.
 
-
 @author: Petar Forai (IMP/IMBA, Austria)
 @author: Kenneth Hoste (Ghent University)
 """
@@ -53,16 +51,16 @@
 from easybuild.tools.toolchain.mpi import Mpi
 
 
-TC_CONSTANT_CRAYPEWRAPPER = "CRAYPEWRAPPER"
+TC_CONSTANT_CRAYPE = "CRAYPE"
 
 
-class CrayPEWrapper(Compiler, Mpi, LinAlg, Fftw):
+class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     """Generic support for using Cray compiler wrappers"""
 
     # no toolchain components, so no modules to list here (empty toolchain definition w.r.t. components)
     # the PrgEnv and craype are loaded, but are not considered actual toolchain components
     COMPILER_MODULE_NAME = []
-    COMPILER_FAMILY = TC_CONSTANT_CRAYPEWRAPPER
+    COMPILER_FAMILY = TC_CONSTANT_CRAYPE
 
     COMPILER_UNIQUE_OPTS = {
         # FIXME: (kehoste) how is this different from the existing 'shared' toolchain option? just map 'shared' to '-dynamic'? (already done)
@@ -104,7 +102,7 @@ class CrayPEWrapper(Compiler, Mpi, LinAlg, Fftw):
     # MPI support
     # no separate module, Cray compiler drivers always provide MPI support
     MPI_MODULE_NAME = []
-    MPI_FAMILY = TC_CONSTANT_CRAYPEWRAPPER
+    MPI_FAMILY = TC_CONSTANT_CRAYPE
     MPI_TYPE = TC_CONSTANT_MPI_TYPE_MPICH
 
     MPI_COMPILER_MPICC = COMPILER_CC
@@ -168,7 +166,7 @@ def _set_optimal_architecture(self):
     def _set_compiler_flags(self):
         """Set compiler flags."""
         self.COMPILER_FLAGS.extend(['dynamic'])
-        super(CrayPEWrapper, self)._set_compiler_flags()
+        super(CrayPE, self)._set_compiler_flags()
 
     def _set_mpi_compiler_variables(self):
         """Set the MPI compiler variables"""
@@ -212,7 +210,7 @@ def _get_software_root(self, name):
                 root = os.path.dirname(incdir)
                 self.log.debug("Obtained install prefix for %s via $%s: %s", name, env_var, root)
         else:
-            root = super(CrayPEWrapper, self)._get_software_root(name)
+            root = super(CrayPE, self)._get_software_root(name)
 
         return root
 
@@ -227,7 +225,7 @@ def _get_software_version(self, name):
             else:
                 self.log.debug("Obtained version for %s via $%s: %s", name, env_var, ver)
         else:
-            ver = super(CrayPEWrapper, self)._get_software_version(name)
+            ver = super(CrayPE, self)._get_software_version(name)
 
         return ver
 
@@ -245,9 +243,9 @@ def definition(self):
 
 
 # Gcc's base is Compiler
-class CrayPEWrapperGNU(CrayPEWrapper):
+class CrayPEGNU(CrayPE):
     """Support for using the Cray GNU compiler wrappers."""
-    TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_GNU'
+    TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_GNU'
 
     # FIXME: make this empty list?
     BLAS_LIB = ['sci_gnu_mpi']
@@ -265,12 +263,12 @@ def _set_compiler_vars(self):
             for attr_name in ['COMPILER_%s' % a for a in comp_attrs]:
                 setattr(self, attr_name, getattr(Gcc, attr_name))
 
-        super(CrayPEWrapperGNU,self)._set_compiler_vars()
+        super(CrayPEGNU,self)._set_compiler_vars()
 
 
-class CrayPEWrapperIntel(CrayPEWrapper):
+class CrayPEIntel(CrayPE):
     """Support for using the Cray Intel compiler wrappers."""
-    TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_INTEL'
+    TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_INTEL'
 
     # FIXME: make this empty list?
     BLAS_LIB = ['sci_intel_mpi']
@@ -288,12 +286,12 @@ def _set_compiler_flags(self):
             for attr_name in ['COMPILER_%s' % a for a in comp_attrs] + ['LINKER_TOGGLE_STATIC_DYNAMIC']:
                 setattr(self, attr_name, getattr(IntelIccIfort, attr_name))
 
-        super(CrayPEWrapperIntel, self).set_compiler_flags()
+        super(CrayPEIntel, self).set_compiler_flags()
 
 
-class CrayPEWrapperCray(CrayPEWrapper):
+class CrayPECray(CrayPE):
     """Support for using the Cray CCE compiler wrappers."""
-    TC_CONSTANT_CRAYPEWRAPPER = TC_CONSTANT_CRAYPEWRAPPER + '_CRAY'
+    TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_CRAY'
 
     # FIXME: make this empty list?
     BLAS_LIB = ['sci_cray_mpi']
diff --git a/easybuild/toolchains/craycce.py b/easybuild/toolchains/craycce.py
index 612d28c58e..18c799c7ae 100644
--- a/easybuild/toolchains/craycce.py
+++ b/easybuild/toolchains/craycce.py
@@ -27,8 +27,8 @@
 """
 
 
-from easybuild.toolchains.compiler.craypewrappers import CrayPEWrapperCray
+from easybuild.toolchains.compiler.craype import CrayPECray
 
-class CrayCCE(CrayPEWrapperCray):
+class CrayCCE(CrayPECray):
     """Compiler toolchain for Cray Programming Environment for Cray Compiling Environment (CCE) (PrgEnv-cray)."""
     NAME = 'CrayCCE'
diff --git a/easybuild/toolchains/craygnu.py b/easybuild/toolchains/craygnu.py
index eb8cdeed41..2386dcaa0e 100644
--- a/easybuild/toolchains/craygnu.py
+++ b/easybuild/toolchains/craygnu.py
@@ -27,8 +27,8 @@
 """
 
 
-from easybuild.toolchains.compiler.craypewrappers import CrayPEWrapperGNU
+from easybuild.toolchains.compiler.craype import CrayPEGNU
 
-class CrayGNU(CrayPEWrapperGNU):
+class CrayGNU(CrayPEGNU):
     """Compiler toolchain for Cray Programming Environment for GCC compilers (PrgEnv-gnu)."""
     NAME = 'CrayGNU'
diff --git a/easybuild/toolchains/crayintel.py b/easybuild/toolchains/crayintel.py
index 8d546bf1c4..b2049902a3 100644
--- a/easybuild/toolchains/crayintel.py
+++ b/easybuild/toolchains/crayintel.py
@@ -27,8 +27,8 @@
 """
 
 
-from easybuild.toolchains.compiler.craypewrappers import CrayPEWrapperIntel
+from easybuild.toolchains.compiler.craype import CrayPEIntel
 
-class CrayIntel(CrayPEWrapperIntel):
+class CrayIntel(CrayPEIntel):
     """Compiler toolchain for Cray Programming Environment for Intel compilers (PrgEnv-intel)."""
     NAME = 'CrayIntel'

From 96aac6f0ad2407b2851b6d32207e65cbd5928ca7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 21:17:11 +0200
Subject: [PATCH 0884/1356] use empty BLAS_LIB/BLAS_LIB_MT lists (required
 #1263)

---
 easybuild/toolchains/compiler/craype.py | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 25dc10b68f..48b7d4f2b8 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -122,9 +122,8 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     # see https://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/
     BLAS_MODULE_NAME = ['cray-libsci']
     # specific library depends on PrgEnv flavor
-    # FIXME: make this (always) empty list?
-    BLAS_LIB = None
-    BLAS_LIB_MT = None
+    BLAS_LIB = []
+    BLAS_LIB_MT = []
 
     LAPACK_MODULE_NAME = ['cray-libsci']
     LAPACK_IS_BLAS = True
@@ -242,15 +241,10 @@ def definition(self):
         return {}
 
 
-# Gcc's base is Compiler
 class CrayPEGNU(CrayPE):
     """Support for using the Cray GNU compiler wrappers."""
     TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_GNU'
 
-    # FIXME: make this empty list?
-    BLAS_LIB = ['sci_gnu_mpi']
-    BLAS_LIB_MT = ['sci_gnu_mpi_mp']
-
     PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
 
     def _set_compiler_vars(self):
@@ -270,10 +264,6 @@ class CrayPEIntel(CrayPE):
     """Support for using the Cray Intel compiler wrappers."""
     TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_INTEL'
 
-    # FIXME: make this empty list?
-    BLAS_LIB = ['sci_intel_mpi']
-    BLAS_LIB_MT = ['sci_intel_mpi_mp']
-
     PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
 
     def _set_compiler_flags(self):
@@ -293,8 +283,4 @@ class CrayPECray(CrayPE):
     """Support for using the Cray CCE compiler wrappers."""
     TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_CRAY'
 
-    # FIXME: make this empty list?
-    BLAS_LIB = ['sci_cray_mpi']
-    BLAS_LIB_MT = ['sci_cray_mpi_mp']
-
     PRGENV_MODULE_NAME_SUFFIX = 'cray'  # PrgEnv-cray

From 278e3faf73a8ee29756da307681bc1de6d4aa4db Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Apr 2015 21:35:13 +0200
Subject: [PATCH 0885/1356] use setdefault

---
 easybuild/tools/variables.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/variables.py b/easybuild/tools/variables.py
index a480f58eb3..a6ec60c62f 100644
--- a/easybuild/tools/variables.py
+++ b/easybuild/tools/variables.py
@@ -483,7 +483,7 @@ def join(self, name, *others):
         self.log.debug("join name %s others %s" % (name, others))
 
         # make sure name is defined, even if 'others' list is empty
-        self[name] = []
+        self.setdefault(name)
 
         for other in others:
             if other in self:

From 00f374c70d428970d499a78811b6c466d0e625da Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 22 Apr 2015 14:16:37 +0200
Subject: [PATCH 0886/1356] avoid issue with _set_compiler_flags super call wrt
 multiple inheritance (-dynamic appearing multiple times in $CFLAGS)

---
 easybuild/toolchains/compiler/craype.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 48b7d4f2b8..70e5a85de6 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -142,6 +142,12 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     # template for craype module (determines code generator backend of Cray compiler wrappers)
     CRAYPE_MODULE_NAME_TEMPLATE = 'craype-%(optarch)s'
 
+    def __init__(self, *args, **kwargs):
+        """Constructor."""
+        super(CrayPE, self).__init__(*args, **kwargs)
+        # 'register'  additional toolchain options that correspond to a compiler flag
+        self.COMPILER_FLAGS.extend(['dynamic'])
+
     def _pre_prepare(self):
         """Load PrgEnv module."""
         prgenv_mod_name = self.PRGENV_MODULE_NAME_TEMPLATE % {
@@ -162,11 +168,6 @@ def _set_optimal_architecture(self):
         # no compiler flag when optarch toolchain option is enabled
         self.options.options_map['optarch'] = ''
 
-    def _set_compiler_flags(self):
-        """Set compiler flags."""
-        self.COMPILER_FLAGS.extend(['dynamic'])
-        super(CrayPE, self)._set_compiler_flags()
-
     def _set_mpi_compiler_variables(self):
         """Set the MPI compiler variables"""
         for var_tuple in COMPILER_VARIABLES:

From f6471ac069c544ac0acbca323e111a6f67c6bf94 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 22 Apr 2015 14:26:23 +0200
Subject: [PATCH 0887/1356] use PrgEnv as compiler module name, don't redefine
 toolchain definition as being empty

---
 easybuild/toolchains/compiler/craype.py | 17 +++--------------
 1 file changed, 3 insertions(+), 14 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 70e5a85de6..62e270993e 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -134,9 +134,8 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     # FFT support, via Cray-provided fftw module
     FFT_MODULE_NAME = ['fftw']
 
-    # template and name suffix for PrgEnv module that matches this toolchain
+    # suffix for PrgEnv module that matches this toolchain
     # e.g. 'gnu' => 'PrgEnv-gnu/<version>'
-    PRGENV_MODULE_NAME_TEMPLATE = 'PrgEnv-%(suffix)s/%(version)s'
     PRGENV_MODULE_NAME_SUFFIX = None
 
     # template for craype module (determines code generator backend of Cray compiler wrappers)
@@ -148,14 +147,8 @@ def __init__(self, *args, **kwargs):
         # 'register'  additional toolchain options that correspond to a compiler flag
         self.COMPILER_FLAGS.extend(['dynamic'])
 
-    def _pre_prepare(self):
-        """Load PrgEnv module."""
-        prgenv_mod_name = self.PRGENV_MODULE_NAME_TEMPLATE % {
-            'suffix': self.PRGENV_MODULE_NAME_SUFFIX,
-            'version': self.version,
-        }
-        self.log.info("Loading PrgEnv module '%s' for Cray toolchain %s" % (prgenv_mod_name, self.mod_short_name))
-        self.modules_tool.load([prgenv_mod_name])
+        # use name of PrgEnv module as name of module that provides compiler
+        self.COMPILER_MODULE_NAME = ['PrgEnv-%s' % self.PRGENV_MODULE_NAME_SUFFIX]
 
     def _set_optimal_architecture(self):
         """Load craype module specified via 'optarch' build option."""
@@ -237,10 +230,6 @@ def _set_scalapack_variables(self):
         """Skip setting ScaLAPACK related variables"""
         pass
 
-    def definition(self):
-        """Empty toolchain definition (no modules listed as toolchain dependencies)."""
-        return {}
-
 
 class CrayPEGNU(CrayPE):
     """Support for using the Cray GNU compiler wrappers."""

From fe9d9e6fff4dad782cc098d66febc936dd046a44 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 22 Apr 2015 16:47:54 +0200
Subject: [PATCH 0888/1356] set correct compiler/MPI family for Cray toolchains

---
 easybuild/toolchains/compiler/craype.py | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 62e270993e..df814386fd 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -39,10 +39,10 @@
 """
 import os
 
-from easybuild.toolchains.compiler.gcc import Gcc
-from easybuild.toolchains.compiler.inteliccifort import IntelIccIfort
+from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC, Gcc
+from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP, IntelIccIfort
 from easybuild.toolchains.fft.fftw import Fftw
-from easybuild.toolchains.mpi.mpich import TC_CONSTANT_MPI_TYPE_MPICH
+from easybuild.toolchains.mpi.mpich import TC_CONSTANT_MPICH, TC_CONSTANT_MPI_TYPE_MPICH
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.toolchain.compiler import Compiler
@@ -51,16 +51,17 @@
 from easybuild.tools.toolchain.mpi import Mpi
 
 
-TC_CONSTANT_CRAYPE = "CRAYPE"
+TC_CONSTANT_CRAYPE = "CrayPE"
+TC_CONSTANT_CRAYCE = "CrayCE"
 
 
 class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     """Generic support for using Cray compiler wrappers"""
 
-    # no toolchain components, so no modules to list here (empty toolchain definition w.r.t. components)
-    # the PrgEnv and craype are loaded, but are not considered actual toolchain components
-    COMPILER_MODULE_NAME = []
-    COMPILER_FAMILY = TC_CONSTANT_CRAYPE
+    # compiler module name is PrgEnv, suffix name depends on CrayPE flavor (gnu, intel, cray)
+    COMPILER_MODULE_NAME = None
+    # compiler family depends on CrayPE flavor
+    COMPILER_FAMILY = None
 
     COMPILER_UNIQUE_OPTS = {
         # FIXME: (kehoste) how is this different from the existing 'shared' toolchain option? just map 'shared' to '-dynamic'? (already done)
@@ -102,7 +103,7 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     # MPI support
     # no separate module, Cray compiler drivers always provide MPI support
     MPI_MODULE_NAME = []
-    MPI_FAMILY = TC_CONSTANT_CRAYPE
+    MPI_FAMILY = TC_CONSTANT_MPICH
     MPI_TYPE = TC_CONSTANT_MPI_TYPE_MPICH
 
     MPI_COMPILER_MPICC = COMPILER_CC
@@ -236,6 +237,7 @@ class CrayPEGNU(CrayPE):
     TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_GNU'
 
     PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
+    COMPILER_FAMILY = TC_CONSTANT_GCC
 
     def _set_compiler_vars(self):
         """Set compiler variables, either for the compiler wrapper, or the underlying compiler."""
@@ -255,6 +257,7 @@ class CrayPEIntel(CrayPE):
     TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_INTEL'
 
     PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
+    COMPILER_FAMILY = TC_CONSTANT_INTELCOMP
 
     def _set_compiler_flags(self):
         """Set compiler variables, either for the compiler wrapper, or the underlying compiler."""
@@ -274,3 +277,4 @@ class CrayPECray(CrayPE):
     TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_CRAY'
 
     PRGENV_MODULE_NAME_SUFFIX = 'cray'  # PrgEnv-cray
+    COMPILER_FAMILY = TC_CONSTANT_CRAYCE

From ab980dbc5550842310e862f0d3ccf62af506eb90 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 09:29:15 +0200
Subject: [PATCH 0889/1356] get rid of $PROFILEREAD hack when running commands,
 not needed anymore

---
 easybuild/tools/run.py | 24 ------------------------
 test/framework/run.py  | 24 ------------------------
 2 files changed, 48 deletions(-)

diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index 56544bdeff..651042651e 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -60,29 +60,6 @@
 strictness = WARN
 
 
-def adjust_cmd(func):
-    """Make adjustments to given command, if required."""
-
-    def inner(cmd, *args, **kwargs):
-        # SuSE hack
-        # - profile is not resourced, and functions (e.g. module) is not inherited
-        if 'PROFILEREAD' in os.environ and (len(os.environ['PROFILEREAD']) > 0):
-            filepaths = ['/etc/profile.d/modules.sh']
-            extra = ''
-            for fp in filepaths:
-                if os.path.exists(fp):
-                    extra = ". %s &&%s" % (fp, extra)
-                else:
-                    _log.warning("Can't find file %s" % fp)
-
-            cmd = "%s %s" % (extra, cmd)
-
-        return func(cmd, *args, **kwargs)
-
-    return inner
-
-
-@adjust_cmd
 def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True, log_output=False, path=None):
     """
     Executes a command cmd
@@ -153,7 +130,6 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
     return parse_cmd_output(cmd, stdouterr, ec, simple, log_all, log_ok, regexp)
 
 
-@adjust_cmd
 def run_cmd_qa(cmd, qa, no_qa=None, log_ok=True, log_all=False, simple=False, regexp=True, std_qa=None, path=None):
     """
     Executes a command cmd
diff --git a/test/framework/run.py b/test/framework/run.py
index 48b33efcdd..4d46392ddf 100644
--- a/test/framework/run.py
+++ b/test/framework/run.py
@@ -95,30 +95,6 @@ def test_parse_log_error(self):
         errors = parse_log_for_error("error failed", True)
         self.assertEqual(len(errors), 1)
 
-    def test_run_cmd_suse(self):
-        """Test run_cmd on SuSE systems, which have $PROFILEREAD set."""
-        # avoid warning messages
-        run_log_level = run_log.getEffectiveLevel()
-        run_log.setLevel('ERROR')
-
-        # run_cmd should also work if $PROFILEREAD is set (very relevant for SuSE systems)
-        profileread = os.environ.get('PROFILEREAD', None)
-        os.environ['PROFILEREAD'] = 'profilereadxxx'
-        try:
-            (out, ec) = run_cmd("echo hello")
-        except Exception, err:
-            out, ec = "ERROR: %s" % err, 1
-
-        # make sure it's restored again before we can fail the test
-        if profileread is not None:
-            os.environ['PROFILEREAD'] = profileread
-        else:
-            del os.environ['PROFILEREAD']
-
-        self.assertEqual(out, "hello\n")
-        self.assertEqual(ec, 0)
-        run_log.setLevel(run_log_level)
-
 
 def suite():
     """ returns all the testcases in this module """

From fd246c958305bc7b254608a2af61d155220292e6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 12:02:13 +0200
Subject: [PATCH 0890/1356] add support for --external-modules-metadata, pick
 up metadata when parsing dependencies

---
 easybuild/framework/easyconfig/easyconfig.py | 10 ++++++-
 easybuild/tools/config.py                    |  1 +
 easybuild/tools/options.py                   |  8 +++++
 easybuild/tools/toolchain/toolchain.py       |  2 +-
 test/framework/config.py                     | 31 ++++++++++++++++++++
 5 files changed, 50 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index bd161ab708..d4870614f5 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -169,6 +169,8 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
             'stop': self.valid_stops,
         }
 
+        self.external_modules_metadata = build_option('external_modules_metadata')
+
         # parse easyconfig file
         self.build_specs = build_specs
         self.parse()
@@ -549,7 +551,8 @@ def _parse_dependency(self, dep, hidden=False):
             'version': None,
             'versionsuffix': '',
             'hidden': hidden,
-            'external_module': False
+            'external_module': False,
+            'root': None,
         }
         if isinstance(dep, dict):
             dependency.update(dep)
@@ -573,6 +576,11 @@ def _parse_dependency(self, dep, hidden=False):
                     dependency['external_module'] = True
                     dependency['short_mod_name'] = dep[0]
                     dependency['full_mod_name'] = dep[0]
+                    if dep[0] in self.external_modules_metadata:
+                        dependency.update(self.external_modules_metadata[dep[0]])
+                        self.log.info("Updated dependency info with metadata for external module: %s", dependency)
+                    else:
+                        self.log.info("No metadata available for external module %s", dep[0])
                 else:
                     raise EasyBuildError("Incorrect external dependency specification: %s", dep)
             else:
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 7b398be0aa..1d7b37c55b 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -83,6 +83,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'download_timeout',
         'dump_test_report',
         'easyblock',
+        'external_modules_metadata',
         'filter_deps',
         'hide_deps',
         'from_pr',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 0b62665209..fc6224f109 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -54,6 +54,7 @@
 from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
+from easybuild.tools.configobj import ConfigObj
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
@@ -235,6 +236,7 @@ def config_options(self):
             'avail-repositories': ("Show all repository types (incl. non-usable)",
                                    None, "store_true", False,),
             'buildpath': ("Temporary build path", None, 'store', mk_full_default_path('buildpath')),
+            'external-modules-metadata': ("File specifying metadata for external modules", None, 'store', None),
             'ignore-dirs': ("Directory names to ignore when searching for files/dirs",
                             'strlist', 'store', ['.git', '.svn']),
             'installpath': ("Install path for software and modules",
@@ -444,6 +446,12 @@ def postprocess(self):
             if token is None:
                 raise EasyBuildError("Failed to obtain required GitHub token for user '%s'", self.options.github_user)
 
+        # parse file specifying metadata for external modules
+        if self.options.external_modules_metadata:
+            self.options.external_modules_metadata = ConfigObj(self.options.external_modules_metadata)
+        else:
+            self.options.external_modules_metadata = {}
+
         self._postprocess_config()
 
     def _postprocess_config(self):
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index d183bcda83..a97e701dea 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -415,7 +415,7 @@ def _add_dependency_variables(self, names=None, cpp=None, ld=None):
         else:
             deps = [{'name': name} for name in names if name is not None]
 
-        for root in self.get_software_root([dep['name'] for dep in deps]):
+        for root in self.get_software_root([dep['name'] for dep in deps if not dep.get('external_module', False)]):
             self.variables.append_subdirs("CPPFLAGS", root, subdirs=cpp_paths)
             self.variables.append_subdirs("LDFLAGS", root, subdirs=ld_paths)
 
diff --git a/test/framework/config.py b/test/framework/config.py
index f10342e093..873f2f39db 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -46,6 +46,16 @@
 from easybuild.tools.filetools import mkdir, write_file
 from easybuild.tools.options import CONFIG_ENV_VAR_PREFIX
 
+EXTERNAL_MODULES_METADATA = """[cray-netcdf/4.3.2]
+name = netCDF,netCDF-Fortran
+root=NETCDF_DIR
+version = 4.3.2
+ 
+[cray-hdf5/1.8.13]
+name = HDF5
+root = HDF5_DIR
+version = 1.8.13
+"""
 
 class EasyBuildConfigTest(EnhancedTestCase):
     """Test cases for EasyBuild configuration."""
@@ -584,6 +594,27 @@ def test_flex_robot_paths(self):
 
         sys.path[:] = orig_sys_path
 
+    def test_external_modules_metadata(self):
+        """Test --external-modules-metadata."""
+        testcfgtxt = EXTERNAL_MODULES_METADATA
+        testcfg = os.path.join(self.test_prefix, 'test_external_modules_metadata.cfg')
+        write_file(testcfg, testcfgtxt)
+
+        cfg = init_config(args=['--external-modules-metadata=%s' % testcfg])
+
+        netcdf = {
+            'name': ['netCDF', 'netCDF-Fortran'],
+            'root': 'NETCDF_DIR',
+            'version': '4.3.2',
+        }
+        self.assertEqual(cfg.external_modules_metadata['cray-netcdf/4.3.2'], netcdf)
+        hdf5 = {
+            'name': 'HDF5',
+            'root': 'HDF5_DIR',
+            'version': '1.8.13',
+        }
+        self.assertEqual(cfg.external_modules_metadata['cray-hdf5/1.8.13'], hdf5)
+
 
 def suite():
     return TestLoader().loadTestsFromTestCase(EasyBuildConfigTest)

From 1b5d84c8c28fbc34244322c4583041875f117331 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 14:07:34 +0200
Subject: [PATCH 0891/1356] fix remarks

---
 easybuild/framework/easyconfig/easyconfig.py |  2 +-
 easybuild/tools/options.py                   | 27 +++++++++++++++-----
 test/framework/config.py                     |  8 +++---
 3 files changed, 25 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index d4870614f5..4c206f5604 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -552,7 +552,7 @@ def _parse_dependency(self, dep, hidden=False):
             'versionsuffix': '',
             'hidden': hidden,
             'external_module': False,
-            'root': None,
+            'prefix': None,  # installation prefix (only relevant for external modules)
         }
         if isinstance(dep, dict):
             dependency.update(dep)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index fc6224f109..1af6d96211 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -54,7 +54,7 @@
 from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import get_pretend_installpath
 from easybuild.tools.config import mk_full_default_path
-from easybuild.tools.configobj import ConfigObj
+from easybuild.tools.configobj import ConfigObj, ConfigObjError
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
 from easybuild.tools.modules import avail_modules_tools
@@ -236,7 +236,8 @@ def config_options(self):
             'avail-repositories': ("Show all repository types (incl. non-usable)",
                                    None, "store_true", False,),
             'buildpath': ("Temporary build path", None, 'store', mk_full_default_path('buildpath')),
-            'external-modules-metadata': ("File specifying metadata for external modules", None, 'store', None),
+            'external-modules-metadata': ("List of files specifying metadata for external modules (INI format)",
+                                          'strlist', 'store', []),
             'ignore-dirs': ("Directory names to ignore when searching for files/dirs",
                             'strlist', 'store', ['.git', '.svn']),
             'installpath': ("Install path for software and modules",
@@ -446,14 +447,26 @@ def postprocess(self):
             if token is None:
                 raise EasyBuildError("Failed to obtain required GitHub token for user '%s'", self.options.github_user)
 
-        # parse file specifying metadata for external modules
-        if self.options.external_modules_metadata:
-            self.options.external_modules_metadata = ConfigObj(self.options.external_modules_metadata)
-        else:
-            self.options.external_modules_metadata = {}
+        self._postprocess_external_modules_metadata()
 
         self._postprocess_config()
 
+    def _postprocess_external_modules_metadata(self):
+        """Parse file(s) specifying metadata for external modules."""
+        parsed_external_modules_metadata = ConfigObj()
+        for path in self.options.external_modules_metadata:
+            if os.path.exists(path):
+                try:
+                    parsed = ConfigObj(path)
+                except ConfigObjError, err:
+                    raise EasyBuildError("Failed to parse %s with external modules metadata: %s", path, err)
+                parsed_external_modules_metadata.merge(parsed)
+            else:
+                raise EasyBuildError("Specified path for file with external modules metadata does not exist: %s", path)
+
+        self.options.external_modules_metadata = parsed_external_modules_metadata
+        self.log.debug("External modules metadata: %s", self.options.external_modules_metadata)
+
     def _postprocess_config(self):
         """Postprocessing of configuration options"""
         if self.options.prefix is not None:
diff --git a/test/framework/config.py b/test/framework/config.py
index 873f2f39db..a1b3d6caae 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -48,13 +48,13 @@
 
 EXTERNAL_MODULES_METADATA = """[cray-netcdf/4.3.2]
 name = netCDF,netCDF-Fortran
-root=NETCDF_DIR
 version = 4.3.2
+prefix = NETCDF_DIR
  
 [cray-hdf5/1.8.13]
 name = HDF5
-root = HDF5_DIR
 version = 1.8.13
+prefix = HDF5_DIR
 """
 
 class EasyBuildConfigTest(EnhancedTestCase):
@@ -604,14 +604,14 @@ def test_external_modules_metadata(self):
 
         netcdf = {
             'name': ['netCDF', 'netCDF-Fortran'],
-            'root': 'NETCDF_DIR',
             'version': '4.3.2',
+            'prefix': 'NETCDF_DIR',
         }
         self.assertEqual(cfg.external_modules_metadata['cray-netcdf/4.3.2'], netcdf)
         hdf5 = {
             'name': 'HDF5',
-            'root': 'HDF5_DIR',
             'version': '1.8.13',
+            'prefix': 'HDF5_DIR',
         }
         self.assertEqual(cfg.external_modules_metadata['cray-hdf5/1.8.13'], hdf5)
 

From 603a224a54ed3db0377d4d3e5405c4c8c960d511 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 14:51:17 +0200
Subject: [PATCH 0892/1356] enhance test for parsing deps in easyconfig

---
 easybuild/framework/easyconfig/easyconfig.py |  2 +-
 test/framework/easyconfig.py                 | 21 ++++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 4c206f5604..cbe9e4d65b 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -546,7 +546,7 @@ def _parse_dependency(self, dep, hidden=False):
             'dummy': False,
             'full_mod_name': None,  # full module name
             'short_mod_name': None,  # short module name
-            'name': None,  # software name
+            'name': None,  # software name (may be a list of names, e.g. for external modules)
             'toolchain': None,
             'version': None,
             'versionsuffix': '',
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 34c365110e..99101cd999 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -50,6 +50,7 @@
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak_one
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import module_classes
+from easybuild.tools.configobj import ConfigObj
 from easybuild.tools.filetools import read_file, write_file
 from easybuild.tools.module_naming_scheme.toolchain import det_toolchain_compilers, det_toolchain_mpi
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
@@ -1047,6 +1048,11 @@ def test_external_dependencies(self):
         ectxt += "\nbuilddependencies = [('somebuilddep/0.1', EXTERNAL_MODULE)]"
         write_file(toy_ec, ectxt)
 
+        build_options = {
+            'valid_module_classes': module_classes(),
+            'external_modules_metadata': ConfigObj(),
+        }
+        init_config(build_options=build_options)
         ec = EasyConfig(toy_ec)
 
         builddeps = ec.builddependencies()
@@ -1061,6 +1067,21 @@ def test_external_dependencies(self):
         self.assertEqual([d['full_mod_name'] for d in deps], ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1'])
         self.assertEqual([d['external_module'] for d in deps], [False, True, True])
 
+        metadata = os.path.join(self.test_prefix, 'external_modules_metadata.cfg')
+        metadatatxt = '\n'.join(['[foobar/1.2.3]', 'name = foobar,bar', 'version = 1.2.3', 'prefix = /foo/bar'])
+        write_file(metadata, metadatatxt)
+        build_options = {
+            'valid_module_classes': module_classes(),
+            'external_modules_metadata': ConfigObj(metadata),
+        }
+        init_config(build_options=build_options)
+        ec = EasyConfig(toy_ec)
+        self.assertEqual(ec.dependencies()[1]['short_mod_name'], 'foobar/1.2.3')
+        self.assertEqual(ec.dependencies()[1]['external_module'], True)
+        self.assertEqual(ec.dependencies()[1]['name'], ['foobar', 'bar'])
+        self.assertEqual(ec.dependencies()[1]['version'], '1.2.3')
+        self.assertEqual(ec.dependencies()[1]['prefix'], '/foo/bar')
+
     def test_update(self):
         """Test use of update() method for EasyConfig instances."""
         toy_ebfile = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb')

From 5d31d96b993b4c89dc1bcb83e1fd8ff35e5885df Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 14:52:09 +0200
Subject: [PATCH 0893/1356] style fixes + better logging

---
 easybuild/tools/environment.py | 3 ++-
 easybuild/tools/modules.py     | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/environment.py b/easybuild/tools/environment.py
index 15e05b0b59..5ce354f788 100644
--- a/easybuild/tools/environment.py
+++ b/easybuild/tools/environment.py
@@ -84,10 +84,11 @@ def setvar(key, value):
     put key in the environment with value
     tracks added keys until write_changes has been called
     """
+    oldval = os.environ.get(key, 'None (not defined)')
     # os.putenv() is not necessary. os.environ will call this.
     os.environ[key] = value
     _changes[key] = value
-    _log.info("Environment variable %s set to %s" % (key, value))
+    _log.info("Environment variable %s set to %s (previous value: %s)", key, value, oldval)
 
 
 def unset_env_vars(keys):
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 433559e8e3..43a2e2ff87 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -848,7 +848,7 @@ def prepend_module_path(self, path):
 def get_software_root_env_var_name(name):
     """Return name of environment variable for software root."""
     newname = convert_name(name, upper=True)
-    return ''.join([ROOT_ENV_VAR_NAME_PREFIX, newname])
+    return ROOT_ENV_VAR_NAME_PREFIX + newname
 
 
 def get_software_root(name, with_env_var=False):
@@ -910,7 +910,7 @@ def get_software_libdir(name, only_one=True, fs=None):
 def get_software_version_env_var_name(name):
     """Return name of environment variable for software root."""
     newname = convert_name(name, upper=True)
-    return ''.join([VERSION_ENV_VAR_NAME_PREFIX, newname])
+    return VERSION_ENV_VAR_NAME_PREFIX + newname
 
 
 def get_software_version(name):

From c9e3f73de16e3518ea7771c47c80a3d2d5ca86f3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 15:18:35 +0200
Subject: [PATCH 0894/1356] define $EB* env vars for external modules via
 toolchain prepare mechanism

---
 easybuild/tools/toolchain/toolchain.py | 40 +++++++++++++--
 test/framework/toolchain.py            | 70 ++++++++++++++++++++++++++
 2 files changed, 107 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index a97e701dea..8c584d160b 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -38,7 +38,8 @@
 from easybuild.tools.config import build_option, install_path
 from easybuild.tools.environment import setvar
 from easybuild.tools.module_generator import dependencies_for
-from easybuild.tools.modules import get_software_root, get_software_version, modules_tool
+from easybuild.tools.modules import get_software_root, get_software_root_env_var_name
+from easybuild.tools.modules import get_software_version, get_software_version_env_var_name, modules_tool
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
 from easybuild.tools.toolchain.options import ToolchainOptions
 from easybuild.tools.toolchain.toolchainvariables import ToolchainVariables
@@ -317,6 +318,39 @@ def is_dep_in_toolchain_module(self, name):
         """Check whether a specific software name is listed as a dependency in the module for this toolchain."""
         return any(map(lambda m: self.mns.is_short_modname_for(m, name), self.toolchain_dep_mods))
 
+    def _prepare_dependencies(self):
+        """Load modules for dependencies, and handle special cases like external modules."""
+        # load modules for all dependencies
+        self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
+
+        # define $EBROOT* and $EBVERSION* for external modules, if metadata is available
+        for dep in self.dependencies:
+            names = dep['name']
+            if isinstance(names, basestring):
+                names = [names]
+
+            if dep['external_module'] and names is not None:
+                for name in names:
+                    self.log.debug("Defining $EB* environment variables for external module %s under name %s",
+                                   dep['short_mod_name'], name)
+
+                    # install prefix, picked up by get_software_root
+                    prefix = dep['prefix']
+                    if prefix is not None:
+                        if prefix in os.environ:
+                            prefix = os.environ[prefix]
+                            self.log.debug("Using value of $%s as prefix for external module %s: %s",
+                                           dep['prefix'], dep['short_mod_name'], prefix)
+                        else:
+                            self.log.debug("Using specified prefix for external module %s: %s",
+                                           dep['short_mod_name'], prefix)
+
+                        setvar(get_software_root_env_var_name(name), prefix)
+
+                    # $EBVERSION
+                    if dep['version'] is not None:
+                        setvar(get_software_version_env_var_name(name), dep['version'])
+
     def prepare(self, onlymod=None):
         """
         Prepare a set of environment parameters based on name/version of toolchain
@@ -338,7 +372,7 @@ def prepare(self, onlymod=None):
                 self.log.info('prepare: toolchain dummy mode, dummy version; not loading dependencies')
             else:
                 self.log.info('prepare: toolchain dummy mode and loading dependencies')
-                self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
+                self._prepare_dependencies()
             return
 
         # Load the toolchain and dependencies modules
@@ -349,7 +383,7 @@ def prepare(self, onlymod=None):
             for modpath in self.init_modpaths:
                 self.modules_tool.prepend_module_path(os.path.join(install_path('mod'), mod_path_suffix, modpath))
         self.modules_tool.load([self.det_short_module_name()])
-        self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
+        self._prepare_dependencies()
 
         # determine direct toolchain dependencies
         mod_name = self.det_short_module_name()
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 217b60977e..cf6d54e586 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -39,6 +39,7 @@
 from easybuild.framework.easyconfig.easyconfig import EasyConfig, ActiveMNS
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import write_file
+from easybuild.tools.modules import modules_tool
 from easybuild.tools.toolchain.utilities import search_toolchain
 from test.framework.utilities import find_full_path
 
@@ -543,6 +544,75 @@ def test_mpi_cmd_for(self):
         shutil.rmtree(tmpdir)
         write_file(imkl_module_path, imkl_module_txt)
 
+    def test_prepare_deps(self):
+        """Test preparing for a toolchain when dependencies are involved."""
+        tc = self.get_toolchain('GCC', version='4.6.4')
+        deps = [
+            {
+                'name': 'OpenMPI',
+                'version': '1.6.4',
+                'full_mod_name': 'OpenMPI/1.6.4-GCC-4.6.4',
+                'short_mod_name': 'OpenMPI/1.6.4-GCC-4.6.4',
+                'external_module': False,
+            },
+        ]
+        tc.add_dependencies(deps)
+        tc.prepare()
+        mods = ['GCC/4.6.4', 'hwloc/1.6.2-GCC-4.6.4', 'OpenMPI/1.6.4-GCC-4.6.4']
+        self.assertTrue([m['mod_name'] for m in modules_tool().list()], mods)
+
+    def test_prepare_deps_external(self):
+        """Test preparing for a toolchain when dependencies and external modules are involved."""
+        deps = [
+            {
+                'name': 'OpenMPI',
+                'version': '1.6.4',
+                'full_mod_name': 'OpenMPI/1.6.4-GCC-4.6.4',
+                'short_mod_name': 'OpenMPI/1.6.4-GCC-4.6.4',
+                'external_module': False,
+            },
+            # no metadata available
+            {
+                'name': None,
+                'version': None,
+                'full_mod_name': 'toy/0.0',
+                'short_mod_name': 'toy/0.0',
+                'external_module': True,
+            }
+        ]
+        tc = self.get_toolchain('GCC', version='4.6.4')
+        tc.add_dependencies(deps)
+        tc.prepare()
+        mods = ['GCC/4.6.4', 'hwloc/1.6.2-GCC-4.6.4', 'OpenMPI/1.6.4-GCC-4.6.4', 'toy/0.0']
+        self.assertTrue([m['mod_name'] for m in modules_tool().list()], mods)
+        self.assertTrue(os.environ['EBROOTTOY'].endswith('software/toy/0.0'))
+        self.assertEqual(os.environ['EBVERSIONTOY'], '0.0')
+        self.assertFalse('EBROOTFOOBAR' in os.environ)
+
+        # with metadata
+        deps[1] = {
+            'name': ['toy', 'foobar'],
+            'version': '1.2.3.4.5',
+            'prefix': 'FOOBAR_PREFIX',
+            'full_mod_name': 'toy/0.0',
+            'short_mod_name': 'toy/0.0',
+            'external_module': True,
+        }
+        tc = self.get_toolchain('GCC', version='4.6.4')
+        tc.add_dependencies(deps)
+        os.environ['FOOBAR_PREFIX'] = '/foo/bar'
+        tc.prepare()
+        mods = ['GCC/4.6.4', 'hwloc/1.6.2-GCC-4.6.4', 'OpenMPI/1.6.4-GCC-4.6.4', 'toy/0.0']
+        self.assertTrue([m['mod_name'] for m in modules_tool().list()], mods)
+        self.assertEqual(os.environ['EBROOTTOY'], '/foo/bar')
+        self.assertEqual(os.environ['EBVERSIONTOY'], '1.2.3.4.5')
+        self.assertEqual(os.environ['EBROOTFOOBAR'], '/foo/bar')
+        self.assertEqual(os.environ['EBVERSIONFOOBAR'], '1.2.3.4.5')
+
+        self.assertEqual(modules.get_software_root('foobar'), '/foo/bar')
+        self.assertEqual(modules.get_software_version('toy'), '1.2.3.4.5')
+
+
 def suite():
     """ return all the tests"""
     return TestLoader().loadTestsFromTestCase(ToolchainTest)

From 4d5d816183438d1a41d6db717e62284b22e1a34d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 15:20:24 +0200
Subject: [PATCH 0895/1356] remove unused pre_prepare hackish workaround

---
 easybuild/tools/toolchain/toolchain.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 31a3c869e9..c43ae6f014 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -317,10 +317,6 @@ def is_dep_in_toolchain_module(self, name):
         """Check whether a specific software name is listed as a dependency in the module for this toolchain."""
         return any(map(lambda m: self.mns.is_short_modname_for(m, name), self.toolchain_dep_mods))
 
-    def _pre_prepare(self):
-        """Toolchain-specific preparations thay should be done first."""
-        pass
-
     def prepare(self, onlymod=None):
         """
         Prepare a set of environment parameters based on name/version of toolchain
@@ -336,9 +332,6 @@ def prepare(self, onlymod=None):
 
         if not self._toolchain_exists():
             raise EasyBuildError("No module found for toolchain: %s", self.mod_short_name)
-
-        # preliminary preparations first
-        self._pre_prepare()
         
         if self.name == DUMMY_TOOLCHAIN_NAME:
             if self.version == DUMMY_TOOLCHAIN_VERSION:

From 5f96460ca6f2dd1da337cf0305a1c51594447fd1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 15:44:36 +0200
Subject: [PATCH 0896/1356] cleanup handling of external modules in
 toolchain.prepare

---
 easybuild/tools/toolchain/toolchain.py | 54 ++++++++++++++------------
 1 file changed, 29 insertions(+), 25 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 8c584d160b..453aa0772c 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -321,35 +321,39 @@ def is_dep_in_toolchain_module(self, name):
     def _prepare_dependencies(self):
         """Load modules for dependencies, and handle special cases like external modules."""
         # load modules for all dependencies
-        self.modules_tool.load([dep['short_mod_name'] for dep in self.dependencies])
+        dep_mods = [dep['short_mod_name'] for dep in self.dependencies]
+        self.log.debug("Loading modules for dependencies: %s" % dep_mods)
+        self.modules_tool.load(dep_mods)
 
         # define $EBROOT* and $EBVERSION* for external modules, if metadata is available
-        for dep in self.dependencies:
-            names = dep['name']
+        for dep in [d for d in self.dependencies if d['external_module']]:
+            self.log.debug("Defining $EB* environment variables for external module %s", dep['short_mod_name'])
+
+            names = dep['name'] or []
             if isinstance(names, basestring):
                 names = [names]
-
-            if dep['external_module'] and names is not None:
-                for name in names:
-                    self.log.debug("Defining $EB* environment variables for external module %s under name %s",
-                                   dep['short_mod_name'], name)
-
-                    # install prefix, picked up by get_software_root
-                    prefix = dep['prefix']
-                    if prefix is not None:
-                        if prefix in os.environ:
-                            prefix = os.environ[prefix]
-                            self.log.debug("Using value of $%s as prefix for external module %s: %s",
-                                           dep['prefix'], dep['short_mod_name'], prefix)
-                        else:
-                            self.log.debug("Using specified prefix for external module %s: %s",
-                                           dep['short_mod_name'], prefix)
-
-                        setvar(get_software_root_env_var_name(name), prefix)
-
-                    # $EBVERSION
-                    if dep['version'] is not None:
-                        setvar(get_software_version_env_var_name(name), dep['version'])
+            self.log.debug("Software names for external module %s: %s", dep['short_mod_name'], names)
+
+            for name in names:
+                self.log.debug("Defining $EB* environment variables for external module %s under name %s",
+                               dep['short_mod_name'], name)
+
+                # install prefix, picked up by get_software_root
+                prefix = dep['prefix']
+                if prefix is not None:
+                    if prefix in os.environ:
+                        prefix = os.environ[prefix]
+                        self.log.debug("Using value of $%s as prefix for external module %s: %s",
+                                       dep['prefix'], dep['short_mod_name'], prefix)
+                    else:
+                        self.log.debug("Using specified prefix for external module %s: %s",
+                                       dep['short_mod_name'], prefix)
+
+                    setvar(get_software_root_env_var_name(name), prefix)
+
+                # $EBVERSION
+                if dep['version'] is not None:
+                    setvar(get_software_version_env_var_name(name), dep['version'])
 
     def prepare(self, onlymod=None):
         """

From 8281b32cd02be6d68bd5f3ee81b0f11c7d4f88a9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 16:22:14 +0200
Subject: [PATCH 0897/1356] fix broken test + minor cleanup

---
 easybuild/tools/toolchain/toolchain.py | 8 +++++---
 test/framework/easyconfig.py           | 3 +++
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 453aa0772c..c7671bb861 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -453,9 +453,11 @@ def _add_dependency_variables(self, names=None, cpp=None, ld=None):
         else:
             deps = [{'name': name} for name in names if name is not None]
 
-        for root in self.get_software_root([dep['name'] for dep in deps if not dep.get('external_module', False)]):
-            self.variables.append_subdirs("CPPFLAGS", root, subdirs=cpp_paths)
-            self.variables.append_subdirs("LDFLAGS", root, subdirs=ld_paths)
+        # name or root may be None for external modules
+        for root in self.get_software_root([dep['name'] for dep in deps if dep['name'] is not None]):
+            if root is not None:
+                self.variables.append_subdirs("CPPFLAGS", root, subdirs=cpp_paths)
+                self.variables.append_subdirs("LDFLAGS", root, subdirs=ld_paths)
 
     def _setenv_variables(self, donotset=None):
         """Actually set the environment variables"""
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 99101cd999..646d2cccc4 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -580,6 +580,7 @@ def test_obtain_easyconfig(self):
                 'full_mod_name': 'foo/1.2.3-GCC-4.4.5',
                 'hidden': False,
                 'external_module': False,
+                'prefix': None,
             },
             {
                 'name': 'bar',
@@ -591,6 +592,7 @@ def test_obtain_easyconfig(self):
                 'full_mod_name': 'bar/666-gompi-1.4.10-bleh',
                 'hidden': False,
                 'external_module': False,
+                'prefix': None,
             },
             {
                 'name': 'test',
@@ -602,6 +604,7 @@ def test_obtain_easyconfig(self):
                 'full_mod_name': 'test/.3.2.1-GCC-4.4.5',
                 'hidden': True,
                 'external_module': False,
+                'prefix': None,
             },
         ]
 

From 46389500cac336ebbbc463f8f90486ad156451ff Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 17:25:44 +0200
Subject: [PATCH 0898/1356] handle possible list of names for external modules
 in _add_dependency_variables

---
 easybuild/tools/toolchain/toolchain.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index c7671bb861..a32edf3eef 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -453,8 +453,17 @@ def _add_dependency_variables(self, names=None, cpp=None, ld=None):
         else:
             deps = [{'name': name} for name in names if name is not None]
 
-        # name or root may be None for external modules
-        for root in self.get_software_root([dep['name'] for dep in deps if dep['name'] is not None]):
+        dep_names = []
+        for dep in deps:
+            # name may be None or a list of names for external modules
+            if dep['name'] is not None:
+                if isinstance(dep['name'], list):
+                    dep_names.extend(dep['name'])
+                else:
+                    dep_names.append(dep['name'])
+
+        for root in self.get_software_root(dep_names):
+            # software install prefix may be None for external modules
             if root is not None:
                 self.variables.append_subdirs("CPPFLAGS", root, subdirs=cpp_paths)
                 self.variables.append_subdirs("LDFLAGS", root, subdirs=ld_paths)

From 70801eda6b4656d16837a228e3a110d58dba08a6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Apr 2015 20:06:17 +0200
Subject: [PATCH 0899/1356] add FIXMEs

---
 easybuild/toolchains/compiler/craype.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index df814386fd..c91c664fe3 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -64,8 +64,8 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     COMPILER_FAMILY = None
 
     COMPILER_UNIQUE_OPTS = {
-        # FIXME: (kehoste) how is this different from the existing 'shared' toolchain option? just map 'shared' to '-dynamic'? (already done)
         'dynamic': (False, "Generate dynamically linked executable"),
+        # FIXME: drop unused mpich-mt, usewrappedcompiler support?
         'mpich-mt': (False, "Directs the driver to link in an alternate version of the Cray-MPICH library which \
                              provides fine-grained multi-threading support to applications that perform \
                              MPI operations within threaded regions."),
@@ -75,18 +75,19 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-        #'pic': 'shared',  # FIXME (use compiler-specific setting?)
         'shared': 'shared',
         'dynamic': 'dynamic',
         'static': 'static',
         'verbose': 'craype-verbose',
         'mpich-mt': 'craympich-mt',
         # no optimization flags
+        # FIXME enable?
         'noopt': [],
         'lowopt': [],
         'defaultopt': [],
         'opt': [],
         # no precision flags
+        # FIXME enable?
         'strict': [],
         'precise': [],
         'defaultprec': [],
@@ -111,6 +112,7 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     MPI_COMPILER_MPIF77 = COMPILER_F77
     MPI_COMPILER_MPIF90 = COMPILER_F90
 
+    # no MPI wrappers, so no need to specify serial compiler
     MPI_SHARED_OPTION_MAP = {
         '_opt_MPICC': '',
         '_opt_MPICXX': '',
@@ -121,7 +123,7 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     # BLAS/LAPACK support
     # via cray-libsci module, which gets loaded via the PrgEnv module
     # see https://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/
-    BLAS_MODULE_NAME = ['cray-libsci']
+    BLAS_MODULE_NAME = ['cray-libsci']  # FIXME: let this load via PrgEnv, and so not list it here (or filter it out of definition)?
     # specific library depends on PrgEnv flavor
     BLAS_LIB = []
     BLAS_LIB_MT = []
@@ -151,6 +153,8 @@ def __init__(self, *args, **kwargs):
         # use name of PrgEnv module as name of module that provides compiler
         self.COMPILER_MODULE_NAME = ['PrgEnv-%s' % self.PRGENV_MODULE_NAME_SUFFIX]
 
+        # FIXME: force use of --experimental
+
     def _set_optimal_architecture(self):
         """Load craype module specified via 'optarch' build option."""
         optarch = build_option('optarch')
@@ -239,6 +243,7 @@ class CrayPEGNU(CrayPE):
     PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
     COMPILER_FAMILY = TC_CONSTANT_GCC
 
+    # FIXME: drop this?
     def _set_compiler_vars(self):
         """Set compiler variables, either for the compiler wrapper, or the underlying compiler."""
         if self.options.option('usewrappedcompiler'):
@@ -259,6 +264,7 @@ class CrayPEIntel(CrayPE):
     PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
     COMPILER_FAMILY = TC_CONSTANT_INTELCOMP
 
+    # FIXME: drop this?
     def _set_compiler_flags(self):
         """Set compiler variables, either for the compiler wrapper, or the underlying compiler."""
         if self.options.option("usewrappedcompiler"):

From 6f0c2f68f93f013c514f408f542c106c524fac5f Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Thu, 23 Apr 2015 23:26:04 +0300
Subject: [PATCH 0900/1356] One more FIXME for MT BLAS.

---
 easybuild/toolchains/compiler/craype.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index c91c664fe3..6782738ee8 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -125,6 +125,8 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     # see https://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/
     BLAS_MODULE_NAME = ['cray-libsci']  # FIXME: let this load via PrgEnv, and so not list it here (or filter it out of definition)?
     # specific library depends on PrgEnv flavor
+
+    #FIXME: need to revisit this, on numpy we ended up with a serial BLAS through the wrapper.
     BLAS_LIB = []
     BLAS_LIB_MT = []
 

From 7b1b258e3df856a3ae0caf59a00fff2382e6f9a9 Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Thu, 23 Apr 2015 23:32:11 +0300
Subject: [PATCH 0901/1356] added fixme wrt to hugepage and accelerator targets

---
 easybuild/toolchains/compiler/craype.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 6782738ee8..5e79d783ae 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -146,6 +146,10 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     # template for craype module (determines code generator backend of Cray compiler wrappers)
     CRAYPE_MODULE_NAME_TEMPLATE = 'craype-%(optarch)s'
 
+    # FIXME: add support for hugepages and accelerator modules that belong to CrayPE and allow to load modules
+    # CRAYPE_HUGEMEM_MODULE_NAME_TEMPLATE = 'craype-hugepages%(hugemagesize)s'
+    # CRAYPE_ACCEL_MODULE_NAME_TEMPLATE = 'craype-accel-%(acceltgt)s' 
+
     def __init__(self, *args, **kwargs):
         """Constructor."""
         super(CrayPE, self).__init__(*args, **kwargs)

From 54e72978046d38e09d920ef2a69a69cf8190f8bc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 09:15:08 +0200
Subject: [PATCH 0902/1356] clean up implementation of --only-module, add unit
 test for it

---
 easybuild/framework/easyblock.py | 31 ++++++++++++++++++++-----------
 easybuild/tools/options.py       |  2 +-
 test/framework/toy_build.py      | 25 +++++++++++++++++++++++++
 3 files changed, 46 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index be4da82a44..3746d6a75b 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1580,7 +1580,11 @@ def sanity_check_step(self, custom_paths=None, custom_commands=None, extension=F
                 self.log.warning("Sanity check: %s" % self.sanity_check_fail_msgs[-1])
 
         # chdir to installdir (better environment for running tests)
-        os.chdir(self.installdir)
+        if os.path.exists(self.installdir):
+            try:
+                os.chdir(self.installdir)
+            except OSError, err:
+                raise EasyBuildError("Failed to move to installdir %s: %s", self.installdir, err)
 
         # run sanity check commands
         commands = self.cfg['sanity_check_commands']
@@ -1728,30 +1732,35 @@ def run_step(self, step, methods, skippable=False):
         """
         Run step, returns false when execution should be stopped
         """
+        only_module = build_option('only_module')
+        force = build_option('force')
         skip = False
+
         # skip step if specified, either as individual (skippable) step, or when only generating module file
         # still run sanity check when only generating module
         skip_individual_step = skippable and (self.skip or step in self.cfg['skipsteps'])
-        only_module_skip = build_option('only_module') and not step in ['sanitycheck', 'module']
+        only_module_skip = only_module and not step in ['sanitycheck', 'module']
         if skip_individual_step or only_module_skip:
-            self.log.info("Skipping %s step" % step)
+            self.log.info("Skipping %s step", step)
             skip = True
-        # allow skipping sanity check too when only generating module via --force
-        elif build_option('only_module') and step == 'sanitycheck' and build_option('force'):
-            self.log.info("Skipping %s step, due to combo of --only-module and --force" in ['sanitycheck'])
+
+        # allow skipping sanity check too when only generating module and --force is enable
+        elif only_module and step == 'sanitycheck' and force:
+            self.log.info("Skipping %s step, due to combo of --only-module and --force", step)
             skip = True
 
-        if not skip:
-            self.log.info("Starting %s step" % step)
-            # update the config templates
-            self.update_config_template_run_step()
+        else:
+            self.log.debug("Not skipping %s step (skippable: %s, skip: %s, skipsteps: %s, only_module: %s, force: %s",
+                           step, skippable, self.skip, self.cfg['skipsteps'], only_module, force)
 
+            self.log.info("Starting %s step", step)
+            self.update_config_template_run_step()
             for m in methods:
                 self.log.info("Running method %s part of step %s" % ('_'.join(m.func_code.co_names), step))
                 m(self)
 
         if self.cfg['stop'] == step:
-            self.log.info("Stopping after %s step." % step)
+            self.log.info("Stopping after %s step.", step)
             raise StopException(step)
 
     @staticmethod
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 444c737919..2cedc68bb0 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -207,7 +207,7 @@ def override_options(self):
                           "(e.g. --hide-deps=zlib,ncurses)", 'strlist', 'extend', None),
             'oldstyleconfig':   ("Look for and use the oldstyle configuration file.",
                                  None, 'store_true', True),
-            'only-module': ("Only (re)generate module file", None, 'store_true', False),
+            'only-module': ("Only generate module file", None, 'store_true', False),
             'optarch': ("Set architecture optimization, overriding native architecture optimizations",
                         None, 'store', None),
             'pretend': (("Does the build/installation in a test directory located in $HOME/easybuildinstall"),
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index ce14cda823..877a992913 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -880,6 +880,31 @@ def test_external_dependencies(self):
         outtxt = self.test_toy_build(ec_file=toy_ec, verbose=True, extra_args=['--dry-run'], verify=False)
         self.assertTrue(re.search(r"^ \* \[ \] .* \(module: toy/0.0-external-deps-broken2\)", outtxt, re.M))
 
+    def test_only_module(self):
+        """Test use of --only-module."""
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0.eb')
+        toy_mod = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0')
+
+        # hide all existing modules
+        self.reset_modulepath([os.path.join(self.test_installpath, 'modules', 'all')])
+
+        # sanity check fails without --force if software is not installed yet
+        common_args = [
+            ec_file,
+            '--sourcepath=%s' % self.test_sourcepath,
+            '--buildpath=%s' % self.test_buildpath,
+            '--installpath=%s' % self.test_installpath,
+            '--debug',
+            '--unittest-file=%s' % self.logfile,
+        ]
+        args = common_args + ['--only-module']
+        err_msg = "Sanity check failed"
+        self.assertErrorRegex(EasyBuildError, err_msg, self.eb_main, args, do_build=True, raise_error=True)
+        self.assertFalse(os.path.exists(toy_mod))
+
+        self.eb_main(args + ['--force'], do_build=True, raise_error=True)
+        self.assertTrue(os.path.exists(toy_mod))
+
 
 def suite():
     """ return all the tests in this file """

From fee2b98470efff02ba4226f2ad7ae2ae3e69f12c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 14:26:50 +0200
Subject: [PATCH 0903/1356] add support for
 --software-installdir-naming-scheme, enhance test for --only-module

---
 easybuild/framework/easyblock.py | 15 ++++++++--
 easybuild/tools/config.py        |  1 +
 easybuild/tools/options.py       |  2 ++
 test/framework/toy_build.py      | 51 +++++++++++++++++++++++++++++++-
 4 files changed, 66 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3746d6a75b..cbb480eb1e 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -68,7 +68,7 @@
 from easybuild.tools.run import run_cmd
 from easybuild.tools.jenkins import write_to_xml
 from easybuild.tools.module_generator import ModuleGeneratorLua, ModuleGeneratorTcl, module_generator
-from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
+from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
 from easybuild.tools.modules import ROOT_ENV_VAR_NAME_PREFIX, VERSION_ENV_VAR_NAME_PREFIX, DEVEL_ENV_VAR_NAME_PREFIX
 from easybuild.tools.modules import get_software_root, modules_tool
 from easybuild.tools.repository.repository import init_repository
@@ -674,7 +674,18 @@ def gen_installdir(self):
         """
         basepath = install_path()
         if basepath:
-            self.install_subdir = ActiveMNS().det_full_module_name(self.cfg, force_visible=True)
+            install_subdir_ns = build_option('software_installdir_naming_scheme')
+            if install_subdir_ns is None:
+                self.install_subdir = ActiveMNS().det_full_module_name(self.cfg, force_visible=True)
+                self.log.debug("Determined name of install subdir using active module naming scheme: %s",
+                               self.install_subdir)
+            else:
+                avail_mnss = avail_module_naming_schemes()
+                if install_subdir_ns in avail_mnss:
+                    self.install_subdir = avail_mnss[install_subdir_ns]().det_full_module_name(self.cfg)
+                    self.log.debug("Determined name of install subdir using specified naming scheme %s: %s",
+                                   install_subdir_ns, self.install_subdir)
+
             installdir = os.path.join(basepath, self.install_subdir)
             self.installdir = os.path.abspath(installdir)
             self.log.info("Install dir set to %s" % self.installdir)
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index b96a0987fb..5aaac3c143 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -95,6 +95,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'optarch',
         'regtest_output_dir',
         'skip',
+        'software_installdir_naming_scheme',
         'stop',
         'suffix_modules_path',
         'test_report_env_filter',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 2cedc68bb0..4a901d7488 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -269,6 +269,8 @@ def config_options(self):
                                 "(is passed as list of arguments to create the repository instance). "
                                 "For more info, use --avail-repositories."),
                                'strlist', 'store', self.default_repositorypath),
+            'software-installdir-naming-scheme': ("Naming scheme for software install (sub)directory "
+                                                  "(default: same as --module-naming-scheme)", None, 'store', None),
             'sourcepath': ("Path(s) to where sources should be downloaded (string, colon-separated)",
                            None, 'store', mk_full_default_path('sourcepath')),
             'subdir-modules': ("Installpath subdir for modules", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_modules']),
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 877a992913..599ac83dc5 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -44,7 +44,7 @@
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import get_module_syntax
-from easybuild.tools.filetools import mkdir, read_file, write_file
+from easybuild.tools.filetools import mkdir, read_file, which, write_file
 from easybuild.tools.modules import modules_tool
 
 
@@ -905,6 +905,55 @@ def test_only_module(self):
         self.eb_main(args + ['--force'], do_build=True, raise_error=True)
         self.assertTrue(os.path.exists(toy_mod))
 
+        os.remove(toy_mod)
+
+        # installing another module under a different naming scheme and using Lua module syntax works fine
+
+        # first actually build and install toy software + module
+        prefix = os.path.join(self.test_installpath, 'software', 'toy', '0.0')
+        self.eb_main(common_args + ['--force'], do_build=True, raise_error=True)
+        self.assertTrue(os.path.exists(toy_mod))
+        self.assertTrue(os.path.exists(os.path.join(self.test_installpath, 'software', 'toy', '0.0', 'bin')))
+        modtxt = read_file(toy_mod)
+        self.assertTrue(re.search("set root %s" % prefix, modtxt))
+        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 1)
+        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software', 'toy'))), 1)
+
+        # install (only) additional module under a hierarchical MNS
+        args = common_args + [
+            '--only-module',
+            '--software-installdir-naming-scheme=EasyBuildMNS',
+            '--module-naming-scheme=HierarchicalMNS',
+        ]
+        toy_core_mod = os.path.join(self.test_installpath, 'modules', 'all', 'Core', 'toy', '0.0')
+        self.assertFalse(os.path.exists(toy_core_mod))
+        self.eb_main(args, do_build=True, raise_error=True)
+        self.assertTrue(os.path.exists(toy_core_mod))
+        # existing install is reused
+        modtxt2 = read_file(toy_core_mod)
+        self.assertTrue(re.search("set root %s" % prefix, modtxt2))
+        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 1)
+        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software', 'toy'))), 1)
+
+        os.remove(toy_mod)
+        os.remove(toy_core_mod)
+
+        # test installing (only) additional module in Lua syntax (if Lmod is available)
+        lmod_abspath = which('lmod')
+        if lmod_abspath is not None:
+            args = common_args + [
+                '--only-module',
+                '--module-syntax=Lua',
+                '--modules-tool=Lmod',
+            ]
+            self.assertFalse(os.path.exists(toy_mod + '.lua'))
+            self.eb_main(args, do_build=True, raise_error=True)
+            self.assertTrue(os.path.exists(toy_mod + '.lua'))
+            # existing install is reused
+            modtxt3 = read_file(toy_mod + '.lua')
+            self.assertTrue(re.search('local root = "%s"' % prefix, modtxt3))
+            self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 1)
+            self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software', 'toy'))), 1)
 
 def suite():
     """ return all the tests in this file """

From 4141c21a9683204160530d59ec27fab316c06f0f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 16:26:06 +0200
Subject: [PATCH 0904/1356] rename to --module-only fix style remarks, force
 Tcl syntax in --module-only unit test

---
 easybuild/framework/easyblock.py | 64 +++++++++++++++++++-------------
 easybuild/tools/config.py        |  2 +-
 easybuild/tools/options.py       |  2 +-
 test/framework/toy_build.py      | 13 ++++---
 4 files changed, 47 insertions(+), 34 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index cbb480eb1e..03118015f4 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -685,6 +685,9 @@ def gen_installdir(self):
                     self.install_subdir = avail_mnss[install_subdir_ns]().det_full_module_name(self.cfg)
                     self.log.debug("Determined name of install subdir using specified naming scheme %s: %s",
                                    install_subdir_ns, self.install_subdir)
+                else:
+                    raise EasyBuildError("Unknown naming scheme specified for software install (sub)directory: %s",
+                                         install_subdir_ns)
 
             installdir = os.path.join(basepath, self.install_subdir)
             self.installdir = os.path.abspath(installdir)
@@ -963,7 +966,7 @@ def make_module_req(self):
         requirements = self.make_module_req_guess()
 
         lines = []
-        if os.path.exists(self.installdir):
+        if os.path.isdir(self.installdir):
             try:
                 os.chdir(self.installdir)
             except OSError, err:
@@ -1591,7 +1594,7 @@ def sanity_check_step(self, custom_paths=None, custom_commands=None, extension=F
                 self.log.warning("Sanity check: %s" % self.sanity_check_fail_msgs[-1])
 
         # chdir to installdir (better environment for running tests)
-        if os.path.exists(self.installdir):
+        if os.path.isdir(self.installdir):
             try:
                 os.chdir(self.installdir)
             except OSError, err:
@@ -1739,36 +1742,42 @@ def update_config_template_run_step(self):
             self.cfg.template_values[name[0]] = str(getattr(self, name[0], None))
         self.cfg.generate_template_values()
 
-    def run_step(self, step, methods, skippable=False):
-        """
-        Run step, returns false when execution should be stopped
-        """
-        only_module = build_option('only_module')
+    def _skip_step(self, step, skippable):
+        """Dedice whether or not to skip the specified step."""
+        module_only = build_option('module_only')
         force = build_option('force')
         skip = False
 
-        # skip step if specified, either as individual (skippable) step, or when only generating module file
-        # still run sanity check when only generating module
-        skip_individual_step = skippable and (self.skip or step in self.cfg['skipsteps'])
-        only_module_skip = only_module and not step in ['sanitycheck', 'module']
-        if skip_individual_step or only_module_skip:
-            self.log.info("Skipping %s step", step)
+        # skip step if specified as individual (skippable) step
+        if skippable and (self.skip or step in self.cfg['skipsteps']):
+            self.log.info("Skipping %s step (skip: %s, skipsteps: %s)", step, self.skip, self.cfg['skipsteps'])
+            skip = True
+
+        # skip step when only generating module file; still run sanity check without use of force
+        elif module_only and not step in ['sanitycheck', 'module']:
+            self.log.info("Skipping %s step (only generating module)", step)
             skip = True
 
-        # allow skipping sanity check too when only generating module and --force is enable
-        elif only_module and step == 'sanitycheck' and force:
-            self.log.info("Skipping %s step, due to combo of --only-module and --force", step)
+        # allow skipping sanity check too when only generating module and force is used
+        elif module_only and step == 'sanitycheck' and force:
+            self.log.info("Skipping %s step because of forced module-only mode", step)
             skip = True
 
         else:
-            self.log.debug("Not skipping %s step (skippable: %s, skip: %s, skipsteps: %s, only_module: %s, force: %s",
-                           step, skippable, self.skip, self.cfg['skipsteps'], only_module, force)
+            self.log.debug("Not skipping %s step (skippable: %s, skip: %s, skipsteps: %s, module_only: %s, force: %s",
+                           step, skippable, self.skip, self.cfg['skipsteps'], module_only, force)
 
-            self.log.info("Starting %s step", step)
-            self.update_config_template_run_step()
-            for m in methods:
-                self.log.info("Running method %s part of step %s" % ('_'.join(m.func_code.co_names), step))
-                m(self)
+        return skip
+
+    def run_step(self, step, methods):
+        """
+        Run step, returns false when execution should be stopped
+        """
+        self.log.info("Starting %s step", step)
+        self.update_config_template_run_step()
+        for m in methods:
+            self.log.info("Running method %s part of step %s" % ('_'.join(m.func_code.co_names), step))
+            m(self)
 
         if self.cfg['stop'] == step:
             self.log.info("Stopping after %s step.", step)
@@ -1880,9 +1889,12 @@ def run_all_steps(self, run_test_cases):
 
         print_msg("building and installing %s..." % self.full_mod_name, self.log, silent=self.silent)
         try:
-            for (stop_name, descr, step_methods, skippable) in steps:
-                print_msg("%s..." % descr, self.log, silent=self.silent)
-                self.run_step(stop_name, step_methods, skippable=skippable)
+            for (step_name, descr, step_methods, skippable) in steps:
+                if self._skip_step(step_name, skippable):
+                    print_msg("%s [skipped]" % descr, self.log, silent=self.silent)
+                else:
+                    print_msg("%s..." % descr, self.log, silent=self.silent)
+                    self.run_step(step_name, step_methods)
 
         except StopException:
             pass
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 5aaac3c143..31516a9e81 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -91,7 +91,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'ignore_dirs',
         'modules_footer',
         'only_blocks',
-        'only_module',
+        'module_only',
         'optarch',
         'regtest_output_dir',
         'skip',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 4a901d7488..a67e9b35c6 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -207,7 +207,7 @@ def override_options(self):
                           "(e.g. --hide-deps=zlib,ncurses)", 'strlist', 'extend', None),
             'oldstyleconfig':   ("Look for and use the oldstyle configuration file.",
                                  None, 'store_true', True),
-            'only-module': ("Only generate module file", None, 'store_true', False),
+            'module-only': ("Only generate module file (and run sanity check)", None, 'store_true', False),
             'optarch': ("Set architecture optimization, overriding native architecture optimizations",
                         None, 'store', None),
             'pretend': (("Does the build/installation in a test directory located in $HOME/easybuildinstall"),
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 599ac83dc5..4d42b1d49a 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -880,8 +880,8 @@ def test_external_dependencies(self):
         outtxt = self.test_toy_build(ec_file=toy_ec, verbose=True, extra_args=['--dry-run'], verify=False)
         self.assertTrue(re.search(r"^ \* \[ \] .* \(module: toy/0.0-external-deps-broken2\)", outtxt, re.M))
 
-    def test_only_module(self):
-        """Test use of --only-module."""
+    def test_module_only(self):
+        """Test use of --module-only."""
         ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0.eb')
         toy_mod = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0')
 
@@ -896,8 +896,9 @@ def test_only_module(self):
             '--installpath=%s' % self.test_installpath,
             '--debug',
             '--unittest-file=%s' % self.logfile,
+            '--module-syntax=Tcl',
         ]
-        args = common_args + ['--only-module']
+        args = common_args + ['--module-only']
         err_msg = "Sanity check failed"
         self.assertErrorRegex(EasyBuildError, err_msg, self.eb_main, args, do_build=True, raise_error=True)
         self.assertFalse(os.path.exists(toy_mod))
@@ -921,7 +922,7 @@ def test_only_module(self):
 
         # install (only) additional module under a hierarchical MNS
         args = common_args + [
-            '--only-module',
+            '--module-only',
             '--software-installdir-naming-scheme=EasyBuildMNS',
             '--module-naming-scheme=HierarchicalMNS',
         ]
@@ -941,8 +942,8 @@ def test_only_module(self):
         # test installing (only) additional module in Lua syntax (if Lmod is available)
         lmod_abspath = which('lmod')
         if lmod_abspath is not None:
-            args = common_args + [
-                '--only-module',
+            args = common_args[:-1] + [
+                '--module-only',
                 '--module-syntax=Lua',
                 '--modules-tool=Lmod',
             ]

From 30eaa095a0c5169282462cb39e3206a0f97746ee Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 16:49:34 +0200
Subject: [PATCH 0905/1356] drop --software-installdir-naming-scheme, extend
 MNS API with det_install_subdir

---
 easybuild/framework/easyblock.py              | 19 +---------
 easybuild/framework/easyconfig/easyconfig.py  |  7 ++++
 easybuild/tools/config.py                     |  1 -
 easybuild/tools/module_naming_scheme/mns.py   | 12 ++++++
 easybuild/tools/options.py                    |  2 -
 .../migrate_from_eb_to_hmns.py                | 37 +++++++++++++++++++
 test/framework/toy_build.py                   |  3 +-
 7 files changed, 59 insertions(+), 22 deletions(-)
 create mode 100644 test/framework/sandbox/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 03118015f4..74f2396baa 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -674,23 +674,8 @@ def gen_installdir(self):
         """
         basepath = install_path()
         if basepath:
-            install_subdir_ns = build_option('software_installdir_naming_scheme')
-            if install_subdir_ns is None:
-                self.install_subdir = ActiveMNS().det_full_module_name(self.cfg, force_visible=True)
-                self.log.debug("Determined name of install subdir using active module naming scheme: %s",
-                               self.install_subdir)
-            else:
-                avail_mnss = avail_module_naming_schemes()
-                if install_subdir_ns in avail_mnss:
-                    self.install_subdir = avail_mnss[install_subdir_ns]().det_full_module_name(self.cfg)
-                    self.log.debug("Determined name of install subdir using specified naming scheme %s: %s",
-                                   install_subdir_ns, self.install_subdir)
-                else:
-                    raise EasyBuildError("Unknown naming scheme specified for software install (sub)directory: %s",
-                                         install_subdir_ns)
-
-            installdir = os.path.join(basepath, self.install_subdir)
-            self.installdir = os.path.abspath(installdir)
+            self.install_subdir = ActiveMNS().det_install_subdir(self.cfg)
+            self.installdir = os.path.join(os.path.abspath(basepath), self.install_subdir)
             self.log.info("Install dir set to %s" % self.installdir)
         else:
             raise EasyBuildError("Can't set installation directory")
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index bd161ab708..b906186aff 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1090,6 +1090,13 @@ def det_full_module_name(self, ec, force_visible=False):
         self.log.debug("Obtained valid full module name %s" % mod_name)
         return mod_name
 
+    def det_install_subdir(self, ec):
+        """Determine name of software installation subdirectory."""
+        self.log.debug("Determining software installation subdir for %s", ec)
+        subdir = self.mns.det_install_subdir(self.check_ec_type(ec))
+        self.log.debug("Obtained subdir %s", subdir)
+        return subdir
+
     def det_devel_module_filename(self, ec, force_visible=False):
         """Determine devel module filename."""
         modname = self.det_full_module_name(ec, force_visible=force_visible)
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 31516a9e81..85e62878fc 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -95,7 +95,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'optarch',
         'regtest_output_dir',
         'skip',
-        'software_installdir_naming_scheme',
         'stop',
         'suffix_modules_path',
         'test_report_env_filter',
diff --git a/easybuild/tools/module_naming_scheme/mns.py b/easybuild/tools/module_naming_scheme/mns.py
index 29fbb1f3ff..670493fb78 100644
--- a/easybuild/tools/module_naming_scheme/mns.py
+++ b/easybuild/tools/module_naming_scheme/mns.py
@@ -84,6 +84,18 @@ def det_short_module_name(self, ec):
         # by default: full module name doesn't include a $MODULEPATH subdir
         return self.det_full_module_name(ec)
 
+    def det_install_subdir(self, ec):
+        """
+        Determine name of software installation subdirectory of install path.
+
+        @param ec: dict-like object with easyconfig parameter values; for now only the 'name',
+                   'version', 'versionsuffix' and 'toolchain' parameters are guaranteed to be available
+
+        @return: string with name of subdirectory, e.g.: '<compiler>/<mpi_lib>/<name>/<version>'
+        """
+        # by default: use full module name as name for install subdir
+        return self.det_full_module_name(ec)
+
     def det_module_subdir(self, ec):
         """
         Determine subdirectory for module file in $MODULEPATH.
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index a67e9b35c6..4561f66554 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -269,8 +269,6 @@ def config_options(self):
                                 "(is passed as list of arguments to create the repository instance). "
                                 "For more info, use --avail-repositories."),
                                'strlist', 'store', self.default_repositorypath),
-            'software-installdir-naming-scheme': ("Naming scheme for software install (sub)directory "
-                                                  "(default: same as --module-naming-scheme)", None, 'store', None),
             'sourcepath': ("Path(s) to where sources should be downloaded (string, colon-separated)",
                            None, 'store', mk_full_default_path('sourcepath')),
             'subdir-modules': ("Installpath subdir for modules", None, 'store', DEFAULT_PATH_SUBDIRS['subdir_modules']),
diff --git a/test/framework/sandbox/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py b/test/framework/sandbox/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
new file mode 100644
index 0000000000..13c1634b3d
--- /dev/null
+++ b/test/framework/sandbox/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
@@ -0,0 +1,37 @@
+##
+# Copyright 2013-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Implementation of a test module naming scheme that can be used to migrate from EasyBuildMNS to HierarchicalMNS.
+
+@author: Kenneth Hoste (Ghent University)
+"""
+from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS
+from easybuild.tools.module_naming_scheme.hierarchical_mns import HierarchicalMNS
+
+class MigrateFromEBToHMNS(HierarchicalMNS, EasyBuildMNS):
+
+    def det_install_subdir(self, ec):
+        """Determine name of software installation subdirectory of install path, using EasyBuild MNS."""
+        return EasyBuildMNS.det_full_module_name(self, ec)
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 4d42b1d49a..2a577f3b3b 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -923,8 +923,7 @@ def test_module_only(self):
         # install (only) additional module under a hierarchical MNS
         args = common_args + [
             '--module-only',
-            '--software-installdir-naming-scheme=EasyBuildMNS',
-            '--module-naming-scheme=HierarchicalMNS',
+            '--module-naming-scheme=MigrateFromEBToHMNS',
         ]
         toy_core_mod = os.path.join(self.test_installpath, 'modules', 'all', 'Core', 'toy', '0.0')
         self.assertFalse(os.path.exists(toy_core_mod))

From 7cccdb76b532ee1af0b13a9b7fba306c19dbcc41 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 17:08:00 +0200
Subject: [PATCH 0906/1356] define toolchain_family to be used in easyblocks

---
 easybuild/toolchains/compiler/craype.py | 9 +++------
 easybuild/tools/toolchain/toolchain.py  | 5 +++++
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index c91c664fe3..a3a9bd950b 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -58,6 +58,9 @@
 class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     """Generic support for using Cray compiler wrappers"""
 
+    # toolchain family
+    FAMILY = TC_CONSTANT_CRAYPE
+
     # compiler module name is PrgEnv, suffix name depends on CrayPE flavor (gnu, intel, cray)
     COMPILER_MODULE_NAME = None
     # compiler family depends on CrayPE flavor
@@ -238,8 +241,6 @@ def _set_scalapack_variables(self):
 
 class CrayPEGNU(CrayPE):
     """Support for using the Cray GNU compiler wrappers."""
-    TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_GNU'
-
     PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
     COMPILER_FAMILY = TC_CONSTANT_GCC
 
@@ -259,8 +260,6 @@ def _set_compiler_vars(self):
 
 class CrayPEIntel(CrayPE):
     """Support for using the Cray Intel compiler wrappers."""
-    TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_INTEL'
-
     PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
     COMPILER_FAMILY = TC_CONSTANT_INTELCOMP
 
@@ -280,7 +279,5 @@ def _set_compiler_flags(self):
 
 class CrayPECray(CrayPE):
     """Support for using the Cray CCE compiler wrappers."""
-    TC_CONSTANT_CRAYPE = TC_CONSTANT_CRAYPE + '_CRAY'
-
     PRGENV_MODULE_NAME_SUFFIX = 'cray'  # PrgEnv-cray
     COMPILER_FAMILY = TC_CONSTANT_CRAYCE
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index c43ae6f014..7d0298012f 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -55,6 +55,7 @@ class Toolchain(object):
 
     NAME = None
     VERSION = None
+    FAMILY = None
 
     # class method
     def _is_toolchain_for(cls, name):
@@ -448,6 +449,10 @@ def get_flag(self, name):
         """Get compiler flag for a certain option."""
         return "-%s" % self.options.option(name)
 
+    def toolchain_family(self):
+        """Return toolchain family for this toolchain."""
+        return self.FAMILY
+
     def comp_family(self):
         """ Return compiler family used in this toolchain (abstract method)."""
         raise NotImplementedError

From 9f7593c6767423e7c0d8f6886b78f596d47aab3c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 18:32:09 +0200
Subject: [PATCH 0907/1356] fix parsing of external modules metadata, make sure
 name/version are always lists

---
 easybuild/tools/options.py | 12 ++++++++++--
 test/framework/config.py   |  8 ++++----
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 1af6d96211..b150ac5d2a 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -456,14 +456,22 @@ def _postprocess_external_modules_metadata(self):
         parsed_external_modules_metadata = ConfigObj()
         for path in self.options.external_modules_metadata:
             if os.path.exists(path):
+                self.log.debug("Parsing %s with external modules metadata", path)
                 try:
-                    parsed = ConfigObj(path)
+                    parsed_external_modules_metadata.merge(ConfigObj(path))
                 except ConfigObjError, err:
                     raise EasyBuildError("Failed to parse %s with external modules metadata: %s", path, err)
-                parsed_external_modules_metadata.merge(parsed)
             else:
                 raise EasyBuildError("Specified path for file with external modules metadata does not exist: %s", path)
 
+        # make sure name/version values are always lists
+        for mod, entry in parsed_external_modules_metadata.items():
+            for key in ['name', 'version']:
+                if isinstance(entry[key], basestring):
+                    entry[key] = [entry[key]]
+                    self.log.debug("Transformed external module metadata value %s for %s into a single-value list: %s",
+                                   key, mod, entry[key])
+
         self.options.external_modules_metadata = parsed_external_modules_metadata
         self.log.debug("External modules metadata: %s", self.options.external_modules_metadata)
 
diff --git a/test/framework/config.py b/test/framework/config.py
index a1b3d6caae..74fb0f4083 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -48,7 +48,7 @@
 
 EXTERNAL_MODULES_METADATA = """[cray-netcdf/4.3.2]
 name = netCDF,netCDF-Fortran
-version = 4.3.2
+version = 4.3.2,4.3.2
 prefix = NETCDF_DIR
  
 [cray-hdf5/1.8.13]
@@ -604,13 +604,13 @@ def test_external_modules_metadata(self):
 
         netcdf = {
             'name': ['netCDF', 'netCDF-Fortran'],
-            'version': '4.3.2',
+            'version': ['4.3.2', '4.3.2'],
             'prefix': 'NETCDF_DIR',
         }
         self.assertEqual(cfg.external_modules_metadata['cray-netcdf/4.3.2'], netcdf)
         hdf5 = {
-            'name': 'HDF5',
-            'version': '1.8.13',
+            'name': ['HDF5'],
+            'version': ['1.8.13'],
             'prefix': 'HDF5_DIR',
         }
         self.assertEqual(cfg.external_modules_metadata['cray-hdf5/1.8.13'], hdf5)

From f100ddb4370443f99b9e89cff1a09bb6f87379f7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 20:40:33 +0200
Subject: [PATCH 0908/1356] fix remarks

---
 easybuild/framework/easyconfig/easyconfig.py | 25 ++++--
 easybuild/tools/environment.py               |  7 +-
 easybuild/tools/options.py                   | 10 ++-
 easybuild/tools/toolchain/toolchain.py       | 80 ++++++++++----------
 test/framework/config.py                     | 18 +++++
 test/framework/toolchain.py                  | 16 ++--
 6 files changed, 99 insertions(+), 57 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index cbe9e4d65b..ba6a717bc4 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -543,16 +543,24 @@ def _parse_dependency(self, dep, hidden=False):
 
         attr = ['name', 'version', 'versionsuffix', 'toolchain']
         dependency = {
-            'dummy': False,
-            'full_mod_name': None,  # full module name
-            'short_mod_name': None,  # short module name
-            'name': None,  # software name (may be a list of names, e.g. for external modules)
-            'toolchain': None,
+            # full/short module names
+            'full_mod_name': None,
+            'short_mod_name': None,
+            # software name, version, versionsuffix
+            'name': None,
             'version': None,
             'versionsuffix': '',
+            # toolchain with which this dependency is installed
+            'toolchain': None,
+            # boolean indicating whether we're dealing with a dummy toolchain for this dependency
+            'dummy': False,
+            # boolean indicating whether the module for this dependency is (to be) installed hidden
             'hidden': hidden,
+            # boolean indicating whether this dependency should be resolved via an external module
             'external_module': False,
-            'prefix': None,  # installation prefix (only relevant for external modules)
+            # metadata in case this is an external module;
+            # provides information on what this module represents (software name/version, install prefix, ...)
+            'external_modules_metadata': {},
         }
         if isinstance(dep, dict):
             dependency.update(dep)
@@ -577,8 +585,9 @@ def _parse_dependency(self, dep, hidden=False):
                     dependency['short_mod_name'] = dep[0]
                     dependency['full_mod_name'] = dep[0]
                     if dep[0] in self.external_modules_metadata:
-                        dependency.update(self.external_modules_metadata[dep[0]])
-                        self.log.info("Updated dependency info with metadata for external module: %s", dependency)
+                        dependency['external_modules_metadata'].update(self.external_modules_metadata[dep[0]])
+                        self.log.info("Updated dependency info with available metadata for external module %s: %s",
+                                      dep[0], dependency['external_modules_metadata'])
                     else:
                         self.log.info("No metadata available for external module %s", dep[0])
                 else:
diff --git a/easybuild/tools/environment.py b/easybuild/tools/environment.py
index 5ce354f788..cd6b290d77 100644
--- a/easybuild/tools/environment.py
+++ b/easybuild/tools/environment.py
@@ -84,11 +84,14 @@ def setvar(key, value):
     put key in the environment with value
     tracks added keys until write_changes has been called
     """
-    oldval = os.environ.get(key, 'None (not defined)')
+    if key in os.environ:
+        oldval_info = "previous value: '%s'" % os.environ[key]
+    else:
+        oldval_info = "previously undefined"
     # os.putenv() is not necessary. os.environ will call this.
     os.environ[key] = value
     _changes[key] = value
-    _log.info("Environment variable %s set to %s (previous value: %s)", key, value, oldval)
+    _log.info("Environment variable %s set to %s (%s)", key, value, oldval_info)
 
 
 def unset_env_vars(keys):
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index b150ac5d2a..b80a651442 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -464,14 +464,20 @@ def _postprocess_external_modules_metadata(self):
             else:
                 raise EasyBuildError("Specified path for file with external modules metadata does not exist: %s", path)
 
-        # make sure name/version values are always lists
+        # make sure name/version values are always lists, make sure they're equal length
         for mod, entry in parsed_external_modules_metadata.items():
             for key in ['name', 'version']:
-                if isinstance(entry[key], basestring):
+                if isinstance(entry.get(key), basestring):
                     entry[key] = [entry[key]]
                     self.log.debug("Transformed external module metadata value %s for %s into a single-value list: %s",
                                    key, mod, entry[key])
 
+            # if both names and versions are available, lists must be of same length
+            names, versions = entry.get('name'), entry.get('version')
+            if names is not None and versions is not None and len(names) != len(versions):
+                raise EasyBuildError("Different length for lists of names/versions in metadata for external module %s: "
+                                     "names: %s; versions: %s", mod, names, versions)
+
         self.options.external_modules_metadata = parsed_external_modules_metadata
         self.log.debug("External modules metadata: %s", self.options.external_modules_metadata)
 
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index a32edf3eef..6c260cee74 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -318,6 +318,35 @@ def is_dep_in_toolchain_module(self, name):
         """Check whether a specific software name is listed as a dependency in the module for this toolchain."""
         return any(map(lambda m: self.mns.is_short_modname_for(m, name), self.toolchain_dep_mods))
 
+    def _prepare_dependency_external_module(self, dep):
+        """Set environment variables picked up by utility functions for dependencies specified as external modules."""
+        mod_name = dep['full_mod_name']
+        metadata = dep['external_module_metadata']
+        self.log.debug("Defining $EB* environment variables for external module %s", mod_name)
+
+        names = metadata.get('name', [])
+        versions = metadata.get('version', [None]*len(names))
+        self.log.debug("Metadata for external module %s: %s", mod_name, metadata)
+
+        for name, version in zip(names, versions):
+            self.log.debug("Defining $EB* environment variables for external module %s under name %s",
+                           mod_name, name)
+
+            # define $EBROOT env var for install prefix, picked up by get_software_root
+            prefix = metadata.get('prefix')
+            if prefix is not None:
+                if prefix in os.environ:
+                    val = os.environ[prefix]
+                    self.log.debug("Using value of $%s as prefix for external module %s: %s", prefix, mod_name, val)
+                else:
+                    val = prefix
+                    self.log.debug("Using specified prefix for external module %s: %s", mod_name, val)
+                setvar(get_software_root_env_var_name(name), val)
+
+            # define $EBVERSION env var for software version, picked up by get_software_version
+            if version is not None:
+                setvar(get_software_version_env_var_name(name), version)
+
     def _prepare_dependencies(self):
         """Load modules for dependencies, and handle special cases like external modules."""
         # load modules for all dependencies
@@ -327,33 +356,7 @@ def _prepare_dependencies(self):
 
         # define $EBROOT* and $EBVERSION* for external modules, if metadata is available
         for dep in [d for d in self.dependencies if d['external_module']]:
-            self.log.debug("Defining $EB* environment variables for external module %s", dep['short_mod_name'])
-
-            names = dep['name'] or []
-            if isinstance(names, basestring):
-                names = [names]
-            self.log.debug("Software names for external module %s: %s", dep['short_mod_name'], names)
-
-            for name in names:
-                self.log.debug("Defining $EB* environment variables for external module %s under name %s",
-                               dep['short_mod_name'], name)
-
-                # install prefix, picked up by get_software_root
-                prefix = dep['prefix']
-                if prefix is not None:
-                    if prefix in os.environ:
-                        prefix = os.environ[prefix]
-                        self.log.debug("Using value of $%s as prefix for external module %s: %s",
-                                       dep['prefix'], dep['short_mod_name'], prefix)
-                    else:
-                        self.log.debug("Using specified prefix for external module %s: %s",
-                                       dep['short_mod_name'], prefix)
-
-                    setvar(get_software_root_env_var_name(name), prefix)
-
-                # $EBVERSION
-                if dep['version'] is not None:
-                    setvar(get_software_version_env_var_name(name), dep['version'])
+            self._prepare_dependency_external_module(dep)
 
     def prepare(self, onlymod=None):
         """
@@ -453,20 +456,19 @@ def _add_dependency_variables(self, names=None, cpp=None, ld=None):
         else:
             deps = [{'name': name} for name in names if name is not None]
 
-        dep_names = []
+        # collect software install prefixes for dependencies
+        roots = []
         for dep in deps:
-            # name may be None or a list of names for external modules
-            if dep['name'] is not None:
-                if isinstance(dep['name'], list):
-                    dep_names.extend(dep['name'])
-                else:
-                    dep_names.append(dep['name'])
+            if dep.get('external_module', False):
+                # for software names provided via external modules, install prefix may be unknown
+                names = dep['external_module_metadata'].get('name', [])
+                roots.extend([root for root in self.get_software_root(names) if root is not None])
+            else:
+                roots.extend(self.get_software_root(dep['name']))
 
-        for root in self.get_software_root(dep_names):
-            # software install prefix may be None for external modules
-            if root is not None:
-                self.variables.append_subdirs("CPPFLAGS", root, subdirs=cpp_paths)
-                self.variables.append_subdirs("LDFLAGS", root, subdirs=ld_paths)
+        for root in roots:
+            self.variables.append_subdirs("CPPFLAGS", root, subdirs=cpp_paths)
+            self.variables.append_subdirs("LDFLAGS", root, subdirs=ld_paths)
 
     def _setenv_variables(self, donotset=None):
         """Actually set the environment variables"""
diff --git a/test/framework/config.py b/test/framework/config.py
index 74fb0f4083..82474bd55d 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -55,6 +55,14 @@
 name = HDF5
 version = 1.8.13
 prefix = HDF5_DIR
+
+[foo]
+name = Foo
+prefix = /foo
+
+[bar/1.2.3]
+name = bar
+version = 1.2.3
 """
 
 class EasyBuildConfigTest(EnhancedTestCase):
@@ -615,6 +623,16 @@ def test_external_modules_metadata(self):
         }
         self.assertEqual(cfg.external_modules_metadata['cray-hdf5/1.8.13'], hdf5)
 
+        # impartial metadata is fine
+        self.assertEqual(cfg.external_modules_metadata['foo'], {'name': ['Foo'], 'prefix': '/foo'})
+        self.assertEqual(cfg.external_modules_metadata['bar/1.2.3'], {'name': ['bar'], 'version': ['1.2.3']})
+
+        # if both names and versions are specified, lists must have same lengths
+        write_file(testcfg, '\n'.join(['[foo/1.2.3]', 'name = foo,bar', 'version = 1.2.3']))
+        args = ['--external-modules-metadata=%s' % testcfg]
+        err_msg = "Different length for lists of names/versions in metadata for external module"
+        self.assertErrorRegex(EasyBuildError, err_msg, init_config, args=args)
+
 
 def suite():
     return TestLoader().loadTestsFromTestCase(EasyBuildConfigTest)
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index cf6d54e586..e5f1d9890f 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -570,6 +570,7 @@ def test_prepare_deps_external(self):
                 'full_mod_name': 'OpenMPI/1.6.4-GCC-4.6.4',
                 'short_mod_name': 'OpenMPI/1.6.4-GCC-4.6.4',
                 'external_module': False,
+                'external_module_metadata': {},
             },
             # no metadata available
             {
@@ -578,6 +579,7 @@ def test_prepare_deps_external(self):
                 'full_mod_name': 'toy/0.0',
                 'short_mod_name': 'toy/0.0',
                 'external_module': True,
+                'external_module_metadata': {},
             }
         ]
         tc = self.get_toolchain('GCC', version='4.6.4')
@@ -591,12 +593,14 @@ def test_prepare_deps_external(self):
 
         # with metadata
         deps[1] = {
-            'name': ['toy', 'foobar'],
-            'version': '1.2.3.4.5',
-            'prefix': 'FOOBAR_PREFIX',
             'full_mod_name': 'toy/0.0',
             'short_mod_name': 'toy/0.0',
             'external_module': True,
+            'external_module_metadata': {
+                'name': ['toy', 'foobar'],
+                'version': ['1.2.3', '4.5'],
+                'prefix': 'FOOBAR_PREFIX',
+            }
         }
         tc = self.get_toolchain('GCC', version='4.6.4')
         tc.add_dependencies(deps)
@@ -605,12 +609,12 @@ def test_prepare_deps_external(self):
         mods = ['GCC/4.6.4', 'hwloc/1.6.2-GCC-4.6.4', 'OpenMPI/1.6.4-GCC-4.6.4', 'toy/0.0']
         self.assertTrue([m['mod_name'] for m in modules_tool().list()], mods)
         self.assertEqual(os.environ['EBROOTTOY'], '/foo/bar')
-        self.assertEqual(os.environ['EBVERSIONTOY'], '1.2.3.4.5')
+        self.assertEqual(os.environ['EBVERSIONTOY'], '1.2.3')
         self.assertEqual(os.environ['EBROOTFOOBAR'], '/foo/bar')
-        self.assertEqual(os.environ['EBVERSIONFOOBAR'], '1.2.3.4.5')
+        self.assertEqual(os.environ['EBVERSIONFOOBAR'], '4.5')
 
         self.assertEqual(modules.get_software_root('foobar'), '/foo/bar')
-        self.assertEqual(modules.get_software_version('toy'), '1.2.3.4.5')
+        self.assertEqual(modules.get_software_version('toy'), '1.2.3')
 
 
 def suite():

From bbbceb15212219c597cd27a61e6f8721998a9e9b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 21:51:26 +0200
Subject: [PATCH 0909/1356] fix broken tests

---
 easybuild/framework/easyconfig/easyconfig.py |  6 +++---
 easybuild/tools/toolchain/toolchain.py       |  3 +--
 test/framework/easyconfig.py                 | 20 ++++++++++++--------
 3 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index ba6a717bc4..a9a2653abc 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -560,7 +560,7 @@ def _parse_dependency(self, dep, hidden=False):
             'external_module': False,
             # metadata in case this is an external module;
             # provides information on what this module represents (software name/version, install prefix, ...)
-            'external_modules_metadata': {},
+            'external_module_metadata': {},
         }
         if isinstance(dep, dict):
             dependency.update(dep)
@@ -585,9 +585,9 @@ def _parse_dependency(self, dep, hidden=False):
                     dependency['short_mod_name'] = dep[0]
                     dependency['full_mod_name'] = dep[0]
                     if dep[0] in self.external_modules_metadata:
-                        dependency['external_modules_metadata'].update(self.external_modules_metadata[dep[0]])
+                        dependency['external_module_metadata'].update(self.external_modules_metadata[dep[0]])
                         self.log.info("Updated dependency info with available metadata for external module %s: %s",
-                                      dep[0], dependency['external_modules_metadata'])
+                                      dep[0], dependency['external_module_metadata'])
                     else:
                         self.log.info("No metadata available for external module %s", dep[0])
                 else:
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 6c260cee74..3b43b22df5 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -329,8 +329,7 @@ def _prepare_dependency_external_module(self, dep):
         self.log.debug("Metadata for external module %s: %s", mod_name, metadata)
 
         for name, version in zip(names, versions):
-            self.log.debug("Defining $EB* environment variables for external module %s under name %s",
-                           mod_name, name)
+            self.log.debug("Defining $EB* environment variables for external module %s under name %s", mod_name, name)
 
             # define $EBROOT env var for install prefix, picked up by get_software_root
             prefix = metadata.get('prefix')
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 646d2cccc4..9fae6bd83e 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -580,7 +580,7 @@ def test_obtain_easyconfig(self):
                 'full_mod_name': 'foo/1.2.3-GCC-4.4.5',
                 'hidden': False,
                 'external_module': False,
-                'prefix': None,
+                'external_module_metadata': {},
             },
             {
                 'name': 'bar',
@@ -592,7 +592,7 @@ def test_obtain_easyconfig(self):
                 'full_mod_name': 'bar/666-gompi-1.4.10-bleh',
                 'hidden': False,
                 'external_module': False,
-                'prefix': None,
+                'external_module_metadata': {},
             },
             {
                 'name': 'test',
@@ -604,7 +604,7 @@ def test_obtain_easyconfig(self):
                 'full_mod_name': 'test/.3.2.1-GCC-4.4.5',
                 'hidden': True,
                 'external_module': False,
-                'prefix': None,
+                'external_module_metadata': {},
             },
         ]
 
@@ -1071,19 +1071,23 @@ def test_external_dependencies(self):
         self.assertEqual([d['external_module'] for d in deps], [False, True, True])
 
         metadata = os.path.join(self.test_prefix, 'external_modules_metadata.cfg')
-        metadatatxt = '\n'.join(['[foobar/1.2.3]', 'name = foobar,bar', 'version = 1.2.3', 'prefix = /foo/bar'])
+        metadatatxt = '\n'.join(['[foobar/1.2.3]', 'name = foo,bar', 'version = 1.2.3,3.2.1', 'prefix = /foo/bar'])
         write_file(metadata, metadatatxt)
+        cfg = init_config(args=['--external-modules-metadata=%s' % metadata])
         build_options = {
+            'external_modules_metadata': cfg.external_modules_metadata,
             'valid_module_classes': module_classes(),
-            'external_modules_metadata': ConfigObj(metadata),
         }
         init_config(build_options=build_options)
         ec = EasyConfig(toy_ec)
         self.assertEqual(ec.dependencies()[1]['short_mod_name'], 'foobar/1.2.3')
         self.assertEqual(ec.dependencies()[1]['external_module'], True)
-        self.assertEqual(ec.dependencies()[1]['name'], ['foobar', 'bar'])
-        self.assertEqual(ec.dependencies()[1]['version'], '1.2.3')
-        self.assertEqual(ec.dependencies()[1]['prefix'], '/foo/bar')
+        metadata = {
+            'name': ['foo', 'bar'],
+            'version': ['1.2.3', '3.2.1'],
+            'prefix': '/foo/bar',
+        }
+        self.assertEqual(ec.dependencies()[1]['external_module_metadata'], metadata)
 
     def test_update(self):
         """Test use of update() method for EasyConfig instances."""

From fcda0a9c3bf767982214e54dbeafe51774f21d23 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 22:02:19 +0200
Subject: [PATCH 0910/1356] remove unused usewrappercompiler option

---
 easybuild/toolchains/compiler/craype.py | 39 ++++---------------------
 1 file changed, 5 insertions(+), 34 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index a3a9bd950b..e987ebcc06 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -39,8 +39,8 @@
 """
 import os
 
-from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC, Gcc
-from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP, IntelIccIfort
+from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC
+from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP
 from easybuild.toolchains.fft.fftw import Fftw
 from easybuild.toolchains.mpi.mpich import TC_CONSTANT_MPICH, TC_CONSTANT_MPI_TYPE_MPICH
 from easybuild.tools.build_log import EasyBuildError
@@ -57,7 +57,6 @@
 
 class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     """Generic support for using Cray compiler wrappers"""
-
     # toolchain family
     FAMILY = TC_CONSTANT_CRAYPE
 
@@ -68,13 +67,11 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
 
     COMPILER_UNIQUE_OPTS = {
         'dynamic': (False, "Generate dynamically linked executable"),
-        # FIXME: drop unused mpich-mt, usewrappedcompiler support?
         'mpich-mt': (False, "Directs the driver to link in an alternate version of the Cray-MPICH library which \
                              provides fine-grained multi-threading support to applications that perform \
                              MPI operations within threaded regions."),
-        'usewrappedcompiler': (False, "Use the embedded compiler instead of the wrapper"),
-        'verbose': (True, "Verbose output"),
         'optarch': (False, "Enable architecture optimizations"),
+        'verbose': (True, "Verbose output"),
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
@@ -126,8 +123,8 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     # BLAS/LAPACK support
     # via cray-libsci module, which gets loaded via the PrgEnv module
     # see https://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/
-    BLAS_MODULE_NAME = ['cray-libsci']  # FIXME: let this load via PrgEnv, and so not list it here (or filter it out of definition)?
-    # specific library depends on PrgEnv flavor
+    BLAS_MODULE_NAME = ['cray-libsci']
+    # no need to specify libraries, compiler driver takes care of linking the right libraries
     BLAS_LIB = []
     BLAS_LIB_MT = []
 
@@ -244,38 +241,12 @@ class CrayPEGNU(CrayPE):
     PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
     COMPILER_FAMILY = TC_CONSTANT_GCC
 
-    # FIXME: drop this?
-    def _set_compiler_vars(self):
-        """Set compiler variables, either for the compiler wrapper, or the underlying compiler."""
-        if self.options.option('usewrappedcompiler'):
-            self.log.info("Using underlying compiler, as specified by the %s class" % Gcc)
-
-            comp_attrs = ['UNIQUE_OPTS', 'UNIQUE_OPTION_MAP', 'CC', 'CXX', 'C_UNIQUE_FLAGS',
-                          'F77', 'F90', 'F_UNIQUE_FLAGS']
-            for attr_name in ['COMPILER_%s' % a for a in comp_attrs]:
-                setattr(self, attr_name, getattr(Gcc, attr_name))
-
-        super(CrayPEGNU,self)._set_compiler_vars()
-
 
 class CrayPEIntel(CrayPE):
     """Support for using the Cray Intel compiler wrappers."""
     PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
     COMPILER_FAMILY = TC_CONSTANT_INTELCOMP
 
-    # FIXME: drop this?
-    def _set_compiler_flags(self):
-        """Set compiler variables, either for the compiler wrapper, or the underlying compiler."""
-        if self.options.option("usewrappedcompiler"):
-            self.log.info("Using underlying compiler, as specified by the %s class" % IntelIccIfort)
-
-            comp_attrs = ['UNIQUE_OPTS', 'UNIQUE_OPTION_MAP', 'CC', 'CXX', 'C_UNIQUE_FLAGS',
-                          'F77', 'F90', 'F_UNIQUE_FLAGS']
-            for attr_name in ['COMPILER_%s' % a for a in comp_attrs] + ['LINKER_TOGGLE_STATIC_DYNAMIC']:
-                setattr(self, attr_name, getattr(IntelIccIfort, attr_name))
-
-        super(CrayPEIntel, self).set_compiler_flags()
-
 
 class CrayPECray(CrayPE):
     """Support for using the Cray CCE compiler wrappers."""

From 20186ec78cc10b5f0d73e539b1f8cbb8571bfe3f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 23:17:46 +0200
Subject: [PATCH 0911/1356] refactor Cray support in separate modules for
 different toolchain components

---
 easybuild/toolchains/compiler/craype.py | 148 ++----------------------
 easybuild/toolchains/craycce.py         |  18 ++-
 easybuild/toolchains/craygnu.py         |  20 +++-
 easybuild/toolchains/crayintel.py       |  20 +++-
 easybuild/toolchains/fft/crayfftw.py    |  71 ++++++++++++
 easybuild/toolchains/linalg/libsci.py   |  76 ++++++++++++
 easybuild/toolchains/mpi/craype.py      |  79 +++++++++++++
 easybuild/tools/toolchain/toolchain.py  |   4 +-
 8 files changed, 279 insertions(+), 157 deletions(-)
 create mode 100644 easybuild/toolchains/fft/crayfftw.py
 create mode 100644 easybuild/toolchains/linalg/libsci.py
 create mode 100644 easybuild/toolchains/mpi/craype.py

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index d7e6ee3ffc..c9af95fea2 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -37,28 +37,20 @@
 @author: Petar Forai (IMP/IMBA, Austria)
 @author: Kenneth Hoste (Ghent University)
 """
-import os
-
 from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC
 from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP
-from easybuild.toolchains.fft.fftw import Fftw
-from easybuild.toolchains.mpi.mpich import TC_CONSTANT_MPICH, TC_CONSTANT_MPI_TYPE_MPICH
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.toolchain.compiler import Compiler
-from easybuild.tools.toolchain.constants import COMPILER_VARIABLES, MPI_COMPILER_TEMPLATE, SEQ_COMPILER_TEMPLATE
-from easybuild.tools.toolchain.linalg import LinAlg
-from easybuild.tools.toolchain.mpi import Mpi
 
 
 TC_CONSTANT_CRAYPE = "CrayPE"
 TC_CONSTANT_CRAYCE = "CrayCE"
 
 
-class CrayPE(Compiler, Mpi, LinAlg, Fftw):
-    """Generic support for using Cray compiler wrappers"""
-    # toolchain family
-    FAMILY = TC_CONSTANT_CRAYPE
+class CrayPECompiler(Compiler):
+    """Generic support for using Cray compiler drivers."""
+    TOOLCHAIN_FAMILY = TC_CONSTANT_CRAYPE
 
     # compiler module name is PrgEnv, suffix name depends on CrayPE flavor (gnu, intel, cray)
     COMPILER_MODULE_NAME = None
@@ -80,19 +72,6 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
         'static': 'static',
         'verbose': 'craype-verbose',
         'mpich-mt': 'craympich-mt',
-        # no optimization flags
-        # FIXME enable?
-        'noopt': [],
-        'lowopt': [],
-        'defaultopt': [],
-        'opt': [],
-        # no precision flags
-        # FIXME enable?
-        'strict': [],
-        'precise': [],
-        'defaultprec': [],
-        'loose': [],
-        'veryloose': [],
     }
 
     COMPILER_CC = 'cc'
@@ -101,44 +80,6 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     COMPILER_F77 = 'ftn'
     COMPILER_F90 = 'ftn'
 
-    # MPI support
-    # no separate module, Cray compiler drivers always provide MPI support
-    MPI_MODULE_NAME = []
-    MPI_FAMILY = TC_CONSTANT_MPICH
-    MPI_TYPE = TC_CONSTANT_MPI_TYPE_MPICH
-
-    MPI_COMPILER_MPICC = COMPILER_CC
-    MPI_COMPILER_MPICXX = COMPILER_CXX
-    MPI_COMPILER_MPIF77 = COMPILER_F77
-    MPI_COMPILER_MPIF90 = COMPILER_F90
-
-    # no MPI wrappers, so no need to specify serial compiler
-    MPI_SHARED_OPTION_MAP = {
-        '_opt_MPICC': '',
-        '_opt_MPICXX': '',
-        '_opt_MPIF77': '',
-        '_opt_MPIF90': '',
-    }
-
-    # BLAS/LAPACK support
-    # via cray-libsci module, which gets loaded via the PrgEnv module
-    # see https://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/
-    BLAS_MODULE_NAME = ['cray-libsci']
-
-    # no need to specify libraries, compiler driver takes care of linking the right libraries
-    # FIXME: need to revisit this, on numpy we ended up with a serial BLAS through the wrapper.
-    BLAS_LIB = []
-    BLAS_LIB_MT = []
-
-    LAPACK_MODULE_NAME = ['cray-libsci']
-    LAPACK_IS_BLAS = True
-
-    BLACS_MODULE_NAME = []
-    SCALAPACK_MODULE_NAME = []
-
-    # FFT support, via Cray-provided fftw module
-    FFT_MODULE_NAME = ['fftw']
-
     # suffix for PrgEnv module that matches this toolchain
     # e.g. 'gnu' => 'PrgEnv-gnu/<version>'
     PRGENV_MODULE_NAME_SUFFIX = None
@@ -146,21 +87,15 @@ class CrayPE(Compiler, Mpi, LinAlg, Fftw):
     # template for craype module (determines code generator backend of Cray compiler wrappers)
     CRAYPE_MODULE_NAME_TEMPLATE = 'craype-%(optarch)s'
 
-    # FIXME: add support for hugepages and accelerator modules that belong to CrayPE and allow to load modules
-    # CRAYPE_HUGEMEM_MODULE_NAME_TEMPLATE = 'craype-hugepages%(hugemagesize)s'
-    # CRAYPE_ACCEL_MODULE_NAME_TEMPLATE = 'craype-accel-%(acceltgt)s' 
-
     def __init__(self, *args, **kwargs):
         """Constructor."""
-        super(CrayPE, self).__init__(*args, **kwargs)
+        super(CrayPECompiler, self).__init__(*args, **kwargs)
         # 'register'  additional toolchain options that correspond to a compiler flag
         self.COMPILER_FLAGS.extend(['dynamic'])
 
         # use name of PrgEnv module as name of module that provides compiler
         self.COMPILER_MODULE_NAME = ['PrgEnv-%s' % self.PRGENV_MODULE_NAME_SUFFIX]
 
-        # FIXME: force use of --experimental
-
     def _set_optimal_architecture(self):
         """Load craype module specified via 'optarch' build option."""
         optarch = build_option('optarch')
@@ -172,89 +107,20 @@ def _set_optimal_architecture(self):
         # no compiler flag when optarch toolchain option is enabled
         self.options.options_map['optarch'] = ''
 
-    def _set_mpi_compiler_variables(self):
-        """Set the MPI compiler variables"""
-        for var_tuple in COMPILER_VARIABLES:
-            c_var = var_tuple[0]  # [1] is the description
-            var = MPI_COMPILER_TEMPLATE % {'c_var':c_var}
-
-            value = getattr(self, 'MPI_COMPILER_%s' % var.upper(), None)
-            if value is None:
-                raise EasyBuildError("_set_mpi_compiler_variables: mpi compiler variable %s undefined", var)
-            self.variables.nappend_el(var, value)
-
-            if self.options.get('usempi', None):
-                var_seq = SEQ_COMPILER_TEMPLATE % {'c_var': c_var}
-                seq_comp = self.variables[c_var]
-                self.log.debug('_set_mpi_compiler_variables: usempi set: defining %s as %s', var_seq, seq_comp)
-                self.variables[var_seq] = seq_comp
-
-        if self.options.get('cciscxx', None):
-            self.log.debug("_set_mpi_compiler_variables: cciscxx set: switching MPICXX %s for MPICC value %s" %
-                           (self.variables['MPICXX'], self.variables['MPICC']))
-            self.variables['MPICXX'] = self.variables['MPICC']
-
-    def _get_software_root(self, name):
-        """Get install prefix for specified software name; special treatment for Cray modules."""
-        if name == 'cray-libsci':
-            # Cray-provided LibSci module
-            env_var = 'CRAY_LIBSCI_PREFIX_DIR'
-            root = os.getenv(env_var, None)
-            if root is None:
-                raise EasyBuildError("Failed to determine install prefix for %s via $%s", name, env_var)
-            else:
-                self.log.debug("Obtained install prefix for %s via $%s: %s", name, env_var, root)
-        elif name == 'fftw':
-            # Cray-provided fftw module
-            env_var = 'FFTW_INC'
-            incdir = os.getenv(env_var, None)
-            if incdir is None:
-                raise EasyBuildError("Failed to determine install prefix for %s via $%s", name, env_var)
-            else:
-                root = os.path.dirname(incdir)
-                self.log.debug("Obtained install prefix for %s via $%s: %s", name, env_var, root)
-        else:
-            root = super(CrayPE, self)._get_software_root(name)
-
-        return root
-
-    def _get_software_version(self, name):
-        """Get version for specified software name; special treatment for Cray modules."""
-        if name == 'fftw':
-            # Cray-provided fftw module
-            env_var = 'FFTW_VERSION'
-            ver = os.getenv(env_var, None)
-            if ver is None:
-                raise EasyBuildError("Failed to determine version for %s via $%s", name, env_var)
-            else:
-                self.log.debug("Obtained version for %s via $%s: %s", name, env_var, ver)
-        else:
-            ver = super(CrayPE, self)._get_software_version(name)
-
-        return ver
-
-    def _set_blacs_variables(self):
-        """Skip setting BLACS related variables"""
-        pass
-
-    def _set_scalapack_variables(self):
-        """Skip setting ScaLAPACK related variables"""
-        pass
-
 
-class CrayPEGNU(CrayPE):
+class CrayPEGCC(CrayPECompiler):
     """Support for using the Cray GNU compiler wrappers."""
     PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
     COMPILER_FAMILY = TC_CONSTANT_GCC
 
 
-class CrayPEIntel(CrayPE):
+class CrayPEIntel(CrayPECompiler):
     """Support for using the Cray Intel compiler wrappers."""
     PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
     COMPILER_FAMILY = TC_CONSTANT_INTELCOMP
 
 
-class CrayPECray(CrayPE):
+class CrayPECray(CrayPECompiler):
     """Support for using the Cray CCE compiler wrappers."""
     PRGENV_MODULE_NAME_SUFFIX = 'cray'  # PrgEnv-cray
     COMPILER_FAMILY = TC_CONSTANT_CRAYCE
diff --git a/easybuild/toolchains/craycce.py b/easybuild/toolchains/craycce.py
index 18c799c7ae..94e166e3ff 100644
--- a/easybuild/toolchains/craycce.py
+++ b/easybuild/toolchains/craycce.py
@@ -23,12 +23,22 @@
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
 """
-@author: Petar Forai
-"""
-
+CrayCCE toolchain: Cray compilers (CCE) and MPI via Cray compiler drivers + LibSci (PrgEnv-cray) and Cray FFTW
 
+@author: Petar Forai (IMP/IMBA, Austria)
+@author: Kenneth Hoste (Ghent University)
+"""
 from easybuild.toolchains.compiler.craype import CrayPECray
+from easybuild.toolchains.fft.crayfftw import CrayFFTW
+from easybuild.toolchains.linalg.libsci import LibSci
+from easybuild.toolchains.mpi.craype import CrayPEMPI
 
-class CrayCCE(CrayPECray):
+
+class CrayCCE(CrayPECray, CrayPEMPI, LibSci, CrayFFTW):
     """Compiler toolchain for Cray Programming Environment for Cray Compiling Environment (CCE) (PrgEnv-cray)."""
     NAME = 'CrayCCE'
+
+    def prepare(self, *args, **kwargs):
+        """Prepare to use this toolchain; marked as experimental."""
+        super(CrayCCE, self).prepare(*args, **kwargs)
+        self.log.experimental("%s toolchain", self.NAME)
diff --git a/easybuild/toolchains/craygnu.py b/easybuild/toolchains/craygnu.py
index 2386dcaa0e..8ef88b7b01 100644
--- a/easybuild/toolchains/craygnu.py
+++ b/easybuild/toolchains/craygnu.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2014 Petar Forai
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -23,12 +23,22 @@
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
 """
-@author: Petar Forai
-"""
+CrayGNU toolchain: GCC and MPI via Cray compiler drivers + LibSci (PrgEnv-gnu) and Cray FFTW
 
+@author: Petar Forai (IMP/IMBA, Austria)
+@author: Kenneth Hoste (Ghent University)
+"""
+from easybuild.toolchains.compiler.craype import CrayPEGCC
+from easybuild.toolchains.fft.crayfftw import CrayFFTW
+from easybuild.toolchains.linalg.libsci import LibSci
+from easybuild.toolchains.mpi.craype import CrayPEMPI
 
-from easybuild.toolchains.compiler.craype import CrayPEGNU
 
-class CrayGNU(CrayPEGNU):
+class CrayGNU(CrayPEGCC, CrayPEMPI, LibSci, CrayFFTW):
     """Compiler toolchain for Cray Programming Environment for GCC compilers (PrgEnv-gnu)."""
     NAME = 'CrayGNU'
+
+    def prepare(self, *args, **kwargs):
+        """Prepare to use this toolchain; marked as experimental."""
+        super(CrayGNU, self).prepare(*args, **kwargs)
+        self.log.experimental("%s toolchain", self.NAME)
diff --git a/easybuild/toolchains/crayintel.py b/easybuild/toolchains/crayintel.py
index b2049902a3..3a5c0e0fdb 100644
--- a/easybuild/toolchains/crayintel.py
+++ b/easybuild/toolchains/crayintel.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2014 Petar Forai
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -23,12 +23,22 @@
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
 """
-@author: Petar Forai
-"""
-
+CrayIntel toolchain: Intel compilers and MPI via Cray compiler drivers + LibSci (PrgEnv-intel) and Cray FFTW
 
+@author: Petar Forai (IMP/IMBA, Austria)
+@author: Kenneth Hoste (Ghent University)
+"""
 from easybuild.toolchains.compiler.craype import CrayPEIntel
+from easybuild.toolchains.fft.crayfftw import CrayFFTW
+from easybuild.toolchains.linalg.libsci import LibSci
+from easybuild.toolchains.mpi.craype import CrayPEMPI
 
-class CrayIntel(CrayPEIntel):
+
+class CrayIntel(CrayPEIntel, CrayPEMPI, LibSci, CrayFFTW):
     """Compiler toolchain for Cray Programming Environment for Intel compilers (PrgEnv-intel)."""
     NAME = 'CrayIntel'
+
+    def prepare(self, *args, **kwargs):
+        """Prepare to use this toolchain; marked as experimental."""
+        super(CrayIntel, self).prepare(*args, **kwargs)
+        self.log.experimental("%s toolchain", self.NAME)
diff --git a/easybuild/toolchains/fft/crayfftw.py b/easybuild/toolchains/fft/crayfftw.py
new file mode 100644
index 0000000000..b575cbc9d9
--- /dev/null
+++ b/easybuild/toolchains/fft/crayfftw.py
@@ -0,0 +1,71 @@
+##
+# Copyright 2014-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Support for Cray FFTW.
+
+@author: Petar Forai (IMP/IMBA, Austria)
+@author: Kenneth Hoste (Ghent University)
+"""
+import os
+
+from easybuild.toolchains.fft.fftw import Fftw
+from easybuild.tools.build_log import EasyBuildError
+
+
+class CrayFFTW(Fftw):
+    """Support for Cray FFTW."""
+    # FFT support, via Cray-provided fftw module
+    FFT_MODULE_NAME = ['fftw']
+
+    def _get_software_root(self, name):
+        """Get install prefix for specified software name; special treatment for Cray modules."""
+        if name == 'fftw':
+            # Cray-provided fftw module
+            env_var = 'FFTW_INC'
+            incdir = os.getenv(env_var, None)
+            if incdir is None:
+                raise EasyBuildError("Failed to determine install prefix for %s via $%s", name, env_var)
+            else:
+                root = os.path.dirname(incdir)
+                self.log.debug("Obtained install prefix for %s via $%s: %s", name, env_var, root)
+        else:
+            root = super(CrayFFTW, self)._get_software_root(name)
+
+        return root
+
+    def _get_software_version(self, name):
+        """Get version for specified software name; special treatment for Cray modules."""
+        if name == 'fftw':
+            # Cray-provided fftw module
+            env_var = 'FFTW_VERSION'
+            ver = os.getenv(env_var, None)
+            if ver is None:
+                raise EasyBuildError("Failed to determine version for %s via $%s", name, env_var)
+            else:
+                self.log.debug("Obtained version for %s via $%s: %s", name, env_var, ver)
+        else:
+            ver = super(CrayFFTW, self)._get_software_version(name)
+
+        return ver
diff --git a/easybuild/toolchains/linalg/libsci.py b/easybuild/toolchains/linalg/libsci.py
new file mode 100644
index 0000000000..e8a8f93505
--- /dev/null
+++ b/easybuild/toolchains/linalg/libsci.py
@@ -0,0 +1,76 @@
+##
+# Copyright 2014-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Support for Cray's LibSci library, which provides BLAS/LAPACK support.
+cfr. https://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/
+
+@author: Petar Forai (IMP/IMBA, Austria)
+@author: Kenneth Hoste (Ghent University)
+"""
+import os
+
+from easybuild.tools.toolchain.linalg import LinAlg
+
+
+class LibSci(LinAlg):
+    """Support for Cray's LibSci library, which provides BLAS/LAPACK support."""
+    # BLAS/LAPACK support
+    # via cray-libsci module, which gets loaded via the PrgEnv module
+    # see https://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/
+    BLAS_MODULE_NAME = ['cray-libsci']
+
+    # no need to specify libraries, compiler driver takes care of linking the right libraries
+    # FIXME: need to revisit this, on numpy we ended up with a serial BLAS through the wrapper.
+    BLAS_LIB = []
+    BLAS_LIB_MT = []
+
+    LAPACK_MODULE_NAME = ['cray-libsci']
+    LAPACK_IS_BLAS = True
+
+    BLACS_MODULE_NAME = []
+    SCALAPACK_MODULE_NAME = []
+
+    def _get_software_root(self, name):
+        """Get install prefix for specified software name; special treatment for Cray modules."""
+        if name == 'cray-libsci':
+            # Cray-provided LibSci module
+            env_var = 'CRAY_LIBSCI_PREFIX_DIR'
+            root = os.getenv(env_var, None)
+            if root is None:
+                raise EasyBuildError("Failed to determine install prefix for %s via $%s", name, env_var)
+            else:
+                self.log.debug("Obtained install prefix for %s via $%s: %s", name, env_var, root)
+        else:
+            root = super(LibSci, self)._get_software_root(name)
+
+        return root
+
+    def _set_blacs_variables(self):
+        """Skip setting BLACS related variables"""
+        pass
+
+    def _set_scalapack_variables(self):
+        """Skip setting ScaLAPACK related variables"""
+        pass
diff --git a/easybuild/toolchains/mpi/craype.py b/easybuild/toolchains/mpi/craype.py
new file mode 100644
index 0000000000..72253c2ffb
--- /dev/null
+++ b/easybuild/toolchains/mpi/craype.py
@@ -0,0 +1,79 @@
+##
+# Copyright 2014-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+MPI support for the Cray Programming Environment (craype).
+
+@author: Petar Forai (IMP/IMBA, Austria)
+@author: Kenneth Hoste (Ghent University)
+"""
+from easybuild.toolchains.compiler.craype import CrayPECompiler
+from easybuild.toolchains.mpi.mpich import TC_CONSTANT_MPICH, TC_CONSTANT_MPI_TYPE_MPICH
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.toolchain.constants import COMPILER_VARIABLES, MPI_COMPILER_TEMPLATE, SEQ_COMPILER_TEMPLATE
+from easybuild.tools.toolchain.mpi import Mpi
+
+
+class CrayPEMPI(Mpi):
+    """Generic support for using Cray compiler wrappers"""
+    # MPI support
+    # no separate module, Cray compiler drivers always provide MPI support
+    MPI_MODULE_NAME = []
+    MPI_FAMILY = TC_CONSTANT_MPICH
+    MPI_TYPE = TC_CONSTANT_MPI_TYPE_MPICH
+
+    MPI_COMPILER_MPICC = CrayPECompiler.COMPILER_CC
+    MPI_COMPILER_MPICXX = CrayPECompiler.COMPILER_CXX
+    MPI_COMPILER_MPIF77 = CrayPECompiler.COMPILER_F77
+    MPI_COMPILER_MPIF90 = CrayPECompiler.COMPILER_F90
+
+    # no MPI wrappers, so no need to specify serial compiler
+    MPI_SHARED_OPTION_MAP = {
+        '_opt_MPICC': '',
+        '_opt_MPICXX': '',
+        '_opt_MPIF77': '',
+        '_opt_MPIF90': '',
+    }
+
+    def _set_mpi_compiler_variables(self):
+        """Set the MPI compiler variables"""
+        for var_tuple in COMPILER_VARIABLES:
+            c_var = var_tuple[0]  # [1] is the description
+            var = MPI_COMPILER_TEMPLATE % {'c_var':c_var}
+
+            value = getattr(self, 'MPI_COMPILER_%s' % var.upper(), None)
+            if value is None:
+                raise EasyBuildError("_set_mpi_compiler_variables: mpi compiler variable %s undefined", var)
+            self.variables.nappend_el(var, value)
+
+            if self.options.get('usempi', None):
+                var_seq = SEQ_COMPILER_TEMPLATE % {'c_var': c_var}
+                seq_comp = self.variables[c_var]
+                self.log.debug('_set_mpi_compiler_variables: usempi set: defining %s as %s', var_seq, seq_comp)
+                self.variables[var_seq] = seq_comp
+
+        if self.options.get('cciscxx', None):
+            self.log.debug("_set_mpi_compiler_variables: cciscxx set: switching MPICXX %s for MPICC value %s" %
+                           (self.variables['MPICXX'], self.variables['MPICC']))
+            self.variables['MPICXX'] = self.variables['MPICC']
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 7d0298012f..0909e1c9eb 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -55,7 +55,7 @@ class Toolchain(object):
 
     NAME = None
     VERSION = None
-    FAMILY = None
+    TOOLCHAIN_FAMILY = None
 
     # class method
     def _is_toolchain_for(cls, name):
@@ -451,7 +451,7 @@ def get_flag(self, name):
 
     def toolchain_family(self):
         """Return toolchain family for this toolchain."""
-        return self.FAMILY
+        return self.TOOLCHAIN_FAMILY
 
     def comp_family(self):
         """ Return compiler family used in this toolchain (abstract method)."""

From ec2118197ec033e3664f467a54f13420515d8a22 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 23:22:37 +0200
Subject: [PATCH 0912/1356] push up experimental

---
 easybuild/toolchains/craycce.py   | 2 +-
 easybuild/toolchains/craygnu.py   | 2 +-
 easybuild/toolchains/crayintel.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/toolchains/craycce.py b/easybuild/toolchains/craycce.py
index 94e166e3ff..770267521b 100644
--- a/easybuild/toolchains/craycce.py
+++ b/easybuild/toolchains/craycce.py
@@ -40,5 +40,5 @@ class CrayCCE(CrayPECray, CrayPEMPI, LibSci, CrayFFTW):
 
     def prepare(self, *args, **kwargs):
         """Prepare to use this toolchain; marked as experimental."""
-        super(CrayCCE, self).prepare(*args, **kwargs)
         self.log.experimental("%s toolchain", self.NAME)
+        super(CrayCCE, self).prepare(*args, **kwargs)
diff --git a/easybuild/toolchains/craygnu.py b/easybuild/toolchains/craygnu.py
index 8ef88b7b01..5f5eaa259d 100644
--- a/easybuild/toolchains/craygnu.py
+++ b/easybuild/toolchains/craygnu.py
@@ -40,5 +40,5 @@ class CrayGNU(CrayPEGCC, CrayPEMPI, LibSci, CrayFFTW):
 
     def prepare(self, *args, **kwargs):
         """Prepare to use this toolchain; marked as experimental."""
-        super(CrayGNU, self).prepare(*args, **kwargs)
         self.log.experimental("%s toolchain", self.NAME)
+        super(CrayGNU, self).prepare(*args, **kwargs)
diff --git a/easybuild/toolchains/crayintel.py b/easybuild/toolchains/crayintel.py
index 3a5c0e0fdb..7d827de055 100644
--- a/easybuild/toolchains/crayintel.py
+++ b/easybuild/toolchains/crayintel.py
@@ -40,5 +40,5 @@ class CrayIntel(CrayPEIntel, CrayPEMPI, LibSci, CrayFFTW):
 
     def prepare(self, *args, **kwargs):
         """Prepare to use this toolchain; marked as experimental."""
-        super(CrayIntel, self).prepare(*args, **kwargs)
         self.log.experimental("%s toolchain", self.NAME)
+        super(CrayIntel, self).prepare(*args, **kwargs)

From 3dbfe720c0639ad8affce1111f60950637d01e32 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Apr 2015 23:33:43 +0200
Subject: [PATCH 0913/1356] fix issues w.r.t. precision compiler flags

---
 easybuild/toolchains/compiler/craype.py | 22 ++++++++++++++++++++--
 easybuild/toolchains/craycce.py         |  2 +-
 easybuild/toolchains/craygnu.py         |  2 +-
 easybuild/toolchains/crayintel.py       |  2 +-
 4 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index c9af95fea2..9a4fa7abbf 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -37,8 +37,8 @@
 @author: Petar Forai (IMP/IMBA, Austria)
 @author: Kenneth Hoste (Ghent University)
 """
-from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC
-from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP
+from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC, Gcc
+from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP, IntelIccIfort
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.toolchain.compiler import Compiler
@@ -113,14 +113,32 @@ class CrayPEGCC(CrayPECompiler):
     PRGENV_MODULE_NAME_SUFFIX = 'gnu'  # PrgEnv-gnu
     COMPILER_FAMILY = TC_CONSTANT_GCC
 
+    def __init__(self, *args, **kwargs):
+        """CrayPEGCC constructor."""
+        super(CrayPEGCC, self).__init__(*args, **kwargs)
+        for precflag in self.COMPILER_PREC_FLAGS:
+            self.COMPILER_UNIQUE_OPTION_MAP[precflag] = Gcc.COMPILER_UNIQUE_OPTION_MAP[precflag]
+
 
 class CrayPEIntel(CrayPECompiler):
     """Support for using the Cray Intel compiler wrappers."""
     PRGENV_MODULE_NAME_SUFFIX = 'intel'  # PrgEnv-intel
     COMPILER_FAMILY = TC_CONSTANT_INTELCOMP
 
+    def __init__(self, *args, **kwargs):
+        """CrayPEIntel constructor."""
+        super(CrayPEIntel, self).__init__(*args, **kwargs)
+        for precflag in self.COMPILER_PREC_FLAGS:
+            self.COMPILER_UNIQUE_OPTION_MAP[precflag] = IntelIccIfort.COMPILER_UNIQUE_OPTION_MAP[precflag]
+
 
 class CrayPECray(CrayPECompiler):
     """Support for using the Cray CCE compiler wrappers."""
     PRGENV_MODULE_NAME_SUFFIX = 'cray'  # PrgEnv-cray
     COMPILER_FAMILY = TC_CONSTANT_CRAYCE
+
+    def __init__(self, *args, **kwargs):
+        """CrayPEIntel constructor."""
+        super(CrayPEIntel, self).__init__(*args, **kwargs)
+        for precflag in self.COMPILER_PREC_FLAGS:
+            self.COMPILER_UNIQUE_OPTION_MAP[precflag] = []
diff --git a/easybuild/toolchains/craycce.py b/easybuild/toolchains/craycce.py
index 770267521b..78c4c41665 100644
--- a/easybuild/toolchains/craycce.py
+++ b/easybuild/toolchains/craycce.py
@@ -40,5 +40,5 @@ class CrayCCE(CrayPECray, CrayPEMPI, LibSci, CrayFFTW):
 
     def prepare(self, *args, **kwargs):
         """Prepare to use this toolchain; marked as experimental."""
-        self.log.experimental("%s toolchain", self.NAME)
+        self.log.experimental("Using %s toolchain", self.NAME)
         super(CrayCCE, self).prepare(*args, **kwargs)
diff --git a/easybuild/toolchains/craygnu.py b/easybuild/toolchains/craygnu.py
index 5f5eaa259d..5dafa0d652 100644
--- a/easybuild/toolchains/craygnu.py
+++ b/easybuild/toolchains/craygnu.py
@@ -40,5 +40,5 @@ class CrayGNU(CrayPEGCC, CrayPEMPI, LibSci, CrayFFTW):
 
     def prepare(self, *args, **kwargs):
         """Prepare to use this toolchain; marked as experimental."""
-        self.log.experimental("%s toolchain", self.NAME)
+        self.log.experimental("Using %s toolchain", self.NAME)
         super(CrayGNU, self).prepare(*args, **kwargs)
diff --git a/easybuild/toolchains/crayintel.py b/easybuild/toolchains/crayintel.py
index 7d827de055..994d80228c 100644
--- a/easybuild/toolchains/crayintel.py
+++ b/easybuild/toolchains/crayintel.py
@@ -40,5 +40,5 @@ class CrayIntel(CrayPEIntel, CrayPEMPI, LibSci, CrayFFTW):
 
     def prepare(self, *args, **kwargs):
         """Prepare to use this toolchain; marked as experimental."""
-        self.log.experimental("%s toolchain", self.NAME)
+        self.log.experimental("Using %s toolchain", self.NAME)
         super(CrayIntel, self).prepare(*args, **kwargs)

From 2500a00966ed044d25aa1b3b86b1b98744b93c6b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 25 Apr 2015 01:25:57 +0200
Subject: [PATCH 0914/1356] exclude cray-libsci from toolchain definition

---
 easybuild/toolchains/linalg/libsci.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/easybuild/toolchains/linalg/libsci.py b/easybuild/toolchains/linalg/libsci.py
index e8a8f93505..d332b8d3d0 100644
--- a/easybuild/toolchains/linalg/libsci.py
+++ b/easybuild/toolchains/linalg/libsci.py
@@ -34,19 +34,22 @@
 from easybuild.tools.toolchain.linalg import LinAlg
 
 
+CRAY_LIBSCI_MODULE_NAME = 'cray-libsci'
+
+
 class LibSci(LinAlg):
     """Support for Cray's LibSci library, which provides BLAS/LAPACK support."""
     # BLAS/LAPACK support
     # via cray-libsci module, which gets loaded via the PrgEnv module
     # see https://www.nersc.gov/users/software/programming-libraries/math-libraries/libsci/
-    BLAS_MODULE_NAME = ['cray-libsci']
+    BLAS_MODULE_NAME = [CRAY_LIBSCI_MODULE_NAME]
 
     # no need to specify libraries, compiler driver takes care of linking the right libraries
     # FIXME: need to revisit this, on numpy we ended up with a serial BLAS through the wrapper.
     BLAS_LIB = []
     BLAS_LIB_MT = []
 
-    LAPACK_MODULE_NAME = ['cray-libsci']
+    LAPACK_MODULE_NAME = [CRAY_LIBSCI_MODULE_NAME]
     LAPACK_IS_BLAS = True
 
     BLACS_MODULE_NAME = []
@@ -74,3 +77,14 @@ def _set_blacs_variables(self):
     def _set_scalapack_variables(self):
         """Skip setting ScaLAPACK related variables"""
         pass
+
+    def definition(self):
+        """
+        Filter BLAS module from toolchain definition.
+        The cray-libsci module is loaded indirectly (and versionless) via the PrgEnv module,
+        and thus is not a direct toolchain component.
+        """
+        tc_def = super(LibSci, self).definition()
+        tc_def['BLAS'] = []
+        tc_def['LAPACK'] = []
+        return tc_def

From fd625b3ce17c3e578fc8caea151da62555ac6f8e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 25 Apr 2015 01:27:39 +0200
Subject: [PATCH 0915/1356] rename CrayPEMPI to CrayMPICH

---
 easybuild/toolchains/craycce.py                      | 4 ++--
 easybuild/toolchains/craygnu.py                      | 4 ++--
 easybuild/toolchains/crayintel.py                    | 4 ++--
 easybuild/toolchains/mpi/{craype.py => craympich.py} | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)
 rename easybuild/toolchains/mpi/{craype.py => craympich.py} (99%)

diff --git a/easybuild/toolchains/craycce.py b/easybuild/toolchains/craycce.py
index 78c4c41665..cd35a3d9de 100644
--- a/easybuild/toolchains/craycce.py
+++ b/easybuild/toolchains/craycce.py
@@ -31,10 +31,10 @@
 from easybuild.toolchains.compiler.craype import CrayPECray
 from easybuild.toolchains.fft.crayfftw import CrayFFTW
 from easybuild.toolchains.linalg.libsci import LibSci
-from easybuild.toolchains.mpi.craype import CrayPEMPI
+from easybuild.toolchains.mpi.craympich import CrayMPICH
 
 
-class CrayCCE(CrayPECray, CrayPEMPI, LibSci, CrayFFTW):
+class CrayCCE(CrayPECray, CrayMPICH, LibSci, CrayFFTW):
     """Compiler toolchain for Cray Programming Environment for Cray Compiling Environment (CCE) (PrgEnv-cray)."""
     NAME = 'CrayCCE'
 
diff --git a/easybuild/toolchains/craygnu.py b/easybuild/toolchains/craygnu.py
index 5dafa0d652..9deef321ec 100644
--- a/easybuild/toolchains/craygnu.py
+++ b/easybuild/toolchains/craygnu.py
@@ -31,10 +31,10 @@
 from easybuild.toolchains.compiler.craype import CrayPEGCC
 from easybuild.toolchains.fft.crayfftw import CrayFFTW
 from easybuild.toolchains.linalg.libsci import LibSci
-from easybuild.toolchains.mpi.craype import CrayPEMPI
+from easybuild.toolchains.mpi.craympich import CrayMPICH
 
 
-class CrayGNU(CrayPEGCC, CrayPEMPI, LibSci, CrayFFTW):
+class CrayGNU(CrayPEGCC, CrayMPICH, LibSci, CrayFFTW):
     """Compiler toolchain for Cray Programming Environment for GCC compilers (PrgEnv-gnu)."""
     NAME = 'CrayGNU'
 
diff --git a/easybuild/toolchains/crayintel.py b/easybuild/toolchains/crayintel.py
index 994d80228c..92ee0e9b1a 100644
--- a/easybuild/toolchains/crayintel.py
+++ b/easybuild/toolchains/crayintel.py
@@ -31,10 +31,10 @@
 from easybuild.toolchains.compiler.craype import CrayPEIntel
 from easybuild.toolchains.fft.crayfftw import CrayFFTW
 from easybuild.toolchains.linalg.libsci import LibSci
-from easybuild.toolchains.mpi.craype import CrayPEMPI
+from easybuild.toolchains.mpi.craympich import CrayMPICH
 
 
-class CrayIntel(CrayPEIntel, CrayPEMPI, LibSci, CrayFFTW):
+class CrayIntel(CrayPEIntel, CrayMPICH, LibSci, CrayFFTW):
     """Compiler toolchain for Cray Programming Environment for Intel compilers (PrgEnv-intel)."""
     NAME = 'CrayIntel'
 
diff --git a/easybuild/toolchains/mpi/craype.py b/easybuild/toolchains/mpi/craympich.py
similarity index 99%
rename from easybuild/toolchains/mpi/craype.py
rename to easybuild/toolchains/mpi/craympich.py
index 72253c2ffb..e2ec238008 100644
--- a/easybuild/toolchains/mpi/craype.py
+++ b/easybuild/toolchains/mpi/craympich.py
@@ -35,7 +35,7 @@
 from easybuild.tools.toolchain.mpi import Mpi
 
 
-class CrayPEMPI(Mpi):
+class CrayMPICH(Mpi):
     """Generic support for using Cray compiler wrappers"""
     # MPI support
     # no separate module, Cray compiler drivers always provide MPI support

From fdcfbfa831b2158c6b4cf5e0d931f8324e016d1d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 25 Apr 2015 01:33:42 +0200
Subject: [PATCH 0916/1356] fix typo

---
 easybuild/toolchains/compiler/craype.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 9a4fa7abbf..8e23a81dcb 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -139,6 +139,6 @@ class CrayPECray(CrayPECompiler):
 
     def __init__(self, *args, **kwargs):
         """CrayPEIntel constructor."""
-        super(CrayPEIntel, self).__init__(*args, **kwargs)
+        super(CrayPECray, self).__init__(*args, **kwargs)
         for precflag in self.COMPILER_PREC_FLAGS:
             self.COMPILER_UNIQUE_OPTION_MAP[precflag] = []

From ace0f89df6f6ba719d2bfd71e7fb15102bb8b99a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 25 Apr 2015 01:42:14 +0200
Subject: [PATCH 0917/1356] tiny fixes

---
 easybuild/toolchains/craycce.py        | 2 +-
 easybuild/tools/toolchain/toolchain.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/toolchains/craycce.py b/easybuild/toolchains/craycce.py
index cd35a3d9de..db86c0b266 100644
--- a/easybuild/toolchains/craycce.py
+++ b/easybuild/toolchains/craycce.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2014 Petar Forai
+# Copyright 2014-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 0909e1c9eb..411769f971 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -333,7 +333,7 @@ def prepare(self, onlymod=None):
 
         if not self._toolchain_exists():
             raise EasyBuildError("No module found for toolchain: %s", self.mod_short_name)
-        
+
         if self.name == DUMMY_TOOLCHAIN_NAME:
             if self.version == DUMMY_TOOLCHAIN_VERSION:
                 self.log.info('prepare: toolchain dummy mode, dummy version; not loading dependencies')

From 2beac2e7d1dd92e5af18aab5b60f8393ff43c19a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 26 Apr 2015 10:38:11 +0200
Subject: [PATCH 0918/1356] also include mpich-mt in list of CrayPE compiler
 flags

---
 easybuild/toolchains/compiler/craype.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 8e23a81dcb..f5fa020a42 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -91,7 +91,7 @@ def __init__(self, *args, **kwargs):
         """Constructor."""
         super(CrayPECompiler, self).__init__(*args, **kwargs)
         # 'register'  additional toolchain options that correspond to a compiler flag
-        self.COMPILER_FLAGS.extend(['dynamic'])
+        self.COMPILER_FLAGS.extend(['dynamic', 'mpich-mt'])
 
         # use name of PrgEnv module as name of module that provides compiler
         self.COMPILER_MODULE_NAME = ['PrgEnv-%s' % self.PRGENV_MODULE_NAME_SUFFIX]

From 51533c9f614aa7af730c0ac05679f054d2553505 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 26 Apr 2015 16:23:04 +0200
Subject: [PATCH 0919/1356] bump version to 2.1.0 and update release notes

---
 RELEASE_NOTES              | 41 ++++++++++++++++++++++++++++++++++++++
 easybuild/tools/version.py |  4 ++--
 2 files changed, 43 insertions(+), 2 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 7068649c36..a01e81e032 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,6 +3,47 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
+v2.1.0 (April 28th 2015)
+------------------------
+
+feature + bugfix release
+- bump required vsc-base version to 2.2.0
+- add support for only (re)generating module files: --module-only (#1018)
+    - module naming scheme API is enhanced to include det_install_subdir method
+    - FIXME docs see
+- add support for generating module files in Lua syntax (note: required Lmod as modules tool) (#1060, #1255, #1256)
+    - see --module-syntax configuration option
+- deprecate log.error in favor of raising EasyBuildError exception (#1218)
+    - see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#depr-error-reporting
+- add support for using external modules as dependencies, and to provide metadata for external modules (#1230, #1265)
+    - see http://easybuild.readthedocs.org/en/latest/Using_external_modules.html
+- add experimental support for Cray toolchains on top of PrgEnv modules: CrayGNU, CrayIntel, CrayCCE (#1234)
+    - FIXME see (wiki)
+- various other enhancements, including:
+    - sort the results of searching for files (e.g., --search output) (#1214)
+    - enhance test w.r.t. use of templates in cfgfile (#1217)
+    - define %(DEFAULT_REPOSITORYPATH)s template for cfgfiles (see eb --avail-cfgfile-constants) (#1220)
+    - also reset $LD_PRELOAD when running module commands, in case module defined $LD_PRELOAD (#1222)
+    - move location of 'module use' statements in generated module file (*after* 'module load' statements) (#1232)
+    - add support for --show-default-configfiles (#1240)
+    - report error on missing configuration files, rather than ignoring them (#1240)
+    - clean up commit message used in easyconfig git repository (#1248)
+    - add --hide-deps configuration option to specify names of software that must be installed as hidden modules (#1250)
+        - FIXME docs
+    - add support for appending/prepending to --robot-paths to avoid overwriting default robot search path (#1252)
+    - enable detection of use of unknown $EASYBUILD-prefixed environment variables (#1253)
+    - add --installpath-modules and --installpath-software configuration options (#1258)
+    - use dedicated subdirectory in temporary directory for each test to ensure better cleanup (#1260)
+    - get rid of $PROFILEREAD hack when running commands, not needed anymore (#1264)
+- various bug fixes, including:
+    - make bootstrap script robust against having 'vsc-base' already available in Python search path (#1212, #1215)
+    - set default value for unpack_options easyconfig parameter to '', so self.cfg.update works on it (#1229)
+    - also copy rotated log files (#1238)
+    - fix parsing of --download-timeout value (#1242)
+    - make test_XDG_CONFIG_env_vars unit test robust against existing user config file in default location (#1259)
+    - fix minor robustness issues w.r.t. $XDG_CONFIG* and $PYTHONPATH in unit tests (#1262)
+    - fix issue with handling empty toolchain variables (#1263)
+
 v2.0.0 (March 6th 2015)
 -----------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 1a243e6bba..cb77b7a3dc 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,8 +37,8 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion("2.1.0dev")
-UNKNOWN = "UNKNOWN"
+VERSION = LooseVersion('2.1.0')
+UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():
     """

From 4aca5efbc4876ef2f34342f07c67253b7bf962c0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 26 Apr 2015 19:16:49 +0200
Subject: [PATCH 0920/1356] do not fiddle with
 options.self.options.external_modules_metadata if --external-modules-metadata
 was not set

---
 easybuild/tools/options.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index f215d8c8fa..43d89a7465 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -454,6 +454,11 @@ def postprocess(self):
 
     def _postprocess_external_modules_metadata(self):
         """Parse file(s) specifying metadata for external modules."""
+        # leave external_modules_metadata untouched if no files are provided
+        if not self.options.external_modules_metadata:
+            self.log.debug("No metadata provided for external modules.")
+            return
+
         parsed_external_modules_metadata = ConfigObj()
         for path in self.options.external_modules_metadata:
             if os.path.exists(path):

From a7c147ecdc8ac13a08e0d4d0e8f587fd83e055fb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 26 Apr 2015 19:23:55 +0200
Subject: [PATCH 0921/1356] enhance tests

---
 test/framework/config.py  |  4 ++++
 test/framework/options.py | 11 +++++++++++
 2 files changed, 15 insertions(+)

diff --git a/test/framework/config.py b/test/framework/config.py
index 82474bd55d..57223c5b96 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -604,6 +604,10 @@ def test_flex_robot_paths(self):
 
     def test_external_modules_metadata(self):
         """Test --external-modules-metadata."""
+        # empty list by default
+        cfg = init_config()
+        self.assertEqual(cfg.external_modules_metadata, [])
+
         testcfgtxt = EXTERNAL_MODULES_METADATA
         testcfg = os.path.join(self.test_prefix, 'test_external_modules_metadata.cfg')
         write_file(testcfg, testcfgtxt)
diff --git a/test/framework/options.py b/test/framework/options.py
index 38028a2a4a..6538678590 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1648,6 +1648,17 @@ def test_show_default_configfiles(self):
         os.environ['HOME'] = home
         reload(easybuild.tools.options)
 
+    def test_generate_cmd_line(self):
+        """Test for generate_cmd_line."""
+        ebopts = EasyBuildOptions()
+        self.assertEqual(ebopts.generate_cmd_line(), [])
+
+        ebopts = EasyBuildOptions(go_args=['--force'])
+        self.assertEqual(ebopts.generate_cmd_line(), ['--force'])
+
+        ebopts = EasyBuildOptions(go_args=['--search=bar', '--search', 'foobar'])
+        self.assertEqual(ebopts.generate_cmd_line(), ['--search=foobar'])
+
 
 def suite():
     """ returns all the testcases in this module """

From bd2ed2cb0c5d56c5e78c4ff28ad068ce1a0af756 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 26 Apr 2015 20:43:15 +0200
Subject: [PATCH 0922/1356] include PR #1267

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index a01e81e032..5807e809af 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -15,7 +15,7 @@ feature + bugfix release
     - see --module-syntax configuration option
 - deprecate log.error in favor of raising EasyBuildError exception (#1218)
     - see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#depr-error-reporting
-- add support for using external modules as dependencies, and to provide metadata for external modules (#1230, #1265)
+- add support for using external modules as dependencies, and to provide metadata for external modules (#1230, #1265, #1267)
     - see http://easybuild.readthedocs.org/en/latest/Using_external_modules.html
 - add experimental support for Cray toolchains on top of PrgEnv modules: CrayGNU, CrayIntel, CrayCCE (#1234)
     - FIXME see (wiki)

From 1e1e917a081a44b4e526d9dc03d46a4028943ffc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 26 Apr 2015 20:54:23 +0200
Subject: [PATCH 0923/1356] check whether craype exists before loading it

---
 easybuild/toolchains/compiler/craype.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index f5fa020a42..19a854876b 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -102,7 +102,12 @@ def _set_optimal_architecture(self):
         if optarch is None:
             raise EasyBuildError("Don't know which 'craype' module to load, 'optarch' build option is unspecified.")
         else:
-            self.modules_tool.load([self.CRAYPE_MODULE_NAME_TEMPLATE % {'optarch': optarch}])
+            craype_mod_name = self.CRAYPE_MODULE_NAME_TEMPLATE % {'optarch': optarch}
+            if self.modules_tool.exist([craype_mod_name])[0]:
+                self.modules_tool.load([craype_mod_name])
+            else:
+                raise EasyBuildError("Necessary craype module with name '%s' is not available (optarch: '%s')",
+                                     craype_mod_name, optarch)
 
         # no compiler flag when optarch toolchain option is enabled
         self.options.options_map['optarch'] = ''

From 7b774e1c8b1ffaec4078dcca58427cecb63a1da9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 26 Apr 2015 22:34:26 +0200
Subject: [PATCH 0924/1356] include PR #1268 in release notes

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 5807e809af..d6eec3e9bc 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -17,7 +17,7 @@ feature + bugfix release
     - see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#depr-error-reporting
 - add support for using external modules as dependencies, and to provide metadata for external modules (#1230, #1265, #1267)
     - see http://easybuild.readthedocs.org/en/latest/Using_external_modules.html
-- add experimental support for Cray toolchains on top of PrgEnv modules: CrayGNU, CrayIntel, CrayCCE (#1234)
+- add experimental support for Cray toolchains on top of PrgEnv modules: CrayGNU, CrayIntel, CrayCCE (#1234, #1268)
     - FIXME see (wiki)
 - various other enhancements, including:
     - sort the results of searching for files (e.g., --search output) (#1214)

From d78593400b8a2937fb57c36ca11edb3576d9af70 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 28 Apr 2015 10:26:38 +0200
Subject: [PATCH 0925/1356] add docs URLs, list vsc-base enhancements, fix date

---
 RELEASE_NOTES | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index d6eec3e9bc..0a4fab5a41 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -7,18 +7,21 @@ v2.1.0 (April 28th 2015)
 ------------------------
 
 feature + bugfix release
-- bump required vsc-base version to 2.2.0
+- requires vsc-base v2.2.0 or more recent
+    - added support for LoggedException
+    - added support for add_flex action in GeneralOption
+    - added support to GeneralOption to act on unknown configuration environment variables
 - add support for only (re)generating module files: --module-only (#1018)
     - module naming scheme API is enhanced to include det_install_subdir method
-    - FIXME docs see
+    - see http://easybuild.readthedocs.org/en/latest/Partial_installations.html#module-only
 - add support for generating module files in Lua syntax (note: required Lmod as modules tool) (#1060, #1255, #1256)
-    - see --module-syntax configuration option
-- deprecate log.error in favor of raising EasyBuildError exception (#1218)
+    - see --module-syntax configuration option and http://easybuild.readthedocs.org/en/latest/Configuration.html#module-syntax
+- deprecate log.error method in favor of raising EasyBuildError exception (#1218)
     - see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#depr-error-reporting
 - add support for using external modules as dependencies, and to provide metadata for external modules (#1230, #1265, #1267)
     - see http://easybuild.readthedocs.org/en/latest/Using_external_modules.html
 - add experimental support for Cray toolchains on top of PrgEnv modules: CrayGNU, CrayIntel, CrayCCE (#1234, #1268)
-    - FIXME see (wiki)
+    - see https://github.com/hpcugent/easybuild/wiki/EasyBuild-on-Cray for more information
 - various other enhancements, including:
     - sort the results of searching for files (e.g., --search output) (#1214)
     - enhance test w.r.t. use of templates in cfgfile (#1217)
@@ -26,17 +29,21 @@ feature + bugfix release
     - also reset $LD_PRELOAD when running module commands, in case module defined $LD_PRELOAD (#1222)
     - move location of 'module use' statements in generated module file (*after* 'module load' statements) (#1232)
     - add support for --show-default-configfiles (#1240)
+      - see http://easybuild.readthedocs.org/en/latest/Configuration.html#default-configuration-files
     - report error on missing configuration files, rather than ignoring them (#1240)
+      - see http://easybuild.readthedocs.org/en/latest/Configuration.html#configuration-env-vars
     - clean up commit message used in easyconfig git repository (#1248)
     - add --hide-deps configuration option to specify names of software that must be installed as hidden modules (#1250)
-        - FIXME docs
+        - see http://easybuild.readthedocs.org/en/latest/Manipulating_dependencies.html#hide-deps
     - add support for appending/prepending to --robot-paths to avoid overwriting default robot search path (#1252)
+        - see also http://easybuild.readthedocs.org/en/latest/Using_the_EasyBuild_command_line.html#robot-search-path-prepend-append
     - enable detection of use of unknown $EASYBUILD-prefixed environment variables (#1253)
     - add --installpath-modules and --installpath-software configuration options (#1258)
+      - see http://easybuild.readthedocs.org/en/latest/Configuration.html#installpath
     - use dedicated subdirectory in temporary directory for each test to ensure better cleanup (#1260)
     - get rid of $PROFILEREAD hack when running commands, not needed anymore (#1264)
 - various bug fixes, including:
-    - make bootstrap script robust against having 'vsc-base' already available in Python search path (#1212, #1215)
+    - make bootstrap script robust against having vsc-base already available in Python search path (#1212, #1215)
     - set default value for unpack_options easyconfig parameter to '', so self.cfg.update works on it (#1229)
     - also copy rotated log files (#1238)
     - fix parsing of --download-timeout value (#1242)

From ad5351e8f2c844bc7c06cf7faf4abb2964c3510c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Apr 2015 07:27:25 +0200
Subject: [PATCH 0926/1356] really fix date

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 0a4fab5a41..7637de7e5e 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,7 +3,7 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-v2.1.0 (April 28th 2015)
+v2.1.0 (April 30th 2015)
 ------------------------
 
 feature + bugfix release

From f136347456afce562995f0a83e3ab731ea39af7c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Apr 2015 14:44:59 +0200
Subject: [PATCH 0927/1356] fix broken tests: don't try setting unknown
 easyconfig parameter via --try-amend, due to changes in tweak_one

---
 test/framework/easyconfig.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 5f662ccbf2..d9bf0ce25e 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -367,7 +367,6 @@ def test_tweaking(self):
             'toolchain_name': tcname,
             'patches': new_patches[:1],
             'homepage': homepage,
-            'foo': "bar"
         }
 
         tweak_one(self.eb_file, tweaked_fn, tweaks)
@@ -515,7 +514,7 @@ def test_obtain_easyconfig(self):
             'toolchain_name': tcname,
             'toolchain_version': tcver,
             'version': ver,
-            'foo': 'bar123'
+            'start_dir': 'bar123'
         })
         res = obtain_ec_for(specs, [self.ec_dir], None)
         self.assertEqual(res[1], "%s-%s-%s-%s%s.eb" % (name, ver, tcname, tcver, suff))
@@ -526,11 +525,16 @@ def test_obtain_easyconfig(self):
         self.assertEqual(ec['version'], specs['version'])
         self.assertEqual(ec['versionsuffix'], specs['versionsuffix'])
         self.assertEqual(ec['toolchain'], {'name': tcname, 'version': tcver})
-        # can't check for key 'foo', because EasyConfig ignores parameter names it doesn't know about
-        txt = read_file(res[1])
-        self.assertTrue(re.search('foo = "%s"' % specs['foo'], txt))
+        self.assertEqual(ec['start_dir'], specs['start_dir'])
         os.remove(res[1])
 
+        specs.update({
+            'foo': 'bar123'
+        })
+        self.assertErrorRegex(EasyBuildError, "Unkown easyconfig parameter: foo",
+                              obtain_ec_for, specs, [self.ec_dir], None)
+        del specs['foo']
+
         # should pick correct version, i.e. not newer than what's specified, if a choice needs to be made
         ver = '3.14'
         specs.update({'version': ver})

From aea378c273df85ffde3434ee6b8728998c23b1c0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Apr 2015 15:45:51 +0200
Subject: [PATCH 0928/1356] fix help statement in Lua module files

---
 easybuild/tools/module_generator.py | 2 +-
 test/framework/module_generator.py  | 2 +-
 test/framework/toy_build.py         | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 1332f3f3e5..d0ae5c2df0 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -323,7 +323,7 @@ def get_description(self, conflict=True):
         description = "%s - Homepage: %s" % (self.app.cfg['description'], self.app.cfg['homepage'])
 
         lines = [
-            "help = [[%(description)s]]",
+            "help([[%(description)s]])",
             "whatis([[Name: %(name)s]])",
             "whatis([[Version: %(version)s]])",
             "whatis([[Description: %(description)s]])",
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index f898bf913f..9391193707 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -93,7 +93,7 @@ def test_descr(self):
 
         else:
             expected = '\n'.join([
-                'help = [[%s]]' % gzip_txt,
+                'help([[%s]])' % gzip_txt,
                 "whatis([[Name: gzip]])" ,
                 "whatis([[Version: 1.4]])" ,
                 "whatis([[Description: %s]])" % gzip_txt,
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 2a577f3b3b..741f8abf5f 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -769,7 +769,7 @@ def test_toy_module_fulltxt(self):
 
         if get_module_syntax() == 'Lua':
             mod_txt_regex_pattern = '\n'.join([
-                r'help = \[\[Toy C program. - Homepage: http://hpcugent.github.com/easybuild\]\]',
+                r'help(\[\[Toy C program. - Homepage: http://hpcugent.github.com/easybuild\]\])',
                 r'whatis\(\[\[Name: toy\]\]\)',
                 r'whatis\(\[\[Version: 0.0\]\]\)',
                 r'whatis\(\[\[Description: Toy C program. - Homepage: http://hpcugent.github.com/easybuild\]\]\)',

From a2887f8cb8f7594cb1d5abc07afe135dc811593f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Apr 2015 21:02:56 +0200
Subject: [PATCH 0929/1356] fix broken test

---
 test/framework/toy_build.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 741f8abf5f..ab172f92a6 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -769,7 +769,7 @@ def test_toy_module_fulltxt(self):
 
         if get_module_syntax() == 'Lua':
             mod_txt_regex_pattern = '\n'.join([
-                r'help(\[\[Toy C program. - Homepage: http://hpcugent.github.com/easybuild\]\])',
+                r'help\(\[\[Toy C program. - Homepage: http://hpcugent.github.com/easybuild\]\]\)',
                 r'whatis\(\[\[Name: toy\]\]\)',
                 r'whatis\(\[\[Version: 0.0\]\]\)',
                 r'whatis\(\[\[Description: Toy C program. - Homepage: http://hpcugent.github.com/easybuild\]\]\)',

From e4205d6fefdd729a61d90cfbf303553efbb9e282 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Apr 2015 22:35:47 +0200
Subject: [PATCH 0930/1356] include PRs #1169 and #1270 in release notes

---
 RELEASE_NOTES | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 7637de7e5e..6c1b3ecbc9 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -14,7 +14,7 @@ feature + bugfix release
 - add support for only (re)generating module files: --module-only (#1018)
     - module naming scheme API is enhanced to include det_install_subdir method
     - see http://easybuild.readthedocs.org/en/latest/Partial_installations.html#module-only
-- add support for generating module files in Lua syntax (note: required Lmod as modules tool) (#1060, #1255, #1256)
+- add support for generating module files in Lua syntax (note: required Lmod as modules tool) (#1060, #1255, #1256, #1270)
     - see --module-syntax configuration option and http://easybuild.readthedocs.org/en/latest/Configuration.html#module-syntax
 - deprecate log.error method in favor of raising EasyBuildError exception (#1218)
     - see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#depr-error-reporting
@@ -23,6 +23,7 @@ feature + bugfix release
 - add experimental support for Cray toolchains on top of PrgEnv modules: CrayGNU, CrayIntel, CrayCCE (#1234, #1268)
     - see https://github.com/hpcugent/easybuild/wiki/EasyBuild-on-Cray for more information
 - various other enhancements, including:
+    - clear list of checksums when using --try-software-version (#1169)
     - sort the results of searching for files (e.g., --search output) (#1214)
     - enhance test w.r.t. use of templates in cfgfile (#1217)
     - define %(DEFAULT_REPOSITORYPATH)s template for cfgfiles (see eb --avail-cfgfile-constants) (#1220)

From 7c4b0e65a4683a04fc866658a6c2173b17ac039a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 Apr 2015 08:53:36 +0200
Subject: [PATCH 0931/1356] fix typo

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 6c1b3ecbc9..d5997570ec 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -14,7 +14,7 @@ feature + bugfix release
 - add support for only (re)generating module files: --module-only (#1018)
     - module naming scheme API is enhanced to include det_install_subdir method
     - see http://easybuild.readthedocs.org/en/latest/Partial_installations.html#module-only
-- add support for generating module files in Lua syntax (note: required Lmod as modules tool) (#1060, #1255, #1256, #1270)
+- add support for generating module files in Lua syntax (note: requires Lmod as modules tool) (#1060, #1255, #1256, #1270)
     - see --module-syntax configuration option and http://easybuild.readthedocs.org/en/latest/Configuration.html#module-syntax
 - deprecate log.error method in favor of raising EasyBuildError exception (#1218)
     - see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html#depr-error-reporting

From aefd06bfe99c7cab3690fb78d2f310c47e869bb2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 Apr 2015 12:53:28 +0200
Subject: [PATCH 0932/1356] bump version to v2.1.1dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index cb77b7a3dc..dcaa0ec56e 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.1.0')
+VERSION = LooseVersion('2.1.1dev')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From 57d8de9c1a511b2de93ec9275134ed1adb2258e9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 30 Apr 2015 16:04:44 +0200
Subject: [PATCH 0933/1356] bump version to v2.2.0dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index dcaa0ec56e..2efb989a88 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.1.1dev')
+VERSION = LooseVersion('2.2.0dev')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From 6ceecb347d5c8ddc02a2feef93e35e52f4af7981 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 3 May 2015 16:04:24 +0200
Subject: [PATCH 0934/1356] fix generate_software_list.py script

---
 easybuild/scripts/generate_software_list.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/scripts/generate_software_list.py b/easybuild/scripts/generate_software_list.py
index d4995d87c6..26feaab3b2 100644
--- a/easybuild/scripts/generate_software_list.py
+++ b/easybuild/scripts/generate_software_list.py
@@ -101,7 +101,7 @@
 # configure EasyBuild, by parsing options
 eb_go = eboptions.parse_options(args=args)
 config.init(eb_go.options, eb_go.get_options_by_section('config'))
-config.init_build_options({'validate': False})
+config.init_build_options({'validate': False, 'external_modules_metadata': {}})
 
 
 configs = []
@@ -125,7 +125,7 @@
             ec = EasyConfig(ec_file)
             log.info("found valid easyconfig %s" % ec)
             if not ec.name in names:
-                log.info("found new software package %s" % ec)
+                log.info("found new software package %s" % ec.name)
                 ec.easyblock = None
                 # check if an easyblock exists
                 ebclass = get_easyblock_class(None, name=ec.name, default_fallback=False)

From 5206426e687836e5ca3c2bc3654dfdd3f68385a6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 6 May 2015 07:14:06 +0300
Subject: [PATCH 0935/1356] only use environment variable to find module
 command binary if command can't be found in $PATH

---
 easybuild/tools/modules.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 43a2e2ff87..566c2872c4 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -122,7 +122,7 @@ class ModulesTool(object):
     TERSE_OPTION = (0, '--terse')
     # module command to use
     COMMAND = None
-    # environment variable to determine the module command (instead of COMMAND)
+    # environment variable that may refer to module command
     COMMAND_ENVIRONMENT = None
     # run module command explicitly using this shell
     COMMAND_SHELL = None
@@ -156,8 +156,8 @@ def __init__(self, mod_paths=None, testing=False):
 
         # actual module command (i.e., not the 'module' wrapper function, but the binary)
         self.cmd = self.COMMAND
-        if self.COMMAND_ENVIRONMENT is not None and self.COMMAND_ENVIRONMENT in os.environ:
-            self.log.debug('Set command via environment variable %s' % self.COMMAND_ENVIRONMENT)
+        if which(self.cmd) is None and self.COMMAND_ENVIRONMENT in os.environ:
+            self.log.debug('Set command via environment variable %s: %s', self.COMMAND_ENVIRONMENT, self.cmd)
             self.cmd = os.environ[self.COMMAND_ENVIRONMENT]
 
         if self.cmd is None:

From a211351a194bf497bceb08a59b6b6980566b4c8f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 6 May 2015 07:45:14 +0300
Subject: [PATCH 0936/1356] fix issue with missing load statements when
 --module-only is used, don't skip ready/prepare steps

---
 easybuild/framework/easyblock.py |  6 ++++--
 test/framework/toy_build.py      | 30 ++++++++++++++++++++++--------
 2 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 74f2396baa..d509614459 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1738,8 +1738,10 @@ def _skip_step(self, step, skippable):
             self.log.info("Skipping %s step (skip: %s, skipsteps: %s)", step, self.skip, self.cfg['skipsteps'])
             skip = True
 
-        # skip step when only generating module file; still run sanity check without use of force
-        elif module_only and not step in ['sanitycheck', 'module']:
+        # skip step when only generating module file
+        # * still run sanity check without use of force
+        # * always run ready & prepare step to set up toolchain + deps
+        elif module_only and not step in ['ready', 'prepare', 'sanitycheck', 'module']:
             self.log.info("Skipping %s step (only generating module)", step)
             skip = True
 
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index ab172f92a6..b40000a6ea 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -882,8 +882,9 @@ def test_external_dependencies(self):
 
     def test_module_only(self):
         """Test use of --module-only."""
-        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0.eb')
-        toy_mod = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0')
+        ec_files_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        ec_file = os.path.join(ec_files_path, 'toy-0.0-deps.eb')
+        toy_mod = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0-deps')
 
         # hide all existing modules
         self.reset_modulepath([os.path.join(self.test_installpath, 'modules', 'all')])
@@ -896,6 +897,7 @@ def test_module_only(self):
             '--installpath=%s' % self.test_installpath,
             '--debug',
             '--unittest-file=%s' % self.logfile,
+            '--robot=%s' % ec_files_path,
             '--module-syntax=Tcl',
         ]
         args = common_args + ['--module-only']
@@ -906,18 +908,22 @@ def test_module_only(self):
         self.eb_main(args + ['--force'], do_build=True, raise_error=True)
         self.assertTrue(os.path.exists(toy_mod))
 
+        # make sure load statements for dependencies are included in additional module file generated with --module-only
+        modtxt = read_file(toy_mod)
+        self.assertTrue(re.search('load.*ictce/4.1.13', modtxt), "load statement for ictce/4.1.13 found in module")
+
         os.remove(toy_mod)
 
         # installing another module under a different naming scheme and using Lua module syntax works fine
 
         # first actually build and install toy software + module
-        prefix = os.path.join(self.test_installpath, 'software', 'toy', '0.0')
+        prefix = os.path.join(self.test_installpath, 'software', 'toy', '0.0-deps')
         self.eb_main(common_args + ['--force'], do_build=True, raise_error=True)
         self.assertTrue(os.path.exists(toy_mod))
-        self.assertTrue(os.path.exists(os.path.join(self.test_installpath, 'software', 'toy', '0.0', 'bin')))
+        self.assertTrue(os.path.exists(os.path.join(self.test_installpath, 'software', 'toy', '0.0-deps', 'bin')))
         modtxt = read_file(toy_mod)
         self.assertTrue(re.search("set root %s" % prefix, modtxt))
-        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 1)
+        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 2)  # toy + ictce
         self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software', 'toy'))), 1)
 
         # install (only) additional module under a hierarchical MNS
@@ -925,16 +931,20 @@ def test_module_only(self):
             '--module-only',
             '--module-naming-scheme=MigrateFromEBToHMNS',
         ]
-        toy_core_mod = os.path.join(self.test_installpath, 'modules', 'all', 'Core', 'toy', '0.0')
+        toy_core_mod = os.path.join(self.test_installpath, 'modules', 'all', 'Core', 'toy', '0.0-deps')
         self.assertFalse(os.path.exists(toy_core_mod))
         self.eb_main(args, do_build=True, raise_error=True)
         self.assertTrue(os.path.exists(toy_core_mod))
         # existing install is reused
         modtxt2 = read_file(toy_core_mod)
         self.assertTrue(re.search("set root %s" % prefix, modtxt2))
-        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 1)
+        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 2)
         self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software', 'toy'))), 1)
 
+        # make sure load statements for dependencies are included
+        modtxt = read_file(toy_core_mod)
+        self.assertTrue(re.search('load.*ictce/4.1.13', modtxt), "load statement for ictce/4.1.13 found in module")
+
         os.remove(toy_mod)
         os.remove(toy_core_mod)
 
@@ -952,9 +962,13 @@ def test_module_only(self):
             # existing install is reused
             modtxt3 = read_file(toy_mod + '.lua')
             self.assertTrue(re.search('local root = "%s"' % prefix, modtxt3))
-            self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 1)
+            self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 2)
             self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software', 'toy'))), 1)
 
+            # make sure load statements for dependencies are included
+            modtxt = read_file(toy_mod + '.lua')
+            self.assertTrue(re.search('load.*ictce/4.1.13', modtxt), "load statement for ictce/4.1.13 found in module")
+
 def suite():
     """ return all the tests in this file """
     return TestLoader().loadTestsFromTestCase(ToyBuildTest)

From 8904f10c69c047d4a2888fdbe33bb32b7b9461a6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 6 May 2015 09:40:16 +0300
Subject: [PATCH 0937/1356] add log message in case module command paths
 obtained via $PATH and $LMOD_CMD are different

---
 easybuild/tools/modules.py | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 566c2872c4..2021bd5a24 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -122,7 +122,8 @@ class ModulesTool(object):
     TERSE_OPTION = (0, '--terse')
     # module command to use
     COMMAND = None
-    # environment variable that may refer to module command
+    # environment variable to determine path to module command;
+    # used as fallback in case command is not available in $PATH
     COMMAND_ENVIRONMENT = None
     # run module command explicitly using this shell
     COMMAND_SHELL = None
@@ -155,11 +156,20 @@ def __init__(self, mod_paths=None, testing=False):
         self._modules = []
 
         # actual module command (i.e., not the 'module' wrapper function, but the binary)
-        self.cmd = self.COMMAND
-        if which(self.cmd) is None and self.COMMAND_ENVIRONMENT in os.environ:
+        self.cmd = which(self.COMMAND)
+        env_cmd_path = os.environ.get(self.COMMAND_ENVIRONMENT)
+
+        # only use command path in environment variable if command in not available in $PATH
+        if self.cmd is None and env_cmd_path is not None:
             self.log.debug('Set command via environment variable %s: %s', self.COMMAND_ENVIRONMENT, self.cmd)
-            self.cmd = os.environ[self.COMMAND_ENVIRONMENT]
+            self.cmd = env_cmd_path
+
+        # check whether paths obtained via $PATH and $LMOD_CMD are different
+        elif self.cmd != env_cmd_path:
+            self.log.debug("Different paths found for module command '%s' via which/$PATH and $%s: %s vs %s",
+                           self.COMMAND, self.COMMAND_ENVIRONMENT, self.cmd, env_cmd_path)
 
+        # make sure the module command was found
         if self.cmd is None:
             raise EasyBuildError("No command set.")
         else:

From 704e211ff8ad48d4748ae0d709dea674e66ced94 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 6 May 2015 10:08:25 +0300
Subject: [PATCH 0938/1356] stick to initially using non-relative path for
 module command found via $PATH, enhance test_lmod_specific unit test

---
 easybuild/tools/modules.py    |  6 +++---
 test/framework/modulestool.py | 21 ++++++++++++++++++---
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 2021bd5a24..3700a1a8ab 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -156,16 +156,16 @@ def __init__(self, mod_paths=None, testing=False):
         self._modules = []
 
         # actual module command (i.e., not the 'module' wrapper function, but the binary)
-        self.cmd = which(self.COMMAND)
+        self.cmd = self.COMMAND
         env_cmd_path = os.environ.get(self.COMMAND_ENVIRONMENT)
 
         # only use command path in environment variable if command in not available in $PATH
-        if self.cmd is None and env_cmd_path is not None:
+        if which(self.cmd) is None and env_cmd_path is not None:
             self.log.debug('Set command via environment variable %s: %s', self.COMMAND_ENVIRONMENT, self.cmd)
             self.cmd = env_cmd_path
 
         # check whether paths obtained via $PATH and $LMOD_CMD are different
-        elif self.cmd != env_cmd_path:
+        elif which(self.cmd) != env_cmd_path:
             self.log.debug("Different paths found for module command '%s' via which/$PATH and $%s: %s vs %s",
                            self.COMMAND, self.COMMAND_ENVIRONMENT, self.cmd, env_cmd_path)
 
diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index f6ca56b8a8..6130e33564 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -29,6 +29,7 @@
 """
 import os
 import re
+import stat
 import tempfile
 from vsc.utils import fancylogger
 
@@ -41,7 +42,7 @@
 from easybuild.tools import config, modules
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import which
+from easybuild.tools.filetools import which, write_file
 from easybuild.tools.modules import modules_tool, Lmod
 from test.framework.utilities import init_config
 
@@ -95,7 +96,8 @@ def test_environment_command(self):
             # should never get here
             self.assertTrue(False, 'BrokenMockModulesTool should fail')
         except EasyBuildError, err:
-            self.assertTrue('command is not available' in str(err))
+            err_msg = "command is not available"
+            self.assertTrue(err_msg in str(err), "'%s' found in: %s" % (err_msg, err))
 
         os.environ[BrokenMockModulesTool.COMMAND_ENVIRONMENT] = MockModulesTool.COMMAND
         os.environ['module'] = "() { /bin/echo $*\n}"
@@ -160,6 +162,9 @@ def test_lmod_specific(self):
             }
             init_config(build_options=build_options)
 
+            lmod = Lmod(testing=True)
+            self.assertEqual(lmod.cmd, lmod_abspath)
+
             # drop any location where 'lmod' or 'spider' can be found from $PATH
             paths = os.environ.get('PATH', '').split(os.pathsep)
             new_paths = []
@@ -173,8 +178,18 @@ def test_lmod_specific(self):
             # make sure $MODULEPATH contains path that provides some modules
             os.environ['MODULEPATH'] = os.path.abspath(os.path.join(os.path.dirname(__file__), 'modules'))
 
-            # initialize Lmod modules tool, pass full path to 'lmod' via $LMOD_CMD
+            # initialize Lmod modules tool, pass (fake) full path to 'lmod' via $LMOD_CMD
+            fake_path = os.path.join(self.test_installpath, 'lmod')
+            write_file(fake_path, '#!/bin/bash\necho "Modules based on Lua: Version %s " >&2' % Lmod.REQ_VERSION)
+            os.chmod(fake_path, stat.S_IRUSR|stat.S_IXUSR)
+            os.environ['LMOD_CMD'] = fake_path
+            init_config(build_options=build_options)
+            lmod = Lmod(testing=True)
+            self.assertEqual(lmod.cmd, fake_path)
+
+            # use correct full path for 'lmod' via $LMOD_CMD
             os.environ['LMOD_CMD'] = lmod_abspath
+            init_config(build_options=build_options)
             lmod = Lmod(testing=True)
 
             # obtain list of availabe modules, should be non-empty

From 466ba4b2a8b530ee3a173e3e8332c86307b68eae Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 6 May 2015 22:56:53 +0300
Subject: [PATCH 0939/1356] introduce constants for step names, update
 --module-only help msg

---
 easybuild/framework/easyblock.py | 53 ++++++++++++++++++++++----------
 easybuild/tools/options.py       | 11 +++----
 test/framework/config.py         |  3 --
 3 files changed, 41 insertions(+), 26 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index d509614459..3c03555429 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -78,6 +78,25 @@
 from easybuild.tools.version import this_is_easybuild, VERBOSE_VERSION, VERSION
 
 
+BUILD_STEP = 'build'
+CLEANUP_STEP = 'cleanup'
+CONFIGURE_STEP = 'configure'
+EXTENSIONS_STEP = 'extensions'
+FETCH_STEP = 'fetch'
+MODULE_STEP = 'module'
+PACKAGE_STEP = 'package'
+PATCH_STEP = 'patch'
+POSTPROC_STEP = 'postproc'
+PREPARE_STEP = 'prepare'
+READY_STEP = 'ready'
+SANITYCHECK_STEP = 'sanitycheck'
+SOURCE_STEP = 'source'
+TEST_STEP = 'test'
+TESTCASES_STEP = 'testcases'
+
+MODULE_ONLY_STEPS = [MODULE_STEP, PREPARE_STEP, READY_STEP, SANITYCHECK_STEP]
+
+
 _log = fancylogger.getLogger('easyblock')
 
 
@@ -1741,12 +1760,12 @@ def _skip_step(self, step, skippable):
         # skip step when only generating module file
         # * still run sanity check without use of force
         # * always run ready & prepare step to set up toolchain + deps
-        elif module_only and not step in ['ready', 'prepare', 'sanitycheck', 'module']:
+        elif module_only and not step in MODULE_ONLY_STEPS:
             self.log.info("Skipping %s step (only generating module)", step)
             skip = True
 
         # allow skipping sanity check too when only generating module and force is used
-        elif module_only and step == 'sanitycheck' and force:
+        elif module_only and step == SANITYCHECK_STEP and force:
             self.log.info("Skipping %s step because of forced module-only mode", step)
             skip = True
 
@@ -1786,14 +1805,14 @@ def get_step(tag, descr, substeps, skippable, initial=True):
             (True, lambda x: env.reset_changes()),
             (True, lambda x: x.handle_iterate_opts()),
         ]
-        ready_step_spec = lambda initial: get_step('ready', "creating build dir, resetting environment",
+        ready_step_spec = lambda initial: get_step(READY_STEP, "creating build dir, resetting environment",
                                                    ready_substeps, False, initial=initial)
 
         source_substeps = [
             (False, lambda x: x.checksum_step()),
             (True, lambda x: x.extract_step()),
         ]
-        source_step_spec = lambda initial: get_step('source', "unpacking", source_substeps, True, initial=initial)
+        source_step_spec = lambda initial: get_step(SOURCE_STEP, "unpacking", source_substeps, True, initial=initial)
 
         def prepare_step_spec(initial):
             """Return prepare step specification."""
@@ -1801,7 +1820,7 @@ def prepare_step_spec(initial):
                 substeps = [lambda x: x.prepare_step()]
             else:
                 substeps = [lambda x: x.guess_start_dir()]
-            return ('prepare', 'preparing', substeps, False)
+            return (PREPARE_STEP, 'preparing', substeps, False)
 
         install_substeps = [
             (False, lambda x: x.stage_install_step()),
@@ -1813,14 +1832,14 @@ def prepare_step_spec(initial):
         # format for step specifications: (stop_name: (description, list of functions, skippable))
 
         # core steps that are part of the iterated loop
-        patch_step_spec = ('patch', 'patching', [lambda x: x.patch_step()], True)
-        configure_step_spec = ('configure', 'configuring', [lambda x: x.configure_step()], True)
-        build_step_spec = ('build', 'building', [lambda x: x.build_step()], True)
-        test_step_spec = ('test', 'testing', [lambda x: x.test_step()], True)
+        patch_step_spec = (PATCH_STEP, 'patching', [lambda x: x.patch_step()], True)
+        configure_step_spec = (CONFIGURE_STEP, 'configuring', [lambda x: x.configure_step()], True)
+        build_step_spec = (BUILD_STEP, 'building', [lambda x: x.build_step()], True)
+        test_step_spec = (TEST_STEP, 'testing', [lambda x: x.test_step()], True)
 
         # part 1: pre-iteration + first iteration
         steps_part1 = [
-            ('fetch', 'fetching files', [lambda x: x.fetch_step()], False),
+            (FETCH_STEP, 'fetching files', [lambda x: x.fetch_step()], False),
             ready_step_spec(True),
             source_step_spec(True),
             patch_step_spec,
@@ -1845,19 +1864,19 @@ def prepare_step_spec(initial):
         ] * (iteration_count - 1)
         # part 3: post-iteration part
         steps_part3 = [
-            ('extensions', 'taking care of extensions', [lambda x: x.extensions_step()], False),
-            ('package', 'packaging', [lambda x: x.package_step()], True),
-            ('postproc', 'postprocessing', [lambda x: x.post_install_step()], True),
-            ('sanitycheck', 'sanity checking', [lambda x: x.sanity_check_step()], False),
-            ('cleanup', 'cleaning up', [lambda x: x.cleanup_step()], False),
-            ('module', 'creating module', [lambda x: x.make_module_step()], False),
+            (EXTENSIONS_STEP, 'taking care of extensions', [lambda x: x.extensions_step()], False),
+            (PACKAGE_STEP, 'packaging', [lambda x: x.package_step()], True),
+            (POSTPROC_STEP, 'postprocessing', [lambda x: x.post_install_step()], True),
+            (SANITYCHECK_STEP, 'sanity checking', [lambda x: x.sanity_check_step()], False),
+            (CLEANUP_STEP, 'cleaning up', [lambda x: x.cleanup_step()], False),
+            (MODULE_STEP, 'creating module', [lambda x: x.make_module_step()], False),
         ]
 
         # full list of steps, included iterated steps
         steps = steps_part1 + steps_part2 + steps_part3
 
         if run_test_cases:
-            steps.append(('testcases', 'running test cases', [
+            steps.append((TESTCASES_STEP, 'running test cases', [
                 lambda x: x.load_module(),
                 lambda x: x.test_cases_step(),
             ], False))
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 43d89a7465..573b535051 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -40,7 +40,7 @@
 from distutils.version import LooseVersion
 from vsc.utils.missing import nub
 
-from easybuild.framework.easyblock import EasyBlock
+from easybuild.framework.easyblock import MODULE_ONLY_STEPS, SOURCE_STEP, EasyBlock
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.constants import constant_documentation
 from easybuild.framework.easyconfig.format.pyheaderconfigobj import build_easyconfig_constants_dict
@@ -134,7 +134,8 @@ def basic_options(self):
                             'pathlist', 'add_flex', self.default_robot_paths, {'metavar': 'PATH[%sPATH]' % os.pathsep}),
             'skip': ("Skip existing software (useful for installing additional packages)",
                      None, 'store_true', False, 'k'),
-            'stop': ("Stop the installation after certain step", 'choice', 'store_or_None', 'source', 's', all_stops),
+            'stop': ("Stop the installation after certain step",
+                     'choice', 'store_or_None', SOURCE_STEP, 's', all_stops),
             'strict': ("Set strictness level", 'choice', 'store', run.WARN, strictness_options),
         })
 
@@ -206,9 +207,8 @@ def override_options(self):
                             'strlist', 'extend', None),
             'hide-deps': ("Comma separated list of dependencies that you want automatically hidden, "
                           "(e.g. --hide-deps=zlib,ncurses)", 'strlist', 'extend', None),
-            'oldstyleconfig':   ("Look for and use the oldstyle configuration file.",
-                                 None, 'store_true', True),
-            'module-only': ("Only generate module file (and run sanity check)", None, 'store_true', False),
+            'module-only': ("Only generate module file(s); skip all steps except for %s" % ', '.join(MODULE_ONLY_STEPS),
+                            None, 'store_true', False),
             'optarch': ("Set architecture optimization, overriding native architecture optimizations",
                         None, 'store', None),
             'pretend': (("Does the build/installation in a test directory located in $HOME/easybuildinstall"),
@@ -405,7 +405,6 @@ def validate(self):
     def postprocess(self):
         """Do some postprocessing, in particular print stuff"""
         build_log.EXPERIMENTAL = self.options.experimental
-        config.SUPPORT_OLDSTYLE = self.options.oldstyleconfig
 
         # set strictness of run module
         if self.options.strict:
diff --git a/test/framework/config.py b/test/framework/config.py
index 57223c5b96..07e0fe262e 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -251,14 +251,11 @@ def test_generaloption_config_file(self):
         """Test use of new-style configuration file."""
         self.purge_environment()
 
-        oldstyle_config_file = os.path.join(self.tmpdir, 'nooldconfig.py')
         config_file = os.path.join(self.tmpdir, 'testconfig.cfg')
 
         testpath1 = os.path.join(self.tmpdir, 'test1')
         testpath2 = os.path.join(self.tmpdir, 'testtwo')
 
-        write_file(oldstyle_config_file, '')
-
         # test with config file passed via command line
         cfgtxt = '\n'.join([
             '[config]',

From 55e956c6535574005afd345f71cfeec94b1ff89c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 6 May 2015 07:14:06 +0300
Subject: [PATCH 0940/1356] only use environment variable to find module
 command binary if command can't be found in $PATH

---
 easybuild/tools/modules.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 43a2e2ff87..566c2872c4 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -122,7 +122,7 @@ class ModulesTool(object):
     TERSE_OPTION = (0, '--terse')
     # module command to use
     COMMAND = None
-    # environment variable to determine the module command (instead of COMMAND)
+    # environment variable that may refer to module command
     COMMAND_ENVIRONMENT = None
     # run module command explicitly using this shell
     COMMAND_SHELL = None
@@ -156,8 +156,8 @@ def __init__(self, mod_paths=None, testing=False):
 
         # actual module command (i.e., not the 'module' wrapper function, but the binary)
         self.cmd = self.COMMAND
-        if self.COMMAND_ENVIRONMENT is not None and self.COMMAND_ENVIRONMENT in os.environ:
-            self.log.debug('Set command via environment variable %s' % self.COMMAND_ENVIRONMENT)
+        if which(self.cmd) is None and self.COMMAND_ENVIRONMENT in os.environ:
+            self.log.debug('Set command via environment variable %s: %s', self.COMMAND_ENVIRONMENT, self.cmd)
             self.cmd = os.environ[self.COMMAND_ENVIRONMENT]
 
         if self.cmd is None:

From 0ab6957fdf18e3c0ac2d732f1521db627cdc8d89 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 6 May 2015 09:40:16 +0300
Subject: [PATCH 0941/1356] add log message in case module command paths
 obtained via $PATH and $LMOD_CMD are different

---
 easybuild/tools/modules.py | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 566c2872c4..2021bd5a24 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -122,7 +122,8 @@ class ModulesTool(object):
     TERSE_OPTION = (0, '--terse')
     # module command to use
     COMMAND = None
-    # environment variable that may refer to module command
+    # environment variable to determine path to module command;
+    # used as fallback in case command is not available in $PATH
     COMMAND_ENVIRONMENT = None
     # run module command explicitly using this shell
     COMMAND_SHELL = None
@@ -155,11 +156,20 @@ def __init__(self, mod_paths=None, testing=False):
         self._modules = []
 
         # actual module command (i.e., not the 'module' wrapper function, but the binary)
-        self.cmd = self.COMMAND
-        if which(self.cmd) is None and self.COMMAND_ENVIRONMENT in os.environ:
+        self.cmd = which(self.COMMAND)
+        env_cmd_path = os.environ.get(self.COMMAND_ENVIRONMENT)
+
+        # only use command path in environment variable if command in not available in $PATH
+        if self.cmd is None and env_cmd_path is not None:
             self.log.debug('Set command via environment variable %s: %s', self.COMMAND_ENVIRONMENT, self.cmd)
-            self.cmd = os.environ[self.COMMAND_ENVIRONMENT]
+            self.cmd = env_cmd_path
+
+        # check whether paths obtained via $PATH and $LMOD_CMD are different
+        elif self.cmd != env_cmd_path:
+            self.log.debug("Different paths found for module command '%s' via which/$PATH and $%s: %s vs %s",
+                           self.COMMAND, self.COMMAND_ENVIRONMENT, self.cmd, env_cmd_path)
 
+        # make sure the module command was found
         if self.cmd is None:
             raise EasyBuildError("No command set.")
         else:

From df1a533a91816346fc5b319ce8f83216f8ca8b06 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 6 May 2015 10:08:25 +0300
Subject: [PATCH 0942/1356] stick to initially using non-relative path for
 module command found via $PATH, enhance test_lmod_specific unit test

---
 easybuild/tools/modules.py    |  6 +++---
 test/framework/modulestool.py | 21 ++++++++++++++++++---
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 2021bd5a24..3700a1a8ab 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -156,16 +156,16 @@ def __init__(self, mod_paths=None, testing=False):
         self._modules = []
 
         # actual module command (i.e., not the 'module' wrapper function, but the binary)
-        self.cmd = which(self.COMMAND)
+        self.cmd = self.COMMAND
         env_cmd_path = os.environ.get(self.COMMAND_ENVIRONMENT)
 
         # only use command path in environment variable if command in not available in $PATH
-        if self.cmd is None and env_cmd_path is not None:
+        if which(self.cmd) is None and env_cmd_path is not None:
             self.log.debug('Set command via environment variable %s: %s', self.COMMAND_ENVIRONMENT, self.cmd)
             self.cmd = env_cmd_path
 
         # check whether paths obtained via $PATH and $LMOD_CMD are different
-        elif self.cmd != env_cmd_path:
+        elif which(self.cmd) != env_cmd_path:
             self.log.debug("Different paths found for module command '%s' via which/$PATH and $%s: %s vs %s",
                            self.COMMAND, self.COMMAND_ENVIRONMENT, self.cmd, env_cmd_path)
 
diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index f6ca56b8a8..6130e33564 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -29,6 +29,7 @@
 """
 import os
 import re
+import stat
 import tempfile
 from vsc.utils import fancylogger
 
@@ -41,7 +42,7 @@
 from easybuild.tools import config, modules
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import which
+from easybuild.tools.filetools import which, write_file
 from easybuild.tools.modules import modules_tool, Lmod
 from test.framework.utilities import init_config
 
@@ -95,7 +96,8 @@ def test_environment_command(self):
             # should never get here
             self.assertTrue(False, 'BrokenMockModulesTool should fail')
         except EasyBuildError, err:
-            self.assertTrue('command is not available' in str(err))
+            err_msg = "command is not available"
+            self.assertTrue(err_msg in str(err), "'%s' found in: %s" % (err_msg, err))
 
         os.environ[BrokenMockModulesTool.COMMAND_ENVIRONMENT] = MockModulesTool.COMMAND
         os.environ['module'] = "() { /bin/echo $*\n}"
@@ -160,6 +162,9 @@ def test_lmod_specific(self):
             }
             init_config(build_options=build_options)
 
+            lmod = Lmod(testing=True)
+            self.assertEqual(lmod.cmd, lmod_abspath)
+
             # drop any location where 'lmod' or 'spider' can be found from $PATH
             paths = os.environ.get('PATH', '').split(os.pathsep)
             new_paths = []
@@ -173,8 +178,18 @@ def test_lmod_specific(self):
             # make sure $MODULEPATH contains path that provides some modules
             os.environ['MODULEPATH'] = os.path.abspath(os.path.join(os.path.dirname(__file__), 'modules'))
 
-            # initialize Lmod modules tool, pass full path to 'lmod' via $LMOD_CMD
+            # initialize Lmod modules tool, pass (fake) full path to 'lmod' via $LMOD_CMD
+            fake_path = os.path.join(self.test_installpath, 'lmod')
+            write_file(fake_path, '#!/bin/bash\necho "Modules based on Lua: Version %s " >&2' % Lmod.REQ_VERSION)
+            os.chmod(fake_path, stat.S_IRUSR|stat.S_IXUSR)
+            os.environ['LMOD_CMD'] = fake_path
+            init_config(build_options=build_options)
+            lmod = Lmod(testing=True)
+            self.assertEqual(lmod.cmd, fake_path)
+
+            # use correct full path for 'lmod' via $LMOD_CMD
             os.environ['LMOD_CMD'] = lmod_abspath
+            init_config(build_options=build_options)
             lmod = Lmod(testing=True)
 
             # obtain list of availabe modules, should be non-empty

From ee76ee8e1c7f82f579ec70abfd87e056bd6b5764 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 7 May 2015 01:21:38 +0300
Subject: [PATCH 0943/1356] Merge pull request #1275 from boegel/LMOD_CMD

only use environment variable to find module command binary if command can't be found in $PATH

From c5cb3b80808fcc1777c64b8d4b50825a51dee606 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 7 May 2015 11:30:20 +0300
Subject: [PATCH 0944/1356] fix location of module_only build option w.r.t.
 default value

---
 easybuild/tools/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index ca66b9e1d3..f44171b5d2 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -92,7 +92,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'ignore_dirs',
         'modules_footer',
         'only_blocks',
-        'module_only',
         'optarch',
         'regtest_output_dir',
         'skip',
@@ -108,6 +107,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'experimental',
         'force',
         'hidden',
+        'module_only',
         'robot',
         'sequential',
         'set_gid_bit',

From 9286b19488adaa4510d1197e2cbb604d2954b687 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 7 May 2015 11:30:20 +0300
Subject: [PATCH 0945/1356] fix location of module_only build option w.r.t.
 default value

---
 easybuild/tools/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index ca66b9e1d3..f44171b5d2 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -92,7 +92,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'ignore_dirs',
         'modules_footer',
         'only_blocks',
-        'module_only',
         'optarch',
         'regtest_output_dir',
         'skip',
@@ -108,6 +107,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'experimental',
         'force',
         'hidden',
+        'module_only',
         'robot',
         'sequential',
         'set_gid_bit',

From 21975ddd453a3e0a1ece491b75145ea256c2f2b8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 8 May 2015 02:00:04 +0300
Subject: [PATCH 0946/1356] Merge pull request #1277 from
 boegel/module_only_build_opt

fix location of module_only build option w.r.t. default value

From b73f03c07c28297bef8935bc7cf77e899cde313e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 11 May 2015 19:12:42 +0200
Subject: [PATCH 0947/1356] check whether hidden dependency was already marked
 as hidden (via --hide-deps)

---
 easybuild/framework/easyconfig/easyconfig.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index e3c0569ec3..9da551fcd5 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -393,10 +393,14 @@ def filter_hidden_deps(self):
         faulty_deps = []
         for hidden_dep in self['hiddendependencies']:
             # check whether hidden dep is a listed dep using *visible* module name, not hidden one
+            hidden_mod_name = ActiveMNS().det_full_module_name(hidden_dep)
             visible_mod_name = ActiveMNS().det_full_module_name(hidden_dep, force_visible=True)
             if visible_mod_name in dep_mod_names:
                 self['dependencies'] = [d for d in self['dependencies'] if d['full_mod_name'] != visible_mod_name]
                 self.log.debug("Removed dependency matching hidden dependency %s" % hidden_dep)
+            elif hidden_mod_name in dep_mod_names:
+                self['dependencies'] = [d for d in self['dependencies'] if d['full_mod_name'] != hidden_mod_name]
+                self.log.debug("Hidden dependency %s is already marked to be installed as hidden module", hidden_dep)
             else:
                 # hidden dependencies must also be included in list of dependencies;
                 # this is done to try and make easyconfigs portable w.r.t. site-specific policies with minimal effort,

From 960b26cffe7bb50f3e74305690e61022c9ff9b5a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 11 May 2015 19:13:24 +0200
Subject: [PATCH 0948/1356] add unit test to test combining --hide-deps with
 hiddendependencies

---
 test/framework/easyconfig.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index b538231271..95beba08e8 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1114,6 +1114,22 @@ def test_update(self):
         ec.update('patches', ['foo.patch', 'bar.patch'])
         self.assertEqual(ec['patches'], ['toy-0.0_typo.patch', 'foo.patch', 'bar.patch'])
 
+    def test_hide_hidden_deps(self):
+        """Test use of --hide-deps on hiddendependencies."""
+        test_dir = os.path.dirname(os.path.abspath(__file__))
+        ec_file = os.path.join(test_dir, 'easyconfigs', 'gzip-1.4-GCC-4.6.3.eb')
+        ec = EasyConfig(ec_file)
+        self.assertEqual(ec['hiddendependencies'][0]['full_mod_name'], 'toy/.0.0-deps')
+        self.assertEqual(ec['dependencies'], [])
+
+        build_options = {
+            'hide_deps': ['toy'],
+            'valid_module_classes': module_classes(),
+        }
+        init_config(build_options=build_options)
+        ec = EasyConfig(ec_file)
+        self.assertEqual(ec['hiddendependencies'][0]['full_mod_name'], 'toy/.0.0-deps')
+        self.assertEqual(ec['dependencies'], [])
 
 def suite():
     """ returns all the testcases in this module """

From d2b25d2793d61d5fdc44a160375632d209756409 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 11 May 2015 22:03:08 +0200
Subject: [PATCH 0949/1356] enhance --search: only consider actual filename
 (not entire path), use regex syntax

---
 easybuild/tools/filetools.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 4e635bf9b0..804dadfea8 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -342,6 +342,8 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
         raise EasyBuildError("search_file: ignore_dirs (%s) should be of type list, not %s",
                              ignore_dirs, type(ignore_dirs))
 
+    query = re.compile(query.lower())
+
     var_lines = []
     hit_lines = []
     var_index = 1
@@ -349,18 +351,16 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
     for path in paths:
         hits = []
         hit_in_path = False
-        print_msg("Searching (case-insensitive) for '%s' in %s " % (query, path), log=_log, silent=silent)
+        print_msg("Searching (case-insensitive) for '%s' in %s " % (query.pattern, path), log=_log, silent=silent)
 
-        query = query.lower()
         for (dirpath, dirnames, filenames) in os.walk(path, topdown=True):
             for filename in filenames:
-                filename = os.path.join(dirpath, filename)
-                if filename.lower().find(query) != -1:
+                if query.search(filename.lower()):
                     if not hit_in_path:
                         var = "CFGS%d" % var_index
                         var_index += 1
                         hit_in_path = True
-                    hits.append(filename)
+                    hits.append(os.path.join(dirpath, filename))
 
             # do not consider (certain) hidden directories
             # note: we still need to consider e.g., .local !

From 02349bd3a6bd9f8bcdb8f88dc4071c2a8a213694 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 11 May 2015 19:12:42 +0200
Subject: [PATCH 0950/1356] check whether hidden dependency was already marked
 as hidden (via --hide-deps)

---
 easybuild/framework/easyconfig/easyconfig.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index e3c0569ec3..9da551fcd5 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -393,10 +393,14 @@ def filter_hidden_deps(self):
         faulty_deps = []
         for hidden_dep in self['hiddendependencies']:
             # check whether hidden dep is a listed dep using *visible* module name, not hidden one
+            hidden_mod_name = ActiveMNS().det_full_module_name(hidden_dep)
             visible_mod_name = ActiveMNS().det_full_module_name(hidden_dep, force_visible=True)
             if visible_mod_name in dep_mod_names:
                 self['dependencies'] = [d for d in self['dependencies'] if d['full_mod_name'] != visible_mod_name]
                 self.log.debug("Removed dependency matching hidden dependency %s" % hidden_dep)
+            elif hidden_mod_name in dep_mod_names:
+                self['dependencies'] = [d for d in self['dependencies'] if d['full_mod_name'] != hidden_mod_name]
+                self.log.debug("Hidden dependency %s is already marked to be installed as hidden module", hidden_dep)
             else:
                 # hidden dependencies must also be included in list of dependencies;
                 # this is done to try and make easyconfigs portable w.r.t. site-specific policies with minimal effort,

From c5031214c607de76d9bb010509f9466693796d3a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 11 May 2015 19:13:24 +0200
Subject: [PATCH 0951/1356] add unit test to test combining --hide-deps with
 hiddendependencies

---
 test/framework/easyconfig.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index b538231271..95beba08e8 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1114,6 +1114,22 @@ def test_update(self):
         ec.update('patches', ['foo.patch', 'bar.patch'])
         self.assertEqual(ec['patches'], ['toy-0.0_typo.patch', 'foo.patch', 'bar.patch'])
 
+    def test_hide_hidden_deps(self):
+        """Test use of --hide-deps on hiddendependencies."""
+        test_dir = os.path.dirname(os.path.abspath(__file__))
+        ec_file = os.path.join(test_dir, 'easyconfigs', 'gzip-1.4-GCC-4.6.3.eb')
+        ec = EasyConfig(ec_file)
+        self.assertEqual(ec['hiddendependencies'][0]['full_mod_name'], 'toy/.0.0-deps')
+        self.assertEqual(ec['dependencies'], [])
+
+        build_options = {
+            'hide_deps': ['toy'],
+            'valid_module_classes': module_classes(),
+        }
+        init_config(build_options=build_options)
+        ec = EasyConfig(ec_file)
+        self.assertEqual(ec['hiddendependencies'][0]['full_mod_name'], 'toy/.0.0-deps')
+        self.assertEqual(ec['dependencies'], [])
 
 def suite():
     """ returns all the testcases in this module """

From 3d64d66bd3b0fd934c6b2f52e6ba6f99e0ee9ede Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 11 May 2015 22:15:26 +0200
Subject: [PATCH 0952/1356] Merge pull request #1280 from boegel/fix_hide_deps

fix combined use of --hide-deps and hiddendependencies

From 196bdf997159139fd0b5c5e8a40deacc86c1ded5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 May 2015 07:41:03 +0200
Subject: [PATCH 0953/1356] use case-insensitive compiled regex when searching
 easyconfigs + enhance unit test

---
 easybuild/tools/filetools.py |  5 +++--
 test/framework/options.py    | 20 ++++++++++++++++++++
 2 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 804dadfea8..f073381f48 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -342,7 +342,8 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
         raise EasyBuildError("search_file: ignore_dirs (%s) should be of type list, not %s",
                              ignore_dirs, type(ignore_dirs))
 
-    query = re.compile(query.lower())
+    # compile regex, case-insensitive
+    query = re.compile(query, re.I)
 
     var_lines = []
     hit_lines = []
@@ -355,7 +356,7 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
 
         for (dirpath, dirnames, filenames) in os.walk(path, topdown=True):
             for filename in filenames:
-                if query.search(filename.lower()):
+                if query.search(filename):
                     if not hit_in_path:
                         var = "CFGS%d" % var_index
                         var_index += 1
diff --git a/test/framework/options.py b/test/framework/options.py
index 6538678590..cc2ba6ac0e 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -574,6 +574,26 @@ def test_search(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
+        write_file(self.logfile, '')
+
+        args = [
+            '--search=^gcc.*2.eb',
+            '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+            '--unittest-file=%s' % self.logfile,
+        ]
+        self.eb_main(args, logfile=dummylogfn)
+        logtxt = read_file(self.logfile)
+
+        info_msg = r"Searching \(case-insensitive\) for '\^gcc.\*2.eb' in"
+        self.assertTrue(re.search(info_msg, logtxt), "Info message when searching for easyconfigs in '%s'" % logtxt)
+        for ec in ['GCC-4.7.2.eb', 'GCC-4.8.2.eb', 'GCC-4.9.2.eb']:
+            self.assertTrue(re.search(r" \* \S*%s$" % ec, logtxt, re.M), "Found easyconfig %s in '%s'" % (ec, logtxt))
+
+        if os.path.exists(dummylogfn):
+            os.remove(dummylogfn)
+
+        write_file(self.logfile, '')
+
         for search_arg in ['-S', '--search-short']:
             open(self.logfile, 'w').write('')
             args = [

From 6d98f1d9b8070e5c185af4dbb789ed06ef76f3c7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 11 May 2015 22:03:08 +0200
Subject: [PATCH 0954/1356] enhance --search: only consider actual filename
 (not entire path), use regex syntax

---
 easybuild/tools/filetools.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 4e635bf9b0..804dadfea8 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -342,6 +342,8 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
         raise EasyBuildError("search_file: ignore_dirs (%s) should be of type list, not %s",
                              ignore_dirs, type(ignore_dirs))
 
+    query = re.compile(query.lower())
+
     var_lines = []
     hit_lines = []
     var_index = 1
@@ -349,18 +351,16 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
     for path in paths:
         hits = []
         hit_in_path = False
-        print_msg("Searching (case-insensitive) for '%s' in %s " % (query, path), log=_log, silent=silent)
+        print_msg("Searching (case-insensitive) for '%s' in %s " % (query.pattern, path), log=_log, silent=silent)
 
-        query = query.lower()
         for (dirpath, dirnames, filenames) in os.walk(path, topdown=True):
             for filename in filenames:
-                filename = os.path.join(dirpath, filename)
-                if filename.lower().find(query) != -1:
+                if query.search(filename.lower()):
                     if not hit_in_path:
                         var = "CFGS%d" % var_index
                         var_index += 1
                         hit_in_path = True
-                    hits.append(filename)
+                    hits.append(os.path.join(dirpath, filename))
 
             # do not consider (certain) hidden directories
             # note: we still need to consider e.g., .local !

From 15853ef4588890fd9c8d01007ad8b32b57439007 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 May 2015 07:41:03 +0200
Subject: [PATCH 0955/1356] use case-insensitive compiled regex when searching
 easyconfigs + enhance unit test

---
 easybuild/tools/filetools.py |  5 +++--
 test/framework/options.py    | 20 ++++++++++++++++++++
 2 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 804dadfea8..f073381f48 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -342,7 +342,8 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
         raise EasyBuildError("search_file: ignore_dirs (%s) should be of type list, not %s",
                              ignore_dirs, type(ignore_dirs))
 
-    query = re.compile(query.lower())
+    # compile regex, case-insensitive
+    query = re.compile(query, re.I)
 
     var_lines = []
     hit_lines = []
@@ -355,7 +356,7 @@ def search_file(paths, query, short=False, ignore_dirs=None, silent=False):
 
         for (dirpath, dirnames, filenames) in os.walk(path, topdown=True):
             for filename in filenames:
-                if query.search(filename.lower()):
+                if query.search(filename):
                     if not hit_in_path:
                         var = "CFGS%d" % var_index
                         var_index += 1
diff --git a/test/framework/options.py b/test/framework/options.py
index 6538678590..cc2ba6ac0e 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -574,6 +574,26 @@ def test_search(self):
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
 
+        write_file(self.logfile, '')
+
+        args = [
+            '--search=^gcc.*2.eb',
+            '--robot=%s' % os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+            '--unittest-file=%s' % self.logfile,
+        ]
+        self.eb_main(args, logfile=dummylogfn)
+        logtxt = read_file(self.logfile)
+
+        info_msg = r"Searching \(case-insensitive\) for '\^gcc.\*2.eb' in"
+        self.assertTrue(re.search(info_msg, logtxt), "Info message when searching for easyconfigs in '%s'" % logtxt)
+        for ec in ['GCC-4.7.2.eb', 'GCC-4.8.2.eb', 'GCC-4.9.2.eb']:
+            self.assertTrue(re.search(r" \* \S*%s$" % ec, logtxt, re.M), "Found easyconfig %s in '%s'" % (ec, logtxt))
+
+        if os.path.exists(dummylogfn):
+            os.remove(dummylogfn)
+
+        write_file(self.logfile, '')
+
         for search_arg in ['-S', '--search-short']:
             open(self.logfile, 'w').write('')
             args = [

From bff9a513839df34ab554f8422f1f24bac42a214f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 May 2015 10:23:01 +0200
Subject: [PATCH 0956/1356] Merge pull request #1281 from
 boegel/search_basename

enhance --search: only consider actual filename (not entire path), use regex syntax

From 8d380aaddcb4a81f3fa7854d7134c087eb49f671 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 15:25:41 +0200
Subject: [PATCH 0957/1356] force quicker log rotation to minize amount of disk
 space used by removed log files

---
 test/framework/suite.py     |  8 ++++++++
 test/framework/utilities.py | 27 +++++++++++++++++----------
 2 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 2b6001221f..b533118677 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -37,6 +37,14 @@
 import unittest
 from vsc.utils import fancylogger
 
+origLogToFile = fancylogger.logToFile
+def tweakedLogToFile(*args, **kwargs):
+    """Modified logToFile, with 100KB max log file size and no rotation."""
+    kwargs['max_bytes'] = 1024*1024
+    kwargs['backup_count'] = 1
+    return origLogToFile(*args, **kwargs)
+fancylogger.logToFile = tweakedLogToFile
+
 # initialize EasyBuild logging, so we disable it
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import set_tmpdir
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 7d18614830..25f28edcc9 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -48,7 +48,7 @@
 from easybuild.tools import config
 from easybuild.tools.config import module_classes, set_tmpdir
 from easybuild.tools.environment import modify_env
-from easybuild.tools.filetools import mkdir, read_file
+from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.options import CONFIG_ENV_VAR_PREFIX, EasyBuildOptions
@@ -152,15 +152,22 @@ def tearDown(self):
         # restore original Python search path
         sys.path = self.orig_sys_path
 
-        # cleanup
-        for path in [self.logfile, self.test_buildpath, self.test_installpath, self.test_prefix]:
-            try:
-                if os.path.isdir(path):
-                    shutil.rmtree(path)
-                else:
-                    os.remove(path)
-            except OSError, err:
-                pass
+        # cleanup: remove test directory, but restores log files (empty)
+        # log rotation only kicks in when *all* log handles are out of scope
+        try:
+            logfiles = []
+            for root, _, filenames in os.walk(self.test_prefix):
+                for filename in filenames:
+                    if filename.endswith('.log'):
+                        logfiles.append(os.path.join(root, filename))
+
+            shutil.rmtree(self.test_prefix)
+
+            for logfile in logfiles:
+                mkdir(os.path.dirname(logfile), parents=True)
+                write_file(logfile, '')
+        except OSError, err:
+            pass
 
         # restore original 'parent' tmpdir
         for var in ['TMPDIR', 'TEMP', 'TMP']:

From a638a0a79947f6e610f9a1e4a8ef832dfa297f56 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 15:30:32 +0200
Subject: [PATCH 0958/1356] zero backups

---
 test/framework/suite.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index b533118677..95321cfe5d 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -41,7 +41,7 @@
 def tweakedLogToFile(*args, **kwargs):
     """Modified logToFile, with 100KB max log file size and no rotation."""
     kwargs['max_bytes'] = 1024*1024
-    kwargs['backup_count'] = 1
+    kwargs['backup_count'] = 0
     return origLogToFile(*args, **kwargs)
 fancylogger.logToFile = tweakedLogToFile
 

From 854100e79361476e97973e0b4f4902a98d7d19b7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 15:45:16 +0200
Subject: [PATCH 0959/1356] better comments

---
 test/framework/suite.py     | 6 +++---
 test/framework/utilities.py | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 95321cfe5d..3b9dfe203a 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -39,9 +39,9 @@
 
 origLogToFile = fancylogger.logToFile
 def tweakedLogToFile(*args, **kwargs):
-    """Modified logToFile, with 100KB max log file size and no rotation."""
-    kwargs['max_bytes'] = 1024*1024
-    kwargs['backup_count'] = 0
+    """Modified logToFile, with 1MB max log file size and no rotation."""
+    kwargs['max_bytes'] = 1024*1024  # 1MB
+    kwargs['backup_count'] = 0  # don't keep any rotated logs
     return origLogToFile(*args, **kwargs)
 fancylogger.logToFile = tweakedLogToFile
 
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 25f28edcc9..86d6bc6c21 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -153,7 +153,8 @@ def tearDown(self):
         sys.path = self.orig_sys_path
 
         # cleanup: remove test directory, but restores log files (empty)
-        # log rotation only kicks in when *all* log handles are out of scope
+        # log rotation only kicks in when *all* log handles are out of scope (when this TestCase object is removed);
+        # log files should still be in place at that time
         try:
             logfiles = []
             for root, _, filenames in os.walk(self.test_prefix):

From efda786e578931122d34ff44fded96fbb2634439 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 16:04:37 +0200
Subject: [PATCH 0960/1356] don't use mkdir or write_file which relies on
 config too much, ignore IOErrors too

---
 test/framework/utilities.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 86d6bc6c21..a46696d85f 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -48,7 +48,7 @@
 from easybuild.tools import config
 from easybuild.tools.config import module_classes, set_tmpdir
 from easybuild.tools.environment import modify_env
-from easybuild.tools.filetools import mkdir, read_file, write_file
+from easybuild.tools.filetools import mkdir, read_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.options import CONFIG_ENV_VAR_PREFIX, EasyBuildOptions
@@ -152,9 +152,9 @@ def tearDown(self):
         # restore original Python search path
         sys.path = self.orig_sys_path
 
-        # cleanup: remove test directory, but restores log files (empty)
+        # cleanup: remove test directory, but restore log files (as empty files)
         # log rotation only kicks in when *all* log handles are out of scope (when this TestCase object is removed);
-        # log files should still be in place at that time
+        # log files must still be in place at that time
         try:
             logfiles = []
             for root, _, filenames in os.walk(self.test_prefix):
@@ -165,9 +165,12 @@ def tearDown(self):
             shutil.rmtree(self.test_prefix)
 
             for logfile in logfiles:
-                mkdir(os.path.dirname(logfile), parents=True)
-                write_file(logfile, '')
-        except OSError, err:
+                os.makedirs(os.path.dirname(logfile))
+                f = open(logfile, 'w')
+                f.write('')
+                f.close()
+                sys.stderr.write('Restored %s\n' % logfile)
+        except (OSError, IOError), err:
             pass
 
         # restore original 'parent' tmpdir

From f3e26e1c9d6f4c60d4d8c527b6438ba92f272b0c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 18:14:02 +0200
Subject: [PATCH 0961/1356] clean up log handlers added by main

---
 test/framework/utilities.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index a46696d85f..15f0c77229 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -169,7 +169,6 @@ def tearDown(self):
                 f = open(logfile, 'w')
                 f.write('')
                 f.close()
-                sys.stderr.write('Restored %s\n' % logfile)
         except (OSError, IOError), err:
             pass
 
@@ -215,6 +214,8 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
 
         env_before = copy.deepcopy(os.environ)
 
+        log = fancylogger.getLogger(fname=False)
+        orig_log_handlers = log.handlers[:]
         try:
             main((args, logfile, do_build))
         except SystemExit:
@@ -224,6 +225,12 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
             if verbose:
                 print "err: %s" % err
 
+        # remove any log handlers that were added by main()
+        new_log_handlers = [h for h in log.handlers if h not in orig_log_handlers]
+        for log_handler in new_log_handlers:
+            log_handler.close()
+            log.removeHandler(log_handler)
+
         logtxt = read_file(logfile)
 
         os.chdir(self.cwd)

From f3bae0f657a484bdfb14ba7f7ea2d57efda05f95 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 19:27:05 +0200
Subject: [PATCH 0962/1356] remove log handles that were added during the test
 in tearDown

---
 test/framework/suite.py     |  8 ------
 test/framework/utilities.py | 54 ++++++++++++-------------------------
 2 files changed, 17 insertions(+), 45 deletions(-)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 3b9dfe203a..2b6001221f 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -37,14 +37,6 @@
 import unittest
 from vsc.utils import fancylogger
 
-origLogToFile = fancylogger.logToFile
-def tweakedLogToFile(*args, **kwargs):
-    """Modified logToFile, with 1MB max log file size and no rotation."""
-    kwargs['max_bytes'] = 1024*1024  # 1MB
-    kwargs['backup_count'] = 0  # don't keep any rotated logs
-    return origLogToFile(*args, **kwargs)
-fancylogger.logToFile = tweakedLogToFile
-
 # initialize EasyBuild logging, so we disable it
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import set_tmpdir
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 15f0c77229..4c24d5ec9c 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -83,6 +83,10 @@ def setUp(self):
         """Set up testcase."""
         super(EnhancedTestCase, self).setUp()
 
+        # keep track of log handlers
+        log = fancylogger.getLogger(fname=False)
+        self.orig_log_handlers = log.handlers[:]
+
         self.orig_tmpdir = tempfile.gettempdir()
         # use a subdirectory for this test (which we can clean up easily after the test completes)
         self.test_prefix = set_tmpdir()
@@ -98,10 +102,6 @@ def setUp(self):
         # keep track of original environment/Python search path to restore
         self.orig_sys_path = sys.path[:]
 
-        self.orig_paths = {}
-        for path in ['buildpath', 'installpath', 'sourcepath']:
-            self.orig_paths[path] = os.environ.get('EASYBUILD_%s' % path.upper(), None)
-
         testdir = os.path.dirname(os.path.abspath(__file__))
 
         self.test_sourcepath = os.path.join(testdir, 'sandbox', 'sources')
@@ -145,31 +145,27 @@ def setUp(self):
     def tearDown(self):
         """Clean up after running testcase."""
         super(EnhancedTestCase, self).tearDown()
+
+        # go back to where we were before
         os.chdir(self.cwd)
+
+        # restore original environment
         modify_env(os.environ, self.orig_environ)
-        tempfile.tempdir = None
 
         # restore original Python search path
         sys.path = self.orig_sys_path
 
-        # cleanup: remove test directory, but restore log files (as empty files)
-        # log rotation only kicks in when *all* log handles are out of scope (when this TestCase object is removed);
-        # log files must still be in place at that time
-        try:
-            logfiles = []
-            for root, _, filenames in os.walk(self.test_prefix):
-                for filename in filenames:
-                    if filename.endswith('.log'):
-                        logfiles.append(os.path.join(root, filename))
+        # remove any log handlers that were added (so that log files can be effectively removed)
+        log = fancylogger.getLogger(fname=False)
+        new_log_handlers = [h for h in log.handlers if h not in self.orig_log_handlers]
+        for log_handler in new_log_handlers:
+            log_handler.close()
+            log.removeHandler(log_handler)
 
+        # cleanup test tmp dir
+        try:
             shutil.rmtree(self.test_prefix)
-
-            for logfile in logfiles:
-                os.makedirs(os.path.dirname(logfile))
-                f = open(logfile, 'w')
-                f.write('')
-                f.close()
-        except (OSError, IOError), err:
+        except (OSError, IOError):
             pass
 
         # restore original 'parent' tmpdir
@@ -179,14 +175,6 @@ def tearDown(self):
         # reset to make sure tempfile picks up new temporary directory to use
         tempfile.tempdir = None
 
-        for path in ['buildpath', 'installpath', 'sourcepath']:
-            if self.orig_paths[path] is not None:
-                os.environ['EASYBUILD_%s' % path.upper()] = self.orig_paths[path]
-            else:
-                if 'EASYBUILD_%s' % path.upper() in os.environ:
-                    del os.environ['EASYBUILD_%s' % path.upper()]
-        init_config()
-
     def reset_modulepath(self, modpaths):
         """Reset $MODULEPATH with specified paths."""
         modtool = modules_tool()
@@ -214,8 +202,6 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
 
         env_before = copy.deepcopy(os.environ)
 
-        log = fancylogger.getLogger(fname=False)
-        orig_log_handlers = log.handlers[:]
         try:
             main((args, logfile, do_build))
         except SystemExit:
@@ -225,12 +211,6 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
             if verbose:
                 print "err: %s" % err
 
-        # remove any log handlers that were added by main()
-        new_log_handlers = [h for h in log.handlers if h not in orig_log_handlers]
-        for log_handler in new_log_handlers:
-            log_handler.close()
-            log.removeHandler(log_handler)
-
         logtxt = read_file(logfile)
 
         os.chdir(self.cwd)

From 4a7044de18f2182c06b69f7dd4db2e329f70a674 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 15:25:41 +0200
Subject: [PATCH 0963/1356] force quicker log rotation to minize amount of disk
 space used by removed log files

---
 test/framework/suite.py     |  8 ++++++++
 test/framework/utilities.py | 27 +++++++++++++++++----------
 2 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 2b6001221f..b533118677 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -37,6 +37,14 @@
 import unittest
 from vsc.utils import fancylogger
 
+origLogToFile = fancylogger.logToFile
+def tweakedLogToFile(*args, **kwargs):
+    """Modified logToFile, with 100KB max log file size and no rotation."""
+    kwargs['max_bytes'] = 1024*1024
+    kwargs['backup_count'] = 1
+    return origLogToFile(*args, **kwargs)
+fancylogger.logToFile = tweakedLogToFile
+
 # initialize EasyBuild logging, so we disable it
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import set_tmpdir
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 7d18614830..25f28edcc9 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -48,7 +48,7 @@
 from easybuild.tools import config
 from easybuild.tools.config import module_classes, set_tmpdir
 from easybuild.tools.environment import modify_env
-from easybuild.tools.filetools import mkdir, read_file
+from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.options import CONFIG_ENV_VAR_PREFIX, EasyBuildOptions
@@ -152,15 +152,22 @@ def tearDown(self):
         # restore original Python search path
         sys.path = self.orig_sys_path
 
-        # cleanup
-        for path in [self.logfile, self.test_buildpath, self.test_installpath, self.test_prefix]:
-            try:
-                if os.path.isdir(path):
-                    shutil.rmtree(path)
-                else:
-                    os.remove(path)
-            except OSError, err:
-                pass
+        # cleanup: remove test directory, but restores log files (empty)
+        # log rotation only kicks in when *all* log handles are out of scope
+        try:
+            logfiles = []
+            for root, _, filenames in os.walk(self.test_prefix):
+                for filename in filenames:
+                    if filename.endswith('.log'):
+                        logfiles.append(os.path.join(root, filename))
+
+            shutil.rmtree(self.test_prefix)
+
+            for logfile in logfiles:
+                mkdir(os.path.dirname(logfile), parents=True)
+                write_file(logfile, '')
+        except OSError, err:
+            pass
 
         # restore original 'parent' tmpdir
         for var in ['TMPDIR', 'TEMP', 'TMP']:

From b0a520dedde5b39d2df40c899be19a08e1227016 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 15:30:32 +0200
Subject: [PATCH 0964/1356] zero backups

---
 test/framework/suite.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index b533118677..95321cfe5d 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -41,7 +41,7 @@
 def tweakedLogToFile(*args, **kwargs):
     """Modified logToFile, with 100KB max log file size and no rotation."""
     kwargs['max_bytes'] = 1024*1024
-    kwargs['backup_count'] = 1
+    kwargs['backup_count'] = 0
     return origLogToFile(*args, **kwargs)
 fancylogger.logToFile = tweakedLogToFile
 

From 171647cdf537247930242a9e13c17e7a22b658bc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 15:45:16 +0200
Subject: [PATCH 0965/1356] better comments

---
 test/framework/suite.py     | 6 +++---
 test/framework/utilities.py | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 95321cfe5d..3b9dfe203a 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -39,9 +39,9 @@
 
 origLogToFile = fancylogger.logToFile
 def tweakedLogToFile(*args, **kwargs):
-    """Modified logToFile, with 100KB max log file size and no rotation."""
-    kwargs['max_bytes'] = 1024*1024
-    kwargs['backup_count'] = 0
+    """Modified logToFile, with 1MB max log file size and no rotation."""
+    kwargs['max_bytes'] = 1024*1024  # 1MB
+    kwargs['backup_count'] = 0  # don't keep any rotated logs
     return origLogToFile(*args, **kwargs)
 fancylogger.logToFile = tweakedLogToFile
 
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 25f28edcc9..86d6bc6c21 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -153,7 +153,8 @@ def tearDown(self):
         sys.path = self.orig_sys_path
 
         # cleanup: remove test directory, but restores log files (empty)
-        # log rotation only kicks in when *all* log handles are out of scope
+        # log rotation only kicks in when *all* log handles are out of scope (when this TestCase object is removed);
+        # log files should still be in place at that time
         try:
             logfiles = []
             for root, _, filenames in os.walk(self.test_prefix):

From 3749b0093f254d353c1d3b63648f870e34a0ab23 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 16:04:37 +0200
Subject: [PATCH 0966/1356] don't use mkdir or write_file which relies on
 config too much, ignore IOErrors too

---
 test/framework/utilities.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 86d6bc6c21..a46696d85f 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -48,7 +48,7 @@
 from easybuild.tools import config
 from easybuild.tools.config import module_classes, set_tmpdir
 from easybuild.tools.environment import modify_env
-from easybuild.tools.filetools import mkdir, read_file, write_file
+from easybuild.tools.filetools import mkdir, read_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.options import CONFIG_ENV_VAR_PREFIX, EasyBuildOptions
@@ -152,9 +152,9 @@ def tearDown(self):
         # restore original Python search path
         sys.path = self.orig_sys_path
 
-        # cleanup: remove test directory, but restores log files (empty)
+        # cleanup: remove test directory, but restore log files (as empty files)
         # log rotation only kicks in when *all* log handles are out of scope (when this TestCase object is removed);
-        # log files should still be in place at that time
+        # log files must still be in place at that time
         try:
             logfiles = []
             for root, _, filenames in os.walk(self.test_prefix):
@@ -165,9 +165,12 @@ def tearDown(self):
             shutil.rmtree(self.test_prefix)
 
             for logfile in logfiles:
-                mkdir(os.path.dirname(logfile), parents=True)
-                write_file(logfile, '')
-        except OSError, err:
+                os.makedirs(os.path.dirname(logfile))
+                f = open(logfile, 'w')
+                f.write('')
+                f.close()
+                sys.stderr.write('Restored %s\n' % logfile)
+        except (OSError, IOError), err:
             pass
 
         # restore original 'parent' tmpdir

From 1964af20c23f58bf4431c0a896db97652df526f6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 18:14:02 +0200
Subject: [PATCH 0967/1356] clean up log handlers added by main

---
 test/framework/utilities.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index a46696d85f..15f0c77229 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -169,7 +169,6 @@ def tearDown(self):
                 f = open(logfile, 'w')
                 f.write('')
                 f.close()
-                sys.stderr.write('Restored %s\n' % logfile)
         except (OSError, IOError), err:
             pass
 
@@ -215,6 +214,8 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
 
         env_before = copy.deepcopy(os.environ)
 
+        log = fancylogger.getLogger(fname=False)
+        orig_log_handlers = log.handlers[:]
         try:
             main((args, logfile, do_build))
         except SystemExit:
@@ -224,6 +225,12 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
             if verbose:
                 print "err: %s" % err
 
+        # remove any log handlers that were added by main()
+        new_log_handlers = [h for h in log.handlers if h not in orig_log_handlers]
+        for log_handler in new_log_handlers:
+            log_handler.close()
+            log.removeHandler(log_handler)
+
         logtxt = read_file(logfile)
 
         os.chdir(self.cwd)

From 4fcbf8125b22974b2ea587986a9d791e98413248 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 19:27:05 +0200
Subject: [PATCH 0968/1356] remove log handles that were added during the test
 in tearDown

---
 test/framework/suite.py     |  8 ------
 test/framework/utilities.py | 54 ++++++++++++-------------------------
 2 files changed, 17 insertions(+), 45 deletions(-)

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 3b9dfe203a..2b6001221f 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -37,14 +37,6 @@
 import unittest
 from vsc.utils import fancylogger
 
-origLogToFile = fancylogger.logToFile
-def tweakedLogToFile(*args, **kwargs):
-    """Modified logToFile, with 1MB max log file size and no rotation."""
-    kwargs['max_bytes'] = 1024*1024  # 1MB
-    kwargs['backup_count'] = 0  # don't keep any rotated logs
-    return origLogToFile(*args, **kwargs)
-fancylogger.logToFile = tweakedLogToFile
-
 # initialize EasyBuild logging, so we disable it
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import set_tmpdir
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 15f0c77229..4c24d5ec9c 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -83,6 +83,10 @@ def setUp(self):
         """Set up testcase."""
         super(EnhancedTestCase, self).setUp()
 
+        # keep track of log handlers
+        log = fancylogger.getLogger(fname=False)
+        self.orig_log_handlers = log.handlers[:]
+
         self.orig_tmpdir = tempfile.gettempdir()
         # use a subdirectory for this test (which we can clean up easily after the test completes)
         self.test_prefix = set_tmpdir()
@@ -98,10 +102,6 @@ def setUp(self):
         # keep track of original environment/Python search path to restore
         self.orig_sys_path = sys.path[:]
 
-        self.orig_paths = {}
-        for path in ['buildpath', 'installpath', 'sourcepath']:
-            self.orig_paths[path] = os.environ.get('EASYBUILD_%s' % path.upper(), None)
-
         testdir = os.path.dirname(os.path.abspath(__file__))
 
         self.test_sourcepath = os.path.join(testdir, 'sandbox', 'sources')
@@ -145,31 +145,27 @@ def setUp(self):
     def tearDown(self):
         """Clean up after running testcase."""
         super(EnhancedTestCase, self).tearDown()
+
+        # go back to where we were before
         os.chdir(self.cwd)
+
+        # restore original environment
         modify_env(os.environ, self.orig_environ)
-        tempfile.tempdir = None
 
         # restore original Python search path
         sys.path = self.orig_sys_path
 
-        # cleanup: remove test directory, but restore log files (as empty files)
-        # log rotation only kicks in when *all* log handles are out of scope (when this TestCase object is removed);
-        # log files must still be in place at that time
-        try:
-            logfiles = []
-            for root, _, filenames in os.walk(self.test_prefix):
-                for filename in filenames:
-                    if filename.endswith('.log'):
-                        logfiles.append(os.path.join(root, filename))
+        # remove any log handlers that were added (so that log files can be effectively removed)
+        log = fancylogger.getLogger(fname=False)
+        new_log_handlers = [h for h in log.handlers if h not in self.orig_log_handlers]
+        for log_handler in new_log_handlers:
+            log_handler.close()
+            log.removeHandler(log_handler)
 
+        # cleanup test tmp dir
+        try:
             shutil.rmtree(self.test_prefix)
-
-            for logfile in logfiles:
-                os.makedirs(os.path.dirname(logfile))
-                f = open(logfile, 'w')
-                f.write('')
-                f.close()
-        except (OSError, IOError), err:
+        except (OSError, IOError):
             pass
 
         # restore original 'parent' tmpdir
@@ -179,14 +175,6 @@ def tearDown(self):
         # reset to make sure tempfile picks up new temporary directory to use
         tempfile.tempdir = None
 
-        for path in ['buildpath', 'installpath', 'sourcepath']:
-            if self.orig_paths[path] is not None:
-                os.environ['EASYBUILD_%s' % path.upper()] = self.orig_paths[path]
-            else:
-                if 'EASYBUILD_%s' % path.upper() in os.environ:
-                    del os.environ['EASYBUILD_%s' % path.upper()]
-        init_config()
-
     def reset_modulepath(self, modpaths):
         """Reset $MODULEPATH with specified paths."""
         modtool = modules_tool()
@@ -214,8 +202,6 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
 
         env_before = copy.deepcopy(os.environ)
 
-        log = fancylogger.getLogger(fname=False)
-        orig_log_handlers = log.handlers[:]
         try:
             main((args, logfile, do_build))
         except SystemExit:
@@ -225,12 +211,6 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
             if verbose:
                 print "err: %s" % err
 
-        # remove any log handlers that were added by main()
-        new_log_handlers = [h for h in log.handlers if h not in orig_log_handlers]
-        for log_handler in new_log_handlers:
-            log_handler.close()
-            log.removeHandler(log_handler)
-
         logtxt = read_file(logfile)
 
         os.chdir(self.cwd)

From ce0d7740f21547c72bb9358e93ac1bc2aa8d6ea8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 May 2015 20:30:53 +0200
Subject: [PATCH 0969/1356] Merge pull request #1282 from
 boegel/trim_tests_tmp_disk_space

remove log handlers that were added during tests, to ensure effective cleanup of log files

From 540fe47c0526b1789ead3becfc69ce704c2d97e4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 15 May 2015 10:46:34 +0200
Subject: [PATCH 0970/1356] define $CRAYPE_LINK_TYPE if 'dynamic' toolchain
 option is enabled

---
 easybuild/toolchains/compiler/craype.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 19a854876b..443a4f42d4 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -37,6 +37,7 @@
 @author: Petar Forai (IMP/IMBA, Austria)
 @author: Kenneth Hoste (Ghent University)
 """
+import easybuild.tools.environment as env
 from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC, Gcc
 from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP, IntelIccIfort
 from easybuild.tools.build_log import EasyBuildError
@@ -112,6 +113,13 @@ def _set_optimal_architecture(self):
         # no compiler flag when optarch toolchain option is enabled
         self.options.options_map['optarch'] = ''
 
+    def prepare(self, *args, **kwargs):
+        """Prepare to use this toolchain; define $CRAYPE_LINK_TYPE if 'dynamic' toolchain option is enabled."""
+        super(CrayPECompiler, self).prepare(*args, **kwargs)
+
+        if self.options['dynamic']:
+            env.setvar('CRAYPE_LINK_TYPE', 'dynamic')
+
 
 class CrayPEGCC(CrayPECompiler):
     """Support for using the Cray GNU compiler wrappers."""

From 0373d6a37fb55f0ab890728192342e296d617fda Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Fri, 15 May 2015 23:27:17 +0300
Subject: [PATCH 0971/1356] expose $CRAYPE_LINK_TYPE=dynamic in case of either
 shared or dynamic toolchain option is set.

---
 easybuild/toolchains/compiler/craype.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 443a4f42d4..b93494b9d5 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -68,8 +68,9 @@ class CrayPECompiler(Compiler):
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-        'shared': 'shared',
-        'dynamic': 'dynamic',
+	#handled shared and dynamic always via CRAYPE_LINK_TYPE environment variable, dont pass flags to wrapper.
+        'shared': '',
+        'dynamic': '',
         'static': 'static',
         'verbose': 'craype-verbose',
         'mpich-mt': 'craympich-mt',
@@ -117,7 +118,7 @@ def prepare(self, *args, **kwargs):
         """Prepare to use this toolchain; define $CRAYPE_LINK_TYPE if 'dynamic' toolchain option is enabled."""
         super(CrayPECompiler, self).prepare(*args, **kwargs)
 
-        if self.options['dynamic']:
+        if self.options['dynamic'] or self.options['shared']:
             env.setvar('CRAYPE_LINK_TYPE', 'dynamic')
 
 

From fbe5ada451f5e3c67c8e7de1593a7605c1e0f62a Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Fri, 15 May 2015 23:44:29 +0300
Subject: [PATCH 0972/1356] Dropped tabs. Sry.

---
 easybuild/toolchains/compiler/craype.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index b93494b9d5..da730a3f42 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -68,7 +68,7 @@ class CrayPECompiler(Compiler):
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-	#handled shared and dynamic always via CRAYPE_LINK_TYPE environment variable, dont pass flags to wrapper.
+        #handled shared and dynamic always via CRAYPE_LINK_TYPE environment variable, dont pass flags to wrapper.
         'shared': '',
         'dynamic': '',
         'static': 'static',

From 2b3d3b57a096a901734e3628125bf0a0a5d29abb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 16 May 2015 10:03:22 +0200
Subject: [PATCH 0973/1356] style fixes, extra debug log message, don't
 redefine static flag

---
 easybuild/toolchains/compiler/craype.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index da730a3f42..8250c2b9f5 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -68,10 +68,9 @@ class CrayPECompiler(Compiler):
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-        #handled shared and dynamic always via CRAYPE_LINK_TYPE environment variable, dont pass flags to wrapper.
+        # handle shared and dynamic always via $CRAYPE_LINK_TYPE environment variable, don't pass flags to wrapper
         'shared': '',
         'dynamic': '',
-        'static': 'static',
         'verbose': 'craype-verbose',
         'mpich-mt': 'craympich-mt',
     }
@@ -119,6 +118,7 @@ def prepare(self, *args, **kwargs):
         super(CrayPECompiler, self).prepare(*args, **kwargs)
 
         if self.options['dynamic'] or self.options['shared']:
+            self.log.debug("Enabling building of shared libs/dynamically linked executables via $CRAYPE_LINK_TYPE")
             env.setvar('CRAYPE_LINK_TYPE', 'dynamic')
 
 

From 681fc0ac59b4a8547018646fec74d93c0cc44433 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 15 May 2015 10:46:34 +0200
Subject: [PATCH 0974/1356] define $CRAYPE_LINK_TYPE if 'dynamic' toolchain
 option is enabled

---
 easybuild/toolchains/compiler/craype.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 19a854876b..443a4f42d4 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -37,6 +37,7 @@
 @author: Petar Forai (IMP/IMBA, Austria)
 @author: Kenneth Hoste (Ghent University)
 """
+import easybuild.tools.environment as env
 from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC, Gcc
 from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP, IntelIccIfort
 from easybuild.tools.build_log import EasyBuildError
@@ -112,6 +113,13 @@ def _set_optimal_architecture(self):
         # no compiler flag when optarch toolchain option is enabled
         self.options.options_map['optarch'] = ''
 
+    def prepare(self, *args, **kwargs):
+        """Prepare to use this toolchain; define $CRAYPE_LINK_TYPE if 'dynamic' toolchain option is enabled."""
+        super(CrayPECompiler, self).prepare(*args, **kwargs)
+
+        if self.options['dynamic']:
+            env.setvar('CRAYPE_LINK_TYPE', 'dynamic')
+
 
 class CrayPEGCC(CrayPECompiler):
     """Support for using the Cray GNU compiler wrappers."""

From b0eeb0e304722e060d96ee5fa2807e902b21c419 Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Fri, 15 May 2015 23:27:17 +0300
Subject: [PATCH 0975/1356] expose $CRAYPE_LINK_TYPE=dynamic in case of either
 shared or dynamic toolchain option is set.

---
 easybuild/toolchains/compiler/craype.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 443a4f42d4..b93494b9d5 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -68,8 +68,9 @@ class CrayPECompiler(Compiler):
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-        'shared': 'shared',
-        'dynamic': 'dynamic',
+	#handled shared and dynamic always via CRAYPE_LINK_TYPE environment variable, dont pass flags to wrapper.
+        'shared': '',
+        'dynamic': '',
         'static': 'static',
         'verbose': 'craype-verbose',
         'mpich-mt': 'craympich-mt',
@@ -117,7 +118,7 @@ def prepare(self, *args, **kwargs):
         """Prepare to use this toolchain; define $CRAYPE_LINK_TYPE if 'dynamic' toolchain option is enabled."""
         super(CrayPECompiler, self).prepare(*args, **kwargs)
 
-        if self.options['dynamic']:
+        if self.options['dynamic'] or self.options['shared']:
             env.setvar('CRAYPE_LINK_TYPE', 'dynamic')
 
 

From 0df07cc14e032300e27221d84cf664ed2778ea5b Mon Sep 17 00:00:00 2001
From: pforai <pfo@pseudoterminal.org>
Date: Fri, 15 May 2015 23:44:29 +0300
Subject: [PATCH 0976/1356] Dropped tabs. Sry.

---
 easybuild/toolchains/compiler/craype.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index b93494b9d5..da730a3f42 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -68,7 +68,7 @@ class CrayPECompiler(Compiler):
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-	#handled shared and dynamic always via CRAYPE_LINK_TYPE environment variable, dont pass flags to wrapper.
+        #handled shared and dynamic always via CRAYPE_LINK_TYPE environment variable, dont pass flags to wrapper.
         'shared': '',
         'dynamic': '',
         'static': 'static',

From 42021ffe37055adfac041b0f5a61d31b3ccb6563 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 16 May 2015 10:03:22 +0200
Subject: [PATCH 0977/1356] style fixes, extra debug log message, don't
 redefine static flag

---
 easybuild/toolchains/compiler/craype.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index da730a3f42..8250c2b9f5 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -68,10 +68,9 @@ class CrayPECompiler(Compiler):
     }
 
     COMPILER_UNIQUE_OPTION_MAP = {
-        #handled shared and dynamic always via CRAYPE_LINK_TYPE environment variable, dont pass flags to wrapper.
+        # handle shared and dynamic always via $CRAYPE_LINK_TYPE environment variable, don't pass flags to wrapper
         'shared': '',
         'dynamic': '',
-        'static': 'static',
         'verbose': 'craype-verbose',
         'mpich-mt': 'craympich-mt',
     }
@@ -119,6 +118,7 @@ def prepare(self, *args, **kwargs):
         super(CrayPECompiler, self).prepare(*args, **kwargs)
 
         if self.options['dynamic'] or self.options['shared']:
+            self.log.debug("Enabling building of shared libs/dynamically linked executables via $CRAYPE_LINK_TYPE")
             env.setvar('CRAYPE_LINK_TYPE', 'dynamic')
 
 

From 43bba338cbe7ac6e9833be0e3b564462bb0521ac Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 16 May 2015 11:06:39 +0200
Subject: [PATCH 0978/1356] Merge pull request #1283 from
 boegel/craype_link_type

define $CRAYPE_LINK_TYPE if 'dynamic' toolchain option is enabled

From 38978aeb3426ae8d3b51820c263130734b6fdb9d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 16 May 2015 11:54:09 +0200
Subject: [PATCH 0979/1356] bump version to 2.1.1 and update release notes

---
 RELEASE_NOTES              | 14 ++++++++++++++
 easybuild/tools/version.py |  2 +-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index d5997570ec..b63d342ada 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,6 +3,20 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
+v2.1.1 (May 18th 2015)
+----------------------
+
+bugfix release
+- various bug fixes, including:
+    - only use $LMOD_CMD value if lmod binary can't be found in $PATH (#1275)
+    - fix issue with missing load statements when --module-only is used, don't skip ready/prepare steps (#1276)
+    - fix location of module_only build option w.r.t. default value (#1277)
+    - fix combined use of --hide-deps and hiddendependencies (#1280)
+    - enhance --search: only consider actual filename (not entire path), use regex syntax (#1281)
+    - remove log handlers that were added during tests, to ensure effective cleanup of log files (#1282)
+        - this makes the unit test suite run ~3x faster!
+    - define $CRAYPE_LINK_TYPE if 'dynamic' toolchain option is enabled for Cray compiler wrappers (#1283)
+
 v2.1.0 (April 30th 2015)
 ------------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index dcaa0ec56e..53156b5c7b 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.1.1dev')
+VERSION = LooseVersion('2.1.1')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From 3aad4a461fc125b05736e6bdc684a77827529c34 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 16 May 2015 12:03:50 +0200
Subject: [PATCH 0980/1356] focus on major changes in release notes

---
 RELEASE_NOTES | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index b63d342ada..bb5c1656a1 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -7,12 +7,12 @@ v2.1.1 (May 18th 2015)
 ----------------------
 
 bugfix release
-- various bug fixes, including:
+- fix issue with missing load statements when --module-only is used, don't skip ready/prepare steps (#1276)
+- enhance --search: only consider actual filename (not entire path), use regex syntax (#1281)
+- various other bug fixes, including:
     - only use $LMOD_CMD value if lmod binary can't be found in $PATH (#1275)
-    - fix issue with missing load statements when --module-only is used, don't skip ready/prepare steps (#1276)
     - fix location of module_only build option w.r.t. default value (#1277)
     - fix combined use of --hide-deps and hiddendependencies (#1280)
-    - enhance --search: only consider actual filename (not entire path), use regex syntax (#1281)
     - remove log handlers that were added during tests, to ensure effective cleanup of log files (#1282)
         - this makes the unit test suite run ~3x faster!
     - define $CRAYPE_LINK_TYPE if 'dynamic' toolchain option is enabled for Cray compiler wrappers (#1283)

From 0b04f6760b7f38c9b11809a8755fb920fd2fa44f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 18 May 2015 13:52:06 +0200
Subject: [PATCH 0981/1356] include dependency marked as external module in
 test easyconfigs

---
 test/framework/easyconfig.py               | 15 ++++++++-------
 test/framework/easyconfigs/toy-0.0-deps.eb |  5 ++++-
 test/framework/module_generator.py         |  1 +
 test/framework/toy_build.py                | 11 ++++++-----
 4 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 95beba08e8..6454cf1087 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1069,10 +1069,11 @@ def test_external_dependencies(self):
         self.assertEqual(builddeps[0]['external_module'], True)
 
         deps = ec.dependencies()
-        self.assertEqual(len(deps), 3)
-        self.assertEqual([d['short_mod_name'] for d in deps], ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1'])
-        self.assertEqual([d['full_mod_name'] for d in deps], ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1'])
-        self.assertEqual([d['external_module'] for d in deps], [False, True, True])
+        self.assertEqual(len(deps), 4)
+        correct_deps = ['ictce/4.1.13', 'GCC/4.7.2', 'foobar/1.2.3', 'somebuilddep/0.1']
+        self.assertEqual([d['short_mod_name'] for d in deps], correct_deps)
+        self.assertEqual([d['full_mod_name'] for d in deps], correct_deps)
+        self.assertEqual([d['external_module'] for d in deps], [False, True, True, True])
 
         metadata = os.path.join(self.test_prefix, 'external_modules_metadata.cfg')
         metadatatxt = '\n'.join(['[foobar/1.2.3]', 'name = foo,bar', 'version = 1.2.3,3.2.1', 'prefix = /foo/bar'])
@@ -1084,14 +1085,14 @@ def test_external_dependencies(self):
         }
         init_config(build_options=build_options)
         ec = EasyConfig(toy_ec)
-        self.assertEqual(ec.dependencies()[1]['short_mod_name'], 'foobar/1.2.3')
-        self.assertEqual(ec.dependencies()[1]['external_module'], True)
+        self.assertEqual(ec.dependencies()[2]['short_mod_name'], 'foobar/1.2.3')
+        self.assertEqual(ec.dependencies()[2]['external_module'], True)
         metadata = {
             'name': ['foo', 'bar'],
             'version': ['1.2.3', '3.2.1'],
             'prefix': '/foo/bar',
         }
-        self.assertEqual(ec.dependencies()[1]['external_module_metadata'], metadata)
+        self.assertEqual(ec.dependencies()[2]['external_module_metadata'], metadata)
 
     def test_update(self):
         """Test use of update() method for EasyConfig instances."""
diff --git a/test/framework/easyconfigs/toy-0.0-deps.eb b/test/framework/easyconfigs/toy-0.0-deps.eb
index 646f9db067..84e6e22bc1 100644
--- a/test/framework/easyconfigs/toy-0.0-deps.eb
+++ b/test/framework/easyconfigs/toy-0.0-deps.eb
@@ -18,7 +18,10 @@ checksums = [[
 ]]
 patches = ['toy-0.0_typo.patch']
 
-dependencies = [('ictce', '4.1.13', '', True)]
+dependencies = [
+    ('ictce', '4.1.13', '', True),
+    ('GCC/4.7.2', EXTERNAL_MODULE),
+]
 
 sanity_check_paths = {
     'files': [('bin/yot', 'bin/toy')],
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 9391193707..5f6029cda5 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -269,6 +269,7 @@ def test_module_naming_scheme(self):
 
         build_options = {
             'check_osdeps': False,
+            'external_modules_metadata': {},
             'robot_path': [ecs_dir],
             'valid_stops': all_stops,
             'validate': False,
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index b40000a6ea..46797db2d1 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -849,7 +849,7 @@ def test_external_dependencies(self):
 
         # install dummy modules
         modulepath = os.path.join(self.test_prefix, 'modules')
-        for mod in ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1']:
+        for mod in ['ictce/4.1.13', 'GCC/4.7.2', 'foobar/1.2.3', 'somebuilddep/0.1']:
             mkdir(os.path.join(modulepath, os.path.dirname(mod)), parents=True)
             write_file(os.path.join(modulepath, mod), "#%Module")
 
@@ -858,7 +858,7 @@ def test_external_dependencies(self):
 
         modules_tool().load(['toy/0.0-external-deps'])
         # note build dependency is not loaded
-        mods = ['ictce/4.1.13', 'foobar/1.2.3', 'toy/0.0-external-deps']
+        mods = ['ictce/4.1.13', 'GCC/4.7.2', 'foobar/1.2.3', 'toy/0.0-external-deps']
         self.assertEqual([x['mod_name'] for x in modules_tool().list()], mods)
 
         # check behaviour when a non-existing external (build) dependency is included
@@ -886,8 +886,8 @@ def test_module_only(self):
         ec_file = os.path.join(ec_files_path, 'toy-0.0-deps.eb')
         toy_mod = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0-deps')
 
-        # hide all existing modules
-        self.reset_modulepath([os.path.join(self.test_installpath, 'modules', 'all')])
+        # only consider provided test modules
+        self.reset_modulepath([os.path.join(os.path.dirname(os.path.abspath(__file__)), 'modules')])
 
         # sanity check fails without --force if software is not installed yet
         common_args = [
@@ -911,6 +911,7 @@ def test_module_only(self):
         # make sure load statements for dependencies are included in additional module file generated with --module-only
         modtxt = read_file(toy_mod)
         self.assertTrue(re.search('load.*ictce/4.1.13', modtxt), "load statement for ictce/4.1.13 found in module")
+        self.assertTrue(re.search('load.*GCC/4.7.2', modtxt), "load statement for GCC/4.7.2 found in module")
 
         os.remove(toy_mod)
 
@@ -923,7 +924,7 @@ def test_module_only(self):
         self.assertTrue(os.path.exists(os.path.join(self.test_installpath, 'software', 'toy', '0.0-deps', 'bin')))
         modtxt = read_file(toy_mod)
         self.assertTrue(re.search("set root %s" % prefix, modtxt))
-        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 2)  # toy + ictce
+        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 1)
         self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software', 'toy'))), 1)
 
         # install (only) additional module under a hierarchical MNS

From 640fb2e4629534f6187da8e163ea4a2a68d63e98 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 18 May 2015 14:02:02 +0200
Subject: [PATCH 0982/1356] include #1273 in v2.1.1 release notes

---
 RELEASE_NOTES | 1 +
 1 file changed, 1 insertion(+)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index bb5c1656a1..241f8b3d8c 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -10,6 +10,7 @@ bugfix release
 - fix issue with missing load statements when --module-only is used, don't skip ready/prepare steps (#1276)
 - enhance --search: only consider actual filename (not entire path), use regex syntax (#1281)
 - various other bug fixes, including:
+    - fix generate_software_list.py script w.r.t. dependencies marked as external modules (#1273)
     - only use $LMOD_CMD value if lmod binary can't be found in $PATH (#1275)
     - fix location of module_only build option w.r.t. default value (#1277)
     - fix combined use of --hide-deps and hiddendependencies (#1280)

From 680c831bcc7c690f217126028c0cdd390dd87d48 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 3 May 2015 16:04:24 +0200
Subject: [PATCH 0983/1356] fix generate_software_list.py script

---
 easybuild/scripts/generate_software_list.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/scripts/generate_software_list.py b/easybuild/scripts/generate_software_list.py
index d4995d87c6..26feaab3b2 100644
--- a/easybuild/scripts/generate_software_list.py
+++ b/easybuild/scripts/generate_software_list.py
@@ -101,7 +101,7 @@
 # configure EasyBuild, by parsing options
 eb_go = eboptions.parse_options(args=args)
 config.init(eb_go.options, eb_go.get_options_by_section('config'))
-config.init_build_options({'validate': False})
+config.init_build_options({'validate': False, 'external_modules_metadata': {}})
 
 
 configs = []
@@ -125,7 +125,7 @@
             ec = EasyConfig(ec_file)
             log.info("found valid easyconfig %s" % ec)
             if not ec.name in names:
-                log.info("found new software package %s" % ec)
+                log.info("found new software package %s" % ec.name)
                 ec.easyblock = None
                 # check if an easyblock exists
                 ebclass = get_easyblock_class(None, name=ec.name, default_fallback=False)

From e47a944e55f2c9e14e3228ef184e7046d8b7432d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 18 May 2015 13:52:06 +0200
Subject: [PATCH 0984/1356] include dependency marked as external module in
 test easyconfigs

---
 test/framework/easyconfig.py               | 15 ++++++++-------
 test/framework/easyconfigs/toy-0.0-deps.eb |  5 ++++-
 test/framework/module_generator.py         |  1 +
 test/framework/toy_build.py                | 11 ++++++-----
 4 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 95beba08e8..6454cf1087 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1069,10 +1069,11 @@ def test_external_dependencies(self):
         self.assertEqual(builddeps[0]['external_module'], True)
 
         deps = ec.dependencies()
-        self.assertEqual(len(deps), 3)
-        self.assertEqual([d['short_mod_name'] for d in deps], ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1'])
-        self.assertEqual([d['full_mod_name'] for d in deps], ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1'])
-        self.assertEqual([d['external_module'] for d in deps], [False, True, True])
+        self.assertEqual(len(deps), 4)
+        correct_deps = ['ictce/4.1.13', 'GCC/4.7.2', 'foobar/1.2.3', 'somebuilddep/0.1']
+        self.assertEqual([d['short_mod_name'] for d in deps], correct_deps)
+        self.assertEqual([d['full_mod_name'] for d in deps], correct_deps)
+        self.assertEqual([d['external_module'] for d in deps], [False, True, True, True])
 
         metadata = os.path.join(self.test_prefix, 'external_modules_metadata.cfg')
         metadatatxt = '\n'.join(['[foobar/1.2.3]', 'name = foo,bar', 'version = 1.2.3,3.2.1', 'prefix = /foo/bar'])
@@ -1084,14 +1085,14 @@ def test_external_dependencies(self):
         }
         init_config(build_options=build_options)
         ec = EasyConfig(toy_ec)
-        self.assertEqual(ec.dependencies()[1]['short_mod_name'], 'foobar/1.2.3')
-        self.assertEqual(ec.dependencies()[1]['external_module'], True)
+        self.assertEqual(ec.dependencies()[2]['short_mod_name'], 'foobar/1.2.3')
+        self.assertEqual(ec.dependencies()[2]['external_module'], True)
         metadata = {
             'name': ['foo', 'bar'],
             'version': ['1.2.3', '3.2.1'],
             'prefix': '/foo/bar',
         }
-        self.assertEqual(ec.dependencies()[1]['external_module_metadata'], metadata)
+        self.assertEqual(ec.dependencies()[2]['external_module_metadata'], metadata)
 
     def test_update(self):
         """Test use of update() method for EasyConfig instances."""
diff --git a/test/framework/easyconfigs/toy-0.0-deps.eb b/test/framework/easyconfigs/toy-0.0-deps.eb
index 646f9db067..84e6e22bc1 100644
--- a/test/framework/easyconfigs/toy-0.0-deps.eb
+++ b/test/framework/easyconfigs/toy-0.0-deps.eb
@@ -18,7 +18,10 @@ checksums = [[
 ]]
 patches = ['toy-0.0_typo.patch']
 
-dependencies = [('ictce', '4.1.13', '', True)]
+dependencies = [
+    ('ictce', '4.1.13', '', True),
+    ('GCC/4.7.2', EXTERNAL_MODULE),
+]
 
 sanity_check_paths = {
     'files': [('bin/yot', 'bin/toy')],
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 9391193707..5f6029cda5 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -269,6 +269,7 @@ def test_module_naming_scheme(self):
 
         build_options = {
             'check_osdeps': False,
+            'external_modules_metadata': {},
             'robot_path': [ecs_dir],
             'valid_stops': all_stops,
             'validate': False,
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index b40000a6ea..46797db2d1 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -849,7 +849,7 @@ def test_external_dependencies(self):
 
         # install dummy modules
         modulepath = os.path.join(self.test_prefix, 'modules')
-        for mod in ['ictce/4.1.13', 'foobar/1.2.3', 'somebuilddep/0.1']:
+        for mod in ['ictce/4.1.13', 'GCC/4.7.2', 'foobar/1.2.3', 'somebuilddep/0.1']:
             mkdir(os.path.join(modulepath, os.path.dirname(mod)), parents=True)
             write_file(os.path.join(modulepath, mod), "#%Module")
 
@@ -858,7 +858,7 @@ def test_external_dependencies(self):
 
         modules_tool().load(['toy/0.0-external-deps'])
         # note build dependency is not loaded
-        mods = ['ictce/4.1.13', 'foobar/1.2.3', 'toy/0.0-external-deps']
+        mods = ['ictce/4.1.13', 'GCC/4.7.2', 'foobar/1.2.3', 'toy/0.0-external-deps']
         self.assertEqual([x['mod_name'] for x in modules_tool().list()], mods)
 
         # check behaviour when a non-existing external (build) dependency is included
@@ -886,8 +886,8 @@ def test_module_only(self):
         ec_file = os.path.join(ec_files_path, 'toy-0.0-deps.eb')
         toy_mod = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0-deps')
 
-        # hide all existing modules
-        self.reset_modulepath([os.path.join(self.test_installpath, 'modules', 'all')])
+        # only consider provided test modules
+        self.reset_modulepath([os.path.join(os.path.dirname(os.path.abspath(__file__)), 'modules')])
 
         # sanity check fails without --force if software is not installed yet
         common_args = [
@@ -911,6 +911,7 @@ def test_module_only(self):
         # make sure load statements for dependencies are included in additional module file generated with --module-only
         modtxt = read_file(toy_mod)
         self.assertTrue(re.search('load.*ictce/4.1.13', modtxt), "load statement for ictce/4.1.13 found in module")
+        self.assertTrue(re.search('load.*GCC/4.7.2', modtxt), "load statement for GCC/4.7.2 found in module")
 
         os.remove(toy_mod)
 
@@ -923,7 +924,7 @@ def test_module_only(self):
         self.assertTrue(os.path.exists(os.path.join(self.test_installpath, 'software', 'toy', '0.0-deps', 'bin')))
         modtxt = read_file(toy_mod)
         self.assertTrue(re.search("set root %s" % prefix, modtxt))
-        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 2)  # toy + ictce
+        self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software'))), 1)
         self.assertEqual(len(os.listdir(os.path.join(self.test_installpath, 'software', 'toy'))), 1)
 
         # install (only) additional module under a hierarchical MNS

From c7bd5ee12efb0bc320cbc12d336dbd3ce100340b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 18 May 2015 14:26:49 +0200
Subject: [PATCH 0985/1356] Merge pull request #1273 from
 boegel/fix_generate_software_list

fix generate_software_list.py script

From f16f0ae57cefd8072aed7296c30337875d4cf543 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 18 May 2015 19:07:37 +0200
Subject: [PATCH 0986/1356] use https for PyPI URLs

---
 easybuild/framework/easyconfig/templates.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/templates.py b/easybuild/framework/easyconfig/templates.py
index 046ce3e43f..7608aeece5 100644
--- a/easybuild/framework/easyconfig/templates.py
+++ b/easybuild/framework/easyconfig/templates.py
@@ -88,9 +88,9 @@
      'googlecode.com source url'),
     ('LAUNCHPAD_SOURCE', 'https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/%(version)s/+download/',
      'launchpad.net source url'),
-    ('PYPI_SOURCE', 'http://pypi.python.org/packages/source/%(nameletter)s/%(name)s',
+    ('PYPI_SOURCE', 'https://pypi.python.org/packages/source/%(nameletter)s/%(name)s',
      'pypi source url'),  # e.g., Cython, Sphinx
-    ('PYPI_LOWER_SOURCE', 'http://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s',
+    ('PYPI_LOWER_SOURCE', 'https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s',
      'pypi source url (lowercase name)'),  # e.g., Greenlet, PyZMQ
     ('R_SOURCE', 'http://cran.r-project.org/src/base/R-%(version_major)s',
      'cran.r-project.org (base) source url'),

From dd047a8ff392cb0670b68802a29ecc44422518bf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 20 May 2015 09:14:18 +0200
Subject: [PATCH 0987/1356] add GNU toolchain definition

---
 easybuild/toolchains/gnu.py | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 easybuild/toolchains/gnu.py

diff --git a/easybuild/toolchains/gnu.py b/easybuild/toolchains/gnu.py
new file mode 100644
index 0000000000..8b7f97ad70
--- /dev/null
+++ b/easybuild/toolchains/gnu.py
@@ -0,0 +1,36 @@
+##
+# Copyright 2012-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for GCC compiler toolchain.
+
+@author: Kenneth Hoste (Ghent University)
+"""
+
+from easybuild.toolchains.compiler.gcc import Gcc
+
+
+class GNU(Gcc):
+    """Compiler-only toolchain, including only GCC and binutils."""
+    NAME = 'GNU'

From 13f717e899e9d146974d1fd6f29129edac495d62 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 27 May 2015 07:46:29 +0200
Subject: [PATCH 0988/1356] exclude 'easyblocks' pkg from sys.path, make sure
 $EASYBUILD_BOOTSTRAP* env vars are undefined via pop

---
 easybuild/scripts/bootstrap_eb.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 115f92121f..17a6055513 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -57,7 +57,7 @@
 EASYBUILD_PACKAGES = [VSC_BASE, 'easybuild-framework', 'easybuild-easyblocks', 'easybuild-easyconfigs']
 
 # set print_debug to True for detailed progress info
-print_debug = os.environ.get('EASYBUILD_BOOTSTRAP_DEBUG', False)
+print_debug = os.environ.pop('EASYBUILD_BOOTSTRAP_DEBUG', False)
 
 # don't add user site directory to sys.path (equivalent to python -s), see https://www.python.org/dev/peps/pep-0370/
 os.environ['PYTHONNOUSERSITE'] = '1'
@@ -439,11 +439,11 @@ def main():
         error("Usage: %s <install path>" % sys.argv[0])
     install_path = os.path.abspath(sys.argv[1])
 
-    sourcepath = os.environ.get('EASYBUILD_BOOTSTRAP_SOURCEPATH')
+    sourcepath = os.environ.pop('EASYBUILD_BOOTSTRAP_SOURCEPATH', None)
     if sourcepath is not None:
         info("Fetching sources from %s..." % sourcepath)
 
-    skip_stage0 = os.environ.get('EASYBUILD_BOOTSTRAP_SKIP_STAGE0', False)
+    skip_stage0 = os.environ.pop('EASYBUILD_BOOTSTRAP_SKIP_STAGE0', False)
 
     # create temporary dir for temporary installations
     tmpdir = tempfile.mkdtemp()
@@ -459,7 +459,7 @@ def main():
     for path in orig_sys_path:
         include_path = True
         # exclude path if it's potentially an EasyBuild/VSC package, providing the 'easybuild'/'vsc' namespace, resp.
-        if any([os.path.exists(os.path.join(path, pkg, '__init__.py')) for pkg in ['easybuild', 'vsc']]):
+        if any([os.path.exists(os.path.join(path, pkg, '__init__.py')) for pkg in ['easyblocks', 'easybuild', 'vsc']]):
             include_path = False
         # exclude any .egg paths
         if path.endswith('.egg'):

From 5541b418632c82a7996639fc5320e3c6ccb29890 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 28 May 2015 11:47:56 +0200
Subject: [PATCH 0989/1356] improve error reporting/robustness in
 fix_broken_easyconfigs.py script

---
 easybuild/scripts/fix_broken_easyconfigs.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/easybuild/scripts/fix_broken_easyconfigs.py b/easybuild/scripts/fix_broken_easyconfigs.py
index e8f60cee62..7f1cc626a0 100755
--- a/easybuild/scripts/fix_broken_easyconfigs.py
+++ b/easybuild/scripts/fix_broken_easyconfigs.py
@@ -30,14 +30,13 @@
 import os
 import re
 import sys
-import tempfile
 from vsc.utils import fancylogger
 from vsc.utils.generaloption import SimpleOption
 
-from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.config import init_build_options
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.framework.easyconfig.parser import REPLACED_PARAMETERS, fetch_parameters_from_easyconfig
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import init_build_options
 from easybuild.tools.filetools import find_easyconfigs, read_file, write_file
 
 
@@ -119,7 +118,7 @@ def process_easyconfig_file(ec_file):
     log = go.log
 
     fancylogger.logToScreen(enable=True, stdout=True)
-    log.setLevel('INFO')
+    fancylogger.setLogLevel('WARNING')
 
     try:
         import easybuild.easyblocks.generic.configuremake
@@ -136,7 +135,11 @@ def process_easyconfig_file(ec_file):
 
     log.info("Processing %d easyconfigs" % len(ec_files))
     for ec_file in ec_files:
-        process_easyconfig_file(ec_file)
+        try:
+            process_easyconfig_file(ec_file)
+        except EasyBuildError, err:
+            log.warning("Ignoring issue when processing %s: %s", ec_file, err)
 
 except EasyBuildError, err:
+    sys.stderr.write("ERROR: %s\n" % err)
     sys.exit(1)

From de704ff18a7861658fcea8d2141eaf4f33e3319f Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Thu, 4 Jun 2015 20:57:17 -0400
Subject: [PATCH 0990/1356] Adding lstrip to stop double -- in versions of
 packages and deps

---
 easybuild/tools/packaging.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index cc729e709c..77e9f0959e 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -68,7 +68,7 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
 
     pkgname = pkgtemplate % {
         'toolchain' : toolchain_name,
-        'version': '-'.join([x for x in [easyblock.cfg.get('versionprefix', ''), easyblock.cfg['version'], easyblock.cfg['versionsuffix']] if x]),
+        'version': '-'.join([x for x in [easyblock.cfg.get('versionprefix', ''), easyblock.cfg['version'], easyblock.cfg['versionsuffix'].lstrip('-')] if x]),
         'name' : easyblock.name,
     }
     
@@ -87,7 +87,7 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
         _log.debug("The dep added looks like %s " % dep)
         dep_pkgname = pkgtemplate % {
             'name': dep['name'],
-            'version': '-'.join([x for x in [dep.get('versionprefix',''), dep['version'], dep['versionsuffix']] if x]),
+            'version': '-'.join([x for x in [dep.get('versionprefix',''), dep['version'], dep['versionsuffix'].lstrip('-')] if x]),
             'toolchain': "%s-%s" % (dep['toolchain']['name'], dep['toolchain']['version']),
         }
         depstring += " --depends '%s'" % ( dep_pkgname)

From 02e85d9ce1516b022be870dc103916c00a738ab1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 09:08:16 +0200
Subject: [PATCH 0991/1356] reset keep toolchain component class 'constants'
 every time

---
 easybuild/toolchains/compiler/inteliccifort.py |  5 ++++-
 easybuild/toolchains/linalg/acml.py            | 10 +++++++---
 easybuild/toolchains/linalg/intelmkl.py        | 15 ++++++++++-----
 3 files changed, 21 insertions(+), 9 deletions(-)

diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index 2e071033a2..8214933f61 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -87,7 +87,7 @@ class IntelIccIfort(Compiler):
         'dynamic':'-Bdynamic',
     }
 
-    LIB_MULTITHREAD = ['iomp5', 'pthread']  ## iomp5 is OpenMP related
+    LIB_MULTITHREAD = None
 
     def _set_compiler_vars(self):
         """Intel compilers-specific adjustments after setting compiler variables."""
@@ -104,6 +104,9 @@ def _set_compiler_vars(self):
             raise EasyBuildError("_set_compiler_vars: mismatch between icc version %s and ifort version %s",
                                  icc_version, ifort_version)
 
+        # reset LIB_MULTITHREAD every time,
+        # to avoid problems when multiple Intel compilers versions are used in a single session
+        self.LIB_MULTITHREAD = ['iomp5', 'pthread']  # iomp5 is OpenMP related
         if LooseVersion(icc_version) < LooseVersion('2011'):
             self.LIB_MULTITHREAD.insert(1, "guide")
 
diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index 9594fa428a..befed0aaf9 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -43,9 +43,8 @@ class Acml(LinAlg):
     Provides ACML BLAS/LAPACK support.
     """
     BLAS_MODULE_NAME = ['ACML']
-    # full list of libraries is highly dependent on ACML version and toolchain compiler (ifort, gfortran, ...)
-    BLAS_LIB = ['acml']
-    BLAS_LIB_MT = ['acml_mp']
+    BLAS_LIB = None
+    BLAS_LIB_MT = None
 
     # is completed in _set_blas_variables, depends on compiler used
     BLAS_LIB_DIR = []
@@ -73,6 +72,11 @@ def _set_blas_variables(self):
             raise EasyBuildError("_set_blas_variables: ACML set LDFLAGS/CPPFLAGS unknown entry in ACML_SUBDIRS_MAP "
                                  "with compiler family %s", self.COMPILER_FAMILY)
 
+        # reset BLAS_LIB(_MT) every time, to avoid problems when multiple ACML versions are used in a single session
+        # full list of libraries is highly dependent on ACML version and toolchain compiler (ifort, gfortran, ...)
+        self.BLAS_LIB = ['acml']
+        self.BLAS_LIB_MT = ['acml_mp']
+
         # version before 5.x still featured the acml_mv library
         ver = self.get_software_version(self.BLAS_MODULE_NAME)[0]
         if LooseVersion(ver) < LooseVersion("5"):
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index 6d1886212a..2c86cc680b 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -67,9 +67,9 @@ class IntelMKL(LinAlg):
     BLACS_LIB_STATIC = True
 
     SCALAPACK_MODULE_NAME = ['imkl']
-    SCALAPACK_LIB = ["mkl_scalapack%(lp64_sc)s"]
-    SCALAPACK_LIB_MT = ["mkl_scalapack%(lp64_sc)s"]
-    SCALAPACK_LIB_MAP = {"lp64_sc":"_lp64"}
+    SCALAPACK_LIB = None
+    SCALAPACK_LIB_MT = None
+    SCALAPACK_LIB_MAP = None
     SCALAPACK_REQUIRES = ['LIBBLACS', 'LIBBLAS']
     SCALAPACK_LIB_GROUP = True
     SCALAPACK_LIB_STATIC = True
@@ -101,10 +101,10 @@ def _set_blas_variables(self):
 
         if self.options.get('32bit', None):
             # 32bit
-            self.BLAS_LIB_MAP.update({"lp64":''})
+            self.BLAS_LIB_MAP.update({"lp64":''})  # FIXME
         if self.options.get('i8', None):
             # ilp64/i8
-            self.BLAS_LIB_MAP.update({"lp64":'_ilp64'})
+            self.BLAS_LIB_MAP.update({"lp64":'_ilp64'})  # FIXME
             # CPP / CFLAGS
             self.variables.nappend_el('CFLAGS', 'DMKL_ILP64')
 
@@ -150,6 +150,11 @@ def _set_blacs_variables(self):
         super(IntelMKL, self)._set_blacs_variables()
 
     def _set_scalapack_variables(self):
+        # reset SCALAPACK_LIB* every time, to avoid problems when multiple imkl versions are used in a single session
+        self.SCALAPACK_LIB = ["mkl_scalapack%(lp64_sc)s"]
+        self.SCALAPACK_LIB_MT = ["mkl_scalapack%(lp64_sc)s"]
+        self.SCALAPACK_LIB_MAP = {'lp64_sc': '_lp64'}
+
         imkl_version = self.get_software_version(self.BLAS_MODULE_NAME)[0]
         if LooseVersion(imkl_version) < LooseVersion('10.3'):
             self.SCALAPACK_LIB.append("mkl_solver%(lp64)s_sequential")

From f532b8d6cd95580e9e86fa06630fe7157623134e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 09:48:35 +0200
Subject: [PATCH 0992/1356] add unit test to verify fix w.r.t. toolchain
 constants

---
 test/framework/modules/icc/11.1.073    |  7 +++++
 test/framework/modules/ictce/3.2.2.u3  | 36 +++++++++++++++++++++
 test/framework/modules/ifort/11.1.073  |  7 +++++
 test/framework/modules/imkl/10.2.6.038 |  7 +++++
 test/framework/modules/impi/4.0.0.028  |  7 +++++
 test/framework/toolchain.py            | 43 ++++++++++++++++++++++++--
 6 files changed, 104 insertions(+), 3 deletions(-)
 create mode 100644 test/framework/modules/icc/11.1.073
 create mode 100644 test/framework/modules/ictce/3.2.2.u3
 create mode 100644 test/framework/modules/ifort/11.1.073
 create mode 100644 test/framework/modules/imkl/10.2.6.038
 create mode 100644 test/framework/modules/impi/4.0.0.028

diff --git a/test/framework/modules/icc/11.1.073 b/test/framework/modules/icc/11.1.073
new file mode 100644
index 0000000000..f78c11207f
--- /dev/null
+++ b/test/framework/modules/icc/11.1.073
@@ -0,0 +1,7 @@
+#%Module
+
+set root /tmp/icc/11.1.073
+
+setenv EBROOTICC "$root"
+setenv EBVERSIONICC "11.1.073"
+setenv  EBDEVELICC "$root/easybuild/icc-11.1.073-easybuild-devel"
diff --git a/test/framework/modules/ictce/3.2.2.u3 b/test/framework/modules/ictce/3.2.2.u3
new file mode 100644
index 0000000000..453b686f4c
--- /dev/null
+++ b/test/framework/modules/ictce/3.2.2.u3
@@ -0,0 +1,36 @@
+#%Module
+
+proc ModulesHelp { } {
+    puts stderr {   Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/
+    }
+}
+
+module-whatis {Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/}
+
+set root    /tmp/ictce/3.2.2.u3
+
+conflict    ictce
+
+if { ![is-loaded icc/11.1.073] } {
+    module load icc/11.1.073
+}
+
+if { ![is-loaded ifort/11.1.073] } {
+    module load ifort/11.1.073
+}
+
+if { ![is-loaded impi/4.0.0.028] } {
+    module load impi/4.0.0.028
+}
+
+if { ![is-loaded imkl/10.2.6.038] } {
+    module load imkl/10.2.6.038
+}
+
+
+setenv	EBROOTICTCE		"$root"
+setenv	EBVERSIONICTCE		"3.2.2.u3"
+setenv	EBDEVELICTCE		"$root/easybuild/ictce-3.2.2.u3-easybuild-devel"
+
+
+# built with EasyBuild version 1.9.0dev
diff --git a/test/framework/modules/ifort/11.1.073 b/test/framework/modules/ifort/11.1.073
new file mode 100644
index 0000000000..66e68eef4e
--- /dev/null
+++ b/test/framework/modules/ifort/11.1.073
@@ -0,0 +1,7 @@
+#%Module
+
+set root /tmp/ifort/11.1.073
+
+setenv EBROOTIFORT "$root"
+setenv EBVERSIONIFORT "11.1.073"
+setenv  EBDEVELIFORT "$root/easybuild/ifort-11.1.073-easybuild-devel"
diff --git a/test/framework/modules/imkl/10.2.6.038 b/test/framework/modules/imkl/10.2.6.038
new file mode 100644
index 0000000000..c539b9e5f7
--- /dev/null
+++ b/test/framework/modules/imkl/10.2.6.038
@@ -0,0 +1,7 @@
+#%Module
+
+set root	/var/folders/8s/_frgh9sj6m744mxt5w5lyztr0000gn/T/eb-SGdeX9/tmptwWn9I
+
+setenv EBROOTIMKL "$root"
+setenv EBVERSIONIMKL "10.2.6.038"
+setenv  EBDEVELIMKL "$root/easybuild/imkl-10.2.6.038-easybuild-devel"
diff --git a/test/framework/modules/impi/4.0.0.028 b/test/framework/modules/impi/4.0.0.028
new file mode 100644
index 0000000000..ec11aaef29
--- /dev/null
+++ b/test/framework/modules/impi/4.0.0.028
@@ -0,0 +1,7 @@
+#%Module
+
+set root /tmp/impi/4.0.0.028
+
+setenv EBROOTIMPI "$root"
+setenv EBVERSIONIMPI "4.0.0.028"
+setenv  EBDEVELIMPI "$root/easybuild/impi-4.0.0.028-easybuild-devel"
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index e5f1d9890f..f37a3c2870 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -431,14 +431,14 @@ def test_goolfc(self):
         # check CUDA runtime lib
         self.assertTrue("-lrt -lcudart" in tc.get_variable('LIBS'))
 
-    def setup_sandbox_for_intel_fftw(self):
+    def setup_sandbox_for_intel_fftw(self, imklver='10.3.12.361'):
         """Set up sandbox for Intel FFTW"""
         # hack to make Intel FFTW lib check pass
         # rewrite $root in imkl module so we can put required lib*.a files in place
         tmpdir = tempfile.mkdtemp()
 
         test_modules_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'modules'))
-        imkl_module_path = os.path.join(test_modules_path, 'imkl', '10.3.12.361')
+        imkl_module_path = os.path.join(test_modules_path, 'imkl', imklver)
         imkl_module_txt = open(imkl_module_path, 'r').read()
         regex = re.compile('^(set\s*root).*$', re.M)
         imkl_module_alt_txt = regex.sub(r'\1\t%s' % tmpdir, imkl_module_txt)
@@ -446,7 +446,7 @@ def setup_sandbox_for_intel_fftw(self):
 
         fftw_libs = ['fftw3xc_intel', 'fftw3x_cdft', 'mkl_cdft_core', 'mkl_blacs_intelmpi_lp64']
         fftw_libs += ['mkl_blacs_intelmpi_lp64', 'mkl_intel_lp64', 'mkl_sequential', 'mkl_core']
-        for subdir in ['mkl/lib/intel64', 'compiler/lib/intel64']:
+        for subdir in ['mkl/lib/intel64', 'compiler/lib/intel64', 'lib/em64t']:
             os.makedirs(os.path.join(tmpdir, subdir))
             for fftlib in fftw_libs:
                 write_file(os.path.join(tmpdir, subdir, 'lib%s.a' % fftlib), 'foo')
@@ -616,6 +616,43 @@ def test_prepare_deps_external(self):
         self.assertEqual(modules.get_software_root('foobar'), '/foo/bar')
         self.assertEqual(modules.get_software_version('toy'), '1.2.3')
 
+    def test_old_new_iccifort(self):
+        """Test whether preparing for old/new Intel compilers works correctly."""
+        tmpdir1, imkl_module_path1, imkl_module_txt1 = self.setup_sandbox_for_intel_fftw(imklver='10.3.12.361')
+        tmpdir2, imkl_module_path2, imkl_module_txt2 = self.setup_sandbox_for_intel_fftw(imklver='10.2.6.038')
+
+        # incl. -lguide
+        libblas_mt_old = "-Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
+        libblas_mt_old += " -Wl,--end-group -Wl,-Bdynamic -liomp5 -lguide -lpthread"
+
+        # no -lguide
+        libblas_mt_new = "-Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
+        libblas_mt_new += " -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread"
+
+        tc = self.get_toolchain('ictce', version='4.1.13')
+        tc.prepare()
+        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_new)
+        modules_tool().purge()
+
+        tc = self.get_toolchain('ictce', version='3.2.2.u3')
+        tc.prepare()
+        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_old)
+        modules_tool().purge()
+
+        tc = self.get_toolchain('ictce', version='4.1.13')
+        tc.prepare()
+        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_new)
+        modules_tool().purge()
+
+        tc = self.get_toolchain('ictce', version='3.2.2.u3')
+        tc.prepare()
+        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_old)
+
+        # cleanup
+        shutil.rmtree(tmpdir1)
+        shutil.rmtree(tmpdir2)
+        write_file(imkl_module_path1, imkl_module_txt1)
+        write_file(imkl_module_path2, imkl_module_txt2)
 
 def suite():
     """ return all the tests"""

From 2cee2ad8a1b9ecf0255b5833bf269a74afa7a94f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 10:28:42 +0200
Subject: [PATCH 0993/1356] fix modules count in modules.py test module

---
 test/framework/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 487cbb8ccb..aa201c095a 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -46,7 +46,7 @@
 
 
 # number of modules included for testing purposes
-TEST_MODULES_COUNT = 58
+TEST_MODULES_COUNT = 63
 
 
 class ModulesTest(EnhancedTestCase):

From 5c94dd18f7ef71412fdc15678597b071736d6135 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 11:01:17 +0200
Subject: [PATCH 0994/1356] make fix inheritance-safe

---
 easybuild/toolchains/compiler/inteliccifort.py |  6 ++++--
 easybuild/toolchains/linalg/acml.py            | 11 +++++++----
 easybuild/toolchains/linalg/intelmkl.py        | 16 ++++++++++------
 3 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index 8214933f61..7532468998 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -87,7 +87,9 @@ class IntelIccIfort(Compiler):
         'dynamic':'-Bdynamic',
     }
 
-    LIB_MULTITHREAD = None
+    LIB_MULTITHREAD = ['iomp5', 'pthread']  # iomp5 is OpenMP related
+    # keep track of original value, needs to be restored every time since we append to class 'constant' LIB_MULTITHREAD
+    _INIT_LIB_MULTITHREAD = LIB_MULTITHREAD[:]
 
     def _set_compiler_vars(self):
         """Intel compilers-specific adjustments after setting compiler variables."""
@@ -106,7 +108,7 @@ def _set_compiler_vars(self):
 
         # reset LIB_MULTITHREAD every time,
         # to avoid problems when multiple Intel compilers versions are used in a single session
-        self.LIB_MULTITHREAD = ['iomp5', 'pthread']  # iomp5 is OpenMP related
+        self.LIB_MULTITHREAD = self._INIT_LIB_MULTITHREAD[:]
         if LooseVersion(icc_version) < LooseVersion('2011'):
             self.LIB_MULTITHREAD.insert(1, "guide")
 
diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index befed0aaf9..13876777f3 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -43,8 +43,11 @@ class Acml(LinAlg):
     Provides ACML BLAS/LAPACK support.
     """
     BLAS_MODULE_NAME = ['ACML']
-    BLAS_LIB = None
-    BLAS_LIB_MT = None
+    BLAS_LIB = ['acml']
+    BLAS_LIB_MT = ['acml_mp']
+    # keep track of original values, need to be restored every time since we append to class 'constants' BLAS_LIB*
+    _INIT_BLAS_LIB = BLAS_LIB[:]
+    _INIT_BLAS_LIB_MT = BLAS_LIB_MT[:]
 
     # is completed in _set_blas_variables, depends on compiler used
     BLAS_LIB_DIR = []
@@ -74,8 +77,8 @@ def _set_blas_variables(self):
 
         # reset BLAS_LIB(_MT) every time, to avoid problems when multiple ACML versions are used in a single session
         # full list of libraries is highly dependent on ACML version and toolchain compiler (ifort, gfortran, ...)
-        self.BLAS_LIB = ['acml']
-        self.BLAS_LIB_MT = ['acml_mp']
+        self.BLAS_LIB = self._INIT_BLAS_LIB[:]
+        self.BLAS_LIB_MT = self._INIT_BLAS_LIB_MT[:]
 
         # version before 5.x still featured the acml_mv library
         ver = self.get_software_version(self.BLAS_MODULE_NAME)[0]
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index 2c86cc680b..2cc5cb663e 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -67,12 +67,16 @@ class IntelMKL(LinAlg):
     BLACS_LIB_STATIC = True
 
     SCALAPACK_MODULE_NAME = ['imkl']
-    SCALAPACK_LIB = None
-    SCALAPACK_LIB_MT = None
-    SCALAPACK_LIB_MAP = None
     SCALAPACK_REQUIRES = ['LIBBLACS', 'LIBBLAS']
     SCALAPACK_LIB_GROUP = True
     SCALAPACK_LIB_STATIC = True
+    SCALAPACK_LIB = ["mkl_scalapack%(lp64_sc)s"]
+    SCALAPACK_LIB_MT = ["mkl_scalapack%(lp64_sc)s"]
+    SCALAPACK_LIB_MAP = {'lp64_sc': '_lp64'}
+    # keep track of original values, need to be restored every time since we append to class 'constants' SCALAPACK_LIB*
+    _INIT_SCALAPACK_LIB = SCALAPACK_LIB[:]
+    _INIT_SCALAPACK_LIB_MT = SCALAPACK_LIB_MT[:]
+    _INIT_SCALAPACK_LIB_MAP = SCALAPACK_LIB_MAP[:]
 
     def _set_blas_variables(self):
         """Fix the map a bit"""
@@ -151,9 +155,9 @@ def _set_blacs_variables(self):
 
     def _set_scalapack_variables(self):
         # reset SCALAPACK_LIB* every time, to avoid problems when multiple imkl versions are used in a single session
-        self.SCALAPACK_LIB = ["mkl_scalapack%(lp64_sc)s"]
-        self.SCALAPACK_LIB_MT = ["mkl_scalapack%(lp64_sc)s"]
-        self.SCALAPACK_LIB_MAP = {'lp64_sc': '_lp64'}
+        self.SCALAPACK_LIB = self._INIT_SCALAPACK_LIB
+        self.SCALAPACK_LIB_MT = self._INIT_SCALAPACK_LIB_MT
+        self.SCALAPACK_LIB_MAP = self._INIT_SCALAPACK_LIB_MAP
 
         imkl_version = self.get_software_version(self.BLAS_MODULE_NAME)[0]
         if LooseVersion(imkl_version) < LooseVersion('10.3'):

From 8d1cdf425d824fc5560f4a2fb596624895ee45aa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 11:17:34 +0200
Subject: [PATCH 0995/1356] fix resetting of self.SCALAPACK_LIB_MAP, enhance
 test

---
 easybuild/toolchains/linalg/intelmkl.py | 10 +++++-----
 test/framework/toolchain.py             | 21 ++++++++++++++++++++-
 2 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index 2cc5cb663e..ae3a3e7914 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -28,7 +28,7 @@
 @author: Stijn De Weirdt (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
-
+import copy
 from distutils.version import LooseVersion
 
 from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP
@@ -76,7 +76,7 @@ class IntelMKL(LinAlg):
     # keep track of original values, need to be restored every time since we append to class 'constants' SCALAPACK_LIB*
     _INIT_SCALAPACK_LIB = SCALAPACK_LIB[:]
     _INIT_SCALAPACK_LIB_MT = SCALAPACK_LIB_MT[:]
-    _INIT_SCALAPACK_LIB_MAP = SCALAPACK_LIB_MAP[:]
+    _INIT_SCALAPACK_LIB_MAP = copy.deepcopy(SCALAPACK_LIB_MAP)
 
     def _set_blas_variables(self):
         """Fix the map a bit"""
@@ -155,9 +155,9 @@ def _set_blacs_variables(self):
 
     def _set_scalapack_variables(self):
         # reset SCALAPACK_LIB* every time, to avoid problems when multiple imkl versions are used in a single session
-        self.SCALAPACK_LIB = self._INIT_SCALAPACK_LIB
-        self.SCALAPACK_LIB_MT = self._INIT_SCALAPACK_LIB_MT
-        self.SCALAPACK_LIB_MAP = self._INIT_SCALAPACK_LIB_MAP
+        self.SCALAPACK_LIB = self._INIT_SCALAPACK_LIB[:]
+        self.SCALAPACK_LIB_MT = self._INIT_SCALAPACK_LIB_MT[:]
+        self.SCALAPACK_LIB_MAP = copy.deepcopy(self._INIT_SCALAPACK_LIB_MAP)
 
         imkl_version = self.get_software_version(self.BLAS_MODULE_NAME)[0]
         if LooseVersion(imkl_version) < LooseVersion('10.3'):
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index f37a3c2870..7fee7d0831 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -445,7 +445,7 @@ def setup_sandbox_for_intel_fftw(self, imklver='10.3.12.361'):
         open(imkl_module_path, 'w').write(imkl_module_alt_txt)
 
         fftw_libs = ['fftw3xc_intel', 'fftw3x_cdft', 'mkl_cdft_core', 'mkl_blacs_intelmpi_lp64']
-        fftw_libs += ['mkl_blacs_intelmpi_lp64', 'mkl_intel_lp64', 'mkl_sequential', 'mkl_core']
+        fftw_libs += ['mkl_blacs_intelmpi_lp64', 'mkl_intel_lp64', 'mkl_sequential', 'mkl_core', 'mkl_intel_ilp64']
         for subdir in ['mkl/lib/intel64', 'compiler/lib/intel64', 'lib/em64t']:
             os.makedirs(os.path.join(tmpdir, subdir))
             for fftlib in fftw_libs:
@@ -629,24 +629,43 @@ def test_old_new_iccifort(self):
         libblas_mt_new = "-Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
         libblas_mt_new += " -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread"
 
+        # incl. -lmkl_solver*
+        libscalack_old = "-lmkl_scalapack_lp64 -lmkl_solver_lp64_sequential -lmkl_blacs_intelmpi_lp64"
+        libscalack_old += " -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
+
+        # no -lmkl_solver*
+        libscalack_new = "-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
+
         tc = self.get_toolchain('ictce', version='4.1.13')
         tc.prepare()
         self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_new)
+        self.assertTrue(libscalack_new in os.environ['LIBSCALAPACK'])
         modules_tool().purge()
 
         tc = self.get_toolchain('ictce', version='3.2.2.u3')
         tc.prepare()
         self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_old)
+        self.assertTrue(libscalack_old in os.environ['LIBSCALAPACK'])
         modules_tool().purge()
 
         tc = self.get_toolchain('ictce', version='4.1.13')
         tc.prepare()
         self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_new)
+        self.assertTrue(libscalack_new in os.environ['LIBSCALAPACK'])
         modules_tool().purge()
 
         tc = self.get_toolchain('ictce', version='3.2.2.u3')
         tc.prepare()
         self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_old)
+        self.assertTrue(libscalack_old in os.environ['LIBSCALAPACK'])
+        modules_tool().purge()
+
+        libscalack_new = libscalack_new.replace('_lp64', '_ilp64')
+        tc = self.get_toolchain('ictce', version='4.1.13')
+        opts = {'i8': True}
+        tc.set_options(opts)
+        tc.prepare()
+        self.assertTrue(libscalack_new in os.environ['LIBSCALAPACK'])
 
         # cleanup
         shutil.rmtree(tmpdir1)

From 57d01a644beaea8ad76c72f19d883883e03791b1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 13:00:44 +0200
Subject: [PATCH 0996/1356] make --strict also a build option

---
 easybuild/tools/config.py  |  5 +++++
 easybuild/tools/options.py |  5 ++---
 test/framework/config.py   | 13 ++++++++++++-
 3 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index f44171b5d2..976bc3e7e5 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -44,6 +44,7 @@
 from vsc.utils.patterns import Singleton
 
 import easybuild.tools.environment as env
+from easybuild.tools import run
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.run import run_cmd
 
@@ -65,6 +66,7 @@
 }
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
+DEFAULT_STRICT = run.WARN
 
 
 # utility function for obtaining default paths
@@ -119,6 +121,9 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
     True: [
         'cleanup_builddir',
     ],
+    DEFAULT_STRICT: [
+        'strict',
+    ],
 }
 # build option that do not have a perfectly matching command line option
 BUILD_OPTIONS_OTHER = {
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 573b535051..ebb1a3ef1e 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -52,8 +52,7 @@
 from easybuild.tools.build_log import EasyBuildError, raise_easybuilderror
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX, DEFAULT_MODULES_TOOL
 from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
-from easybuild.tools.config import get_pretend_installpath
-from easybuild.tools.config import mk_full_default_path
+from easybuild.tools.config import DEFAULT_STRICT, get_pretend_installpath, mk_full_default_path
 from easybuild.tools.configobj import ConfigObj, ConfigObjError
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
@@ -136,7 +135,7 @@ def basic_options(self):
                      None, 'store_true', False, 'k'),
             'stop': ("Stop the installation after certain step",
                      'choice', 'store_or_None', SOURCE_STEP, 's', all_stops),
-            'strict': ("Set strictness level", 'choice', 'store', run.WARN, strictness_options),
+            'strict': ("Set strictness level", 'choice', 'store', DEFAULT_STRICT, strictness_options),
         })
 
         self.log.debug("basic_options: descr %s opts %s" % (descr, opts))
diff --git a/test/framework/config.py b/test/framework/config.py
index 07e0fe262e..ecbb28fe2c 100644
--- a/test/framework/config.py
+++ b/test/framework/config.py
@@ -38,8 +38,9 @@
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 
 import easybuild.tools.options as eboptions
+from easybuild.tools import run
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.config import build_path, source_paths, install_path, get_repositorypath
+from easybuild.tools.config import build_option, build_path, source_paths, install_path, get_repositorypath
 from easybuild.tools.config import set_tmpdir, BuildOptions, ConfigurationVariables
 from easybuild.tools.config import get_build_log_path, DEFAULT_PATH_SUBDIRS, init_build_options
 from easybuild.tools.environment import modify_env
@@ -634,6 +635,16 @@ def test_external_modules_metadata(self):
         err_msg = "Different length for lists of names/versions in metadata for external module"
         self.assertErrorRegex(EasyBuildError, err_msg, init_config, args=args)
 
+    def test_strict(self):
+        """Test use of --strict."""
+        # check default
+        self.assertEqual(build_option('strict'), run.WARN)
+
+        for strict_str, strict_val in [('error', run.ERROR), ('ignore', run.IGNORE), ('warn', run.WARN)]:
+            options = init_config(args=['--strict=%s' % strict_str])
+            init_config(build_options={'strict': options.strict})
+            self.assertEqual(build_option('strict'), strict_val)
+
 
 def suite():
     return TestLoader().loadTestsFromTestCase(EasyBuildConfigTest)

From 391cc62e6052425c580102925d6e5e975711a398 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 16:54:30 +0200
Subject: [PATCH 0997/1356] implement central solution for restoring Toolchain
 class 'constants'

---
 easybuild/toolchains/compiler/cuda.py         |  2 +-
 .../toolchains/compiler/inteliccifort.py      | 10 ++--
 easybuild/toolchains/linalg/acml.py           | 13 ++---
 easybuild/toolchains/linalg/intelmkl.py       | 14 ++----
 easybuild/tools/toolchain/toolchain.py        | 35 ++++++++++++-
 test/framework/toolchain.py                   | 49 ++++++++++++-------
 6 files changed, 82 insertions(+), 41 deletions(-)

diff --git a/easybuild/toolchains/compiler/cuda.py b/easybuild/toolchains/compiler/cuda.py
index 9397a9a584..ffbe45099c 100644
--- a/easybuild/toolchains/compiler/cuda.py
+++ b/easybuild/toolchains/compiler/cuda.py
@@ -96,7 +96,7 @@ def _set_compiler_flags(self):
         self.variables.nappend('CUDA_CXXFLAGS', cuda_flags)
 
         # add gencode compiler flags to list of flags for compiler variables
-        for gencode_val in self.options['cuda_gencode']:
+        for gencode_val in self.options.get('cuda_gencode', []):
             gencode_option = 'gencode %s' % gencode_val
             self.variables.nappend('CUDA_CFLAGS', gencode_option)
             self.variables.nappend('CUDA_CXXFLAGS', gencode_option)
diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index 7532468998..d024b0aaad 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -88,8 +88,11 @@ class IntelIccIfort(Compiler):
     }
 
     LIB_MULTITHREAD = ['iomp5', 'pthread']  # iomp5 is OpenMP related
-    # keep track of original value, needs to be restored every time since we append to class 'constant' LIB_MULTITHREAD
-    _INIT_LIB_MULTITHREAD = LIB_MULTITHREAD[:]
+
+    def __init__(self, *args, **kwargs):
+        """Toolchain constructor."""
+        self.CLASS_CONSTANTS_TO_RESTORE.append('LIB_MULTITHREAD')
+        super(IntelIccIfort, self).__init__(*args, **kwargs)
 
     def _set_compiler_vars(self):
         """Intel compilers-specific adjustments after setting compiler variables."""
@@ -106,9 +109,6 @@ def _set_compiler_vars(self):
             raise EasyBuildError("_set_compiler_vars: mismatch between icc version %s and ifort version %s",
                                  icc_version, ifort_version)
 
-        # reset LIB_MULTITHREAD every time,
-        # to avoid problems when multiple Intel compilers versions are used in a single session
-        self.LIB_MULTITHREAD = self._INIT_LIB_MULTITHREAD[:]
         if LooseVersion(icc_version) < LooseVersion('2011'):
             self.LIB_MULTITHREAD.insert(1, "guide")
 
diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index 13876777f3..26ced341b4 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -45,9 +45,6 @@ class Acml(LinAlg):
     BLAS_MODULE_NAME = ['ACML']
     BLAS_LIB = ['acml']
     BLAS_LIB_MT = ['acml_mp']
-    # keep track of original values, need to be restored every time since we append to class 'constants' BLAS_LIB*
-    _INIT_BLAS_LIB = BLAS_LIB[:]
-    _INIT_BLAS_LIB_MT = BLAS_LIB_MT[:]
 
     # is completed in _set_blas_variables, depends on compiler used
     BLAS_LIB_DIR = []
@@ -60,6 +57,11 @@ class Acml(LinAlg):
         TC_CONSTANT_GCC: ['gfortran64', 'gfortran64_mp'],
     }
 
+    def __init__(self, *args, **kwargs):
+        """Toolchain constructor."""
+        self.CLASS_CONSTANTS_TO_RESTORE.extend(['BLAS_LIB', 'BLAS_LIB_MT'])
+        super(Acml, self).__init__(*args, **kwargs)
+
     def _set_blas_variables(self):
         """Fix the map a bit"""
         if self.options.get('32bit', None):
@@ -75,11 +77,6 @@ def _set_blas_variables(self):
             raise EasyBuildError("_set_blas_variables: ACML set LDFLAGS/CPPFLAGS unknown entry in ACML_SUBDIRS_MAP "
                                  "with compiler family %s", self.COMPILER_FAMILY)
 
-        # reset BLAS_LIB(_MT) every time, to avoid problems when multiple ACML versions are used in a single session
-        # full list of libraries is highly dependent on ACML version and toolchain compiler (ifort, gfortran, ...)
-        self.BLAS_LIB = self._INIT_BLAS_LIB[:]
-        self.BLAS_LIB_MT = self._INIT_BLAS_LIB_MT[:]
-
         # version before 5.x still featured the acml_mv library
         ver = self.get_software_version(self.BLAS_MODULE_NAME)[0]
         if LooseVersion(ver) < LooseVersion("5"):
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index ae3a3e7914..0e1eceefaf 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -73,10 +73,11 @@ class IntelMKL(LinAlg):
     SCALAPACK_LIB = ["mkl_scalapack%(lp64_sc)s"]
     SCALAPACK_LIB_MT = ["mkl_scalapack%(lp64_sc)s"]
     SCALAPACK_LIB_MAP = {'lp64_sc': '_lp64'}
-    # keep track of original values, need to be restored every time since we append to class 'constants' SCALAPACK_LIB*
-    _INIT_SCALAPACK_LIB = SCALAPACK_LIB[:]
-    _INIT_SCALAPACK_LIB_MT = SCALAPACK_LIB_MT[:]
-    _INIT_SCALAPACK_LIB_MAP = copy.deepcopy(SCALAPACK_LIB_MAP)
+
+    def __init__(self, *args, **kwargs):
+        """Toolchain constructor."""
+        self.CLASS_CONSTANTS_TO_RESTORE.extend(['SCALAPACK_LIB', 'SCALAPACK_LIB_MT', 'SCALAPACK_LIB_MAP'])
+        super(IntelMKL, self).__init__(*args, **kwargs)
 
     def _set_blas_variables(self):
         """Fix the map a bit"""
@@ -154,11 +155,6 @@ def _set_blacs_variables(self):
         super(IntelMKL, self)._set_blacs_variables()
 
     def _set_scalapack_variables(self):
-        # reset SCALAPACK_LIB* every time, to avoid problems when multiple imkl versions are used in a single session
-        self.SCALAPACK_LIB = self._INIT_SCALAPACK_LIB[:]
-        self.SCALAPACK_LIB_MT = self._INIT_SCALAPACK_LIB_MT[:]
-        self.SCALAPACK_LIB_MAP = copy.deepcopy(self._INIT_SCALAPACK_LIB_MAP)
-
         imkl_version = self.get_software_version(self.BLAS_MODULE_NAME)[0]
         if LooseVersion(imkl_version) < LooseVersion('10.3'):
             self.SCALAPACK_LIB.append("mkl_solver%(lp64)s_sequential")
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index a5cad572be..b63e3265d3 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -30,7 +30,7 @@
 @author: Stijn De Weirdt (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
-
+import copy
 import os
 from vsc.utils import fancylogger
 
@@ -58,6 +58,10 @@ class Toolchain(object):
     VERSION = None
     TOOLCHAIN_FAMILY = None
 
+    # list of class 'constants' that should be restored for every new instance of this class
+    CLASS_CONSTANTS_TO_RESTORE = []
+    CLASS_CONSTANT_COPIES = {}
+
     # class method
     def _is_toolchain_for(cls, name):
         """see if this class can provide support for toolchain named name"""
@@ -95,6 +99,9 @@ def __init__(self, name=None, version=None, mns=None):
 
         self.vars = None
 
+        self._copy_class_constants()
+        self._restore_class_constants()
+
         self.modules_tool = modules_tool()
         self.mns = mns
         self.mod_full_name = None
@@ -122,6 +129,32 @@ def base_init(self):
             if hasattr(self, 'LINKER_TOGGLE_STATIC_DYNAMIC'):
                 self.variables.LINKER_TOGGLE_STATIC_DYNAMIC = self.LINKER_TOGGLE_STATIC_DYNAMIC
 
+    def _copy_class_constants(self):
+        """Copy class constants that needs to be restored again when a new instance is created."""
+        # this only needs to be done the first time (for this class, taking inheritance into account is key)
+        key = self.__class__
+        if key not in self.CLASS_CONSTANT_COPIES:
+            self.CLASS_CONSTANT_COPIES[key] = {}
+            for cst in self.CLASS_CONSTANTS_TO_RESTORE:
+                if hasattr(self, cst):
+                    self.CLASS_CONSTANT_COPIES[key][cst] = copy.deepcopy(getattr(self, cst))
+                else:
+                    raise EasyBuildError("Class constant '%s' to be restored does not exist", cst)
+
+            self.log.debug("Copied class constants: %s", self.CLASS_CONSTANT_COPIES[key])
+
+    def _restore_class_constants(self):
+        """Restored class constants that need to be restored when a new instance is created."""
+        key = self.__class__
+        for cst in self.CLASS_CONSTANT_COPIES[key]:
+            newval = copy.deepcopy(self.CLASS_CONSTANT_COPIES[key][cst])
+            if hasattr(self, cst):
+                self.log.debug("Restoring class constant '%s' to %s (was: %s)", cst, newval, getattr(self, cst))
+            else:
+                self.log.debug("Restoring (currently undefined) class constant '%s' to %s", cst, newval)
+
+            setattr(self, cst, newval)
+
     def get_variable(self, name, typ=str):
         """Get value for specified variable.
         typ: indicates what type of return value is expected"""
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 7fee7d0831..faf64fface 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -622,50 +622,65 @@ def test_old_new_iccifort(self):
         tmpdir2, imkl_module_path2, imkl_module_txt2 = self.setup_sandbox_for_intel_fftw(imklver='10.2.6.038')
 
         # incl. -lguide
-        libblas_mt_old = "-Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
-        libblas_mt_old += " -Wl,--end-group -Wl,-Bdynamic -liomp5 -lguide -lpthread"
+        libblas_mt_ictce3 = "-Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
+        libblas_mt_ictce3 += " -Wl,--end-group -Wl,-Bdynamic -liomp5 -lguide -lpthread"
 
         # no -lguide
-        libblas_mt_new = "-Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
-        libblas_mt_new += " -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread"
+        libblas_mt_ictce4 = "-Wl,-Bstatic -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core"
+        libblas_mt_ictce4 += " -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread"
 
         # incl. -lmkl_solver*
-        libscalack_old = "-lmkl_scalapack_lp64 -lmkl_solver_lp64_sequential -lmkl_blacs_intelmpi_lp64"
-        libscalack_old += " -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
+        libscalack_ictce3 = "-lmkl_scalapack_lp64 -lmkl_solver_lp64_sequential -lmkl_blacs_intelmpi_lp64"
+        libscalack_ictce3 += " -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
 
         # no -lmkl_solver*
-        libscalack_new = "-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
+        libscalack_ictce4 = "-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
+
+        libblas_mt_goolfc = "-lopenblas -lgfortran"
+        libscalack_goolfc = "-lscalapack -lopenblas -lgfortran"
+
+        tc = self.get_toolchain('goolfc', version='1.3.12')
+        tc.prepare()
+        self.assertEqual(os.environ['LIBBLAS_MT'], libblas_mt_goolfc)
+        self.assertEqual(os.environ['LIBSCALAPACK'], libscalack_goolfc)
+        modules_tool().purge()
 
         tc = self.get_toolchain('ictce', version='4.1.13')
         tc.prepare()
-        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_new)
-        self.assertTrue(libscalack_new in os.environ['LIBSCALAPACK'])
+        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_ictce4)
+        self.assertTrue(libscalack_ictce4 in os.environ['LIBSCALAPACK'])
         modules_tool().purge()
 
         tc = self.get_toolchain('ictce', version='3.2.2.u3')
         tc.prepare()
-        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_old)
-        self.assertTrue(libscalack_old in os.environ['LIBSCALAPACK'])
+        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_ictce3)
+        self.assertTrue(libscalack_ictce3 in os.environ['LIBSCALAPACK'])
         modules_tool().purge()
 
         tc = self.get_toolchain('ictce', version='4.1.13')
         tc.prepare()
-        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_new)
-        self.assertTrue(libscalack_new in os.environ['LIBSCALAPACK'])
+        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_ictce4)
+        self.assertTrue(libscalack_ictce4 in os.environ['LIBSCALAPACK'])
         modules_tool().purge()
 
         tc = self.get_toolchain('ictce', version='3.2.2.u3')
         tc.prepare()
-        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_old)
-        self.assertTrue(libscalack_old in os.environ['LIBSCALAPACK'])
+        self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_ictce3)
+        self.assertTrue(libscalack_ictce3 in os.environ['LIBSCALAPACK'])
         modules_tool().purge()
 
-        libscalack_new = libscalack_new.replace('_lp64', '_ilp64')
+        libscalack_ictce4 = libscalack_ictce4.replace('_lp64', '_ilp64')
         tc = self.get_toolchain('ictce', version='4.1.13')
         opts = {'i8': True}
         tc.set_options(opts)
         tc.prepare()
-        self.assertTrue(libscalack_new in os.environ['LIBSCALAPACK'])
+        self.assertTrue(libscalack_ictce4 in os.environ['LIBSCALAPACK'])
+        modules_tool().purge()
+
+        tc = self.get_toolchain('goolfc', version='1.3.12')
+        tc.prepare()
+        self.assertEqual(os.environ['LIBBLAS_MT'], libblas_mt_goolfc)
+        self.assertEqual(os.environ['LIBSCALAPACK'], libscalack_goolfc)
 
         # cleanup
         shutil.rmtree(tmpdir1)

From 0671a434e3cb9b9310991c4a1b213f56f9be3ee2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 16:56:44 +0200
Subject: [PATCH 0998/1356] cleanup

---
 easybuild/toolchains/linalg/acml.py     |  1 +
 easybuild/toolchains/linalg/intelmkl.py | 11 ++++++-----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index 26ced341b4..0dc899b2e6 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -43,6 +43,7 @@ class Acml(LinAlg):
     Provides ACML BLAS/LAPACK support.
     """
     BLAS_MODULE_NAME = ['ACML']
+    # full list of libraries is highly dependent on ACML version and toolchain compiler (ifort, gfortran, ...)
     BLAS_LIB = ['acml']
     BLAS_LIB_MT = ['acml_mp']
 
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index 0e1eceefaf..78cc87de2f 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -67,15 +67,16 @@ class IntelMKL(LinAlg):
     BLACS_LIB_STATIC = True
 
     SCALAPACK_MODULE_NAME = ['imkl']
-    SCALAPACK_REQUIRES = ['LIBBLACS', 'LIBBLAS']
-    SCALAPACK_LIB_GROUP = True
-    SCALAPACK_LIB_STATIC = True
     SCALAPACK_LIB = ["mkl_scalapack%(lp64_sc)s"]
     SCALAPACK_LIB_MT = ["mkl_scalapack%(lp64_sc)s"]
     SCALAPACK_LIB_MAP = {'lp64_sc': '_lp64'}
+    SCALAPACK_REQUIRES = ['LIBBLACS', 'LIBBLAS']
+    SCALAPACK_LIB_GROUP = True
+    SCALAPACK_LIB_STATIC = True
 
     def __init__(self, *args, **kwargs):
         """Toolchain constructor."""
+        self.CLASS_CONSTANTS_TO_RESTORE.append('BLAS_LIB_MAP')
         self.CLASS_CONSTANTS_TO_RESTORE.extend(['SCALAPACK_LIB', 'SCALAPACK_LIB_MT', 'SCALAPACK_LIB_MAP'])
         super(IntelMKL, self).__init__(*args, **kwargs)
 
@@ -106,10 +107,10 @@ def _set_blas_variables(self):
 
         if self.options.get('32bit', None):
             # 32bit
-            self.BLAS_LIB_MAP.update({"lp64":''})  # FIXME
+            self.BLAS_LIB_MAP.update({"lp64":''})
         if self.options.get('i8', None):
             # ilp64/i8
-            self.BLAS_LIB_MAP.update({"lp64":'_ilp64'})  # FIXME
+            self.BLAS_LIB_MAP.update({"lp64":'_ilp64'})
             # CPP / CFLAGS
             self.variables.nappend_el('CFLAGS', 'DMKL_ILP64')
 

From d4c5fc6673715eafdf152ee3ce595d2652fdc969 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 17:54:57 +0200
Subject: [PATCH 0999/1356] don't define Toolchain class constant as empty
 list, not inheritance-safe

---
 easybuild/toolchains/compiler/inteliccifort.py |  2 +-
 easybuild/toolchains/linalg/acml.py            |  2 +-
 easybuild/toolchains/linalg/intelmkl.py        |  3 +--
 easybuild/tools/toolchain/toolchain.py         | 12 ++++++++++--
 4 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index d024b0aaad..d2a71dac7b 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -91,7 +91,7 @@ class IntelIccIfort(Compiler):
 
     def __init__(self, *args, **kwargs):
         """Toolchain constructor."""
-        self.CLASS_CONSTANTS_TO_RESTORE.append('LIB_MULTITHREAD')
+        self.add_class_constants_to_restore(['LIB_MULTITHREAD'])
         super(IntelIccIfort, self).__init__(*args, **kwargs)
 
     def _set_compiler_vars(self):
diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index 0dc899b2e6..e6f8da07e5 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -60,7 +60,7 @@ class Acml(LinAlg):
 
     def __init__(self, *args, **kwargs):
         """Toolchain constructor."""
-        self.CLASS_CONSTANTS_TO_RESTORE.extend(['BLAS_LIB', 'BLAS_LIB_MT'])
+        self.add_class_constants_to_restore(['BLAS_LIB', 'BLAS_LIB_MT'])
         super(Acml, self).__init__(*args, **kwargs)
 
     def _set_blas_variables(self):
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index 78cc87de2f..c10969ed21 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -76,8 +76,7 @@ class IntelMKL(LinAlg):
 
     def __init__(self, *args, **kwargs):
         """Toolchain constructor."""
-        self.CLASS_CONSTANTS_TO_RESTORE.append('BLAS_LIB_MAP')
-        self.CLASS_CONSTANTS_TO_RESTORE.extend(['SCALAPACK_LIB', 'SCALAPACK_LIB_MT', 'SCALAPACK_LIB_MAP'])
+        self.add_class_constants_to_restore(['BLAS_LIB_MAP', 'SCALAPACK_LIB', 'SCALAPACK_LIB_MT', 'SCALAPACK_LIB_MAP'])
         super(IntelMKL, self).__init__(*args, **kwargs)
 
     def _set_blas_variables(self):
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index b63e3265d3..9548ceb41a 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -59,7 +59,7 @@ class Toolchain(object):
     TOOLCHAIN_FAMILY = None
 
     # list of class 'constants' that should be restored for every new instance of this class
-    CLASS_CONSTANTS_TO_RESTORE = []
+    CLASS_CONSTANTS_TO_RESTORE = None
     CLASS_CONSTANT_COPIES = {}
 
     # class method
@@ -99,6 +99,7 @@ def __init__(self, name=None, version=None, mns=None):
 
         self.vars = None
 
+        self.add_class_constants_to_restore([])  # make sure self.CLASS_CONSTANTS_TO_RESTORE is initialised
         self._copy_class_constants()
         self._restore_class_constants()
 
@@ -115,6 +116,13 @@ def __init__(self, name=None, version=None, mns=None):
                 self.mod_short_name = self.mns.det_short_module_name(tc_dict)
                 self.init_modpaths = self.mns.det_init_modulepaths(tc_dict)
 
+    def add_class_constants_to_restore(self, names):
+        """Add given constants to list of class constants to restore with each new instance."""
+        if self.CLASS_CONSTANTS_TO_RESTORE is None:
+            self.CLASS_CONSTANTS_TO_RESTORE = names[:]
+        else:
+            self.CLASS_CONSTANTS_TO_RESTORE.extend(names)
+
     def base_init(self):
         if not hasattr(self, 'log'):
             self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
@@ -139,7 +147,7 @@ def _copy_class_constants(self):
                 if hasattr(self, cst):
                     self.CLASS_CONSTANT_COPIES[key][cst] = copy.deepcopy(getattr(self, cst))
                 else:
-                    raise EasyBuildError("Class constant '%s' to be restored does not exist", cst)
+                    raise EasyBuildError("Class constant '%s' to be restored does not exist in %s", cst, self)
 
             self.log.debug("Copied class constants: %s", self.CLASS_CONSTANT_COPIES[key])
 

From 77cf7f6c6718a2d8e9399fa46b9d828e9c7f0947 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jun 2015 18:50:13 +0200
Subject: [PATCH 1000/1356] drop unused import

---
 easybuild/toolchains/linalg/intelmkl.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index c10969ed21..2102c6e02e 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -28,7 +28,6 @@
 @author: Stijn De Weirdt (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
-import copy
 from distutils.version import LooseVersion
 
 from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP

From 6a97117120170b89b781621196d7c97b6a471413 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Fri, 5 Jun 2015 22:19:39 +0200
Subject: [PATCH 1001/1356] Only redefine `gc3libs.log` if GC3Pie is available

---
 easybuild/tools/job/gc3pie.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 1639b7ecdb..62ebfb3523 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -48,10 +48,11 @@
 
 from vsc.utils import fancylogger
 
-# inject EasyBuild logger into GC3Pie
-gc3libs.log = fancylogger.getLogger('gc3pie', fname=False)
-# make handling of log.error compatible with stdlib logging
-gc3libs.log.raiseError = False
+if HAVE_GC3PIE:
+    # inject EasyBuild logger into GC3Pie
+    gc3libs.log = fancylogger.getLogger('gc3pie', fname=False)
+    # make handling of log.error compatible with stdlib logging
+    gc3libs.log.raiseError = False
 
 
 # eb --job --job-backend=GC3Pie

From 415fa87aec1c4531e059dabc15e68c7eb26878b8 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Fri, 5 Jun 2015 22:23:38 +0200
Subject: [PATCH 1002/1356] Add back `prepare_first` into arguments of
 `build_easyconfigs_in_parallel`.

Thanks @boegel for spotting the error!
---
 easybuild/tools/parallelbuild.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 082086dd2c..80f952705d 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -53,7 +53,9 @@ def _to_key(dep):
     """Determine key for specified dependency."""
     return ActiveMNS().det_full_module_name(dep)
 
-def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybuild-build'):
+def build_easyconfigs_in_parallel(build_command, easyconfigs,
+                                  output_dir='easybuild-build',
+                                  prepare_first=True):
     """
     Build easyconfigs in parallel by submitting jobs to a batch-queuing system.
     Return list of jobs submitted.

From cf16ee292980ac42a6f73e86ff234f6ce594a9df Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 8 Jun 2015 10:01:35 +0200
Subject: [PATCH 1003/1356] fix remarks

---
 .../toolchains/compiler/inteliccifort.py      |  3 ++-
 easybuild/toolchains/linalg/acml.py           |  3 ++-
 easybuild/toolchains/linalg/intelmkl.py       |  3 ++-
 easybuild/tools/toolchain/toolchain.py        | 25 +++++++++++--------
 4 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index d2a71dac7b..e9af5dc722 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -91,7 +91,8 @@ class IntelIccIfort(Compiler):
 
     def __init__(self, *args, **kwargs):
         """Toolchain constructor."""
-        self.add_class_constants_to_restore(['LIB_MULTITHREAD'])
+        class_constants = kwargs.setdefault('class_constants', [])
+        class_constants.append('LIB_MULTITHREAD')
         super(IntelIccIfort, self).__init__(*args, **kwargs)
 
     def _set_compiler_vars(self):
diff --git a/easybuild/toolchains/linalg/acml.py b/easybuild/toolchains/linalg/acml.py
index e6f8da07e5..fb7c5def68 100644
--- a/easybuild/toolchains/linalg/acml.py
+++ b/easybuild/toolchains/linalg/acml.py
@@ -60,7 +60,8 @@ class Acml(LinAlg):
 
     def __init__(self, *args, **kwargs):
         """Toolchain constructor."""
-        self.add_class_constants_to_restore(['BLAS_LIB', 'BLAS_LIB_MT'])
+        class_constants = kwargs.setdefault('class_constants', [])
+        class_constants.extend(['BLAS_LIB', 'BLAS_LIB_MT'])
         super(Acml, self).__init__(*args, **kwargs)
 
     def _set_blas_variables(self):
diff --git a/easybuild/toolchains/linalg/intelmkl.py b/easybuild/toolchains/linalg/intelmkl.py
index 2102c6e02e..81ae047c63 100644
--- a/easybuild/toolchains/linalg/intelmkl.py
+++ b/easybuild/toolchains/linalg/intelmkl.py
@@ -75,7 +75,8 @@ class IntelMKL(LinAlg):
 
     def __init__(self, *args, **kwargs):
         """Toolchain constructor."""
-        self.add_class_constants_to_restore(['BLAS_LIB_MAP', 'SCALAPACK_LIB', 'SCALAPACK_LIB_MT', 'SCALAPACK_LIB_MAP'])
+        class_constants = kwargs.setdefault('class_constants', [])
+        class_constants.extend(['BLAS_LIB_MAP', 'SCALAPACK_LIB', 'SCALAPACK_LIB_MT', 'SCALAPACK_LIB_MAP'])
         super(IntelMKL, self).__init__(*args, **kwargs)
 
     def _set_blas_variables(self):
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index 9548ceb41a..907bb65734 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -77,7 +77,7 @@ def _is_toolchain_for(cls, name):
 
     _is_toolchain_for = classmethod(_is_toolchain_for)
 
-    def __init__(self, name=None, version=None, mns=None):
+    def __init__(self, name=None, version=None, mns=None, class_constants=None):
         """Toolchain constructor."""
 
         self.base_init()
@@ -99,9 +99,7 @@ def __init__(self, name=None, version=None, mns=None):
 
         self.vars = None
 
-        self.add_class_constants_to_restore([])  # make sure self.CLASS_CONSTANTS_TO_RESTORE is initialised
-        self._copy_class_constants()
-        self._restore_class_constants()
+        self._init_class_constants(class_constants)
 
         self.modules_tool = modules_tool()
         self.mns = mns
@@ -116,14 +114,8 @@ def __init__(self, name=None, version=None, mns=None):
                 self.mod_short_name = self.mns.det_short_module_name(tc_dict)
                 self.init_modpaths = self.mns.det_init_modulepaths(tc_dict)
 
-    def add_class_constants_to_restore(self, names):
-        """Add given constants to list of class constants to restore with each new instance."""
-        if self.CLASS_CONSTANTS_TO_RESTORE is None:
-            self.CLASS_CONSTANTS_TO_RESTORE = names[:]
-        else:
-            self.CLASS_CONSTANTS_TO_RESTORE.extend(names)
-
     def base_init(self):
+        """Initialise missing class attributes (log, options, variables)."""
         if not hasattr(self, 'log'):
             self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
@@ -137,6 +129,17 @@ def base_init(self):
             if hasattr(self, 'LINKER_TOGGLE_STATIC_DYNAMIC'):
                 self.variables.LINKER_TOGGLE_STATIC_DYNAMIC = self.LINKER_TOGGLE_STATIC_DYNAMIC
 
+    def _init_class_constants(self, class_constants):
+        """Initialise class 'constants'."""
+        # make sure self.CLASS_CONSTANTS_TO_RESTORE is initialised
+        if class_constants is None:
+            self.CLASS_CONSTANTS_TO_RESTORE = []
+        else:
+            self.CLASS_CONSTANTS_TO_RESTORE = class_constants[:]
+
+        self._copy_class_constants()
+        self._restore_class_constants()
+
     def _copy_class_constants(self):
         """Copy class constants that needs to be restored again when a new instance is created."""
         # this only needs to be done the first time (for this class, taking inheritance into account is key)

From 84f125aed13fa5f1db5eddf8dfaab5ffa15f0297 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 8 Jun 2015 16:01:57 +0200
Subject: [PATCH 1004/1356] make unit test suite pass, rename JobServer to
 JobBackend, fix default for --job-bakcend

---
 easybuild/tools/config.py         |  3 +--
 easybuild/tools/job/__init__.py   | 20 ++--------------
 easybuild/tools/job/gc3pie.py     |  6 ++---
 easybuild/tools/job/pbs_python.py | 13 ++++++----
 easybuild/tools/options.py        | 13 +++++-----
 easybuild/tools/parallelbuild.py  |  8 +++----
 test/framework/parallelbuild.py   | 40 +++++++++++++++++++++----------
 7 files changed, 50 insertions(+), 53 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index e0352afd5f..a3199dadd8 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -52,6 +52,7 @@
 _log = fancylogger.getLogger('config', fname=False)
 
 
+DEFAULT_JOB_BACKEND = 'PbsPython'
 DEFAULT_LOGFILE_FORMAT = ("easybuild", "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
 DEFAULT_MNS = 'EasyBuildMNS'
 DEFAULT_MODULE_SYNTAX = 'Tcl'
@@ -68,8 +69,6 @@
 DEFAULT_REPOSITORY = 'FileRepository'
 DEFAULT_STRICT = run.WARN
 
-PREFERRED_JOB_BACKENDS = ('Pbs', 'GC3Pie')
-
 
 # utility function for obtaining default paths
 def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 5d11408053..194e469358 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -30,11 +30,10 @@
 from vsc.utils.missing import get_subclasses
 
 from easybuild.tools.config import get_job_backend
-from easybuild.tools.config import PREFERRED_JOB_BACKENDS
 from easybuild.tools.utilities import import_available_modules
 
 
-class JobServer(object):
+class JobBackend(object):
     __metaclass__ = ABCMeta
 
     USABLE = False
@@ -92,9 +91,7 @@ def avail_job_backends(check_usable=True):
     Return all known job execution backends.
     """
     import_available_modules('easybuild.tools.job')
-    class_dict = dict([(x.__name__, x)
-                       for x in get_subclasses(JobServer)
-                       if (x.USABLE or not check_usable)])
+    class_dict = dict([(x.__name__, x) for x in get_subclasses(JobBackend)])
     return class_dict
 
 
@@ -107,16 +104,3 @@ def job_backend():
         return None
     job_backend_class = avail_job_backends().get(job_backend)
     return job_backend_class()
-
-
-def preferred_job_backend(order=PREFERRED_JOB_BACKENDS):
-    """
-    Return name of preferred concrete `JobServer` instance, or `None`
-    if none is available.
-    """
-    available_backends = avail_job_backends()
-    for backend in order:
-        if backend in available_backends:
-            return backend
-            break
-    return None
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 62ebfb3523..ecf375dda3 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -44,7 +44,7 @@
     HAVE_GC3PIE = False
 
 from easybuild.tools.build_log import print_msg
-from easybuild.tools.job import JobServer
+from easybuild.tools.job import JobBackend
 
 from vsc.utils import fancylogger
 
@@ -56,7 +56,7 @@
 
 
 # eb --job --job-backend=GC3Pie
-class GC3Pie(JobServer):
+class GC3Pie(JobBackend):
     """
     Use the GC3Pie__ framework to submit and monitor compilation jobs.
 
@@ -83,7 +83,7 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         Create and return a job object with the given parameters.
 
         First argument `server` is an instance of the corresponding
-        `JobServer` class, i.e., a `GC3Pie`:class: instance in this case.
+        `JobBackend` class, i.e., a `GC3Pie`:class: instance in this case.
 
         Second argument `script` is the content of the job script
         itself, i.e., the sequence of shell commands that will be
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 15323d4f5b..e334157199 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -36,7 +36,7 @@
 from vsc.utils import fancylogger
 
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.job import JobServer
+from easybuild.tools.job import JobBackend
 
 
 _log = fancylogger.getLogger('pbs_python', fname=False)
@@ -58,27 +58,30 @@ def only_if_pbs_import_successful(fn):
     HAVE_PBS_PYTHON = True
 except ImportError:
     _log.debug("Failed to import pbs from pbs_python."
-               " Silently ignoring, this is a real issue only with --job=pbs")
+               " Silently ignoring, this is a real issue only when pbs_python is used as backend for --job")
     # no `pbs_python` available, turn function into a no-op
     def only_if_pbs_import_successful(fn):
         def instead(*args, **kwargs):
             """This is a no-op since `pbs_python` is not available."""
             errmsg = ("PBSQuery or pbs modules not available."
                       " Please make sure `pbs_python` is installed and usable.")
-            _log.error(errmsg)
-            raise RuntimeError(errmsg)
+            raise EasyBuildError(errmsg)
         return instead
     HAVE_PBS_PYTHON = False
 
 
-class Pbs(JobServer):
+class PbsPython(JobBackend):
     """
     Manage PBS server communication and create `PbsJob` objects.
     """
 
     USABLE = HAVE_PBS_PYTHON
 
+    @only_if_pbs_import_successful
     def __init__(self, pbs_server=None):
+        _init()
+
+    def _init(self, pbs_server=None):
         self.pbs_server = pbs_server or pbs.pbs_default()
         self.conn = None
         self._ppn = None
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 5aa5e2cbf8..8780b2c12e 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -48,16 +48,15 @@
 from easybuild.framework.easyconfig.templates import template_documentation
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
-from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
+from easybuild.tools import build_log, config, run  # build_log should always stay there, to ensure EasyBuildLog
 from easybuild.tools.build_log import EasyBuildError, raise_easybuilderror
-from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX, DEFAULT_MODULES_TOOL
-from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
-from easybuild.tools.config import DEFAULT_STRICT, get_pretend_installpath, mk_full_default_path
-from easybuild.tools.config import PREFERRED_JOB_BACKENDS
+from easybuild.tools.config import DEFAULT_JOB_BACKEND, DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX
+from easybuild.tools.config import DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX
+from easybuild.tools.config import DEFAULT_REPOSITORY, DEFAULT_STRICT, get_pretend_installpath, mk_full_default_path
 from easybuild.tools.configobj import ConfigObj, ConfigObjError
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
-from easybuild.tools.job import avail_job_backends, preferred_job_backend
+from easybuild.tools.job import avail_job_backends
 from easybuild.tools.modules import avail_modules_tools
 from easybuild.tools.module_generator import ModuleGeneratorLua, avail_module_generators
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
@@ -249,7 +248,7 @@ def config_options(self):
             'installpath-software': ("Install path for software (if None, combine --installpath and --subdir-software)",
                                      None, 'store', None),
             'job-backend': ("What job runner to use", 'choice', 'store',
-                            preferred_job_backend(), (avail_job_backends().keys())),
+                            DEFAULT_JOB_BACKEND, avail_job_backends().keys()),
             # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 80f952705d..bc42d775a4 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -72,14 +72,12 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs,
 
     job_server = job_backend()
     if job_server is None:
-        _log.error("Cannot use --job if no job backend is available.")
+        raise EasyBuildError("Cannot use --job if no job backend is available.")
 
     try:
         job_server.begin()
-    except RuntimeError, err:
-        _log.error("connection to server failed (%s: %s), can't submit jobs."
-                   % (err.__class__.__name__, err))
-        return None # XXX: should this `raise` instead?
+    except RuntimeError as err:
+        raise EasyBuildError("connection to server failed (%s: %s), can't submit jobs.", err.__class__.__name__, err)
 
     # dependencies have already been resolved,
     # so one can linearly walk over the list and use previous job id's
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 76d9b90715..a910b763bc 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -33,7 +33,9 @@
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 
 from easybuild.framework.easyconfig.tools import process_easyconfig
-from easybuild.tools import config, parallelbuild
+from easybuild.tools import config, job
+from easybuild.tools.job import pbs_python
+from easybuild.tools.job.pbs_python import PbsPython
 from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
 from easybuild.tools.robot import resolve_dependencies
 
@@ -59,37 +61,49 @@ def cleanup(self, *args, **kwargs):
     def has_holds(self, *args, **kwargs):
         pass
 
-    def submit(self, *args, **kwargs):
+    def _submit(self, *args, **kwargs):
         pass
 
 
 class ParallelBuildTest(EnhancedTestCase):
     """ Testcase for run module """
 
-    def setUp(self):
-        """Set up testcase."""
-        super(ParallelBuildTest, self).setUp()
+    def test_build_easyconfigs_in_parallel_pbs_python(self):
+        """Basic test for build_easyconfigs_in_parallel function."""
+        # put mocked functions in place
+        PbsPython__init__ = PbsPython.__init__
+        PbsPython_commit = PbsPython.commit
+        PbsPython_connect_to_server = PbsPython.connect_to_server
+        PbsPython_ppn = PbsPython.ppn
+        pbs_python_PbsJob = pbs_python.PbsJob
+
+        PbsPython.__init__ = lambda self: PbsPython._init(self, pbs_server='localhost')
+        PbsPython.commit = mock
+        PbsPython.connect_to_server = mock
+        PbsPython.ppn = mock
+        pbs_python.PbsJob = MockPbsJob
+
         build_options = {
             'robot_path': os.path.join(os.path.dirname(__file__), 'easyconfigs'),
             'valid_module_classes': config.module_classes(),
             'validate': False,
         }
-        init_config(build_options=build_options)
+        init_config(args=['--job-backend=PbsPython'], build_options=build_options)
 
-        # put mocked functions in place
-        parallelbuild.connect_to_server = mock
-        parallelbuild.disconnect_from_server = mock
-        parallelbuild.get_ppn = mock
-        parallelbuild.PbsJob = MockPbsJob
 
-    def test_build_easyconfigs_in_parallel(self):
-        """Basic test for build_easyconfigs_in_parallel function."""
         easyconfig_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'gzip-1.5-goolf-1.4.10.eb')
         easyconfigs = process_easyconfig(easyconfig_file)
         ordered_ecs = resolve_dependencies(easyconfigs)
         jobs = build_easyconfigs_in_parallel("echo %(spec)s", ordered_ecs, prepare_first=False)
         self.assertEqual(len(jobs), 8)
 
+        # restore mocked stuff
+        PbsPython.__init__ = PbsPython__init__
+        PbsPython.commit = PbsPython_commit
+        PbsPython.connect_to_server = PbsPython_connect_to_server
+        PbsPython.ppn = PbsPython_ppn
+        pbs_python.PbsJob = pbs_python_PbsJob
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(ParallelBuildTest)

From 9c1dfc57349344968800dd87998149542c31b167 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Mon, 8 Jun 2015 18:05:52 +0200
Subject: [PATCH 1005/1356] Fix reporting of job count.

---
 easybuild/tools/job/gc3pie.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index ecf375dda3..127cfe0194 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -146,8 +146,6 @@ def commit(self):
         No more job submissions should be attempted after `commit()`
         has been called, until `begin()` is invoked again.
         """
-        total = len(self._jobs)
-
         # Create an instance of `Engine` using the configuration file present
         # in your home directory.
         self._engine = create_engine()
@@ -174,13 +172,13 @@ def commit(self):
                 'RUNNING',
                 'ok',
                 'failed',
-            ], total=total)
+            ])
 
             # Wait a few seconds...
             time.sleep(30)
 
         # final status report
-        self._print_status_report(['total', 'ok', 'failed'], total=total)
+        self._print_status_report(['total', 'ok', 'failed'])
 
     def _print_status_report(self, states=('total', 'ok', 'failed'), **override):
         """

From a295d2c12c292988c66c28ed52b94c702055e453 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Mon, 8 Jun 2015 18:37:32 +0200
Subject: [PATCH 1006/1356] Set base output directory for the entire task
 collection.

---
 easybuild/tools/job/gc3pie.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 127cfe0194..b5cb8cf079 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -76,7 +76,8 @@ def begin(self):
 
         Removes any reference to previously-submitted jobs.
         """
-        self._jobs = DependentTaskCollection()
+        self._jobs = DependentTaskCollection(
+            output_dir=os.path.join(os.getcwd(), 'easybuild-jobs'))
 
     def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         """
@@ -117,7 +118,7 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
             inputs=[],
             outputs=[],
             # where should the output (STDOUT/STDERR) files be downloaded to?
-            output_dir=os.path.join(os.getcwd(), 'easybuild-jobs', name),
+            output_dir=os.path.join(self._jobs.output_dir, name),
             # capture STDOUT and STDERR
             stdout='stdout.log',
             join=True,

From a4c78b6b7213db4b05f99a32a1431e43a29827d6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 9 Jun 2015 11:20:23 +0200
Subject: [PATCH 1007/1356] add unit test for GC3Pie

---
 easybuild/tools/job/gc3pie.py   | 24 +++-----------
 test/framework/parallelbuild.py | 58 ++++++++++++++++++++++++++++++---
 2 files changed, 58 insertions(+), 24 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index b5cb8cf079..c6611f4ea1 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -44,6 +44,7 @@
     HAVE_GC3PIE = False
 
 from easybuild.tools.build_log import print_msg
+from easybuild.tools.config import build_option
 from easybuild.tools.job import JobBackend
 
 from vsc.utils import fancylogger
@@ -167,16 +168,10 @@ def commit(self):
             self._engine.progress()
 
             # report progress
-            self._print_status_report([
-                'total',
-                'SUBMITTED',
-                'RUNNING',
-                'ok',
-                'failed',
-            ])
+            self._print_status_report(['total', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
 
             # Wait a few seconds...
-            time.sleep(30)
+            time.sleep(30)  # FIXME: don't hardcode (at least use a class constant that can be tweaked)
 
         # final status report
         self._print_status_report(['total', 'ok', 'failed'])
@@ -192,14 +187,5 @@ def _print_status_report(self, states=('total', 'ok', 'failed'), **override):
         report the number of total jobs right from the start.
         """
         stats = self._engine.stats(only=Application)
-        print_msg(
-            "build jobs: "
-            + ", ".join([
-                ("%d %s" % (
-                    override.get(state, stats[state]),
-                    state.lower(),
-                ))
-                for state in states
-                if stats[state] > 0
-            ]),
-            log=override.get('log', gc3libs.log))
+        job_overview = ', '.join(["%d %s" % (override.get(s, stats[s]), s.lower()) for s in states if stats[s]])
+        print_msg("build jobs: %s" % job_overview, log=override.get('log', gc3libs.log), silent=build_option('silent'))
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index a910b763bc..a5afd7fc75 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -33,13 +33,29 @@
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 
 from easybuild.framework.easyconfig.tools import process_easyconfig
-from easybuild.tools import config, job
+from easybuild.tools import config
+from easybuild.tools.filetools import write_file
 from easybuild.tools.job import pbs_python
 from easybuild.tools.job.pbs_python import PbsPython
 from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
 from easybuild.tools.robot import resolve_dependencies
 
 
+GC3PIE_LOCAL_CONFIGURATION = """[resource/localhost]
+enabled = yes
+type = shellcmd
+frontend = localhost
+transport = local
+max_cores_per_job = 1
+max_memory_per_core = 1GiB
+max_walltime = 8 hours
+# this doubles as "maximum concurrent jobs"
+max_cores = 4
+architecture = x86_64
+auth = none
+override = no
+"""
+
 def mock(*args, **kwargs):
     """Function used for mocking several functions imported in parallelbuild module."""
     return 1
@@ -69,7 +85,7 @@ class ParallelBuildTest(EnhancedTestCase):
     """ Testcase for run module """
 
     def test_build_easyconfigs_in_parallel_pbs_python(self):
-        """Basic test for build_easyconfigs_in_parallel function."""
+        """Test build_easyconfigs_in_parallel(), using (mocked) pbs_python as backend for --job."""
         # put mocked functions in place
         PbsPython__init__ = PbsPython.__init__
         PbsPython_commit = PbsPython.commit
@@ -90,9 +106,8 @@ def test_build_easyconfigs_in_parallel_pbs_python(self):
         }
         init_config(args=['--job-backend=PbsPython'], build_options=build_options)
 
-
-        easyconfig_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'gzip-1.5-goolf-1.4.10.eb')
-        easyconfigs = process_easyconfig(easyconfig_file)
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'gzip-1.5-goolf-1.4.10.eb')
+        easyconfigs = process_easyconfig(ec_file)
         ordered_ecs = resolve_dependencies(easyconfigs)
         jobs = build_easyconfigs_in_parallel("echo %(spec)s", ordered_ecs, prepare_first=False)
         self.assertEqual(len(jobs), 8)
@@ -104,6 +119,39 @@ def test_build_easyconfigs_in_parallel_pbs_python(self):
         PbsPython.ppn = PbsPython_ppn
         pbs_python.PbsJob = pbs_python_PbsJob
 
+    def test_build_easyconfigs_in_parallel_gc3pie(self):
+        """Test build_easyconfigs_in_parallel(), using GC3Pie with local config as backend for --job."""
+        try:
+            import gc3libs
+        except ImportError:
+            print "GC3Pie not available, skipping test"
+            return
+
+        build_options = {
+            'robot_path': os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+            'silent': True,
+            'valid_module_classes': config.module_classes(),
+            'validate': False,
+        }
+        init_config(args=['--job-backend=GC3Pie'], build_options=build_options)
+
+        # put GC3Pie config in place to use local host and fork/exec
+        gc3pie_cfgfile = os.path.join(self.test_prefix, 'gc3pie_local.ini')
+        write_file(gc3pie_cfgfile, GC3PIE_LOCAL_CONFIGURATION)
+        # inject configuration file
+        gc3libs.Default.CONFIG_FILE_LOCATIONS.append(gc3pie_cfgfile)
+
+        ec_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
+        easyconfigs = process_easyconfig(ec_file)
+        ordered_ecs = resolve_dependencies(easyconfigs)
+        topdir = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+        test_easyblocks_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox')
+        cmd = "PYTHONPATH=%s:%s:$PYTHONPATH eb %%(spec)s -df" % (topdir, test_easyblocks_path)
+        jobs = build_easyconfigs_in_parallel(cmd, ordered_ecs, prepare_first=False)
+
+        self.assertTrue(os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0'))
+        self.assertTrue(os.path.join(self.test_installpath, 'software', 'toy', '0.0', 'bin', 'toy'))
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(ParallelBuildTest)

From 103e1787b09eadd436cc5c51b94af94b4c87ef1f Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 9 Jun 2015 11:50:27 +0200
Subject: [PATCH 1008/1356] Make polling interval a class-level constant.

So it can be tweaked, e.g., in test cases when we know
it's safe to do so.
---
 easybuild/tools/job/gc3pie.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index c6611f4ea1..1feed7cbec 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -71,6 +71,12 @@ class GC3Pie(JobBackend):
 
     USABLE = HAVE_GC3PIE
 
+    # After polling for job status, sleep for this time duration
+    # before polling again. Duration is expressed in seconds.
+    #
+    # XXX: should this be configurable via a command-line option?
+    POLL_INTERVAL = 30
+
     def begin(self):
         """
         Start a bulk job submission.
@@ -171,7 +177,7 @@ def commit(self):
             self._print_status_report(['total', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
 
             # Wait a few seconds...
-            time.sleep(30)  # FIXME: don't hardcode (at least use a class constant that can be tweaked)
+            time.sleep(self.POLL_INTERVAL)
 
         # final status report
         self._print_status_report(['total', 'ok', 'failed'])

From 7777dd6486449b3d25c6d720e4b43d5086aa4c74 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 9 Jun 2015 11:50:27 +0200
Subject: [PATCH 1009/1356] Make polling interval a class-level constant.

So it can be tweaked, e.g., in test cases when we know
it's safe to do so.
---
 easybuild/tools/job/gc3pie.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 1feed7cbec..ad638c7480 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -73,8 +73,6 @@ class GC3Pie(JobBackend):
 
     # After polling for job status, sleep for this time duration
     # before polling again. Duration is expressed in seconds.
-    #
-    # XXX: should this be configurable via a command-line option?
     POLL_INTERVAL = 30
 
     def begin(self):
@@ -177,7 +175,11 @@ def commit(self):
             self._print_status_report(['total', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
 
             # Wait a few seconds...
+<<<<<<< HEAD
             time.sleep(self.POLL_INTERVAL)
+=======
+            time.sleep(POLL_INTERVAL)
+>>>>>>> Make polling interval a class-level constant.
 
         # final status report
         self._print_status_report(['total', 'ok', 'failed'])

From 0c7dc0e03a81c6258d49ce3b6e0e6a5b23c25af2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 9 Jun 2015 12:01:11 +0200
Subject: [PATCH 1010/1356] fix use of POLL_INTERVAL constant, use it in GC3Pie
 job backend unit test

---
 easybuild/tools/job/gc3pie.py   | 4 ++++
 test/framework/parallelbuild.py | 3 +++
 2 files changed, 7 insertions(+)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index ad638c7480..2b0ec12f43 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -175,11 +175,15 @@ def commit(self):
             self._print_status_report(['total', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
 
             # Wait a few seconds...
+<<<<<<< HEAD
 <<<<<<< HEAD
             time.sleep(self.POLL_INTERVAL)
 =======
             time.sleep(POLL_INTERVAL)
 >>>>>>> Make polling interval a class-level constant.
+=======
+            time.sleep(self.POLL_INTERVAL)
+>>>>>>> fix use of POLL_INTERVAL constant, use it in GC3Pie job backend unit test
 
         # final status report
         self._print_status_report(['total', 'ok', 'failed'])
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index a5afd7fc75..c8615a8fe7 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -36,6 +36,7 @@
 from easybuild.tools import config
 from easybuild.tools.filetools import write_file
 from easybuild.tools.job import pbs_python
+from easybuild.tools.job.gc3pie import GC3Pie
 from easybuild.tools.job.pbs_python import PbsPython
 from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
 from easybuild.tools.robot import resolve_dependencies
@@ -127,6 +128,8 @@ def test_build_easyconfigs_in_parallel_gc3pie(self):
             print "GC3Pie not available, skipping test"
             return
 
+        GC3Pie.POLL_INTERVAL = 0.5  # poll every 0.5 seconds to speed up the test
+
         build_options = {
             'robot_path': os.path.join(os.path.dirname(__file__), 'easyconfigs'),
             'silent': True,

From 17ed8989e78b153b80bc48d206aa5a5a8d8f68ac Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 9 Jun 2015 12:06:42 +0200
Subject: [PATCH 1011/1356] move JobBackend & utility functions to
 easybuild.tools.job.backend module

---
 easybuild/tools/job/__init__.py   |  90 +++----------------------
 easybuild/tools/job/backend.py    | 106 ++++++++++++++++++++++++++++++
 easybuild/tools/job/gc3pie.py     |   2 +-
 easybuild/tools/job/pbs_python.py |   2 +-
 easybuild/tools/options.py        |   2 +-
 easybuild/tools/parallelbuild.py  |   2 +-
 6 files changed, 119 insertions(+), 85 deletions(-)
 create mode 100644 easybuild/tools/job/backend.py

diff --git a/easybuild/tools/job/__init__.py b/easybuild/tools/job/__init__.py
index 194e469358..ce6a4a99ce 100644
--- a/easybuild/tools/job/__init__.py
+++ b/easybuild/tools/job/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2015-2015 Ghent University
+# Copyright 2011-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -22,85 +22,13 @@
 # You should have received a copy of the GNU General Public License
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
-"""Abstract interface for submitting jobs and related utilities."""
+"""
+Declares easybuild.tools.job namespace, in an extendable way.
 
+@author: Jens Timmerman (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+"""
+from pkgutil import extend_path
 
-from abc import ABCMeta, abstractmethod
-
-from vsc.utils.missing import get_subclasses
-
-from easybuild.tools.config import get_job_backend
-from easybuild.tools.utilities import import_available_modules
-
-
-class JobBackend(object):
-    __metaclass__ = ABCMeta
-
-    USABLE = False
-
-    @abstractmethod
-    def begin(self):
-        """
-        Start a bulk job submission.
-
-        Jobs may be queued and only actually submitted when `commit()`
-        is called.
-        """
-        pass
-
-    @abstractmethod
-    def make_job(self, script, name, env_vars=None, hours=None, cores=None):
-        """
-        Create and return a `Job` object with the given parameters.
-
-        See the `Job`:class: constructor for an explanation of what
-        the arguments are.
-        """
-        pass
-
-    @abstractmethod
-    def submit(self, job, after=frozenset()):
-        """
-        Submit a job to the batch-queueing system.
-
-        If second optional argument `after` is given, it must be a
-        sequence of jobs that must be successfully terminated before
-        the new job can run.
-
-        Note that actual submission may be delayed until `commit()` is
-        called.
-        """
-        pass
-
-    @abstractmethod
-    def commit(self):
-        """
-        End a bulk job submission.
-
-        Releases any jobs that were possibly queued since the last
-        `begin()` call.
-
-        No more job submissions should be attempted after `commit()`
-        has been called, until a `begin()` is invoked again.
-        """
-        pass
-
-
-def avail_job_backends(check_usable=True):
-    """
-    Return all known job execution backends.
-    """
-    import_available_modules('easybuild.tools.job')
-    class_dict = dict([(x.__name__, x) for x in get_subclasses(JobBackend)])
-    return class_dict
-
-
-def job_backend():
-    """
-    Return interface to job server, or `None` if none is available.
-    """
-    job_backend = get_job_backend()
-    if job_backend is None:
-        return None
-    job_backend_class = avail_job_backends().get(job_backend)
-    return job_backend_class()
+# we're not the only ones in this namespace
+__path__ = extend_path(__path__, __name__)  #@ReservedAssignment
diff --git a/easybuild/tools/job/backend.py b/easybuild/tools/job/backend.py
new file mode 100644
index 0000000000..194e469358
--- /dev/null
+++ b/easybuild/tools/job/backend.py
@@ -0,0 +1,106 @@
+##
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""Abstract interface for submitting jobs and related utilities."""
+
+
+from abc import ABCMeta, abstractmethod
+
+from vsc.utils.missing import get_subclasses
+
+from easybuild.tools.config import get_job_backend
+from easybuild.tools.utilities import import_available_modules
+
+
+class JobBackend(object):
+    __metaclass__ = ABCMeta
+
+    USABLE = False
+
+    @abstractmethod
+    def begin(self):
+        """
+        Start a bulk job submission.
+
+        Jobs may be queued and only actually submitted when `commit()`
+        is called.
+        """
+        pass
+
+    @abstractmethod
+    def make_job(self, script, name, env_vars=None, hours=None, cores=None):
+        """
+        Create and return a `Job` object with the given parameters.
+
+        See the `Job`:class: constructor for an explanation of what
+        the arguments are.
+        """
+        pass
+
+    @abstractmethod
+    def submit(self, job, after=frozenset()):
+        """
+        Submit a job to the batch-queueing system.
+
+        If second optional argument `after` is given, it must be a
+        sequence of jobs that must be successfully terminated before
+        the new job can run.
+
+        Note that actual submission may be delayed until `commit()` is
+        called.
+        """
+        pass
+
+    @abstractmethod
+    def commit(self):
+        """
+        End a bulk job submission.
+
+        Releases any jobs that were possibly queued since the last
+        `begin()` call.
+
+        No more job submissions should be attempted after `commit()`
+        has been called, until a `begin()` is invoked again.
+        """
+        pass
+
+
+def avail_job_backends(check_usable=True):
+    """
+    Return all known job execution backends.
+    """
+    import_available_modules('easybuild.tools.job')
+    class_dict = dict([(x.__name__, x) for x in get_subclasses(JobBackend)])
+    return class_dict
+
+
+def job_backend():
+    """
+    Return interface to job server, or `None` if none is available.
+    """
+    job_backend = get_job_backend()
+    if job_backend is None:
+        return None
+    job_backend_class = avail_job_backends().get(job_backend)
+    return job_backend_class()
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 2b0ec12f43..80b360b7e2 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -45,7 +45,7 @@
 
 from easybuild.tools.build_log import print_msg
 from easybuild.tools.config import build_option
-from easybuild.tools.job import JobBackend
+from easybuild.tools.job.backend import JobBackend
 
 from vsc.utils import fancylogger
 
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index e334157199..3810a9020c 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -36,7 +36,7 @@
 from vsc.utils import fancylogger
 
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.job import JobBackend
+from easybuild.tools.job.backend import JobBackend
 
 
 _log = fancylogger.getLogger('pbs_python', fname=False)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 8780b2c12e..86c0ffb93c 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -56,7 +56,7 @@
 from easybuild.tools.configobj import ConfigObj, ConfigObjError
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
-from easybuild.tools.job import avail_job_backends
+from easybuild.tools.job.backend import avail_job_backends
 from easybuild.tools.modules import avail_modules_tools
 from easybuild.tools.module_generator import ModuleGeneratorLua, avail_module_generators
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index bc42d775a4..19e1a48217 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -42,7 +42,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
-from easybuild.tools.job import job_backend
+from easybuild.tools.job.backend import job_backend
 from easybuild.tools.repository.repository import init_repository
 from vsc.utils import fancylogger
 

From 0c66ba81bbea74871482d2d1e679b05cac7d40f7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 9 Jun 2015 14:15:02 +0200
Subject: [PATCH 1012/1356] rename JobBackend API: init/queue/complete

---
 easybuild/tools/job/backend.py    | 24 ++++++++---------
 easybuild/tools/job/gc3pie.py     | 28 +++++++-------------
 easybuild/tools/job/pbs_python.py | 43 +++++++++++++++++--------------
 easybuild/tools/parallelbuild.py  |  6 ++---
 test/framework/parallelbuild.py   |  8 +++---
 5 files changed, 53 insertions(+), 56 deletions(-)

diff --git a/easybuild/tools/job/backend.py b/easybuild/tools/job/backend.py
index 194e469358..ad27701e0a 100644
--- a/easybuild/tools/job/backend.py
+++ b/easybuild/tools/job/backend.py
@@ -39,11 +39,11 @@ class JobBackend(object):
     USABLE = False
 
     @abstractmethod
-    def begin(self):
+    def init(self):
         """
-        Start a bulk job submission.
+        Initialise the job backend, to start a bulk job submission.
 
-        Jobs may be queued and only actually submitted when `commit()`
+        Jobs may be queued and only actually submitted when `complete()`
         is called.
         """
         pass
@@ -59,29 +59,29 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         pass
 
     @abstractmethod
-    def submit(self, job, after=frozenset()):
+    def queue(self, job, dependencies=frozenset()):
         """
-        Submit a job to the batch-queueing system.
+        Add a job to the queue.
 
-        If second optional argument `after` is given, it must be a
+        If second optional argument `dependencies` is given, it must be a
         sequence of jobs that must be successfully terminated before
         the new job can run.
 
-        Note that actual submission may be delayed until `commit()` is
+        Note that actual submission may be delayed until `complete()` is
         called.
         """
         pass
 
     @abstractmethod
-    def commit(self):
+    def complete(self):
         """
-        End a bulk job submission.
+        Complete a bulk job submission.
 
         Releases any jobs that were possibly queued since the last
-        `begin()` call.
+        `init()` call.
 
-        No more job submissions should be attempted after `commit()`
-        has been called, until a `begin()` is invoked again.
+        No more job submissions should be attempted after `complete()`
+        has been called, until a `init()` is invoked again.
         """
         pass
 
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 80b360b7e2..0d8ea74b65 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -75,11 +75,11 @@ class GC3Pie(JobBackend):
     # before polling again. Duration is expressed in seconds.
     POLL_INTERVAL = 30
 
-    def begin(self):
+    def init(self):
         """
-        Start a bulk job submission.
+        Initialise the job backend.
 
-        Removes any reference to previously-submitted jobs.
+        Start a new list of submitted jobs.
         """
         self._jobs = DependentTaskCollection(
             output_dir=os.path.join(os.getcwd(), 'easybuild-jobs'))
@@ -130,27 +130,19 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
             **extra_args
             )
 
-    def submit(self, job, after=frozenset()):
+    def queue(self, job, dependencies=frozenset()):
         """
-        Submit a job to the batch-queueing system, optionally specifying dependencies.
+        Add a job to the queue, optionally specifying dependencies.
 
-        If second optional argument `after` is given, it must be a
-        sequence of jobs that must be successfully terminated before
-        the new job can run.
-
-        Actual submission is delayed until `commit()` is called.
+        @param dependencies: jobs on which this job depends.
         """
-        self._jobs.add(job, after)
+        self._jobs.add(job, dependencies)
 
-    def commit(self):
+    def complete(self):
         """
-        End a bulk job submission.
-
-        Releases any jobs that were possibly queued since the last
-        `begin()` call.
+        Complete a bulk job submission.
 
-        No more job submissions should be attempted after `commit()`
-        has been called, until `begin()` is invoked again.
+        Create engine, and progress it until all jobs have terminated.
         """
         # Create an instance of `Engine` using the configuration file present
         # in your home directory.
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 3810a9020c..dec41de85e 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -77,16 +77,18 @@ class PbsPython(JobBackend):
 
     USABLE = HAVE_PBS_PYTHON
 
-    @only_if_pbs_import_successful
     def __init__(self, pbs_server=None):
-        _init()
-
-    def _init(self, pbs_server=None):
+        """Constructor."""
         self.pbs_server = pbs_server or pbs.pbs_default()
         self.conn = None
         self._ppn = None
 
-    def begin(self):
+    def init(self):
+        """
+        Initialise the job backend.
+
+        Connect to the PBS server & reset list of submitted jobs.
+        """
         self.connect_to_server()
         self._submitted = []
 
@@ -97,27 +99,31 @@ def connect_to_server(self):
             self.conn = pbs.pbs_connect(self.pbs_server)
         return self.conn
 
-    def submit(self, job, after=frozenset()):
-        assert isinstance(job, PbsJob)
-        if after:
-            job.add_dependencies(after)
+    def queue(self, job, dependencies=frozenset()):
+        """
+        Add a job to the queue.
+
+        @param dependencies: jobs on which this job depends.
+        """
+        if dependencies:
+            job.add_dependencies(dependencies)
         job._submit()
         self._submitted.append(job)
 
-    def commit(self):
-        # release all user holds on jobs after submission is completed
+    def complete(self):
+        """
+        Complete a bulk job submission.
+
+        Release all user holds on submitted jobs, and disconnect from server.
+        """
         for job in self._submitted:
             if job.has_holds():
                 _log.info("releasing user hold on job %s" % job.jobid)
                 job.release_hold()
         self.disconnect_from_server()
         if self._submitted:
-            _log.info(
-                "List of submitted jobs:"
-                + "; ".join([
-                    ("%s (%s): %s" % (job.name, job.module, job.jobid))
-                    for job in self._submitted
-                ]))
+            submitted_jobs = '; '.join(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in self._submitted])
+            _log.info("List of submitted jobs: %s", submitted_jobs)
 
     @only_if_pbs_import_successful
     def disconnect_from_server(self):
@@ -150,8 +156,7 @@ def _get_ppn(self):
 
     def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         """Create and return a `PbsJob` object with the given parameters."""
-        return PbsJob(self, script, name, env_vars, hours, cores,
-                      conn=self.conn, ppn=self.ppn)
+        return PbsJob(self, script, name, env_vars, hours, cores, conn=self.conn, ppn=self.ppn)
 
 
 class PbsJob(object):
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 19e1a48217..2f1e0560e5 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -75,7 +75,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs,
         raise EasyBuildError("Cannot use --job if no job backend is available.")
 
     try:
-        job_server.begin()
+        job_server.init()
     except RuntimeError as err:
         raise EasyBuildError("connection to server failed (%s: %s), can't submit jobs.", err.__class__.__name__, err)
 
@@ -101,7 +101,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs,
         job_deps = [module_to_job[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in module_to_job]
 
         # actually (try to) submit job
-        job_server.submit(new_job, job_deps)
+        job_server.queue(new_job, job_deps)
         _log.info(
             "job %s for module %s has been submitted"
             % (new_job, new_job.module))
@@ -110,7 +110,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs,
         module_to_job[new_job.module] = new_job
         jobs.append(new_job)
 
-    job_server.commit()
+    job_server.complete()
 
     return jobs
 
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index c8615a8fe7..19e9d949d0 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -89,13 +89,13 @@ def test_build_easyconfigs_in_parallel_pbs_python(self):
         """Test build_easyconfigs_in_parallel(), using (mocked) pbs_python as backend for --job."""
         # put mocked functions in place
         PbsPython__init__ = PbsPython.__init__
-        PbsPython_commit = PbsPython.commit
+        PbsPython_complete = PbsPython.complete
         PbsPython_connect_to_server = PbsPython.connect_to_server
         PbsPython_ppn = PbsPython.ppn
         pbs_python_PbsJob = pbs_python.PbsJob
 
-        PbsPython.__init__ = lambda self: PbsPython._init(self, pbs_server='localhost')
-        PbsPython.commit = mock
+        PbsPython.__init__ = lambda self: PbsPython__init__(self, pbs_server='localhost')
+        PbsPython.complete = mock
         PbsPython.connect_to_server = mock
         PbsPython.ppn = mock
         pbs_python.PbsJob = MockPbsJob
@@ -115,7 +115,7 @@ def test_build_easyconfigs_in_parallel_pbs_python(self):
 
         # restore mocked stuff
         PbsPython.__init__ = PbsPython__init__
-        PbsPython.commit = PbsPython_commit
+        PbsPython.complete = PbsPython_complete
         PbsPython.connect_to_server = PbsPython_connect_to_server
         PbsPython.ppn = PbsPython_ppn
         pbs_python.PbsJob = pbs_python_PbsJob

From 75d824e9754bfa3659e2cc6119112cdfb89138e5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 9 Jun 2015 14:29:09 +0200
Subject: [PATCH 1013/1356] fix merge conflict fail

---
 easybuild/tools/job/gc3pie.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 0d8ea74b65..57a9a54a1d 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -167,15 +167,7 @@ def complete(self):
             self._print_status_report(['total', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
 
             # Wait a few seconds...
-<<<<<<< HEAD
-<<<<<<< HEAD
             time.sleep(self.POLL_INTERVAL)
-=======
-            time.sleep(POLL_INTERVAL)
->>>>>>> Make polling interval a class-level constant.
-=======
-            time.sleep(self.POLL_INTERVAL)
->>>>>>> fix use of POLL_INTERVAL constant, use it in GC3Pie job backend unit test
 
         # final status report
         self._print_status_report(['total', 'ok', 'failed'])

From 7c77b9cbd6ab9ccc7ec66bb439a7106e88118033 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 9 Jun 2015 15:27:53 +0200
Subject: [PATCH 1014/1356] apply (only) decorator approach for
 pbs_python/GC3Pie + style cleanup

---
 easybuild/tools/job/backend.py    |   2 -
 easybuild/tools/job/gc3pie.py     | 114 ++++++++++++++++++------------
 easybuild/tools/job/pbs_python.py |  37 +++++-----
 3 files changed, 89 insertions(+), 64 deletions(-)

diff --git a/easybuild/tools/job/backend.py b/easybuild/tools/job/backend.py
index ad27701e0a..25bfcdc5d4 100644
--- a/easybuild/tools/job/backend.py
+++ b/easybuild/tools/job/backend.py
@@ -36,8 +36,6 @@
 class JobBackend(object):
     __metaclass__ = ABCMeta
 
-    USABLE = False
-
     @abstractmethod
     def init(self):
         """
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 57a9a54a1d..080340943c 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -27,63 +27,79 @@
 Interface for submitting jobs via GC3Pie.
 
 @author: Riccardo Murri (University of Zurich)
+@author: Kenneth Hoste (Ghent University)
 """
-
-
 import os
 import time
 
+from vsc.utils import fancylogger
+
+from easybuild.tools.build_log import EasyBuildError, print_msg
+from easybuild.tools.config import build_option
+from easybuild.tools.job.backend import JobBackend
+
+
+_log = fancylogger.getLogger('gc3pie', fname=False)
+
+
 try:
     import gc3libs
     from gc3libs import Application, Run, create_engine
     from gc3libs.core import Engine
     from gc3libs.quantity import hours as hr
     from gc3libs.workflow import DependentTaskCollection
-    HAVE_GC3PIE = True
-except ImportError:
-    HAVE_GC3PIE = False
-
-from easybuild.tools.build_log import print_msg
-from easybuild.tools.config import build_option
-from easybuild.tools.job.backend import JobBackend
-
-from vsc.utils import fancylogger
 
-if HAVE_GC3PIE:
     # inject EasyBuild logger into GC3Pie
     gc3libs.log = fancylogger.getLogger('gc3pie', fname=False)
     # make handling of log.error compatible with stdlib logging
     gc3libs.log.raiseError = False
 
+    # GC3Pie is available, no need guard against import errors
+    def gc3pie_imported(fn):
+        """No-op decorator."""
+        return fn
+
+except ImportError as err:
+    _log.debug("Failed to import gc3libs from GC3Pie."
+               " Silently ignoring, this is a real issue only when GC3Pie is used as backend for --job")
+
+    # GC3Pie not available, turn method in a raised EasyBuildError
+    def gc3pie_imported(_):
+        """Decorator which raises an EasyBuildError because GC3Pie is not available."""
+        def fail(_):
+            """Raise EasyBuildError since GC3Pie is not available."""
+            errmsg = "gc3libs not available. Please make sure GC3Pie is installed and usable: %s"
+            raise EasyBuildError(errmsg, err)
+
+        return fail
+
 
 # eb --job --job-backend=GC3Pie
 class GC3Pie(JobBackend):
     """
-    Use the GC3Pie__ framework to submit and monitor compilation jobs.
+    Use the GC3Pie framework to submit and monitor compilation jobs,
+    see http://gc3pie.readthedocs.org/.
 
     In contrast with accessing an external service, GC3Pie implements
     its own workflow manager, which means ``eb --job
     --job-backend=GC3Pie`` will keep running until all jobs have
     terminated.
-
-    .. __: http://gc3pie.googlecode.com/
     """
-
-    USABLE = HAVE_GC3PIE
-
     # After polling for job status, sleep for this time duration
     # before polling again. Duration is expressed in seconds.
     POLL_INTERVAL = 30
 
+    @gc3pie_imported
     def init(self):
         """
         Initialise the job backend.
 
         Start a new list of submitted jobs.
         """
-        self._jobs = DependentTaskCollection(
-            output_dir=os.path.join(os.getcwd(), 'easybuild-jobs'))
+        self.output_dir = os.path.join(os.getcwd(), 'easybuild-gc3pie-jobs')
+        self.jobs = DependentTaskCollection(output_dir=self.output_dir)
 
+    @gc3pie_imported
     def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         """
         Create and return a job object with the given parameters.
@@ -106,38 +122,47 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         * hours must be in the range 1 .. MAX_WALLTIME;
         * cores depends on which cluster the job is being run.
         """
-        extra_args = {
+        named_args = {
             'jobname': name, # job name in GC3Pie
-            'name':    name, # same in EasyBuild
+            'name':    name, # job name in EasyBuild
         }
+
+        # environment
         if env_vars:
-            extra_args['environment'] = env_vars
+            named_args['environment'] = env_vars
+
+        # input/output files for job (none)
+        named_args['inputs'] = []
+        named_args['outputs'] = []
+
+        # job logs
+        named_args.update({
+            # join stdout/stderr in a single log
+            'join': True,
+            # location for log file
+            'output_dir': os.path.join(self.output_dir, name),
+            # log file name
+            'stdout': 'eb.log',
+        })
+
+        # resources
         if hours:
-            extra_args['requested_walltime'] = hours*hr
+            named_args['requested_walltime'] = hours * hr
         if cores:
-            extra_args['requested_cores'] = cores
-        return Application(
-            # arguments
-            ['/bin/sh', '-c', script],
-            # no need to stage files in or out
-            inputs=[],
-            outputs=[],
-            # where should the output (STDOUT/STDERR) files be downloaded to?
-            output_dir=os.path.join(self._jobs.output_dir, name),
-            # capture STDOUT and STDERR
-            stdout='stdout.log',
-            join=True,
-            **extra_args
-            )
+            named_args['requested_cores'] = cores
+
+        return Application(['/bin/sh', '-c', script], **named_args)
 
+    @gc3pie_imported
     def queue(self, job, dependencies=frozenset()):
         """
         Add a job to the queue, optionally specifying dependencies.
 
         @param dependencies: jobs on which this job depends.
         """
-        self._jobs.add(job, dependencies)
+        self.jobs.add(job, dependencies)
 
+    @gc3pie_imported
     def complete(self):
         """
         Complete a bulk job submission.
@@ -151,13 +176,13 @@ def complete(self):
         # Add your application to the engine. This will NOT submit
         # your application yet, but will make the engine *aware* of
         # the application.
-        self._engine.add(self._jobs)
+        self._engine.add(self.jobs)
 
         # in case you want to select a specific resource, call
         # `Engine.select_resource(<resource_name>)`
 
         # Periodically check the status of your application.
-        while self._jobs.execution.state != Run.State.TERMINATED:
+        while self.jobs.execution.state != Run.State.TERMINATED:
             # `Engine.progress()` will do the GC3Pie magic:
             # submit new jobs, update status of submitted jobs, get
             # results of terminating jobs etc...
@@ -172,7 +197,8 @@ def complete(self):
         # final status report
         self._print_status_report(['total', 'ok', 'failed'])
 
-    def _print_status_report(self, states=('total', 'ok', 'failed'), **override):
+    @gc3pie_imported
+    def _print_status_report(self, states=('total', 'ok', 'failed')):
         """
         Print a job status report to STDOUT and the log file.
 
@@ -183,5 +209,5 @@ def _print_status_report(self, states=('total', 'ok', 'failed'), **override):
         report the number of total jobs right from the start.
         """
         stats = self._engine.stats(only=Application)
-        job_overview = ', '.join(["%d %s" % (override.get(s, stats[s]), s.lower()) for s in states if stats[s]])
-        print_msg("build jobs: %s" % job_overview, log=override.get('log', gc3libs.log), silent=build_option('silent'))
+        job_overview = ', '.join(["%d %s" % (stats[s], s.lower()) for s in states if stats[s]])
+        print_msg("GC3Pie job overview: %s" % job_overview, log=_log, silent=build_option('silent'))
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index dec41de85e..31807e8cf5 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -52,31 +52,31 @@
     from PBSQuery import PBSQuery
     import pbs
     KNOWN_HOLD_TYPES = [pbs.USER_HOLD, pbs.OTHER_HOLD, pbs.SYSTEM_HOLD]
-    # `pbs_python` available, no need guard against import errors
-    def only_if_pbs_import_successful(fn):
+
+    # `pbs_python` is available, no need guard against import errors
+    def pbs_python_imported(fn):
+        """No-op decorator."""
         return fn
-    HAVE_PBS_PYTHON = True
-except ImportError:
+
+except ImportError as err:
     _log.debug("Failed to import pbs from pbs_python."
                " Silently ignoring, this is a real issue only when pbs_python is used as backend for --job")
-    # no `pbs_python` available, turn function into a no-op
-    def only_if_pbs_import_successful(fn):
-        def instead(*args, **kwargs):
-            """This is a no-op since `pbs_python` is not available."""
-            errmsg = ("PBSQuery or pbs modules not available."
-                      " Please make sure `pbs_python` is installed and usable.")
-            raise EasyBuildError(errmsg)
-        return instead
-    HAVE_PBS_PYTHON = False
+
+    # `pbs_python` not available, turn method in a raised EasyBuildError
+    def pbs_python_imported(_):
+        """Decorator which raises an EasyBuildError because pbs_python is not available."""
+        def fail(_):
+            """Raise EasyBuildError since `pbs_python` is not available."""
+            errmsg = "PBSQuery or pbs modules not available. Please make sure `pbs_python` is installed and usable: %s"
+            raise EasyBuildError(errmsg, err)
+
+        return fail
 
 
 class PbsPython(JobBackend):
     """
     Manage PBS server communication and create `PbsJob` objects.
     """
-
-    USABLE = HAVE_PBS_PYTHON
-
     def __init__(self, pbs_server=None):
         """Constructor."""
         self.pbs_server = pbs_server or pbs.pbs_default()
@@ -92,7 +92,7 @@ def init(self):
         self.connect_to_server()
         self._submitted = []
 
-    @only_if_pbs_import_successful
+    @pbs_python_imported
     def connect_to_server(self):
         """Connect to PBS server, set and return connection."""
         if not self.conn:
@@ -125,12 +125,13 @@ def complete(self):
             submitted_jobs = '; '.join(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in self._submitted])
             _log.info("List of submitted jobs: %s", submitted_jobs)
 
-    @only_if_pbs_import_successful
+    @pbs_python_imported
     def disconnect_from_server(self):
         """Disconnect current connection."""
         pbs.pbs_disconnect(self.conn)
         self.conn = None
 
+    @pbs_python_imported
     def _get_ppn(self):
         """Guess PBS' `ppn` value for a full node."""
         # cache this value as it's not likely going to change over the

From ba943947c20670cf3ce2dd14f1c39e8711b6b398 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Tue, 9 Jun 2015 18:36:35 +0200
Subject: [PATCH 1015/1356] Do not limit the "failed import" decorators to
 unary functions.

Functions of any arity and any arbitrary keyword arguments can now be
decorated.
---
 easybuild/tools/job/gc3pie.py     | 2 +-
 easybuild/tools/job/pbs_python.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 080340943c..0525f54472 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -66,7 +66,7 @@ def gc3pie_imported(fn):
     # GC3Pie not available, turn method in a raised EasyBuildError
     def gc3pie_imported(_):
         """Decorator which raises an EasyBuildError because GC3Pie is not available."""
-        def fail(_):
+        def fail(*args, **kwargs):
             """Raise EasyBuildError since GC3Pie is not available."""
             errmsg = "gc3libs not available. Please make sure GC3Pie is installed and usable: %s"
             raise EasyBuildError(errmsg, err)
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 31807e8cf5..2a7c16bd3e 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -65,7 +65,7 @@ def pbs_python_imported(fn):
     # `pbs_python` not available, turn method in a raised EasyBuildError
     def pbs_python_imported(_):
         """Decorator which raises an EasyBuildError because pbs_python is not available."""
-        def fail(_):
+        def fail(*args, **kwargs):
             """Raise EasyBuildError since `pbs_python` is not available."""
             errmsg = "PBSQuery or pbs modules not available. Please make sure `pbs_python` is installed and usable: %s"
             raise EasyBuildError(errmsg, err)

From b7e06ac15da8497564bfaabd360c3ff0b97de44f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 11 Jun 2015 13:32:16 +0200
Subject: [PATCH 1016/1356] add extra configuration options related to --job

---
 easybuild/tools/config.py         |  4 ++++
 easybuild/tools/job/gc3pie.py     | 33 +++++++++++++++++++++----------
 easybuild/tools/job/pbs_python.py | 30 +++++++++++++++++-----------
 easybuild/tools/options.py        | 19 ++++++++++++++++--
 easybuild/tools/parallelbuild.py  |  2 +-
 5 files changed, 64 insertions(+), 24 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index a3199dadd8..3b5c772454 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -93,6 +93,10 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'github_user',
         'group',
         'ignore_dirs',
+        'job_backend_config',
+        'job_output_dir',
+        'job_polling_interval',
+        'job_target_resource',
         'modules_footer',
         'only_blocks',
         'optarch',
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 0525f54472..c00a2f52e0 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -85,9 +85,6 @@ class GC3Pie(JobBackend):
     --job-backend=GC3Pie`` will keep running until all jobs have
     terminated.
     """
-    # After polling for job status, sleep for this time duration
-    # before polling again. Duration is expressed in seconds.
-    POLL_INTERVAL = 30
 
     @gc3pie_imported
     def init(self):
@@ -96,9 +93,19 @@ def init(self):
 
         Start a new list of submitted jobs.
         """
-        self.output_dir = os.path.join(os.getcwd(), 'easybuild-gc3pie-jobs')
+        cfgfile = build_option('job_backend_config')
+        if cfgfile:
+            # FIXME: is there a better way?
+            gc3libs.Default.CONFIG_FILE_LOCATIONS.append(cfgfile)
+
+        # additional subdirectory, since GC3Pie cleans up the output dir?!
+        self.output_dir = os.path.join(build_option('job_output_dir'), 'eb-gc3pie-jobs')
         self.jobs = DependentTaskCollection(output_dir=self.output_dir)
 
+        # after polling for job status, sleep for this time duration
+        # before polling again (in seconds)
+        self.poll_interval = build_option('job_polling_interval')
+
     @gc3pie_imported
     def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         """
@@ -140,14 +147,20 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
             # join stdout/stderr in a single log
             'join': True,
             # location for log file
-            'output_dir': os.path.join(self.output_dir, name),
+            # FIXME: does GC3Pie blindly remove this entire directory?!
+            'output_dir': self.output_dir,
             # log file name
-            'stdout': 'eb.log',
+            'stdout': 'eb-%s-gc3pie-job.log' % name,
         })
 
         # resources
-        if hours:
-            named_args['requested_walltime'] = hours * hr
+        if hours is None:
+            hours = build_option('job_max_walltime')
+        if hours > max_walltime:
+            self.log.warn("Specified %s hours, but this is impossible. (resetting to %s hours)" % (hours, max_walltime))
+            hours = max_walltime
+        named_args['requested_walltime'] = hours * hr
+
         if cores:
             named_args['requested_cores'] = cores
 
@@ -179,7 +192,7 @@ def complete(self):
         self._engine.add(self.jobs)
 
         # in case you want to select a specific resource, call
-        # `Engine.select_resource(<resource_name>)`
+        self._engine.select_resource(build_option('job_target_resource'))
 
         # Periodically check the status of your application.
         while self.jobs.execution.state != Run.State.TERMINATED:
@@ -192,7 +205,7 @@ def complete(self):
             self._print_status_report(['total', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
 
             # Wait a few seconds...
-            time.sleep(self.POLL_INTERVAL)
+            time.sleep(self.poll_interval)
 
         # final status report
         self._print_status_report(['total', 'ok', 'failed'])
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 2a7c16bd3e..35a960aff7 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -36,13 +36,13 @@
 from vsc.utils import fancylogger
 
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import build_option
 from easybuild.tools.job.backend import JobBackend
 
 
 _log = fancylogger.getLogger('pbs_python', fname=False)
 
 
-MAX_WALLTIME = 72
 # extend paramater should be 'NULL' in some functions because this is required by the python api
 NULL = 'NULL'
 # list of known hold types
@@ -79,7 +79,7 @@ class PbsPython(JobBackend):
     """
     def __init__(self, pbs_server=None):
         """Constructor."""
-        self.pbs_server = pbs_server or pbs.pbs_default()
+        self.pbs_server = pbs_server or build_option('job_target_resource') or pbs.pbs_default()
         self.conn = None
         self._ppn = None
 
@@ -169,7 +169,7 @@ def __init__(self, server, script, name, env_vars=None,
         create a new Job to be submitted to PBS
         env_vars is a dictionary with key-value pairs of environment variables that should be passed on to the job
         hours and cores should be integer values.
-        hours can be 1 - MAX_WALLTIME, cores depends on which cluster it is being run.
+        hours can be 1 - (max walltime), cores depends on which cluster it is being run.
         """
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
@@ -189,11 +189,12 @@ def __init__(self, server, script, name, env_vars=None,
         # setup the resources requested
 
         # validate requested resources!
+        max_walltime = build_option('job_max_walltime')
         if hours is None:
-            hours = MAX_WALLTIME
-        if hours > MAX_WALLTIME:
-            self.log.warn("Specified %s hours, but this is impossible. (resetting to %s hours)" % (hours, MAX_WALLTIME))
-            hours = MAX_WALLTIME
+            hours = max_walltime
+        if hours > max_walltime:
+            self.log.warn("Specified %s hours, but this is impossible. (resetting to %s hours)" % (hours, max_walltime))
+            hours = max_walltime
 
         if ppn is None:
             max_cores = server.ppn
@@ -207,9 +208,9 @@ def __init__(self, server, script, name, env_vars=None,
 
         # only allow cores and hours for now.
         self.resources = {
-                          "walltime": "%s:00:00" % hours,
-                          "nodes": "1:ppn=%s" % cores
-                         }
+            'walltime': '%s:00:00' % hours,
+            'nodes': '1:ppn=%s' % cores,
+        }
         # don't specify any queue name to submit to, use the default
         self.queue = None
         # job id of this job
@@ -238,10 +239,17 @@ def _submit(self):
         self.log.debug("Going to submit script %s" % txt)
 
         # Build default pbs_attributes list
-        pbs_attributes = pbs.new_attropl(1)
+        pbs_attributes = pbs.new_attropl(3)
         pbs_attributes[0].name = pbs.ATTR_N  # Job_Name
         pbs_attributes[0].value = self.name
 
+        output_dir = build_option('output_dir')
+        pbs_attributes[1].name = pbs.ATTR_o
+        pbs_attributes[1].value = os.path.join(output_dir, '%s.o$PBS_JOBID' % self.name)
+
+        pbs_attributes[2].name = pbs.ATTR_e
+        pbs_attributes[2].value = os.path.join(output_dir, '%s.e$PBS_JOBID' % self.name)
+
         # set resource requirements
         resource_attributes = pbs.new_attropl(len(self.resources))
         idx = 0
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 86c0ffb93c..565fdea566 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -247,8 +247,8 @@ def config_options(self):
                                     None, 'store', None),
             'installpath-software': ("Install path for software (if None, combine --installpath and --subdir-software)",
                                      None, 'store', None),
-            'job-backend': ("What job runner to use", 'choice', 'store',
-                            DEFAULT_JOB_BACKEND, avail_job_backends().keys()),
+            'job-backend': ("Backend to use for submitting jobs", 'choice', 'store',
+                            DEFAULT_JOB_BACKEND, sorted(avail_job_backends().keys())),
             # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
@@ -357,6 +357,21 @@ def easyconfig_options(self):
         self.log.debug("easyconfig_options: descr %s opts %s" % (descr, opts))
         self.add_group_parser(opts, descr, prefix='easyconfig')
 
+    def job_options(self):
+        """Option related to --job."""
+        descr = ("Options for job backend", "Options for job backend (only relevant when --job is used)")
+
+        opts = OrderedDict({
+            'backend-config': ("Configuration file for job backend", None, 'store', None),
+            'max-walltime': ("Maximum walltime for jobs (in hours)", 'int', 'store', 24),
+            'output-dir': ("Output directory for jobs (default: current directory)", None, 'store', os.getcwd()),
+            'polling-interval': ("Interval between polls for status of jobs (in seconds)", int, 'store', 30),
+            'target-resource': ("Target resource for jobs", None, 'store', None),
+        })
+
+        self.log.debug("job_options: descr %s opts %s", descr, opts)
+        self.add_group_parser(opts, descr, prefix='job')
+
     def easyblock_options(self):
         # easyblock options (to be passed to easyblock instance)
         descr = ("Options for Easyblocks", "Options to be passed to all Easyblocks.")
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 2f1e0560e5..04a50d7491 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -72,7 +72,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs,
 
     job_server = job_backend()
     if job_server is None:
-        raise EasyBuildError("Cannot use --job if no job backend is available.")
+        raise EasyBuildError("Can not use --job if no job backend is available.")
 
     try:
         job_server.init()

From 7671f2be3524262d26c2cebed92fb1e08b436406 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Thu, 11 Jun 2015 07:50:42 -0400
Subject: [PATCH 1017/1356] readding a couple of options that got dropped in a
 develop merge

---
 easybuild/tools/config.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index fe9d7c786e..1b1db96dfa 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -191,6 +191,8 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'buildpath',
         'config',
         'installpath',
+        'installpath_modules',
+        'installpath_software',
         'logfile_format',
         'moduleclasses',
         'module_naming_scheme',

From e4d5675befb3383a7c481f486a9eab2ff665c60b Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Thu, 11 Jun 2015 08:03:37 -0400
Subject: [PATCH 1018/1356] removing deprecated log.errors

---
 easybuild/tools/packaging.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 77e9f0959e..efe9d507b6 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -43,6 +43,7 @@
 from easybuild.tools.config import install_path, package_template
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
+from easybuild.tools.build_log import EasyBuildError
 
 _log = fancylogger.getLogger('tools.packaging')
 
@@ -57,7 +58,7 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
     try:
         os.chdir(workdir)
     except OSError, err:
-        _log.error("Failed to chdir into workdir: %s : %s" % (workdir, err))
+        raise EasybBuildError("Failed to chdir into workdir: %s : %s", workdir, err)
 
     # default package_template is "eb-%(toolchain)s-%(name)s"
     pkgtemplate = package_template()

From e7bf08d83dbf0ebed2abfbc21fc33a6cce654ef3 Mon Sep 17 00:00:00 2001
From: Riccardo Murri <riccardo.murri@gmail.com>
Date: Thu, 11 Jun 2015 14:51:07 +0200
Subject: [PATCH 1019/1356] Use publicly-supported interface to use
 other/additional configuration files.

---
 easybuild/tools/job/gc3pie.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index c00a2f52e0..234613f78b 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -93,10 +93,15 @@ def init(self):
 
         Start a new list of submitted jobs.
         """
+        # List of config files for GC3Pie; non-existing ones will be
+        # silently ignored.  The list here copies GC3Pie's default,
+        # for the principle of minimal surprise, but there is no
+        # strict requirement that this be done and EB could actually
+        # choose to use a completely distinct set of conf. files.
+        self.config_files = gc3libs.Default.CONFIG_FILE_LOCATIONS[:]
         cfgfile = build_option('job_backend_config')
         if cfgfile:
-            # FIXME: is there a better way?
-            gc3libs.Default.CONFIG_FILE_LOCATIONS.append(cfgfile)
+            self.config_files.append(cfgfile)
 
         # additional subdirectory, since GC3Pie cleans up the output dir?!
         self.output_dir = os.path.join(build_option('job_output_dir'), 'eb-gc3pie-jobs')
@@ -184,7 +189,7 @@ def complete(self):
         """
         # Create an instance of `Engine` using the configuration file present
         # in your home directory.
-        self._engine = create_engine()
+        self._engine = create_engine(* self.config_files)
 
         # Add your application to the engine. This will NOT submit
         # your application yet, but will make the engine *aware* of

From b815d6643f7a7b5da9c61f55c54d34ac37127a46 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Thu, 11 Jun 2015 15:40:00 -0400
Subject: [PATCH 1020/1356] adding some extra checks for experimental, package
 existance and options

---
 easybuild/framework/easyblock.py | 11 +++++++++--
 easybuild/tools/options.py       | 11 ++++++++++-
 easybuild/tools/packaging.py     | 16 ++++++++++++++++
 3 files changed, 35 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index eb92b13af7..b0fad7c021 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1499,6 +1499,8 @@ def package_step(self):
         packagedir_dest = os.path.abspath(package_path())
 
         packaging_tool = build_option('package_tool')
+        opt_force = build_option('force')
+
         if packaging_tool == "fpm":
             packaging_type = build_option('package_type') if build_option('package_type') else "rpm"
              
@@ -1507,8 +1509,13 @@ def package_step(self):
             if not os.path.exists(packagedir_dest):
                 mkdir(packagedir_dest)
         
-            for file in glob.glob(os.path.join(packagedir_src, "*.%s" % packaging_type)):
-                shutil.copy(file, packagedir_dest)
+            for src_file in glob.glob(os.path.join(packagedir_src, "*.%s" % packaging_type)):
+                src_filename = os.path.basename(src_file)
+                dest_file = os.path.join(packagedir_dest, src_filename)
+                if os.path.exists(dest_file) and not opt_force:
+                    raise EasyBuildError("Unable to copy file, dest already exists. Look in src for packages dest: %s src: %s ", dest_file, src_file)
+                else:
+                    shutil.copy(src_file, packagedir_dest)
         else:
             _log.debug('Skipping package step')
 
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ef8757e7a1..6e1e70bd1d 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -48,7 +48,7 @@
 from easybuild.framework.easyconfig.templates import template_documentation
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
-from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
+from easybuild.tools import build_log, config, run, packaging  # @UnusedImport make sure config is always initialized!
 from easybuild.tools.build_log import EasyBuildError, raise_easybuilderror
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX, DEFAULT_MODULES_TOOL
 from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PACKAGE_TEMPLATE, DEFAULT_PATH_SUBDIRS
@@ -459,6 +459,15 @@ def postprocess(self):
 
         self._postprocess_config()
 
+        #Check experimental option dependencies (for now packaging)
+        #print "Got config_options: %s" % packaging.config_options
+        package_options = [ getattr(self.options, x) for x in packaging.config_options if getattr(self.options, x) ]
+        if any( package_options ):
+            packaging.option_postprocess()
+        else:
+            self.log.debug("Didn't find any packaging options")
+
+
     def _postprocess_external_modules_metadata(self):
         """Parse file(s) specifying metadata for external modules."""
         # leave external_modules_metadata untouched if no files are provided
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index efe9d507b6..811b1711d7 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -44,8 +44,10 @@
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import which
 
 _log = fancylogger.getLogger('tools.packaging')
+config_options = [ 'package_tool', 'package_type' ]
 
 def package_fpm(easyblock, modfile_path, package_type="rpm" ):
     '''
@@ -115,3 +117,17 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
 
     return workdir
 
+
+def option_postprocess():
+    '''
+    Called from easybuild.tools.options.postprocess to check that experimental is triggered and fpm is available
+    '''
+
+    _log.experimental("Using the packaging module, This is experimental")
+    fpm_path = which('fpm')
+    rpmbuild_path = which('rpmbuild')
+    if fpm_path and rpmbuild_path:
+        _log.info("fpm found at: %s" % fpm_path)
+    else:
+        raise EasyBuildError("Need both fpm and rpmbuild. Found fpm: %s rpmbuild: %s", fpm_path, rpmbuild_path)
+

From 33f80facfb49a2187673107f9117ffbca9746413 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 11 Jun 2015 22:49:59 +0200
Subject: [PATCH 1021/1356] correct use of job configuration parameters, use
 them in the gc3pie unit test

---
 easybuild/tools/config.py        |  1 +
 easybuild/tools/job/gc3pie.py    | 14 ++++++++------
 easybuild/tools/parallelbuild.py |  2 +-
 test/framework/parallelbuild.py  | 19 +++++++++----------
 4 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 3b5c772454..b6bb7c910f 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -94,6 +94,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'group',
         'ignore_dirs',
         'job_backend_config',
+        'job_max_walltime',
         'job_output_dir',
         'job_polling_interval',
         'job_target_resource',
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 234613f78b..dac6c2ccf4 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -159,8 +159,9 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         })
 
         # resources
+        max_walltime = build_option('job_max_walltime')
         if hours is None:
-            hours = build_option('job_max_walltime')
+            hours = max_walltime
         if hours > max_walltime:
             self.log.warn("Specified %s hours, but this is impossible. (resetting to %s hours)" % (hours, max_walltime))
             hours = max_walltime
@@ -187,9 +188,8 @@ def complete(self):
 
         Create engine, and progress it until all jobs have terminated.
         """
-        # Create an instance of `Engine` using the configuration file present
-        # in your home directory.
-        self._engine = create_engine(* self.config_files)
+        # create an instance of `Engine` using the list of configuration files
+        self._engine = create_engine(*self.config_files)
 
         # Add your application to the engine. This will NOT submit
         # your application yet, but will make the engine *aware* of
@@ -197,7 +197,9 @@ def complete(self):
         self._engine.add(self.jobs)
 
         # in case you want to select a specific resource, call
-        self._engine.select_resource(build_option('job_target_resource'))
+        target_resource = build_option('job_target_resource')
+        if target_resource:
+            self._engine.select_resource(target_resource)
 
         # Periodically check the status of your application.
         while self.jobs.execution.state != Run.State.TERMINATED:
@@ -207,7 +209,7 @@ def complete(self):
             self._engine.progress()
 
             # report progress
-            self._print_status_report(['total', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
+            self._print_status_report(['total', 'NEW', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
 
             # Wait a few seconds...
             time.sleep(self.poll_interval)
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 04a50d7491..8844c9d678 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -125,7 +125,7 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
     curdir = os.getcwd()
 
     # the options to ignore (help options can't reach here)
-    ignore_opts = ['robot', 'job', 'job-backend']
+    ignore_opts = ['robot', 'job']
 
     # generate_cmd_line returns the options in form --longopt=value
     opts = [x for x in cmd_line_opts if not x.split('=')[0] in ['--%s' % y for y in ignore_opts]]
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 19e9d949d0..520b2fef5c 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -36,7 +36,6 @@
 from easybuild.tools import config
 from easybuild.tools.filetools import write_file
 from easybuild.tools.job import pbs_python
-from easybuild.tools.job.gc3pie import GC3Pie
 from easybuild.tools.job.pbs_python import PbsPython
 from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
 from easybuild.tools.robot import resolve_dependencies
@@ -128,21 +127,21 @@ def test_build_easyconfigs_in_parallel_gc3pie(self):
             print "GC3Pie not available, skipping test"
             return
 
-        GC3Pie.POLL_INTERVAL = 0.5  # poll every 0.5 seconds to speed up the test
+        # put GC3Pie config in place to use local host and fork/exec
+        gc3pie_cfgfile = os.path.join(self.test_prefix, 'gc3pie_local.ini')
+        write_file(gc3pie_cfgfile, GC3PIE_LOCAL_CONFIGURATION)
 
         build_options = {
-            'robot_path': os.path.join(os.path.dirname(__file__), 'easyconfigs'),
+            'job_backend_config': gc3pie_cfgfile,
+            'job_max_walltime': 24,
+            'job_output_dir': self.test_prefix,
+            'job_polling_interval': 1,
+            'robot_path': os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs'),
             'silent': True,
             'valid_module_classes': config.module_classes(),
             'validate': False,
         }
-        init_config(args=['--job-backend=GC3Pie'], build_options=build_options)
-
-        # put GC3Pie config in place to use local host and fork/exec
-        gc3pie_cfgfile = os.path.join(self.test_prefix, 'gc3pie_local.ini')
-        write_file(gc3pie_cfgfile, GC3PIE_LOCAL_CONFIGURATION)
-        # inject configuration file
-        gc3libs.Default.CONFIG_FILE_LOCATIONS.append(gc3pie_cfgfile)
+        options = init_config(args=['--job-backend=GC3Pie'], build_options=build_options)
 
         ec_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
         easyconfigs = process_easyconfig(ec_file)

From 8d3e7f081cdbaec73ce8ac9134178a9aed8796f6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Jun 2015 12:14:13 +0200
Subject: [PATCH 1022/1356] add check on select_resource return value, make
 GC3Pie unit test more robust

---
 easybuild/tools/job/gc3pie.py   |  4 +++-
 easybuild/tools/options.py      |  2 +-
 test/framework/parallelbuild.py | 16 ++++++++++------
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index dac6c2ccf4..d69463ac88 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -199,7 +199,9 @@ def complete(self):
         # in case you want to select a specific resource, call
         target_resource = build_option('job_target_resource')
         if target_resource:
-            self._engine.select_resource(target_resource)
+            res = self._engine.select_resource(target_resource)
+            if res == 0:
+                raise EasyBuildError("Failed to select target resource '%s' in GC3Pie", target_resource)
 
         # Periodically check the status of your application.
         while self.jobs.execution.state != Run.State.TERMINATED:
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 565fdea566..ea0f375268 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -365,7 +365,7 @@ def job_options(self):
             'backend-config': ("Configuration file for job backend", None, 'store', None),
             'max-walltime': ("Maximum walltime for jobs (in hours)", 'int', 'store', 24),
             'output-dir': ("Output directory for jobs (default: current directory)", None, 'store', os.getcwd()),
-            'polling-interval': ("Interval between polls for status of jobs (in seconds)", int, 'store', 30),
+            'polling-interval': ("Interval between polls for status of jobs (in seconds)", float, 'store', 30.0),
             'target-resource': ("Target resource for jobs", None, 'store', None),
         })
 
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 520b2fef5c..aaab04f88b 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -41,19 +41,21 @@
 from easybuild.tools.robot import resolve_dependencies
 
 
-GC3PIE_LOCAL_CONFIGURATION = """[resource/localhost]
+# test GC3Pie configuration with large resource specs
+GC3PIE_LOCAL_CONFIGURATION = """[resource/ebtestlocalhost]
 enabled = yes
 type = shellcmd
 frontend = localhost
 transport = local
 max_cores_per_job = 1
-max_memory_per_core = 1GiB
-max_walltime = 8 hours
+max_memory_per_core = 1000GiB
+max_walltime = 1000 hours
 # this doubles as "maximum concurrent jobs"
-max_cores = 4
+max_cores = 1000
 architecture = x86_64
 auth = none
 override = no
+resourcedir = %(resourcedir)s
 """
 
 def mock(*args, **kwargs):
@@ -128,14 +130,16 @@ def test_build_easyconfigs_in_parallel_gc3pie(self):
             return
 
         # put GC3Pie config in place to use local host and fork/exec
+        resourcedir = os.path.join(self.test_prefix, 'gc3pie')
         gc3pie_cfgfile = os.path.join(self.test_prefix, 'gc3pie_local.ini')
-        write_file(gc3pie_cfgfile, GC3PIE_LOCAL_CONFIGURATION)
+        write_file(gc3pie_cfgfile, GC3PIE_LOCAL_CONFIGURATION % {'resourcedir': resourcedir})
 
         build_options = {
             'job_backend_config': gc3pie_cfgfile,
             'job_max_walltime': 24,
             'job_output_dir': self.test_prefix,
-            'job_polling_interval': 1,
+            'job_polling_interval': 0.2,  # quick polling
+            'job_target_resource': 'ebtestlocalhost',
             'robot_path': os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs'),
             'silent': True,
             'valid_module_classes': config.module_classes(),

From 582319e421be7edc1db1fe1b760e1a51c357b369 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Jun 2015 19:47:54 +0200
Subject: [PATCH 1023/1356] include version check for pbs_python and GC3Pie

---
 easybuild/tools/job/backend.py    |  9 ++++++++
 easybuild/tools/job/gc3pie.py     | 34 ++++++++++++++++++++++++++++---
 easybuild/tools/job/pbs_python.py | 30 +++++++++++++++++++++++----
 test/framework/parallelbuild.py   |  3 +++
 4 files changed, 69 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/job/backend.py b/easybuild/tools/job/backend.py
index 25bfcdc5d4..ade1575da2 100644
--- a/easybuild/tools/job/backend.py
+++ b/easybuild/tools/job/backend.py
@@ -36,6 +36,15 @@
 class JobBackend(object):
     __metaclass__ = ABCMeta
 
+    def __init__(self):
+        """Constructor."""
+        self._check_version()
+
+    @abstractmethod
+    def _check_version(self):
+        """Check whether version of backend complies with required version."""
+        pass
+
     @abstractmethod
     def init(self):
         """
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index d69463ac88..c5a8d5cd4a 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -29,7 +29,9 @@
 @author: Riccardo Murri (University of Zurich)
 @author: Kenneth Hoste (Ghent University)
 """
+from distutils.version import LooseVersion
 import os
+import re
 import time
 
 from vsc.utils import fancylogger
@@ -86,12 +88,38 @@ class GC3Pie(JobBackend):
     terminated.
     """
 
+    REQ_VERSION = '2.3.0'
+    DEVELOPMENT_VERSION = 'development'  # 'magic' version string indicated non-released version
+    REQ_SVN_REVISION = 4218  # use integer value, not a string!
+
+    @gc3pie_imported
+    def _check_version(self):
+        """Check whether GC3Pie version complies with required version."""
+        version_regex = re.compile(r'^(?P<version>\S*) version \(SVN \$Revision: (?P<svn_rev>\d+)\s*\$\)')
+        version_str = gc3libs.__version__
+        res = version_regex.search(version_str)
+        if res:
+            version = res.group('version')
+            svn_rev = int(res.group('svn_rev'))
+            _log.debug("Parsed GC3Pie version info: '%s' (SVN rev: '%s')", version, svn_rev)
+
+            if version == self.DEVELOPMENT_VERSION:
+                # fall back to checking SVN revision for development versions
+                if svn_rev < self.REQ_SVN_REVISION:
+                    raise EasyBuildError("Found GC3Pie SVN revision %d, but revision %d or newer is required",
+                                         svn_rev, self.REQ_SVN_REVISION)
+            else:
+                if LooseVersion(version) < LooseVersion(self.REQ_VERSION):
+                    raise EasyBuildError("Found GC3Pie version %s, but version %s or more recent is required",
+                                         version, self.REQ_VERSION)
+        else:
+            raise EasyBuildError("Failed to parse GC3Pie version string '%s' using pattern %s",
+                                 version_str, version_regex.pattern)
+
     @gc3pie_imported
     def init(self):
         """
-        Initialise the job backend.
-
-        Start a new list of submitted jobs.
+        Initialise the GC3Pie job backend.
         """
         # List of config files for GC3Pie; non-existing ones will be
         # silently ignored.  The list here copies GC3Pie's default,
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 35a960aff7..af46356a7b 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -29,10 +29,10 @@
 @author: Toon Willems (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
-
+from distutils.version import LooseVersion
 import os
+import re
 import tempfile
-import time
 from vsc.utils import fancylogger
 
 from easybuild.tools.build_log import EasyBuildError
@@ -49,8 +49,8 @@
 KNOWN_HOLD_TYPES = []
 
 try:
-    from PBSQuery import PBSQuery
     import pbs
+    from PBSQuery import PBSQuery
     KNOWN_HOLD_TYPES = [pbs.USER_HOLD, pbs.OTHER_HOLD, pbs.SYSTEM_HOLD]
 
     # `pbs_python` is available, no need guard against import errors
@@ -77,8 +77,30 @@ class PbsPython(JobBackend):
     """
     Manage PBS server communication and create `PbsJob` objects.
     """
-    def __init__(self, pbs_server=None):
+
+    # pbs_python 4.1.0 introduces the pbs.version variable we rely on
+    REQ_VERSION = '4.1.0'
+
+    @pbs_python_imported
+    def _check_version(self):
+        """Check whether pbs_python version complies with required version."""
+        version_regex = re.compile('pbs_python version (?P<version>.*)')
+        res = version_regex.search(pbs.version)
+        if res:
+            version = res.group('version')
+            if LooseVersion(version) < LooseVersion(self.REQ_VERSION):
+                raise EasyBuildError("Found pbs_python version %s, but version %s or more recent is required",
+                                     version, self.REQ_VERSION)
+        else:
+            raise EasyBuildError("Failed to parse pbs_python version string '%s' using pattern %s",
+                                 pbs.version, version_regex.pattern)
+
+    def __init__(self, *args, **kwargs):
         """Constructor."""
+        pbs_server = kwargs.pop('pbs_server', None)
+
+        super(PbsPython, self).__init__(*args, **kwargs)
+
         self.pbs_server = pbs_server or build_option('job_target_resource') or pbs.pbs_default()
         self.conn = None
         self._ppn = None
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index aaab04f88b..8bd8f9bf79 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -90,12 +90,14 @@ def test_build_easyconfigs_in_parallel_pbs_python(self):
         """Test build_easyconfigs_in_parallel(), using (mocked) pbs_python as backend for --job."""
         # put mocked functions in place
         PbsPython__init__ = PbsPython.__init__
+        PbsPython_check_version = PbsPython._check_version
         PbsPython_complete = PbsPython.complete
         PbsPython_connect_to_server = PbsPython.connect_to_server
         PbsPython_ppn = PbsPython.ppn
         pbs_python_PbsJob = pbs_python.PbsJob
 
         PbsPython.__init__ = lambda self: PbsPython__init__(self, pbs_server='localhost')
+        PbsPython._check_version = lambda _: True
         PbsPython.complete = mock
         PbsPython.connect_to_server = mock
         PbsPython.ppn = mock
@@ -116,6 +118,7 @@ def test_build_easyconfigs_in_parallel_pbs_python(self):
 
         # restore mocked stuff
         PbsPython.__init__ = PbsPython__init__
+        PbsPython._check_version = PbsPython_check_version
         PbsPython.complete = PbsPython_complete
         PbsPython.connect_to_server = PbsPython_connect_to_server
         PbsPython.ppn = PbsPython_ppn

From 0bec5974468aa4a87e20f8cd4cf1e65586dcdf0e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 12 Jun 2015 23:24:45 +0200
Subject: [PATCH 1024/1356] fix required GC3Pie SVN revision, should be 4223
 (fix for Core.select_resource())

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index c5a8d5cd4a..08a5683841 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -90,7 +90,7 @@ class GC3Pie(JobBackend):
 
     REQ_VERSION = '2.3.0'
     DEVELOPMENT_VERSION = 'development'  # 'magic' version string indicated non-released version
-    REQ_SVN_REVISION = 4218  # use integer value, not a string!
+    REQ_SVN_REVISION = 4223  # use integer value, not a string!
 
     @gc3pie_imported
     def _check_version(self):

From 5afde751d81f78219d074f4e9b7f9b51622beaaf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 13 Jun 2015 10:24:23 +0200
Subject: [PATCH 1025/1356] fix purging of loaded modules in unit tests' setUp

---
 test/framework/utilities.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 4c24d5ec9c..5b00a5a21f 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -138,9 +138,9 @@ def setUp(self):
         reload(easybuild.tools.module_naming_scheme)  # required to run options unit tests stand-alone
 
         modtool = modules_tool()
-        self.reset_modulepath([os.path.join(testdir, 'modules')])
         # purge out any loaded modules with original $MODULEPATH before running each test
         modtool.purge()
+        self.reset_modulepath([os.path.join(testdir, 'modules')])
 
     def tearDown(self):
         """Clean up after running testcase."""

From 932814560069882b4fe6dbee0a2dfdf256d498b1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 13 Jun 2015 10:32:06 +0200
Subject: [PATCH 1026/1356] use gc3libs.core.__version__ as GC3Pie version
 string

---
 easybuild/tools/job/gc3pie.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 08a5683841..fa90240e46 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -88,6 +88,8 @@ class GC3Pie(JobBackend):
     terminated.
     """
 
+    # location of __version__ to use may change, depending on the minimal required SVN revision for development versions
+    VERSION_STR = gc3libs.core.__version__
     REQ_VERSION = '2.3.0'
     DEVELOPMENT_VERSION = 'development'  # 'magic' version string indicated non-released version
     REQ_SVN_REVISION = 4223  # use integer value, not a string!
@@ -96,8 +98,7 @@ class GC3Pie(JobBackend):
     def _check_version(self):
         """Check whether GC3Pie version complies with required version."""
         version_regex = re.compile(r'^(?P<version>\S*) version \(SVN \$Revision: (?P<svn_rev>\d+)\s*\$\)')
-        version_str = gc3libs.__version__
-        res = version_regex.search(version_str)
+        res = version_regex.search(self.VERSION_STR)
         if res:
             version = res.group('version')
             svn_rev = int(res.group('svn_rev'))
@@ -114,7 +115,7 @@ def _check_version(self):
                                          version, self.REQ_VERSION)
         else:
             raise EasyBuildError("Failed to parse GC3Pie version string '%s' using pattern %s",
-                                 version_str, version_regex.pattern)
+                                 self.VERSION_STR, version_regex.pattern)
 
     @gc3pie_imported
     def init(self):

From 7493478a6ed23d85c55d9ceefe0c5abc02369917 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Jun 2015 11:22:13 +0200
Subject: [PATCH 1027/1356] fix issue with cleaning up (no) logfile if
 --logtostdout/-l is used

---
 easybuild/tools/build_log.py |  3 ++-
 test/framework/options.py    | 11 ++++++++++-
 test/framework/utilities.py  | 12 ++++++++----
 3 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/build_log.py b/easybuild/tools/build_log.py
index 3bf2a09527..bd9f50853b 100644
--- a/easybuild/tools/build_log.py
+++ b/easybuild/tools/build_log.py
@@ -201,7 +201,8 @@ def stop_logging(logfile, logtostdout=False):
     """Stop logging."""
     if logtostdout:
         fancylogger.logToScreen(enable=False, stdout=True)
-    fancylogger.logToFile(logfile, enable=False)
+    if logfile is not None:
+        fancylogger.logToFile(logfile, enable=False)
 
 
 def get_log(name=None):
diff --git a/test/framework/options.py b/test/framework/options.py
index cc2ba6ac0e..a18479caeb 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -324,9 +324,18 @@ def test_zzz_logtostdout(self):
             # cleanup
             os.remove(fn)
 
+        stdoutorig = sys.stdout
+        sys.stdout = open("/dev/null", 'w')
+
+        toy_ecfile = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0.eb')
+        self.logfile = None
+        out = self.eb_main([toy_ecfile, '--debug', '-l', '--force'], raise_error=True)
+
         if os.path.exists(dummylogfn):
             os.remove(dummylogfn)
-        fancylogger.logToFile(self.logfile)
+
+        sys.stdout.close()
+        sys.stdout = stdoutorig
 
     def test_avail_easyconfig_params(self):
         """Test listing available easyconfig parameters."""
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 5b00a5a21f..0c209f501d 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -196,9 +196,10 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
         if logfile is None:
             logfile = self.logfile
         # clear log file
-        f = open(logfile, 'w')
-        f.write('')
-        f.close()
+        if logfile:
+            f = open(logfile, 'w')
+            f.write('')
+            f.close()
 
         env_before = copy.deepcopy(os.environ)
 
@@ -211,7 +212,10 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
             if verbose:
                 print "err: %s" % err
 
-        logtxt = read_file(logfile)
+        if logfile:
+            logtxt = read_file(logfile)
+        else:
+            logtxt = None
 
         os.chdir(self.cwd)
 

From ae88385de4bf3ba00926589a3229c847ca83ecd6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Jun 2015 12:56:29 +0200
Subject: [PATCH 1028/1356] stop making ModulesTool class a singleton

---
 easybuild/framework/easyblock.py | 8 +++-----
 easybuild/tools/modules.py       | 2 --
 test/framework/modulestool.py    | 3 ---
 3 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3c03555429..b2828a6d41 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1029,8 +1029,7 @@ def load_fake_module(self, purge=False):
         fake_mod_path = self.make_module_step(True)
 
         # load fake module
-        modtool = modules_tool()
-        modtool.prepend_module_path(fake_mod_path)
+        self.modules_tool.prepend_module_path(fake_mod_path)
         self.load_module(purge=purge)
 
         return (fake_mod_path, env)
@@ -1044,9 +1043,8 @@ def clean_up_fake_module(self, fake_mod_data):
         # self.full_mod_name might not be set (e.g. during unit tests)
         if fake_mod_path and self.full_mod_name is not None:
             try:
-                modtool = modules_tool()
-                modtool.unload([self.full_mod_name])
-                modtool.remove_module_path(fake_mod_path)
+                self.modules_tool.unload([self.full_mod_name])
+                self.modules_tool.remove_module_path(fake_mod_path)
                 rmtree2(os.path.dirname(fake_mod_path))
             except OSError, err:
                 raise EasyBuildError("Failed to clean up fake module dir %s: %s", fake_mod_path, err)
diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 3700a1a8ab..17e366bae9 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -136,8 +136,6 @@ class ModulesTool(object):
     # modules tool user cache directory
     USER_CACHE_DIR = None
 
-    __metaclass__ = Singleton
-
     def __init__(self, mod_paths=None, testing=False):
         """
         Create a ModulesTool object
diff --git a/test/framework/modulestool.py b/test/framework/modulestool.py
index 6130e33564..4eadb8d0d1 100644
--- a/test/framework/modulestool.py
+++ b/test/framework/modulestool.py
@@ -101,7 +101,6 @@ def test_environment_command(self):
 
         os.environ[BrokenMockModulesTool.COMMAND_ENVIRONMENT] = MockModulesTool.COMMAND
         os.environ['module'] = "() { /bin/echo $*\n}"
-        BrokenMockModulesTool._instances.pop(BrokenMockModulesTool, None)
         bmmt = BrokenMockModulesTool(mod_paths=[], testing=True)
         cmd_abspath = which(MockModulesTool.COMMAND)
 
@@ -135,13 +134,11 @@ def test_module_mismatch(self):
 
         # redefine 'module' function with correct module command
         os.environ['module'] = "() {  eval `/bin/echo $*`\n}"
-        MockModulesTool._instances.pop(MockModulesTool)
         mt = MockModulesTool(testing=True)
         self.assertTrue(isinstance(mt.loaded_modules(), list))  # dummy usage
 
         # a warning should be logged if the 'module' function is undefined
         del os.environ['module']
-        MockModulesTool._instances.pop(MockModulesTool)
         mt = MockModulesTool(testing=True)
         f = open(self.logfile, 'r')
         logtxt = f.read()

From 1fb7d34e9aebfd8857c06dd31a5fe353bef903fa Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 Jun 2015 17:29:22 +0200
Subject: [PATCH 1029/1356] don't use gc3libs before it's imported

---
 easybuild/tools/job/gc3pie.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index fa90240e46..a337b260e9 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -88,8 +88,6 @@ class GC3Pie(JobBackend):
     terminated.
     """
 
-    # location of __version__ to use may change, depending on the minimal required SVN revision for development versions
-    VERSION_STR = gc3libs.core.__version__
     REQ_VERSION = '2.3.0'
     DEVELOPMENT_VERSION = 'development'  # 'magic' version string indicated non-released version
     REQ_SVN_REVISION = 4223  # use integer value, not a string!
@@ -97,8 +95,11 @@ class GC3Pie(JobBackend):
     @gc3pie_imported
     def _check_version(self):
         """Check whether GC3Pie version complies with required version."""
+        # location of __version__ to use may change, depending on the minimal required SVN revision for development versions
+        version_str = gc3libs.core.__version__
+
         version_regex = re.compile(r'^(?P<version>\S*) version \(SVN \$Revision: (?P<svn_rev>\d+)\s*\$\)')
-        res = version_regex.search(self.VERSION_STR)
+        res = version_regex.search(version_str)
         if res:
             version = res.group('version')
             svn_rev = int(res.group('svn_rev'))
@@ -115,7 +116,7 @@ def _check_version(self):
                                          version, self.REQ_VERSION)
         else:
             raise EasyBuildError("Failed to parse GC3Pie version string '%s' using pattern %s",
-                                 self.VERSION_STR, version_regex.pattern)
+                                 version_str, version_regex.pattern)
 
     @gc3pie_imported
     def init(self):

From 4acd6500b6477eac71f3ad116d50ca0696d40650 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Jun 2015 16:34:01 +0200
Subject: [PATCH 1030/1356] enhance unit test for prepend_paths

---
 test/framework/module_generator.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 5f6029cda5..b7294bb4ef 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -179,7 +179,10 @@ def test_prepend_paths(self):
                 "prepend-path\tkey\t\t$root/path2\n",
                 "prepend-path\tkey\t\t$root\n",
             ])
-            self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2", '']))
+            paths = ['path1', 'path2', '']
+            self.assertEqual(expected, self.modgen.prepend_paths("key", paths))
+            # 2nd call should still give same result, no side-effects like manipulating passed list 'paths'!
+            self.assertEqual(expected, self.modgen.prepend_paths("key", paths))
 
             expected = "prepend-path\tbar\t\t$root/foo\n"
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))

From d3c3905b20b7ce0fa9261c512d918b0fc391465d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Jun 2015 16:35:49 +0200
Subject: [PATCH 1031/1356] don't modify values of 'paths' list passed as
 argument to prepend_paths

---
 easybuild/tools/module_generator.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index d0ae5c2df0..6ce72b8dce 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -226,18 +226,21 @@ def prepend_paths(self, key, paths, allow_abs=False):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s" % (paths, key))
             paths = [paths]
 
-        for i, path in enumerate(paths):
+        abspaths = []
+        for path in paths:
             if os.path.isabs(path) and not allow_abs:
                 raise EasyBuildError("Absolute path %s passed to prepend_paths which only expects relative paths.",
                                      path)
             elif not os.path.isabs(path):
                 # prepend $root (= installdir) for (non-empty) relative paths
                 if path:
-                    paths[i] = os.path.join('$root', path)
+                    abspaths.append(os.path.join('$root', path))
                 else:
-                    paths[i] = '$root'
+                    abspaths.append('$root')
+            else:
+                abspaths.append(path)
 
-        statements = [template % (key, p) for p in paths]
+        statements = [template % (key, p) for p in abspaths]
         return ''.join(statements)
 
     def use(self, paths):

From 2bb995e861e66a3586ee9e605acdd3b93d5e234c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Jun 2015 20:44:18 +0200
Subject: [PATCH 1032/1356] add unit test to verify statelessness of
 ModulesTool

---
 test/framework/modules.py | 52 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 51 insertions(+), 1 deletion(-)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 487cbb8ccb..156ebf3875 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -41,7 +41,7 @@
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools import config
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import read_file, write_file
+from easybuild.tools.filetools import mkdir, read_file, write_file
 from easybuild.tools.modules import get_software_root, get_software_version, get_software_libdir, modules_tool
 
 
@@ -322,6 +322,56 @@ def test_path_to_top_of_module_tree_categorized_hmns(self):
         path = modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
         self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
 
+    def test_modules_tool_stateless(self):
+        """Check whether ModulesTool instance is stateless between runs."""
+        test_modules_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'modules')
+
+        # copy test Core/Compiler modules, we need to rewrite the 'module use' statement in the one we're going to load
+        shutil.copytree(os.path.join(test_modules_path, 'Core'), os.path.join(self.test_prefix, 'Core'))
+        shutil.copytree(os.path.join(test_modules_path, 'Compiler'), os.path.join(self.test_prefix, 'Compiler'))
+
+        modtxt = read_file(os.path.join(self.test_prefix, 'Core', 'GCC', '4.7.2'))
+        modpath_extension = os.path.join(self.test_prefix, 'Compiler', 'GCC', '4.7.2')
+        modtxt = re.sub('module use .*', 'module use %s' % modpath_extension, modtxt, re.M)
+        write_file(os.path.join(self.test_prefix, 'Core', 'GCC', '4.7.2'), modtxt)
+
+        modtxt = read_file(os.path.join(self.test_prefix, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'))
+        modpath_extension = os.path.join(self.test_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
+        mkdir(modpath_extension, parents=True)
+        modtxt = re.sub('module use .*', 'module use %s' % modpath_extension, modtxt, re.M)
+        write_file(os.path.join(self.test_prefix, 'Compiler', 'GCC', '4.7.2', 'OpenMPI', '1.6.4'), modtxt)
+
+        # force reset of any singletons by reinitiating config
+        init_config()
+
+        os.environ['MODULEPATH'] = os.path.join(self.test_prefix, 'Core')
+        modtool = modules_tool()
+
+        # GCC/4.6.3 is *not* an available Core module
+        self.assertErrorRegex(EasyBuildError, "Unable to locate a modulefile", modtool.load, ['GCC/4.6.3'])
+
+        # GCC/4.7.2 is one of the available Core modules
+        modtool.load(['GCC/4.7.2'])
+
+        # OpenMPI/1.6.4 becomes available after loading GCC/4.7.2 module
+        modtool.load(['OpenMPI/1.6.4'])
+        modtool.purge()
+
+        # reset $MODULEPATH, obtain new ModulesTool instance,
+        # which should not remember anything w.r.t. previous $MODULEPATH value
+        os.environ['MODULEPATH'] = test_modules_path
+        modtool = modules_tool()
+
+        # GCC/4.6.3 is available
+        modtool.load(['GCC/4.6.3'])
+        modtool.purge()
+
+        # GCC/4.7.2 is available (note: also as non-Core module outside of hierarchy)
+        modtool.load(['GCC/4.7.2'])
+
+        # OpenMPI/1.6.4 is *not* available with current $MODULEPATH (loaded GCC/4.7.2 was not a hierarchical module)
+        self.assertErrorRegex(EasyBuildError, "Unable to locate a modulefile", modtool.load, ['OpenMPI/1.6.4'])
+
 
 def suite():
     """ returns all the testcases in this module """

From 9e0b50a30a94075deb0f5201afeeb4d71682a872 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Jun 2015 21:17:45 +0200
Subject: [PATCH 1033/1356] fix load error msg for Lmod in unit test

---
 test/framework/modules.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 156ebf3875..3dc882a7fa 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -42,7 +42,7 @@
 from easybuild.tools import config
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import mkdir, read_file, write_file
-from easybuild.tools.modules import get_software_root, get_software_version, get_software_libdir, modules_tool
+from easybuild.tools.modules import Lmod, get_software_root, get_software_version, get_software_libdir, modules_tool
 
 
 # number of modules included for testing purposes
@@ -347,8 +347,13 @@ def test_modules_tool_stateless(self):
         os.environ['MODULEPATH'] = os.path.join(self.test_prefix, 'Core')
         modtool = modules_tool()
 
+        if isinstance(modtool, Lmod):
+            load_err_msg = "cannot[\s\n]*be[\s\n]*loaded"
+        else:
+            load_err_msg = "Unable to locate a modulefile"
+
         # GCC/4.6.3 is *not* an available Core module
-        self.assertErrorRegex(EasyBuildError, "Unable to locate a modulefile", modtool.load, ['GCC/4.6.3'])
+        self.assertErrorRegex(EasyBuildError, load_err_msg, modtool.load, ['GCC/4.6.3'])
 
         # GCC/4.7.2 is one of the available Core modules
         modtool.load(['GCC/4.7.2'])
@@ -370,7 +375,7 @@ def test_modules_tool_stateless(self):
         modtool.load(['GCC/4.7.2'])
 
         # OpenMPI/1.6.4 is *not* available with current $MODULEPATH (loaded GCC/4.7.2 was not a hierarchical module)
-        self.assertErrorRegex(EasyBuildError, "Unable to locate a modulefile", modtool.load, ['OpenMPI/1.6.4'])
+        self.assertErrorRegex(EasyBuildError, load_err_msg, modtool.load, ['OpenMPI/1.6.4'])
 
 
 def suite():

From 099d73098b86f3c81292b5c6ae60c195690d63d2 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Tue, 16 Jun 2015 20:50:08 -0400
Subject: [PATCH 1034/1356] just some docs

---
 easybuild/tools/packaging.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 811b1711d7..68ac779b31 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -47,6 +47,8 @@
 from easybuild.tools.filetools import which
 
 _log = fancylogger.getLogger('tools.packaging')
+# This is an abbreviated list of the package options, eventually it might make sense to set them
+# all in the "plugin" rather than in tools.options
 config_options = [ 'package_tool', 'package_type' ]
 
 def package_fpm(easyblock, modfile_path, package_type="rpm" ):

From 0a4d82c3b1e3ad04fd22cdd01acc49362a68a71e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 17 Jun 2015 21:16:10 +0200
Subject: [PATCH 1035/1356] don't skip package_step, add --package option,
 group package-related options together

---
 easybuild/framework/easyblock.py | 15 +++++++++------
 easybuild/tools/config.py        |  9 ++-------
 easybuild/tools/options.py       | 20 ++++++++++++++------
 easybuild/tools/packaging.py     |  6 +++---
 4 files changed, 28 insertions(+), 22 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index b0fad7c021..b576b8fd24 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1501,14 +1501,17 @@ def package_step(self):
         packaging_tool = build_option('package_tool')
         opt_force = build_option('force')
 
-        if packaging_tool == "fpm":
+        if not build_option('package'):
+            _log.info("Skipping package step (not enabled)")
+
+        elif packaging_tool == "fpm":
             packaging_type = build_option('package_type') if build_option('package_type') else "rpm"
-             
+
             packagedir_src = package_fpm(self, path_to_module_file, package_type=packaging_type)
-   
+
             if not os.path.exists(packagedir_dest):
                 mkdir(packagedir_dest)
-        
+
             for src_file in glob.glob(os.path.join(packagedir_src, "*.%s" % packaging_type)):
                 src_filename = os.path.basename(src_file)
                 dest_file = os.path.join(packagedir_dest, src_filename)
@@ -1517,7 +1520,7 @@ def package_step(self):
                 else:
                     shutil.copy(src_file, packagedir_dest)
         else:
-            _log.debug('Skipping package step')
+            raise EasyBuildError("Unknown packaging tool specified: %s", packaging_tool)
 
 
     def post_install_step(self):
@@ -1894,7 +1897,7 @@ def prepare_step_spec(initial):
             (SANITYCHECK_STEP, 'sanity checking', [lambda x: x.sanity_check_step()], False),
             (CLEANUP_STEP, 'cleaning up', [lambda x: x.cleanup_step()], False),
             (MODULE_STEP, 'creating module', [lambda x: x.make_module_step()], False),
-            (PACKAGE_STEP, 'packaging', [lambda x: x.package_step()], True),
+            (PACKAGE_STEP, 'packaging', [lambda x: x.package_step()], False),
         ]
 
         # full list of steps, included iterated steps
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 1b1db96dfa..34589cc955 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -96,6 +96,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'modules_footer',
         'only_blocks',
         'optarch',
+        'package_template',
         'package_tool',
         'package_type',
         'regtest_output_dir',
@@ -113,6 +114,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'force',
         'hidden',
         'module_only',
+        'package',
         'robot',
         'sequential',
         'set_gid_bit',
@@ -199,7 +201,6 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'module_syntax',
         'modules_tool',
         'packagepath',
-        'package_template',
         'prefix',
         'repository',
         'repositorypath',
@@ -373,12 +374,6 @@ def package_path():
     """
     return ConfigurationVariables()['packagepath']
 
-def package_template():
-    """
-    Returns the package template
-    """
-    return ConfigurationVariables()['package_template']
-
 def get_modules_tool():
     """
     Return modules tool (EnvironmentModulesC, Lmod, ...)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 6e1e70bd1d..d9afdb4273 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -261,12 +261,6 @@ def config_options(self):
                                None, 'store_or_None', None, {'metavar': "PATH"}),
             'modules-tool': ("Modules tool to use",
                              'choice', 'store', DEFAULT_MODULES_TOOL, sorted(avail_modules_tools().keys())),
-            'package-tool': ("Packaging tool to use",
-                             None, 'store_or_None', None),
-            'package-type': ("Packaging type to output to",
-                             None, 'store_or_None', None),
-            'package-template': ("A template string to name the package",
-                             None, 'store', DEFAULT_PACKAGE_TEMPLATE),
             'packagepath': ("The destination path for the packages built by package-tool",
                              None, 'store', mk_full_default_path('packagepath')),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
@@ -355,6 +349,20 @@ def regtest_options(self):
         self.log.debug("regtest_options: descr %s opts %s" % (descr, opts))
         self.add_group_parser(opts, descr)
 
+    def package_options(self):
+        # package-related options
+        descr = ("Package options", "Control packaging performed by EasyBuild.")
+
+        opts = OrderedDict({
+            'package': ("Enabling packaging", None, 'store_true', False),
+            'package-template': ("A template string to name the package", None, 'store', DEFAULT_PACKAGE_TEMPLATE),
+            'package-tool': ("Packaging tool to use", None, 'store_or_None', None),
+            'package-type': ("Packaging type to output to", None, 'store_or_None', None),
+        })
+
+        self.log.debug("package_options: descr %s opts %s" % (descr, opts))
+        self.add_group_parser(opts, descr)
+
     def easyconfig_options(self):
         # easyconfig options (to be passed to easyconfig instance)
         descr = ("Options for Easyconfigs", "Options to be passed to all Easyconfig.")
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/packaging.py
index 811b1711d7..0b434f742e 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/packaging.py
@@ -40,7 +40,7 @@
 from vsc.utils import fancylogger
 
 from easybuild.tools.run import run_cmd
-from easybuild.tools.config import install_path, package_template
+from easybuild.tools.config import build_option
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.build_log import EasyBuildError
@@ -60,10 +60,10 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
     try:
         os.chdir(workdir)
     except OSError, err:
-        raise EasybBuildError("Failed to chdir into workdir: %s : %s", workdir, err)
+        raise EasyBuildError("Failed to chdir into workdir: %s : %s", workdir, err)
 
     # default package_template is "eb-%(toolchain)s-%(name)s"
-    pkgtemplate = package_template()
+    pkgtemplate = build_option('package_template')
     full_ec_version = det_full_ec_version(easyblock.cfg)
     _log.debug("I got a package template that looks like: %s " % pkgtemplate )
 

From 5e9d0f44c7ee45e366714c4c7ce3a1eab8f641ba Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Wed, 17 Jun 2015 22:02:51 -0400
Subject: [PATCH 1036/1356] creating a packaging_naming_scheme structure

---
 easybuild/framework/easyblock.py              |  2 +-
 easybuild/tools/config.py                     |  1 -
 easybuild/tools/options.py                    |  7 ++-
 easybuild/tools/package/__init__.py           |  8 ++++
 easybuild/tools/package/activepns.py          | 46 +++++++++++++++++++
 .../tools/package/packaging_naming_scheme.py  | 24 ++++++++++
 .../packaging_naming_scheme/__init__.py       |  0
 .../packaging_naming_scheme/easybuild_pns.py  | 42 +++++++++++++++++
 .../package/packaging_naming_scheme/pns.py    | 25 ++++++++++
 .../{packaging.py => package/utilities.py}    | 29 ++++--------
 10 files changed, 158 insertions(+), 26 deletions(-)
 create mode 100644 easybuild/tools/package/__init__.py
 create mode 100644 easybuild/tools/package/activepns.py
 create mode 100644 easybuild/tools/package/packaging_naming_scheme.py
 create mode 100644 easybuild/tools/package/packaging_naming_scheme/__init__.py
 create mode 100644 easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
 create mode 100644 easybuild/tools/package/packaging_naming_scheme/pns.py
 rename easybuild/tools/{packaging.py => package/utilities.py} (78%)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index b0fad7c021..25af96a60a 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -56,7 +56,7 @@
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP
-from easybuild.tools.packaging import package_fpm
+from easybuild.tools.package.utilities import package_fpm
 from easybuild.tools.build_details import get_build_stats
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 1b1db96dfa..2790039857 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -67,7 +67,6 @@
 }
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
-DEFAULT_PACKAGE_TEMPLATE = "eb-%(name)s-%(version)s-%(toolchain)s"
 DEFAULT_STRICT = run.WARN
 
 # utility function for obtaining default paths
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 6e1e70bd1d..f575f7f4b2 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -48,10 +48,10 @@
 from easybuild.framework.easyconfig.templates import template_documentation
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
-from easybuild.tools import build_log, config, run, packaging  # @UnusedImport make sure config is always initialized!
+from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
 from easybuild.tools.build_log import EasyBuildError, raise_easybuilderror
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX, DEFAULT_MODULES_TOOL
-from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PACKAGE_TEMPLATE, DEFAULT_PATH_SUBDIRS
+from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS
 from easybuild.tools.config import DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import DEFAULT_STRICT, get_pretend_installpath, mk_full_default_path
 from easybuild.tools.configobj import ConfigObj, ConfigObjError
@@ -63,6 +63,7 @@
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
 from easybuild.tools.modules import Lmod
 from easybuild.tools.ordereddict import OrderedDict
+import easybuild.tools.package.utilities as packaging
 from easybuild.tools.toolchain.utilities import search_toolchain
 from easybuild.tools.repository.repository import avail_repositories
 from easybuild.tools.version import this_is_easybuild
@@ -265,8 +266,6 @@ def config_options(self):
                              None, 'store_or_None', None),
             'package-type': ("Packaging type to output to",
                              None, 'store_or_None', None),
-            'package-template': ("A template string to name the package",
-                             None, 'store', DEFAULT_PACKAGE_TEMPLATE),
             'packagepath': ("The destination path for the packages built by package-tool",
                              None, 'store', mk_full_default_path('packagepath')),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
diff --git a/easybuild/tools/package/__init__.py b/easybuild/tools/package/__init__.py
new file mode 100644
index 0000000000..de858db457
--- /dev/null
+++ b/easybuild/tools/package/__init__.py
@@ -0,0 +1,8 @@
+"""
+The packaging module, will contain code for packaging and naming-schemes that can be
+overriden to cover site customizations
+
+"""
+
+
+
diff --git a/easybuild/tools/package/activepns.py b/easybuild/tools/package/activepns.py
new file mode 100644
index 0000000000..d9184eec70
--- /dev/null
+++ b/easybuild/tools/package/activepns.py
@@ -0,0 +1,46 @@
+
+
+from vsc.utils import fancylogger
+from vsc.utils.patterns import Singleton
+from easybuild.tools.config import build_option
+from easybuild.tools.utilities import import_available_modules
+from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
+
+def avail_package_naming_scheme():
+    '''
+    Returns the list of valed naming schemes that are in the easybuild.package.package_naming_scheme namespace
+    '''
+    pns = import_available_modules('easybuild.tools.package.packaging_naming_scheme')
+
+    return pns
+
+class ActivePNS(object):
+    """
+    The wrapper class for Package Naming Schmese, follows the model of Module Naming Schemes, mostly
+    """
+    
+    __metaclass__ = Singleton
+    
+    def __init__(self, *args, **kwargs):
+        """Initialize logger and find available PNSes to load"""
+        self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
+
+        avail_pns = avail_package_naming_scheme()
+        sel_pns = build_option("package-naming-scheme")
+        if sel_pns in avail_pns:
+            self.pns = avail_pns[sel_pns]()
+        else:
+            raise EasyBuildError("Selected package naming scheme %s could not be found in %s",
+                                    sel_pns, avail_pns.keys())
+
+    def name(self):
+        name = self.pns.name()
+        return name
+
+    def version(self):
+        version = self.pns.version()
+        return version
+
+    def release(self):
+        release = self.pns.release()
+        return release
diff --git a/easybuild/tools/package/packaging_naming_scheme.py b/easybuild/tools/package/packaging_naming_scheme.py
new file mode 100644
index 0000000000..bfe620d2ea
--- /dev/null
+++ b/easybuild/tools/package/packaging_naming_scheme.py
@@ -0,0 +1,24 @@
+
+from vsc.utils import fancylogger
+
+options = [ "package-naming-name-template", "package-naming-version-template", "package-naming-toolchain-template" ]
+
+class PackagingNamingScheme(object):
+    """Abstract class for package naming scheme"""
+
+
+    def __init__(self, *args, **kwargs):
+        """initialize logger."""
+        self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
+
+    def name:
+        """Return name of the package, by default would include name, version, toolchain"""
+
+        
+    def name_version:
+
+    def version_version:
+
+    def release:
+
+
diff --git a/easybuild/tools/package/packaging_naming_scheme/__init__.py b/easybuild/tools/package/packaging_naming_scheme/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
new file mode 100644
index 0000000000..e0ab409e74
--- /dev/null
+++ b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
@@ -0,0 +1,42 @@
+
+
+
+"""
+Default implementation of the EasyBuild packaging naming scheme
+
+@author: Rob Schmidt (Ottawa Hospital Research Institute)
+@author: Kenneth Hoste (Ghent University)
+"""
+
+from easybuild.tools.package.packaging_naming_scheme.pns import PackagingNamingScheme
+
+
+class EasyBuildPNS(PackagingNamingScheme):
+    """Class implmenting the default EasyBuild packaging naming scheme."""
+
+    REQUIRED_KEYS = ['name', 'version', 'versionsuffix', 'toolchain']
+
+    def name(self, ec):
+        name_template = "eb-%(name)s-%(version)s-%(toolchain)s"
+        pkg_name = name_template % {
+            'toolchain' : self.toolchain(ec),
+            'version': '-'.join([x for x in [ec.get('versionprefix', ''), ec['version'], ec['versionsuffix'].lstrip('-')] if x]),
+            'name' : eb.name,
+    }
+
+    def _toolchain(self, eb):
+        toolchain_template = "%(toolchain_name)s-%(toolchain_version)s"
+        pkg_toolchain = toolchain_template % {
+            'toolchain_name': eb.toolchain.name,
+            'toolchain_version': eb.toolchain.version,
+        }
+
+
+    def version(self, eb):
+        return eb.cfg['version']
+
+        
+
+    def release(self):
+        return 1
+
diff --git a/easybuild/tools/package/packaging_naming_scheme/pns.py b/easybuild/tools/package/packaging_naming_scheme/pns.py
new file mode 100644
index 0000000000..f4427465ca
--- /dev/null
+++ b/easybuild/tools/package/packaging_naming_scheme/pns.py
@@ -0,0 +1,25 @@
+
+from vsc.utils import fancylogger
+
+options = [ "package-naming-name-template", "package-naming-version-template", "package-naming-toolchain-template" ]
+
+class PackagingNamingScheme(object):
+    """Abstract class for package naming scheme"""
+
+
+    def __init__(self, *args, **kwargs):
+        """initialize logger."""
+        self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
+
+    def name(self):
+        """Return name of the package, by default would include name, version, toolchain"""
+
+        
+    def version(self):
+        """The version in the version part of the package"""
+
+    def release(self):
+        """Just the release"""
+        return 1
+
+
diff --git a/easybuild/tools/packaging.py b/easybuild/tools/package/utilities.py
similarity index 78%
rename from easybuild/tools/packaging.py
rename to easybuild/tools/package/utilities.py
index 68ac779b31..d346f7932d 100644
--- a/easybuild/tools/packaging.py
+++ b/easybuild/tools/package/utilities.py
@@ -45,6 +45,7 @@
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import which
+from easybuild.tools.package.activepns import ActivePNS
 
 _log = fancylogger.getLogger('tools.packaging')
 # This is an abbreviated list of the package options, eventually it might make sense to set them
@@ -64,19 +65,12 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
     except OSError, err:
         raise EasybBuildError("Failed to chdir into workdir: %s : %s", workdir, err)
 
-    # default package_template is "eb-%(toolchain)s-%(name)s"
-    pkgtemplate = package_template()
-    full_ec_version = det_full_ec_version(easyblock.cfg)
-    _log.debug("I got a package template that looks like: %s " % pkgtemplate )
+    package_naming_scheme = ActivePNS()
 
-    toolchain_name = "%s-%s" % (easyblock.toolchain.name, easyblock.toolchain.version)
-
-    pkgname = pkgtemplate % {
-        'toolchain' : toolchain_name,
-        'version': '-'.join([x for x in [easyblock.cfg.get('versionprefix', ''), easyblock.cfg['version'], easyblock.cfg['versionsuffix'].lstrip('-')] if x]),
-        'name' : easyblock.name,
-    }
-    
+    pkgname = package_naming_scheme.name(easyblock.cfg)
+    pkgver  = package_naming_scheme.version(easyblock.cfg)
+    pkgrel  = package_naming_scheme.release(easyblock.cfg)
+ 
     deps = []
     if easyblock.toolchain.name != DUMMY_TOOLCHAIN_NAME:
         toolchain_dict = easyblock.toolchain.as_dict()
@@ -87,14 +81,8 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
     _log.debug("The dependencies to be added to the package are: " + pprint.pformat([easyblock.toolchain.as_dict()]+easyblock.cfg.dependencies()))
     depstring = ""    
     for dep in deps:
-        full_dep_version = det_full_ec_version(dep)
-        #by default will only build iteration 1 packages, do we need to enhance this?
         _log.debug("The dep added looks like %s " % dep)
-        dep_pkgname = pkgtemplate % {
-            'name': dep['name'],
-            'version': '-'.join([x for x in [dep.get('versionprefix',''), dep['version'], dep['versionsuffix'].lstrip('-')] if x]),
-            'toolchain': "%s-%s" % (dep['toolchain']['name'], dep['toolchain']['version']),
-        }
+        dep_pkgname = package_naming_scheme.name(dep)
         depstring += " --depends '%s'" % ( dep_pkgname)
 
     cmdlist=[
@@ -104,7 +92,7 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
         '--provides', pkgname,
         '-t', package_type, # target
         '-s', 'dir', # source
-        '--version', "eb",
+        '--version', pkgver,
     ]
     cmdlist.extend([ depstring ])
     cmdlist.extend([
@@ -133,3 +121,4 @@ def option_postprocess():
     else:
         raise EasyBuildError("Need both fpm and rpmbuild. Found fpm: %s rpmbuild: %s", fpm_path, rpmbuild_path)
 
+

From 44797ea87cbfabebf7864ce9647a0dcfb5a6f117 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Wed, 17 Jun 2015 22:03:23 -0400
Subject: [PATCH 1037/1356] moving this file out of the default file name of
 the sub module

---
 .../tools/package/packaging_naming_scheme.py  | 24 -------------------
 1 file changed, 24 deletions(-)
 delete mode 100644 easybuild/tools/package/packaging_naming_scheme.py

diff --git a/easybuild/tools/package/packaging_naming_scheme.py b/easybuild/tools/package/packaging_naming_scheme.py
deleted file mode 100644
index bfe620d2ea..0000000000
--- a/easybuild/tools/package/packaging_naming_scheme.py
+++ /dev/null
@@ -1,24 +0,0 @@
-
-from vsc.utils import fancylogger
-
-options = [ "package-naming-name-template", "package-naming-version-template", "package-naming-toolchain-template" ]
-
-class PackagingNamingScheme(object):
-    """Abstract class for package naming scheme"""
-
-
-    def __init__(self, *args, **kwargs):
-        """initialize logger."""
-        self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
-
-    def name:
-        """Return name of the package, by default would include name, version, toolchain"""
-
-        
-    def name_version:
-
-    def version_version:
-
-    def release:
-
-

From 2a3127dd7bd99d9b1ff65ff30ae2a7f0da7255d1 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Wed, 17 Jun 2015 22:46:51 -0400
Subject: [PATCH 1038/1356] broken, but closer. Pick up options and config
 (keyerror causing problems)

---
 easybuild/tools/config.py            |  8 +++++++-
 easybuild/tools/options.py           |  4 +++-
 easybuild/tools/package/activepns.py | 14 +++++++++-----
 easybuild/tools/package/utilities.py |  2 ++
 4 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index d48ff5c7b0..31cac9add6 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -95,7 +95,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'modules_footer',
         'only_blocks',
         'optarch',
-        'package_template',
         'package_tool',
         'package_type',
         'regtest_output_dir',
@@ -200,6 +199,7 @@ class ConfigurationVariables(FrozenDictKnownKeys):
         'module_syntax',
         'modules_tool',
         'packagepath',
+        'package_naming_scheme',
         'prefix',
         'repository',
         'repositorypath',
@@ -367,6 +367,12 @@ def get_repositorypath():
     """
     return ConfigurationVariables()['repositorypath']
 
+def get_package_naming_scheme():
+    """
+    Return the package naming scheme
+    """
+    return ConfigurationVariables()['package_naming_scheme']
+
 def package_path():
     """
     Return the path where built packages are copied to
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index d894560292..47a355eccc 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -64,6 +64,8 @@
 from easybuild.tools.modules import Lmod
 from easybuild.tools.ordereddict import OrderedDict
 import easybuild.tools.package.utilities as packaging
+from easybuild.tools.package.utilities import DEFAULT_PNS
+from easybuild.tools.package.activepns import avail_package_naming_scheme
 from easybuild.tools.toolchain.utilities import search_toolchain
 from easybuild.tools.repository.repository import avail_repositories
 from easybuild.tools.version import this_is_easybuild
@@ -356,9 +358,9 @@ def package_options(self):
 
         opts = OrderedDict({
             'package': ("Enabling packaging", None, 'store_true', False),
-            'package-template': ("A template string to name the package", None, 'store', DEFAULT_PACKAGE_TEMPLATE),
             'package-tool': ("Packaging tool to use", None, 'store_or_None', None),
             'package-type': ("Packaging type to output to", None, 'store_or_None', None),
+            'package-naming-scheme': ("Packaging naming scheme choice", 'choice', 'store', DEFAULT_PNS, sorted(avail_package_naming_scheme().keys()))
         })
 
         self.log.debug("package_options: descr %s opts %s" % (descr, opts))
diff --git a/easybuild/tools/package/activepns.py b/easybuild/tools/package/activepns.py
index d9184eec70..5c4983854a 100644
--- a/easybuild/tools/package/activepns.py
+++ b/easybuild/tools/package/activepns.py
@@ -1,18 +1,22 @@
 
 
 from vsc.utils import fancylogger
+from vsc.utils.missing import get_subclasses
 from vsc.utils.patterns import Singleton
-from easybuild.tools.config import build_option
-from easybuild.tools.utilities import import_available_modules
+from easybuild.tools.config import get_package_naming_scheme
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
+from easybuild.tools.package.packaging_naming_scheme.pns import PackagingNamingScheme
+from easybuild.tools.utilities import import_available_modules
 
 def avail_package_naming_scheme():
     '''
     Returns the list of valed naming schemes that are in the easybuild.package.package_naming_scheme namespace
     '''
-    pns = import_available_modules('easybuild.tools.package.packaging_naming_scheme')
+    import_available_modules('easybuild.tools.package.packaging_naming_scheme')
+
+    class_dict = dict([(x.__name__, x) for x in get_subclasses(PackagingNamingScheme)])
 
-    return pns
+    return class_dict
 
 class ActivePNS(object):
     """
@@ -26,7 +30,7 @@ def __init__(self, *args, **kwargs):
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
         avail_pns = avail_package_naming_scheme()
-        sel_pns = build_option("package-naming-scheme")
+        sel_pns = get_package_naming_scheme()
         if sel_pns in avail_pns:
             self.pns = avail_pns[sel_pns]()
         else:
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index 8d94826b52..c4c53c2419 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -47,6 +47,8 @@
 from easybuild.tools.filetools import which
 from easybuild.tools.package.activepns import ActivePNS
 
+DEFAULT_PNS = 'EasyBuildPNS'
+
 _log = fancylogger.getLogger('tools.packaging')
 # This is an abbreviated list of the package options, eventually it might make sense to set them
 # all in the "plugin" rather than in tools.options

From 2362b208ed43d0a13ec7fdfb070724b5c7f1aaa5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 18 Jun 2015 16:14:25 +0200
Subject: [PATCH 1039/1356] add support for --include-*

---
 easybuild/main.py          |  15 ++---
 easybuild/tools/include.py | 113 +++++++++++++++++++++++++++++++++++++
 easybuild/tools/options.py |  60 ++++++++++++++++----
 3 files changed, 168 insertions(+), 20 deletions(-)
 create mode 100644 easybuild/tools/include.py

diff --git a/easybuild/main.py b/easybuild/main.py
index 0c42cd6a2e..74b81d2804 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -163,9 +163,6 @@ def main(testing_data=(None, None, None)):
         new_umask = int(options.umask, 8)
         old_umask = os.umask(new_umask)
 
-    # set temporary directory to use
-    eb_tmpdir = set_tmpdir(options.tmpdir)
-
     # initialise logging for main
     global _log
     _log, logfile = init_logging(logfile, logtostdout=options.logtostdout, testing=testing)
@@ -177,7 +174,7 @@ def main(testing_data=(None, None, None)):
 
     # log startup info
     eb_cmd_line = eb_go.generate_cmd_line() + eb_go.args
-    log_start(eb_cmd_line, eb_tmpdir)
+    log_start(eb_cmd_line, options.tmpdir)
 
     if options.umask is not None:
         _log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
@@ -189,7 +186,7 @@ def main(testing_data=(None, None, None)):
     # determine robot path
     # --try-X, --dep-graph, --search use robot path for searching, so enable it with path of installed easyconfigs
     tweaked_ecs = try_to_generate and build_specs
-    tweaked_ecs_path, pr_path = alt_easyconfig_paths(eb_tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
+    tweaked_ecs_path, pr_path = alt_easyconfig_paths(options.tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
     auto_robot = try_to_generate or options.dep_graph or options.search or options.search_short
     robot_path = det_robot_path(options.robot_paths, tweaked_ecs_path, pr_path, auto_robot=auto_robot)
     _log.debug("Full robot path: %s" % robot_path)
@@ -266,7 +263,7 @@ def main(testing_data=(None, None, None)):
 
     # cleanup and exit after dry run, searching easyconfigs or submitting regression test
     if any([options.dry_run, options.dry_run_short, options.regtest, options.search, options.search_short]):
-        cleanup(logfile, eb_tmpdir, testing)
+        cleanup(logfile, options.tmpdir, testing)
         sys.exit(0)
 
     # skip modules that are already installed unless forced
@@ -299,7 +296,7 @@ def main(testing_data=(None, None, None)):
         job_info_txt = submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
         if not testing:
             print_msg("Submitted parallel build jobs, exiting now: %s" % job_info_txt)
-            cleanup(logfile, eb_tmpdir, testing)
+            cleanup(logfile, options.tmpdir, testing)
             sys.exit(0)
 
     # build software, will exit when errors occurs (except when testing)
@@ -328,10 +325,10 @@ def main(testing_data=(None, None, None)):
         if 'original_spec' in ec and os.path.isfile(ec['spec']):
             os.remove(ec['spec'])
 
-    # stop logging and cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir path)
+    # stop logging and cleanup tmp log file, unless one build failed (individual logs are located in options.tmpdir)
     stop_logging(logfile, logtostdout=options.logtostdout)
     if overall_success:
-        cleanup(logfile, eb_tmpdir, testing)
+        cleanup(logfile, options.tmpdir, testing)
 
 
 if __name__ == "__main__":
diff --git a/easybuild/tools/include.py b/easybuild/tools/include.py
new file mode 100644
index 0000000000..5b3b8c60c5
--- /dev/null
+++ b/easybuild/tools/include.py
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+# #
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Support for including additional Python modules, for easyblocks, module naming schemes and toolchains.
+
+@author: Kenneth Hoste (Ghent University)
+"""
+import glob
+import os
+import sys
+from vsc.utils.missing import nub
+from vsc.utils import fancylogger
+
+import easybuild.easyblocks  # just so we can reload it later
+from easybuild.tools.build_log import EasyBuildError
+
+
+_log = fancylogger.getLogger('tools.include', fname=False)
+
+
+PKG_INIT_BODY = """
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)
+"""
+
+
+def set_up_eb_package(parent_path, eb_pkg_name):
+    """Set up new easybuild subnamespace in specified path."""
+    if not eb_pkg_name.startswith('easybuild'):
+        raise EasyBuildError("Specified EasyBuild package name does not start with 'easybuild': %s", eb_pkg_name)
+
+    pkgpath = os.path.join(parent_path, eb_pkg_name.replace('.', os.path.sep))
+    # note: can't use mkdir, since that required build options to be initialised
+    os.makedirs(pkgpath)
+
+    # put __init__.py files in place, with required pkgutil.extend_path statement
+    while pkgpath != parent_path:
+        # note: can't use write_file, since that required build options to be initialised
+        handle = open(os.path.join(pkgpath, '__init__.py'), 'w')
+        handle.write(PKG_INIT_BODY)
+        handle.close()
+
+        pkgpath = os.path.dirname(pkgpath)
+
+
+def include_easyblocks(tmpdir, paths):
+    """Include generic and software-specific easyblocks found in specified locations."""
+    easyblocks_path = os.path.join(tmpdir, 'included-easyblocks')
+
+    # covers both easybuild.easyblocks and easybuild.easyblocks.generic namespaces
+    set_up_eb_package(easyblocks_path, 'easybuild.easyblocks.generic')
+
+    easyblocks_dir = os.path.join(easyblocks_path, 'easybuild', 'easyblocks')
+
+    allpaths = nub([y for x in paths for y in glob.glob(x)])
+    for easyblock_module in allpaths:
+        filename = os.path.basename(easyblock_module)
+
+        # generic easyblocks are expected to be in a directory named 'generic'
+        if os.path.basename(os.path.dirname(easyblock_module)) == 'generic':
+            target_path = os.path.join(easyblocks_dir, 'generic', filename)
+        else:
+            target_path = os.path.join(easyblocks_dir, filename)
+
+        try:
+            os.symlink(easyblock_module, target_path)
+            _log.info("Symlinking %s to %s", easyblock_module, target_path)
+        except OSError as err:
+            raise EasyBuildError("Symlinking %s to %s failed: %s", easyblock_module, target_path, err)
+
+    included_easyblocks = [x for x in os.listdir(easyblocks_dir) if x not in ['__init__.py', 'generic']]
+    included_generic_easyblocks = [x for x in os.listdir(os.path.join(easyblocks_dir, 'generic')) if x != '__init__.py']
+    _log.debug("Included generic easyblocks: %s", included_easyblocks)
+    _log.debug("Included software-specific easyblocks: %s", included_generic_easyblocks)
+
+    # inject path into Python search path, and reload easybuild.easyblocks to get it 'registered' in sys.modules
+    sys.path.insert(0, easyblocks_path)
+    reload(easybuild.easyblocks)
+
+
+def include_module_naming_schemes(tmpdir, paths):
+    """Include module naming schemes at specified locations."""
+    # FIXME todo
+    raise NotImplementedError
+
+
+def include_toolchains(tmpdir, paths):
+    """Include toolchains and toolchain components at specified locations."""
+    # FIXME todo
+    raise NotImplementedError
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ebb1a3ef1e..34120cbccb 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -36,6 +36,7 @@
 import glob
 import os
 import re
+import shutil
 import sys
 from distutils.version import LooseVersion
 from vsc.utils.missing import nub
@@ -52,10 +53,11 @@
 from easybuild.tools.build_log import EasyBuildError, raise_easybuilderror
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX, DEFAULT_MODULES_TOOL
 from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
-from easybuild.tools.config import DEFAULT_STRICT, get_pretend_installpath, mk_full_default_path
+from easybuild.tools.config import DEFAULT_STRICT, get_pretend_installpath, mk_full_default_path, set_tmpdir
 from easybuild.tools.configobj import ConfigObj, ConfigObjError
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
 from easybuild.tools.github import HAVE_GITHUB_API, HAVE_KEYRING, fetch_github_token
+from easybuild.tools.include import include_easyblocks, include_module_naming_schemes, include_toolchains
 from easybuild.tools.modules import avail_modules_tools
 from easybuild.tools.module_generator import ModuleGeneratorLua, avail_module_generators
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
@@ -240,6 +242,11 @@ def config_options(self):
                                           'strlist', 'store', []),
             'ignore-dirs': ("Directory names to ignore when searching for files/dirs",
                             'strlist', 'store', ['.git', '.svn']),
+            'include-easyblocks': ("Location(s) of extra or customized easyblocks", 'strlist', 'store', []),
+            'include-module-naming-schemes': ("Location(s) of extra or customized module naming schemes",
+                                              'strlist', 'store', []),
+            'include-toolchains': ("Location(s) of extra or customized toolchains or toolchain components",
+                                   'strlist', 'store', []),
             'installpath': ("Install path for software and modules",
                             None, 'store', mk_full_default_path('installpath')),
             'installpath-modules': ("Install path for modules (if None, combine --installpath and --subdir-modules)",
@@ -417,6 +424,12 @@ def postprocess(self):
         if self.options.unittest_file:
             fancylogger.logToFile(self.options.unittest_file)
 
+        # set tmpdir
+        self.options.tmpdir = set_tmpdir(self.options.tmpdir)
+
+        # take --include options into account
+        self._postprocess_include()
+
         # prepare for --list/--avail
         if any([self.options.avail_easyconfig_params, self.options.avail_easyconfig_templates,
                 self.options.list_easyblocks, self.options.list_toolchains, self.options.avail_cfgfile_constants,
@@ -485,6 +498,13 @@ def _postprocess_external_modules_metadata(self):
         self.options.external_modules_metadata = parsed_external_modules_metadata
         self.log.debug("External modules metadata: %s", self.options.external_modules_metadata)
 
+    def _postprocess_include(self):
+        """Postprocess --include options."""
+        # set up included easyblocks, module naming schemes and toolchains/toolchain components
+        include_easyblocks(self.options.tmpdir, self.options.include_easyblocks)
+        #include_module_naming_schemes(self.options.tmpdir, self.options.include_module_naming_schemes)
+        #include_toolchains(self.options.tmpdir, self.options.include_toolchains)
+
     def _postprocess_config(self):
         """Postprocessing of configuration options"""
         if self.options.prefix is not None:
@@ -568,6 +588,13 @@ def _postprocess_list_avail(self):
             self.log.info(msg)
         else:
             print msg
+
+        # cleanup tmpdir
+        try:
+            shutil.rmtree(self.options.tmpdir)
+        except OSError as err:
+            raise EasyBuildError("Failed to clean up temporary directory %s: %s", self.options.tmpdir, err)
+
         sys.exit(0)
 
     def avail_cfgfile_constants(self):
@@ -587,17 +614,21 @@ def avail_cfgfile_constants(self):
                 lines.append("* %s: %s [value: %s]" % (cst_name, cst_help, cst_value))
         return '\n'.join(lines)
 
-    def avail_classes_tree(self, classes, classNames, detailed, depth=0):
+    def avail_classes_tree(self, classes, class_names, locations, detailed, depth=0):
         """Print list of classes as a tree."""
         txt = []
-        for className in classNames:
-            classInfo = classes[className]
+        for class_name in class_names:
+            class_info = classes[class_name]
             if detailed:
-                txt.append("%s|-- %s (%s)" % ("|   " * depth, className, classInfo['module']))
+                mod = class_info['module']
+                loc = ''
+                if mod in locations:
+                    loc = '@ %s' % locations[mod]
+                txt.append("%s|-- %s (%s %s)" % ("|   " * depth, class_name, mod, loc))
             else:
-                txt.append("%s|-- %s" % ("|   " * depth, className))
-            if 'children' in classInfo:
-                txt.extend(self.avail_classes_tree(classes, classInfo['children'], detailed, depth + 1))
+                txt.append("%s|-- %s" % ("|   " * depth, class_name))
+            if 'children' in class_info:
+                txt.extend(self.avail_classes_tree(classes, class_info['children'], locations, detailed, depth + 1))
         return txt
 
     def avail_easyblocks(self):
@@ -608,6 +639,7 @@ def avail_easyblocks(self):
         # finish initialisation of the toolchain module (ie set the TC_CONSTANT constants)
         search_toolchain('')
 
+        locations = {}
         for package in ["easybuild.easyblocks", "easybuild.easyblocks.generic"]:
             __import__(package)
 
@@ -620,7 +652,9 @@ def avail_easyblocks(self):
                     for f in os.listdir(path):
                         res = module_regexp.match(f)
                         if res:
-                            __import__("%s.%s" % (package, res.group(1)))
+                            easyblock = '%s.%s' % (package, res.group(1))
+                            __import__(easyblock)
+                            locations.update({easyblock: os.path.join(path, f)})
 
         def add_class(classes, cls):
             """Add a new class, and all of its subclasses."""
@@ -643,11 +677,15 @@ def add_class(classes, cls):
         for root in roots:
             root = root.__name__
             if detailed:
-                txt.append("%s (%s)" % (root, classes[root]['module']))
+                mod = classes[root]['module']
+                loc = ''
+                if mod in locations:
+                    loc = '@ %s' % locations[mod]
+                txt.append("%s (%s %s)" % (root, mod, loc))
             else:
                 txt.append("%s" % root)
             if 'children' in classes[root]:
-                txt.extend(self.avail_classes_tree(classes, classes[root]['children'], detailed))
+                txt.extend(self.avail_classes_tree(classes, classes[root]['children'], locations, detailed))
                 txt.append("")
 
         return "\n".join(txt)

From 25169739b790062eec2280cebb4da15cce2a4871 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Jun 2015 13:48:14 +0200
Subject: [PATCH 1040/1356] guard __import__ statement in
 import_available_modules for ImportErrors

---
 easybuild/tools/utilities.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index fb3ac98fe0..5023177028 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -32,7 +32,10 @@
 import string
 import sys
 from vsc.utils import fancylogger
+
 import easybuild.tools.environment as env
+from easybuild.tools.build_log import EasyBuildError
+
 
 _log = fancylogger.getLogger('tools.utilities')
 
@@ -99,5 +102,9 @@ def import_available_modules(namespace):
                 mod_name = module.split(os.path.sep)[-1].split('.')[0]
                 modpath = '.'.join([namespace, mod_name])
                 _log.debug("importing module %s" % modpath)
-                modules.append(__import__(modpath, globals(), locals(), ['']))
+                try:
+                    mod = __import__(modpath, globals(), locals(), [''])
+                except ImportError as err:
+                    raise EasyBuildError("import_available_modules: Failed to import %s: %s", modpath, err)
+                modules.append(mod)
     return modules

From 6ea369a33fb09062ab9b1b03bdf2dc21b28ca903 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 Jun 2015 13:48:40 +0200
Subject: [PATCH 1041/1356] complete implementation for
 --include-module-naming-schemes and --include-toolchains + refactor

---
 easybuild/tools/include.py | 121 ++++++++++++++++++++++++++++++-------
 easybuild/tools/options.py |   6 +-
 2 files changed, 101 insertions(+), 26 deletions(-)

diff --git a/easybuild/tools/include.py b/easybuild/tools/include.py
index 5b3b8c60c5..ab0b49ee4e 100644
--- a/easybuild/tools/include.py
+++ b/easybuild/tools/include.py
@@ -34,8 +34,16 @@
 from vsc.utils.missing import nub
 from vsc.utils import fancylogger
 
-import easybuild.easyblocks  # just so we can reload it later
 from easybuild.tools.build_log import EasyBuildError
+# these are imported just to we can reload them later
+import easybuild.easyblocks
+import easybuild.easyblocks.generic
+import easybuild.tools.module_naming_scheme
+import easybuild.toolchains
+import easybuild.toolchains.compiler
+import easybuild.toolchains.fft
+import easybuild.toolchains.linalg
+import easybuild.toolchains.mpi
 
 
 _log = fancylogger.getLogger('tools.include', fname=False)
@@ -46,32 +54,55 @@
 __path__ = extend_path(__path__, __name__)
 """
 
+def create_pkg(path):
+    """Write package __init__.py file at specified path."""
+    init_path = os.path.join(path, '__init__.py')
+    try:
+        # note: can't use mkdir, since that required build options to be initialised
+        if not os.path.exists(path):
+            os.makedirs(path)
 
-def set_up_eb_package(parent_path, eb_pkg_name):
+        # put __init__.py files in place, with required pkgutil.extend_path statement
+        # note: can't use write_file, since that required build options to be initialised
+        handle = open(init_path, 'w')
+        handle.write(PKG_INIT_BODY)
+        handle.close()
+    except (IOError, OSError) as err:
+        raise EasyBuildError("Failed to write %s: %s", init_path, err)
+
+
+def set_up_eb_package(parent_path, eb_pkg_name, subpkgs=None):
     """Set up new easybuild subnamespace in specified path."""
     if not eb_pkg_name.startswith('easybuild'):
         raise EasyBuildError("Specified EasyBuild package name does not start with 'easybuild': %s", eb_pkg_name)
 
     pkgpath = os.path.join(parent_path, eb_pkg_name.replace('.', os.path.sep))
-    # note: can't use mkdir, since that required build options to be initialised
-    os.makedirs(pkgpath)
 
-    # put __init__.py files in place, with required pkgutil.extend_path statement
-    while pkgpath != parent_path:
-        # note: can't use write_file, since that required build options to be initialised
-        handle = open(os.path.join(pkgpath, '__init__.py'), 'w')
-        handle.write(PKG_INIT_BODY)
-        handle.close()
+    # handle subpackages first
+    if subpkgs:
+        for subpkg in subpkgs:
+            create_pkg(os.path.join(pkgpath, subpkg))
 
+    # creata package dirs on each level
+    while pkgpath != parent_path:
+        create_pkg(pkgpath)
         pkgpath = os.path.dirname(pkgpath)
 
 
+def safe_symlink(source_path, symlink_path):
+    """Create a symlink at the specified path for the given path."""
+    try:
+        os.symlink(os.path.abspath(source_path), symlink_path)
+        _log.info("Symlinked %s to %s", source_path, symlink_path)
+    except OSError as err:
+        raise EasyBuildError("Symlinking %s to %s failed: %s", source_path, symlink_path, err)
+
+
 def include_easyblocks(tmpdir, paths):
     """Include generic and software-specific easyblocks found in specified locations."""
     easyblocks_path = os.path.join(tmpdir, 'included-easyblocks')
 
-    # covers both easybuild.easyblocks and easybuild.easyblocks.generic namespaces
-    set_up_eb_package(easyblocks_path, 'easybuild.easyblocks.generic')
+    set_up_eb_package(easyblocks_path, 'easybuild.easyblocks', subpkgs=['generic'])
 
     easyblocks_dir = os.path.join(easyblocks_path, 'easybuild', 'easyblocks')
 
@@ -80,34 +111,78 @@ def include_easyblocks(tmpdir, paths):
         filename = os.path.basename(easyblock_module)
 
         # generic easyblocks are expected to be in a directory named 'generic'
-        if os.path.basename(os.path.dirname(easyblock_module)) == 'generic':
+        parent_dir = os.path.basename(os.path.dirname(easyblock_module))
+        if parent_dir == 'generic':
             target_path = os.path.join(easyblocks_dir, 'generic', filename)
         else:
             target_path = os.path.join(easyblocks_dir, filename)
 
-        try:
-            os.symlink(easyblock_module, target_path)
-            _log.info("Symlinking %s to %s", easyblock_module, target_path)
-        except OSError as err:
-            raise EasyBuildError("Symlinking %s to %s failed: %s", easyblock_module, target_path, err)
+        safe_symlink(easyblock_module, target_path)
 
     included_easyblocks = [x for x in os.listdir(easyblocks_dir) if x not in ['__init__.py', 'generic']]
     included_generic_easyblocks = [x for x in os.listdir(os.path.join(easyblocks_dir, 'generic')) if x != '__init__.py']
     _log.debug("Included generic easyblocks: %s", included_easyblocks)
     _log.debug("Included software-specific easyblocks: %s", included_generic_easyblocks)
 
-    # inject path into Python search path, and reload easybuild.easyblocks to get it 'registered' in sys.modules
+    # inject path into Python search path, and reload modules to get it 'registered' in sys.modules
     sys.path.insert(0, easyblocks_path)
     reload(easybuild.easyblocks)
+    reload(easybuild.easyblocks.generic)
 
 
 def include_module_naming_schemes(tmpdir, paths):
     """Include module naming schemes at specified locations."""
-    # FIXME todo
-    raise NotImplementedError
+    mns_path = os.path.join(tmpdir, 'included-module-naming-schemes')
+
+    set_up_eb_package(mns_path, 'easybuild.tools.module_naming_scheme')
+
+    mns_dir = os.path.join(mns_path, 'easybuild', 'tools', 'module_naming_scheme')
+
+    allpaths = nub([y for x in paths for y in glob.glob(x)])
+    for mns_module in allpaths:
+        filename = os.path.basename(mns_module)
+        target_path = os.path.join(mns_dir, filename)
+        safe_symlink(mns_module, target_path)
+
+    included_mns = [x for x in os.listdir(mns_dir) if x not in ['__init__.py']]
+    _log.debug("Included module naming schemes: %s", included_mns)
+
+    # inject path into Python search path, and reload modules to get it 'registered' in sys.modules
+    sys.path.insert(0, mns_path)
+    reload(easybuild.tools.module_naming_scheme)
 
 
 def include_toolchains(tmpdir, paths):
     """Include toolchains and toolchain components at specified locations."""
-    # FIXME todo
-    raise NotImplementedError
+    toolchains_path = os.path.join(tmpdir, 'included-toolchains')
+    toolchain_subpkgs = ['compiler', 'fft', 'linalg', 'mpi']
+
+    set_up_eb_package(toolchains_path, 'easybuild.toolchains', subpkgs=toolchain_subpkgs)
+
+    toolchains_dir = os.path.join(toolchains_path, 'easybuild', 'toolchains')
+
+    allpaths = nub([y for x in paths for y in glob.glob(x)])
+    for toolchain_module in allpaths:
+        filename = os.path.basename(toolchain_module)
+
+        parent_dir = os.path.basename(os.path.dirname(toolchain_module))
+
+        # generic toolchains are expected to be in a directory named 'generic'
+        if parent_dir in toolchain_subpkgs:
+            target_path = os.path.join(toolchains_dir, parent_dir, filename)
+        else:
+            target_path = os.path.join(toolchains_dir, filename)
+
+        safe_symlink(toolchain_module, target_path)
+
+    included_toolchains = [x for x in os.listdir(toolchains_dir) if x not in ['__init__.py'] + toolchain_subpkgs]
+    _log.debug("Included toolchains: %s", included_toolchains)
+    for subpkg in toolchain_subpkgs:
+        included_subpkg_modules = [x for x in os.listdir(os.path.join(toolchains_dir, subpkg)) if x != '__init__.py']
+        _log.debug("Included toolchain %s components: %s", subpkg, included_subpkg_modules)
+
+    # inject path into Python search path, and reload modules to get it 'registered' in sys.modules
+    sys.path.insert(0, toolchains_path)
+    reload(easybuild.toolchains)
+    for subpkg in toolchain_subpkgs:
+        reload(sys.modules['easybuild.toolchains.%s' % subpkg])
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 34120cbccb..5e18bf090a 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -49,7 +49,7 @@
 from easybuild.framework.easyconfig.templates import template_documentation
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
-from easybuild.tools import build_log, config, run  # build_log should always stay there, to ensure EasyBuildLog
+from easybuild.tools import build_log, run  # build_log should always stay there, to ensure EasyBuildLog
 from easybuild.tools.build_log import EasyBuildError, raise_easybuilderror
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX, DEFAULT_MODULES_TOOL
 from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
@@ -502,8 +502,8 @@ def _postprocess_include(self):
         """Postprocess --include options."""
         # set up included easyblocks, module naming schemes and toolchains/toolchain components
         include_easyblocks(self.options.tmpdir, self.options.include_easyblocks)
-        #include_module_naming_schemes(self.options.tmpdir, self.options.include_module_naming_schemes)
-        #include_toolchains(self.options.tmpdir, self.options.include_toolchains)
+        include_module_naming_schemes(self.options.tmpdir, self.options.include_module_naming_schemes)
+        include_toolchains(self.options.tmpdir, self.options.include_toolchains)
 
     def _postprocess_config(self):
         """Postprocessing of configuration options"""

From 786719f6ef327dd93287c1e5acd6692a722760e0 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Fri, 19 Jun 2015 09:59:07 -0400
Subject: [PATCH 1042/1356] working to build a basic package again, with the
 default package naming scheme

---
 easybuild/tools/options.py                     |  3 ++-
 easybuild/tools/package/activepns.py           | 10 +++++-----
 .../packaging_naming_scheme/easybuild_pns.py   | 18 ++++++++++--------
 .../package/packaging_naming_scheme/pns.py     |  6 +++---
 easybuild/tools/package/utilities.py           |  3 ++-
 5 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 47a355eccc..117bf054e3 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -266,6 +266,8 @@ def config_options(self):
                              'choice', 'store', DEFAULT_MODULES_TOOL, sorted(avail_modules_tools().keys())),
             'packagepath': ("The destination path for the packages built by package-tool",
                              None, 'store', mk_full_default_path('packagepath')),
+            'package-naming-scheme': ("Packaging naming scheme choice", 
+                                      'choice', 'store', DEFAULT_PNS, sorted(avail_package_naming_scheme().keys())),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
                         "(used prefix for defaults %s)" % DEFAULT_PREFIX),
                        None, 'store', None),
@@ -360,7 +362,6 @@ def package_options(self):
             'package': ("Enabling packaging", None, 'store_true', False),
             'package-tool': ("Packaging tool to use", None, 'store_or_None', None),
             'package-type': ("Packaging type to output to", None, 'store_or_None', None),
-            'package-naming-scheme': ("Packaging naming scheme choice", 'choice', 'store', DEFAULT_PNS, sorted(avail_package_naming_scheme().keys()))
         })
 
         self.log.debug("package_options: descr %s opts %s" % (descr, opts))
diff --git a/easybuild/tools/package/activepns.py b/easybuild/tools/package/activepns.py
index 5c4983854a..7267bc014d 100644
--- a/easybuild/tools/package/activepns.py
+++ b/easybuild/tools/package/activepns.py
@@ -37,14 +37,14 @@ def __init__(self, *args, **kwargs):
             raise EasyBuildError("Selected package naming scheme %s could not be found in %s",
                                     sel_pns, avail_pns.keys())
 
-    def name(self):
-        name = self.pns.name()
+    def name(self, ec):
+        name = self.pns.name(ec)
         return name
 
-    def version(self):
-        version = self.pns.version()
+    def version(self, ec):
+        version = self.pns.version(ec)
         return version
 
-    def release(self):
+    def release(self, ec):
         release = self.pns.release()
         return release
diff --git a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
index e0ab409e74..b6dd702528 100644
--- a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
+++ b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
@@ -19,21 +19,23 @@ class EasyBuildPNS(PackagingNamingScheme):
     def name(self, ec):
         name_template = "eb-%(name)s-%(version)s-%(toolchain)s"
         pkg_name = name_template % {
-            'toolchain' : self.toolchain(ec),
+            'toolchain' : self._toolchain(ec),
             'version': '-'.join([x for x in [ec.get('versionprefix', ''), ec['version'], ec['versionsuffix'].lstrip('-')] if x]),
-            'name' : eb.name,
-    }
+            'name' : ec.name,
+        }
+        return pkg_name
 
-    def _toolchain(self, eb):
+    def _toolchain(self, ec):
         toolchain_template = "%(toolchain_name)s-%(toolchain_version)s"
         pkg_toolchain = toolchain_template % {
-            'toolchain_name': eb.toolchain.name,
-            'toolchain_version': eb.toolchain.version,
+            'toolchain_name': ec.toolchain.name,
+            'toolchain_version': ec.toolchain.version,
         }
+        return pkg_toolchain
 
 
-    def version(self, eb):
-        return eb.cfg['version']
+    def version(self, ec):
+        return ec['version']
 
         
 
diff --git a/easybuild/tools/package/packaging_naming_scheme/pns.py b/easybuild/tools/package/packaging_naming_scheme/pns.py
index f4427465ca..9d60949b6f 100644
--- a/easybuild/tools/package/packaging_naming_scheme/pns.py
+++ b/easybuild/tools/package/packaging_naming_scheme/pns.py
@@ -11,14 +11,14 @@ def __init__(self, *args, **kwargs):
         """initialize logger."""
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
-    def name(self):
+    def name(self,ec):
         """Return name of the package, by default would include name, version, toolchain"""
 
         
-    def version(self):
+    def version(self,ec):
         """The version in the version part of the package"""
 
-    def release(self):
+    def release(self,ec):
         """Just the release"""
         return 1
 
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index c4c53c2419..1df0382a53 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -72,7 +72,8 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
     pkgname = package_naming_scheme.name(easyblock.cfg)
     pkgver  = package_naming_scheme.version(easyblock.cfg)
     pkgrel  = package_naming_scheme.release(easyblock.cfg)
- 
+
+    _log.debug("Got the pns values for (name, version, release): (%s, %s, %s)" % (pkgname, pkgver, pkgrel)) 
     deps = []
     if easyblock.toolchain.name != DUMMY_TOOLCHAIN_NAME:
         toolchain_dict = easyblock.toolchain.as_dict()

From 965452981eefcb1f22662fd3e092a046538ce0ad Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 20 Jun 2015 07:52:50 +0200
Subject: [PATCH 1043/1356] add unit tests for --include-*

---
 easybuild/tools/include.py |  36 +++++--
 test/framework/include.py  | 212 +++++++++++++++++++++++++++++++++++++
 test/framework/suite.py    |   3 +-
 3 files changed, 243 insertions(+), 8 deletions(-)
 create mode 100644 test/framework/include.py

diff --git a/easybuild/tools/include.py b/easybuild/tools/include.py
index ab0b49ee4e..af857ec175 100644
--- a/easybuild/tools/include.py
+++ b/easybuild/tools/include.py
@@ -36,14 +36,19 @@
 
 from easybuild.tools.build_log import EasyBuildError
 # these are imported just to we can reload them later
-import easybuild.easyblocks
-import easybuild.easyblocks.generic
 import easybuild.tools.module_naming_scheme
 import easybuild.toolchains
 import easybuild.toolchains.compiler
 import easybuild.toolchains.fft
 import easybuild.toolchains.linalg
 import easybuild.toolchains.mpi
+# importing easyblocks namespace may fail if easybuild-easyblocks is not available
+# for now, we don't really care
+try:
+    import easybuild.easyblocks
+    import easybuild.easyblocks.generic
+except ImportError:
+    pass
 
 
 _log = fancylogger.getLogger('tools.include', fname=False)
@@ -89,6 +94,15 @@ def set_up_eb_package(parent_path, eb_pkg_name, subpkgs=None):
         pkgpath = os.path.dirname(pkgpath)
 
 
+def expand_glob_paths(glob_paths):
+    """Expand specified glob paths to a list of unique non-glob paths to only files."""
+    paths = []
+    for glob_path in glob_paths:
+        paths.extend([f for f in glob.glob(glob_path) if os.path.isfile(f)])
+
+    return nub(paths)
+
+
 def safe_symlink(source_path, symlink_path):
     """Create a symlink at the specified path for the given path."""
     try:
@@ -106,7 +120,7 @@ def include_easyblocks(tmpdir, paths):
 
     easyblocks_dir = os.path.join(easyblocks_path, 'easybuild', 'easyblocks')
 
-    allpaths = nub([y for x in paths for y in glob.glob(x)])
+    allpaths = expand_glob_paths(paths)
     for easyblock_module in allpaths:
         filename = os.path.basename(easyblock_module)
 
@@ -126,8 +140,12 @@ def include_easyblocks(tmpdir, paths):
 
     # inject path into Python search path, and reload modules to get it 'registered' in sys.modules
     sys.path.insert(0, easyblocks_path)
-    reload(easybuild.easyblocks)
-    reload(easybuild.easyblocks.generic)
+    reload(easybuild)
+    if 'easybuild.easyblocks' in sys.modules:
+        reload(easybuild.easyblocks)
+        reload(easybuild.easyblocks.generic)
+
+    return easyblocks_path
 
 
 def include_module_naming_schemes(tmpdir, paths):
@@ -138,7 +156,7 @@ def include_module_naming_schemes(tmpdir, paths):
 
     mns_dir = os.path.join(mns_path, 'easybuild', 'tools', 'module_naming_scheme')
 
-    allpaths = nub([y for x in paths for y in glob.glob(x)])
+    allpaths = expand_glob_paths(paths)
     for mns_module in allpaths:
         filename = os.path.basename(mns_module)
         target_path = os.path.join(mns_dir, filename)
@@ -151,6 +169,8 @@ def include_module_naming_schemes(tmpdir, paths):
     sys.path.insert(0, mns_path)
     reload(easybuild.tools.module_naming_scheme)
 
+    return mns_path
+
 
 def include_toolchains(tmpdir, paths):
     """Include toolchains and toolchain components at specified locations."""
@@ -161,7 +181,7 @@ def include_toolchains(tmpdir, paths):
 
     toolchains_dir = os.path.join(toolchains_path, 'easybuild', 'toolchains')
 
-    allpaths = nub([y for x in paths for y in glob.glob(x)])
+    allpaths = expand_glob_paths(paths)
     for toolchain_module in allpaths:
         filename = os.path.basename(toolchain_module)
 
@@ -186,3 +206,5 @@ def include_toolchains(tmpdir, paths):
     reload(easybuild.toolchains)
     for subpkg in toolchain_subpkgs:
         reload(sys.modules['easybuild.toolchains.%s' % subpkg])
+
+    return toolchains_path
diff --git a/test/framework/include.py b/test/framework/include.py
new file mode 100644
index 0000000000..07b6d3bfc7
--- /dev/null
+++ b/test/framework/include.py
@@ -0,0 +1,212 @@
+# #
+# Copyright 2013-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Unit tests for eb command line options.
+
+@author: Kenneth Hoste (Ghent University)
+"""
+import os
+import sys
+from test.framework.utilities import EnhancedTestCase
+from unittest import TestLoader
+from unittest import main as unittestmain
+
+from easybuild.tools.filetools import mkdir, write_file
+from easybuild.tools.include import include_easyblocks, include_module_naming_schemes, include_toolchains
+
+
+def up(path, cnt):
+    """Return path N times up."""
+    if cnt > 0:
+        path = up(os.path.dirname(path), cnt-1)
+    return path
+
+
+class IncludeTest(EnhancedTestCase):
+    """Testcases for command line options."""
+
+    logfile = None
+
+    def tearDown(self):
+        # FIXME avoid cleanup
+        pass
+
+    def test_include_easyblocks(self):
+        """Test include_easyblocks()."""
+        test_easyblocks = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'easybuild', 'easyblocks')
+
+        # put a couple of custom easyblocks in place, to test
+        myeasyblocks = os.path.join(self.test_prefix, 'myeasyblocks')
+        mkdir(os.path.join(myeasyblocks, 'generic'), parents=True)
+
+        myfoo_easyblock_txt = '\n'.join([
+            "from easybuild.easyblocks.generic.configuremake import ConfigureMake",
+            "class EB_Foo(ConfigureMake):",
+            "   pass",
+        ])
+        write_file(os.path.join(myeasyblocks, 'myfoo.py'), myfoo_easyblock_txt)
+
+        mybar_easyblock_txt = '\n'.join([
+            "from easybuild.framework.easyblock import EasyBlock",
+            "class Bar(EasyBlock):",
+            "   pass",
+        ])
+        write_file(os.path.join(myeasyblocks, 'generic', 'mybar.py'), mybar_easyblock_txt)
+
+        # expand set of known easyblocks with our custom ones
+        glob_paths = [os.path.join(myeasyblocks, '*'), os.path.join(myeasyblocks, '*/*.py')]
+        included_easyblocks_path = include_easyblocks(self.test_prefix, glob_paths)
+
+        expected_paths = ['__init__.py', 'easyblocks/__init__.py', 'easyblocks/myfoo.py',
+                          'easyblocks/generic/__init__.py', 'easyblocks/generic/mybar.py']
+        for filepath in expected_paths:
+            fullpath = os.path.join(included_easyblocks_path, 'easybuild', filepath)
+            self.assertTrue(os.path.exists(fullpath), "%s exists" % fullpath)
+
+        # path to included easyblocks should be prepended to Python search path
+        self.assertEqual(sys.path[0], included_easyblocks_path)
+
+        # importing custom easyblocks should work
+        import easybuild.easyblocks.myfoo
+        myfoo_pyc_path = easybuild.easyblocks.myfoo.__file__
+        myfoo_real_py_path = os.path.realpath(os.path.join(os.path.dirname(myfoo_pyc_path), 'myfoo.py'))
+        self.assertTrue(os.path.samefile(up(myfoo_real_py_path, 1), myeasyblocks))
+
+        import easybuild.easyblocks.generic.mybar
+        mybar_pyc_path = easybuild.easyblocks.generic.mybar.__file__
+        mybar_real_py_path = os.path.realpath(os.path.join(os.path.dirname(mybar_pyc_path), 'mybar.py'))
+        self.assertTrue(os.path.samefile(up(mybar_real_py_path, 2), myeasyblocks))
+
+        # existing (test) easyblocks are unaffected
+        import easybuild.easyblocks.foofoo
+        foofoo_path = os.path.dirname(easybuild.easyblocks.foofoo.__file__)
+        self.assertTrue(os.path.samefile(foofoo_path, test_easyblocks))
+
+    def test_include_easyblocks_priority(self):
+        """Test whether easyblocks included via include_easyblocks() get prioroity over others."""
+        test_easyblocks = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'easybuild', 'easyblocks')
+
+        # make sure that test 'foo' easyblocks is there
+        import easybuild.easyblocks.foo
+        foo_path = os.path.dirname(easybuild.easyblocks.foo.__file__)
+        self.assertTrue(os.path.samefile(foo_path, test_easyblocks))
+
+        # inject custom 'foo' easyblocks
+        myeasyblocks = os.path.join(self.test_prefix, 'myeasyblocks')
+        mkdir(myeasyblocks)
+
+        foo_easyblock_txt = '\n'.join([
+            "from easybuild.framework.easyblock import EasyBlock",
+            "class EB_Foo(EasyBlock):",
+            "   pass",
+        ])
+        write_file(os.path.join(myeasyblocks, 'foo.py'), foo_easyblock_txt)
+        included_easyblocks_path = include_easyblocks(self.test_prefix, [os.path.join(myeasyblocks, 'foo.py')])
+
+        reload(easybuild.easyblocks.foo)
+        foo_pyc_path = easybuild.easyblocks.foo.__file__
+        foo_real_py_path = os.path.realpath(os.path.join(os.path.dirname(foo_pyc_path), 'foo.py'))
+        self.assertFalse(os.path.samefile(os.path.dirname(foo_pyc_path), test_easyblocks))
+        self.assertTrue(os.path.samefile(foo_real_py_path, os.path.join(myeasyblocks, 'foo.py')))
+
+    def test_include_mns(self):
+        """Test include_module_naming_schemes()."""
+        testdir = os.path.dirname(os.path.abspath(__file__))
+        test_mns = os.path.join(testdir, 'sandbox', 'easybuild', 'module_naming_scheme')
+
+        my_mns = os.path.join(self.test_prefix, 'my_mns')
+        mkdir(my_mns)
+
+        my_mns_txt = '\n'.join([
+            "from easybuild.tools.module_naming_scheme import ModuleNamingScheme",
+            "class MyMNS(ModuleNamingScheme):",
+            "   pass",
+        ])
+        write_file(os.path.join(my_mns, 'my_mns.py'), my_mns_txt)
+
+        # include custom MNS
+        included_mns_path = include_module_naming_schemes(self.test_prefix, [os.path.join(my_mns, '*.py')])
+
+        expected_paths = ['__init__.py', 'tools/__init__.py', 'tools/module_naming_scheme/__init__.py',
+                          'tools/module_naming_scheme/my_mns.py']
+        for filepath in expected_paths:
+            fullpath = os.path.join(included_mns_path, 'easybuild', filepath)
+            self.assertTrue(os.path.exists(fullpath), "%s exists" % fullpath)
+
+        # path to included MNSs should be prepended to Python search path
+        self.assertEqual(sys.path[0], included_mns_path)
+
+        # importing custom MNS should work
+        import easybuild.tools.module_naming_scheme.my_mns
+        my_mns_pyc_path = easybuild.tools.module_naming_scheme.my_mns.__file__
+        my_mns_real_py_path = os.path.realpath(os.path.join(os.path.dirname(my_mns_pyc_path), 'my_mns.py'))
+        self.assertTrue(os.path.samefile(up(my_mns_real_py_path, 1), my_mns))
+
+    def test_include_toolchains(self):
+        """Test include_toolchains()."""
+        my_toolchains = os.path.join(self.test_prefix, 'my_toolchains')
+        mkdir(my_toolchains)
+        for subdir in ['compiler', 'fft', 'linalg', 'mpi']:
+            mkdir(os.path.join(my_toolchains, subdir))
+
+        my_tc_txt = '\n'.join([
+            "from easybuild.toolchains.compiler.my_compiler import MyCompiler",
+            "class MyTc(MyCompiler):",
+            "   pass",
+        ])
+        write_file(os.path.join(my_toolchains, 'my_tc.py'), my_tc_txt)
+
+        my_compiler_txt = '\n'.join([
+            "from easybuild.tools.toolchain.compiler import Compiler",
+            "class MyCompiler(Compiler):",
+            "   pass",
+        ])
+        write_file(os.path.join(my_toolchains, 'compiler', 'my_compiler.py'), my_compiler_txt)
+
+        # include custom MNS
+        glob_paths = [os.path.join(my_toolchains, '*.py'), os.path.join(my_toolchains, '*', '*.py')]
+        included_tcs_path = include_toolchains(self.test_prefix, glob_paths)
+
+        expected_paths = ['__init__.py', 'toolchains/__init__.py', 'toolchains/compiler/__init__.py',
+                          'toolchains/my_tc.py', 'toolchains/compiler/my_compiler.py']
+        for filepath in expected_paths:
+            fullpath = os.path.join(included_tcs_path, 'easybuild', filepath)
+            self.assertTrue(os.path.exists(fullpath), "%s exists" % fullpath)
+
+        # path to included MNSs should be prepended to Python search path
+        self.assertEqual(sys.path[0], included_tcs_path)
+
+        # importing custom MNS should work
+        import easybuild.toolchains.my_tc
+        my_tc_pyc_path = easybuild.toolchains.my_tc.__file__
+        my_tc_real_py_path = os.path.realpath(os.path.join(os.path.dirname(my_tc_pyc_path), 'my_tc.py'))
+        self.assertTrue(os.path.samefile(up(my_tc_real_py_path, 1), my_toolchains))
+
+def suite():
+    """ returns all the testcases in this module """
+    return TestLoader().loadTestsFromTestCase(IncludeTest)
+
+if __name__ == '__main__':
+    unittestmain()
diff --git a/test/framework/suite.py b/test/framework/suite.py
index 2b6001221f..5ea7582141 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -66,6 +66,7 @@
 import test.framework.format_convert as f_c
 import test.framework.general as gen
 import test.framework.github as g
+import test.framework.include as i
 import test.framework.license as l
 import test.framework.module_generator as mg
 import test.framework.modules as m
@@ -100,7 +101,7 @@
 
 # call suite() for each module and then run them all
 # note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
-tests = [gen, bl, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p]
+tests = [gen, bl, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p, i]
 
 SUITE = unittest.TestSuite([x.suite() for x in tests])
 

From ba6613132821188ee4496ca6777f023543d8ad32 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 22 Jun 2015 11:25:46 +0200
Subject: [PATCH 1044/1356] don't redefine options.tmpdir, fix broken tests

---
 easybuild/main.py           | 18 +++++++++++-------
 easybuild/tools/options.py  | 16 ++++++++--------
 test/framework/filetools.py |  2 +-
 test/framework/include.py   |  4 ----
 test/framework/utilities.py |  2 ++
 5 files changed, 22 insertions(+), 20 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 74b81d2804..770aa39869 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -38,6 +38,7 @@
 import copy
 import os
 import sys
+import tempfile
 import traceback
 
 # IMPORTANT this has to be the first easybuild import as it customises the logging
@@ -51,7 +52,7 @@
 from easybuild.framework.easyconfig.tools import alt_easyconfig_paths, dep_graph, det_easyconfig_paths
 from easybuild.framework.easyconfig.tools import get_paths_for, parse_easyconfigs, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak
-from easybuild.tools.config import get_repository, get_repositorypath, set_tmpdir
+from easybuild.tools.config import get_repository, get_repositorypath
 from easybuild.tools.filetools import cleanup, write_file
 from easybuild.tools.options import process_software_build_specs
 from easybuild.tools.robot import det_robot_path, dry_run, resolve_dependencies, search_easyconfigs
@@ -163,6 +164,9 @@ def main(testing_data=(None, None, None)):
         new_umask = int(options.umask, 8)
         old_umask = os.umask(new_umask)
 
+    # set by option parsers via set_tmpdir
+    eb_tmpdir = tempfile.gettempdir()
+
     # initialise logging for main
     global _log
     _log, logfile = init_logging(logfile, logtostdout=options.logtostdout, testing=testing)
@@ -174,7 +178,7 @@ def main(testing_data=(None, None, None)):
 
     # log startup info
     eb_cmd_line = eb_go.generate_cmd_line() + eb_go.args
-    log_start(eb_cmd_line, options.tmpdir)
+    log_start(eb_cmd_line, eb_tmpdir)
 
     if options.umask is not None:
         _log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
@@ -186,7 +190,7 @@ def main(testing_data=(None, None, None)):
     # determine robot path
     # --try-X, --dep-graph, --search use robot path for searching, so enable it with path of installed easyconfigs
     tweaked_ecs = try_to_generate and build_specs
-    tweaked_ecs_path, pr_path = alt_easyconfig_paths(options.tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
+    tweaked_ecs_path, pr_path = alt_easyconfig_paths(eb_tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
     auto_robot = try_to_generate or options.dep_graph or options.search or options.search_short
     robot_path = det_robot_path(options.robot_paths, tweaked_ecs_path, pr_path, auto_robot=auto_robot)
     _log.debug("Full robot path: %s" % robot_path)
@@ -263,7 +267,7 @@ def main(testing_data=(None, None, None)):
 
     # cleanup and exit after dry run, searching easyconfigs or submitting regression test
     if any([options.dry_run, options.dry_run_short, options.regtest, options.search, options.search_short]):
-        cleanup(logfile, options.tmpdir, testing)
+        cleanup(logfile, eb_tmpdir, testing)
         sys.exit(0)
 
     # skip modules that are already installed unless forced
@@ -296,7 +300,7 @@ def main(testing_data=(None, None, None)):
         job_info_txt = submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
         if not testing:
             print_msg("Submitted parallel build jobs, exiting now: %s" % job_info_txt)
-            cleanup(logfile, options.tmpdir, testing)
+            cleanup(logfile, eb_tmpdir, testing)
             sys.exit(0)
 
     # build software, will exit when errors occurs (except when testing)
@@ -325,10 +329,10 @@ def main(testing_data=(None, None, None)):
         if 'original_spec' in ec and os.path.isfile(ec['spec']):
             os.remove(ec['spec'])
 
-    # stop logging and cleanup tmp log file, unless one build failed (individual logs are located in options.tmpdir)
+    # stop logging and cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir)
     stop_logging(logfile, logtostdout=options.logtostdout)
     if overall_success:
-        cleanup(logfile, options.tmpdir, testing)
+        cleanup(logfile, eb_tmpdir, testing)
 
 
 if __name__ == "__main__":
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 5e18bf090a..b9c84c4f8d 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -425,10 +425,10 @@ def postprocess(self):
             fancylogger.logToFile(self.options.unittest_file)
 
         # set tmpdir
-        self.options.tmpdir = set_tmpdir(self.options.tmpdir)
+        tmpdir = set_tmpdir(self.options.tmpdir)
 
         # take --include options into account
-        self._postprocess_include()
+        self._postprocess_include(tmpdir)
 
         # prepare for --list/--avail
         if any([self.options.avail_easyconfig_params, self.options.avail_easyconfig_templates,
@@ -498,12 +498,12 @@ def _postprocess_external_modules_metadata(self):
         self.options.external_modules_metadata = parsed_external_modules_metadata
         self.log.debug("External modules metadata: %s", self.options.external_modules_metadata)
 
-    def _postprocess_include(self):
+    def _postprocess_include(self, tmpdir):
         """Postprocess --include options."""
         # set up included easyblocks, module naming schemes and toolchains/toolchain components
-        include_easyblocks(self.options.tmpdir, self.options.include_easyblocks)
-        include_module_naming_schemes(self.options.tmpdir, self.options.include_module_naming_schemes)
-        include_toolchains(self.options.tmpdir, self.options.include_toolchains)
+        include_easyblocks(tmpdir, self.options.include_easyblocks)
+        include_module_naming_schemes(tmpdir, self.options.include_module_naming_schemes)
+        include_toolchains(tmpdir, self.options.include_toolchains)
 
     def _postprocess_config(self):
         """Postprocessing of configuration options"""
@@ -680,8 +680,8 @@ def add_class(classes, cls):
                 mod = classes[root]['module']
                 loc = ''
                 if mod in locations:
-                    loc = '@ %s' % locations[mod]
-                txt.append("%s (%s %s)" % (root, mod, loc))
+                    loc = ' @ %s' % locations[mod]
+                txt.append("%s (%s%s)" % (root, mod, loc))
             else:
                 txt.append("%s" % root)
             if 'children' in classes[root]:
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index a6545454f6..afedd291aa 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -343,7 +343,7 @@ def test_move_logs(self):
         logs = ['bar.log', 'bar.log.1', 'bar.log_0', 'bar.log_1',
                 os.path.basename(self.logfile),
                 'foo.log', 'foo.log.1']
-        self.assertEqual(sorted([f for f in os.listdir(self.test_prefix) if not f.startswith('tmp')]), logs)
+        self.assertEqual(sorted([f for f in os.listdir(self.test_prefix) if 'log' in f]), logs)
         self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log_0')), 'bar')
         self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log_1')), 'barbar')
         self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log')), 'moarbar')
diff --git a/test/framework/include.py b/test/framework/include.py
index 07b6d3bfc7..d02551b1f6 100644
--- a/test/framework/include.py
+++ b/test/framework/include.py
@@ -49,10 +49,6 @@ class IncludeTest(EnhancedTestCase):
 
     logfile = None
 
-    def tearDown(self):
-        # FIXME avoid cleanup
-        pass
-
     def test_include_easyblocks(self):
         """Test include_easyblocks()."""
         test_easyblocks = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox', 'easybuild', 'easyblocks')
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 0c209f501d..5e6e204e9e 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -312,6 +312,8 @@ def cleanup():
     easyconfig._easyconfig_files_cache.clear()
     mns_toolchain._toolchain_details_cache.clear()
 
+    # reset to make sure tempfile picks up new temporary directory to use
+    tempfile.tempdir = None
 
 def init_config(args=None, build_options=None):
     """(re)initialize configuration"""

From b2bd260a6f82b5dac62ff8c91d6c6752f40db971 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 22 Jun 2015 18:38:14 +0200
Subject: [PATCH 1045/1356] only set up include symlinks if something to
 include has been specified

---
 easybuild/tools/options.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index b9c84c4f8d..bbc256eafe 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -501,9 +501,14 @@ def _postprocess_external_modules_metadata(self):
     def _postprocess_include(self, tmpdir):
         """Postprocess --include options."""
         # set up included easyblocks, module naming schemes and toolchains/toolchain components
-        include_easyblocks(tmpdir, self.options.include_easyblocks)
-        include_module_naming_schemes(tmpdir, self.options.include_module_naming_schemes)
-        include_toolchains(tmpdir, self.options.include_toolchains)
+        if self.options.include_easyblocks:
+            include_easyblocks(tmpdir, self.options.include_easyblocks)
+
+        if self.options.include_module_naming_schemes:
+            include_module_naming_schemes(tmpdir, self.options.include_module_naming_schemes)
+
+        if self.options.include_toolchains:
+            include_toolchains(tmpdir, self.options.include_toolchains)
 
     def _postprocess_config(self):
         """Postprocessing of configuration options"""

From 598cb157f5c8f4c8f3255e3f1870a5bccc36a93b Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Mon, 22 Jun 2015 22:38:38 -0400
Subject: [PATCH 1046/1356] fix error message, add release option, bug fixes

---
 easybuild/framework/easyblock.py                 |  2 +-
 easybuild/tools/config.py                        |  1 +
 easybuild/tools/options.py                       |  1 +
 .../packaging_naming_scheme/easybuild_pns.py     | 16 ++++------------
 .../tools/package/packaging_naming_scheme/pns.py |  8 +++++---
 easybuild/tools/package/utilities.py             |  1 +
 6 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 6962c929e8..3c88e9121f 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1514,7 +1514,7 @@ def package_step(self):
                 src_filename = os.path.basename(src_file)
                 dest_file = os.path.join(packagedir_dest, src_filename)
                 if os.path.exists(dest_file) and not opt_force:
-                    raise EasyBuildError("Unable to copy file, dest already exists. Look in src for packages dest: %s src: %s ", dest_file, src_file)
+                    raise EasyBuildError("Unable to copy package: %s as it already exists in %s. Your package should still be in %s", src_filename, dest_file, packagedir_src)
                 else:
                     shutil.copy(src_file, packagedir_dest)
         else:
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 31cac9add6..62a5ce0fcd 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -97,6 +97,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'optarch',
         'package_tool',
         'package_type',
+        'package_release',
         'regtest_output_dir',
         'skip',
         'stop',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 117bf054e3..79eb82ac64 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -362,6 +362,7 @@ def package_options(self):
             'package': ("Enabling packaging", None, 'store_true', False),
             'package-tool': ("Packaging tool to use", None, 'store_or_None', None),
             'package-type': ("Packaging type to output to", None, 'store_or_None', None),
+            'package-release': ("Package release iteration number", None, 'store', "1"),
         })
 
         self.log.debug("package_options: descr %s opts %s" % (descr, opts))
diff --git a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
index b6dd702528..855c831a51 100644
--- a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
+++ b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
@@ -17,28 +17,20 @@ class EasyBuildPNS(PackagingNamingScheme):
     REQUIRED_KEYS = ['name', 'version', 'versionsuffix', 'toolchain']
 
     def name(self, ec):
+        self.log.debug("easyconfig dict for name looks like %s " % ec )
         name_template = "eb-%(name)s-%(version)s-%(toolchain)s"
         pkg_name = name_template % {
             'toolchain' : self._toolchain(ec),
             'version': '-'.join([x for x in [ec.get('versionprefix', ''), ec['version'], ec['versionsuffix'].lstrip('-')] if x]),
-            'name' : ec.name,
+            'name' : ec['name'],
         }
         return pkg_name
 
     def _toolchain(self, ec):
         toolchain_template = "%(toolchain_name)s-%(toolchain_version)s"
         pkg_toolchain = toolchain_template % {
-            'toolchain_name': ec.toolchain.name,
-            'toolchain_version': ec.toolchain.version,
+            'toolchain_name': ec['toolchain']['name'],
+            'toolchain_version': ec['toolchain']['version'],
         }
         return pkg_toolchain
 
-
-    def version(self, ec):
-        return ec['version']
-
-        
-
-    def release(self):
-        return 1
-
diff --git a/easybuild/tools/package/packaging_naming_scheme/pns.py b/easybuild/tools/package/packaging_naming_scheme/pns.py
index 9d60949b6f..3062682ab1 100644
--- a/easybuild/tools/package/packaging_naming_scheme/pns.py
+++ b/easybuild/tools/package/packaging_naming_scheme/pns.py
@@ -1,5 +1,6 @@
 
 from vsc.utils import fancylogger
+from easybuild.tools.config import build_option
 
 options = [ "package-naming-name-template", "package-naming-version-template", "package-naming-toolchain-template" ]
 
@@ -13,13 +14,14 @@ def __init__(self, *args, **kwargs):
 
     def name(self,ec):
         """Return name of the package, by default would include name, version, toolchain"""
-
+        raise NotImplementedError
         
     def version(self,ec):
         """The version in the version part of the package"""
+        return ec['version']    
 
-    def release(self,ec):
+    def release(self,ec=None):
         """Just the release"""
-        return 1
+        return build_option('package_release')
 
 
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index 1df0382a53..ccaef6bd38 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -96,6 +96,7 @@ def package_fpm(easyblock, modfile_path, package_type="rpm" ):
         '-t', package_type, # target
         '-s', 'dir', # source
         '--version', pkgver,
+        '--iteration', pkgrel,
     ]
     cmdlist.extend([ depstring ])
     cmdlist.extend([

From 0fac3673945e2444a1abb88f2104691a57489603 Mon Sep 17 00:00:00 2001
From: Robert Schmidt <rjeschmi@gmail.com>
Date: Mon, 22 Jun 2015 22:50:49 -0400
Subject: [PATCH 1047/1356] add eb version to default name

---
 .../tools/package/packaging_naming_scheme/easybuild_pns.py     | 3 ++-
 easybuild/tools/package/packaging_naming_scheme/pns.py         | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
index 855c831a51..1dae429657 100644
--- a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
+++ b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
@@ -18,11 +18,12 @@ class EasyBuildPNS(PackagingNamingScheme):
 
     def name(self, ec):
         self.log.debug("easyconfig dict for name looks like %s " % ec )
-        name_template = "eb-%(name)s-%(version)s-%(toolchain)s"
+        name_template = "eb%(eb_ver)s-%(name)s-%(version)s-%(toolchain)s"
         pkg_name = name_template % {
             'toolchain' : self._toolchain(ec),
             'version': '-'.join([x for x in [ec.get('versionprefix', ''), ec['version'], ec['versionsuffix'].lstrip('-')] if x]),
             'name' : ec['name'],
+            'eb_ver': self.eb_ver,
         }
         return pkg_name
 
diff --git a/easybuild/tools/package/packaging_naming_scheme/pns.py b/easybuild/tools/package/packaging_naming_scheme/pns.py
index 3062682ab1..408a1b6904 100644
--- a/easybuild/tools/package/packaging_naming_scheme/pns.py
+++ b/easybuild/tools/package/packaging_naming_scheme/pns.py
@@ -1,7 +1,7 @@
 
 from vsc.utils import fancylogger
 from easybuild.tools.config import build_option
-
+from easybuild.tools.version import VERSION as EASYBUILD_VERSION
 options = [ "package-naming-name-template", "package-naming-version-template", "package-naming-toolchain-template" ]
 
 class PackagingNamingScheme(object):
@@ -11,6 +11,7 @@ class PackagingNamingScheme(object):
     def __init__(self, *args, **kwargs):
         """initialize logger."""
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
+        self.eb_ver = EASYBUILD_VERSION
 
     def name(self,ec):
         """Return name of the package, by default would include name, version, toolchain"""

From 084f8282abed18866f6d033b9729129d805e0c2a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 24 Jun 2015 11:00:03 +0200
Subject: [PATCH 1048/1356] promote MigrateFromEBToHMNS to a 'production' MNS

---
 .../tools/module_naming_scheme/migrate_from_eb_to_hmns.py       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename {test/framework/sandbox/easybuild => easybuild}/tools/module_naming_scheme/migrate_from_eb_to_hmns.py (93%)

diff --git a/test/framework/sandbox/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py b/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
similarity index 93%
rename from test/framework/sandbox/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
rename to easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
index 13c1634b3d..747303d9c5 100644
--- a/test/framework/sandbox/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
+++ b/easybuild/tools/module_naming_scheme/migrate_from_eb_to_hmns.py
@@ -23,7 +23,7 @@
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
 """
-Implementation of a test module naming scheme that can be used to migrate from EasyBuildMNS to HierarchicalMNS.
+Implementation of a module naming scheme that can be used to migrate from EasyBuildMNS to HierarchicalMNS.
 
 @author: Kenneth Hoste (Ghent University)
 """

From e4c6e508711131859a835d6934c13863305764d1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 24 Jun 2015 21:44:21 +0200
Subject: [PATCH 1049/1356] improve error missing on missing Python modules for
 job backend

---
 easybuild/tools/job/gc3pie.py     | 2 +-
 easybuild/tools/job/pbs_python.py | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index a337b260e9..96363398e6 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -70,7 +70,7 @@ def gc3pie_imported(_):
         """Decorator which raises an EasyBuildError because GC3Pie is not available."""
         def fail(*args, **kwargs):
             """Raise EasyBuildError since GC3Pie is not available."""
-            errmsg = "gc3libs not available. Please make sure GC3Pie is installed and usable: %s"
+            errmsg = "Python modules 'gc3libs' is not available. Please make sure GC3Pie is installed and usable: %s"
             raise EasyBuildError(errmsg, err)
 
         return fail
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index af46356a7b..da1eae5530 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -67,7 +67,8 @@ def pbs_python_imported(_):
         """Decorator which raises an EasyBuildError because pbs_python is not available."""
         def fail(*args, **kwargs):
             """Raise EasyBuildError since `pbs_python` is not available."""
-            errmsg = "PBSQuery or pbs modules not available. Please make sure `pbs_python` is installed and usable: %s"
+            errmsg = "Python modules 'PBSQuery' and 'pbs' are not available. "
+            errmsg += "Please make sure `pbs_python` is installed and usable: %s"
             raise EasyBuildError(errmsg, err)
 
         return fail

From c0195f78ddfe9429bfe6292d53ad5b5cae24a908 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 24 Jun 2015 21:59:21 +0200
Subject: [PATCH 1050/1356] fix wrong build option: job_output_dir

---
 easybuild/tools/job/pbs_python.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index da1eae5530..93f3c47ed5 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -266,7 +266,7 @@ def _submit(self):
         pbs_attributes[0].name = pbs.ATTR_N  # Job_Name
         pbs_attributes[0].value = self.name
 
-        output_dir = build_option('output_dir')
+        output_dir = build_option('job_output_dir')
         pbs_attributes[1].name = pbs.ATTR_o
         pbs_attributes[1].value = os.path.join(output_dir, '%s.o$PBS_JOBID' % self.name)
 

From c56c34d6e597667f133d530dd602c81564d89ab3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 25 Jun 2015 21:09:51 +0200
Subject: [PATCH 1051/1356] catch errors when creating GC3Pie engine

---
 easybuild/tools/job/gc3pie.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 96363398e6..7b6cd2616c 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -46,6 +46,7 @@
 
 try:
     import gc3libs
+    import gc3libs.exceptions
     from gc3libs import Application, Run, create_engine
     from gc3libs.core import Engine
     from gc3libs.quantity import hours as hr
@@ -219,7 +220,11 @@ def complete(self):
         Create engine, and progress it until all jobs have terminated.
         """
         # create an instance of `Engine` using the list of configuration files
-        self._engine = create_engine(*self.config_files)
+        try:
+            self._engine = create_engine(*self.config_files)
+
+        except gc3libs.exceptions.Error as err:
+            raise EasyBuildError("Failed to create GC3Pie engine: %s", err)
 
         # Add your application to the engine. This will NOT submit
         # your application yet, but will make the engine *aware* of

From 3a3a90f76e6dcd0a0e44dfe24c6996bf2ba91bb8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 25 Jun 2015 21:28:53 +0200
Subject: [PATCH 1052/1356] add --job-cores option (WIP)

---
 easybuild/tools/config.py     | 1 +
 easybuild/tools/job/gc3pie.py | 6 +++++-
 easybuild/tools/options.py    | 1 +
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index b6bb7c910f..a68d56a908 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -94,6 +94,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'group',
         'ignore_dirs',
         'job_backend_config',
+        'job_cores',
         'job_max_walltime',
         'job_output_dir',
         'job_polling_interval',
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 7b6cd2616c..b80dd448ae 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -189,7 +189,7 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
             'stdout': 'eb-%s-gc3pie-job.log' % name,
         })
 
-        # resources
+        # walltime
         max_walltime = build_option('job_max_walltime')
         if hours is None:
             hours = max_walltime
@@ -200,6 +200,10 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
 
         if cores:
             named_args['requested_cores'] = cores
+        elif build_option('job_cores'):
+            named_args['requested_cores'] = build_option('job_cores')
+        else:
+            # FIXME: ask GC3Pie to guess core count per node (see _get_ppn in job/pbs_python.py)
 
         return Application(['/bin/sh', '-c', script], **named_args)
 
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ea0f375268..6cdbb953ed 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -363,6 +363,7 @@ def job_options(self):
 
         opts = OrderedDict({
             'backend-config': ("Configuration file for job backend", None, 'store', None),
+            'cores': ("Number of cores to request per job", None, 'int', 'store', None),
             'max-walltime': ("Maximum walltime for jobs (in hours)", 'int', 'store', 24),
             'output-dir': ("Output directory for jobs (default: current directory)", None, 'store', os.getcwd()),
             'polling-interval': ("Interval between polls for status of jobs (in seconds)", float, 'store', 30.0),

From 3504714c3364c11df2d0635689634e1a08a02f5a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 26 Jun 2015 10:23:41 +0200
Subject: [PATCH 1053/1356] add --read-only-installdir and
 --group-writeable-installdir configuration options

---
 easybuild/framework/easyblock.py | 11 ++++++++---
 easybuild/tools/config.py        | 12 ++----------
 easybuild/tools/options.py       |  4 ++++
 3 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index b2828a6d41..cd82d9d28f 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -59,7 +59,7 @@
 from easybuild.tools.build_details import get_build_stats
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
-from easybuild.tools.config import install_path, log_path, read_only_installdir, source_paths
+from easybuild.tools.config import install_path, log_path, source_paths
 from easybuild.tools.environment import restore_env
 from easybuild.tools.filetools import DEFAULT_CHECKSUM
 from easybuild.tools.filetools import adjust_permissions, apply_patch, convert_name, download_file, encode_class_name
@@ -1519,13 +1519,18 @@ def post_install_step(self):
                 raise EasyBuildError("Unable to change group permissions of file(s): %s", err)
             self.log.info("Successfully made software only available for group %s (gid %s)" % self.group)
 
-        if read_only_installdir():
+        if build_option('read_only_installdir'):
             # remove write permissions for everyone
             perms = stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH
             adjust_permissions(self.installdir, perms, add=False, recursive=True, relative=True, ignore_errors=True)
             self.log.info("Successfully removed write permissions recursively for *EVERYONE* on install dir.")
+        elif build_option('group_writable_installdir'):
+            # enable write permissions for group
+            perms = stat.S_IWGRP
+            adjust_permissions(self.installdir, perms, add=True, recursive=True, relative=True, ignore_errors=True)
+            self.log.info("Successfully enabled write permissions recursively for group on install dir.")
         else:
-            # remove write permissions for group and other to protect installation
+            # remove write permissions for group and other
             perms = stat.S_IWGRP | stat.S_IWOTH
             adjust_permissions(self.installdir, perms, add=False, recursive=True, relative=True, ignore_errors=True)
             self.log.info("Successfully removed write permissions recursively for group/other on install dir.")
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 976bc3e7e5..2a6c34e7d0 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -108,8 +108,10 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'debug',
         'experimental',
         'force',
+        'group_writable_installdir',
         'hidden',
         'module_only',
+        'read_only_installdir',
         'robot',
         'sequential',
         'set_gid_bit',
@@ -448,16 +450,6 @@ def get_log_filename(name, version, add_salt=False):
     return filepath
 
 
-def read_only_installdir():
-    """
-    Return whether installation dir should be fully read-only after installation.
-    """
-    # FIXME (see issue #123): add a config option to set this, should be True by default (?)
-    # this also needs to be checked when --force is used;
-    # install dir will have to (temporarily) be made writeable again for owner in that case
-    return False
-
-
 def module_classes():
     """
     Return list of module classes specified in config file.
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index ebb1a3ef1e..71585b00ae 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -199,6 +199,8 @@ def override_options(self):
             'experimental': ("Allow experimental code (with behaviour that can be changed/removed at any given time).",
                              None, 'store_true', False),
             'group': ("Group to be used for software installations (only verified, not set)", None, 'store', None),
+            'group-writable-installdir': ("Enable group write permissions on installation directory after installation",
+                                          None, 'store_true', False),
             'hidden': ("Install 'hidden' module file(s) by prefixing their name with '.'", None, 'store_true', False),
             'ignore-osdeps': ("Ignore any listed OS dependencies", None, 'store_true', False),
             'filter-deps': ("Comma separated list of dependencies that you DON'T want to install with EasyBuild, "
@@ -212,6 +214,8 @@ def override_options(self):
                         None, 'store', None),
             'pretend': (("Does the build/installation in a test directory located in $HOME/easybuildinstall"),
                         None, 'store_true', False, 'p'),
+            'read-only-installdir': ("Set read-only permissions on installation directory after installation",
+                                     None, 'store_true', False),
             'set-gid-bit': ("Set group ID bit on newly created directories", None, 'store_true', False),
             'sticky-bit': ("Set sticky bit on newly created directories", None, 'store_true', False),
             'skip-test-cases': ("Skip running test cases", None, 'store_true', False, 't'),

From 9d9bd3ddf4e5046875021d5f3a00f1eece0ef7ce Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 26 Jun 2015 15:41:37 +0200
Subject: [PATCH 1054/1356] reorganize test easyblocks to mimic
 easybuild-easyblocks setup

---
 .../sandbox/easybuild/easyblocks/__init__.py         | 12 ++++++++++--
 .../sandbox/easybuild/easyblocks/f/__init__.py       |  0
 .../sandbox/easybuild/easyblocks/{ => f}/foo.py      |  0
 .../sandbox/easybuild/easyblocks/{ => f}/foofoo.py   |  0
 .../sandbox/easybuild/easyblocks/h/__init__.py       |  0
 .../sandbox/easybuild/easyblocks/{ => h}/hpl.py      |  0
 .../sandbox/easybuild/easyblocks/s/__init__.py       |  0
 .../easybuild/easyblocks/{ => s}/scalapack.py        |  0
 .../sandbox/easybuild/easyblocks/t/__init__.py       |  0
 .../sandbox/easybuild/easyblocks/{ => t}/toy.py      |  0
 .../easybuild/easyblocks/{ => t}/toy_buggy.py        |  0
 11 files changed, 10 insertions(+), 2 deletions(-)
 create mode 100644 test/framework/sandbox/easybuild/easyblocks/f/__init__.py
 rename test/framework/sandbox/easybuild/easyblocks/{ => f}/foo.py (100%)
 rename test/framework/sandbox/easybuild/easyblocks/{ => f}/foofoo.py (100%)
 create mode 100644 test/framework/sandbox/easybuild/easyblocks/h/__init__.py
 rename test/framework/sandbox/easybuild/easyblocks/{ => h}/hpl.py (100%)
 create mode 100644 test/framework/sandbox/easybuild/easyblocks/s/__init__.py
 rename test/framework/sandbox/easybuild/easyblocks/{ => s}/scalapack.py (100%)
 create mode 100644 test/framework/sandbox/easybuild/easyblocks/t/__init__.py
 rename test/framework/sandbox/easybuild/easyblocks/{ => t}/toy.py (100%)
 rename test/framework/sandbox/easybuild/easyblocks/{ => t}/toy_buggy.py (100%)

diff --git a/test/framework/sandbox/easybuild/easyblocks/__init__.py b/test/framework/sandbox/easybuild/easyblocks/__init__.py
index 5b5529273b..a2bc4d6715 100644
--- a/test/framework/sandbox/easybuild/easyblocks/__init__.py
+++ b/test/framework/sandbox/easybuild/easyblocks/__init__.py
@@ -1,4 +1,12 @@
 from pkgutil import extend_path
 
-# we're not the only ones in this namespace
-__path__ = extend_path(__path__, __name__)  #@ReservedAssignment
+# Extend path so python finds our easyblocks in the subdirectories where they are located
+subdirs = [chr(l) for l in range(ord('a'), ord('z') + 1)] + ['0']
+for subdir in subdirs:
+    __path__ = extend_path(__path__, '%s.%s' % (__name__, subdir))
+
+# And let python know this is not the only place to look for them, so we can have multiple
+# easybuild/easyblock paths in your python search path, next to the official easyblocks distribution
+__path__ = extend_path(__path__, __name__)  # @ReservedAssignment
+
+del subdir, subdirs, l
diff --git a/test/framework/sandbox/easybuild/easyblocks/f/__init__.py b/test/framework/sandbox/easybuild/easyblocks/f/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/framework/sandbox/easybuild/easyblocks/foo.py b/test/framework/sandbox/easybuild/easyblocks/f/foo.py
similarity index 100%
rename from test/framework/sandbox/easybuild/easyblocks/foo.py
rename to test/framework/sandbox/easybuild/easyblocks/f/foo.py
diff --git a/test/framework/sandbox/easybuild/easyblocks/foofoo.py b/test/framework/sandbox/easybuild/easyblocks/f/foofoo.py
similarity index 100%
rename from test/framework/sandbox/easybuild/easyblocks/foofoo.py
rename to test/framework/sandbox/easybuild/easyblocks/f/foofoo.py
diff --git a/test/framework/sandbox/easybuild/easyblocks/h/__init__.py b/test/framework/sandbox/easybuild/easyblocks/h/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/framework/sandbox/easybuild/easyblocks/hpl.py b/test/framework/sandbox/easybuild/easyblocks/h/hpl.py
similarity index 100%
rename from test/framework/sandbox/easybuild/easyblocks/hpl.py
rename to test/framework/sandbox/easybuild/easyblocks/h/hpl.py
diff --git a/test/framework/sandbox/easybuild/easyblocks/s/__init__.py b/test/framework/sandbox/easybuild/easyblocks/s/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/framework/sandbox/easybuild/easyblocks/scalapack.py b/test/framework/sandbox/easybuild/easyblocks/s/scalapack.py
similarity index 100%
rename from test/framework/sandbox/easybuild/easyblocks/scalapack.py
rename to test/framework/sandbox/easybuild/easyblocks/s/scalapack.py
diff --git a/test/framework/sandbox/easybuild/easyblocks/t/__init__.py b/test/framework/sandbox/easybuild/easyblocks/t/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/test/framework/sandbox/easybuild/easyblocks/toy.py b/test/framework/sandbox/easybuild/easyblocks/t/toy.py
similarity index 100%
rename from test/framework/sandbox/easybuild/easyblocks/toy.py
rename to test/framework/sandbox/easybuild/easyblocks/t/toy.py
diff --git a/test/framework/sandbox/easybuild/easyblocks/toy_buggy.py b/test/framework/sandbox/easybuild/easyblocks/t/toy_buggy.py
similarity index 100%
rename from test/framework/sandbox/easybuild/easyblocks/toy_buggy.py
rename to test/framework/sandbox/easybuild/easyblocks/t/toy_buggy.py

From 2616f461868efbe027c01082e91ab382cd7d862f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 27 Jun 2015 20:57:44 +0200
Subject: [PATCH 1055/1356] fix remarks + enhance and extend unit tests, to
 also cover --include-* options

---
 easybuild/tools/filetools.py |  20 ++++-
 easybuild/tools/include.py   |  82 +++++++++++--------
 easybuild/tools/options.py   |  26 +++---
 test/framework/easyblock.py  |   2 +-
 test/framework/include.py    |   5 +-
 test/framework/options.py    | 149 +++++++++++++++++++++++++++++++----
 6 files changed, 221 insertions(+), 63 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index f073381f48..99dfb1a317 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -43,8 +43,8 @@
 import urllib2
 import zlib
 from vsc.utils import fancylogger
+from vsc.utils.missing import nub
 
-import easybuild.tools.environment as env
 from easybuild.tools.build_log import EasyBuildError, print_msg  # import build_log must stay, to use of EasyBuildLog
 from easybuild.tools.config import build_option
 from easybuild.tools import run
@@ -851,6 +851,24 @@ def mkdir(path, parents=False, set_gid=None, sticky=None):
         _log.debug("Not creating existing path %s" % path)
 
 
+def expand_glob_paths(glob_paths):
+    """Expand specified glob paths to a list of unique non-glob paths to only files."""
+    paths = []
+    for glob_path in glob_paths:
+        paths.extend([f for f in glob.glob(glob_path) if os.path.isfile(f)])
+
+    return nub(paths)
+
+
+def symlink(source_path, symlink_path):
+    """Create a symlink at the specified path to the given path."""
+    try:
+        os.symlink(os.path.abspath(source_path), symlink_path)
+        _log.info("Symlinked %s to %s", source_path, symlink_path)
+    except OSError as err:
+        raise EasyBuildError("Symlinking %s to %s failed: %s", source_path, symlink_path, err)
+
+
 def path_matches(path, paths):
     """Check whether given path matches any of the provided paths."""
     if not os.path.exists(path):
diff --git a/easybuild/tools/include.py b/easybuild/tools/include.py
index af857ec175..f2e6f875bb 100644
--- a/easybuild/tools/include.py
+++ b/easybuild/tools/include.py
@@ -28,13 +28,12 @@
 
 @author: Kenneth Hoste (Ghent University)
 """
-import glob
 import os
 import sys
-from vsc.utils.missing import nub
 from vsc.utils import fancylogger
 
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import expand_glob_paths, symlink
 # these are imported just to we can reload them later
 import easybuild.tools.module_naming_scheme
 import easybuild.toolchains
@@ -54,12 +53,34 @@
 _log = fancylogger.getLogger('tools.include', fname=False)
 
 
+# body for __init__.py file in package directory, which takes care of making sure the package can be distributed
+# across multiple directories
 PKG_INIT_BODY = """
 from pkgutil import extend_path
+
+# extend path so Python knows this is not the only place to look for modules in this package
 __path__ = extend_path(__path__, __name__)
 """
 
-def create_pkg(path):
+# more extensive __init__.py specific to easybuild.easyblocks package;
+# this is required because of the way in which the easyblock Python modules are organised in the easybuild-easyblocks
+# repository, i.e. in first-letter subdirectories
+EASYBLOCKS_PKG_INIT_BODY = """
+from pkgutil import extend_path
+
+# extend path so Python finds our easyblocks in the subdirectories where they are located
+subdirs = [chr(l) for l in range(ord('a'), ord('z') + 1)] + ['0']
+for subdir in subdirs:
+    __path__ = extend_path(__path__, '%s.%s' % (__name__, subdir))
+
+# extend path so Python knows this is not the only place to look for modules in this package
+__path__ = extend_path(__path__, __name__)
+
+del subdir, subdirs, l
+"""
+
+
+def create_pkg(path, pkg_init_body=None):
     """Write package __init__.py file at specified path."""
     init_path = os.path.join(path, '__init__.py')
     try:
@@ -69,15 +90,25 @@ def create_pkg(path):
 
         # put __init__.py files in place, with required pkgutil.extend_path statement
         # note: can't use write_file, since that required build options to be initialised
-        handle = open(init_path, 'w')
-        handle.write(PKG_INIT_BODY)
-        handle.close()
+        with open(init_path, 'w') as handle:
+            if pkg_init_body is None:
+                handle.write(PKG_INIT_BODY)
+            else:
+                handle.write(pkg_init_body)
+
     except (IOError, OSError) as err:
-        raise EasyBuildError("Failed to write %s: %s", init_path, err)
+        raise EasyBuildError("Failed to create package at %s: %s", path, err)
+
 
+def set_up_eb_package(parent_path, eb_pkg_name, subpkgs=None, pkg_init_body=None):
+    """
+    Set up new easybuild subnamespace in specified path.
 
-def set_up_eb_package(parent_path, eb_pkg_name, subpkgs=None):
-    """Set up new easybuild subnamespace in specified path."""
+    @param parent_path: directory to create package in, using 'easybuild' namespace
+    @param eb_pkg_name: full package name, must start with 'easybuild'
+    @param subpkgs: list of subpackages to create
+    @parak pkg_init_body: body of package's __init__.py file (does not apply to subpackages)
+    """
     if not eb_pkg_name.startswith('easybuild'):
         raise EasyBuildError("Specified EasyBuild package name does not start with 'easybuild': %s", eb_pkg_name)
 
@@ -90,33 +121,16 @@ def set_up_eb_package(parent_path, eb_pkg_name, subpkgs=None):
 
     # creata package dirs on each level
     while pkgpath != parent_path:
-        create_pkg(pkgpath)
+        create_pkg(pkgpath, pkg_init_body=pkg_init_body)
         pkgpath = os.path.dirname(pkgpath)
 
 
-def expand_glob_paths(glob_paths):
-    """Expand specified glob paths to a list of unique non-glob paths to only files."""
-    paths = []
-    for glob_path in glob_paths:
-        paths.extend([f for f in glob.glob(glob_path) if os.path.isfile(f)])
-
-    return nub(paths)
-
-
-def safe_symlink(source_path, symlink_path):
-    """Create a symlink at the specified path for the given path."""
-    try:
-        os.symlink(os.path.abspath(source_path), symlink_path)
-        _log.info("Symlinked %s to %s", source_path, symlink_path)
-    except OSError as err:
-        raise EasyBuildError("Symlinking %s to %s failed: %s", source_path, symlink_path, err)
-
-
 def include_easyblocks(tmpdir, paths):
     """Include generic and software-specific easyblocks found in specified locations."""
     easyblocks_path = os.path.join(tmpdir, 'included-easyblocks')
 
-    set_up_eb_package(easyblocks_path, 'easybuild.easyblocks', subpkgs=['generic'])
+    set_up_eb_package(easyblocks_path, 'easybuild.easyblocks',
+                      subpkgs=['generic'], pkg_init_body=EASYBLOCKS_PKG_INIT_BODY)
 
     easyblocks_dir = os.path.join(easyblocks_path, 'easybuild', 'easyblocks')
 
@@ -131,12 +145,12 @@ def include_easyblocks(tmpdir, paths):
         else:
             target_path = os.path.join(easyblocks_dir, filename)
 
-        safe_symlink(easyblock_module, target_path)
+        symlink(easyblock_module, target_path)
 
     included_easyblocks = [x for x in os.listdir(easyblocks_dir) if x not in ['__init__.py', 'generic']]
     included_generic_easyblocks = [x for x in os.listdir(os.path.join(easyblocks_dir, 'generic')) if x != '__init__.py']
-    _log.debug("Included generic easyblocks: %s", included_easyblocks)
-    _log.debug("Included software-specific easyblocks: %s", included_generic_easyblocks)
+    _log.debug("Included generic easyblocks: %s", included_generic_easyblocks)
+    _log.debug("Included software-specific easyblocks: %s", included_easyblocks)
 
     # inject path into Python search path, and reload modules to get it 'registered' in sys.modules
     sys.path.insert(0, easyblocks_path)
@@ -160,7 +174,7 @@ def include_module_naming_schemes(tmpdir, paths):
     for mns_module in allpaths:
         filename = os.path.basename(mns_module)
         target_path = os.path.join(mns_dir, filename)
-        safe_symlink(mns_module, target_path)
+        symlink(mns_module, target_path)
 
     included_mns = [x for x in os.listdir(mns_dir) if x not in ['__init__.py']]
     _log.debug("Included module naming schemes: %s", included_mns)
@@ -193,7 +207,7 @@ def include_toolchains(tmpdir, paths):
         else:
             target_path = os.path.join(toolchains_dir, filename)
 
-        safe_symlink(toolchain_module, target_path)
+        symlink(toolchain_module, target_path)
 
     included_toolchains = [x for x in os.listdir(toolchains_dir) if x not in ['__init__.py'] + toolchain_subpkgs]
     _log.debug("Included toolchains: %s", included_toolchains)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index bbc256eafe..2cef64f5a6 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -425,10 +425,10 @@ def postprocess(self):
             fancylogger.logToFile(self.options.unittest_file)
 
         # set tmpdir
-        tmpdir = set_tmpdir(self.options.tmpdir)
+        self.tmpdir = set_tmpdir(self.options.tmpdir)
 
         # take --include options into account
-        self._postprocess_include(tmpdir)
+        self._postprocess_include()
 
         # prepare for --list/--avail
         if any([self.options.avail_easyconfig_params, self.options.avail_easyconfig_templates,
@@ -498,17 +498,17 @@ def _postprocess_external_modules_metadata(self):
         self.options.external_modules_metadata = parsed_external_modules_metadata
         self.log.debug("External modules metadata: %s", self.options.external_modules_metadata)
 
-    def _postprocess_include(self, tmpdir):
+    def _postprocess_include(self):
         """Postprocess --include options."""
         # set up included easyblocks, module naming schemes and toolchains/toolchain components
         if self.options.include_easyblocks:
-            include_easyblocks(tmpdir, self.options.include_easyblocks)
+            include_easyblocks(self.tmpdir, self.options.include_easyblocks)
 
         if self.options.include_module_naming_schemes:
-            include_module_naming_schemes(tmpdir, self.options.include_module_naming_schemes)
+            include_module_naming_schemes(self.tmpdir, self.options.include_module_naming_schemes)
 
         if self.options.include_toolchains:
-            include_toolchains(tmpdir, self.options.include_toolchains)
+            include_toolchains(self.tmpdir, self.options.include_toolchains)
 
     def _postprocess_config(self):
         """Postprocessing of configuration options"""
@@ -596,9 +596,9 @@ def _postprocess_list_avail(self):
 
         # cleanup tmpdir
         try:
-            shutil.rmtree(self.options.tmpdir)
+            shutil.rmtree(self.tmpdir)
         except OSError as err:
-            raise EasyBuildError("Failed to clean up temporary directory %s: %s", self.options.tmpdir, err)
+            raise EasyBuildError("Failed to clean up temporary directory %s: %s", self.tmpdir, err)
 
         sys.exit(0)
 
@@ -658,8 +658,12 @@ def avail_easyblocks(self):
                         res = module_regexp.match(f)
                         if res:
                             easyblock = '%s.%s' % (package, res.group(1))
-                            __import__(easyblock)
-                            locations.update({easyblock: os.path.join(path, f)})
+                            if easyblock not in locations:
+                                __import__(easyblock)
+                                locations.update({easyblock: os.path.join(path, f)})
+                            else:
+                                self.log.debug("%s already imported from %s, ignoring %s",
+                                               easyblock, locations[easyblock], path)
 
         def add_class(classes, cls):
             """Add a new class, and all of its subclasses."""
@@ -693,7 +697,7 @@ def add_class(classes, cls):
                 txt.extend(self.avail_classes_tree(classes, classes[root]['children'], locations, detailed))
                 txt.append("")
 
-        return "\n".join(txt)
+        return '\n'.join(txt)
 
     def avail_toolchains(self):
         """Show list of known toolchains."""
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 98fb54d10f..5382068066 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -434,7 +434,7 @@ def test_get_easyblock_instance(self):
         self.assertTrue(isinstance(eb, EB_toy))
 
         # check whether 'This is easyblock' log message is there
-        tup = ('EB_toy', 'easybuild.easyblocks.toy', '.*test/framework/sandbox/easybuild/easyblocks/toy.pyc*')
+        tup = ('EB_toy', 'easybuild.easyblocks.toy', '.*test/framework/sandbox/easybuild/easyblocks/t/toy.pyc*')
         eb_log_msg_re = re.compile(r"INFO This is easyblock %s from module %s (%s)" % tup, re.M)
         logtxt = read_file(eb.logfile)
         self.assertTrue(eb_log_msg_re.search(logtxt), "Pattern '%s' found in: %s" % (eb_log_msg_re.pattern, logtxt))
diff --git a/test/framework/include.py b/test/framework/include.py
index d02551b1f6..28b4ed7e29 100644
--- a/test/framework/include.py
+++ b/test/framework/include.py
@@ -97,7 +97,7 @@ def test_include_easyblocks(self):
 
         # existing (test) easyblocks are unaffected
         import easybuild.easyblocks.foofoo
-        foofoo_path = os.path.dirname(easybuild.easyblocks.foofoo.__file__)
+        foofoo_path = os.path.dirname(os.path.dirname(easybuild.easyblocks.foofoo.__file__))
         self.assertTrue(os.path.samefile(foofoo_path, test_easyblocks))
 
     def test_include_easyblocks_priority(self):
@@ -106,7 +106,7 @@ def test_include_easyblocks_priority(self):
 
         # make sure that test 'foo' easyblocks is there
         import easybuild.easyblocks.foo
-        foo_path = os.path.dirname(easybuild.easyblocks.foo.__file__)
+        foo_path = os.path.dirname(os.path.dirname(easybuild.easyblocks.foo.__file__))
         self.assertTrue(os.path.samefile(foo_path, test_easyblocks))
 
         # inject custom 'foo' easyblocks
@@ -200,6 +200,7 @@ def test_include_toolchains(self):
         my_tc_real_py_path = os.path.realpath(os.path.join(os.path.dirname(my_tc_pyc_path), 'my_tc.py'))
         self.assertTrue(os.path.samefile(up(my_tc_real_py_path, 1), my_toolchains))
 
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(IncludeTest)
diff --git a/test/framework/options.py b/test/framework/options.py
index a18479caeb..61ee21a5dd 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -40,6 +40,7 @@
 
 import easybuild.tools.build_log
 import easybuild.tools.options
+import easybuild.tools.toolchain
 from easybuild.framework.easyconfig import BUILD, CUSTOM, DEPENDENCIES, EXTENSIONS, FILEMANAGEMENT, LICENSE
 from easybuild.framework.easyconfig import MANDATORY, MODULES, OTHER, TOOLCHAIN
 from easybuild.tools.build_log import EasyBuildError
@@ -49,6 +50,7 @@
 from easybuild.tools.github import fetch_github_token
 from easybuild.tools.modules import modules_tool
 from easybuild.tools.options import EasyBuildOptions
+from easybuild.tools.toolchain.utilities import TC_CONST_PREFIX
 from easybuild.tools.version import VERSION
 from vsc.utils import fancylogger
 
@@ -504,18 +506,6 @@ def test_list_easyblocks(self):
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
         os.close(fd)
 
-        # adjust PYTHONPATH such that test easyblocks are found
-
-        import easybuild
-        eb_blocks_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'sandbox'))
-        if not eb_blocks_path in sys.path:
-            sys.path.append(eb_blocks_path)
-            easybuild = reload(easybuild)
-
-        import easybuild.easyblocks
-        reload(easybuild.easyblocks)
-        reload(easybuild.tools.module_naming_scheme)  # required to run options unit tests stand-alone
-
         # simple view
         for list_arg in ['--list-easyblocks', '--list-easyblocks=simple']:
 
@@ -526,7 +516,7 @@ def test_list_easyblocks(self):
                     list_arg,
                     '--unittest-file=%s' % self.logfile,
                    ]
-            outtxt = self.eb_main(args, logfile=dummylogfn)
+            self.eb_main(args, logfile=dummylogfn)
             logtxt = read_file(self.logfile)
 
             for pat in [
@@ -546,7 +536,7 @@ def test_list_easyblocks(self):
                 '--list-easyblocks=detailed',
                 '--unittest-file=%s' % self.logfile,
                ]
-        outtxt = self.eb_main(args, logfile=dummylogfn)
+        self.eb_main(args, logfile=dummylogfn)
         logtxt = read_file(self.logfile)
 
         for pat in [
@@ -1688,6 +1678,137 @@ def test_generate_cmd_line(self):
         ebopts = EasyBuildOptions(go_args=['--search=bar', '--search', 'foobar'])
         self.assertEqual(ebopts.generate_cmd_line(), ['--search=foobar'])
 
+    def test_include_easyblocks(self):
+        """Test --include-easyblocks."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        # clear log
+        write_file(self.logfile, '')
+
+        # existing test EB_foo easyblock found without include a custom one
+        args = [
+            '--list-easyblocks=detailed',
+            '--unittest-file=%s' % self.logfile,
+        ]
+        self.eb_main(args, logfile=dummylogfn, raise_error=True)
+        logtxt = read_file(self.logfile)
+
+        test_easyblocks = os.path.dirname(os.path.abspath(__file__))
+        path_pattern = os.path.join(test_easyblocks, 'sandbox', 'easybuild', 'easyblocks', 'f', 'foo.py')
+        foo_regex = re.compile(r"^\|-- EB_foo \(easybuild.easyblocks.foo @ %s\)"  % path_pattern, re.M)
+        self.assertTrue(foo_regex.search(logtxt), "Pattern '%s' found in: %s" % (foo_regex.pattern, logtxt))
+
+        # include extra test easyblocks
+        foo_txt = '\n'.join([
+            'from easybuild.framework.easyblock import EasyBlock',
+            'class EB_foo(EasyBlock):',
+            '   pass',
+            ''
+        ])
+        write_file(os.path.join(self.test_prefix, 'foo.py'), foo_txt)
+
+        # clear log
+        write_file(self.logfile, '')
+
+        args = [
+            '--include-easyblocks=%s/*.py' % self.test_prefix,
+            '--list-easyblocks=detailed',
+            '--unittest-file=%s' % self.logfile,
+        ]
+        self.eb_main(args, logfile=dummylogfn, raise_error=True)
+        logtxt = read_file(self.logfile)
+
+        path_pattern = os.path.join(self.test_prefix, '.*', 'included-easyblocks', 'easybuild', 'easyblocks', 'foo.py')
+        foo_regex = re.compile(r"^\|-- EB_foo \(easybuild.easyblocks.foo @ %s\)"  % path_pattern, re.M)
+        self.assertTrue(foo_regex.search(logtxt), "Pattern '%s' found in: %s" % (foo_regex.pattern, logtxt))
+
+    def test_include_module_naming_schemes(self):
+        """Test --include-module-naming-schemes."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        # clear log
+        write_file(self.logfile, '')
+
+        mns_regex = re.compile(r'^\s*TestIncludedMNS', re.M)
+
+        # TestIncludeMNS module naming scheme is not available by default
+        args = [
+            '--avail-module-naming-schemes',
+            '--unittest-file=%s' % self.logfile,
+        ]
+        self.eb_main(args, logfile=dummylogfn, raise_error=True)
+        logtxt = read_file(self.logfile)
+        self.assertFalse(mns_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (mns_regex.pattern, logtxt))
+
+        # include extra test MNS
+        mns_txt = '\n'.join([
+            'from easybuild.tools.module_naming_scheme import ModuleNamingScheme',
+            'class TestIncludedMNS(ModuleNamingScheme):',
+            '   pass',
+        ])
+        write_file(os.path.join(self.test_prefix, 'test_mns.py'), mns_txt)
+
+        # clear log
+        write_file(self.logfile, '')
+
+        args = [
+            '--avail-module-naming-schemes',
+            '--include-module-naming-schemes=%s/*.py' % self.test_prefix,
+            '--unittest-file=%s' % self.logfile,
+        ]
+        self.eb_main(args, logfile=dummylogfn, raise_error=True)
+        logtxt = read_file(self.logfile)
+        self.assertTrue(mns_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (mns_regex.pattern, logtxt))
+
+    def test_include_toolchains(self):
+        """Test --include-toolchains."""
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        # clear log
+        write_file(self.logfile, '')
+
+        # set processed attribute to false, to trigger rescan in search_toolchain
+        setattr(easybuild.tools.toolchain, '%s_PROCESSED' % TC_CONST_PREFIX, False)
+
+        tc_regex = re.compile(r'^\s*test_included_toolchain: TestIncludedCompiler', re.M)
+
+        # TestIncludeMNS module naming scheme is not available by default
+        args = [
+            '--list-toolchains',
+            '--unittest-file=%s' % self.logfile,
+        ]
+        #self.eb_main(args, logfile=dummylogfn, raise_error=True)
+        #logtxt = read_file(self.logfile)
+        #self.assertFalse(tc_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (tc_regex.pattern, logtxt))
+
+        # include extra test toolchain
+        comp_txt = '\n'.join([
+            'from easybuild.tools.toolchain.compiler import Compiler',
+            'class TestIncludedCompiler(Compiler):',
+            "   COMPILER_MODULE_NAME = ['TestIncludedCompiler']",
+        ])
+        mkdir(os.path.join(self.test_prefix, 'compiler'))
+        write_file(os.path.join(self.test_prefix, 'compiler', 'test_comp.py'), comp_txt)
+
+        tc_txt = '\n'.join([
+            'from easybuild.toolchains.compiler.test_comp import TestIncludedCompiler',
+            'class TestIncludedToolchain(TestIncludedCompiler):',
+            "   NAME = 'test_included_toolchain'",
+        ])
+        write_file(os.path.join(self.test_prefix, 'test_tc.py'), tc_txt)
+
+        args = [
+            '--include-toolchains=%s/*.py,%s/*/*.py' % (self.test_prefix, self.test_prefix),
+            '--list-toolchains',
+            '--unittest-file=%s' % self.logfile,
+        ]
+        self.eb_main(args, logfile=dummylogfn, raise_error=True)
+        logtxt = read_file(self.logfile)
+        self.assertTrue(tc_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (tc_regex.pattern, logtxt))
+
 
 def suite():
     """ returns all the testcases in this module """

From 559a5b15e659f88c013fa1d759308f741439401f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 29 Jun 2015 09:17:58 +0200
Subject: [PATCH 1056/1356] fix FIXMEs

---
 easybuild/tools/job/gc3pie.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index b80dd448ae..5fbcf774b2 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -134,7 +134,7 @@ def init(self):
         if cfgfile:
             self.config_files.append(cfgfile)
 
-        # additional subdirectory, since GC3Pie cleans up the output dir?!
+        # additional subdirectory, since GC3Pie cleans up the output dir!
         self.output_dir = os.path.join(build_option('job_output_dir'), 'eb-gc3pie-jobs')
         self.jobs = DependentTaskCollection(output_dir=self.output_dir)
 
@@ -183,7 +183,6 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
             # join stdout/stderr in a single log
             'join': True,
             # location for log file
-            # FIXME: does GC3Pie blindly remove this entire directory?!
             'output_dir': self.output_dir,
             # log file name
             'stdout': 'eb-%s-gc3pie-job.log' % name,
@@ -203,7 +202,7 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         elif build_option('job_cores'):
             named_args['requested_cores'] = build_option('job_cores')
         else:
-            # FIXME: ask GC3Pie to guess core count per node (see _get_ppn in job/pbs_python.py)
+            self.log.warn("Number of cores to request not specified, falling back to whatever GC3Pie does by default")
 
         return Application(['/bin/sh', '-c', script], **named_args)
 

From f13333458968ef5a18dfd919380591ac279ae9ef Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 29 Jun 2015 16:08:22 +0200
Subject: [PATCH 1057/1356] Replace internal to_str with quote_str

---
 easybuild/framework/easyconfig/easyconfig.py | 18 +++---------------
 easybuild/tools/utilities.py                 | 11 ++++++++---
 2 files changed, 11 insertions(+), 18 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 9da551fcd5..f170f246b0 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -54,7 +54,7 @@
 from easybuild.tools.systemtools import check_os_dependency
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
 from easybuild.tools.toolchain.utilities import get_toolchain
-from easybuild.tools.utilities import remove_unwanted_chars
+from easybuild.tools.utilities import remove_unwanted_chars, quote_str
 from easybuild.framework.easyconfig import MANDATORY
 from easybuild.framework.easyconfig.constants import EXTERNAL_MODULE_MARKER
 from easybuild.framework.easyconfig.default import DEFAULT_CONFIG
@@ -472,18 +472,6 @@ def dump(self, fp):
         """
         eb_file = file(fp, "w")
 
-        def to_str(x):
-            """Return quoted version of x"""
-            if isinstance(x, basestring):
-                if '\n' in x or ('"' in x and "'" in x):
-                    return '"""%s"""' % x
-                elif "'" in x:
-                    return '"%s"' % x
-                else:
-                    return "'%s'" % x
-            else:
-                return "%s" % x
-
         # ordered groups of keys to obtain a nice looking easyconfig file
         grouped_keys = [
             ['name', 'version', 'versionprefix', 'versionsuffix'],
@@ -505,14 +493,14 @@ def to_str(x):
                 for key2, [def_val, _, _] in DEFAULT_CONFIG.items():
                     # only print parameters that are different from the default value
                     if key1 == key2 and val != def_val:
-                        ebtxt.append("%s = %s" % (key1, to_str(val)))
+                        ebtxt.append("%s = %s" % (key1, quote_str(val, True)))
                         printed_keys.append(key1)
             ebtxt.append("")
 
         # print other easyconfig parameters at the end
         for key, [val, _, _] in DEFAULT_CONFIG.items():
             if not key in printed_keys and val != self._config[key][0]:
-                ebtxt.append("%s = %s" % (key, to_str(self._config[key][0])))
+                ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], True)))
 
         eb_file.write('\n'.join(ebtxt))
         eb_file.close()
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index fb3ac98fe0..61d61804e4 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -56,11 +56,13 @@ def flatten(lst):
     return res
 
 
-def quote_str(x):
+def quote_str(x, force_str=False):
     """
     Obtain a new value to be used in string replacement context.
 
     For non-string values, it just returns the exact same value.
+    Non-string values can be converted to string by setting the second
+    parameter to True.
 
     For string values, it tries to escape the string in quotes, e.g.,
     foo becomes 'foo', foo'bar becomes "foo'bar",
@@ -68,14 +70,17 @@ def quote_str(x):
     """
 
     if isinstance(x, basestring):
-        if "'" in x and '"' in x:
+        if '\n' in x or ("'" in x and '"' in x):
             return '"""%s"""' % x
         elif '"' in x:
             return "'%s'" % x
         else:
             return '"%s"' % x
     else:
-        return x
+	if force_str:
+            return str(x)
+	else:
+	    return x
 
 
 def remove_unwanted_chars(inputstring):

From 0604fb7977450a8a14e7182a5de2674f4f19fc6a Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 29 Jun 2015 16:44:15 +0200
Subject: [PATCH 1058/1356] Remove force_str argument

---
 easybuild/framework/easyconfig/easyconfig.py |  4 ++--
 easybuild/tools/utilities.py                 |  7 ++-----
 test.eb                                      | 20 ++++++++++++++++++++
 3 files changed, 24 insertions(+), 7 deletions(-)
 create mode 100644 test.eb

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index f170f246b0..dc98f1dd31 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -493,14 +493,14 @@ def dump(self, fp):
                 for key2, [def_val, _, _] in DEFAULT_CONFIG.items():
                     # only print parameters that are different from the default value
                     if key1 == key2 and val != def_val:
-                        ebtxt.append("%s = %s" % (key1, quote_str(val, True)))
+                        ebtxt.append("%s = %s" % (key1, quote_str(val)))
                         printed_keys.append(key1)
             ebtxt.append("")
 
         # print other easyconfig parameters at the end
         for key, [val, _, _] in DEFAULT_CONFIG.items():
             if not key in printed_keys and val != self._config[key][0]:
-                ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], True)))
+                ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0])))
 
         eb_file.write('\n'.join(ebtxt))
         eb_file.close()
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 61d61804e4..6f83d0f913 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -56,7 +56,7 @@ def flatten(lst):
     return res
 
 
-def quote_str(x, force_str=False):
+def quote_str(x):
     """
     Obtain a new value to be used in string replacement context.
 
@@ -77,10 +77,7 @@ def quote_str(x, force_str=False):
         else:
             return '"%s"' % x
     else:
-	if force_str:
-            return str(x)
-	else:
-	    return x
+	return x
 
 
 def remove_unwanted_chars(inputstring):
diff --git a/test.eb b/test.eb
new file mode 100644
index 0000000000..845628187f
--- /dev/null
+++ b/test.eb
@@ -0,0 +1,20 @@
+name = "Libint"
+version = "1.1.4"
+
+homepage = "https://sourceforge.net/p/libint/"
+description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body
+matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory."""
+
+toolchain = {'version': '1.4.10', 'name': 'goolf'}
+toolchainopts = {'opt': True, 'optarch': True, 'pic': True}
+
+source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download')
+sources = ['%(namelower)s-%(version)s.tar.gz']
+
+
+
+
+
+moduleclass = "chem"
+sanity_check_paths = {'files': ['include/libderiv/libderiv.h', 'include/libint/libint.h', 'include/libr12/libr12.h', 'include/libint/hrr_header.h', 'include/libint/vrr_header.h', 'lib/libderiv.a', 'lib/libint.a', 'lib/libr12.a', 'lib/libderiv.so', 'lib/libint.so', 'lib/libr12.so'], 'dirs': []}
+configopts = "--enable-deriv --enable-r12"
\ No newline at end of file

From 330a4c0be2872982d11750ebfe51b620449d5fb4 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 29 Jun 2015 16:46:28 +0200
Subject: [PATCH 1059/1356] Delete test.eb

---
 test.eb | 20 --------------------
 1 file changed, 20 deletions(-)
 delete mode 100644 test.eb

diff --git a/test.eb b/test.eb
deleted file mode 100644
index 845628187f..0000000000
--- a/test.eb
+++ /dev/null
@@ -1,20 +0,0 @@
-name = "Libint"
-version = "1.1.4"
-
-homepage = "https://sourceforge.net/p/libint/"
-description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body
-matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory."""
-
-toolchain = {'version': '1.4.10', 'name': 'goolf'}
-toolchainopts = {'opt': True, 'optarch': True, 'pic': True}
-
-source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download')
-sources = ['%(namelower)s-%(version)s.tar.gz']
-
-
-
-
-
-moduleclass = "chem"
-sanity_check_paths = {'files': ['include/libderiv/libderiv.h', 'include/libint/libint.h', 'include/libr12/libr12.h', 'include/libint/hrr_header.h', 'include/libint/vrr_header.h', 'lib/libderiv.a', 'lib/libint.a', 'lib/libr12.a', 'lib/libderiv.so', 'lib/libint.so', 'lib/libr12.so'], 'dirs': []}
-configopts = "--enable-deriv --enable-r12"
\ No newline at end of file

From c98f7e3737ce5eaa5b06251a6a2cb54a658518b5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 29 Jun 2015 16:57:01 +0200
Subject: [PATCH 1060/1356] kickstart tests for quote_str/dump

---
 test/framework/easyconfig.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 6454cf1087..dbc8cdcaa8 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -55,6 +55,7 @@
 from easybuild.tools.module_naming_scheme.toolchain import det_toolchain_compilers, det_toolchain_mpi
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.systemtools import get_shared_lib_ext
+from easybuild.tools.utilities import quote_str
 from test.framework.utilities import find_full_path
 
 
@@ -1132,6 +1133,25 @@ def test_hide_hidden_deps(self):
         self.assertEqual(ec['hiddendependencies'][0]['full_mod_name'], 'toy/.0.0-deps')
         self.assertEqual(ec['dependencies'], [])
 
+    def test_quote_str(self):
+        """Test quote_str function."""
+        self.assertEqual(quote_str('foo'), '"foo"')
+        # FIXME: add more test cases
+
+    def test_dump(self):
+        """Test EasyConfig's dump() method."""
+        test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+
+        test_ec = os.path.join(self.test_prefix, 'test.eb')
+
+        ec = EasyConfig(os.path.join(test_ecs_dir, 'toy-0.0.eb'))
+        ec.dump(test_ec)
+        ectxt = read_file(test_ec)
+        version_regex = re.compile('^version = "0.0"', re.M)
+        self.assertTrue(version_regex.search(ectxt))
+        # FIXME: add more test cases (using easyconfigs available in test/framework/easyconfigs)
+
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(EasyConfigTest)

From 5f18519367c60fa7775c2a7dcbe6bc3376935731 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 29 Jun 2015 18:02:06 +0200
Subject: [PATCH 1061/1356] fix required GC3Pie version to just 2.3, provide
 self.log in JobBackend, fix --job-cores option definition

---
 easybuild/tools/job/backend.py    | 2 ++
 easybuild/tools/job/gc3pie.py     | 4 ++--
 easybuild/tools/job/pbs_python.py | 6 +++---
 easybuild/tools/options.py        | 2 +-
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/job/backend.py b/easybuild/tools/job/backend.py
index ade1575da2..25ed7ee9a8 100644
--- a/easybuild/tools/job/backend.py
+++ b/easybuild/tools/job/backend.py
@@ -27,6 +27,7 @@
 
 from abc import ABCMeta, abstractmethod
 
+from vsc.utils import fancylogger
 from vsc.utils.missing import get_subclasses
 
 from easybuild.tools.config import get_job_backend
@@ -38,6 +39,7 @@ class JobBackend(object):
 
     def __init__(self):
         """Constructor."""
+        self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
         self._check_version()
 
     @abstractmethod
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 5fbcf774b2..dbdd4867a6 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -89,7 +89,7 @@ class GC3Pie(JobBackend):
     terminated.
     """
 
-    REQ_VERSION = '2.3.0'
+    REQ_VERSION = '2.3'
     DEVELOPMENT_VERSION = 'development'  # 'magic' version string indicated non-released version
     REQ_SVN_REVISION = 4223  # use integer value, not a string!
 
@@ -104,7 +104,7 @@ def _check_version(self):
         if res:
             version = res.group('version')
             svn_rev = int(res.group('svn_rev'))
-            _log.debug("Parsed GC3Pie version info: '%s' (SVN rev: '%s')", version, svn_rev)
+            self.log.debug("Parsed GC3Pie version info: '%s' (SVN rev: '%s')", version, svn_rev)
 
             if version == self.DEVELOPMENT_VERSION:
                 # fall back to checking SVN revision for development versions
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 93f3c47ed5..5733ccc225 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -141,12 +141,12 @@ def complete(self):
         """
         for job in self._submitted:
             if job.has_holds():
-                _log.info("releasing user hold on job %s" % job.jobid)
+                self.log.info("releasing user hold on job %s" % job.jobid)
                 job.release_hold()
         self.disconnect_from_server()
         if self._submitted:
             submitted_jobs = '; '.join(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in self._submitted])
-            _log.info("List of submitted jobs: %s", submitted_jobs)
+            self.log.info("List of submitted jobs: %s", submitted_jobs)
 
     @pbs_python_imported
     def disconnect_from_server(self):
@@ -170,7 +170,7 @@ def _get_ppn(self):
 
             # return most frequent
             freq_count, freq_np = max([(j, i) for i, j in res.items()])
-            _log.debug("Found most frequent np %s (%s times) in interesting nodes %s" % (freq_np, freq_count, interesting_nodes))
+            self.log.debug("Found most frequent np %s (%s times) in interesting nodes %s" % (freq_np, freq_count, interesting_nodes))
 
             self._ppn = freq_np
 
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 6cdbb953ed..3ec57a984c 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -363,7 +363,7 @@ def job_options(self):
 
         opts = OrderedDict({
             'backend-config': ("Configuration file for job backend", None, 'store', None),
-            'cores': ("Number of cores to request per job", None, 'int', 'store', None),
+            'cores': ("Number of cores to request per job", 'int', 'store', None),
             'max-walltime': ("Maximum walltime for jobs (in hours)", 'int', 'store', 24),
             'output-dir': ("Output directory for jobs (default: current directory)", None, 'store', os.getcwd()),
             'polling-interval': ("Interval between polls for status of jobs (in seconds)", float, 'store', 30.0),

From 291db6455688a5c4be186c0835d4d84a7a2dac52 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 30 Jun 2015 09:37:01 +0200
Subject: [PATCH 1062/1356] Fixed test for load_msg

---
 test/framework/module_generator.py      | 4 ++--
 test/framework/modules/imkl/10.3.12.361 | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 5f6029cda5..1f9af87e32 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -249,8 +249,8 @@ def test_load_msg(self):
             tcl_load_msg = '\n'.join([
                 '',
                 "if { [ module-info mode load ] } {",
-                "    puts stderr \"test \\$test \\$test",
-                "test \\$foo \\$bar\"",
+                "    puts stderr \"\"\"test \\$test \\$test",
+                "test \\$foo \\$bar\"\"\"",
                 "}",
                 '',
             ])
diff --git a/test/framework/modules/imkl/10.3.12.361 b/test/framework/modules/imkl/10.3.12.361
index 780b019c78..d63fb61362 100644
--- a/test/framework/modules/imkl/10.3.12.361
+++ b/test/framework/modules/imkl/10.3.12.361
@@ -13,7 +13,7 @@ module-whatis {Intel Math Kernel Library is a library of highly optimized,
  applications that require maximum performance. Core math functions include
  BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. - Homepage: http://software.intel.com/en-us/intel-mkl/}
 
-set root	/var/folders/6y/x4gmwgjn5qz63b7ftg4j_40m0000gn/T/tmpZg_7A8
+set root	/tmp/eb-bI0pBy/eb-DmuEpJ/eb-leoYDw/eb-UtJJqp/tmp8P3FOY
 
 conflict    imkl
 

From f2e9d80b9a201e79c009cacc320ede8f8115c999 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 30 Jun 2015 09:48:21 +0200
Subject: [PATCH 1063/1356] fix comment on quote_str

---
 easybuild/tools/utilities.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 6f83d0f913..0a2abdd982 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -61,8 +61,6 @@ def quote_str(x):
     Obtain a new value to be used in string replacement context.
 
     For non-string values, it just returns the exact same value.
-    Non-string values can be converted to string by setting the second
-    parameter to True.
 
     For string values, it tries to escape the string in quotes, e.g.,
     foo becomes 'foo', foo'bar becomes "foo'bar",

From 39ab479f5fe6c708a1750ebfa4a0b7da4a011c2f Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 30 Jun 2015 10:14:20 +0200
Subject: [PATCH 1064/1356] tests for quote_str

---
 test/framework/easyconfig.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index dbc8cdcaa8..8b1af96b9f 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1136,7 +1136,20 @@ def test_hide_hidden_deps(self):
     def test_quote_str(self):
         """Test quote_str function."""
         self.assertEqual(quote_str('foo'), '"foo"')
-        # FIXME: add more test cases
+	self.assertEqual(quote_str('foo\'bar'), '"foo\'bar"')
+	self.assertEqual(quote_str('foo\'bar"baz'), '"""foo\'bar"baz"""')
+	self.assertEqual(quote_str("foo'bar\"baz"), '"""foo\'bar"baz"""')
+	self.assertEqual(quote_str("foo \n bar"), '"""foo \n bar"""')	
+
+	""" Non-string values """
+	n = 42
+	self.assertEqual(quote_str(n), 42)
+	l = ["foo", "bar"]
+        self.assertEqual(quote_str(l), ["foo", "bar"])
+	t = ('foo', 'bar')
+	self.assertEqual(quote_str(t), ('foo', 'bar')) 
+	 
+	
 
     def test_dump(self):
         """Test EasyConfig's dump() method."""

From 9d47e3f1c856f716f961bc50306c589a248b84a4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 30 Jun 2015 10:39:44 +0200
Subject: [PATCH 1065/1356] fix comment

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index dbdd4867a6..2f15059d74 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -134,7 +134,7 @@ def init(self):
         if cfgfile:
             self.config_files.append(cfgfile)
 
-        # additional subdirectory, since GC3Pie cleans up the output dir!
+        # additional subdirectory, since GC3Pie renames the output dir if it already exists
         self.output_dir = os.path.join(build_option('job_output_dir'), 'eb-gc3pie-jobs')
         self.jobs = DependentTaskCollection(output_dir=self.output_dir)
 

From 8a867f1b0ff1165e982b207384dcf5337dc3a7f5 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 11:14:17 +0200
Subject: [PATCH 1066/1356] dump/quote_str tests and small changes

---
 easybuild/framework/easyconfig/easyconfig.py | 39 +++++++++++++++++---
 easybuild/tools/utilities.py                 |  8 ++--
 test/framework/easyconfig.py                 | 37 ++++++++++++-------
 test/framework/module_generator.py           |  4 +-
 4 files changed, 64 insertions(+), 24 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index dc98f1dd31..1f63e1ef16 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -466,6 +466,7 @@ def toolchain(self):
             self.log.debug("Initialized toolchain: %s (opts: %s)" % (tc_dict, self['toolchainopts']))
         return self._toolchain
 
+
     def dump(self, fp):
         """
         Dump this easyconfig to file, with the given filename.
@@ -474,14 +475,18 @@ def dump(self, fp):
 
         # ordered groups of keys to obtain a nice looking easyconfig file
         grouped_keys = [
+            ['easyblock'],
             ['name', 'version', 'versionprefix', 'versionsuffix'],
             ['homepage', 'description'],
             ['toolchain', 'toolchainopts'],
-            ['source_urls', 'sources'],
+            ['sources', 'source_urls'],
             ['patches'],
             ['builddependencies', 'dependencies', 'hiddendependencies'],
             ['parallel', 'maxparallel'],
-            ['osdependencies']
+            ['osdependencies'],
+            ['prebuildopts', 'preinstallopts', 'preconfigopts'],
+            ['sanity_check_paths'],
+            ['moduleclass']
         ]
 
         # print easyconfig parameters ordered and in groups specified above
@@ -493,18 +498,42 @@ def dump(self, fp):
                 for key2, [def_val, _, _] in DEFAULT_CONFIG.items():
                     # only print parameters that are different from the default value
                     if key1 == key2 and val != def_val:
-                        ebtxt.append("%s = %s" % (key1, quote_str(val)))
+                        ebtxt.append("%s = %s" % (key1, quote_str(val, esc_newline=True)))
                         printed_keys.append(key1)
             ebtxt.append("")
 
         # print other easyconfig parameters at the end
         for key, [val, _, _] in DEFAULT_CONFIG.items():
             if not key in printed_keys and val != self._config[key][0]:
-                ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0])))
+                ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], esc_newline=True)))
 
-        eb_file.write('\n'.join(ebtxt))
+        eb_file.write(self.wrap('\n'.join(ebtxt), width=120))
         eb_file.close()
 
+    
+    def wrap(self, text, width=80):
+        """ 
+        Word-wrap function to use in dump()
+        Source: http://code.activestate.com/recipes/148061-one-liner-word-wrap-function/
+        """
+        lines = []
+        for paragraph in text.split('\n'):
+            line = []
+            len_line = 0
+            for word in paragraph.split(' '):
+                len_word = len(word)
+                if len_line + len_word <= width:
+                    line.append(word)
+                    len_line += len_word + 1
+                else:
+                    lines.append(' '.join(line))
+                    line = [word]
+                    len_line = len_word + 1
+            lines.append(' '.join(line))
+        return '\n'.join(lines)
+
+
+
     def _validate(self, attr, values):  # private method
         """
         validation helper method. attr is the attribute it will check, values are the possible values.
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 0a2abdd982..92f2c8d5a1 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -56,11 +56,11 @@ def flatten(lst):
     return res
 
 
-def quote_str(x):
+def quote_str(x, esc_newline=False):
     """
     Obtain a new value to be used in string replacement context.
 
-    For non-string values, it just returns the exact same value.
+    For non-string values, it just returns the exact same value.    
 
     For string values, it tries to escape the string in quotes, e.g.,
     foo becomes 'foo', foo'bar becomes "foo'bar",
@@ -68,14 +68,14 @@ def quote_str(x):
     """
 
     if isinstance(x, basestring):
-        if '\n' in x or ("'" in x and '"' in x):
+        if ("'" in x and '"' in x) or (esc_newline and '\n' in x):
             return '"""%s"""' % x
         elif '"' in x:
             return "'%s'" % x
         else:
             return '"%s"' % x
     else:
-	return x
+	    return x
 
 
 def remove_unwanted_chars(inputstring):
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 8b1af96b9f..2779e3e0b9 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1136,33 +1136,44 @@ def test_hide_hidden_deps(self):
     def test_quote_str(self):
         """Test quote_str function."""
         self.assertEqual(quote_str('foo'), '"foo"')
-	self.assertEqual(quote_str('foo\'bar'), '"foo\'bar"')
-	self.assertEqual(quote_str('foo\'bar"baz'), '"""foo\'bar"baz"""')
-	self.assertEqual(quote_str("foo'bar\"baz"), '"""foo\'bar"baz"""')
-	self.assertEqual(quote_str("foo \n bar"), '"""foo \n bar"""')	
-
-	""" Non-string values """
-	n = 42
-	self.assertEqual(quote_str(n), 42)
-	l = ["foo", "bar"]
+        self.assertEqual(quote_str('foo\'bar'), '"foo\'bar"')
+        self.assertEqual(quote_str('foo\'bar"baz'), '"""foo\'bar"baz"""')
+        self.assertEqual(quote_str("foo'bar\"baz"), '"""foo\'bar"baz"""')
+
+        """ Non-string values """
+        n = 42
+        self.assertEqual(quote_str(n), 42)
+        l = ["foo", "bar"]
         self.assertEqual(quote_str(l), ["foo", "bar"])
-	t = ('foo', 'bar')
-	self.assertEqual(quote_str(t), ('foo', 'bar')) 
+        self.assertEqual(quote_str(('foo', 'bar')), ('foo', 'bar')) 
 	 
 	
-
     def test_dump(self):
         """Test EasyConfig's dump() method."""
         test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
 
         test_ec = os.path.join(self.test_prefix, 'test.eb')
+        test_ec2 = os.path.join(self.test_prefix, 'test2.eb')
 
         ec = EasyConfig(os.path.join(test_ecs_dir, 'toy-0.0.eb'))
         ec.dump(test_ec)
         ectxt = read_file(test_ec)
         version_regex = re.compile('^version = "0.0"', re.M)
         self.assertTrue(version_regex.search(ectxt))
-        # FIXME: add more test cases (using easyconfigs available in test/framework/easyconfigs)
+        description_regex = re.compile('^description = "Toy C program."', re.M)
+        self.assertTrue(description_regex.search(ectxt))
+        """ Parse the result again """ 
+        dumped_ec = EasyConfig(test_ec)
+
+        ec2 = EasyConfig(os.path.join(test_ecs_dir, 'goolf-1.4.10.eb'))
+        ec2.dump(test_ec2)
+        ectxt2 = read_file(test_ec2)
+        name_regex = re.compile('^name = "goolf"', re.M)
+        self.assertTrue(name_regex.search(ectxt2))
+        moduleclass_regex = re.compile('^moduleclass = "toolchain"', re.M)
+        self.assertTrue(moduleclass_regex.search(ectxt2))
+
+        dumped_ec2 = EasyConfig(test_ec2)
 
 
 def suite():
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 1f9af87e32..5f6029cda5 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -249,8 +249,8 @@ def test_load_msg(self):
             tcl_load_msg = '\n'.join([
                 '',
                 "if { [ module-info mode load ] } {",
-                "    puts stderr \"\"\"test \\$test \\$test",
-                "test \\$foo \\$bar\"\"\"",
+                "    puts stderr \"test \\$test \\$test",
+                "test \\$foo \\$bar\"",
                 "}",
                 '',
             ])

From 3c2af43e387cb03366a3741748290a6df0f1122f Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 11:16:18 +0200
Subject: [PATCH 1067/1356] fix tab

---
 easybuild/tools/utilities.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 92f2c8d5a1..f04e90f367 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -75,7 +75,7 @@ def quote_str(x, esc_newline=False):
         else:
             return '"%s"' % x
     else:
-	    return x
+        return x
 
 
 def remove_unwanted_chars(inputstring):

From 1d8c0c14f244c7b46864fbb346fe409263bd9b75 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Jul 2015 11:24:09 +0200
Subject: [PATCH 1068/1356] count total number of jobs ourselves, to get a view
 on # jobs in hold

---
 easybuild/tools/job/gc3pie.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 2f15059d74..4c99a4edbb 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -249,16 +249,16 @@ def complete(self):
             self._engine.progress()
 
             # report progress
-            self._print_status_report(['total', 'NEW', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
+            self._print_status_report(['NEW', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
 
             # Wait a few seconds...
             time.sleep(self.poll_interval)
 
         # final status report
-        self._print_status_report(['total', 'ok', 'failed'])
+        self._print_status_report(['ok', 'failed'])
 
     @gc3pie_imported
-    def _print_status_report(self, states=('total', 'ok', 'failed')):
+    def _print_status_report(self, states=('ok', 'failed')):
         """
         Print a job status report to STDOUT and the log file.
 
@@ -269,5 +269,6 @@ def _print_status_report(self, states=('total', 'ok', 'failed')):
         report the number of total jobs right from the start.
         """
         stats = self._engine.stats(only=Application)
-        job_overview = ', '.join(["%d %s" % (stats[s], s.lower()) for s in states if stats[s]])
-        print_msg("GC3Pie job overview: %s" % job_overview, log=_log, silent=build_option('silent'))
+        overview = ', '.join(["%d %s" % (stats[s], s.lower()) for s in states if stats[s]])
+        total = len(self.jobs)
+        print_msg("GC3Pie job overview: %s (total: %s)" % (overview, total), log=_log, silent=build_option('silent'))

From 8b6c8a478b1b5f6d8228b9c824e8a10c4ffd83eb Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 11:56:37 +0200
Subject: [PATCH 1069/1356] fix whitespace

---
 easybuild/tools/utilities.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index f04e90f367..4736dad3aa 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -60,7 +60,7 @@ def quote_str(x, esc_newline=False):
     """
     Obtain a new value to be used in string replacement context.
 
-    For non-string values, it just returns the exact same value.    
+    For non-string values, it just returns the exact same value.
 
     For string values, it tries to escape the string in quotes, e.g.,
     foo becomes 'foo', foo'bar becomes "foo'bar",

From 378611bb82a6a0699b579d5fcbfe107760a82a5e Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 13:26:53 +0200
Subject: [PATCH 1070/1356] undo wrap function

---
 easybuild/framework/easyconfig/easyconfig.py | 26 ++------------------
 1 file changed, 2 insertions(+), 24 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 1f63e1ef16..e47ccb168c 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -39,6 +39,7 @@
 import difflib
 import os
 import re
+import textwrap
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_class_for, nub
 from vsc.utils.patterns import Singleton
@@ -507,33 +508,10 @@ def dump(self, fp):
             if not key in printed_keys and val != self._config[key][0]:
                 ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], esc_newline=True)))
 
-        eb_file.write(self.wrap('\n'.join(ebtxt), width=120))
+        eb_file.write('\n'.join(ebtxt))
         eb_file.close()
 
     
-    def wrap(self, text, width=80):
-        """ 
-        Word-wrap function to use in dump()
-        Source: http://code.activestate.com/recipes/148061-one-liner-word-wrap-function/
-        """
-        lines = []
-        for paragraph in text.split('\n'):
-            line = []
-            len_line = 0
-            for word in paragraph.split(' '):
-                len_word = len(word)
-                if len_line + len_word <= width:
-                    line.append(word)
-                    len_line += len_word + 1
-                else:
-                    lines.append(' '.join(line))
-                    line = [word]
-                    len_line = len_word + 1
-            lines.append(' '.join(line))
-        return '\n'.join(lines)
-
-
-
     def _validate(self, attr, values):  # private method
         """
         validation helper method. attr is the attribute it will check, values are the possible values.

From 92fd3415a51af3aef6ef02bec6503e7c605b9b36 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 13:30:22 +0200
Subject: [PATCH 1071/1356] unused import

---
 easybuild/framework/easyconfig/easyconfig.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index e47ccb168c..fe984784dc 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -39,7 +39,6 @@
 import difflib
 import os
 import re
-import textwrap
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_class_for, nub
 from vsc.utils.patterns import Singleton

From 1dac1478377108ab75ef0c7ee29fa7aee172695d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Jul 2015 14:44:38 +0200
Subject: [PATCH 1072/1356] restore printing report after completing job
 submission

---
 easybuild/tools/job/gc3pie.py     |  3 ++-
 easybuild/tools/job/pbs_python.py | 22 ++++++++++++++++++----
 easybuild/tools/parallelbuild.py  | 26 ++++++++++++--------------
 easybuild/tools/testing.py        | 18 +-----------------
 4 files changed, 33 insertions(+), 36 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 4c99a4edbb..6daa33bb24 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -255,6 +255,7 @@ def complete(self):
             time.sleep(self.poll_interval)
 
         # final status report
+        print_msg("Done processing jobs", log=self.log)
         self._print_status_report(['ok', 'failed'])
 
     @gc3pie_imported
@@ -271,4 +272,4 @@ def _print_status_report(self, states=('ok', 'failed')):
         stats = self._engine.stats(only=Application)
         overview = ', '.join(["%d %s" % (stats[s], s.lower()) for s in states if stats[s]])
         total = len(self.jobs)
-        print_msg("GC3Pie job overview: %s (total: %s)" % (overview, total), log=_log, silent=build_option('silent'))
+        print_msg("GC3Pie job overview: %s (total: %s)" % (overview, total), log=self.log, silent=build_option('silent'))
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 5733ccc225..087ca6d325 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -35,7 +35,7 @@
 import tempfile
 from vsc.utils import fancylogger
 
-from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.config import build_option
 from easybuild.tools.job.backend import JobBackend
 
@@ -143,10 +143,24 @@ def complete(self):
             if job.has_holds():
                 self.log.info("releasing user hold on job %s" % job.jobid)
                 job.release_hold()
+
         self.disconnect_from_server()
-        if self._submitted:
-            submitted_jobs = '; '.join(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in self._submitted])
-            self.log.info("List of submitted jobs: %s", submitted_jobs)
+
+        # print list of submitted jobs
+        submitted_jobs = '; '.join(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in self._submitted])
+        print_msg("List of submitted jobs (%d): %s" % (len(submitted_jobs), submitted_jobs), log=self.log)
+
+        # determine leaf nodes in dependency graph, and report them
+        all_deps = set()
+        for job in self._submitted:
+            all_deps = all_deps.union(job.deps)
+
+        leaf_nodes = []
+        for job in self._submitted:
+            if job.jobid not in all_deps:
+                leaf_nodes.append(str(job.jobid).split('.')[0])
+
+        self.log.info("Job ids of leaf nodes in dep. graph: %s" % ','.join(leaf_nodes))
 
     @pbs_python_imported
     def disconnect_from_server(self):
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 8844c9d678..a830d60f7c 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -53,9 +53,7 @@ def _to_key(dep):
     """Determine key for specified dependency."""
     return ActiveMNS().det_full_module_name(dep)
 
-def build_easyconfigs_in_parallel(build_command, easyconfigs,
-                                  output_dir='easybuild-build',
-                                  prepare_first=True):
+def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybuild-build', prepare_first=True):
     """
     Build easyconfigs in parallel by submitting jobs to a batch-queuing system.
     Return list of jobs submitted.
@@ -67,15 +65,16 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs,
     @param build_command: build command to use
     @param easyconfigs: list of easyconfig files
     @param output_dir: output directory
+    @param prepare_first: prepare by runnning fetch step first for each easyconfig
     """
     _log.info("going to build these easyconfigs in parallel: %s", easyconfigs)
 
-    job_server = job_backend()
-    if job_server is None:
+    job_backend = job_backend()
+    if job_backend is None:
         raise EasyBuildError("Can not use --job if no job backend is available.")
 
     try:
-        job_server.init()
+        job_backend.init()
     except RuntimeError as err:
         raise EasyBuildError("connection to server failed (%s: %s), can't submit jobs.", err.__class__.__name__, err)
 
@@ -95,13 +94,13 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs,
 
         # the new job will only depend on already submitted jobs
         _log.info("creating job for ec: %s" % str(ec))
-        new_job = create_job(job_server, build_command, ec, output_dir=output_dir)
+        new_job = create_job(job_backend, build_command, ec, output_dir=output_dir)
 
         # sometimes unresolved_deps will contain things, not needed to be build
         job_deps = [module_to_job[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in module_to_job]
 
         # actually (try to) submit job
-        job_server.queue(new_job, job_deps)
+        job_backend.queue(new_job, job_deps)
         _log.info(
             "job %s for module %s has been submitted"
             % (new_job, new_job.module))
@@ -110,7 +109,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs,
         module_to_job[new_job.module] = new_job
         jobs.append(new_job)
 
-    job_server.complete()
+    job_backend.complete()
 
     return jobs
 
@@ -139,15 +138,14 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
     if testing:
         _log.debug("Skipping actual submission of jobs since testing mode is enabled")
     else:
-        jobs = build_easyconfigs_in_parallel(command, ordered_ecs)
-        return ("%d jobs required for build." % (len(jobs),))
+        build_easyconfigs_in_parallel(command, ordered_ecs)
 
 
-def create_job(job_server, build_command, easyconfig, output_dir='easybuild-build'):
+def create_job(job_backend, build_command, easyconfig, output_dir='easybuild-build'):
     """
     Creates a job to build a *single* easyconfig.
 
-    @param job_server: A factory object for querying server parameters and creating actual job objects
+    @param job_backend: A factory object for querying server parameters and creating actual job objects
     @param build_command: format string for command, full path to an easyconfig file will be substituted in it
     @param easyconfig: easyconfig as processed by process_easyconfig
     @param output_dir: optional output path; --regtest-output-dir will be used inside the job with this variable
@@ -184,7 +182,7 @@ def create_job(job_server, build_command, easyconfig, output_dir='easybuild-buil
         previous_time = buildstats[-1]['build_time']
         extra['hours'] = int(math.ceil(previous_time * 2 / 60))
 
-    job = job_server.make_job(command, name, easybuild_vars, **extra)
+    job = job_backend.make_job(command, name, easybuild_vars, **extra)
     job.module = easyconfig['ec'].full_mod_name
 
     return job
diff --git a/easybuild/tools/testing.py b/easybuild/tools/testing.py
index e42327e831..c9fb689266 100644
--- a/easybuild/tools/testing.py
+++ b/easybuild/tools/testing.py
@@ -124,24 +124,8 @@ def regtest(easyconfig_paths, build_specs=None):
         # retry twice in case of failure, to avoid fluke errors
         command += "if [ $? -ne 0 ]; then %(cmd)s --force && %(cmd)s --force; fi" % {'cmd': cmd}
 
-        jobs = build_easyconfigs_in_parallel('pbs', command, resolved, output_dir=output_dir)
+        build_easyconfigs_in_parallel(command, resolved, output_dir=output_dir)
 
-        print "List of submitted jobs:"
-        for job in jobs:
-            print "%s: %s" % (job.name, job.jobid)
-        print "(%d jobs submitted)" % len(jobs)
-
-        # determine leaf nodes in dependency graph, and report them
-        all_deps = set()
-        for job in jobs:
-            all_deps = all_deps.union(job.deps)
-
-        leaf_nodes = []
-        for job in jobs:
-            if job.jobid not in all_deps:
-                leaf_nodes.append(str(job.jobid).split('.')[0])
-
-        _log.info("Job ids of leaf nodes in dep. graph: %s" % ','.join(leaf_nodes))
         _log.info("Submitted regression test as jobs, results in %s" % output_dir)
 
         return True  # success

From bffcd166d8a3d165842ef69214204b60c751a852 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Jul 2015 14:50:11 +0200
Subject: [PATCH 1073/1356] fix name clash

---
 easybuild/tools/parallelbuild.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index a830d60f7c..d9567c510f 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -69,12 +69,12 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybu
     """
     _log.info("going to build these easyconfigs in parallel: %s", easyconfigs)
 
-    job_backend = job_backend()
-    if job_backend is None:
+    live_job_backend = job_backend()
+    if live_job_backend is None:
         raise EasyBuildError("Can not use --job if no job backend is available.")
 
     try:
-        job_backend.init()
+        live_job_backend.init()
     except RuntimeError as err:
         raise EasyBuildError("connection to server failed (%s: %s), can't submit jobs.", err.__class__.__name__, err)
 
@@ -94,13 +94,13 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybu
 
         # the new job will only depend on already submitted jobs
         _log.info("creating job for ec: %s" % str(ec))
-        new_job = create_job(job_backend, build_command, ec, output_dir=output_dir)
+        new_job = create_job(live_job_backend, build_command, ec, output_dir=output_dir)
 
         # sometimes unresolved_deps will contain things, not needed to be build
         job_deps = [module_to_job[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in module_to_job]
 
         # actually (try to) submit job
-        job_backend.queue(new_job, job_deps)
+        live_job_backend.queue(new_job, job_deps)
         _log.info(
             "job %s for module %s has been submitted"
             % (new_job, new_job.module))
@@ -109,7 +109,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybu
         module_to_job[new_job.module] = new_job
         jobs.append(new_job)
 
-    job_backend.complete()
+    live_job_backend.complete()
 
     return jobs
 

From 99581f3dc1251d33990de60115d9e359e951d44f Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 14:57:08 +0200
Subject: [PATCH 1074/1356] Order changes + efficiency

---
 easybuild/framework/easyconfig/easyconfig.py | 48 +++++++++++------
 easybuild/tools/utilities.py                 |  8 +--
 test/framework/easyconfig.py                 | 56 ++++++++++----------
 3 files changed, 65 insertions(+), 47 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index fe984784dc..015ebdebfe 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -466,7 +466,6 @@ def toolchain(self):
             self.log.debug("Initialized toolchain: %s (opts: %s)" % (tc_dict, self['toolchainopts']))
         return self._toolchain
 
-
     def dump(self, fp):
         """
         Dump this easyconfig to file, with the given filename.
@@ -482,34 +481,49 @@ def dump(self, fp):
             ['sources', 'source_urls'],
             ['patches'],
             ['builddependencies', 'dependencies', 'hiddendependencies'],
-            ['parallel', 'maxparallel'],
             ['osdependencies'],
-            ['prebuildopts', 'preinstallopts', 'preconfigopts'],
-            ['sanity_check_paths'],
-            ['moduleclass']
+            ['preconfigopts', 'configopts'],
+            ['prebuildopts', 'buildopts'],
+            ['preinstallopts', 'installopts'],
+            ['parallel', 'maxparallel'],
+        ]
+
+        last_keys = [
+            ['sanity_check_paths'], 
+            ['moduleclass'],
         ]
 
+        # internal function; checks for default values
+        def check_and_print(keyset):
+            for group in keyset:
+                printed = False
+                for key1 in group:
+                    val = self._config[key1][0]
+                    for key2, [def_val, _, _] in DEFAULT_CONFIG.items():
+                        # only print parameters that are different from the default value
+                        if key1 == key2 and val != def_val:
+                            ebtxt.append("%s = %s" % (key1, quote_str(val, escape_newline=True)))
+                            printed_keys.append(key1)
+                            printed = True
+                if printed:
+                    ebtxt.append("")
+
+
         # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
         printed_keys = []
-        for group in grouped_keys:
-            for key1 in group:
-                val = self._config[key1][0]
-                for key2, [def_val, _, _] in DEFAULT_CONFIG.items():
-                    # only print parameters that are different from the default value
-                    if key1 == key2 and val != def_val:
-                        ebtxt.append("%s = %s" % (key1, quote_str(val, esc_newline=True)))
-                        printed_keys.append(key1)
-            ebtxt.append("")
+        check_and_print(grouped_keys)
 
         # print other easyconfig parameters at the end
         for key, [val, _, _] in DEFAULT_CONFIG.items():
-            if not key in printed_keys and val != self._config[key][0]:
-                ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], esc_newline=True)))
+            if not key in printed_keys and not key in ['sanity_check_paths', 'moduleclass'] and val != self._config[key][0]:
+                ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], escape_newline=True)))
+
+        # print last two parameters
+        check_and_print(last_keys)
 
         eb_file.write('\n'.join(ebtxt))
         eb_file.close()
-
     
     def _validate(self, attr, values):  # private method
         """
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 4736dad3aa..c0db220be4 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -56,19 +56,21 @@ def flatten(lst):
     return res
 
 
-def quote_str(x, esc_newline=False):
+def quote_str(x, escape_newline=False):
     """
     Obtain a new value to be used in string replacement context.
 
     For non-string values, it just returns the exact same value.
-
+    
     For string values, it tries to escape the string in quotes, e.g.,
     foo becomes 'foo', foo'bar becomes "foo'bar",
     foo'bar"baz becomes \"\"\"foo'bar"baz\"\"\", etc.
+
+    @param escape_newline: wrap strings that include a newline in triple quotes
     """
 
     if isinstance(x, basestring):
-        if ("'" in x and '"' in x) or (esc_newline and '\n' in x):
+        if ("'" in x and '"' in x) or (escape_newline and '\n' in x):
             return '"""%s"""' % x
         elif '"' in x:
             return "'%s'" % x
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 2779e3e0b9..e1f552e6e2 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1135,12 +1135,22 @@ def test_hide_hidden_deps(self):
 
     def test_quote_str(self):
         """Test quote_str function."""
-        self.assertEqual(quote_str('foo'), '"foo"')
-        self.assertEqual(quote_str('foo\'bar'), '"foo\'bar"')
-        self.assertEqual(quote_str('foo\'bar"baz'), '"""foo\'bar"baz"""')
-        self.assertEqual(quote_str("foo'bar\"baz"), '"""foo\'bar"baz"""')
+        teststrings = {
+            'foo' : '"foo"',
+            'foo\'bar' : '"foo\'bar"',
+            'foo\'bar"baz' : '"""foo\'bar"baz"""',
+            "foo'bar\"baz" : '"""foo\'bar"baz"""',
+            "foo\nbar" : '"foo\nbar"'
+        }
+
+        for t in teststrings:
+            self.assertEqual(quote_str(t), teststrings[t])
+
+        # test escape_newline
+        self.assertEqual(quote_str("foo\nbar", escape_newline=False), '"foo\nbar"')
+        self.assertEqual(quote_str("foo\nbar", escape_newline=True), '"""foo\nbar"""')
 
-        """ Non-string values """
+        # non-string values
         n = 42
         self.assertEqual(quote_str(n), 42)
         l = ["foo", "bar"]
@@ -1152,28 +1162,20 @@ def test_dump(self):
         """Test EasyConfig's dump() method."""
         test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
 
-        test_ec = os.path.join(self.test_prefix, 'test.eb')
-        test_ec2 = os.path.join(self.test_prefix, 'test2.eb')
-
-        ec = EasyConfig(os.path.join(test_ecs_dir, 'toy-0.0.eb'))
-        ec.dump(test_ec)
-        ectxt = read_file(test_ec)
-        version_regex = re.compile('^version = "0.0"', re.M)
-        self.assertTrue(version_regex.search(ectxt))
-        description_regex = re.compile('^description = "Toy C program."', re.M)
-        self.assertTrue(description_regex.search(ectxt))
-        """ Parse the result again """ 
-        dumped_ec = EasyConfig(test_ec)
-
-        ec2 = EasyConfig(os.path.join(test_ecs_dir, 'goolf-1.4.10.eb'))
-        ec2.dump(test_ec2)
-        ectxt2 = read_file(test_ec2)
-        name_regex = re.compile('^name = "goolf"', re.M)
-        self.assertTrue(name_regex.search(ectxt2))
-        moduleclass_regex = re.compile('^moduleclass = "toolchain"', re.M)
-        self.assertTrue(moduleclass_regex.search(ectxt2))
-
-        dumped_ec2 = EasyConfig(test_ec2)
+        for f in ['toy-0.0.eb', 'goolf-1.4.10.eb', 'ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb']:
+            test_ec = os.path.join(self.test_prefix, 'test.eb')
+
+            ec = EasyConfig(os.path.join(test_ecs_dir, f))
+            ec.dump(test_ec)
+            ectxt = read_file(test_ec)
+            name_regex = re.compile('^name = "[^"]*"', re.M)
+            description_regex = re.compile('^description = "[^"]*"', re.M)
+            version_regex = re.compile('^version = [0-9\.]*', re.M)
+            self.assertTrue(name_regex.search(ectxt))
+            self.assertTrue(description_regex.search(ectxt))
+            self.assertTrue(version_regex.search(ectxt))
+            # parse result again
+            dumped_ec = EasyConfig(test_ec)
 
 
 def suite():

From 1482a6fdb41944a66218a04bb48633d1188aee92 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 14:59:02 +0200
Subject: [PATCH 1075/1356] Apparently im bad with whitespace

---
 easybuild/tools/utilities.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index c0db220be4..add8dbc57f 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -61,7 +61,7 @@ def quote_str(x, escape_newline=False):
     Obtain a new value to be used in string replacement context.
 
     For non-string values, it just returns the exact same value.
-    
+ 
     For string values, it tries to escape the string in quotes, e.g.,
     foo becomes 'foo', foo'bar becomes "foo'bar",
     foo'bar"baz becomes \"\"\"foo'bar"baz\"\"\", etc.

From 93baad6ce4c7c8d213fec24df72e9e7f3f363b55 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Jul 2015 15:20:43 +0200
Subject: [PATCH 1076/1356] fix job count in printed message for PbsPython
 backend, fix print msg in main after submitting jobs

---
 easybuild/main.py                 | 4 ++--
 easybuild/tools/job/pbs_python.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 0c42cd6a2e..c13e2be6fd 100755
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -296,9 +296,9 @@ def main(testing_data=(None, None, None)):
 
     # submit build as job(s), clean up and exit
     if options.job:
-        job_info_txt = submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
+        submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
         if not testing:
-            print_msg("Submitted parallel build jobs, exiting now: %s" % job_info_txt)
+            print_msg("Submitted parallel build jobs, exiting now")
             cleanup(logfile, eb_tmpdir, testing)
             sys.exit(0)
 
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 087ca6d325..d511093583 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -148,7 +148,7 @@ def complete(self):
 
         # print list of submitted jobs
         submitted_jobs = '; '.join(["%s (%s): %s" % (job.name, job.module, job.jobid) for job in self._submitted])
-        print_msg("List of submitted jobs (%d): %s" % (len(submitted_jobs), submitted_jobs), log=self.log)
+        print_msg("List of submitted jobs (%d): %s" % (len(self._submitted), submitted_jobs), log=self.log)
 
         # determine leaf nodes in dependency graph, and report them
         all_deps = set()

From e4b8253d91470c58df0a08c74650ab2b0d7245ff Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Jul 2015 15:23:03 +0200
Subject: [PATCH 1077/1356] avoid hardcoding list of states in GC3Pie progress
 report implementation

---
 easybuild/tools/job/gc3pie.py | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 6daa33bb24..d2e903e206 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -249,27 +249,25 @@ def complete(self):
             self._engine.progress()
 
             # report progress
-            self._print_status_report(['NEW', 'SUBMITTED', 'RUNNING', 'ok', 'failed'])
+            self._print_status_report()
 
             # Wait a few seconds...
             time.sleep(self.poll_interval)
 
         # final status report
         print_msg("Done processing jobs", log=self.log)
-        self._print_status_report(['ok', 'failed'])
+        self._print_status_report()
 
     @gc3pie_imported
-    def _print_status_report(self, states=('ok', 'failed')):
+    def _print_status_report(self):
         """
         Print a job status report to STDOUT and the log file.
 
-        The number of jobs in any of the given states is reported; the
+        The number of jobs in each states is reported; the
         figures are extracted from the `stats()` method of the
-        currently-running GC3Pie engine.  Additional keyword arguments
-        can override specific stats; this is used, e.g., to correctly
-        report the number of total jobs right from the start.
+        currently-running GC3Pie engine.
         """
         stats = self._engine.stats(only=Application)
-        overview = ', '.join(["%d %s" % (stats[s], s.lower()) for s in states if stats[s]])
+        states = ', '.join(["%d %s" % (stats[s], s.lower()) for s in stats if stats[s]])
         total = len(self.jobs)
-        print_msg("GC3Pie job overview: %s (total: %s)" % (overview, total), log=self.log, silent=build_option('silent'))
+        print_msg("GC3Pie job overview: %s (total: %s)" % (states, total), log=self.log, silent=build_option('silent'))

From 3bb531e30faf2ee630cecd1e4c5516f91599d5d0 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 15:38:27 +0200
Subject: [PATCH 1078/1356] Docstring + flatten list

---
 easybuild/framework/easyconfig/easyconfig.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 015ebdebfe..c05e3e0093 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -489,12 +489,14 @@ def dump(self, fp):
         ]
 
         last_keys = [
-            ['sanity_check_paths'], 
+            ['sanity_check_paths'],
             ['moduleclass'],
         ]
 
-        # internal function; checks for default values
         def check_and_print(keyset):
+            """
+            Internal function checking for default values
+            """
             for group in keyset:
                 printed = False
                 for key1 in group:
@@ -516,7 +518,7 @@ def check_and_print(keyset):
 
         # print other easyconfig parameters at the end
         for key, [val, _, _] in DEFAULT_CONFIG.items():
-            if not key in printed_keys and not key in ['sanity_check_paths', 'moduleclass'] and val != self._config[key][0]:
+            if not key in printed_keys and not key in [k for sublist in last_keys for k in sublist] and val != self._config[key][0]:
                 ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], escape_newline=True)))
 
         # print last two parameters
@@ -524,7 +526,7 @@ def check_and_print(keyset):
 
         eb_file.write('\n'.join(ebtxt))
         eb_file.close()
-    
+
     def _validate(self, attr, values):  # private method
         """
         validation helper method. attr is the attribute it will check, values are the possible values.

From 23c90858dc0d82cbe07712872a27c5f610349820 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Jul 2015 16:12:14 +0200
Subject: [PATCH 1079/1356] do not include count for 'total' jobs as GC3Pie
 sees it

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index d2e903e206..c13d5e8eca 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -268,6 +268,6 @@ def _print_status_report(self):
         currently-running GC3Pie engine.
         """
         stats = self._engine.stats(only=Application)
-        states = ', '.join(["%d %s" % (stats[s], s.lower()) for s in stats if stats[s]])
+        states = ', '.join(["%d %s" % (stats[s], s.lower()) for s in stats if s != 'total' and stats[s]])
         total = len(self.jobs)
         print_msg("GC3Pie job overview: %s (total: %s)" % (states, total), log=self.log, silent=build_option('silent'))

From 5e9bc98097e26a86e2bf95bb2c1dfacad50786f4 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 16:25:07 +0200
Subject: [PATCH 1080/1356] fix unnecessary loop + test

---
 easybuild/framework/easyconfig/easyconfig.py | 25 +++++++++-----------
 test/framework/easyconfig.py                 | 18 +++++++-------
 2 files changed, 20 insertions(+), 23 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index c05e3e0093..d268116ff5 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -488,10 +488,7 @@ def dump(self, fp):
             ['parallel', 'maxparallel'],
         ]
 
-        last_keys = [
-            ['sanity_check_paths'],
-            ['moduleclass'],
-        ]
+        last_keys = ['sanity_check_paths', 'moduleclass']
 
         def check_and_print(keyset):
             """
@@ -499,13 +496,13 @@ def check_and_print(keyset):
             """
             for group in keyset:
                 printed = False
-                for key1 in group:
-                    val = self._config[key1][0]
-                    for key2, [def_val, _, _] in DEFAULT_CONFIG.items():
-                        # only print parameters that are different from the default value
-                        if key1 == key2 and val != def_val:
-                            ebtxt.append("%s = %s" % (key1, quote_str(val, escape_newline=True)))
-                            printed_keys.append(key1)
+                for key in group:
+                    val = self._config[key][0]
+                    if key in DEFAULT_CONFIG:
+                        def_val = DEFAULT_CONFIG[key]
+                        if val not in def_val:
+                            ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
+                            printed_keys.append(key)
                             printed = True
                 if printed:
                     ebtxt.append("")
@@ -517,12 +514,12 @@ def check_and_print(keyset):
         check_and_print(grouped_keys)
 
         # print other easyconfig parameters at the end
-        for key, [val, _, _] in DEFAULT_CONFIG.items():
-            if not key in printed_keys and not key in [k for sublist in last_keys for k in sublist] and val != self._config[key][0]:
+        for key, [val, _, _] in sorted(DEFAULT_CONFIG.items()):
+            if key not in printed_keys and key not in last_keys and val != self._config[key][0]:
                 ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], escape_newline=True)))
 
         # print last two parameters
-        check_and_print(last_keys)
+        check_and_print([[k] for k in last_keys])
 
         eb_file.write('\n'.join(ebtxt))
         eb_file.close()
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index e1f552e6e2..6ac6ece696 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1155,9 +1155,9 @@ def test_quote_str(self):
         self.assertEqual(quote_str(n), 42)
         l = ["foo", "bar"]
         self.assertEqual(quote_str(l), ["foo", "bar"])
-        self.assertEqual(quote_str(('foo', 'bar')), ('foo', 'bar')) 
-	 
-	
+        self.assertEqual(quote_str(('foo', 'bar')), ('foo', 'bar'))
+
+
     def test_dump(self):
         """Test EasyConfig's dump() method."""
         test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
@@ -1168,12 +1168,12 @@ def test_dump(self):
             ec = EasyConfig(os.path.join(test_ecs_dir, f))
             ec.dump(test_ec)
             ectxt = read_file(test_ec)
-            name_regex = re.compile('^name = "[^"]*"', re.M)
-            description_regex = re.compile('^description = "[^"]*"', re.M)
-            version_regex = re.compile('^version = [0-9\.]*', re.M)
-            self.assertTrue(name_regex.search(ectxt))
-            self.assertTrue(description_regex.search(ectxt))
-            self.assertTrue(version_regex.search(ectxt))
+
+            patterns = [r'^name = ["\']', r'^version = ["0-9\.]', r'^description = ["\']']
+            for pattern in patterns:
+                regex = re.compile(pattern, re.M)
+                self.assertTrue(regex.search(ectxt), "Pattern '%s' found in: %s" % (regex.pattern, ectxt))
+
             # parse result again
             dumped_ec = EasyConfig(test_ec)
 

From 6c2eedb8919ade31792fa3b222a0beada6207035 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 16:57:16 +0200
Subject: [PATCH 1081/1356] Raise error when key is not valid

---
 easybuild/framework/easyconfig/easyconfig.py | 4 +++-
 test.eb                                      | 0
 2 files changed, 3 insertions(+), 1 deletion(-)
 create mode 100644 test.eb

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index d268116ff5..8e0abad881 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -497,13 +497,15 @@ def check_and_print(keyset):
             for group in keyset:
                 printed = False
                 for key in group:
-                    val = self._config[key][0]
                     if key in DEFAULT_CONFIG:
+                        val = self._config[key][0]
                         def_val = DEFAULT_CONFIG[key]
                         if val not in def_val:
                             ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
                             printed_keys.append(key)
                             printed = True
+                    else:
+                        raise KeyError('"' + key + '" is not a valid key')
                 if printed:
                     ebtxt.append("")
 
diff --git a/test.eb b/test.eb
new file mode 100644
index 0000000000..e69de29bb2

From 1b1e489fc925406c8fb52297da6cde199f835e53 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 1 Jul 2015 17:07:14 +0200
Subject: [PATCH 1082/1356] Remove check for valid key (KeyError will be
 raised)

---
 easybuild/framework/easyconfig/easyconfig.py | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 8e0abad881..c5252a3f49 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -497,15 +497,12 @@ def check_and_print(keyset):
             for group in keyset:
                 printed = False
                 for key in group:
-                    if key in DEFAULT_CONFIG:
-                        val = self._config[key][0]
-                        def_val = DEFAULT_CONFIG[key]
-                        if val not in def_val:
-                            ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
-                            printed_keys.append(key)
-                            printed = True
-                    else:
-                        raise KeyError('"' + key + '" is not a valid key')
+                    val = self._config[key][0]
+                    def_val = DEFAULT_CONFIG[key]
+                    if val not in def_val:
+                        ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
+                        printed_keys.append(key)
+                        printed = True
                 if printed:
                     ebtxt.append("")
 

From 87a79cef5738f7ab13118d18607de2cff025223e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 Jul 2015 17:17:39 +0200
Subject: [PATCH 1083/1356] tell GC3Pie engine to not rename output directory
 all the time

---
 easybuild/tools/job/gc3pie.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index c13d5e8eca..03baf506e0 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -30,7 +30,7 @@
 @author: Kenneth Hoste (Ghent University)
 """
 from distutils.version import LooseVersion
-import os
+from time import gmtime, strftime
 import re
 import time
 
@@ -134,8 +134,7 @@ def init(self):
         if cfgfile:
             self.config_files.append(cfgfile)
 
-        # additional subdirectory, since GC3Pie renames the output dir if it already exists
-        self.output_dir = os.path.join(build_option('job_output_dir'), 'eb-gc3pie-jobs')
+        self.output_dir = build_option('job_output_dir')
         self.jobs = DependentTaskCollection(output_dir=self.output_dir)
 
         # after polling for job status, sleep for this time duration
@@ -184,8 +183,8 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
             'join': True,
             # location for log file
             'output_dir': self.output_dir,
-            # log file name
-            'stdout': 'eb-%s-gc3pie-job.log' % name,
+            # log file name (including timestamp to try and ensure unique filename)
+            'stdout': 'eb-%s-gc3pie-job-%s.log' % (name, strftime("%Y%M%d-UTC-%H-%M-%S", gmtime()))
         })
 
         # walltime
@@ -229,6 +228,10 @@ def complete(self):
         except gc3libs.exceptions.Error as err:
             raise EasyBuildError("Failed to create GC3Pie engine: %s", err)
 
+        # make sure that all job log files end up in the same directory, rather than renaming the output directory
+        # see https://gc3pie.readthedocs.org/en/latest/programmers/api/gc3libs/core.html#gc3libs.core.Engine
+        self._engine.fetch_output_overwrites = True
+
         # Add your application to the engine. This will NOT submit
         # your application yet, but will make the engine *aware* of
         # the application.

From a9a0309487352890d583f7202eb41d9795ccd1bd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Jul 2015 08:21:35 +0200
Subject: [PATCH 1084/1356] fix remarks

---
 easybuild/tools/job/gc3pie.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 03baf506e0..b13ac3cd18 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -136,6 +136,7 @@ def init(self):
 
         self.output_dir = build_option('job_output_dir')
         self.jobs = DependentTaskCollection(output_dir=self.output_dir)
+        self.job_cnt = 0
 
         # after polling for job status, sleep for this time duration
         # before polling again (in seconds)
@@ -213,6 +214,7 @@ def queue(self, job, dependencies=frozenset()):
         @param dependencies: jobs on which this job depends.
         """
         self.jobs.add(job, dependencies)
+        self.job_cnt += 1
 
     @gc3pie_imported
     def complete(self):
@@ -266,11 +268,11 @@ def _print_status_report(self):
         """
         Print a job status report to STDOUT and the log file.
 
-        The number of jobs in each states is reported; the
+        The number of jobs in each state is reported; the
         figures are extracted from the `stats()` method of the
         currently-running GC3Pie engine.
         """
         stats = self._engine.stats(only=Application)
         states = ', '.join(["%d %s" % (stats[s], s.lower()) for s in stats if s != 'total' and stats[s]])
-        total = len(self.jobs)
-        print_msg("GC3Pie job overview: %s (total: %s)" % (states, total), log=self.log, silent=build_option('silent'))
+        print_msg("GC3Pie job overview: %s (total: %s)" % (states, self.job_cnt),
+                  log=self.log, silent=build_option('silent'))

From 932e0e7f172c02e1cebe2a0a63f67421fd701f80 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Jul 2015 08:23:16 +0200
Subject: [PATCH 1085/1356] include comment on job_cnt

---
 easybuild/tools/job/gc3pie.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index b13ac3cd18..d9a8697ad4 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -214,6 +214,7 @@ def queue(self, job, dependencies=frozenset()):
         @param dependencies: jobs on which this job depends.
         """
         self.jobs.add(job, dependencies)
+        # since it's not trivial to determine the correct job count from self.jobs, we keep track of a count ourselves
         self.job_cnt += 1
 
     @gc3pie_imported

From 71fb772014f3f81f06bf9808587180abdeedfd1d Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Thu, 2 Jul 2015 09:01:48 +0200
Subject: [PATCH 1086/1356] rename internal function in dump()

---
 easybuild/framework/easyconfig/easyconfig.py | 9 +++++----
 test.eb                                      | 0
 2 files changed, 5 insertions(+), 4 deletions(-)
 delete mode 100644 test.eb

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index c5252a3f49..08cc7ad3c6 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -490,9 +490,9 @@ def dump(self, fp):
 
         last_keys = ['sanity_check_paths', 'moduleclass']
 
-        def check_and_print(keyset):
+        def include_defined_parameters(keyset):
             """
-            Internal function checking for default values
+            Internal function to include parameters in the dumped easyconfig file which have a non-default value.
             """
             for group in keyset:
                 printed = False
@@ -510,15 +510,16 @@ def check_and_print(keyset):
         # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
         printed_keys = []
-        check_and_print(grouped_keys)
+        include_defined_parameters(grouped_keys)
 
         # print other easyconfig parameters at the end
         for key, [val, _, _] in sorted(DEFAULT_CONFIG.items()):
             if key not in printed_keys and key not in last_keys and val != self._config[key][0]:
                 ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], escape_newline=True)))
+        ebtxt.append("")
 
         # print last two parameters
-        check_and_print([[k] for k in last_keys])
+        include_defined_parameters([[k] for k in last_keys])
 
         eb_file.write('\n'.join(ebtxt))
         eb_file.close()
diff --git a/test.eb b/test.eb
deleted file mode 100644
index e69de29bb2..0000000000

From b11d26ed6b18417e52719b3706ca184a9cf35815 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Jul 2015 09:31:59 +0200
Subject: [PATCH 1087/1356] add support for *not* expanding relative paths in
 prepend_paths (+ apply #1300 fix to ModuleGeneratorLua)

---
 easybuild/tools/module_generator.py | 33 ++++++++++++++++++++++-------
 test/framework/module_generator.py  | 11 +++++++++-
 2 files changed, 35 insertions(+), 9 deletions(-)

diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 6ce72b8dce..a63dfada92 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -216,9 +216,14 @@ def unload_module(self, mod_name):
         cond_unload = self.conditional_statement("is-loaded %(mod)s", "module unload %(mod)s") % {'mod': mod_name}
         return '\n'.join(['', cond_unload])
 
-    def prepend_paths(self, key, paths, allow_abs=False):
+    def prepend_paths(self, key, paths, allow_abs=False, expand_relpaths=True):
         """
         Generate prepend-path statements for the given list of paths.
+
+        @param key: environment variable to prepend paths to
+        @param paths: list of paths to prepend
+        @param allow_abs: allow providing of absolute paths
+        @param expand_relpaths: expand relative paths into absolute paths (by prefixing install dir)
         """
         template = "prepend-path\t%s\t\t%s\n"
 
@@ -234,7 +239,10 @@ def prepend_paths(self, key, paths, allow_abs=False):
             elif not os.path.isabs(path):
                 # prepend $root (= installdir) for (non-empty) relative paths
                 if path:
-                    abspaths.append(os.path.join('$root', path))
+                    if expand_relpaths:
+                        abspaths.append(os.path.join('$root', path))
+                    else:
+                        abspaths.append(path)
                 else:
                     abspaths.append('$root')
             else:
@@ -373,29 +381,38 @@ def unload_module(self, mod_name):
         cond_unload = self.conditional_statement('isloaded("%(mod)s")', 'unload("%(mod)s")') % {'mod': mod_name}
         return '\n'.join(['', cond_unload])
 
-    def prepend_paths(self, key, paths, allow_abs=False):
+    def prepend_paths(self, key, paths, allow_abs=False, expand_relpaths=True):
         """
         Generate prepend-path statements for the given list of paths
+
+        @param key: environment variable to prepend paths to
+        @param paths: list of paths to prepend
+        @param allow_abs: allow providing of absolute paths
+        @param expand_relpaths: expand relative paths into absolute paths (by prefixing install dir)
         """
         if isinstance(paths, basestring):
             self.log.debug("Wrapping %s into a list before using it to prepend path %s", paths, key)
             paths = [paths]
 
-        for i, path in enumerate(paths):
+        abspaths = []
+        for path in paths:
             if os.path.isabs(path):
                 if allow_abs:
-                    paths[i] = quote_str(path)
+                    abspaths.append(quote_str(path))
                 else:
                     raise EasyBuildError("Absolute path %s passed to prepend_paths which only expects relative paths.",
                                          path)
             else:
                 # use pathJoin for (non-empty) relative paths
                 if path:
-                    paths[i] = self.PATH_JOIN_TEMPLATE % path
+                    if expand_relpaths:
+                        abspaths.append(self.PATH_JOIN_TEMPLATE % path)
+                    else:
+                        abspaths.append(quote_str(path))
                 else:
-                    paths[i] = 'root'
+                    abspaths.append('root')
 
-        statements = [self.PREPEND_PATH_TEMPLATE % (key, p) for p in paths]
+        statements = [self.PREPEND_PATH_TEMPLATE % (key, p) for p in abspaths]
         return ''.join(statements)
 
     def use(self, paths):
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index b7294bb4ef..481d32a85a 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -190,13 +190,19 @@ def test_prepend_paths(self):
             res = self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True)
             self.assertEqual("prepend-path\tkey\t\t/abs/path\n", res)
 
+            res = self.modgen.prepend_paths('key', ['1234@example.com'], expand_relpaths=False)
+            self.assertEqual("prepend-path\tkey\t\t1234@example.com\n", res)
+
         else:
             expected = ''.join([
                 'prepend_path("key", pathJoin(root, "path1"))\n',
                 'prepend_path("key", pathJoin(root, "path2"))\n',
                 'prepend_path("key", root)\n',
             ])
-            self.assertEqual(expected, self.modgen.prepend_paths("key", ["path1", "path2", '']))
+            paths = ['path1', 'path2', '']
+            self.assertEqual(expected, self.modgen.prepend_paths("key", paths))
+            # 2nd call should still give same result, no side-effects like manipulating passed list 'paths'!
+            self.assertEqual(expected, self.modgen.prepend_paths("key", paths))
 
             expected = 'prepend_path("bar", pathJoin(root, "foo"))\n'
             self.assertEqual(expected, self.modgen.prepend_paths("bar", "foo"))
@@ -204,6 +210,9 @@ def test_prepend_paths(self):
             expected = 'prepend_path("key", "/abs/path")\n'
             self.assertEqual(expected, self.modgen.prepend_paths("key", ["/abs/path"], allow_abs=True))
 
+            res = self.modgen.prepend_paths('key', ['1234@example.com'], expand_relpaths=False)
+            self.assertEqual('prepend_path("key", "1234@example.com")\n', res)
+
         self.assertErrorRegex(EasyBuildError, "Absolute path %s/foo passed to prepend_paths " \
                                               "which only expects relative paths." % self.modgen.app.installdir,
                               self.modgen.prepend_paths, "key2", ["bar", "%s/foo" % self.modgen.app.installdir])

From e17593ce22f0f9bb2f2bd506eff0c1e39b0dbdab Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Jul 2015 14:16:24 +0200
Subject: [PATCH 1088/1356] look into making GC3Pie not ignore errors (WIP)

---
 easybuild/tools/job/gc3pie.py   |  4 ++++
 test/framework/parallelbuild.py | 11 +++++++++--
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index d9a8697ad4..03f0b581f5 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -57,6 +57,10 @@
     # make handling of log.error compatible with stdlib logging
     gc3libs.log.raiseError = False
 
+    # instruct GC3Pie to not ignore errors, but raise exceptions instead
+    #gc3libs.UNIGNORE_ALL_ERRORS = True
+    gc3libs.UNIGNORE_ERRORS = set(['fetch_output'])
+
     # GC3Pie is available, no need guard against import errors
     def gc3pie_imported(fn):
         """No-op decorator."""
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 8bd8f9bf79..adaa460616 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -28,13 +28,14 @@
 @author: Kenneth Hoste (Ghent University)
 """
 import os
+import stat
 from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader, main
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
 
 from easybuild.framework.easyconfig.tools import process_easyconfig
 from easybuild.tools import config
-from easybuild.tools.filetools import write_file
+from easybuild.tools.filetools import adjust_permissions, mkdir, write_file
 from easybuild.tools.job import pbs_python
 from easybuild.tools.job.pbs_python import PbsPython
 from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
@@ -137,10 +138,16 @@ def test_build_easyconfigs_in_parallel_gc3pie(self):
         gc3pie_cfgfile = os.path.join(self.test_prefix, 'gc3pie_local.ini')
         write_file(gc3pie_cfgfile, GC3PIE_LOCAL_CONFIGURATION % {'resourcedir': resourcedir})
 
+        output_dir = os.path.join(self.test_prefix, 'subdir', 'gc3pie_output_dir')
+        mkdir(output_dir, parents=True)
+        # remove write permissions on parent dir of specified output dir,
+        # to check that GC3Pie does not try to rename the (already existing) output directory...
+        adjust_permissions(os.path.dirname(output_dir), stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH, add=False)
+
         build_options = {
             'job_backend_config': gc3pie_cfgfile,
             'job_max_walltime': 24,
-            'job_output_dir': self.test_prefix,
+            'job_output_dir': output_dir,
             'job_polling_interval': 0.2,  # quick polling
             'job_target_resource': 'ebtestlocalhost',
             'robot_path': os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs'),

From d1e6733fcb3e586b9a072859bc55996b9f66218a Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Thu, 2 Jul 2015 14:44:55 +0200
Subject: [PATCH 1089/1356] Fixed extra values bug

---
 easybuild/framework/easyconfig/easyconfig.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 08cc7ad3c6..9de1eae5e4 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -148,7 +148,8 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
             tup = (type(self.extra_options), self.extra_options)
             self.log.nosupport("extra_options return value should be of type 'dict', found '%s': %s" % tup, '2.0')
 
-        self._config.update(self.extra_options)
+        # deep copy to make sure self.extra_options remains unchanged
+        self._config.update(copy.deepcopy(self.extra_options))
 
         self.mandatory = MANDATORY_PARAMS[:]
 
@@ -490,6 +491,10 @@ def dump(self, fp):
 
         last_keys = ['sanity_check_paths', 'moduleclass']
 
+        # build dict of default values
+        default_values = dict([(key, DEFAULT_CONFIG[key][0]) for key in DEFAULT_CONFIG])
+        default_values.update(dict([(key, self.extra_options[key][0]) for key in self.extra_options]))
+
         def include_defined_parameters(keyset):
             """
             Internal function to include parameters in the dumped easyconfig file which have a non-default value.
@@ -498,22 +503,20 @@ def include_defined_parameters(keyset):
                 printed = False
                 for key in group:
                     val = self._config[key][0]
-                    def_val = DEFAULT_CONFIG[key]
-                    if val not in def_val:
+                    if val != default_values[key]:
                         ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
                         printed_keys.append(key)
                         printed = True
                 if printed:
                     ebtxt.append("")
 
-
         # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
         printed_keys = []
         include_defined_parameters(grouped_keys)
 
         # print other easyconfig parameters at the end
-        for key, [val, _, _] in sorted(DEFAULT_CONFIG.items()):
+        for (key, val) in default_values.items():
             if key not in printed_keys and key not in last_keys and val != self._config[key][0]:
                 ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], escape_newline=True)))
         ebtxt.append("")

From d9f16c1be0ca3c609524baa984c9ed63a0b0a7b6 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Thu, 2 Jul 2015 15:16:31 +0200
Subject: [PATCH 1090/1356] style fixes

---
 easybuild/framework/easyconfig/easyconfig.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 9de1eae5e4..2516978716 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -502,9 +502,8 @@ def include_defined_parameters(keyset):
             for group in keyset:
                 printed = False
                 for key in group:
-                    val = self._config[key][0]
-                    if val != default_values[key]:
-                        ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
+                    if self[key] != default_values[key]:
+                        ebtxt.append("%s = %s" % (key, quote_str(self[key], escape_newline=True)))
                         printed_keys.append(key)
                         printed = True
                 if printed:
@@ -516,9 +515,10 @@ def include_defined_parameters(keyset):
         include_defined_parameters(grouped_keys)
 
         # print other easyconfig parameters at the end
-        for (key, val) in default_values.items():
-            if key not in printed_keys and key not in last_keys and val != self._config[key][0]:
-                ebtxt.append("%s = %s" % (key, quote_str(self._config[key][0], escape_newline=True)))
+        keys_to_ignore = printed_keys + last_keys
+        for key in default_values:
+            if key not in keys_to_ignore and default_values[key] != self[key]:
+                ebtxt.append("%s = %s" % (key, quote_str(self[key], escape_newline=True)))
         ebtxt.append("")
 
         # print last two parameters

From 380e4593e6f6399eb1d983d7710aa396defa3540 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Jul 2015 15:27:38 +0200
Subject: [PATCH 1091/1356] set retrieve_overwrites to True in GC3Pie engine,
 fix unit test to check whether output dir is NOT renamed

---
 easybuild/tools/job/gc3pie.py   |  7 +++----
 test/framework/parallelbuild.py | 15 ++++++++++++---
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 03f0b581f5..c6990c0f59 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -58,8 +58,7 @@
     gc3libs.log.raiseError = False
 
     # instruct GC3Pie to not ignore errors, but raise exceptions instead
-    #gc3libs.UNIGNORE_ALL_ERRORS = True
-    gc3libs.UNIGNORE_ERRORS = set(['fetch_output'])
+    gc3libs.UNIGNORE_ALL_ERRORS = True
 
     # GC3Pie is available, no need guard against import errors
     def gc3pie_imported(fn):
@@ -237,7 +236,7 @@ def complete(self):
 
         # make sure that all job log files end up in the same directory, rather than renaming the output directory
         # see https://gc3pie.readthedocs.org/en/latest/programmers/api/gc3libs/core.html#gc3libs.core.Engine
-        self._engine.fetch_output_overwrites = True
+        self._engine.retrieve_overwrites = True
 
         # Add your application to the engine. This will NOT submit
         # your application yet, but will make the engine *aware* of
@@ -265,7 +264,7 @@ def complete(self):
             time.sleep(self.poll_interval)
 
         # final status report
-        print_msg("Done processing jobs", log=self.log)
+        print_msg("Done processing jobs", log=self.log, silent=build_option('silent'))
         self._print_status_report()
 
     @gc3pie_imported
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index adaa460616..22f29bcb92 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -35,7 +35,7 @@
 
 from easybuild.framework.easyconfig.tools import process_easyconfig
 from easybuild.tools import config
-from easybuild.tools.filetools import adjust_permissions, mkdir, write_file
+from easybuild.tools.filetools import adjust_permissions, mkdir, which, write_file
 from easybuild.tools.job import pbs_python
 from easybuild.tools.job.pbs_python import PbsPython
 from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
@@ -57,6 +57,7 @@
 auth = none
 override = no
 resourcedir = %(resourcedir)s
+time_cmd = %(time)s
 """
 
 def mock(*args, **kwargs):
@@ -136,13 +137,20 @@ def test_build_easyconfigs_in_parallel_gc3pie(self):
         # put GC3Pie config in place to use local host and fork/exec
         resourcedir = os.path.join(self.test_prefix, 'gc3pie')
         gc3pie_cfgfile = os.path.join(self.test_prefix, 'gc3pie_local.ini')
-        write_file(gc3pie_cfgfile, GC3PIE_LOCAL_CONFIGURATION % {'resourcedir': resourcedir})
+        gc3pie_cfgtxt = GC3PIE_LOCAL_CONFIGURATION % {
+            'resourcedir': resourcedir,
+            'time': which('time'),
+        }
+        write_file(gc3pie_cfgfile, gc3pie_cfgtxt)
 
         output_dir = os.path.join(self.test_prefix, 'subdir', 'gc3pie_output_dir')
+        # purposely pre-create output dir, and put a file in it (to check whether GC3Pie tries to rename the output dir)
         mkdir(output_dir, parents=True)
+        write_file(os.path.join(output_dir, 'foo'), 'bar')
         # remove write permissions on parent dir of specified output dir,
         # to check that GC3Pie does not try to rename the (already existing) output directory...
-        adjust_permissions(os.path.dirname(output_dir), stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH, add=False)
+        adjust_permissions(os.path.dirname(output_dir), stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH,
+                           add=False, recursive=False)
 
         build_options = {
             'job_backend_config': gc3pie_cfgfile,
@@ -168,6 +176,7 @@ def test_build_easyconfigs_in_parallel_gc3pie(self):
         self.assertTrue(os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0'))
         self.assertTrue(os.path.join(self.test_installpath, 'software', 'toy', '0.0', 'bin', 'toy'))
 
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(ParallelBuildTest)

From 914c489caae30b425d1750d9174672da3d79da32 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Thu, 2 Jul 2015 16:26:15 +0200
Subject: [PATCH 1092/1356] dump_extra unit test

---
 test/framework/easyconfig.py | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 6ac6ece696..1e92b3754d 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1177,6 +1177,28 @@ def test_dump(self):
             # parse result again
             dumped_ec = EasyConfig(test_ec)
 
+    def test_dump_extra(self):
+        """Test EasyConfig's dump() method for files containing extra values"""
+
+        rawtxt = '\n'.join([
+            "easyblock = 'EB_foo'",
+            "name = 'foo'",
+            "version = '0.0.1'",
+            "description = 'foo description'",
+            "homepage = 'http://foo.com/'",
+            "toolchain = {'name': 'dummy', 'version': 'dummy'}",
+            "foo_extra1 = 'foobar'",
+        ])
+
+        testec = os.path.join(self.test_prefix, 'test.eb')
+
+        ec = EasyConfig(None, rawtxt=rawtxt)
+        ec.dump(testec)
+        extra_regex = re.compile(r'^foo_extra1 = "foobar"', re.M)
+        self.assertTrue(extra_regex.search(read_file(testec)))
+
+        dumped_ec = EasyConfig(testec)
+
 
 def suite():
     """ returns all the testcases in this module """

From 2541c7b485be8712e2ae2f40b5aa32fb5782ad61 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 2 Jul 2015 18:08:27 +0200
Subject: [PATCH 1093/1356] bump minimal required SVN revision to 4255 (which
 includes fix for auth=none)

---
 easybuild/tools/job/gc3pie.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index c6990c0f59..774cfc9cd1 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -94,7 +94,7 @@ class GC3Pie(JobBackend):
 
     REQ_VERSION = '2.3'
     DEVELOPMENT_VERSION = 'development'  # 'magic' version string indicated non-released version
-    REQ_SVN_REVISION = 4223  # use integer value, not a string!
+    REQ_SVN_REVISION = 4255  # use integer value, not a string!
 
     @gc3pie_imported
     def _check_version(self):

From f0e66c77d87187c9dd61ad351f8fea137881e1ee Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 3 Jul 2015 09:40:40 +0200
Subject: [PATCH 1094/1356] extended test

---
 easybuild/framework/easyconfig/easyconfig.py |  4 ++--
 test/framework/easyconfig.py                 | 25 ++++++++++++--------
 2 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 2516978716..b96ac2c5a6 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -517,14 +517,14 @@ def include_defined_parameters(keyset):
         # print other easyconfig parameters at the end
         keys_to_ignore = printed_keys + last_keys
         for key in default_values:
-            if key not in keys_to_ignore and default_values[key] != self[key]:
+            if key not in keys_to_ignore and self[key] != default_values[key]:
                 ebtxt.append("%s = %s" % (key, quote_str(self[key], escape_newline=True)))
         ebtxt.append("")
 
         # print last two parameters
         include_defined_parameters([[k] for k in last_keys])
 
-        eb_file.write('\n'.join(ebtxt))
+        eb_file.write(('\n'.join(ebtxt)).strip()) # strip for newlines at the end
         eb_file.close()
 
     def _validate(self, attr, values):  # private method
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 1e92b3754d..40946ec994 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1181,21 +1181,26 @@ def test_dump_extra(self):
         """Test EasyConfig's dump() method for files containing extra values"""
 
         rawtxt = '\n'.join([
-            "easyblock = 'EB_foo'",
-            "name = 'foo'",
-            "version = '0.0.1'",
-            "description = 'foo description'",
-            "homepage = 'http://foo.com/'",
-            "toolchain = {'name': 'dummy', 'version': 'dummy'}",
-            "foo_extra1 = 'foobar'",
+            'easyblock = "EB_foo"',
+            '',
+            'name = "foo"',
+            'version = "0.0.1"',
+            '',
+            'homepage = "http://foo.com/"',
+            'description = "foo description"',
+            '',
+            'toolchain = {\'version\': \'dummy\', \'name\': \'dummy\'}',
+            '',
+            'foo_extra1 = "foobar"',
         ])
 
-        testec = os.path.join(self.test_prefix, 'test.eb')
+        handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')
+        os.close(handle)
 
         ec = EasyConfig(None, rawtxt=rawtxt)
         ec.dump(testec)
-        extra_regex = re.compile(r'^foo_extra1 = "foobar"', re.M)
-        self.assertTrue(extra_regex.search(read_file(testec)))
+        ectxt = read_file(testec)
+        self.assertEqual(rawtxt, ectxt)
 
         dumped_ec = EasyConfig(testec)
 

From 18e9a1ebcadd428dd254afe40c6330eb9bcc5f6f Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 3 Jul 2015 12:08:38 +0200
Subject: [PATCH 1095/1356] templated values dumped unresolved

---
 easybuild/framework/easyconfig/easyconfig.py | 5 +++++
 test/framework/easyconfig.py                 | 4 +++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index b96ac2c5a6..69958a6cde 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -491,6 +491,9 @@ def dump(self, fp):
 
         last_keys = ['sanity_check_paths', 'moduleclass']
 
+        tmp = self.enable_templating
+        self.enable_templating = False
+
         # build dict of default values
         default_values = dict([(key, DEFAULT_CONFIG[key][0]) for key in DEFAULT_CONFIG])
         default_values.update(dict([(key, self.extra_options[key][0]) for key in self.extra_options]))
@@ -527,6 +530,8 @@ def include_defined_parameters(keyset):
         eb_file.write(('\n'.join(ebtxt)).strip()) # strip for newlines at the end
         eb_file.close()
 
+        self.enable_tamplating = tmp
+
     def _validate(self, attr, values):  # private method
         """
         validation helper method. attr is the attribute it will check, values are the possible values.
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 40946ec994..3dfda1a253 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1178,7 +1178,7 @@ def test_dump(self):
             dumped_ec = EasyConfig(test_ec)
 
     def test_dump_extra(self):
-        """Test EasyConfig's dump() method for files containing extra values"""
+        """Test EasyConfig's dump() method for files containing extra values and templates"""
 
         rawtxt = '\n'.join([
             'easyblock = "EB_foo"',
@@ -1191,6 +1191,8 @@ def test_dump_extra(self):
             '',
             'toolchain = {\'version\': \'dummy\', \'name\': \'dummy\'}',
             '',
+            'sources = [\'%(name)sV%(version)s.TAR.gz\']',
+            '',
             'foo_extra1 = "foobar"',
         ])
 

From c955fb0b39b2d85ad46de7741b0d68d4636a5498 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 3 Jul 2015 15:42:45 +0200
Subject: [PATCH 1096/1356] template values in dump method + unit test update

---
 easybuild/framework/easyconfig/easyconfig.py | 23 ++++++++++++++--
 test/framework/easyconfig.py                 | 28 ++++++++++++++++++--
 2 files changed, 47 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 69958a6cde..23626f44e1 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -64,7 +64,7 @@
 from easybuild.framework.easyconfig.parser import DEPRECATED_PARAMETERS, REPLACED_PARAMETERS
 from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.templates import template_constant_dict
-
+from easybuild.framework.easyconfig.templates import TEMPLATE_CONSTANTS
 
 _log = fancylogger.getLogger('easyconfig.easyconfig', fname=False)
 
@@ -498,6 +498,24 @@ def dump(self, fp):
         default_values = dict([(key, DEFAULT_CONFIG[key][0]) for key in DEFAULT_CONFIG])
         default_values.update(dict([(key, self.extra_options[key][0]) for key in self.extra_options]))
 
+        template_values = dict([(const[1], const[0]) for const in TEMPLATE_CONSTANTS])
+
+        def replace_templates(value):
+            """ Internal function to replace certain values with constants"""
+            if isinstance(value, basestring):
+                value = template_values.get(value.lower(), value)
+
+            else:
+                if isinstance(value, list):
+                    value = [replace_templates(v) for v in value]
+                elif isinstance(value, tuple):
+                    value = tuple(replace_templates(list(value)))
+                elif isinstance(value, dict):
+                    value = dict([(key, replace_templates(v)) for key, v in value.items()])
+
+            return value
+
+
         def include_defined_parameters(keyset):
             """
             Internal function to include parameters in the dumped easyconfig file which have a non-default value.
@@ -506,7 +524,8 @@ def include_defined_parameters(keyset):
                 printed = False
                 for key in group:
                     if self[key] != default_values[key]:
-                        ebtxt.append("%s = %s" % (key, quote_str(self[key], escape_newline=True)))
+                        val = replace_templates(self[key])
+                        ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
                         printed_keys.append(key)
                         printed = True
                 if printed:
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 3dfda1a253..f0450654db 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1191,8 +1191,6 @@ def test_dump_extra(self):
             '',
             'toolchain = {\'version\': \'dummy\', \'name\': \'dummy\'}',
             '',
-            'sources = [\'%(name)sV%(version)s.TAR.gz\']',
-            '',
             'foo_extra1 = "foobar"',
         ])
 
@@ -1206,6 +1204,32 @@ def test_dump_extra(self):
 
         dumped_ec = EasyConfig(testec)
 
+    def test_dump_template(self):
+        """ Test EasyConfig's dump() method for files containing templates"""
+        rawtxt = '\n'.join([
+            'easyblock = "EB_toy"',
+            '',
+            'name = "foo"',
+            'version = "0.0.1"',
+            '',
+            'homepage = "http://foo.com/"',
+            'description = "foo description"',
+            '',
+            'toolchain = {\'version\': \'dummy\', \'name\': \'dummy\'}',
+            '',
+            'sources = [\'%(namelower)s-%(version)s.TAR.gz\']',
+        ])
+
+        handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')
+        os.close(handle)
+
+        ec = EasyConfig(None, rawtxt=rawtxt)
+        ec.dump(testec)
+        ectxt = read_file(testec)
+
+        regex = re.compile(r'sources \= \[\'SOURCELOWER_TAR_GZ\'\]', re.M)
+        self.assertTrue(regex.search(ectxt))
+
 
 def suite():
     """ returns all the testcases in this module """

From ad223046c4d2af48d726fe5320b73a6f690d6ef7 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 3 Jul 2015 15:58:11 +0200
Subject: [PATCH 1097/1356] Update test doctring

---
 test/framework/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index f0450654db..66fff4a2b4 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1178,7 +1178,7 @@ def test_dump(self):
             dumped_ec = EasyConfig(test_ec)
 
     def test_dump_extra(self):
-        """Test EasyConfig's dump() method for files containing extra values and templates"""
+        """Test EasyConfig's dump() method for files containing extra values"""
 
         rawtxt = '\n'.join([
             'easyblock = "EB_foo"',

From d73f2c6d765f143fea79e7c8984822a42772ac57 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Jul 2015 16:14:56 +0200
Subject: [PATCH 1098/1356] verify whether import of included modules works as
 expected

---
 easybuild/tools/include.py | 56 +++++++++++++++++++++++++++++++-------
 easybuild/tools/options.py |  2 +-
 test/framework/include.py  |  4 ++-
 3 files changed, 50 insertions(+), 12 deletions(-)

diff --git a/easybuild/tools/include.py b/easybuild/tools/include.py
index f2e6f875bb..f6dd8fc1d1 100644
--- a/easybuild/tools/include.py
+++ b/easybuild/tools/include.py
@@ -125,6 +125,24 @@ def set_up_eb_package(parent_path, eb_pkg_name, subpkgs=None, pkg_init_body=None
         pkgpath = os.path.dirname(pkgpath)
 
 
+def verify_imports(pymods, pypkg, from_path):
+    """Verify that import of specified modules from specified package and expected location works."""
+    for pymod in pymods:
+        pymod_spec = '%s.%s' % (pypkg, pymod)
+        try:
+            pymod = __import__(pymod_spec, fromlist=[pypkg])
+        # different types of exceptions may be thrown, not only ImportErrors
+        # e.g. when module being imported contains syntax errors or undefined variables
+        except Exception as err:
+            raise EasyBuildError("Failed to import easyblock %s from %s: %s", pymod_spec, from_path, err)
+
+        if not os.path.samefile(os.path.dirname(pymod.__file__), from_path):
+            raise EasyBuildError("Module %s not imported from expected location (%s): %s",
+                                 pymod_spec, from_path, pymod.__file__)
+
+        _log.debug("Import of %s from %s verified", pymod_spec, from_path)
+
+
 def include_easyblocks(tmpdir, paths):
     """Include generic and software-specific easyblocks found in specified locations."""
     easyblocks_path = os.path.join(tmpdir, 'included-easyblocks')
@@ -147,10 +165,10 @@ def include_easyblocks(tmpdir, paths):
 
         symlink(easyblock_module, target_path)
 
-    included_easyblocks = [x for x in os.listdir(easyblocks_dir) if x not in ['__init__.py', 'generic']]
-    included_generic_easyblocks = [x for x in os.listdir(os.path.join(easyblocks_dir, 'generic')) if x != '__init__.py']
-    _log.debug("Included generic easyblocks: %s", included_generic_easyblocks)
-    _log.debug("Included software-specific easyblocks: %s", included_easyblocks)
+    included_ebs = [x for x in os.listdir(easyblocks_dir) if x not in ['__init__.py', 'generic']]
+    included_generic_ebs = [x for x in os.listdir(os.path.join(easyblocks_dir, 'generic')) if x != '__init__.py']
+    _log.debug("Included generic easyblocks: %s", included_generic_ebs)
+    _log.debug("Included software-specific easyblocks: %s", included_ebs)
 
     # inject path into Python search path, and reload modules to get it 'registered' in sys.modules
     sys.path.insert(0, easyblocks_path)
@@ -159,6 +177,12 @@ def include_easyblocks(tmpdir, paths):
         reload(easybuild.easyblocks)
         reload(easybuild.easyblocks.generic)
 
+    # sanity check: verify that included easyblocks can be imported (from expected location)
+    for subdir, ebs in [('', included_ebs), ('generic', included_generic_ebs)]:
+        pkg = '.'.join(['easybuild', 'easyblocks', subdir]).strip('.')
+        loc = os.path.join(easyblocks_dir, subdir)
+        verify_imports([os.path.splitext(eb)[0] for eb in ebs], pkg, loc)
+
     return easyblocks_path
 
 
@@ -183,6 +207,9 @@ def include_module_naming_schemes(tmpdir, paths):
     sys.path.insert(0, mns_path)
     reload(easybuild.tools.module_naming_scheme)
 
+    # sanity check: verify that included module naming schemes can be imported (from expected location)
+    verify_imports([os.path.splitext(mns)[0] for mns in included_mns], 'easybuild.tools.module_naming_scheme', mns_dir)
+
     return mns_path
 
 
@@ -193,7 +220,7 @@ def include_toolchains(tmpdir, paths):
 
     set_up_eb_package(toolchains_path, 'easybuild.toolchains', subpkgs=toolchain_subpkgs)
 
-    toolchains_dir = os.path.join(toolchains_path, 'easybuild', 'toolchains')
+    tcs_dir = os.path.join(toolchains_path, 'easybuild', 'toolchains')
 
     allpaths = expand_glob_paths(paths)
     for toolchain_module in allpaths:
@@ -203,17 +230,19 @@ def include_toolchains(tmpdir, paths):
 
         # generic toolchains are expected to be in a directory named 'generic'
         if parent_dir in toolchain_subpkgs:
-            target_path = os.path.join(toolchains_dir, parent_dir, filename)
+            target_path = os.path.join(tcs_dir, parent_dir, filename)
         else:
-            target_path = os.path.join(toolchains_dir, filename)
+            target_path = os.path.join(tcs_dir, filename)
 
         symlink(toolchain_module, target_path)
 
-    included_toolchains = [x for x in os.listdir(toolchains_dir) if x not in ['__init__.py'] + toolchain_subpkgs]
+    included_toolchains = [x for x in os.listdir(tcs_dir) if x not in ['__init__.py'] + toolchain_subpkgs]
     _log.debug("Included toolchains: %s", included_toolchains)
+
+    included_subpkg_modules = {}
     for subpkg in toolchain_subpkgs:
-        included_subpkg_modules = [x for x in os.listdir(os.path.join(toolchains_dir, subpkg)) if x != '__init__.py']
-        _log.debug("Included toolchain %s components: %s", subpkg, included_subpkg_modules)
+        included_subpkg_modules[subpkg] = [x for x in os.listdir(os.path.join(tcs_dir, subpkg)) if x != '__init__.py']
+        _log.debug("Included toolchain %s components: %s", subpkg, included_subpkg_modules[subpkg])
 
     # inject path into Python search path, and reload modules to get it 'registered' in sys.modules
     sys.path.insert(0, toolchains_path)
@@ -221,4 +250,11 @@ def include_toolchains(tmpdir, paths):
     for subpkg in toolchain_subpkgs:
         reload(sys.modules['easybuild.toolchains.%s' % subpkg])
 
+    # sanity check: verify that included toolchain modules can be imported (from expected location)
+    verify_imports([os.path.splitext(mns)[0] for mns in included_toolchains], 'easybuild.toolchains', tcs_dir)
+    for subpkg in toolchain_subpkgs:
+        pkg = '.'.join(['easybuild', 'toolchains', subpkg])
+        loc = os.path.join(tcs_dir, subpkg)
+        verify_imports([os.path.splitext(tcmod)[0] for tcmod in included_subpkg_modules[subpkg]], pkg, loc)
+
     return toolchains_path
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 2cef64f5a6..9f8e83cc71 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -786,7 +786,7 @@ def parse_options(args=None):
     try:
         eb_go = EasyBuildOptions(usage=usage, description=description, prog='eb', envvar_prefix=CONFIG_ENV_VAR_PREFIX,
                                  go_args=args, error_env_options=True, error_env_option_method=raise_easybuilderror)
-    except Exception, err:
+    except Exception as err:
         raise EasyBuildError("Failed to parse configuration options: %s" % err)
 
     return eb_go
diff --git a/test/framework/include.py b/test/framework/include.py
index 28b4ed7e29..dc3d3b3c97 100644
--- a/test/framework/include.py
+++ b/test/framework/include.py
@@ -113,6 +113,9 @@ def test_include_easyblocks_priority(self):
         myeasyblocks = os.path.join(self.test_prefix, 'myeasyblocks')
         mkdir(myeasyblocks)
 
+        # 'undo' import of foo easyblock
+        del sys.modules['easybuild.easyblocks.foo']
+
         foo_easyblock_txt = '\n'.join([
             "from easybuild.framework.easyblock import EasyBlock",
             "class EB_Foo(EasyBlock):",
@@ -121,7 +124,6 @@ def test_include_easyblocks_priority(self):
         write_file(os.path.join(myeasyblocks, 'foo.py'), foo_easyblock_txt)
         included_easyblocks_path = include_easyblocks(self.test_prefix, [os.path.join(myeasyblocks, 'foo.py')])
 
-        reload(easybuild.easyblocks.foo)
         foo_pyc_path = easybuild.easyblocks.foo.__file__
         foo_real_py_path = os.path.realpath(os.path.join(os.path.dirname(foo_pyc_path), 'foo.py'))
         self.assertFalse(os.path.samefile(os.path.dirname(foo_pyc_path), test_easyblocks))

From ee8b90a6b2a342ef9c9d6e9a5d723ab0b25f10e0 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 3 Jul 2015 16:42:48 +0200
Subject: [PATCH 1099/1356] replace_templates is no longer an inner function +
 some fixes

---
 easybuild/framework/easyconfig/easyconfig.py | 50 ++++++++++----------
 test/framework/easyconfig.py                 |  6 +--
 2 files changed, 29 insertions(+), 27 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 23626f44e1..320c355cb8 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -63,8 +63,8 @@
 from easybuild.framework.easyconfig.licenses import EASYCONFIG_LICENSES_DICT, License
 from easybuild.framework.easyconfig.parser import DEPRECATED_PARAMETERS, REPLACED_PARAMETERS
 from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig
-from easybuild.framework.easyconfig.templates import template_constant_dict
-from easybuild.framework.easyconfig.templates import TEMPLATE_CONSTANTS
+from easybuild.framework.easyconfig.templates import template_constant_dict, TEMPLATE_CONSTANTS
+
 
 _log = fancylogger.getLogger('easyconfig.easyconfig', fname=False)
 
@@ -491,30 +491,14 @@ def dump(self, fp):
 
         last_keys = ['sanity_check_paths', 'moduleclass']
 
-        tmp = self.enable_templating
-        self.enable_templating = False
+        orig_enable_templating = self.enable_templating
+        self.enable_templating = False # templated values should be dumped unresolved
 
         # build dict of default values
         default_values = dict([(key, DEFAULT_CONFIG[key][0]) for key in DEFAULT_CONFIG])
         default_values.update(dict([(key, self.extra_options[key][0]) for key in self.extra_options]))
 
-        template_values = dict([(const[1], const[0]) for const in TEMPLATE_CONSTANTS])
-
-        def replace_templates(value):
-            """ Internal function to replace certain values with constants"""
-            if isinstance(value, basestring):
-                value = template_values.get(value.lower(), value)
-
-            else:
-                if isinstance(value, list):
-                    value = [replace_templates(v) for v in value]
-                elif isinstance(value, tuple):
-                    value = tuple(replace_templates(list(value)))
-                elif isinstance(value, dict):
-                    value = dict([(key, replace_templates(v)) for key, v in value.items()])
-
-            return value
-
+        templ_const = dict([(const[1], const[0]) for const in TEMPLATE_CONSTANTS])
 
         def include_defined_parameters(keyset):
             """
@@ -524,7 +508,7 @@ def include_defined_parameters(keyset):
                 printed = False
                 for key in group:
                     if self[key] != default_values[key]:
-                        val = replace_templates(self[key])
+                        val = replace_templates(self[key], templ_const)
                         ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
                         printed_keys.append(key)
                         printed = True
@@ -549,7 +533,7 @@ def include_defined_parameters(keyset):
         eb_file.write(('\n'.join(ebtxt)).strip()) # strip for newlines at the end
         eb_file.close()
 
-        self.enable_tamplating = tmp
+        self.enable_tamplating = orig_enable_templating
 
     def _validate(self, attr, values):  # private method
         """
@@ -942,8 +926,26 @@ def resolve_template(value, tmpl_dict):
 
     return value
 
+def replace_templates(value, templ_const):
+    """
+    Given a value, try to substitute constants where possible.
+        - value can be a string, list, tuple, dict or combination thereof
+        - templ_const is a dictionary of constants
+    """
+    if isinstance(value, basestring):
+        value = templ_const.get(value, value)
+
+    else:
+        if isinstance(value, list):
+            value = [replace_templates(v, templ_const) for v in value]
+        elif isinstance(value, tuple):
+            value = tuple(replace_templates(list(value), templ_const))
+        elif isinstance(value, dict):
+            value = dict([(key, replace_templates(v, templ_const)) for key, v in value.items()])
+    return value
+
 
-def process_easyconfig(path, build_specs=None, validate=True, parse_only=False, hidden=None):
+def process_easyconfig(path,ecess_easyconfigbuild_specs=None, validate=True, parse_only=False, hidden=None):
     """
     Process easyconfig, returning some information for each block
     @param path: path to easyconfig file
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index f0450654db..33cd6ac08d 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1189,7 +1189,7 @@ def test_dump_extra(self):
             'homepage = "http://foo.com/"',
             'description = "foo description"',
             '',
-            'toolchain = {\'version\': \'dummy\', \'name\': \'dummy\'}',
+            "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
             'foo_extra1 = "foobar"',
         ])
@@ -1215,9 +1215,9 @@ def test_dump_template(self):
             'homepage = "http://foo.com/"',
             'description = "foo description"',
             '',
-            'toolchain = {\'version\': \'dummy\', \'name\': \'dummy\'}',
+            "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
-            'sources = [\'%(namelower)s-%(version)s.TAR.gz\']',
+            "sources = ['%(namelower)s-%(version)s.tar.gz']",
         ])
 
         handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')

From a2396c5bf2575830e7d833fb918cce5c0ab6ceea Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 3 Jul 2015 16:50:10 +0200
Subject: [PATCH 1100/1356] Fixed a typo

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 320c355cb8..93f3ea4b60 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -945,7 +945,7 @@ def replace_templates(value, templ_const):
     return value
 
 
-def process_easyconfig(path,ecess_easyconfigbuild_specs=None, validate=True, parse_only=False, hidden=None):
+def process_easyconfig(path,build_specs=None, validate=True, parse_only=False, hidden=None):
     """
     Process easyconfig, returning some information for each block
     @param path: path to easyconfig file

From 9439f96f8034ef3d4c8e17eae172552aafadedbb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Jul 2015 17:01:59 +0200
Subject: [PATCH 1101/1356] fix broken test

---
 test/framework/options.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 61ee21a5dd..14b03922eb 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1699,6 +1699,9 @@ def test_include_easyblocks(self):
         foo_regex = re.compile(r"^\|-- EB_foo \(easybuild.easyblocks.foo @ %s\)"  % path_pattern, re.M)
         self.assertTrue(foo_regex.search(logtxt), "Pattern '%s' found in: %s" % (foo_regex.pattern, logtxt))
 
+        # 'undo' import of foo easyblock
+        del sys.modules['easybuild.easyblocks.foo']
+
         # include extra test easyblocks
         foo_txt = '\n'.join([
             'from easybuild.framework.easyblock import EasyBlock',

From d1293cce5b11d1bcf8750ed54d46563a7313e3a0 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 3 Jul 2015 17:08:12 +0200
Subject: [PATCH 1102/1356] to be continued on monday

---
 easybuild/framework/easyconfig/easyconfig.py |  6 ++++++
 test.eb                                      | 16 ++++++++++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 test.eb

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 93f3ea4b60..6b65b29108 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -498,7 +498,12 @@ def dump(self, fp):
         default_values = dict([(key, DEFAULT_CONFIG[key][0]) for key in DEFAULT_CONFIG])
         default_values.update(dict([(key, self.extra_options[key][0]) for key in self.extra_options]))
 
+        self.generate_template_values()
         templ_const = dict([(const[1], const[0]) for const in TEMPLATE_CONSTANTS])
+        templ_const.update([(self.template_values[key], key) for key in self.template_values if key != ''])
+
+        for i in templ_const:
+            print i
 
         def include_defined_parameters(keyset):
             """
@@ -933,6 +938,7 @@ def replace_templates(value, templ_const):
         - templ_const is a dictionary of constants
     """
     if isinstance(value, basestring):
+        # TODO replace template values, not only constants
         value = templ_const.get(value, value)
 
     else:
diff --git a/test.eb b/test.eb
new file mode 100644
index 0000000000..1f8a9f6b54
--- /dev/null
+++ b/test.eb
@@ -0,0 +1,16 @@
+name = "name"
+version = "version"
+
+homepage = "https://www.ruby-lang.org"
+description = """Ruby is a dynamic, open source programming language with 
+ a focus on simplicity and productivity. It has an elegant syntax that is 
+ natural to read and easy to write."""
+
+toolchain = {'version': 'toolchain_version', 'name': 'toolchain_version'}
+
+sources = ['SOURCELOWER_TAR_GZ']
+source_urls = ['http://cache.ruby-lang.org/pub/ruby/']
+
+exts_list = [('ffi', '1.9.8', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('childprocess', '0.5.6', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('json', '1.8.2', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('cabin', '0.7.1', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('backports', '3.6.4', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('arr-pm', '0.0.10', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('clamp', '0.6.5', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']})]
+
+moduleclass = "lang"
\ No newline at end of file

From f09130d1500487ea9c0a570af5ad21424c906864 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 3 Jul 2015 17:10:38 +0200
Subject: [PATCH 1103/1356] Delete test.eb

... again
---
 test.eb | 16 ----------------
 1 file changed, 16 deletions(-)
 delete mode 100644 test.eb

diff --git a/test.eb b/test.eb
deleted file mode 100644
index 1f8a9f6b54..0000000000
--- a/test.eb
+++ /dev/null
@@ -1,16 +0,0 @@
-name = "name"
-version = "version"
-
-homepage = "https://www.ruby-lang.org"
-description = """Ruby is a dynamic, open source programming language with 
- a focus on simplicity and productivity. It has an elegant syntax that is 
- natural to read and easy to write."""
-
-toolchain = {'version': 'toolchain_version', 'name': 'toolchain_version'}
-
-sources = ['SOURCELOWER_TAR_GZ']
-source_urls = ['http://cache.ruby-lang.org/pub/ruby/']
-
-exts_list = [('ffi', '1.9.8', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('childprocess', '0.5.6', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('json', '1.8.2', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('cabin', '0.7.1', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('backports', '3.6.4', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('arr-pm', '0.0.10', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('clamp', '0.6.5', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']})]
-
-moduleclass = "lang"
\ No newline at end of file

From 8b02f1b95a71eb5a93814921a1b16311e9c45b9f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 3 Jul 2015 18:11:37 +0200
Subject: [PATCH 1104/1356] make sure custom foo easyblock is 'unloaded' again

---
 test/framework/include.py | 5 ++++-
 test/framework/options.py | 3 +++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/test/framework/include.py b/test/framework/include.py
index dc3d3b3c97..07e7476b94 100644
--- a/test/framework/include.py
+++ b/test/framework/include.py
@@ -122,13 +122,16 @@ def test_include_easyblocks_priority(self):
             "   pass",
         ])
         write_file(os.path.join(myeasyblocks, 'foo.py'), foo_easyblock_txt)
-        included_easyblocks_path = include_easyblocks(self.test_prefix, [os.path.join(myeasyblocks, 'foo.py')])
+        include_easyblocks(self.test_prefix, [os.path.join(myeasyblocks, 'foo.py')])
 
         foo_pyc_path = easybuild.easyblocks.foo.__file__
         foo_real_py_path = os.path.realpath(os.path.join(os.path.dirname(foo_pyc_path), 'foo.py'))
         self.assertFalse(os.path.samefile(os.path.dirname(foo_pyc_path), test_easyblocks))
         self.assertTrue(os.path.samefile(foo_real_py_path, os.path.join(myeasyblocks, 'foo.py')))
 
+        # 'undo' import of foo easyblock
+        del sys.modules['easybuild.easyblocks.foo']
+
     def test_include_mns(self):
         """Test include_module_naming_schemes()."""
         testdir = os.path.dirname(os.path.abspath(__file__))
diff --git a/test/framework/options.py b/test/framework/options.py
index 14b03922eb..20bf8ca55a 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1726,6 +1726,9 @@ def test_include_easyblocks(self):
         foo_regex = re.compile(r"^\|-- EB_foo \(easybuild.easyblocks.foo @ %s\)"  % path_pattern, re.M)
         self.assertTrue(foo_regex.search(logtxt), "Pattern '%s' found in: %s" % (foo_regex.pattern, logtxt))
 
+        # 'undo' import of foo easyblock
+        del sys.modules['easybuild.easyblocks.foo']
+
     def test_include_module_naming_schemes(self):
         """Test --include-module-naming-schemes."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')

From 6f0c94a3945af696b583d1b0d302f868ba3ab507 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 6 Jul 2015 11:02:43 +0200
Subject: [PATCH 1105/1356] fix comment

---
 easybuild/tools/include.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/include.py b/easybuild/tools/include.py
index f6dd8fc1d1..dbde8e067f 100644
--- a/easybuild/tools/include.py
+++ b/easybuild/tools/include.py
@@ -228,7 +228,7 @@ def include_toolchains(tmpdir, paths):
 
         parent_dir = os.path.basename(os.path.dirname(toolchain_module))
 
-        # generic toolchains are expected to be in a directory named 'generic'
+        # toolchain components are expected to be in a directory named according to the type of component
         if parent_dir in toolchain_subpkgs:
             target_path = os.path.join(tcs_dir, parent_dir, filename)
         else:

From 3169a4754e114dafaa4c9332bb43fe54ce0fd222 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 6 Jul 2015 11:10:54 +0200
Subject: [PATCH 1106/1356] set resource_errors_are_fatal=True in create_engine
 call

---
 easybuild/tools/job/gc3pie.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 774cfc9cd1..60f05ac661 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -92,9 +92,9 @@ class GC3Pie(JobBackend):
     terminated.
     """
 
-    REQ_VERSION = '2.3'
+    REQ_VERSION = '2.4.0'
     DEVELOPMENT_VERSION = 'development'  # 'magic' version string indicated non-released version
-    REQ_SVN_REVISION = 4255  # use integer value, not a string!
+    REQ_SVN_REVISION = 4287  # use integer value, not a string!
 
     @gc3pie_imported
     def _check_version(self):
@@ -229,7 +229,7 @@ def complete(self):
         """
         # create an instance of `Engine` using the list of configuration files
         try:
-            self._engine = create_engine(*self.config_files)
+            self._engine = create_engine(*self.config_files, resource_errors_are_fatal=True)
 
         except gc3libs.exceptions.Error as err:
             raise EasyBuildError("Failed to create GC3Pie engine: %s", err)

From ecb9880b4961161be3ded1a4bc796526ce73ea1f Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 6 Jul 2015 13:07:14 +0200
Subject: [PATCH 1107/1356] Replace strings with template values in dump method

---
 easybuild/framework/easyconfig/easyconfig.py | 39 ++++++++++++--------
 test.eb                                      | 16 --------
 test/framework/easyconfig.py                 |  8 ++--
 3 files changed, 28 insertions(+), 35 deletions(-)
 delete mode 100644 test.eb

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 6b65b29108..899aa62d7e 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1,4 +1,4 @@
-# #
+
 # Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
@@ -500,10 +500,9 @@ def dump(self, fp):
 
         self.generate_template_values()
         templ_const = dict([(const[1], const[0]) for const in TEMPLATE_CONSTANTS])
-        templ_const.update([(self.template_values[key], key) for key in self.template_values if key != ''])
+        templ_val = dict([(self.template_values[key], key) for key in self.template_values if len(self.template_values[key]) > 2])
 
-        for i in templ_const:
-            print i
+        exclude_keys = ['name', 'version', 'description', 'homepage', 'toolchain'] # values will not be templated for these keys
 
         def include_defined_parameters(keyset):
             """
@@ -512,8 +511,10 @@ def include_defined_parameters(keyset):
             for group in keyset:
                 printed = False
                 for key in group:
-                    if self[key] != default_values[key]:
-                        val = replace_templates(self[key], templ_const)
+                    val = self[key]
+                    if val != default_values[key]:
+                        if key not in exclude_keys:
+                            val = replace_templates(val, templ_const, templ_val)
                         ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
                         printed_keys.append(key)
                         printed = True
@@ -931,27 +932,35 @@ def resolve_template(value, tmpl_dict):
 
     return value
 
-def replace_templates(value, templ_const):
+def replace_templates(value, templ_const, templ_val):
     """
-    Given a value, try to substitute constants where possible.
+    Given a value, try to substitute template strings where possible.
         - value can be a string, list, tuple, dict or combination thereof
-        - templ_const is a dictionary of constants
+        - templ_const is a dictionary of template strings (constants)
+        - templ_val is a dictionary of template strings specific for this easyconfig file
     """
     if isinstance(value, basestring):
-        # TODO replace template values, not only constants
-        value = templ_const.get(value, value)
+        old_value = ""
+        while value != old_value:
+            old_value = value
+            if value in templ_const:
+                value = templ_const[value]
+            else:
+                # check for template values - longest strings first
+                for v in sorted(templ_val, key=lambda v: len(v), reverse=True):
+                    value = re.sub(r"\b" + re.escape(v) + r"\b", r'%(' + templ_val[v] + ')s', value)
 
     else:
         if isinstance(value, list):
-            value = [replace_templates(v, templ_const) for v in value]
+            value = [replace_templates(v, templ_const, templ_val) for v in value]
         elif isinstance(value, tuple):
-            value = tuple(replace_templates(list(value), templ_const))
+            value = tuple(replace_templates(list(value), templ_const, templ_val))
         elif isinstance(value, dict):
-            value = dict([(key, replace_templates(v, templ_const)) for key, v in value.items()])
+            value = dict([(key, replace_templates(v, templ_const, templ_val)) for key, v in value.items()])
     return value
 
 
-def process_easyconfig(path,build_specs=None, validate=True, parse_only=False, hidden=None):
+def process_easyconfig(path, build_specs=None, validate=True, parse_only=False, hidden=None):
     """
     Process easyconfig, returning some information for each block
     @param path: path to easyconfig file
diff --git a/test.eb b/test.eb
deleted file mode 100644
index 1f8a9f6b54..0000000000
--- a/test.eb
+++ /dev/null
@@ -1,16 +0,0 @@
-name = "name"
-version = "version"
-
-homepage = "https://www.ruby-lang.org"
-description = """Ruby is a dynamic, open source programming language with 
- a focus on simplicity and productivity. It has an elegant syntax that is 
- natural to read and easy to write."""
-
-toolchain = {'version': 'toolchain_version', 'name': 'toolchain_version'}
-
-sources = ['SOURCELOWER_TAR_GZ']
-source_urls = ['http://cache.ruby-lang.org/pub/ruby/']
-
-exts_list = [('ffi', '1.9.8', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('childprocess', '0.5.6', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('json', '1.8.2', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('cabin', '0.7.1', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('backports', '3.6.4', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('arr-pm', '0.0.10', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']}), ('clamp', '0.6.5', {'source_tmpl': '%(name)s-%(version)s.gem', 'source_urls': ['http://rubygems.org/downloads/']})]
-
-moduleclass = "lang"
\ No newline at end of file
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 68ef5e00c1..1b814e55f5 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1209,7 +1209,7 @@ def test_dump_template(self):
         rawtxt = '\n'.join([
             'easyblock = "EB_toy"',
             '',
-            'name = "foo"',
+            'name = "Foo"',
             'version = "0.0.1"',
             '',
             'homepage = "http://foo.com/"',
@@ -1217,7 +1217,7 @@ def test_dump_template(self):
             '',
             "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
-            "sources = ['%(namelower)s-%(version)s.tar.gz']",
+            "sources = ['foo-0.0.1.tar.gz']",
         ])
 
         handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')
@@ -1227,8 +1227,8 @@ def test_dump_template(self):
         ec.dump(testec)
         ectxt = read_file(testec)
 
-        regex = re.compile(r'sources \= \[\'SOURCELOWER_TAR_GZ\'\]', re.M)
-        self.assertTrue(regex.search(ectxt))
+        regex = re.compile(r"sources \= \['SOURCELOWER_TAR_GZ'\]", re.M)
+        self.assertTrue(regex.search(ectxt), "Pattern '%s' found in: %s" % (regex.pattern, ectxt))
 
 
 def suite():

From 8f771d745e97d05a2978deb21df5f607a2787240 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 6 Jul 2015 13:45:14 +0200
Subject: [PATCH 1108/1356] clumsiness

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 899aa62d7e..6138511f3e 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1,4 +1,4 @@
-
+# #
 # Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,

From 0dceb5d678470be9975dc7f90f2fa8b0abded9d4 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 6 Jul 2015 17:04:33 +0200
Subject: [PATCH 1109/1356] Begin script for generic easyblock documentation

---
 easybuild/tools/docs.py | 63 ++++++++++++++++++++++++++++++++++++++---
 1 file changed, 59 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 628d6d5b2f..795656db59 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -34,25 +34,27 @@
 @author: Ward Poelmans (Ghent University)
 """
 import copy
+import os
 
 from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, HIDDEN, sorted_categories
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.utilities import quote_str
+from easybuild.easyblocks.generic.configuremake import ConfigureMake
 
 
 FORMAT_RST = 'rst'
 FORMAT_TXT = 'txt'
 
+def det_col_width(entries, title):
+    """Determine column width based on column title and list of entries."""
+    return max(map(len, entries + [title]))
+
 
 def avail_easyconfig_params_rst(title, grouped_params):
     """
     Compose overview of available easyconfig parameters, in RST format.
     """
-    def det_col_width(entries, title):
-        """Determine column width based on column title and list of entries."""
-        return max(map(len, entries + [title]))
-
     # main title
     lines = [
         title,
@@ -160,3 +162,56 @@ def avail_easyconfig_params(easyblock, output_format):
         FORMAT_TXT: avail_easyconfig_params_txt,
     }
     return avail_easyconfig_params_functions[output_format](title, grouped_params)
+
+def generic_easyblocks(classname):
+    """
+    Compose overview of available generic easyblocks in rst format
+    """
+    block = globals()[classname]
+    lines = [
+        '``' + classname + '``',
+        '=' * (len(classname)+4),
+        '',
+    ]
+
+    derived = '(derives from '
+    for base in block.__bases__:
+        derived += '``'+base.__name__+'`` '
+    derived += ')'
+    lines.extend([derived, ''])
+
+    lines.extend([block.__doc__.strip(), ''])
+
+    if block.extra_options(None):
+        extra_parameters = 'Extra easyconfig parameters specific to ``' + classname + '`` easyblock'
+        lines.extend([extra_parameters, '-' * len(extra_parameters), ''])
+        ex_opt = block.extra_options()
+
+        ectitle = 'easyconfig parameter'
+        desctitle = 'description'
+        dftitle = 'default value'
+
+        # figure out column widths
+        nw = det_col_width([key for key in ex_opt], ectitle) + 4 # +4 for backticks
+        dw = det_col_width([val[1] for val in ex_opt.values()], desctitle)
+        dfw = det_col_width([str(val[0]) for val in ex_opt.values()], dftitle) + 4 # +4 for backticks
+
+        # table aligning - I may have stolen this from above but hey ho I'll fix that later
+        line_tmpl = "{0:{c}<%s}   {1:{c}<%s}   {2:{c}<%s}" % (nw, dw, dfw)
+        table_line = line_tmpl.format('', '', '', c='=', nw=nw, dw=dw, dfw=dfw)
+
+        lines.append(table_line)
+        lines.append(line_tmpl.format(ectitle, desctitle, dftitle, c=' '))
+        lines.append(table_line)
+
+        for key in ex_opt:
+           lines.append(line_tmpl.format('``'+key+'``', ex_opt[key][1], '``' + str(quote_str(ex_opt[key][0])) + '``', c=' '))
+        lines.append(table_line)
+
+        commonly_used = 'Commonly used easyconfig parameters with ``' + classname + '`` easyblock'
+        lines.extend(['', commonly_used, '-' * len(commonly_used)])
+
+    print '\n'.join(lines)
+
+
+

From 8fbc168a485b308020a035a9cc1bf1fc7688a2b9 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 7 Jul 2015 13:57:40 +0200
Subject: [PATCH 1110/1356] Generic easyblock docs, continued

---
 easybuild/tools/doc_examples/Binary.eb        | 21 ++++++
 easybuild/tools/doc_examples/Bundle.eb        | 17 +++++
 easybuild/tools/doc_examples/CMakeMake.eb     | 30 ++++++++
 easybuild/tools/doc_examples/ConfigureMake.eb | 20 +++++
 .../ConfigureMakePythonPackage.eb             | 33 ++++++++
 easybuild/tools/docs.py                       | 75 ++++++++++++++-----
 6 files changed, 179 insertions(+), 17 deletions(-)
 create mode 100644 easybuild/tools/doc_examples/Binary.eb
 create mode 100644 easybuild/tools/doc_examples/Bundle.eb
 create mode 100644 easybuild/tools/doc_examples/CMakeMake.eb
 create mode 100644 easybuild/tools/doc_examples/ConfigureMake.eb
 create mode 100644 easybuild/tools/doc_examples/ConfigureMakePythonPackage.eb

diff --git a/easybuild/tools/doc_examples/Binary.eb b/easybuild/tools/doc_examples/Binary.eb
new file mode 100644
index 0000000000..2fa31617c3
--- /dev/null
+++ b/easybuild/tools/doc_examples/Binary.eb
@@ -0,0 +1,21 @@
+easyblock = 'Binary'
+
+name = 'Platanus'
+version = '1.2.1'
+versionsuffix = '-linux-x86_64'
+
+homepage = 'http://platanus.bio.titech.ac.jp/'
+description = """PLATform for Assembling NUcleotide Sequences"""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201']
+sources = ['platanus']
+checksums = ['02cf92847ec704d010a54df293b9c60a']
+
+sanity_check_paths = {
+    'files': ['platanus'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/tools/doc_examples/Bundle.eb b/easybuild/tools/doc_examples/Bundle.eb
new file mode 100644
index 0000000000..067ccdbe63
--- /dev/null
+++ b/easybuild/tools/doc_examples/Bundle.eb
@@ -0,0 +1,17 @@
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20150119' # date of the most recent change
+
+homepage = 'http://autotools.io'
+description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
+
+toolchain = {'name': 'GCC', 'version': '4.9.2'}
+
+dependencies = [
+    ('Autoconf', '2.69'), # 20120424
+    ('Automake', '1.15'), # 20150105
+    ('libtool', '2.4.5'), # 20150119
+]
+
+moduleclass = 'devel'
diff --git a/easybuild/tools/doc_examples/CMakeMake.eb b/easybuild/tools/doc_examples/CMakeMake.eb
new file mode 100644
index 0000000000..1e8a2bf6f6
--- /dev/null
+++ b/easybuild/tools/doc_examples/CMakeMake.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'ANTs'
+version = '2.1.0rc3'
+
+homepage = 'http://stnava.github.io/ANTs/'
+description = """ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing,
+ interpreting and visualizing multidimensional data."""
+
+toolchain = {'name': 'goolf', 'version': '1.5.14'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/stnava/ANTs/archive/']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [('CMake', '3.0.2')]
+
+skipsteps = ['install']
+buildopts = ' && mkdir -p %(installdir)s && cp -r * %(installdir)s/'
+
+parallel = 1
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['bin/ANTS'],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'data'
diff --git a/easybuild/tools/doc_examples/ConfigureMake.eb b/easybuild/tools/doc_examples/ConfigureMake.eb
new file mode 100644
index 0000000000..9a0d4bf65e
--- /dev/null
+++ b/easybuild/tools/doc_examples/ConfigureMake.eb
@@ -0,0 +1,20 @@
+easyblock = 'ConfigureMake'
+
+name = 'zsync'
+version = '0.6.2'
+
+homepage = 'http://zsync.moria.org.uk/'
+description = """zsync-0.6.2: Optimising file distribution program, a 1-to-many rsync"""
+
+sources = [SOURCE_TAR_BZ2]
+source_urls = ['http://zsync.moria.org.uk/download/']
+
+
+toolchain = {'name': 'ictce', 'version': '5.3.0'}
+
+sanity_check_paths = {
+                      'files': ['bin/zsync'],
+                      'dirs': []
+                     }
+
+moduleclass = 'tools'
diff --git a/easybuild/tools/doc_examples/ConfigureMakePythonPackage.eb b/easybuild/tools/doc_examples/ConfigureMakePythonPackage.eb
new file mode 100644
index 0000000000..0f9fd09a84
--- /dev/null
+++ b/easybuild/tools/doc_examples/ConfigureMakePythonPackage.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMakePythonPackage'
+
+name = 'PyQt'
+version = '4.11.3'
+
+homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt'
+description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework."""
+
+toolchain = {'name': 'goolf', 'version': '1.5.14'}
+
+sources = ['%(name)s-x11-gpl-%(version)s.tar.gz']
+source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s']
+
+python = 'Python'
+pyver = '2.7.9'
+pythonshortver = '.'.join(pyver.split('.')[:2])
+versionsuffix = '-%s-%s' % (python, pyver)
+
+dependencies = [
+    (python, pyver),
+    ('SIP', '4.16.4', versionsuffix),
+    ('Qt', '4.8.6'),
+]
+
+configopts = "configure-ng.py --confirm-license"
+configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver
+configopts += " --no-sip-files"
+
+options = {'modulename': 'PyQt4'}
+
+modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver}
+
+moduleclass = 'vis'
diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 795656db59..709405dc74 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -34,14 +34,14 @@
 @author: Ward Poelmans (Ghent University)
 """
 import copy
+import inspect
 import os
 
 from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, HIDDEN, sorted_categories
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.tools.ordereddict import OrderedDict
-from easybuild.tools.utilities import quote_str
-from easybuild.easyblocks.generic.configuremake import ConfigureMake
-
+from easybuild.tools.utilities import quote_str, import_available_modules
+from easybuild.tools.filetools import read_file
 
 FORMAT_RST = 'rst'
 FORMAT_TXT = 'txt'
@@ -163,29 +163,56 @@ def avail_easyconfig_params(easyblock, output_format):
     }
     return avail_easyconfig_params_functions[output_format](title, grouped_params)
 
-def generic_easyblocks(classname):
+def generic_easyblocks():
     """
-    Compose overview of available generic easyblocks in rst format
+    Compose overview of all generic easyblocks
     """
-    block = globals()[classname]
+    modules = import_available_modules('easybuild.easyblocks.generic')
+    docs = []
+    seen = []
+
+    for m in modules:
+        for name,obj in inspect.getmembers(m, inspect.isclass):
+            eb_class = getattr(m, name)
+            # skip imported classes that are not easyblocks
+            if eb_class.__module__.startswith('easybuild.easyblocks.generic') and name not in seen:
+                docs.append(doc_easyblock(eb_class))
+                seen.append(name)
+
+    return docs
+
+
+def doc_easyblock(eb_class):
+    """
+    Compose overview of one easyblock given class object of the easyblock in rst format
+    """
+    classname = eb_class.__name__
+
+    common_params = {
+        'ConfigureMake' : ['configopts', 'buildopts', 'installopts'],
+        # to be continued
+    }
+
     lines = [
         '``' + classname + '``',
         '=' * (len(classname)+4),
         '',
     ]
 
-    derived = '(derives from '
-    for base in block.__bases__:
-        derived += '``'+base.__name__+'`` '
-    derived += ')'
+    bases = ['``' + base.__name__ + '``' for base in eb_class.__bases__]
+    derived = '(derives from ' + ', '.join(bases) + ')'
+
+
     lines.extend([derived, ''])
 
-    lines.extend([block.__doc__.strip(), ''])
+    # Description (docstring)
+    lines.extend([eb_class.__doc__.strip(), ''])
 
-    if block.extra_options(None):
+    # Add extra options, if any
+    if eb_class.extra_options():
         extra_parameters = 'Extra easyconfig parameters specific to ``' + classname + '`` easyblock'
         lines.extend([extra_parameters, '-' * len(extra_parameters), ''])
-        ex_opt = block.extra_options()
+        ex_opt = eb_class.extra_options()
 
         ectitle = 'easyconfig parameter'
         desctitle = 'description'
@@ -196,7 +223,7 @@ def generic_easyblocks(classname):
         dw = det_col_width([val[1] for val in ex_opt.values()], desctitle)
         dfw = det_col_width([str(val[0]) for val in ex_opt.values()], dftitle) + 4 # +4 for backticks
 
-        # table aligning - I may have stolen this from above but hey ho I'll fix that later
+        # table aligning
         line_tmpl = "{0:{c}<%s}   {1:{c}<%s}   {2:{c}<%s}" % (nw, dw, dfw)
         table_line = line_tmpl.format('', '', '', c='=', nw=nw, dw=dw, dfw=dfw)
 
@@ -206,12 +233,26 @@ def generic_easyblocks(classname):
 
         for key in ex_opt:
            lines.append(line_tmpl.format('``'+key+'``', ex_opt[key][1], '``' + str(quote_str(ex_opt[key][0])) + '``', c=' '))
-        lines.append(table_line)
+        lines.extend([table_line, ''])
+
 
+    if classname in common_params:
         commonly_used = 'Commonly used easyconfig parameters with ``' + classname + '`` easyblock'
-        lines.extend(['', commonly_used, '-' * len(commonly_used)])
+        lines.extend([commonly_used, '-' * len(commonly_used)])
 
-    print '\n'.join(lines)
+        for opt in common_params[classname]:
+            param = '* ``' + opt + '`` - ' + DEFAULT_CONFIG[opt][1]
+            lines.append(param)
+
+
+    if classname + '.eb' in os.listdir(os.path.join(os.path.dirname(__file__), 'doc_examples')):
+        lines.extend(['', 'Example', '-' * 8, '', '::', ''])
+        f = open(os.path.join(os.path.dirname(__file__), 'doc_examples', classname+'.eb'), "r")
+        for line in f.readlines():
+            lines.append('    ' + line.strip())
+        lines.append('') # empty line after literal block
+
+    return '\n'.join(lines)
 
 
 

From 7cfc6a295425bc06eacde370e1035c24f6ff66c0 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 7 Jul 2015 15:54:47 +0200
Subject: [PATCH 1111/1356] python star operator is gr8

---
 easybuild/tools/docs.py | 69 +++++++++++++++++++++++++++++------------
 1 file changed, 49 insertions(+), 20 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 709405dc74..1e2e701e44 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -179,7 +179,7 @@ def generic_easyblocks():
                 docs.append(doc_easyblock(eb_class))
                 seen.append(name)
 
-    return docs
+    return sorted(docs)
 
 
 def doc_easyblock(eb_class):
@@ -214,26 +214,10 @@ def doc_easyblock(eb_class):
         lines.extend([extra_parameters, '-' * len(extra_parameters), ''])
         ex_opt = eb_class.extra_options()
 
-        ectitle = 'easyconfig parameter'
-        desctitle = 'description'
-        dftitle = 'default value'
+        titles = ['easyconfig parameter', 'description', 'default value']
+        values = [[backtick(key) for key in ex_opt], [val[1] for val in ex_opt.values()], [backtick(str(quote_str(val[0]))) for val in ex_opt.values()]]
 
-        # figure out column widths
-        nw = det_col_width([key for key in ex_opt], ectitle) + 4 # +4 for backticks
-        dw = det_col_width([val[1] for val in ex_opt.values()], desctitle)
-        dfw = det_col_width([str(val[0]) for val in ex_opt.values()], dftitle) + 4 # +4 for backticks
-
-        # table aligning
-        line_tmpl = "{0:{c}<%s}   {1:{c}<%s}   {2:{c}<%s}" % (nw, dw, dfw)
-        table_line = line_tmpl.format('', '', '', c='=', nw=nw, dw=dw, dfw=dfw)
-
-        lines.append(table_line)
-        lines.append(line_tmpl.format(ectitle, desctitle, dftitle, c=' '))
-        lines.append(table_line)
-
-        for key in ex_opt:
-           lines.append(line_tmpl.format('``'+key+'``', ex_opt[key][1], '``' + str(quote_str(ex_opt[key][0])) + '``', c=' '))
-        lines.extend([table_line, ''])
+        lines.extend(mk_rst_table(titles, values))
 
 
     if classname in common_params:
@@ -255,4 +239,49 @@ def doc_easyblock(eb_class):
     return '\n'.join(lines)
 
 
+def mk_rst_table(titles, values):
+    """
+    Returns an rst table with given titles and string values
+    """
+    num_col = len(titles)
+    table = []
+    col_widths = []
+    tmpl = []
+    line= []
+
+    # figure out column widths
+    for i in range(0, num_col):
+        col_widths.append(det_col_width(values[i], titles[i]))
+
+        # make line template
+        tmpl.append('{' + str(i) + ':{c}<' + str(col_widths[i]) + '}')
+        line.append('') # needed for table line
+
+    line_tmpl = '   '.join(tmpl)
+    table_line = line_tmpl.format(*line, c="=")
+
+    table.append(table_line)
+    table.append(line_tmpl.format(*titles, c=' '))
+    table.append(table_line)
+
+    for i in range(0, len(values[0])):
+        table.append(line_tmpl.format(*[v[i] for v in values], c=' '))
+
+    table.extend([table_line, ''])
+
+    return table
+
+
+def backtick(string):
+    return '``' + string + '``'
+
+
+
+
+
+
+
+
+
+
 

From 31587c911254009a42282eb05d12bc86b244b603 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 7 Jul 2015 15:54:47 +0200
Subject: [PATCH 1112/1356] Separate function for making rst tables

---
 easybuild/tools/docs.py | 69 +++++++++++++++++++++++++++++------------
 1 file changed, 49 insertions(+), 20 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 709405dc74..1e2e701e44 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -179,7 +179,7 @@ def generic_easyblocks():
                 docs.append(doc_easyblock(eb_class))
                 seen.append(name)
 
-    return docs
+    return sorted(docs)
 
 
 def doc_easyblock(eb_class):
@@ -214,26 +214,10 @@ def doc_easyblock(eb_class):
         lines.extend([extra_parameters, '-' * len(extra_parameters), ''])
         ex_opt = eb_class.extra_options()
 
-        ectitle = 'easyconfig parameter'
-        desctitle = 'description'
-        dftitle = 'default value'
+        titles = ['easyconfig parameter', 'description', 'default value']
+        values = [[backtick(key) for key in ex_opt], [val[1] for val in ex_opt.values()], [backtick(str(quote_str(val[0]))) for val in ex_opt.values()]]
 
-        # figure out column widths
-        nw = det_col_width([key for key in ex_opt], ectitle) + 4 # +4 for backticks
-        dw = det_col_width([val[1] for val in ex_opt.values()], desctitle)
-        dfw = det_col_width([str(val[0]) for val in ex_opt.values()], dftitle) + 4 # +4 for backticks
-
-        # table aligning
-        line_tmpl = "{0:{c}<%s}   {1:{c}<%s}   {2:{c}<%s}" % (nw, dw, dfw)
-        table_line = line_tmpl.format('', '', '', c='=', nw=nw, dw=dw, dfw=dfw)
-
-        lines.append(table_line)
-        lines.append(line_tmpl.format(ectitle, desctitle, dftitle, c=' '))
-        lines.append(table_line)
-
-        for key in ex_opt:
-           lines.append(line_tmpl.format('``'+key+'``', ex_opt[key][1], '``' + str(quote_str(ex_opt[key][0])) + '``', c=' '))
-        lines.extend([table_line, ''])
+        lines.extend(mk_rst_table(titles, values))
 
 
     if classname in common_params:
@@ -255,4 +239,49 @@ def doc_easyblock(eb_class):
     return '\n'.join(lines)
 
 
+def mk_rst_table(titles, values):
+    """
+    Returns an rst table with given titles and string values
+    """
+    num_col = len(titles)
+    table = []
+    col_widths = []
+    tmpl = []
+    line= []
+
+    # figure out column widths
+    for i in range(0, num_col):
+        col_widths.append(det_col_width(values[i], titles[i]))
+
+        # make line template
+        tmpl.append('{' + str(i) + ':{c}<' + str(col_widths[i]) + '}')
+        line.append('') # needed for table line
+
+    line_tmpl = '   '.join(tmpl)
+    table_line = line_tmpl.format(*line, c="=")
+
+    table.append(table_line)
+    table.append(line_tmpl.format(*titles, c=' '))
+    table.append(table_line)
+
+    for i in range(0, len(values[0])):
+        table.append(line_tmpl.format(*[v[i] for v in values], c=' '))
+
+    table.extend([table_line, ''])
+
+    return table
+
+
+def backtick(string):
+    return '``' + string + '``'
+
+
+
+
+
+
+
+
+
+
 

From 34c2853b4a848e36c1cba294816fc713c6a656dd Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 7 Jul 2015 16:29:40 +0200
Subject: [PATCH 1113/1356] Also use mk_rst_table in avail_easyconfig_params

---
 easybuild/tools/docs.py | 41 ++++++++++++-----------------------------
 1 file changed, 12 insertions(+), 29 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 1e2e701e44..aa6cc45387 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -67,29 +67,14 @@ def avail_easyconfig_params_rst(title, grouped_params):
         lines.append("%s parameters" % grpname)
         lines.extend(['-' * len(lines[-1]), ''])
 
-        name_title = "**Parameter name**"
-        descr_title = "**Description**"
-        dflt_title = "**Default value**"
+        titles = ["**Parameter name**", "**Description**", "**Default value**"]
+        values = [
+            [backtick(name) for name in grouped_params[grpname].keys()],
+            [x[0] for x in grouped_params[grpname].values()],
+            [str(quote_str(x[1])) for x in grouped_params[grpname].values()]
+        ]
 
-        # figure out column widths
-        nw = det_col_width(grouped_params[grpname].keys(), name_title) + 4  # +4 for raw format ("``foo``")
-        dw = det_col_width([x[0] for x in grouped_params[grpname].values()], descr_title)
-        dfw = det_col_width([str(quote_str(x[1])) for x in grouped_params[grpname].values()], dflt_title)
-
-        # 3 columns (name, description, default value), left-aligned, {c} is fill char
-        line_tmpl = "{0:{c}<%s}   {1:{c}<%s}   {2:{c}<%s}" % (nw, dw, dfw)
-        table_line = line_tmpl.format('', '', '', c='=', nw=nw, dw=dw, dfw=dfw)
-
-        # table header
-        lines.append(table_line)
-        lines.append(line_tmpl.format(name_title, descr_title, dflt_title, c=' '))
-        lines.append(line_tmpl.format('', '', '', c='-'))
-
-        # table rows by parameter
-        for name, (descr, dflt) in sorted(grouped_params[grpname].items()):
-            rawname = '``%s``' % name
-            lines.append(line_tmpl.format(rawname, descr, str(quote_str(dflt)), c=' '))
-        lines.append(table_line)
+        lines.extend(mk_rst_table(titles, values))
         lines.append('')
 
     return '\n'.join(lines)
@@ -201,8 +186,6 @@ def doc_easyblock(eb_class):
 
     bases = ['``' + base.__name__ + '``' for base in eb_class.__bases__]
     derived = '(derives from ' + ', '.join(bases) + ')'
-
-
     lines.extend([derived, ''])
 
     # Description (docstring)
@@ -210,7 +193,7 @@ def doc_easyblock(eb_class):
 
     # Add extra options, if any
     if eb_class.extra_options():
-        extra_parameters = 'Extra easyconfig parameters specific to ``' + classname + '`` easyblock'
+        extra_parameters = 'Extra easyconfig parameters specific to ' + backtick(classname) + ' easyblock'
         lines.extend([extra_parameters, '-' * len(extra_parameters), ''])
         ex_opt = eb_class.extra_options()
 
@@ -218,14 +201,14 @@ def doc_easyblock(eb_class):
         values = [[backtick(key) for key in ex_opt], [val[1] for val in ex_opt.values()], [backtick(str(quote_str(val[0]))) for val in ex_opt.values()]]
 
         lines.extend(mk_rst_table(titles, values))
-
+        lines.append('')
 
     if classname in common_params:
-        commonly_used = 'Commonly used easyconfig parameters with ``' + classname + '`` easyblock'
+        commonly_used = 'Commonly used easyconfig parameters with ' + backtick(classname) + ' easyblock'
         lines.extend([commonly_used, '-' * len(commonly_used)])
 
         for opt in common_params[classname]:
-            param = '* ``' + opt + '`` - ' + DEFAULT_CONFIG[opt][1]
+            param = '* ' + backtick(opt) + ' - ' + DEFAULT_CONFIG[opt][1]
             lines.append(param)
 
 
@@ -241,7 +224,7 @@ def doc_easyblock(eb_class):
 
 def mk_rst_table(titles, values):
     """
-    Returns an rst table with given titles and string values
+    Returns an rst table with given titles and values (a nested list of string values for each column)
     """
     num_col = len(titles)
     table = []

From e96df9a754167fcb3bca99493456d2722ceb8a19 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 7 Jul 2015 16:50:42 +0200
Subject: [PATCH 1114/1356] added table of contents

---
 easybuild/tools/docs.py | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index aa6cc45387..65d5b54270 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -164,7 +164,9 @@ def generic_easyblocks():
                 docs.append(doc_easyblock(eb_class))
                 seen.append(name)
 
-    return sorted(docs)
+    toc = ['.. contents:: Available generic easyblocks', '    :depth: 1', '']
+
+    return toc + sorted(docs)
 
 
 def doc_easyblock(eb_class):
@@ -257,14 +259,3 @@ def mk_rst_table(titles, values):
 
 def backtick(string):
     return '``' + string + '``'
-
-
-
-
-
-
-
-
-
-
-

From 2f0cb1b18e94e51a2d7b22a1ebf398217855035c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Jul 2015 20:15:17 +0200
Subject: [PATCH 1115/1356] replace log.error with 'raise EasyBuildError' in
 hgrepo.py

---
 easybuild/tools/repository/hgrepo.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/repository/hgrepo.py b/easybuild/tools/repository/hgrepo.py
index 571377a552..1e764d535b 100644
--- a/easybuild/tools/repository/hgrepo.py
+++ b/easybuild/tools/repository/hgrepo.py
@@ -43,6 +43,7 @@
 import time
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import rmtree2
 from easybuild.tools.repository.filerepo import FileRepository
 
@@ -88,7 +89,7 @@ def setup_repo(self):
         Set up mercurial repository.
         """
         if not HAVE_HG:
-            self.log.error("The python-hglib Python module is not available, which is required for Mercurial support.")
+            raise EasyBuildError("python-hglib is not available, which is required for Mercurial support.")
 
         self.wc = tempfile.mkdtemp(prefix='hg-wc-')
 
@@ -110,18 +111,18 @@ def create_working_copy(self):
             self.log.debug("connection to mercurial repo in %s" % self.wc)
             self.client = hglib.open(self.wc)
         except HgServerError, err:
-            self.log.error("Could not connect to local mercurial repo: %s" % err)
+            raise EasyBuildError("Could not connect to local mercurial repo: %s", err)
         except (HgCapabilityError, HgResponseError), err:
-            self.log.error("Server response: %s", err)
+            raise EasyBuildError("Server response: %s", err)
         except (OSError, ValueError), err:
-            self.log.error("Could not create a local mercurial repo in wc %s: %s" % (self.wc, err))
+            raise EasyBuildError("Could not create a local mercurial repo in wc %s: %s", self.wc, err)
 
         # try to get the remote data in the local repo
         try:
             self.client.pull()
             self.log.debug("pulled succesfully in %s" % self.wc)
         except (HgCommandError, HgServerError, HgResponseError, OSError, ValueError), err:
-            self.log.error("pull in working copy %s went wrong: %s" % (self.wc, err))
+            raise EasyBuildError("pull in working copy %s went wrong: %s", self.wc, err)
 
     def add_easyconfig(self, cfg, name, version, stats, append):
         """
@@ -167,4 +168,4 @@ def cleanup(self):
         try:
             rmtree2(self.wc)
         except IOError, err:
-            self.log.error("Can't remove working copy %s: %s" % (self.wc, err))
+            raise EasyBuildError("Can't remove working copy %s: %s", self.wc, err)

From 2f1ed157ff57b53e15d013d3cb6c41b776a20f14 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Jul 2015 20:15:50 +0200
Subject: [PATCH 1116/1356] fix typo

---
 easybuild/tools/repository/gitrepo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/repository/gitrepo.py b/easybuild/tools/repository/gitrepo.py
index 90ad3472f3..a4cf89a755 100644
--- a/easybuild/tools/repository/gitrepo.py
+++ b/easybuild/tools/repository/gitrepo.py
@@ -77,7 +77,7 @@ class GitRepository(FileRepository):
     def __init__(self, *args):
         """
         Initialize git client to None (will be set later)
-        All the real logic is in the setup_repo and create_wroking_copy methods
+        All the real logic is in the setup_repo and create_working_copy methods
         """
         self.client = None
         FileRepository.__init__(self, *args)

From 218b2b884bbbc7efcc343850a6b76416b993d101 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Jul 2015 21:10:36 +0200
Subject: [PATCH 1117/1356] add unit test for HgRepository

---
 test/framework/repository.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/test/framework/repository.py b/test/framework/repository.py
index 5622e49f65..b1730dc522 100644
--- a/test/framework/repository.py
+++ b/test/framework/repository.py
@@ -37,6 +37,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.repository.filerepo import FileRepository
 from easybuild.tools.repository.gitrepo import GitRepository
+from easybuild.tools.repository.hgrepo import HgRepository
 from easybuild.tools.repository.svnrepo import SvnRepository
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.run import run_cmd
@@ -124,6 +125,23 @@ def test_svnrepo(self):
         self.assertTrue(os.path.exists(os.path.join(repo.wc, 'trunk', 'README.md')))
         shutil.rmtree(repo.wc)
 
+    def test_hgrepo(self):
+        """Test using HgRepository."""
+        # only run this test if pysvn Python module is available
+        try:
+            import hglib
+        except ImportError:
+            print "(skipping HgRepository test)"
+            return
+
+        # GitHub also supports SVN
+        test_repo_url = 'https://kehoste@bitbucket.org/kehoste/testrepository'
+
+        repo = HgRepository(test_repo_url)
+        repo.init()
+        self.assertTrue(os.path.exists(os.path.join(repo.wc, 'README')))
+        shutil.rmtree(repo.wc)
+
     def test_init_repository(self):
         """Test use of init_repository function."""
         repo = init_repository('FileRepository', self.path)

From c5b83ffc0633302db72d852b98693417cbb83cb4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Jul 2015 22:29:39 +0200
Subject: [PATCH 1118/1356] reenable (and fix) accidentally disabled test

---
 test/framework/robot.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/test/framework/robot.py b/test/framework/robot.py
index 5898160f9c..beb16f219a 100644
--- a/test/framework/robot.py
+++ b/test/framework/robot.py
@@ -42,7 +42,8 @@
 from easybuild.framework.easyconfig.tools import skip_available
 from easybuild.tools import config, modules
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import read_file, write_file
+from easybuild.tools.configobj import ConfigObj
+from easybuild.tools.filetools import write_file
 from easybuild.tools.github import fetch_github_token
 from easybuild.tools.robot import resolve_dependencies
 from test.framework.utilities import find_full_path
@@ -92,7 +93,7 @@ def setUp(self):
         super(RobotTest, self).setUp()
         self.github_token = fetch_github_token(GITHUB_TEST_ACCOUNT)
 
-    def xtest_resolve_dependencies(self):
+    def test_resolve_dependencies(self):
         """ Test with some basic testcases (also check if he can find dependencies inside the given directory """
 
         # replace Modules class with something we have control over
@@ -112,6 +113,7 @@ def xtest_resolve_dependencies(self):
         }
         build_options = {
             'allow_modules_tool_mismatch': True,
+            'external_modules_metadata': ConfigObj(),
             'robot_path': None,
             'validate': False,
         }

From d5abf406b4d229225b04d9abb2880b56de19611e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Jul 2015 23:31:35 +0200
Subject: [PATCH 1119/1356] cleanup of support for packaging + kickstart unit
 tests related to packaging support

---
 easybuild/tools/options.py                    |  20 +--
 easybuild/tools/package/activepns.py          |  50 -------
 .../packaging_naming_scheme/easybuild_pns.py  |  34 ++++-
 .../package/packaging_naming_scheme/pns.py    |  57 ++++++--
 easybuild/tools/package/utilities.py          | 133 +++++++++++-------
 test/framework/package.py                     |  79 +++++++++++
 test/framework/suite.py                       |   4 +-
 7 files changed, 244 insertions(+), 133 deletions(-)
 delete mode 100644 easybuild/tools/package/activepns.py
 create mode 100644 test/framework/package.py

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 79eb82ac64..cd7ad8da81 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -48,11 +48,10 @@
 from easybuild.framework.easyconfig.templates import template_documentation
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.extension import Extension
-from easybuild.tools import build_log, config, run  # @UnusedImport make sure config is always initialized!
+from easybuild.tools import build_log, config, run  # build_log should always stay there, to ensure EasyBuildLog
 from easybuild.tools.build_log import EasyBuildError, raise_easybuilderror
 from easybuild.tools.config import DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX, DEFAULT_MODULES_TOOL
-from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS
-from easybuild.tools.config import DEFAULT_PREFIX, DEFAULT_REPOSITORY
+from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX, DEFAULT_REPOSITORY
 from easybuild.tools.config import DEFAULT_STRICT, get_pretend_installpath, mk_full_default_path
 from easybuild.tools.configobj import ConfigObj, ConfigObjError
 from easybuild.tools.docs import FORMAT_RST, FORMAT_TXT, avail_easyconfig_params
@@ -63,9 +62,7 @@
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
 from easybuild.tools.modules import Lmod
 from easybuild.tools.ordereddict import OrderedDict
-import easybuild.tools.package.utilities as packaging
-from easybuild.tools.package.utilities import DEFAULT_PNS
-from easybuild.tools.package.activepns import avail_package_naming_scheme
+from easybuild.tools.package.utilities import DEFAULT_PNS, avail_package_naming_schemes, check_pkg_support
 from easybuild.tools.toolchain.utilities import search_toolchain
 from easybuild.tools.repository.repository import avail_repositories
 from easybuild.tools.version import this_is_easybuild
@@ -267,7 +264,7 @@ def config_options(self):
             'packagepath': ("The destination path for the packages built by package-tool",
                              None, 'store', mk_full_default_path('packagepath')),
             'package-naming-scheme': ("Packaging naming scheme choice", 
-                                      'choice', 'store', DEFAULT_PNS, sorted(avail_package_naming_scheme().keys())),
+                                      'choice', 'store', DEFAULT_PNS, sorted(avail_package_naming_schemes().keys())),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
                         "(used prefix for defaults %s)" % DEFAULT_PREFIX),
                        None, 'store', None),
@@ -472,15 +469,12 @@ def postprocess(self):
 
         self._postprocess_config()
 
-        #Check experimental option dependencies (for now packaging)
-        #print "Got config_options: %s" % packaging.config_options
-        package_options = [ getattr(self.options, x) for x in packaging.config_options if getattr(self.options, x) ]
-        if any( package_options ):
-            packaging.option_postprocess()
+        # check whether packaging is supported when it's being used
+        if any([self.options.package_tool, self.options.package_type]):
+            check_pkg_support()
         else:
             self.log.debug("Didn't find any packaging options")
 
-
     def _postprocess_external_modules_metadata(self):
         """Parse file(s) specifying metadata for external modules."""
         # leave external_modules_metadata untouched if no files are provided
diff --git a/easybuild/tools/package/activepns.py b/easybuild/tools/package/activepns.py
deleted file mode 100644
index 7267bc014d..0000000000
--- a/easybuild/tools/package/activepns.py
+++ /dev/null
@@ -1,50 +0,0 @@
-
-
-from vsc.utils import fancylogger
-from vsc.utils.missing import get_subclasses
-from vsc.utils.patterns import Singleton
-from easybuild.tools.config import get_package_naming_scheme
-from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
-from easybuild.tools.package.packaging_naming_scheme.pns import PackagingNamingScheme
-from easybuild.tools.utilities import import_available_modules
-
-def avail_package_naming_scheme():
-    '''
-    Returns the list of valed naming schemes that are in the easybuild.package.package_naming_scheme namespace
-    '''
-    import_available_modules('easybuild.tools.package.packaging_naming_scheme')
-
-    class_dict = dict([(x.__name__, x) for x in get_subclasses(PackagingNamingScheme)])
-
-    return class_dict
-
-class ActivePNS(object):
-    """
-    The wrapper class for Package Naming Schmese, follows the model of Module Naming Schemes, mostly
-    """
-    
-    __metaclass__ = Singleton
-    
-    def __init__(self, *args, **kwargs):
-        """Initialize logger and find available PNSes to load"""
-        self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
-
-        avail_pns = avail_package_naming_scheme()
-        sel_pns = get_package_naming_scheme()
-        if sel_pns in avail_pns:
-            self.pns = avail_pns[sel_pns]()
-        else:
-            raise EasyBuildError("Selected package naming scheme %s could not be found in %s",
-                                    sel_pns, avail_pns.keys())
-
-    def name(self, ec):
-        name = self.pns.name(ec)
-        return name
-
-    def version(self, ec):
-        version = self.pns.version(ec)
-        return version
-
-    def release(self, ec):
-        release = self.pns.release()
-        return release
diff --git a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
index 1dae429657..bc95cace8a 100644
--- a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
+++ b/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
@@ -1,10 +1,31 @@
-
-
-
+##
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
 """
-Default implementation of the EasyBuild packaging naming scheme
+Implementation of the EasyBuild packaging naming scheme
 
-@author: Rob Schmidt (Ottawa Hospital Research Institute)
+@author: Robert Schmidt (Ottawa Hospital Research Institute)
 @author: Kenneth Hoste (Ghent University)
 """
 
@@ -17,6 +38,7 @@ class EasyBuildPNS(PackagingNamingScheme):
     REQUIRED_KEYS = ['name', 'version', 'versionsuffix', 'toolchain']
 
     def name(self, ec):
+        """Determine package name"""
         self.log.debug("easyconfig dict for name looks like %s " % ec )
         name_template = "eb%(eb_ver)s-%(name)s-%(version)s-%(toolchain)s"
         pkg_name = name_template % {
@@ -28,10 +50,10 @@ def name(self, ec):
         return pkg_name
 
     def _toolchain(self, ec):
+        """Determine toolchain"""
         toolchain_template = "%(toolchain_name)s-%(toolchain_version)s"
         pkg_toolchain = toolchain_template % {
             'toolchain_name': ec['toolchain']['name'],
             'toolchain_version': ec['toolchain']['version'],
         }
         return pkg_toolchain
-
diff --git a/easybuild/tools/package/packaging_naming_scheme/pns.py b/easybuild/tools/package/packaging_naming_scheme/pns.py
index 408a1b6904..b1569d0f66 100644
--- a/easybuild/tools/package/packaging_naming_scheme/pns.py
+++ b/easybuild/tools/package/packaging_naming_scheme/pns.py
@@ -1,28 +1,55 @@
-
+##
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+
+"""
+General package naming scheme.
+
+@author: Robert Schmidt (Ottawa Hospital Research Institute)
+@author: Kenneth Hoste (Ghent University)
+"""
 from vsc.utils import fancylogger
 from easybuild.tools.config import build_option
 from easybuild.tools.version import VERSION as EASYBUILD_VERSION
-options = [ "package-naming-name-template", "package-naming-version-template", "package-naming-toolchain-template" ]
 
-class PackagingNamingScheme(object):
-    """Abstract class for package naming scheme"""
 
+class PackagingNamingScheme(object):
+    """Abstract class for package naming schemes"""
 
-    def __init__(self, *args, **kwargs):
+    def __init__(self):
         """initialize logger."""
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
         self.eb_ver = EASYBUILD_VERSION
 
-    def name(self,ec):
-        """Return name of the package, by default would include name, version, toolchain"""
+    def name(self, ec):
+        """Determine package name"""
         raise NotImplementedError
-        
-    def version(self,ec):
-        """The version in the version part of the package"""
-        return ec['version']    
-
-    def release(self,ec=None):
-        """Just the release"""
-        return build_option('package_release')
 
+    def version(self, ec):
+        """Determine package version"""
+        return ec['version']
 
+    def release(self, ec=None):
+        """Determine package release"""
+        return build_option('package_release')
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index ccaef6bd38..14e215e2ca 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -1,5 +1,5 @@
-# #
-# Copyright 2009-2014 Ghent University
+##
+# Copyright 2015-2015 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -21,10 +21,10 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-# #
+##
 
 """
-A place for packaging functions
+Various utilities related to packaging support.
 
 @author: Marc Litherland
 @author: Gianluca Santarossa (Novartis)
@@ -32,97 +32,134 @@
 @author: Fotis Georgatos (Uni.Lu, NTUA)
 @author: Kenneth Hoste (Ghent University)
 """
-
 import os
 import tempfile
 import pprint
 
 from vsc.utils import fancylogger
+from vsc.utils.missing import get_subclasses
+from vsc.utils.patterns import Singleton
 
-from easybuild.tools.run import run_cmd
-from easybuild.tools.config import build_option
-from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
-from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
+from easybuild.tools.config import get_package_naming_scheme
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import which
-from easybuild.tools.package.activepns import ActivePNS
+from easybuild.tools.package.packaging_naming_scheme.pns import PackagingNamingScheme
+from easybuild.tools.run import run_cmd
+from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
+from easybuild.tools.utilities import import_available_modules
+
 
 DEFAULT_PNS = 'EasyBuildPNS'
 
-_log = fancylogger.getLogger('tools.packaging')
-# This is an abbreviated list of the package options, eventually it might make sense to set them
-# all in the "plugin" rather than in tools.options
-config_options = [ 'package_tool', 'package_type' ]
+_log = fancylogger.getLogger('tools.package')
+
 
-def package_fpm(easyblock, modfile_path, package_type="rpm" ):
-    '''
+def avail_package_naming_schemes():
+    """
+    Returns the list of valed naming schemes that are in the easybuild.package.package_naming_scheme namespace
+    """
+    import_available_modules('easybuild.tools.package.packaging_naming_scheme')
+    class_dict = dict([(x.__name__, x) for x in get_subclasses(PackagingNamingScheme)])
+    return class_dict
+
+
+def package_fpm(easyblock, modfile_path, package_type='rpm'):
+    """
     This function will build a package using fpm and return the directory where the packages are
-    '''
-    
-    workdir = tempfile.mkdtemp()
-    _log.info("Will be writing RPM to %s" % workdir)
+    """
+    workdir = tempfile.mkdtemp(prefix='eb-pkgs')
+    _log.info("Will be creating packages in %s", workdir)
 
     try:
         os.chdir(workdir)
     except OSError, err:
-        raise EasyBuildError("Failed to chdir into workdir: %s : %s", workdir, err)
+        raise EasyBuildError("Failed to chdir into workdir %s: %s", workdir, err)
 
     package_naming_scheme = ActivePNS()
 
     pkgname = package_naming_scheme.name(easyblock.cfg)
-    pkgver  = package_naming_scheme.version(easyblock.cfg)
-    pkgrel  = package_naming_scheme.release(easyblock.cfg)
+    pkgver = package_naming_scheme.version(easyblock.cfg)
+    pkgrel = package_naming_scheme.release(easyblock.cfg)
 
-    _log.debug("Got the pns values for (name, version, release): (%s, %s, %s)" % (pkgname, pkgver, pkgrel)) 
+    _log.debug("Got the PNS values for (name, version, release): (%s, %s, %s)", pkgname, pkgver, pkgrel)
     deps = []
     if easyblock.toolchain.name != DUMMY_TOOLCHAIN_NAME:
         toolchain_dict = easyblock.toolchain.as_dict()
         deps.extend([toolchain_dict])
 
     deps.extend(easyblock.cfg.dependencies())
- 
-    _log.debug("The dependencies to be added to the package are: " + pprint.pformat([easyblock.toolchain.as_dict()]+easyblock.cfg.dependencies()))
-    depstring = ""    
+
+    _log.debug("The dependencies to be added to the package are: %s",
+               pprint.pformat([easyblock.toolchain.as_dict()] + easyblock.cfg.dependencies()))
+    depstring = ''
     for dep in deps:
-        _log.debug("The dep added looks like %s " % dep)
+        _log.debug("The dep added looks like %s ", dep)
         dep_pkgname = package_naming_scheme.name(dep)
-        depstring += " --depends '%s'" % ( dep_pkgname)
+        depstring += " --depends '%s'" % dep_pkgname
 
-    cmdlist=[
+    cmdlist = [
         'fpm',
         '--workdir', workdir,
         '--name', pkgname,
         '--provides', pkgname,
-        '-t', package_type, # target
-        '-s', 'dir', # source
+        '-t', package_type,  # target
+        '-s', 'dir',  # source
         '--version', pkgver,
         '--iteration', pkgrel,
-    ]
-    cmdlist.extend([ depstring ])
-    cmdlist.extend([
+        depstring,
         easyblock.installdir,
-        modfile_path
-    ])
-    cmdstr = " ".join(cmdlist)
-    _log.debug("The flattened cmdlist looks like" + cmdstr)
-    out = run_cmd(cmdstr, log_all=True, simple=True)
-   
-    _log.info("wrote rpm to %s" % (workdir) )
+        modfile_path,
+    ]
+    cmd = ' '.join(cmdlist)
+    _log.debug("The flattened cmdlist looks like: %s", cmd)
+    run_cmd(cmd, log_all=True, simple=True)
+
+    _log.info("Created %s package in %s", package_type, workdir)
 
     return workdir
 
 
-def option_postprocess():
-    '''
-    Called from easybuild.tools.options.postprocess to check that experimental is triggered and fpm is available
-    '''
+def check_pkg_support():
+    """Check whether packaging is supported, i.e. whether the required dependencies are available."""
 
-    _log.experimental("Using the packaging module, This is experimental")
+    _log.experimental("Support for packaging installed software.")
     fpm_path = which('fpm')
     rpmbuild_path = which('rpmbuild')
     if fpm_path and rpmbuild_path:
-        _log.info("fpm found at: %s" % fpm_path)
+        _log.info("fpm found at: %s", fpm_path)
     else:
         raise EasyBuildError("Need both fpm and rpmbuild. Found fpm: %s rpmbuild: %s", fpm_path, rpmbuild_path)
 
 
+class ActivePNS(object):
+    """
+    The wrapper class for Package Naming Schemes.
+    """
+    __metaclass__ = Singleton
+
+    def __init__(self):
+        """Initialize logger and find available PNSes to load"""
+        self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
+
+        avail_pns = avail_package_naming_schemes()
+        sel_pns = get_package_naming_scheme()
+        if sel_pns in avail_pns:
+            self.pns = avail_pns[sel_pns]()
+        else:
+            raise EasyBuildError("Selected package naming scheme %s could not be found in %s",
+                                 sel_pns, avail_pns.keys())
+
+    def name(self, ec):
+        """Determine package name"""
+        name = self.pns.name(ec)
+        return name
+
+    def version(self, ec):
+        """Determine package version"""
+        version = self.pns.version(ec)
+        return version
+
+    def release(self, ec):
+        """Determine package release"""
+        release = self.pns.release()
+        return release
diff --git a/test/framework/package.py b/test/framework/package.py
new file mode 100644
index 0000000000..8b28dc0eef
--- /dev/null
+++ b/test/framework/package.py
@@ -0,0 +1,79 @@
+# #
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Unit tests for packaging support.
+
+@author: Kenneth Hoste (Ghent University)
+"""
+import os
+import stat
+
+from test.framework.utilities import EnhancedTestCase
+from unittest import TestLoader
+from unittest import main as unittestmain
+
+import easybuild.tools.build_log
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import adjust_permissions, write_file
+from easybuild.tools.package.utilities import avail_package_naming_schemes, check_pkg_support
+
+
+class PackageTest(EnhancedTestCase):
+    """Tests for packaging support."""
+
+    def test_avail_package_naming_schemes(self):
+        """Test avail_package_naming_schemes()"""
+        self.assertEqual(sorted(avail_package_naming_schemes().keys()), ['EasyBuildPNS'])
+
+    def test_check_pkg_support(self):
+        """Test check_pkg_support()."""
+        # hard enable experimental
+        orig_experimental = easybuild.tools.build_log.EXPERIMENTAL
+        easybuild.tools.build_log.EXPERIMENTAL = True
+
+        # clear $PATH to make sure fpm/rpmbuild can not be found
+        os.environ['PATH'] = ''
+
+        self.assertErrorRegex(EasyBuildError, "Need both fpm and rpmbuild", check_pkg_support)
+
+        for binary in ['fpm', 'rpmbuild']:
+            binpath = os.path.join(self.test_prefix, binary)
+            write_file(binpath, '#!/bin/bash')
+            adjust_permissions(binpath, stat.S_IXUSR, add=True)
+        os.environ['PATH'] = self.test_prefix
+
+        check_pkg_support()
+
+        # restore
+        easybuild.tools.build_log.EXPERIMENTAL = orig_experimental
+
+
+def suite():
+    """ returns all the testcases in this module """
+    return TestLoader().loadTestsFromTestCase(PackageTest)
+
+
+if __name__ == '__main__':
+    unittestmain()
diff --git a/test/framework/suite.py b/test/framework/suite.py
index 2b6001221f..636966391a 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -72,6 +72,7 @@
 import test.framework.modulestool as mt
 import test.framework.options as o
 import test.framework.parallelbuild as p
+import test.framework.package as pkg
 import test.framework.repository as r
 import test.framework.robot as robot
 import test.framework.run as run
@@ -100,7 +101,8 @@
 
 # call suite() for each module and then run them all
 # note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
-tests = [gen, bl, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p]
+tests = [gen, bl, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw,
+         p, pkg]
 
 SUITE = unittest.TestSuite([x.suite() for x in tests])
 

From f6ff0ac0f69759b35c96d14f5487e465e89d59c6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 Jul 2015 23:39:34 +0200
Subject: [PATCH 1120/1356] keep imports in alphabetical order

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 3c88e9121f..9cfad19244 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -56,7 +56,6 @@
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tools import get_paths_for
 from easybuild.framework.easyconfig.templates import TEMPLATE_NAMES_EASYBLOCK_RUN_STEP
-from easybuild.tools.package.utilities import package_fpm
 from easybuild.tools.build_details import get_build_stats
 from easybuild.tools.build_log import EasyBuildError, print_error, print_msg
 from easybuild.tools.config import build_option, build_path, get_log_filename, get_repository, get_repositorypath
@@ -72,6 +71,7 @@
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
 from easybuild.tools.modules import ROOT_ENV_VAR_NAME_PREFIX, VERSION_ENV_VAR_NAME_PREFIX, DEVEL_ENV_VAR_NAME_PREFIX
 from easybuild.tools.modules import get_software_root, modules_tool
+from easybuild.tools.package.utilities import package_fpm
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.systemtools import det_parallelism, use_group

From 05bd7523e7df3b32396a92176346bea7e6154eca Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 8 Jul 2015 10:52:02 +0200
Subject: [PATCH 1121/1356] Fixed some remarks

---
 :q                      | 275 ++++++++++++++++++++++++++++++++++++++++
 easybuild/tools/docs.py |  43 +++----
 2 files changed, 296 insertions(+), 22 deletions(-)
 create mode 100644 :q

diff --git a/:q b/:q
new file mode 100644
index 0000000000..ee31281b3e
--- /dev/null
+++ b/:q
@@ -0,0 +1,275 @@
+# #
+# Copyright 2009-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Documentation-related functionality
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+@author: Toon Willems (Ghent University)
+@author: Ward Poelmans (Ghent University)
+"""
+import copy
+import inspect
+import os
+
+from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, HIDDEN, sorted_categories
+from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
+from easybuild.tools.ordereddict import OrderedDict
+from easybuild.tools.utilities import quote_str, import_available_modules
+from easybuild.tools.filetools import read_file
+
+FORMAT_RST = 'rst'
+FORMAT_TXT = 'txt'
+
+def det_col_width(entries, title):
+    """Determine column width based on column title and list of entries."""
+    return max(map(len, entries + [title]))
+
+
+def avail_easyconfig_params_rst(title, grouped_params):
+    """
+    Compose overview of available easyconfig parameters, in RST format.
+    """
+    # main title
+    lines = [
+        title,
+        '=' * len(title),
+        '',
+    ]
+
+    for grpname in grouped_params:
+        # group section title
+        lines.append("%s parameters" % grpname)
+        lines.extend(['-' * len(lines[-1]), ''])
+
+        titles = ["**Parameter name**", "**Description**", "**Default value**"]
+        values = [
+            [backtick(name) for name in grouped_params[grpname].keys()],
+            [x[0] for x in grouped_params[grpname].values()],
+            [str(quote_str(x[1])) for x in grouped_params[grpname].values()]
+        ]
+
+        lines.extend(mk_rst_table(titles, values))
+        lines.append('')
+
+    return '\n'.join(lines)
+
+def avail_easyconfig_params_txt(title, grouped_params):
+    """
+    Compose overview of available easyconfig parameters, in plain text format.
+    """
+    # main title
+    lines = [
+        '%s:' % title,
+        '',
+    ]
+
+    for grpname in grouped_params:
+        # group section title
+        lines.append(grpname.upper())
+        lines.append('-' * len(lines[-1]))
+
+        # determine width of 'name' column, to left-align descriptions
+        nw = max(map(len, grouped_params[grpname].keys()))
+
+        # line by parameter
+        for name, (descr, dflt) in sorted(grouped_params[grpname].items()):
+            lines.append("{0:<{nw}}   {1:} [default: {2:}]".format(name, descr, str(quote_str(dflt)), nw=nw))
+        lines.append('')
+
+    return '\n'.join(lines)
+
+def avail_easyconfig_params(easyblock, output_format):
+    """
+    Compose overview of available easyconfig parameters, in specified format.
+    """
+    params = copy.deepcopy(DEFAULT_CONFIG)
+
+    # include list of extra parameters (if any)
+    extra_params = {}
+    app = get_easyblock_class(easyblock, default_fallback=False)
+    if app is not None:
+        extra_params = app.extra_options()
+    params.update(extra_params)
+
+    # compose title
+    title = "Available easyconfig parameters"
+    if extra_params:
+        title += " (* indicates specific to the %s easyblock)" % app.__name__
+
+    # group parameters by category
+    grouped_params = OrderedDict()
+    for category in sorted_categories():
+        # exclude hidden parameters
+        if category[1].upper() in [HIDDEN]:
+            continue
+
+        grpname = category[1]
+        grouped_params[grpname] = {}
+        for name, (dflt, descr, cat) in params.items():
+            if cat == category:
+                if name in extra_params:
+                    # mark easyblock-specific parameters
+                    name = '%s*' % name
+                grouped_params[grpname].update({name: (descr, dflt)})
+
+        if not grouped_params[grpname]:
+            del grouped_params[grpname]
+
+    # compose output, according to specified format (txt, rst, ...)
+    avail_easyconfig_params_functions = {
+        FORMAT_RST: avail_easyconfig_params_rst,
+        FORMAT_TXT: avail_easyconfig_params_txt,
+    }
+    return avail_easyconfig_params_functions[output_format](title, grouped_params)
+
+def generic_easyblocks():
+    """
+    Compose overview of all generic easyblocks
+    """
+    modules = import_available_modules('easybuild.easyblocks.generic')
+    docs = []
+    seen = []
+
+    for m in modules:
+        for name,obj in inspect.getmembers(m, inspect.isclass):
+            eb_class = getattr(m, name)
+            # skip imported classes that are not easyblocks
+            if eb_class.__module__.startswith('easybuild.easyblocks.generic') and name not in seen:
+                docs.append(doc_easyblock(eb_class))
+                seen.append(name)
+
+    toc = ['.. contents:: Available generic easyblocks', '    :depth: 1', '']
+
+    return toc + sorted(docs)
+
+def overriden_functions(eb_class, parent_class):
+    print eb_class.__name__
+    print eb_class
+    print parent_class
+    for func in eb_class.__dict__.keys():
+        child_func = getattr(eb_class, func)
+        parent_func = getattr(parent_class, func)
+        if child_func.__func__ is not parent_func.__func__:
+            print func
+
+
+
+def doc_easyblock(eb_class):
+    """
+    Compose overview of one easyblock given class object of the easyblock in rst format
+    """
+    classname = eb_class.__name__
+
+    common_params = {
+        'ConfigureMake' : ['configopts', 'buildopts', 'installopts'],
+        # to be continued
+    }
+
+    lines = [
+        '``' + classname + '``',
+        '=' * (len(classname)+4),
+        '',
+    ]
+
+    bases = ['``' + base.__name__ + '``' for base in eb_class.__bases__]
+    derived = '(derives from ' + ', '.join(bases) + ')'
+    lines.extend([derived, ''])
+
+    for base in eb_class.__bases__:
+        overriden_functions(eb_class, base)
+
+    # Description (docstring)
+    lines.extend([eb_class.__doc__.strip(), ''])
+
+    # Add extra options, if any
+    if eb_class.extra_options():
+        extra_parameters = 'Extra easyconfig parameters specific to ' + backtick(classname) + ' easyblock'
+        lines.extend([extra_parameters, '-' * len(extra_parameters), ''])
+        ex_opt = eb_class.extra_options()
+
+        titles = ['easyconfig parameter', 'description', 'default value']
+        values = [[backtick(key) for key in ex_opt], [val[1] for val in ex_opt.values()], [backtick(str(quote_str(val[0]))) for val in ex_opt.values()]]
+
+        lines.extend(mk_rst_table(titles, values))
+        lines.append('')
+
+    if classname in common_params:
+        commonly_used = 'Commonly used easyconfig parameters with ' + backtick(classname) + ' easyblock'
+        lines.extend([commonly_used, '-' * len(commonly_used)])
+
+        for opt in common_params[classname]:
+            param = '* ' + backtick(opt) + ' - ' + DEFAULT_CONFIG[opt][1]
+            lines.append(param)
+
+
+    if classname + '.eb' in os.listdir(os.path.join(os.path.dirname(__file__), 'doc_examples')):
+        lines.extend(['', 'Example', '-' * 8, '', '::', ''])
+        f = open(os.path.join(os.path.dirname(__file__), 'doc_examples', classname+'.eb'), "r")
+        for line in f.readlines():
+            lines.append('    ' + line.strip())
+        lines.append('') # empty line after literal block
+
+    return '\n'.join(lines)
+
+
+def mk_rst_table(titles, values):
+    """
+    Returns an rst table with given titles and values (a nested list of string values for each column)
+    """
+    num_col = len(titles)
+    table = []
+    col_widths = []
+    tmpl = []
+    line= []
+
+    # figure out column widths
+    for i in range(0, num_col):
+        col_widths.append(det_col_width(values[i], titles[i]))
+
+        # make line template
+        tmpl.append('{' + str(i) + ':{c}<' + str(col_widths[i]) + '}')
+        line.append('') # needed for table line
+
+    line_tmpl = '   '.join(tmpl)
+    table_line = line_tmpl.format(*line, c="=")
+
+    table.append(table_line)
+    table.append(line_tmpl.format(*titles, c=' '))
+    table.append(table_line)
+
+    for i in range(0, len(values[0])):
+        table.append(line_tmpl.format(*[v[i] for v in values], c=' '))
+
+    table.extend([table_line, ''])
+
+    return table
+
+
+def backtick(string):
+    return '``' + string + '``'
diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 65d5b54270..c2b84520b6 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -46,6 +46,11 @@
 FORMAT_RST = 'rst'
 FORMAT_TXT = 'txt'
 
+COMMON_PARAMS = {
+    'ConfigureMake' : ['configopts', 'buildopts', 'installopts'],
+    # to be continued
+}
+
 def det_col_width(entries, title):
     """Determine column width based on column title and list of entries."""
     return max(map(len, entries + [title]))
@@ -69,7 +74,7 @@ def avail_easyconfig_params_rst(title, grouped_params):
 
         titles = ["**Parameter name**", "**Description**", "**Default value**"]
         values = [
-            [backtick(name) for name in grouped_params[grpname].keys()],
+            ['``' + name + '``' for name in grouped_params[grpname].keys()],
             [x[0] for x in grouped_params[grpname].values()],
             [str(quote_str(x[1])) for x in grouped_params[grpname].values()]
         ]
@@ -153,6 +158,7 @@ def generic_easyblocks():
     Compose overview of all generic easyblocks
     """
     modules = import_available_modules('easybuild.easyblocks.generic')
+    path_to_examples = os.path.join(os.path.dirname(__file__), 'doc_examples') #TODO: move them somewhere else
     docs = []
     seen = []
 
@@ -161,25 +167,19 @@ def generic_easyblocks():
             eb_class = getattr(m, name)
             # skip imported classes that are not easyblocks
             if eb_class.__module__.startswith('easybuild.easyblocks.generic') and name not in seen:
-                docs.append(doc_easyblock(eb_class))
+                docs.append(doc_easyblock(eb_class, path_to_examples))
                 seen.append(name)
 
     toc = ['.. contents:: Available generic easyblocks', '    :depth: 1', '']
 
     return toc + sorted(docs)
 
-
-def doc_easyblock(eb_class):
+def doc_easyblock(eb_class, path_to_examples):
     """
     Compose overview of one easyblock given class object of the easyblock in rst format
     """
     classname = eb_class.__name__
 
-    common_params = {
-        'ConfigureMake' : ['configopts', 'buildopts', 'installopts'],
-        # to be continued
-    }
-
     lines = [
         '``' + classname + '``',
         '=' * (len(classname)+4),
@@ -195,35 +195,37 @@ def doc_easyblock(eb_class):
 
     # Add extra options, if any
     if eb_class.extra_options():
-        extra_parameters = 'Extra easyconfig parameters specific to ' + backtick(classname) + ' easyblock'
+        extra_parameters = 'Extra easyconfig parameters specific to ``' + classname + '`` easyblock'
         lines.extend([extra_parameters, '-' * len(extra_parameters), ''])
         ex_opt = eb_class.extra_options()
 
         titles = ['easyconfig parameter', 'description', 'default value']
-        values = [[backtick(key) for key in ex_opt], [val[1] for val in ex_opt.values()], [backtick(str(quote_str(val[0]))) for val in ex_opt.values()]]
+        values = [
+            ['``' + key + '``' for key in ex_opt],
+            [val[1] for val in ex_opt.values()],
+            ['``' + str(quote_str(val[0])) + '``' for val in ex_opt.values()]
+        ]
 
         lines.extend(mk_rst_table(titles, values))
         lines.append('')
 
-    if classname in common_params:
-        commonly_used = 'Commonly used easyconfig parameters with ' + backtick(classname) + ' easyblock'
+    if classname in COMMON_PARAMS:
+        commonly_used = 'Commonly used easyconfig parameters with ``' + classname + '`` easyblock'
         lines.extend([commonly_used, '-' * len(commonly_used)])
 
-        for opt in common_params[classname]:
-            param = '* ' + backtick(opt) + ' - ' + DEFAULT_CONFIG[opt][1]
+        for opt in COMMON_PARAMS[classname]:
+            param = '* ``' + opt + '`` - ' + DEFAULT_CONFIG[opt][1]
             lines.append(param)
 
 
-    if classname + '.eb' in os.listdir(os.path.join(os.path.dirname(__file__), 'doc_examples')):
+    if classname + '.eb' in os.listdir(os.path.join(path_to_examples)):
         lines.extend(['', 'Example', '-' * 8, '', '::', ''])
-        f = open(os.path.join(os.path.dirname(__file__), 'doc_examples', classname+'.eb'), "r")
-        for line in f.readlines():
+        for line in read_file(os.path.join(path_to_examples, classname+'.eb')).split('\n'):
             lines.append('    ' + line.strip())
         lines.append('') # empty line after literal block
 
     return '\n'.join(lines)
 
-
 def mk_rst_table(titles, values):
     """
     Returns an rst table with given titles and values (a nested list of string values for each column)
@@ -256,6 +258,3 @@ def mk_rst_table(titles, values):
 
     return table
 
-
-def backtick(string):
-    return '``' + string + '``'

From c657025791b533e7fb39ed61e70be0af946a3413 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 8 Jul 2015 10:52:51 +0200
Subject: [PATCH 1122/1356] Delete :q

something went wrong there
---
 :q | 275 -------------------------------------------------------------
 1 file changed, 275 deletions(-)
 delete mode 100644 :q

diff --git a/:q b/:q
deleted file mode 100644
index ee31281b3e..0000000000
--- a/:q
+++ /dev/null
@@ -1,275 +0,0 @@
-# #
-# Copyright 2009-2015 Ghent University
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-# #
-"""
-Documentation-related functionality
-
-@author: Stijn De Weirdt (Ghent University)
-@author: Dries Verdegem (Ghent University)
-@author: Kenneth Hoste (Ghent University)
-@author: Pieter De Baets (Ghent University)
-@author: Jens Timmerman (Ghent University)
-@author: Toon Willems (Ghent University)
-@author: Ward Poelmans (Ghent University)
-"""
-import copy
-import inspect
-import os
-
-from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, HIDDEN, sorted_categories
-from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
-from easybuild.tools.ordereddict import OrderedDict
-from easybuild.tools.utilities import quote_str, import_available_modules
-from easybuild.tools.filetools import read_file
-
-FORMAT_RST = 'rst'
-FORMAT_TXT = 'txt'
-
-def det_col_width(entries, title):
-    """Determine column width based on column title and list of entries."""
-    return max(map(len, entries + [title]))
-
-
-def avail_easyconfig_params_rst(title, grouped_params):
-    """
-    Compose overview of available easyconfig parameters, in RST format.
-    """
-    # main title
-    lines = [
-        title,
-        '=' * len(title),
-        '',
-    ]
-
-    for grpname in grouped_params:
-        # group section title
-        lines.append("%s parameters" % grpname)
-        lines.extend(['-' * len(lines[-1]), ''])
-
-        titles = ["**Parameter name**", "**Description**", "**Default value**"]
-        values = [
-            [backtick(name) for name in grouped_params[grpname].keys()],
-            [x[0] for x in grouped_params[grpname].values()],
-            [str(quote_str(x[1])) for x in grouped_params[grpname].values()]
-        ]
-
-        lines.extend(mk_rst_table(titles, values))
-        lines.append('')
-
-    return '\n'.join(lines)
-
-def avail_easyconfig_params_txt(title, grouped_params):
-    """
-    Compose overview of available easyconfig parameters, in plain text format.
-    """
-    # main title
-    lines = [
-        '%s:' % title,
-        '',
-    ]
-
-    for grpname in grouped_params:
-        # group section title
-        lines.append(grpname.upper())
-        lines.append('-' * len(lines[-1]))
-
-        # determine width of 'name' column, to left-align descriptions
-        nw = max(map(len, grouped_params[grpname].keys()))
-
-        # line by parameter
-        for name, (descr, dflt) in sorted(grouped_params[grpname].items()):
-            lines.append("{0:<{nw}}   {1:} [default: {2:}]".format(name, descr, str(quote_str(dflt)), nw=nw))
-        lines.append('')
-
-    return '\n'.join(lines)
-
-def avail_easyconfig_params(easyblock, output_format):
-    """
-    Compose overview of available easyconfig parameters, in specified format.
-    """
-    params = copy.deepcopy(DEFAULT_CONFIG)
-
-    # include list of extra parameters (if any)
-    extra_params = {}
-    app = get_easyblock_class(easyblock, default_fallback=False)
-    if app is not None:
-        extra_params = app.extra_options()
-    params.update(extra_params)
-
-    # compose title
-    title = "Available easyconfig parameters"
-    if extra_params:
-        title += " (* indicates specific to the %s easyblock)" % app.__name__
-
-    # group parameters by category
-    grouped_params = OrderedDict()
-    for category in sorted_categories():
-        # exclude hidden parameters
-        if category[1].upper() in [HIDDEN]:
-            continue
-
-        grpname = category[1]
-        grouped_params[grpname] = {}
-        for name, (dflt, descr, cat) in params.items():
-            if cat == category:
-                if name in extra_params:
-                    # mark easyblock-specific parameters
-                    name = '%s*' % name
-                grouped_params[grpname].update({name: (descr, dflt)})
-
-        if not grouped_params[grpname]:
-            del grouped_params[grpname]
-
-    # compose output, according to specified format (txt, rst, ...)
-    avail_easyconfig_params_functions = {
-        FORMAT_RST: avail_easyconfig_params_rst,
-        FORMAT_TXT: avail_easyconfig_params_txt,
-    }
-    return avail_easyconfig_params_functions[output_format](title, grouped_params)
-
-def generic_easyblocks():
-    """
-    Compose overview of all generic easyblocks
-    """
-    modules = import_available_modules('easybuild.easyblocks.generic')
-    docs = []
-    seen = []
-
-    for m in modules:
-        for name,obj in inspect.getmembers(m, inspect.isclass):
-            eb_class = getattr(m, name)
-            # skip imported classes that are not easyblocks
-            if eb_class.__module__.startswith('easybuild.easyblocks.generic') and name not in seen:
-                docs.append(doc_easyblock(eb_class))
-                seen.append(name)
-
-    toc = ['.. contents:: Available generic easyblocks', '    :depth: 1', '']
-
-    return toc + sorted(docs)
-
-def overriden_functions(eb_class, parent_class):
-    print eb_class.__name__
-    print eb_class
-    print parent_class
-    for func in eb_class.__dict__.keys():
-        child_func = getattr(eb_class, func)
-        parent_func = getattr(parent_class, func)
-        if child_func.__func__ is not parent_func.__func__:
-            print func
-
-
-
-def doc_easyblock(eb_class):
-    """
-    Compose overview of one easyblock given class object of the easyblock in rst format
-    """
-    classname = eb_class.__name__
-
-    common_params = {
-        'ConfigureMake' : ['configopts', 'buildopts', 'installopts'],
-        # to be continued
-    }
-
-    lines = [
-        '``' + classname + '``',
-        '=' * (len(classname)+4),
-        '',
-    ]
-
-    bases = ['``' + base.__name__ + '``' for base in eb_class.__bases__]
-    derived = '(derives from ' + ', '.join(bases) + ')'
-    lines.extend([derived, ''])
-
-    for base in eb_class.__bases__:
-        overriden_functions(eb_class, base)
-
-    # Description (docstring)
-    lines.extend([eb_class.__doc__.strip(), ''])
-
-    # Add extra options, if any
-    if eb_class.extra_options():
-        extra_parameters = 'Extra easyconfig parameters specific to ' + backtick(classname) + ' easyblock'
-        lines.extend([extra_parameters, '-' * len(extra_parameters), ''])
-        ex_opt = eb_class.extra_options()
-
-        titles = ['easyconfig parameter', 'description', 'default value']
-        values = [[backtick(key) for key in ex_opt], [val[1] for val in ex_opt.values()], [backtick(str(quote_str(val[0]))) for val in ex_opt.values()]]
-
-        lines.extend(mk_rst_table(titles, values))
-        lines.append('')
-
-    if classname in common_params:
-        commonly_used = 'Commonly used easyconfig parameters with ' + backtick(classname) + ' easyblock'
-        lines.extend([commonly_used, '-' * len(commonly_used)])
-
-        for opt in common_params[classname]:
-            param = '* ' + backtick(opt) + ' - ' + DEFAULT_CONFIG[opt][1]
-            lines.append(param)
-
-
-    if classname + '.eb' in os.listdir(os.path.join(os.path.dirname(__file__), 'doc_examples')):
-        lines.extend(['', 'Example', '-' * 8, '', '::', ''])
-        f = open(os.path.join(os.path.dirname(__file__), 'doc_examples', classname+'.eb'), "r")
-        for line in f.readlines():
-            lines.append('    ' + line.strip())
-        lines.append('') # empty line after literal block
-
-    return '\n'.join(lines)
-
-
-def mk_rst_table(titles, values):
-    """
-    Returns an rst table with given titles and values (a nested list of string values for each column)
-    """
-    num_col = len(titles)
-    table = []
-    col_widths = []
-    tmpl = []
-    line= []
-
-    # figure out column widths
-    for i in range(0, num_col):
-        col_widths.append(det_col_width(values[i], titles[i]))
-
-        # make line template
-        tmpl.append('{' + str(i) + ':{c}<' + str(col_widths[i]) + '}')
-        line.append('') # needed for table line
-
-    line_tmpl = '   '.join(tmpl)
-    table_line = line_tmpl.format(*line, c="=")
-
-    table.append(table_line)
-    table.append(line_tmpl.format(*titles, c=' '))
-    table.append(table_line)
-
-    for i in range(0, len(values[0])):
-        table.append(line_tmpl.format(*[v[i] for v in values], c=' '))
-
-    table.extend([table_line, ''])
-
-    return table
-
-
-def backtick(string):
-    return '``' + string + '``'

From 1dd8db7dd61074071bc37263e1f1a1884feeaa4e Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 8 Jul 2015 13:43:42 +0200
Subject: [PATCH 1123/1356] Fixed some remarks

---
 easybuild/framework/easyconfig/easyconfig.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 6138511f3e..47b511ac3d 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -63,7 +63,7 @@
 from easybuild.framework.easyconfig.licenses import EASYCONFIG_LICENSES_DICT, License
 from easybuild.framework.easyconfig.parser import DEPRECATED_PARAMETERS, REPLACED_PARAMETERS
 from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig
-from easybuild.framework.easyconfig.templates import template_constant_dict, TEMPLATE_CONSTANTS
+from easybuild.framework.easyconfig.templates import TEMPLATE_CONSTANTS, template_constant_dict
 
 
 _log = fancylogger.getLogger('easyconfig.easyconfig', fname=False)
@@ -500,9 +500,10 @@ def dump(self, fp):
 
         self.generate_template_values()
         templ_const = dict([(const[1], const[0]) for const in TEMPLATE_CONSTANTS])
-        templ_val = dict([(self.template_values[key], key) for key in self.template_values if len(self.template_values[key]) > 2])
-
-        exclude_keys = ['name', 'version', 'description', 'homepage', 'toolchain'] # values will not be templated for these keys
+        # reverse map of templates longer than 2 characters, to inject template values where possible
+        templ_val = sorted(dict([(val, key) for key, val in self.template_values.items() if len(val) > 2]), key=len(val), reverse=True)
+        # values will not be templated for these keys
+        exclude_keys = ['name', 'version', 'description', 'homepage', 'toolchain']
 
         def include_defined_parameters(keyset):
             """
@@ -514,7 +515,9 @@ def include_defined_parameters(keyset):
                     val = self[key]
                     if val != default_values[key]:
                         if key not in exclude_keys:
+                            self.log.debug("Original value before replacing matching template values: %s", val)
                             val = replace_templates(val, templ_const, templ_val)
+                            self.log.debug("New value after replacing matching template values: %s", val)
                         ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
                         printed_keys.append(key)
                         printed = True
@@ -539,7 +542,7 @@ def include_defined_parameters(keyset):
         eb_file.write(('\n'.join(ebtxt)).strip()) # strip for newlines at the end
         eb_file.close()
 
-        self.enable_tamplating = orig_enable_templating
+        self.enable_templating = orig_enable_templating
 
     def _validate(self, attr, values):  # private method
         """
@@ -940,7 +943,7 @@ def replace_templates(value, templ_const, templ_val):
         - templ_val is a dictionary of template strings specific for this easyconfig file
     """
     if isinstance(value, basestring):
-        old_value = ""
+        old_value = None
         while value != old_value:
             old_value = value
             if value in templ_const:

From cc8da015350afce5f2dd4fbfaf4f211baaf7a020 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 8 Jul 2015 15:11:38 +0200
Subject: [PATCH 1124/1356] added custom step functions to doc

---
 easybuild/tools/docs.py | 37 ++++++++++++++++++++++++-------------
 1 file changed, 24 insertions(+), 13 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index c2b84520b6..27df95800d 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -46,11 +46,6 @@
 FORMAT_RST = 'rst'
 FORMAT_TXT = 'txt'
 
-COMMON_PARAMS = {
-    'ConfigureMake' : ['configopts', 'buildopts', 'installopts'],
-    # to be continued
-}
-
 def det_col_width(entries, title):
     """Determine column width based on column title and list of entries."""
     return max(map(len, entries + [title]))
@@ -153,12 +148,11 @@ def avail_easyconfig_params(easyblock, output_format):
     }
     return avail_easyconfig_params_functions[output_format](title, grouped_params)
 
-def generic_easyblocks():
+def generic_easyblocks(path_to_examples, common_params={}, doc_functions=[]):
     """
     Compose overview of all generic easyblocks
     """
     modules = import_available_modules('easybuild.easyblocks.generic')
-    path_to_examples = os.path.join(os.path.dirname(__file__), 'doc_examples') #TODO: move them somewhere else
     docs = []
     seen = []
 
@@ -167,14 +161,14 @@ def generic_easyblocks():
             eb_class = getattr(m, name)
             # skip imported classes that are not easyblocks
             if eb_class.__module__.startswith('easybuild.easyblocks.generic') and name not in seen:
-                docs.append(doc_easyblock(eb_class, path_to_examples))
+                docs.append(doc_easyblock(eb_class, path_to_examples, common_params, doc_functions))
                 seen.append(name)
 
     toc = ['.. contents:: Available generic easyblocks', '    :depth: 1', '']
 
     return toc + sorted(docs)
 
-def doc_easyblock(eb_class, path_to_examples):
+def doc_easyblock(eb_class, path_to_examples, common_params, doc_functions):
     """
     Compose overview of one easyblock given class object of the easyblock in rst format
     """
@@ -207,17 +201,34 @@ def doc_easyblock(eb_class, path_to_examples):
         ]
 
         lines.extend(mk_rst_table(titles, values))
-        lines.append('')
 
-    if classname in COMMON_PARAMS:
+    # Add commonly used parameters
+    if classname in common_params:
         commonly_used = 'Commonly used easyconfig parameters with ``' + classname + '`` easyblock'
         lines.extend([commonly_used, '-' * len(commonly_used)])
 
-        for opt in COMMON_PARAMS[classname]:
+        for opt in common_params[classname]:
             param = '* ``' + opt + '`` - ' + DEFAULT_CONFIG[opt][1]
             lines.append(param)
+    lines.append('')
+
+    custom = []
+    # Add docstring for custom steps
+    for func in doc_functions:
+        if func in eb_class.__dict__:
+            f = eb_class.__dict__[func]
+        elif func in eb_class.__bases__[0].__dict__:
+            f = eb_class.__bases__[0].__dict__[func]
+
+        if f.__doc__:
+            custom.append('* ``' + func + '`` - ' + f.__doc__.strip())
+
+    if custom:
+        title = 'Customised steps'
+        lines.extend([title, '-' * len(title)] + custom)
+        lines.append('')
 
-
+    # Add example if available
     if classname + '.eb' in os.listdir(os.path.join(path_to_examples)):
         lines.extend(['', 'Example', '-' * 8, '', '::', ''])
         for line in read_file(os.path.join(path_to_examples, classname+'.eb')).split('\n'):

From 09a974276f271f49b94220d29d7a1371848dc735 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 8 Jul 2015 15:22:32 +0200
Subject: [PATCH 1125/1356] remove examples from framework

---
 easybuild/tools/doc_examples/Binary.eb        | 21 ------------
 easybuild/tools/doc_examples/Bundle.eb        | 17 ----------
 easybuild/tools/doc_examples/CMakeMake.eb     | 30 -----------------
 easybuild/tools/doc_examples/ConfigureMake.eb | 20 -----------
 .../ConfigureMakePythonPackage.eb             | 33 -------------------
 5 files changed, 121 deletions(-)
 delete mode 100644 easybuild/tools/doc_examples/Binary.eb
 delete mode 100644 easybuild/tools/doc_examples/Bundle.eb
 delete mode 100644 easybuild/tools/doc_examples/CMakeMake.eb
 delete mode 100644 easybuild/tools/doc_examples/ConfigureMake.eb
 delete mode 100644 easybuild/tools/doc_examples/ConfigureMakePythonPackage.eb

diff --git a/easybuild/tools/doc_examples/Binary.eb b/easybuild/tools/doc_examples/Binary.eb
deleted file mode 100644
index 2fa31617c3..0000000000
--- a/easybuild/tools/doc_examples/Binary.eb
+++ /dev/null
@@ -1,21 +0,0 @@
-easyblock = 'Binary'
-
-name = 'Platanus'
-version = '1.2.1'
-versionsuffix = '-linux-x86_64'
-
-homepage = 'http://platanus.bio.titech.ac.jp/'
-description = """PLATform for Assembling NUcleotide Sequences"""
-
-toolchain = {'name': 'dummy', 'version': 'dummy'}
-
-source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201']
-sources = ['platanus']
-checksums = ['02cf92847ec704d010a54df293b9c60a']
-
-sanity_check_paths = {
-    'files': ['platanus'],
-    'dirs': [],
-}
-
-moduleclass = 'bio'
diff --git a/easybuild/tools/doc_examples/Bundle.eb b/easybuild/tools/doc_examples/Bundle.eb
deleted file mode 100644
index 067ccdbe63..0000000000
--- a/easybuild/tools/doc_examples/Bundle.eb
+++ /dev/null
@@ -1,17 +0,0 @@
-easyblock = 'Bundle'
-
-name = 'Autotools'
-version = '20150119' # date of the most recent change
-
-homepage = 'http://autotools.io'
-description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
-
-toolchain = {'name': 'GCC', 'version': '4.9.2'}
-
-dependencies = [
-    ('Autoconf', '2.69'), # 20120424
-    ('Automake', '1.15'), # 20150105
-    ('libtool', '2.4.5'), # 20150119
-]
-
-moduleclass = 'devel'
diff --git a/easybuild/tools/doc_examples/CMakeMake.eb b/easybuild/tools/doc_examples/CMakeMake.eb
deleted file mode 100644
index 1e8a2bf6f6..0000000000
--- a/easybuild/tools/doc_examples/CMakeMake.eb
+++ /dev/null
@@ -1,30 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'ANTs'
-version = '2.1.0rc3'
-
-homepage = 'http://stnava.github.io/ANTs/'
-description = """ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing,
- interpreting and visualizing multidimensional data."""
-
-toolchain = {'name': 'goolf', 'version': '1.5.14'}
-toolchainopts = {'pic': True}
-
-source_urls = ['https://github.com/stnava/ANTs/archive/']
-sources = ['v%(version)s.tar.gz']
-
-builddependencies = [('CMake', '3.0.2')]
-
-skipsteps = ['install']
-buildopts = ' && mkdir -p %(installdir)s && cp -r * %(installdir)s/'
-
-parallel = 1
-
-separate_build_dir = True
-
-sanity_check_paths = {
-    'files': ['bin/ANTS'],
-    'dirs': ['lib'],
-}
-
-moduleclass = 'data'
diff --git a/easybuild/tools/doc_examples/ConfigureMake.eb b/easybuild/tools/doc_examples/ConfigureMake.eb
deleted file mode 100644
index 9a0d4bf65e..0000000000
--- a/easybuild/tools/doc_examples/ConfigureMake.eb
+++ /dev/null
@@ -1,20 +0,0 @@
-easyblock = 'ConfigureMake'
-
-name = 'zsync'
-version = '0.6.2'
-
-homepage = 'http://zsync.moria.org.uk/'
-description = """zsync-0.6.2: Optimising file distribution program, a 1-to-many rsync"""
-
-sources = [SOURCE_TAR_BZ2]
-source_urls = ['http://zsync.moria.org.uk/download/']
-
-
-toolchain = {'name': 'ictce', 'version': '5.3.0'}
-
-sanity_check_paths = {
-                      'files': ['bin/zsync'],
-                      'dirs': []
-                     }
-
-moduleclass = 'tools'
diff --git a/easybuild/tools/doc_examples/ConfigureMakePythonPackage.eb b/easybuild/tools/doc_examples/ConfigureMakePythonPackage.eb
deleted file mode 100644
index 0f9fd09a84..0000000000
--- a/easybuild/tools/doc_examples/ConfigureMakePythonPackage.eb
+++ /dev/null
@@ -1,33 +0,0 @@
-easyblock = 'ConfigureMakePythonPackage'
-
-name = 'PyQt'
-version = '4.11.3'
-
-homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt'
-description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework."""
-
-toolchain = {'name': 'goolf', 'version': '1.5.14'}
-
-sources = ['%(name)s-x11-gpl-%(version)s.tar.gz']
-source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s']
-
-python = 'Python'
-pyver = '2.7.9'
-pythonshortver = '.'.join(pyver.split('.')[:2])
-versionsuffix = '-%s-%s' % (python, pyver)
-
-dependencies = [
-    (python, pyver),
-    ('SIP', '4.16.4', versionsuffix),
-    ('Qt', '4.8.6'),
-]
-
-configopts = "configure-ng.py --confirm-license"
-configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver
-configopts += " --no-sip-files"
-
-options = {'modulename': 'PyQt4'}
-
-modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver}
-
-moduleclass = 'vis'

From 0299605b9adc9629d613abd5f2389c7c5eac2e41 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 8 Jul 2015 16:25:53 +0200
Subject: [PATCH 1126/1356] added internal references for parent classes

---
 easybuild/tools/docs.py | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 27df95800d..f1d7c4b923 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -154,21 +154,24 @@ def generic_easyblocks(path_to_examples, common_params={}, doc_functions=[]):
     """
     modules = import_available_modules('easybuild.easyblocks.generic')
     docs = []
-    seen = []
+    all_blocks = []
 
+    # get all blocks
     for m in modules:
         for name,obj in inspect.getmembers(m, inspect.isclass):
             eb_class = getattr(m, name)
             # skip imported classes that are not easyblocks
-            if eb_class.__module__.startswith('easybuild.easyblocks.generic') and name not in seen:
-                docs.append(doc_easyblock(eb_class, path_to_examples, common_params, doc_functions))
-                seen.append(name)
+            if eb_class.__module__.startswith('easybuild.easyblocks.generic') and eb_class not in all_blocks:
+                all_blocks.append(eb_class)
+
+    for eb_class in all_blocks:
+        docs.append(doc_easyblock(eb_class, path_to_examples, common_params, doc_functions, all_blocks))
 
     toc = ['.. contents:: Available generic easyblocks', '    :depth: 1', '']
 
     return toc + sorted(docs)
 
-def doc_easyblock(eb_class, path_to_examples, common_params, doc_functions):
+def doc_easyblock(eb_class, path_to_examples, common_params, doc_functions, all_blocks):
     """
     Compose overview of one easyblock given class object of the easyblock in rst format
     """
@@ -180,7 +183,11 @@ def doc_easyblock(eb_class, path_to_examples, common_params, doc_functions):
         '',
     ]
 
-    bases = ['``' + base.__name__ + '``' for base in eb_class.__bases__]
+    bases = []
+    for b in eb_class.__bases__:
+        base = b.__name__ + '_' if b in all_blocks else b.__name__
+        bases.append(base)
+
     derived = '(derives from ' + ', '.join(bases) + ')'
     lines.extend([derived, ''])
 

From 5baa702ae48053eded2faa16b0dded1a6a9315a7 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 8 Jul 2015 16:32:49 +0200
Subject: [PATCH 1127/1356] added mark for inherited functions

---
 easybuild/tools/docs.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index f1d7c4b923..734e97f549 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -219,16 +219,18 @@ def doc_easyblock(eb_class, path_to_examples, common_params, doc_functions, all_
             lines.append(param)
     lines.append('')
 
-    custom = []
     # Add docstring for custom steps
+    custom = []
+    inh = ''
     for func in doc_functions:
         if func in eb_class.__dict__:
             f = eb_class.__dict__[func]
         elif func in eb_class.__bases__[0].__dict__:
             f = eb_class.__bases__[0].__dict__[func]
+            inh = ' (inherited)'
 
         if f.__doc__:
-            custom.append('* ``' + func + '`` - ' + f.__doc__.strip())
+            custom.append('* ``' + func + '`` - ' + f.__doc__.strip() + inh)
 
     if custom:
         title = 'Customised steps'

From 1e35b4295f586527bc609020d3d5fc0adf7668c5 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 8 Jul 2015 16:44:46 +0200
Subject: [PATCH 1128/1356] added page title

---
 easybuild/tools/docs.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 734e97f549..8260b31bf9 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -167,9 +167,10 @@ def generic_easyblocks(path_to_examples, common_params={}, doc_functions=[]):
     for eb_class in all_blocks:
         docs.append(doc_easyblock(eb_class, path_to_examples, common_params, doc_functions, all_blocks))
 
-    toc = ['.. contents:: Available generic easyblocks', '    :depth: 1', '']
+    title = 'Overview of generic easyblocks'
 
-    return toc + sorted(docs)
+    heading = ['=' * len(title), title, '=' * len(title), '', '.. contents:: Available generic easyblocks', '    :depth: 1', '']
+    return heading + sorted(docs)
 
 def doc_easyblock(eb_class, path_to_examples, common_params, doc_functions, all_blocks):
     """

From 09c21da2e228fe402c2b69eef51076da7d8d40ec Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 8 Jul 2015 16:56:24 +0200
Subject: [PATCH 1129/1356] Small fixes

---
 easybuild/tools/docs.py | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 8260b31bf9..e9824cee4c 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -43,9 +43,11 @@
 from easybuild.tools.utilities import quote_str, import_available_modules
 from easybuild.tools.filetools import read_file
 
+
 FORMAT_RST = 'rst'
 FORMAT_TXT = 'txt'
 
+
 def det_col_width(entries, title):
     """Determine column width based on column title and list of entries."""
     return max(map(len, entries + [title]))
@@ -69,9 +71,9 @@ def avail_easyconfig_params_rst(title, grouped_params):
 
         titles = ["**Parameter name**", "**Description**", "**Default value**"]
         values = [
-            ['``' + name + '``' for name in grouped_params[grpname].keys()],
-            [x[0] for x in grouped_params[grpname].values()],
-            [str(quote_str(x[1])) for x in grouped_params[grpname].values()]
+            ['``' + name + '``' for name in grouped_params[grpname].keys()],  # parameter name
+            [x[0] for x in grouped_params[grpname].values()],  # description
+            [str(quote_str(x[1])) for x in grouped_params[grpname].values()]  #default value
         ]
 
         lines.extend(mk_rst_table(titles, values))
@@ -148,9 +150,10 @@ def avail_easyconfig_params(easyblock, output_format):
     }
     return avail_easyconfig_params_functions[output_format](title, grouped_params)
 
-def generic_easyblocks(path_to_examples, common_params={}, doc_functions=[]):
+
+def gen_easyblocks_overview_rst(path_to_examples, common_params={}, doc_functions=[]):
     """
-    Compose overview of all generic easyblocks
+    Compose overview of all generic easyblocks in rst format
     """
     modules = import_available_modules('easybuild.easyblocks.generic')
     docs = []
@@ -165,14 +168,14 @@ def generic_easyblocks(path_to_examples, common_params={}, doc_functions=[]):
                 all_blocks.append(eb_class)
 
     for eb_class in all_blocks:
-        docs.append(doc_easyblock(eb_class, path_to_examples, common_params, doc_functions, all_blocks))
+        docs.append(gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc_functions, all_blocks))
 
     title = 'Overview of generic easyblocks'
 
-    heading = ['=' * len(title), title, '=' * len(title), '', '.. contents:: Available generic easyblocks', '    :depth: 1', '']
+    heading = ['=' * len(title), title, '=' * len(title), '', '.. contents::', '    :depth: 1', '']
     return heading + sorted(docs)
 
-def doc_easyblock(eb_class, path_to_examples, common_params, doc_functions, all_blocks):
+def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc_functions, all_blocks):
     """
     Compose overview of one easyblock given class object of the easyblock in rst format
     """
@@ -203,9 +206,9 @@ def doc_easyblock(eb_class, path_to_examples, common_params, doc_functions, all_
 
         titles = ['easyconfig parameter', 'description', 'default value']
         values = [
-            ['``' + key + '``' for key in ex_opt],
-            [val[1] for val in ex_opt.values()],
-            ['``' + str(quote_str(val[0])) + '``' for val in ex_opt.values()]
+            ['``' + key + '``' for key in ex_opt],  # parameter name
+            [val[1] for val in ex_opt.values()],  # description
+            ['``' + str(quote_str(val[0])) + '``' for val in ex_opt.values()]  # default value
         ]
 
         lines.extend(mk_rst_table(titles, values))

From 1f487a1cea9dd8da027f8454e643da2cbec2c053 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 8 Jul 2015 21:23:56 +0200
Subject: [PATCH 1130/1356] style fixes in job/backend.py and parallelbuild.py

---
 easybuild/tools/job/backend.py   |  6 +++++-
 easybuild/tools/parallelbuild.py | 19 +++++++++----------
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/easybuild/tools/job/backend.py b/easybuild/tools/job/backend.py
index 25ed7ee9a8..ba381005a4 100644
--- a/easybuild/tools/job/backend.py
+++ b/easybuild/tools/job/backend.py
@@ -22,8 +22,12 @@
 # You should have received a copy of the GNU General Public License
 # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
 ##
-"""Abstract interface for submitting jobs and related utilities."""
+"""
+Abstract interface for submitting jobs and related utilities.
 
+@author: Riccardo Murri (University of Zurich)
+@author: Kenneth Hoste (Ghent University)
+"""
 
 from abc import ABCMeta, abstractmethod
 
diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index d9567c510f..a34968772d 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -69,12 +69,12 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybu
     """
     _log.info("going to build these easyconfigs in parallel: %s", easyconfigs)
 
-    live_job_backend = job_backend()
-    if live_job_backend is None:
+    active_job_backend = job_backend()
+    if active_job_backend is None:
         raise EasyBuildError("Can not use --job if no job backend is available.")
 
     try:
-        live_job_backend.init()
+        active_job_backend.init()
     except RuntimeError as err:
         raise EasyBuildError("connection to server failed (%s: %s), can't submit jobs.", err.__class__.__name__, err)
 
@@ -94,22 +94,21 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybu
 
         # the new job will only depend on already submitted jobs
         _log.info("creating job for ec: %s" % str(ec))
-        new_job = create_job(live_job_backend, build_command, ec, output_dir=output_dir)
+        new_job = create_job(active_job_backend, build_command, ec, output_dir=output_dir)
 
         # sometimes unresolved_deps will contain things, not needed to be build
-        job_deps = [module_to_job[dep] for dep in map(_to_key, ec['unresolved_deps']) if dep in module_to_job]
+        dep_mod_names = map(ActiveMNS().det_full_module_name, ec['unresolved_deps'])
+        job_deps = [module_to_job[dep] for dep in dep_mod_names if dep in module_to_job]
 
         # actually (try to) submit job
-        live_job_backend.queue(new_job, job_deps)
-        _log.info(
-            "job %s for module %s has been submitted"
-            % (new_job, new_job.module))
+        active_job_backend.queue(new_job, job_deps)
+        _log.info("job %s for module %s has been submitted", new_job, new_job.module)
 
         # update dictionary
         module_to_job[new_job.module] = new_job
         jobs.append(new_job)
 
-    live_job_backend.complete()
+    active_job_backend.complete()
 
     return jobs
 

From d05cd3025175003d972f75dc26d8a8c7c3d15e7f Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Thu, 9 Jul 2015 09:22:18 +0200
Subject: [PATCH 1131/1356] More fixes

---
 easybuild/tools/docs.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index e9824cee4c..ba406ffb29 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -182,6 +182,8 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
     classname = eb_class.__name__
 
     lines = [
+        '.. ' + classname + ':',
+        '',
         '``' + classname + '``',
         '=' * (len(classname)+4),
         '',
@@ -189,7 +191,7 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
 
     bases = []
     for b in eb_class.__bases__:
-        base = b.__name__ + '_' if b in all_blocks else b.__name__
+        base = ':ref:`' + b.__name__ +'`' if b in all_blocks else b.__name__
         bases.append(base)
 
     derived = '(derives from ' + ', '.join(bases) + ')'
@@ -237,19 +239,21 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
             custom.append('* ``' + func + '`` - ' + f.__doc__.strip() + inh)
 
     if custom:
-        title = 'Customised steps'
+        title = 'Customised steps in ``' + classname + '`` easyblock'
         lines.extend([title, '-' * len(title)] + custom)
         lines.append('')
 
     # Add example if available
-    if classname + '.eb' in os.listdir(os.path.join(path_to_examples)):
-        lines.extend(['', 'Example', '-' * 8, '', '::', ''])
+    if os.path.exists(os.path.join(path_to_examples, '%s.eb' % classname)):
+        title = 'Example for ``' + classname + '`` easyblock'
+        lines.extend(['', title, '-' * len(title), '', '::', ''])
         for line in read_file(os.path.join(path_to_examples, classname+'.eb')).split('\n'):
             lines.append('    ' + line.strip())
         lines.append('') # empty line after literal block
 
     return '\n'.join(lines)
 
+
 def mk_rst_table(titles, values):
     """
     Returns an rst table with given titles and values (a nested list of string values for each column)
@@ -281,4 +285,3 @@ def mk_rst_table(titles, values):
     table.extend([table_line, ''])
 
     return table
-

From 5062e0a43ed4f37f1bc197e778d7c1a8cc5ae1b1 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Thu, 9 Jul 2015 11:32:17 +0200
Subject: [PATCH 1132/1356] Small rst_table unit test

---
 doc_examples/Binary.eb                     | 21 +++++++
 doc_examples/Bundle.eb                     | 17 ++++++
 doc_examples/CMakeMake.eb                  | 30 ++++++++++
 doc_examples/ConfigureMake.eb              | 20 +++++++
 doc_examples/ConfigureMakePythonPackage.eb | 33 +++++++++++
 easybuild/tools/docs.py                    |  1 -
 test/framework/docs.py                     | 65 ++++++++++++++++++++++
 test/framework/suite.py                    |  3 +-
 8 files changed, 188 insertions(+), 2 deletions(-)
 create mode 100644 doc_examples/Binary.eb
 create mode 100644 doc_examples/Bundle.eb
 create mode 100644 doc_examples/CMakeMake.eb
 create mode 100644 doc_examples/ConfigureMake.eb
 create mode 100644 doc_examples/ConfigureMakePythonPackage.eb
 create mode 100644 test/framework/docs.py

diff --git a/doc_examples/Binary.eb b/doc_examples/Binary.eb
new file mode 100644
index 0000000000..2fa31617c3
--- /dev/null
+++ b/doc_examples/Binary.eb
@@ -0,0 +1,21 @@
+easyblock = 'Binary'
+
+name = 'Platanus'
+version = '1.2.1'
+versionsuffix = '-linux-x86_64'
+
+homepage = 'http://platanus.bio.titech.ac.jp/'
+description = """PLATform for Assembling NUcleotide Sequences"""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201']
+sources = ['platanus']
+checksums = ['02cf92847ec704d010a54df293b9c60a']
+
+sanity_check_paths = {
+    'files': ['platanus'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/doc_examples/Bundle.eb b/doc_examples/Bundle.eb
new file mode 100644
index 0000000000..067ccdbe63
--- /dev/null
+++ b/doc_examples/Bundle.eb
@@ -0,0 +1,17 @@
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20150119' # date of the most recent change
+
+homepage = 'http://autotools.io'
+description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
+
+toolchain = {'name': 'GCC', 'version': '4.9.2'}
+
+dependencies = [
+    ('Autoconf', '2.69'), # 20120424
+    ('Automake', '1.15'), # 20150105
+    ('libtool', '2.4.5'), # 20150119
+]
+
+moduleclass = 'devel'
diff --git a/doc_examples/CMakeMake.eb b/doc_examples/CMakeMake.eb
new file mode 100644
index 0000000000..1e8a2bf6f6
--- /dev/null
+++ b/doc_examples/CMakeMake.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'ANTs'
+version = '2.1.0rc3'
+
+homepage = 'http://stnava.github.io/ANTs/'
+description = """ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing,
+ interpreting and visualizing multidimensional data."""
+
+toolchain = {'name': 'goolf', 'version': '1.5.14'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/stnava/ANTs/archive/']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [('CMake', '3.0.2')]
+
+skipsteps = ['install']
+buildopts = ' && mkdir -p %(installdir)s && cp -r * %(installdir)s/'
+
+parallel = 1
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['bin/ANTS'],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'data'
diff --git a/doc_examples/ConfigureMake.eb b/doc_examples/ConfigureMake.eb
new file mode 100644
index 0000000000..9a0d4bf65e
--- /dev/null
+++ b/doc_examples/ConfigureMake.eb
@@ -0,0 +1,20 @@
+easyblock = 'ConfigureMake'
+
+name = 'zsync'
+version = '0.6.2'
+
+homepage = 'http://zsync.moria.org.uk/'
+description = """zsync-0.6.2: Optimising file distribution program, a 1-to-many rsync"""
+
+sources = [SOURCE_TAR_BZ2]
+source_urls = ['http://zsync.moria.org.uk/download/']
+
+
+toolchain = {'name': 'ictce', 'version': '5.3.0'}
+
+sanity_check_paths = {
+                      'files': ['bin/zsync'],
+                      'dirs': []
+                     }
+
+moduleclass = 'tools'
diff --git a/doc_examples/ConfigureMakePythonPackage.eb b/doc_examples/ConfigureMakePythonPackage.eb
new file mode 100644
index 0000000000..0f9fd09a84
--- /dev/null
+++ b/doc_examples/ConfigureMakePythonPackage.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMakePythonPackage'
+
+name = 'PyQt'
+version = '4.11.3'
+
+homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt'
+description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework."""
+
+toolchain = {'name': 'goolf', 'version': '1.5.14'}
+
+sources = ['%(name)s-x11-gpl-%(version)s.tar.gz']
+source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s']
+
+python = 'Python'
+pyver = '2.7.9'
+pythonshortver = '.'.join(pyver.split('.')[:2])
+versionsuffix = '-%s-%s' % (python, pyver)
+
+dependencies = [
+    (python, pyver),
+    ('SIP', '4.16.4', versionsuffix),
+    ('Qt', '4.8.6'),
+]
+
+configopts = "configure-ng.py --confirm-license"
+configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver
+configopts += " --no-sip-files"
+
+options = {'modulename': 'PyQt4'}
+
+modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver}
+
+moduleclass = 'vis'
diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index ba406ffb29..dd94257a94 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -183,7 +183,6 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
 
     lines = [
         '.. ' + classname + ':',
-        '',
         '``' + classname + '``',
         '=' * (len(classname)+4),
         '',
diff --git a/test/framework/docs.py b/test/framework/docs.py
new file mode 100644
index 0000000000..36f0d997f0
--- /dev/null
+++ b/test/framework/docs.py
@@ -0,0 +1,65 @@
+# #
+# Copyright 2012-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+Unit tests for docs.py.
+"""
+
+from test.framework.utilities import EnhancedTestCase, init_config
+from unittest import TestLoader, main
+from easybuild.tools.docs import mk_rst_table
+
+class DocsTest(EnhancedTestCase):
+
+    def test_rst_table(self):
+        """ Test mk_rst_table function """
+        entries_1 = [['one', 'two', 'three']]
+        t1 = 'This title is long'
+        titles_1 = [t1]
+
+        # small table
+        table_1 = '\n'.join(mk_rst_table(titles_1, entries_1))
+        check_1 = '\n'.join([
+            '=' * len(t1),
+            t1,
+            '=' * len(t1),
+            'one' + ' ' * (len(t1) - 3),
+            'two' + ' ' * (len(t1) -3),
+            'three' + ' ' * (len(t1) - 5),
+            '=' * len(t1),
+            '',
+        ])
+
+        self.assertEqual(table_1, check_1)
+
+
+def suite():
+    """ returns all test cases in this module """
+    return TestLoader().loadTestsFromTestCase(DocsTest)
+
+if __name__ == '__main__':
+    # also check the setUp for debug
+    # logToScreen(enable=True)
+    # setLogLevelDebug()
+    main()
diff --git a/test/framework/suite.py b/test/framework/suite.py
index 2b6001221f..447aa9ca9f 100644
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -62,6 +62,7 @@
 import test.framework.easyconfigformat as ef
 import test.framework.ebconfigobj as ebco
 import test.framework.easyconfigversion as ev
+import test.framework.docs as d
 import test.framework.filetools as f
 import test.framework.format_convert as f_c
 import test.framework.general as gen
@@ -100,7 +101,7 @@
 
 # call suite() for each module and then run them all
 # note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
-tests = [gen, bl, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p]
+tests = [gen, bl, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw, p, d]
 
 SUITE = unittest.TestSuite([x.suite() for x in tests])
 

From 00496ba9a7d367bcc573363ea2435d88fc854d7e Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Thu, 9 Jul 2015 14:41:20 +0200
Subject: [PATCH 1133/1356] Fixed some remarks + extended tests

---
 easybuild/framework/easyconfig/easyconfig.py | 15 +++++++------
 test/framework/easyconfig.py                 | 22 ++++++++++++++++----
 2 files changed, 27 insertions(+), 10 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 47b511ac3d..f8f19c70c4 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -51,6 +51,7 @@
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
 from easybuild.tools.module_naming_scheme.utilities import det_hidden_modname, is_valid_module_name
 from easybuild.tools.modules import get_software_root_env_var_name, get_software_version_env_var_name
+from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.systemtools import check_os_dependency
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
 from easybuild.tools.toolchain.utilities import get_toolchain
@@ -500,8 +501,10 @@ def dump(self, fp):
 
         self.generate_template_values()
         templ_const = dict([(const[1], const[0]) for const in TEMPLATE_CONSTANTS])
-        # reverse map of templates longer than 2 characters, to inject template values where possible
-        templ_val = sorted(dict([(val, key) for key, val in self.template_values.items() if len(val) > 2]), key=len(val), reverse=True)
+        # reverse map of templates longer than 2 characters, to inject template values where possible, sorted on length
+        templ_val = OrderedDict([(self.template_values[k], k)
+                        for k in sorted(self.template_values, key=lambda k:len(self.template_values[k]), reverse=True)
+                        if len(self.template_values[k]) > 2])
         # values will not be templated for these keys
         exclude_keys = ['name', 'version', 'description', 'homepage', 'toolchain']
 
@@ -940,7 +943,7 @@ def replace_templates(value, templ_const, templ_val):
     Given a value, try to substitute template strings where possible.
         - value can be a string, list, tuple, dict or combination thereof
         - templ_const is a dictionary of template strings (constants)
-        - templ_val is a dictionary of template strings specific for this easyconfig file
+        - templ_val is an ordered dictionary of template strings specific for this easyconfig file
     """
     if isinstance(value, basestring):
         old_value = None
@@ -949,9 +952,9 @@ def replace_templates(value, templ_const, templ_val):
             if value in templ_const:
                 value = templ_const[value]
             else:
-                # check for template values - longest strings first
-                for v in sorted(templ_val, key=lambda v: len(v), reverse=True):
-                    value = re.sub(r"\b" + re.escape(v) + r"\b", r'%(' + templ_val[v] + ')s', value)
+                # check for template values
+                for k, v in templ_val.items():
+                    value = re.sub(r"\b" + re.escape(k) + r"\b", r'%(' + v + ')s', value)
 
     else:
         if isinstance(value, list):
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 1b814e55f5..cd3dfdef23 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1153,8 +1153,7 @@ def test_quote_str(self):
         # non-string values
         n = 42
         self.assertEqual(quote_str(n), 42)
-        l = ["foo", "bar"]
-        self.assertEqual(quote_str(l), ["foo", "bar"])
+        self.assertEqual(quote_str(["foo", "bar"]), ["foo", "bar"])
         self.assertEqual(quote_str(('foo', 'bar')), ('foo', 'bar'))
 
 
@@ -1218,17 +1217,32 @@ def test_dump_template(self):
             "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
             "sources = ['foo-0.0.1.tar.gz']",
+            '',
+            'configopts = "--opt1=0.0.1"',
+            '',
+            "sanity_check_paths = {'files': ['files/foo/bar'], 'dirs':[] }",
         ])
 
         handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')
         os.close(handle)
 
         ec = EasyConfig(None, rawtxt=rawtxt)
+        ec.enable_templating = True
         ec.dump(testec)
         ectxt = read_file(testec)
 
-        regex = re.compile(r"sources \= \['SOURCELOWER_TAR_GZ'\]", re.M)
-        self.assertTrue(regex.search(ectxt), "Pattern '%s' found in: %s" % (regex.pattern, ectxt))
+        self.assertTrue(ec.enable_templating)
+
+        patterns = [
+            r"sources = \['SOURCELOWER_TAR_GZ'\]",
+            r'description = "foo description"',  # no templating for description
+            r"sanity_check_paths = {'files': \['files/%\(namelower\)s/bar'\]",
+            r'configopts = "--opt1=%\(version\)s"',
+        ]
+
+        for pattern in patterns:
+            regex = re.compile(pattern, re.M)
+            self.assertTrue(regex.search(ectxt), "Pattern '%s' found in: %s" % (regex.pattern, ectxt))
 
 
 def suite():

From 8b2c532f079dc0660fb29dd902f0a8ab61c2a1fb Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Thu, 9 Jul 2015 15:03:38 +0200
Subject: [PATCH 1134/1356] exclude_values is constant value

---
 easybuild/framework/easyconfig/easyconfig.py | 7 ++++---
 test/framework/easyconfig.py                 | 6 ++++--
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index f8f19c70c4..f0b105e0b7 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -75,6 +75,9 @@
 # set of configure/build/install options that can be provided as lists for an iterated build
 ITERATE_OPTIONS = ['preconfigopts', 'configopts', 'prebuildopts', 'buildopts', 'preinstallopts', 'installopts']
 
+# values for these keys will not be templated in dump()
+EXCLUDED_KEYS_REPLACE_TEMPLATES = ['name', 'version', 'description', 'homepage', 'toolchain']
+
 _easyconfig_files_cache = {}
 _easyconfigs_cache = {}
 
@@ -505,8 +508,6 @@ def dump(self, fp):
         templ_val = OrderedDict([(self.template_values[k], k)
                         for k in sorted(self.template_values, key=lambda k:len(self.template_values[k]), reverse=True)
                         if len(self.template_values[k]) > 2])
-        # values will not be templated for these keys
-        exclude_keys = ['name', 'version', 'description', 'homepage', 'toolchain']
 
         def include_defined_parameters(keyset):
             """
@@ -517,7 +518,7 @@ def include_defined_parameters(keyset):
                 for key in group:
                     val = self[key]
                     if val != default_values[key]:
-                        if key not in exclude_keys:
+                        if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
                             self.log.debug("Original value before replacing matching template values: %s", val)
                             val = replace_templates(val, templ_const, templ_val)
                             self.log.debug("New value after replacing matching template values: %s", val)
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index cd3dfdef23..7ffe603137 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1218,7 +1218,8 @@ def test_dump_template(self):
             '',
             "sources = ['foo-0.0.1.tar.gz']",
             '',
-            'configopts = "--opt1=0.0.1"',
+            'preconfigopts = "--opt1=%s" % name',
+            'configopts = "--opt2=0.0.1"',
             '',
             "sanity_check_paths = {'files': ['files/foo/bar'], 'dirs':[] }",
         ])
@@ -1237,7 +1238,8 @@ def test_dump_template(self):
             r"sources = \['SOURCELOWER_TAR_GZ'\]",
             r'description = "foo description"',  # no templating for description
             r"sanity_check_paths = {'files': \['files/%\(namelower\)s/bar'\]",
-            r'configopts = "--opt1=%\(version\)s"',
+            r'preconfigopts = "--opt1=%\(name\)s"',
+            r'configopts = "--opt2=%\(version\)s"',
         ]
 
         for pattern in patterns:

From bf4936988c8d590d0d4c5206a08fad8bece26a9b Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Thu, 9 Jul 2015 15:21:22 +0200
Subject: [PATCH 1135/1356] remove example files

---
 doc_examples/Binary.eb                     | 21 --------------
 doc_examples/Bundle.eb                     | 17 -----------
 doc_examples/CMakeMake.eb                  | 30 --------------------
 doc_examples/ConfigureMake.eb              | 20 -------------
 doc_examples/ConfigureMakePythonPackage.eb | 33 ----------------------
 5 files changed, 121 deletions(-)
 delete mode 100644 doc_examples/Binary.eb
 delete mode 100644 doc_examples/Bundle.eb
 delete mode 100644 doc_examples/CMakeMake.eb
 delete mode 100644 doc_examples/ConfigureMake.eb
 delete mode 100644 doc_examples/ConfigureMakePythonPackage.eb

diff --git a/doc_examples/Binary.eb b/doc_examples/Binary.eb
deleted file mode 100644
index 2fa31617c3..0000000000
--- a/doc_examples/Binary.eb
+++ /dev/null
@@ -1,21 +0,0 @@
-easyblock = 'Binary'
-
-name = 'Platanus'
-version = '1.2.1'
-versionsuffix = '-linux-x86_64'
-
-homepage = 'http://platanus.bio.titech.ac.jp/'
-description = """PLATform for Assembling NUcleotide Sequences"""
-
-toolchain = {'name': 'dummy', 'version': 'dummy'}
-
-source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201']
-sources = ['platanus']
-checksums = ['02cf92847ec704d010a54df293b9c60a']
-
-sanity_check_paths = {
-    'files': ['platanus'],
-    'dirs': [],
-}
-
-moduleclass = 'bio'
diff --git a/doc_examples/Bundle.eb b/doc_examples/Bundle.eb
deleted file mode 100644
index 067ccdbe63..0000000000
--- a/doc_examples/Bundle.eb
+++ /dev/null
@@ -1,17 +0,0 @@
-easyblock = 'Bundle'
-
-name = 'Autotools'
-version = '20150119' # date of the most recent change
-
-homepage = 'http://autotools.io'
-description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
-
-toolchain = {'name': 'GCC', 'version': '4.9.2'}
-
-dependencies = [
-    ('Autoconf', '2.69'), # 20120424
-    ('Automake', '1.15'), # 20150105
-    ('libtool', '2.4.5'), # 20150119
-]
-
-moduleclass = 'devel'
diff --git a/doc_examples/CMakeMake.eb b/doc_examples/CMakeMake.eb
deleted file mode 100644
index 1e8a2bf6f6..0000000000
--- a/doc_examples/CMakeMake.eb
+++ /dev/null
@@ -1,30 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'ANTs'
-version = '2.1.0rc3'
-
-homepage = 'http://stnava.github.io/ANTs/'
-description = """ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing,
- interpreting and visualizing multidimensional data."""
-
-toolchain = {'name': 'goolf', 'version': '1.5.14'}
-toolchainopts = {'pic': True}
-
-source_urls = ['https://github.com/stnava/ANTs/archive/']
-sources = ['v%(version)s.tar.gz']
-
-builddependencies = [('CMake', '3.0.2')]
-
-skipsteps = ['install']
-buildopts = ' && mkdir -p %(installdir)s && cp -r * %(installdir)s/'
-
-parallel = 1
-
-separate_build_dir = True
-
-sanity_check_paths = {
-    'files': ['bin/ANTS'],
-    'dirs': ['lib'],
-}
-
-moduleclass = 'data'
diff --git a/doc_examples/ConfigureMake.eb b/doc_examples/ConfigureMake.eb
deleted file mode 100644
index 9a0d4bf65e..0000000000
--- a/doc_examples/ConfigureMake.eb
+++ /dev/null
@@ -1,20 +0,0 @@
-easyblock = 'ConfigureMake'
-
-name = 'zsync'
-version = '0.6.2'
-
-homepage = 'http://zsync.moria.org.uk/'
-description = """zsync-0.6.2: Optimising file distribution program, a 1-to-many rsync"""
-
-sources = [SOURCE_TAR_BZ2]
-source_urls = ['http://zsync.moria.org.uk/download/']
-
-
-toolchain = {'name': 'ictce', 'version': '5.3.0'}
-
-sanity_check_paths = {
-                      'files': ['bin/zsync'],
-                      'dirs': []
-                     }
-
-moduleclass = 'tools'
diff --git a/doc_examples/ConfigureMakePythonPackage.eb b/doc_examples/ConfigureMakePythonPackage.eb
deleted file mode 100644
index 0f9fd09a84..0000000000
--- a/doc_examples/ConfigureMakePythonPackage.eb
+++ /dev/null
@@ -1,33 +0,0 @@
-easyblock = 'ConfigureMakePythonPackage'
-
-name = 'PyQt'
-version = '4.11.3'
-
-homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt'
-description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework."""
-
-toolchain = {'name': 'goolf', 'version': '1.5.14'}
-
-sources = ['%(name)s-x11-gpl-%(version)s.tar.gz']
-source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s']
-
-python = 'Python'
-pyver = '2.7.9'
-pythonshortver = '.'.join(pyver.split('.')[:2])
-versionsuffix = '-%s-%s' % (python, pyver)
-
-dependencies = [
-    (python, pyver),
-    ('SIP', '4.16.4', versionsuffix),
-    ('Qt', '4.8.6'),
-]
-
-configopts = "configure-ng.py --confirm-license"
-configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver
-configopts += " --no-sip-files"
-
-options = {'modulename': 'PyQt4'}
-
-modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver}
-
-moduleclass = 'vis'

From 3ccbb5a3c7d804cf446a1c849d513f5c113eb202 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 07:54:04 +0200
Subject: [PATCH 1136/1356] style cleanup in package_step

---
 easybuild/framework/easyblock.py     | 46 ++++++++++++++--------------
 easybuild/tools/options.py           |  4 +--
 easybuild/tools/package/utilities.py | 12 +++++---
 3 files changed, 32 insertions(+), 30 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 9cfad19244..4a32e812e0 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -68,10 +68,10 @@
 from easybuild.tools.run import run_cmd
 from easybuild.tools.jenkins import write_to_xml
 from easybuild.tools.module_generator import ModuleGeneratorLua, ModuleGeneratorTcl, module_generator
-from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
+from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.modules import ROOT_ENV_VAR_NAME_PREFIX, VERSION_ENV_VAR_NAME_PREFIX, DEVEL_ENV_VAR_NAME_PREFIX
 from easybuild.tools.modules import get_software_root, modules_tool
-from easybuild.tools.package.utilities import package_fpm
+from easybuild.tools.package.utilities import PKG_TOOL_FPM, package_fpm
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.systemtools import det_parallelism, use_group
@@ -1491,35 +1491,35 @@ def extensions_step(self, fetch=False):
         self.clean_up_fake_module(fake_mod_data)
 
     def package_step(self):
-        """Prepare package software (e.g. into an RPM) with fpm."""
+        """Package installed software (e.g., into an RPM), if requested, using selected package tool."""
 
-        path_to_module_file = os.path.join(install_path('mod'), build_option('suffix_modules_path'), self.full_mod_name)
-        packagedir_dest = os.path.abspath(package_path())
+        if build_option('package'):
 
-        packaging_tool = build_option('package_tool')
-        opt_force = build_option('force')
+            path_to_module_file = self.module_generator.filename
+            pkgdir_dest = os.path.abspath(package_path())
 
-        if not build_option('package'):
-            _log.info("Skipping package step (not enabled)")
+            pkgtool = build_option('package_tool')
+            opt_force = build_option('force')
 
-        elif packaging_tool == "fpm":
-            packaging_type = build_option('package_type') if build_option('package_type') else "rpm"
+            if pkgtool == PKG_TOOL_FPM:
+                pkgtype = build_option('package_type')
+                self.log.info("Generating %s package using %s in %s", pkgtype, pkgtool, pkgdir_dest)
+                pkgdir_src = package_fpm(self, path_to_module_file, pkgtype)
 
-            packagedir_src = package_fpm(self, path_to_module_file, package_type=packaging_type)
+                mkdir(pkgdir_dest)
 
-            if not os.path.exists(packagedir_dest):
-                mkdir(packagedir_dest)
+                for src_file in glob.glob(os.path.join(pkgdir_src, "*.%s" % pkgtype)):
+                    dest_file = os.path.join(pkgdir_dest, os.path.basename(src_file))
+                    if os.path.exists(dest_file) and not opt_force:
+                        raise EasyBuildError("Unable to copy package %s to %s (already exists).", src_file, dest_file)
+                    else:
+                        self.log.info("Copied package %s to %s", src_file, pkgdir_dest)
+                        shutil.copy(src_file, pkgdir_dest)
+            else:
+                raise EasyBuildError("Unknown packaging tool specified: %s", pkgtool)
 
-            for src_file in glob.glob(os.path.join(packagedir_src, "*.%s" % packaging_type)):
-                src_filename = os.path.basename(src_file)
-                dest_file = os.path.join(packagedir_dest, src_filename)
-                if os.path.exists(dest_file) and not opt_force:
-                    raise EasyBuildError("Unable to copy package: %s as it already exists in %s. Your package should still be in %s", src_filename, dest_file, packagedir_src)
-                else:
-                    shutil.copy(src_file, packagedir_dest)
         else:
-            raise EasyBuildError("Unknown packaging tool specified: %s", packaging_tool)
-
+            self.log.info("Skipping package step (not enabled)")
 
     def post_install_step(self):
         """
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 80de25f11a..10a96595dd 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -369,8 +369,8 @@ def package_options(self):
         opts = OrderedDict({
             'package': ("Enabling packaging", None, 'store_true', False),
             'package-tool': ("Packaging tool to use", None, 'store_or_None', None),
-            'package-type': ("Packaging type to output to", None, 'store_or_None', None),
-            'package-release': ("Package release iteration number", None, 'store', "1"),
+            'package-type': ("Type of package to generate", None, 'store_or_None', 'rpm'),
+            'package-release': ("Package release iteration number", None, 'store', '1'),
         })
 
         self.log.debug("package_options: descr %s opts %s" % (descr, opts))
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index 14e215e2ca..11d73a07f6 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -50,6 +50,8 @@
 
 
 DEFAULT_PNS = 'EasyBuildPNS'
+PKG_TOOL_FPM = 'fpm'
+
 
 _log = fancylogger.getLogger('tools.package')
 
@@ -63,7 +65,7 @@ def avail_package_naming_schemes():
     return class_dict
 
 
-def package_fpm(easyblock, modfile_path, package_type='rpm'):
+def package_fpm(easyblock, modfile_path, pkgtype):
     """
     This function will build a package using fpm and return the directory where the packages are
     """
@@ -98,11 +100,11 @@ def package_fpm(easyblock, modfile_path, package_type='rpm'):
         depstring += " --depends '%s'" % dep_pkgname
 
     cmdlist = [
-        'fpm',
+        PKG_TOOL_FPM,
         '--workdir', workdir,
         '--name', pkgname,
         '--provides', pkgname,
-        '-t', package_type,  # target
+        '-t', pkgtype,  # target
         '-s', 'dir',  # source
         '--version', pkgver,
         '--iteration', pkgrel,
@@ -114,7 +116,7 @@ def package_fpm(easyblock, modfile_path, package_type='rpm'):
     _log.debug("The flattened cmdlist looks like: %s", cmd)
     run_cmd(cmd, log_all=True, simple=True)
 
-    _log.info("Created %s package in %s", package_type, workdir)
+    _log.info("Created %s package in %s", pkgtype, workdir)
 
     return workdir
 
@@ -123,7 +125,7 @@ def check_pkg_support():
     """Check whether packaging is supported, i.e. whether the required dependencies are available."""
 
     _log.experimental("Support for packaging installed software.")
-    fpm_path = which('fpm')
+    fpm_path = which(PKG_TOOL_FPM)
     rpmbuild_path = which('rpmbuild')
     if fpm_path and rpmbuild_path:
         _log.info("fpm found at: %s", fpm_path)

From 71e8f8d5d546a890526d591a1d2ecf53e040e92e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 08:08:07 +0200
Subject: [PATCH 1137/1356] add unit test for ActivePNS

---
 easybuild/tools/config.py |  8 ++++++--
 test/framework/package.py | 17 +++++++++++++++--
 2 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 8280413cdc..85ae8def48 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -103,8 +103,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'only_blocks',
         'optarch',
         'package_tool',
-        'package_type',
-        'package_release',
         'regtest_output_dir',
         'skip',
         'stop',
@@ -135,6 +133,12 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
     DEFAULT_STRICT: [
         'strict',
     ],
+    '1': [
+        'package_release',
+    ],
+    'rpm': [
+        'package_type',
+    ],
 }
 # build option that do not have a perfectly matching command line option
 BUILD_OPTIONS_OTHER = {
diff --git a/test/framework/package.py b/test/framework/package.py
index 8b28dc0eef..9a95efc4ae 100644
--- a/test/framework/package.py
+++ b/test/framework/package.py
@@ -30,14 +30,15 @@
 import os
 import stat
 
-from test.framework.utilities import EnhancedTestCase
+from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader
 from unittest import main as unittestmain
 
 import easybuild.tools.build_log
+from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import adjust_permissions, write_file
-from easybuild.tools.package.utilities import avail_package_naming_schemes, check_pkg_support
+from easybuild.tools.package.utilities import ActivePNS, avail_package_naming_schemes, check_pkg_support
 
 
 class PackageTest(EnhancedTestCase):
@@ -69,6 +70,18 @@ def test_check_pkg_support(self):
         # restore
         easybuild.tools.build_log.EXPERIMENTAL = orig_experimental
 
+    def test_active_pns(self):
+        """Test use of ActivePNS."""
+        test_easyconfigs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        ec = EasyConfig(os.path.join(test_easyconfigs, 'OpenMPI-1.6.4-GCC-4.6.4.eb'), validate=False)
+
+        pns = ActivePNS()
+
+        # default: EasyBuild package naming scheme, pkg release 1
+        self.assertEqual(pns.name(ec), 'eb2.2.0dev-OpenMPI-1.6.4-GCC-4.6.4')
+        self.assertEqual(pns.version(ec), '1.6.4')
+        self.assertEqual(pns.release(ec), '1')
+
 
 def suite():
     """ returns all the testcases in this module """

From a187736d6ecd9039cf666054f21b88c2fd9f370e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 08:25:31 +0200
Subject: [PATCH 1138/1356] enhance check_pkg_support function

---
 easybuild/tools/config.py            |  7 ++++++-
 easybuild/tools/options.py           | 11 ++++++-----
 easybuild/tools/package/utilities.py | 24 ++++++++++++++++++------
 test/framework/package.py            |  3 ++-
 4 files changed, 32 insertions(+), 13 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 85ae8def48..1dd1e16b5f 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -102,7 +102,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'modules_footer',
         'only_blocks',
         'optarch',
-        'package_tool',
         'regtest_output_dir',
         'skip',
         'stop',
@@ -136,6 +135,9 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
     '1': [
         'package_release',
     ],
+    'fpm': [
+        'package_tool',
+    ],
     'rpm': [
         'package_type',
     ],
@@ -380,18 +382,21 @@ def get_repositorypath():
     """
     return ConfigurationVariables()['repositorypath']
 
+
 def get_package_naming_scheme():
     """
     Return the package naming scheme
     """
     return ConfigurationVariables()['package_naming_scheme']
 
+
 def package_path():
     """
     Return the path where built packages are copied to
     """
     return ConfigurationVariables()['packagepath']
 
+
 def get_modules_tool():
     """
     Return modules tool (EnvironmentModulesC, Lmod, ...)
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 10a96595dd..f0cacb58c4 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -66,7 +66,8 @@
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
 from easybuild.tools.modules import Lmod
 from easybuild.tools.ordereddict import OrderedDict
-from easybuild.tools.package.utilities import DEFAULT_PNS, avail_package_naming_schemes, check_pkg_support
+from easybuild.tools.package.utilities import DEFAULT_PNS, PKG_TOOL_FPM, PKG_TYPE_RPM
+from easybuild.tools.package.utilities import avail_package_naming_schemes, check_pkg_support
 from easybuild.tools.toolchain.utilities import search_toolchain
 from easybuild.tools.repository.repository import avail_repositories
 from easybuild.tools.version import this_is_easybuild
@@ -368,8 +369,8 @@ def package_options(self):
 
         opts = OrderedDict({
             'package': ("Enabling packaging", None, 'store_true', False),
-            'package-tool': ("Packaging tool to use", None, 'store_or_None', None),
-            'package-type': ("Type of package to generate", None, 'store_or_None', 'rpm'),
+            'package-tool': ("Packaging tool to use", None, 'store_or_None', PKG_TOOL_FPM),
+            'package-type': ("Type of package to generate", None, 'store_or_None', PKG_TYPE_RPM),
             'package-release': ("Package release iteration number", None, 'store', '1'),
         })
 
@@ -503,10 +504,10 @@ def postprocess(self):
         self._postprocess_config()
 
         # check whether packaging is supported when it's being used
-        if any([self.options.package_tool, self.options.package_type]):
+        if self.options.package:
             check_pkg_support()
         else:
-            self.log.debug("Didn't find any packaging options")
+            self.log.debug("Packaging not enabled, so not check for packaging support.")
 
     def _postprocess_external_modules_metadata(self):
         """Parse file(s) specifying metadata for external modules."""
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index 11d73a07f6..f800abf389 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -40,7 +40,7 @@
 from vsc.utils.missing import get_subclasses
 from vsc.utils.patterns import Singleton
 
-from easybuild.tools.config import get_package_naming_scheme
+from easybuild.tools.config import build_option, get_package_naming_scheme
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import which
 from easybuild.tools.package.packaging_naming_scheme.pns import PackagingNamingScheme
@@ -51,6 +51,7 @@
 
 DEFAULT_PNS = 'EasyBuildPNS'
 PKG_TOOL_FPM = 'fpm'
+PKG_TYPE_RPM = 'rpm'
 
 
 _log = fancylogger.getLogger('tools.package')
@@ -124,13 +125,24 @@ def package_fpm(easyblock, modfile_path, pkgtype):
 def check_pkg_support():
     """Check whether packaging is supported, i.e. whether the required dependencies are available."""
 
+    # packaging support is considered experimental for now (requires using --experimental)
     _log.experimental("Support for packaging installed software.")
-    fpm_path = which(PKG_TOOL_FPM)
-    rpmbuild_path = which('rpmbuild')
-    if fpm_path and rpmbuild_path:
-        _log.info("fpm found at: %s", fpm_path)
+
+    pkgtool = build_option('package_tool')
+    pkgtool_path = which(pkgtool)
+    if pkgtool_path:
+        _log.info("Selected packaging tool '%s' found at %s", pkgtool, pkgtool_path)
+
+        # rpmbuild is required for generating RPMs with FPM
+        if pkgtool == PKG_TOOL_FPM and build_option('package_type') == PKG_TYPE_RPM:
+            rpmbuild_path = which('rpmbuild')
+            if rpmbuild_path:
+                _log.info("Required tool 'rpmbuild' found at %s", rpmbuild_path)
+            else:
+                raise EasyBuildError("rpmbuild is required when generating RPM packages with FPM, but was not found")
+
     else:
-        raise EasyBuildError("Need both fpm and rpmbuild. Found fpm: %s rpmbuild: %s", fpm_path, rpmbuild_path)
+        raise EasyBuildError("Selected packaging tool '%s' not found", pkgtool)
 
 
 class ActivePNS(object):
diff --git a/test/framework/package.py b/test/framework/package.py
index 9a95efc4ae..d51412ca58 100644
--- a/test/framework/package.py
+++ b/test/framework/package.py
@@ -57,7 +57,7 @@ def test_check_pkg_support(self):
         # clear $PATH to make sure fpm/rpmbuild can not be found
         os.environ['PATH'] = ''
 
-        self.assertErrorRegex(EasyBuildError, "Need both fpm and rpmbuild", check_pkg_support)
+        self.assertErrorRegex(EasyBuildError, "Selected packaging tool 'fpm' not found", check_pkg_support)
 
         for binary in ['fpm', 'rpmbuild']:
             binpath = os.path.join(self.test_prefix, binary)
@@ -65,6 +65,7 @@ def test_check_pkg_support(self):
             adjust_permissions(binpath, stat.S_IXUSR, add=True)
         os.environ['PATH'] = self.test_prefix
 
+        # no errors => support check passes
         check_pkg_support()
 
         # restore

From 37ad376bc51984afe744217c1df3fc7c6d5d1903 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 08:30:24 +0200
Subject: [PATCH 1139/1356] fix __init__.py's in tools/package, rename to
 PackageNamingScheme (was PackagingNamingScheme)

---
 easybuild/tools/package/__init__.py           | 38 +++++++++++++++++--
 .../package/package_naming_scheme/__init__.py | 37 ++++++++++++++++++
 .../easybuild_pns.py                          |  4 +-
 .../pns.py                                    |  2 +-
 .../packaging_naming_scheme/__init__.py       |  0
 easybuild/tools/package/utilities.py          |  6 +--
 6 files changed, 77 insertions(+), 10 deletions(-)
 create mode 100644 easybuild/tools/package/package_naming_scheme/__init__.py
 rename easybuild/tools/package/{packaging_naming_scheme => package_naming_scheme}/easybuild_pns.py (94%)
 rename easybuild/tools/package/{packaging_naming_scheme => package_naming_scheme}/pns.py (98%)
 delete mode 100644 easybuild/tools/package/packaging_naming_scheme/__init__.py

diff --git a/easybuild/tools/package/__init__.py b/easybuild/tools/package/__init__.py
index de858db457..51a62d3f44 100644
--- a/easybuild/tools/package/__init__.py
+++ b/easybuild/tools/package/__init__.py
@@ -1,8 +1,38 @@
+##
+# Copyright 2009-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
 """
-The packaging module, will contain code for packaging and naming-schemes that can be
-overriden to cover site customizations
+This declares the namespace for the tools.package submodule of EasyBuild,
+which contains support for packaging and package naming schemes that can be overriden to cover site customizations.
 
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
 """
+from pkgutil import extend_path
 
-
-
+# we're not the only ones in this namespace
+__path__ = extend_path(__path__, __name__)  #@ReservedAssignment
diff --git a/easybuild/tools/package/package_naming_scheme/__init__.py b/easybuild/tools/package/package_naming_scheme/__init__.py
new file mode 100644
index 0000000000..6af2449881
--- /dev/null
+++ b/easybuild/tools/package/package_naming_scheme/__init__.py
@@ -0,0 +1,37 @@
+##
+# Copyright 2009-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+This declares the namespace for the tools.package.package_naming_scheme submodule of EasyBuild.
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+"""
+from pkgutil import extend_path
+
+# we're not the only ones in this namespace
+__path__ = extend_path(__path__, __name__)  #@ReservedAssignment
diff --git a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
similarity index 94%
rename from easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
rename to easybuild/tools/package/package_naming_scheme/easybuild_pns.py
index bc95cace8a..2ed2ff2013 100644
--- a/easybuild/tools/package/packaging_naming_scheme/easybuild_pns.py
+++ b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
@@ -29,10 +29,10 @@
 @author: Kenneth Hoste (Ghent University)
 """
 
-from easybuild.tools.package.packaging_naming_scheme.pns import PackagingNamingScheme
+from easybuild.tools.package.package_naming_scheme.pns import PackageNamingScheme
 
 
-class EasyBuildPNS(PackagingNamingScheme):
+class EasyBuildPNS(PackageNamingScheme):
     """Class implmenting the default EasyBuild packaging naming scheme."""
 
     REQUIRED_KEYS = ['name', 'version', 'versionsuffix', 'toolchain']
diff --git a/easybuild/tools/package/packaging_naming_scheme/pns.py b/easybuild/tools/package/package_naming_scheme/pns.py
similarity index 98%
rename from easybuild/tools/package/packaging_naming_scheme/pns.py
rename to easybuild/tools/package/package_naming_scheme/pns.py
index b1569d0f66..e8733c20b6 100644
--- a/easybuild/tools/package/packaging_naming_scheme/pns.py
+++ b/easybuild/tools/package/package_naming_scheme/pns.py
@@ -34,7 +34,7 @@
 from easybuild.tools.version import VERSION as EASYBUILD_VERSION
 
 
-class PackagingNamingScheme(object):
+class PackageNamingScheme(object):
     """Abstract class for package naming schemes"""
 
     def __init__(self):
diff --git a/easybuild/tools/package/packaging_naming_scheme/__init__.py b/easybuild/tools/package/packaging_naming_scheme/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index f800abf389..2b282e30d9 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -43,7 +43,7 @@
 from easybuild.tools.config import build_option, get_package_naming_scheme
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import which
-from easybuild.tools.package.packaging_naming_scheme.pns import PackagingNamingScheme
+from easybuild.tools.package.package_naming_scheme.pns import PackageNamingScheme
 from easybuild.tools.run import run_cmd
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.utilities import import_available_modules
@@ -61,8 +61,8 @@ def avail_package_naming_schemes():
     """
     Returns the list of valed naming schemes that are in the easybuild.package.package_naming_scheme namespace
     """
-    import_available_modules('easybuild.tools.package.packaging_naming_scheme')
-    class_dict = dict([(x.__name__, x) for x in get_subclasses(PackagingNamingScheme)])
+    import_available_modules('easybuild.tools.package.package_naming_scheme')
+    class_dict = dict([(x.__name__, x) for x in get_subclasses(PackageNamingScheme)])
     return class_dict
 
 

From fc8557ef13906d6e856d9ecd34f9f7a69faf815f Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 10 Jul 2015 09:13:59 +0200
Subject: [PATCH 1140/1356] Update on doc for generic easyblocks

---
 easybuild/tools/docs.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index dd94257a94..a46d3b1ed8 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -151,11 +151,11 @@ def avail_easyconfig_params(easyblock, output_format):
     return avail_easyconfig_params_functions[output_format](title, grouped_params)
 
 
-def gen_easyblocks_overview_rst(path_to_examples, common_params={}, doc_functions=[]):
+def gen_easyblocks_overview_rst(package_name, path_to_examples, common_params={}, doc_functions=[]):
     """
-    Compose overview of all generic easyblocks in rst format
+    Compose overview of all easyblocks in the given package in rst format
     """
-    modules = import_available_modules('easybuild.easyblocks.generic')
+    modules = import_available_modules(package_name)
     docs = []
     all_blocks = []
 
@@ -164,7 +164,7 @@ def gen_easyblocks_overview_rst(path_to_examples, common_params={}, doc_function
         for name,obj in inspect.getmembers(m, inspect.isclass):
             eb_class = getattr(m, name)
             # skip imported classes that are not easyblocks
-            if eb_class.__module__.startswith('easybuild.easyblocks.generic') and eb_class not in all_blocks:
+            if eb_class.__module__.startswith(package_name) and eb_class not in all_blocks:
                 all_blocks.append(eb_class)
 
     for eb_class in all_blocks:
@@ -172,7 +172,7 @@ def gen_easyblocks_overview_rst(path_to_examples, common_params={}, doc_function
 
     title = 'Overview of generic easyblocks'
 
-    heading = ['=' * len(title), title, '=' * len(title), '', '.. contents::', '    :depth: 1', '']
+    heading = ['=' * len(title), title, '=' * len(title), '', '.. contents::', '    :depth: 2', '']
     return heading + sorted(docs)
 
 def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc_functions, all_blocks):
@@ -182,7 +182,8 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
     classname = eb_class.__name__
 
     lines = [
-        '.. ' + classname + ':',
+        '.. _' + classname + ':',
+        '',
         '``' + classname + '``',
         '=' * (len(classname)+4),
         '',

From 58021d4b52100e9e1e636720df9a54ec973d8b32 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 13:41:16 +0200
Subject: [PATCH 1141/1356] clean up package naming scheme modules

---
 .../package_naming_scheme/easybuild_pns.py    | 19 +++++--------------
 .../package/package_naming_scheme/pns.py      | 12 +++++++-----
 2 files changed, 12 insertions(+), 19 deletions(-)

diff --git a/easybuild/tools/package/package_naming_scheme/easybuild_pns.py b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
index 2ed2ff2013..a93a5ef69b 100644
--- a/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
+++ b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
@@ -30,30 +30,21 @@
 """
 
 from easybuild.tools.package.package_naming_scheme.pns import PackageNamingScheme
+from easybuild.tools.version import VERSION as EASYBUILD_VERSION
 
 
 class EasyBuildPNS(PackageNamingScheme):
     """Class implmenting the default EasyBuild packaging naming scheme."""
 
-    REQUIRED_KEYS = ['name', 'version', 'versionsuffix', 'toolchain']
-
     def name(self, ec):
         """Determine package name"""
         self.log.debug("easyconfig dict for name looks like %s " % ec )
-        name_template = "eb%(eb_ver)s-%(name)s-%(version)s-%(toolchain)s"
+        name_template = "eb%(eb_ver)s-%(name)s-%(version)s-%(toolchain_name)s-%(toolchain_version)s"
         pkg_name = name_template % {
-            'toolchain' : self._toolchain(ec),
+            'toolchain_name' : ec['toolchain']['name'],
+            'toolchain_version' : ec['toolchain']['version'],
             'version': '-'.join([x for x in [ec.get('versionprefix', ''), ec['version'], ec['versionsuffix'].lstrip('-')] if x]),
             'name' : ec['name'],
-            'eb_ver': self.eb_ver,
+            'eb_ver': EASYBUILD_VERSION,
         }
         return pkg_name
-
-    def _toolchain(self, ec):
-        """Determine toolchain"""
-        toolchain_template = "%(toolchain_name)s-%(toolchain_version)s"
-        pkg_toolchain = toolchain_template % {
-            'toolchain_name': ec['toolchain']['name'],
-            'toolchain_version': ec['toolchain']['version'],
-        }
-        return pkg_toolchain
diff --git a/easybuild/tools/package/package_naming_scheme/pns.py b/easybuild/tools/package/package_naming_scheme/pns.py
index e8733c20b6..deb81c3909 100644
--- a/easybuild/tools/package/package_naming_scheme/pns.py
+++ b/easybuild/tools/package/package_naming_scheme/pns.py
@@ -24,30 +24,32 @@
 ##
 
 """
-General package naming scheme.
+Abstract implementation of a package naming scheme.
 
 @author: Robert Schmidt (Ottawa Hospital Research Institute)
 @author: Kenneth Hoste (Ghent University)
 """
+from abc import ABCMeta, abstractmethod
 from vsc.utils import fancylogger
+
 from easybuild.tools.config import build_option
-from easybuild.tools.version import VERSION as EASYBUILD_VERSION
 
 
 class PackageNamingScheme(object):
     """Abstract class for package naming schemes"""
+    __metaclass__ = ABCMeta
 
     def __init__(self):
         """initialize logger."""
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
-        self.eb_ver = EASYBUILD_VERSION
 
+    @abstractmethod
     def name(self, ec):
         """Determine package name"""
-        raise NotImplementedError
+        pass
 
     def version(self, ec):
-        """Determine package version"""
+        """Determine package version."""
         return ec['version']
 
     def release(self, ec=None):

From aab0716b5f2cdc471be6ce9beb673065950d22d9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 13:52:20 +0200
Subject: [PATCH 1142/1356] use det_full_ec_version in EasyBuildPNS

---
 .../package/package_naming_scheme/easybuild_pns.py     | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/package/package_naming_scheme/easybuild_pns.py b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
index a93a5ef69b..0f7aa12ba3 100644
--- a/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
+++ b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
@@ -28,7 +28,7 @@
 @author: Robert Schmidt (Ottawa Hospital Research Institute)
 @author: Kenneth Hoste (Ghent University)
 """
-
+from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.package.package_naming_scheme.pns import PackageNamingScheme
 from easybuild.tools.version import VERSION as EASYBUILD_VERSION
 
@@ -38,12 +38,10 @@ class EasyBuildPNS(PackageNamingScheme):
 
     def name(self, ec):
         """Determine package name"""
-        self.log.debug("easyconfig dict for name looks like %s " % ec )
-        name_template = "eb%(eb_ver)s-%(name)s-%(version)s-%(toolchain_name)s-%(toolchain_version)s"
+        self.log.debug("easyconfig dict for name looks like: %s ", ec)
+        name_template = "eb%(eb_ver)s-%(name)s-%(fullversion)s"
         pkg_name = name_template % {
-            'toolchain_name' : ec['toolchain']['name'],
-            'toolchain_version' : ec['toolchain']['version'],
-            'version': '-'.join([x for x in [ec.get('versionprefix', ''), ec['version'], ec['versionsuffix'].lstrip('-')] if x]),
+            'fullversion': det_full_ec_version(ec),
             'name' : ec['name'],
             'eb_ver': EASYBUILD_VERSION,
         }

From 016eac4352a11c7186c375b01e3c966cd69bc94a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 19:01:07 +0200
Subject: [PATCH 1143/1356] tweak EasyBuildPNS, add unit test for package_fpm

---
 easybuild/framework/easyblock.py              |  6 +--
 .../package_naming_scheme/easybuild_pns.py    | 14 +++---
 easybuild/tools/package/utilities.py          |  6 +--
 ...1.3.12.eb => toy-0.0-gompi-1.3.12-test.eb} |  1 +
 test/framework/package.py                     | 43 +++++++++++++++++--
 test/framework/toy_build.py                   |  4 +-
 6 files changed, 54 insertions(+), 20 deletions(-)
 rename test/framework/easyconfigs/{toy-0.0-gompi-1.3.12.eb => toy-0.0-gompi-1.3.12-test.eb} (97%)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 4a32e812e0..63b212c5b1 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1495,16 +1495,14 @@ def package_step(self):
 
         if build_option('package'):
 
-            path_to_module_file = self.module_generator.filename
-            pkgdir_dest = os.path.abspath(package_path())
-
             pkgtool = build_option('package_tool')
+            pkgdir_dest = os.path.abspath(package_path())
             opt_force = build_option('force')
 
             if pkgtool == PKG_TOOL_FPM:
                 pkgtype = build_option('package_type')
                 self.log.info("Generating %s package using %s in %s", pkgtype, pkgtool, pkgdir_dest)
-                pkgdir_src = package_fpm(self, path_to_module_file, pkgtype)
+                pkgdir_src = package_fpm(self, pkgtype)
 
                 mkdir(pkgdir_dest)
 
diff --git a/easybuild/tools/package/package_naming_scheme/easybuild_pns.py b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
index 0f7aa12ba3..d1990de6d9 100644
--- a/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
+++ b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
@@ -38,11 +38,9 @@ class EasyBuildPNS(PackageNamingScheme):
 
     def name(self, ec):
         """Determine package name"""
-        self.log.debug("easyconfig dict for name looks like: %s ", ec)
-        name_template = "eb%(eb_ver)s-%(name)s-%(fullversion)s"
-        pkg_name = name_template % {
-            'fullversion': det_full_ec_version(ec),
-            'name' : ec['name'],
-            'eb_ver': EASYBUILD_VERSION,
-        }
-        return pkg_name
+        self.log.debug("Easyconfig dict passed to name() looks like: %s ", ec)
+        return '%s-%s' % (ec['name'], det_full_ec_version(ec))
+
+    def version(self, ec):
+        """Determine package version: EasyBuild version used to build & install."""
+        return 'eb-%s' % EASYBUILD_VERSION
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index 2b282e30d9..007c713723 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -66,11 +66,11 @@ def avail_package_naming_schemes():
     return class_dict
 
 
-def package_fpm(easyblock, modfile_path, pkgtype):
+def package_fpm(easyblock, pkgtype):
     """
     This function will build a package using fpm and return the directory where the packages are
     """
-    workdir = tempfile.mkdtemp(prefix='eb-pkgs')
+    workdir = tempfile.mkdtemp(prefix='eb-pkgs-')
     _log.info("Will be creating packages in %s", workdir)
 
     try:
@@ -111,7 +111,7 @@ def package_fpm(easyblock, modfile_path, pkgtype):
         '--iteration', pkgrel,
         depstring,
         easyblock.installdir,
-        modfile_path,
+        easyblock.module_generator.filename,
     ]
     cmd = ' '.join(cmdlist)
     _log.debug("The flattened cmdlist looks like: %s", cmd)
diff --git a/test/framework/easyconfigs/toy-0.0-gompi-1.3.12.eb b/test/framework/easyconfigs/toy-0.0-gompi-1.3.12-test.eb
similarity index 97%
rename from test/framework/easyconfigs/toy-0.0-gompi-1.3.12.eb
rename to test/framework/easyconfigs/toy-0.0-gompi-1.3.12-test.eb
index 632c832da3..b866a7ee1c 100644
--- a/test/framework/easyconfigs/toy-0.0-gompi-1.3.12.eb
+++ b/test/framework/easyconfigs/toy-0.0-gompi-1.3.12-test.eb
@@ -1,5 +1,6 @@
 name = 'toy'
 version = '0.0'
+versionsuffix = '-test'
 
 homepage = 'http://hpcugent.github.com/easybuild'
 description = "Toy C program."
diff --git a/test/framework/package.py b/test/framework/package.py
index d51412ca58..61bf4272f9 100644
--- a/test/framework/package.py
+++ b/test/framework/package.py
@@ -38,7 +38,20 @@
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import adjust_permissions, write_file
-from easybuild.tools.package.utilities import ActivePNS, avail_package_naming_schemes, check_pkg_support
+from easybuild.tools.package.utilities import ActivePNS, avail_package_naming_schemes, check_pkg_support, package_fpm
+from easybuild.tools.version import VERSION as EASYBUILD_VERSION
+
+
+MOCKED_FPM_RPM = """#!/bin/bash
+# only parse what we need to spit out the expected package file, ignore the rest
+workdir=`echo $@ | sed 's/--workdir \([^ ]*\).*/\\1/g'`
+name=`echo $@ | sed 's/.* --name \([^ ]*\).*/\\1/g'`
+version=`echo $@ | sed 's/.*--version \([^ ]*\).*/\\1/g'`
+iteration=`echo $@ | sed 's/.*--iteration \([^ ]*\).*/\\1/g'`
+target=`echo $@ | sed 's/.*-t \([^ ]*\).*/\\1/g'`
+
+echo "thisisan$target" > ${workdir}/${name}-${version}.${iteration}.${target}
+"""
 
 
 class PackageTest(EnhancedTestCase):
@@ -79,10 +92,34 @@ def test_active_pns(self):
         pns = ActivePNS()
 
         # default: EasyBuild package naming scheme, pkg release 1
-        self.assertEqual(pns.name(ec), 'eb2.2.0dev-OpenMPI-1.6.4-GCC-4.6.4')
-        self.assertEqual(pns.version(ec), '1.6.4')
+        self.assertEqual(pns.name(ec), 'OpenMPI-1.6.4-GCC-4.6.4')
+        self.assertEqual(pns.version(ec), 'eb-%s' % EASYBUILD_VERSION)
         self.assertEqual(pns.release(ec), '1')
 
+    def test_package_fpm(self):
+        """Test package_fpm function."""
+        init_config(build_options={'silent': True})
+
+        test_easyconfigs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        ec = EasyConfig(os.path.join(test_easyconfigs, 'toy-0.0-gompi-1.3.12-test.eb'), validate=False)
+
+        # put mocked 'fpm' command in place, just for testing purposes
+        fpm = os.path.join(self.test_prefix, 'fpm')
+        write_file(fpm, MOCKED_FPM_RPM)
+        adjust_permissions(fpm, stat.S_IXUSR, add=True)
+        os.environ['PATH'] = '%s:%s' % (self.test_prefix, os.environ['PATH'])
+
+        # import needs to be done here, since test easyblocks are only included later
+        from easybuild.easyblocks.toy import EB_toy
+        eb = EB_toy(ec)
+
+        # build & install first
+        eb.run_all_steps(False)
+        pkgdir = package_fpm(eb, 'rpm')
+
+        pkgfile = os.path.join(pkgdir, 'toy-0.0-gompi-1.3.12-test-eb-%s.1.rpm' % EASYBUILD_VERSION)
+        self.assertTrue(os.path.isfile(pkgfile), "Found %s" % pkgfile)
+
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 46797db2d1..25a7c7ad85 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -693,8 +693,8 @@ def test_toy_advanced(self):
         """Test toy build with extensions and non-dummy toolchain."""
         test_dir = os.path.abspath(os.path.dirname(__file__))
         os.environ['MODULEPATH'] = os.path.join(test_dir, 'modules')
-        test_ec = os.path.join(test_dir, 'easyconfigs', 'toy-0.0-gompi-1.3.12.eb')
-        self.test_toy_build(ec_file=test_ec, versionsuffix='-gompi-1.3.12')
+        test_ec = os.path.join(test_dir, 'easyconfigs', 'toy-0.0-gompi-1.3.12-test.eb')
+        self.test_toy_build(ec_file=test_ec, versionsuffix='-gompi-1.3.12-test')
 
     def test_toy_hidden(self):
         """Test installing a hidden module."""

From 8ed418f3d19d7661ae2904b15e7207e74e09df18 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 19:11:22 +0200
Subject: [PATCH 1144/1356] add package() function, move some of the logic down

---
 easybuild/framework/easyblock.py     | 28 ++++++++++++----------------
 easybuild/tools/package/utilities.py | 20 +++++++++++++++++---
 test/framework/package.py            | 14 ++++++++------
 3 files changed, 37 insertions(+), 25 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 63b212c5b1..bd5f4cdc0b 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -71,7 +71,7 @@
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.modules import ROOT_ENV_VAR_NAME_PREFIX, VERSION_ENV_VAR_NAME_PREFIX, DEVEL_ENV_VAR_NAME_PREFIX
 from easybuild.tools.modules import get_software_root, modules_tool
-from easybuild.tools.package.utilities import PKG_TOOL_FPM, package_fpm
+from easybuild.tools.package.utilities import PKG_TOOL_FPM, package
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.systemtools import det_parallelism, use_group
@@ -1495,26 +1495,22 @@ def package_step(self):
 
         if build_option('package'):
 
-            pkgtool = build_option('package_tool')
+            pkgtype = build_option('package_type')
             pkgdir_dest = os.path.abspath(package_path())
             opt_force = build_option('force')
 
-            if pkgtool == PKG_TOOL_FPM:
-                pkgtype = build_option('package_type')
-                self.log.info("Generating %s package using %s in %s", pkgtype, pkgtool, pkgdir_dest)
-                pkgdir_src = package_fpm(self, pkgtype)
+            self.log.info("Generating %s package in %s", pkgtype, pkgdir_dest)
+            pkgdir_src = package(self)
 
-                mkdir(pkgdir_dest)
+            mkdir(pkgdir_dest)
 
-                for src_file in glob.glob(os.path.join(pkgdir_src, "*.%s" % pkgtype)):
-                    dest_file = os.path.join(pkgdir_dest, os.path.basename(src_file))
-                    if os.path.exists(dest_file) and not opt_force:
-                        raise EasyBuildError("Unable to copy package %s to %s (already exists).", src_file, dest_file)
-                    else:
-                        self.log.info("Copied package %s to %s", src_file, pkgdir_dest)
-                        shutil.copy(src_file, pkgdir_dest)
-            else:
-                raise EasyBuildError("Unknown packaging tool specified: %s", pkgtool)
+            for src_file in glob.glob(os.path.join(pkgdir_src, "*.%s" % pkgtype)):
+                dest_file = os.path.join(pkgdir_dest, os.path.basename(src_file))
+                if os.path.exists(dest_file) and not opt_force:
+                    raise EasyBuildError("Unable to copy package %s to %s (already exists).", src_file, dest_file)
+                else:
+                    self.log.info("Copied package %s to %s", src_file, pkgdir_dest)
+                    shutil.copy(src_file, pkgdir_dest)
 
         else:
             self.log.info("Skipping package step (not enabled)")
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index 007c713723..748c4f2d03 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -66,12 +66,26 @@ def avail_package_naming_schemes():
     return class_dict
 
 
-def package_fpm(easyblock, pkgtype):
+def package(easyblock):
+    """
+    Package installed software, according to active packaging configuration settings."""
+    pkgtool = build_option('package_tool')
+
+    if pkgtool == PKG_TOOL_FPM:
+        pkgdir = package_with_fpm(easyblock)
+    else:
+        raise EasyBuildError("Unknown packaging tool specified: %s", pkgtool)
+
+    return pkgdir
+
+
+def package_with_fpm(easyblock):
     """
     This function will build a package using fpm and return the directory where the packages are
     """
     workdir = tempfile.mkdtemp(prefix='eb-pkgs-')
-    _log.info("Will be creating packages in %s", workdir)
+    pkgtype = build_option('package_type')
+    _log.info("Will be creating %s package(s) in %s", pkgtype, workdir)
 
     try:
         os.chdir(workdir)
@@ -117,7 +131,7 @@ def package_fpm(easyblock, pkgtype):
     _log.debug("The flattened cmdlist looks like: %s", cmd)
     run_cmd(cmd, log_all=True, simple=True)
 
-    _log.info("Created %s package in %s", pkgtype, workdir)
+    _log.info("Created %s package(s) in %s", pkgtype, workdir)
 
     return workdir
 
diff --git a/test/framework/package.py b/test/framework/package.py
index 61bf4272f9..e3892ebbce 100644
--- a/test/framework/package.py
+++ b/test/framework/package.py
@@ -38,7 +38,7 @@
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import adjust_permissions, write_file
-from easybuild.tools.package.utilities import ActivePNS, avail_package_naming_schemes, check_pkg_support, package_fpm
+from easybuild.tools.package.utilities import ActivePNS, avail_package_naming_schemes, check_pkg_support, package
 from easybuild.tools.version import VERSION as EASYBUILD_VERSION
 
 
@@ -96,8 +96,8 @@ def test_active_pns(self):
         self.assertEqual(pns.version(ec), 'eb-%s' % EASYBUILD_VERSION)
         self.assertEqual(pns.release(ec), '1')
 
-    def test_package_fpm(self):
-        """Test package_fpm function."""
+    def test_package(self):
+        """Test package function."""
         init_config(build_options={'silent': True})
 
         test_easyconfigs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
@@ -111,11 +111,13 @@ def test_package_fpm(self):
 
         # import needs to be done here, since test easyblocks are only included later
         from easybuild.easyblocks.toy import EB_toy
-        eb = EB_toy(ec)
+        easyblock = EB_toy(ec)
 
         # build & install first
-        eb.run_all_steps(False)
-        pkgdir = package_fpm(eb, 'rpm')
+        easyblock.run_all_steps(False)
+
+        # package using default packaging configuration (FPM to build RPM packages)
+        pkgdir = package(easyblock)
 
         pkgfile = os.path.join(pkgdir, 'toy-0.0-gompi-1.3.12-test-eb-%s.1.rpm' % EASYBUILD_VERSION)
         self.assertTrue(os.path.isfile(pkgfile), "Found %s" % pkgfile)

From 5c5e78b03d0eab8e3d59ec0f3149d23c586c1070 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 20:47:34 +0200
Subject: [PATCH 1145/1356] add unit tests for --package* (+ --skip)

---
 easybuild/main.py                    |  7 ++++++
 easybuild/tools/options.py           | 12 +++-------
 easybuild/tools/package/utilities.py |  7 +++++-
 test/framework/options.py            |  2 ++
 test/framework/package.py            | 23 +++++++++++++-----
 test/framework/toy_build.py          | 35 ++++++++++++++++++++++++++++
 6 files changed, 70 insertions(+), 16 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index c0f90b4b65..a5307a8c97 100755
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -56,6 +56,7 @@
 from easybuild.tools.filetools import cleanup, write_file
 from easybuild.tools.options import process_software_build_specs
 from easybuild.tools.robot import det_robot_path, dry_run, resolve_dependencies, search_easyconfigs
+from easybuild.tools.package.utilities import check_pkg_support
 from easybuild.tools.parallelbuild import submit_jobs
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.testing import create_test_report, overall_test_report, regtest, session_module_list, session_state
@@ -210,6 +211,12 @@ def main(testing_data=(None, None, None)):
     config.init(options, config_options_dict)
     config.init_build_options(build_options=build_options, cmdline_options=options)
 
+    # check whether packaging is supported when it's being used
+    if options.package:
+        check_pkg_support()
+    else:
+        _log.debug("Packaging not enabled, so not check for packaging support.")
+
     # update session state
     eb_config = eb_go.generate_cmd_line(add_default=True)
     modlist = session_module_list(testing=testing)  # build options must be initialized first before 'module list' works
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index f0cacb58c4..7dbfd59dd2 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -67,7 +67,7 @@
 from easybuild.tools.modules import Lmod
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.package.utilities import DEFAULT_PNS, PKG_TOOL_FPM, PKG_TYPE_RPM
-from easybuild.tools.package.utilities import avail_package_naming_schemes, check_pkg_support
+from easybuild.tools.package.utilities import avail_package_naming_schemes
 from easybuild.tools.toolchain.utilities import search_toolchain
 from easybuild.tools.repository.repository import avail_repositories
 from easybuild.tools.version import this_is_easybuild
@@ -369,8 +369,8 @@ def package_options(self):
 
         opts = OrderedDict({
             'package': ("Enabling packaging", None, 'store_true', False),
-            'package-tool': ("Packaging tool to use", None, 'store_or_None', PKG_TOOL_FPM),
-            'package-type': ("Type of package to generate", None, 'store_or_None', PKG_TYPE_RPM),
+            'package-tool': ("Packaging tool to use", None, 'store', PKG_TOOL_FPM),
+            'package-type': ("Type of package to generate", None, 'store', PKG_TYPE_RPM),
             'package-release': ("Package release iteration number", None, 'store', '1'),
         })
 
@@ -503,12 +503,6 @@ def postprocess(self):
 
         self._postprocess_config()
 
-        # check whether packaging is supported when it's being used
-        if self.options.package:
-            check_pkg_support()
-        else:
-            self.log.debug("Packaging not enabled, so not check for packaging support.")
-
     def _postprocess_external_modules_metadata(self):
         """Parse file(s) specifying metadata for external modules."""
         # leave external_modules_metadata untouched if no files are provided
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index 748c4f2d03..3e70c1c776 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -88,6 +88,7 @@ def package_with_fpm(easyblock):
     _log.info("Will be creating %s package(s) in %s", pkgtype, workdir)
 
     try:
+        origdir = os.getcwd()
         os.chdir(workdir)
     except OSError, err:
         raise EasyBuildError("Failed to chdir into workdir %s: %s", workdir, err)
@@ -133,12 +134,16 @@ def package_with_fpm(easyblock):
 
     _log.info("Created %s package(s) in %s", pkgtype, workdir)
 
+    try:
+        os.chdir(origdir)
+    except OSError, err:
+        raise EasyBuildError("Failed to chdir back to %s: %s", origdir, err)
+
     return workdir
 
 
 def check_pkg_support():
     """Check whether packaging is supported, i.e. whether the required dependencies are available."""
-
     # packaging support is considered experimental for now (requires using --experimental)
     _log.experimental("Support for packaging installed software.")
 
diff --git a/test/framework/options.py b/test/framework/options.py
index 20bf8ca55a..0f6f7ce693 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1815,6 +1815,8 @@ def test_include_toolchains(self):
         logtxt = read_file(self.logfile)
         self.assertTrue(tc_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (tc_regex.pattern, logtxt))
 
+    def test_package(self):
+        """Test use of --package."""
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/package.py b/test/framework/package.py
index e3892ebbce..53feaf504f 100644
--- a/test/framework/package.py
+++ b/test/framework/package.py
@@ -42,7 +42,7 @@
 from easybuild.tools.version import VERSION as EASYBUILD_VERSION
 
 
-MOCKED_FPM_RPM = """#!/bin/bash
+MOCKED_FPM = """#!/bin/bash
 # only parse what we need to spit out the expected package file, ignore the rest
 workdir=`echo $@ | sed 's/--workdir \([^ ]*\).*/\\1/g'`
 name=`echo $@ | sed 's/.* --name \([^ ]*\).*/\\1/g'`
@@ -54,6 +54,21 @@
 """
 
 
+def mock_fpm(tmpdir):
+    """Put mocked version of fpm command in place in specified tmpdir."""
+    # put mocked 'fpm' command in place, just for testing purposes
+    fpm = os.path.join(tmpdir, 'fpm')
+    write_file(fpm, MOCKED_FPM)
+    adjust_permissions(fpm, stat.S_IXUSR, add=True)
+
+    # also put mocked rpmbuild in place
+    rpmbuild = os.path.join(tmpdir, 'rpmbuild')
+    write_file(rpmbuild, '#!/bin/bash')  # only needs to be there, doesn't need to actually do something...
+    adjust_permissions(rpmbuild, stat.S_IXUSR, add=True)
+
+    os.environ['PATH'] = '%s:%s' % (tmpdir, os.environ['PATH'])
+
+
 class PackageTest(EnhancedTestCase):
     """Tests for packaging support."""
 
@@ -103,11 +118,7 @@ def test_package(self):
         test_easyconfigs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         ec = EasyConfig(os.path.join(test_easyconfigs, 'toy-0.0-gompi-1.3.12-test.eb'), validate=False)
 
-        # put mocked 'fpm' command in place, just for testing purposes
-        fpm = os.path.join(self.test_prefix, 'fpm')
-        write_file(fpm, MOCKED_FPM_RPM)
-        adjust_permissions(fpm, stat.S_IXUSR, add=True)
-        os.environ['PATH'] = '%s:%s' % (self.test_prefix, os.environ['PATH'])
+        mock_fpm(self.test_prefix)
 
         # import needs to be done here, since test easyblocks are only included later
         from easybuild.easyblocks.toy import EB_toy
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 25a7c7ad85..0f7414e593 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -36,6 +36,7 @@
 import sys
 import tempfile
 from test.framework.utilities import EnhancedTestCase
+from test.framework.package import mock_fpm
 from unittest import TestLoader
 from unittest import main as unittestmain
 from vsc.utils.fancylogger import setLogLevelDebug, logToScreen
@@ -46,6 +47,7 @@
 from easybuild.tools.config import get_module_syntax
 from easybuild.tools.filetools import mkdir, read_file, which, write_file
 from easybuild.tools.modules import modules_tool
+from easybuild.tools.version import VERSION as EASYBUILD_VERSION
 
 
 class ToyBuildTest(EnhancedTestCase):
@@ -970,6 +972,39 @@ def test_module_only(self):
             modtxt = read_file(toy_mod + '.lua')
             self.assertTrue(re.search('load.*ictce/4.1.13', modtxt), "load statement for ictce/4.1.13 found in module")
 
+    def test_package(self):
+        """Test use of --package and accompanying package configuration settings."""
+        mock_fpm(self.test_prefix)
+        pkgpath = os.path.join(self.test_prefix, 'pkgs')
+
+        extra_args = [
+            '--experimental',
+            '--package',
+            '--package-release=321',
+            '--package-tool=fpm',
+            '--package-type=foo',
+            '--packagepath=%s' % pkgpath,
+        ]
+
+        self.test_toy_build(extra_args=extra_args)
+
+        toypkg = os.path.join(pkgpath, 'toy-0.0-eb-%s.321.foo' % EASYBUILD_VERSION)
+        self.assertTrue(os.path.exists(toypkg), "%s is there" % toypkg)
+
+    def test_package_skip(self):
+        """Test use of --package with --skip."""
+        mock_fpm(self.test_prefix)
+        pkgpath = os.path.join(self.test_prefix, 'packages')  # default path
+
+        self.test_toy_build(['--packagepath=%s' % pkgpath])
+        self.assertFalse(os.path.exists(pkgpath), "%s is not created without use of --package" % pkgpath)
+
+        self.test_toy_build(extra_args=['--experimental', '--package', '--skip'], verify=False)
+
+        toypkg = os.path.join(pkgpath, 'toy-0.0-eb-%s.1.rpm' % EASYBUILD_VERSION)
+        self.assertTrue(os.path.exists(toypkg), "%s is there" % toypkg)
+
+
 def suite():
     """ return all the tests in this file """
     return TestLoader().loadTestsFromTestCase(ToyBuildTest)

From 1d54b440921dc525cafb9b11fdbf9059da0f8f98 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 23:55:44 +0200
Subject: [PATCH 1146/1356] move changing of permissions into a separate
 'finalize' step, add unit test for --read-only-install and
 --group-writable-installdir

---
 easybuild/framework/easyblock.py | 70 +++++++++++++++++++-------------
 easybuild/main.py                | 12 +++++-
 test/framework/toy_build.py      | 27 +++++++++++-
 3 files changed, 78 insertions(+), 31 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index cd82d9d28f..31ba2040c8 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -83,6 +83,7 @@
 CONFIGURE_STEP = 'configure'
 EXTENSIONS_STEP = 'extensions'
 FETCH_STEP = 'fetch'
+FINALIZE_STEP = 'finalize'
 MODULE_STEP = 'module'
 PACKAGE_STEP = 'package'
 PATCH_STEP = 'patch'
@@ -1497,8 +1498,6 @@ def post_install_step(self):
         """
         Do some postprocessing
         - run post install commands if any were specified
-        - set file permissions ....
-        Installing user must be member of the group that it is changed to
         """
         if self.cfg['postinstallcmds'] is not None:
             # make sure we have a list of commands
@@ -1509,32 +1508,6 @@ def post_install_step(self):
                     raise EasyBuildError("Invalid element in 'postinstallcmds', not a string: %s", cmd)
                 run_cmd(cmd, simple=True, log_ok=True, log_all=True)
 
-        if self.group is not None:
-            # remove permissions for others, and set group ID
-            try:
-                perms = stat.S_IROTH | stat.S_IWOTH | stat.S_IXOTH
-                adjust_permissions(self.installdir, perms, add=False, recursive=True, group_id=self.group[1],
-                                   relative=True, ignore_errors=True)
-            except EasyBuildError, err:
-                raise EasyBuildError("Unable to change group permissions of file(s): %s", err)
-            self.log.info("Successfully made software only available for group %s (gid %s)" % self.group)
-
-        if build_option('read_only_installdir'):
-            # remove write permissions for everyone
-            perms = stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH
-            adjust_permissions(self.installdir, perms, add=False, recursive=True, relative=True, ignore_errors=True)
-            self.log.info("Successfully removed write permissions recursively for *EVERYONE* on install dir.")
-        elif build_option('group_writable_installdir'):
-            # enable write permissions for group
-            perms = stat.S_IWGRP
-            adjust_permissions(self.installdir, perms, add=True, recursive=True, relative=True, ignore_errors=True)
-            self.log.info("Successfully enabled write permissions recursively for group on install dir.")
-        else:
-            # remove write permissions for group and other
-            perms = stat.S_IWGRP | stat.S_IWOTH
-            adjust_permissions(self.installdir, perms, add=False, recursive=True, relative=True, ignore_errors=True)
-            self.log.info("Successfully removed write permissions recursively for group/other on install dir.")
-
     def sanity_check_step(self, custom_paths=None, custom_commands=None, extension=False):
         """
         Do a sanity check on the installation
@@ -1720,6 +1693,39 @@ def make_module_step(self, fake=False):
 
         return modpath
 
+    def finalize_step(self):
+        """
+        Finalize installation procedure: adjust permissions as configured, change group ownership (if requested).
+        Installing user must be member of the group that it is changed to.
+        """
+        if self.group is not None:
+            # remove permissions for others, and set group ID
+            try:
+                perms = stat.S_IROTH | stat.S_IWOTH | stat.S_IXOTH
+                adjust_permissions(self.installdir, perms, add=False, recursive=True, group_id=self.group[1],
+                                   relative=True, ignore_errors=True)
+            except EasyBuildError, err:
+                raise EasyBuildError("Unable to change group permissions of file(s): %s", err)
+            self.log.info("Successfully made software only available for group %s (gid %s)" % self.group)
+
+        if build_option('read_only_installdir'):
+            # remove write permissions for everyone
+            perms = stat.S_IWUSR | stat.S_IWGRP | stat.S_IWOTH
+            adjust_permissions(self.installdir, perms, add=False, recursive=True, relative=True, ignore_errors=True)
+            self.log.info("Successfully removed write permissions recursively for *EVERYONE* on install dir.")
+
+        elif build_option('group_writable_installdir'):
+            # enable write permissions for group
+            perms = stat.S_IWGRP
+            adjust_permissions(self.installdir, perms, add=True, recursive=True, relative=True, ignore_errors=True)
+            self.log.info("Successfully enabled write permissions recursively for group on install dir.")
+
+        else:
+            # remove write permissions for group and other
+            perms = stat.S_IWGRP | stat.S_IWOTH
+            adjust_permissions(self.installdir, perms, add=False, recursive=True, relative=True, ignore_errors=True)
+            self.log.info("Successfully removed write permissions recursively for group/other on install dir.")
+
     def test_cases_step(self):
         """
         Run provided test cases.
@@ -1873,6 +1879,7 @@ def prepare_step_spec(initial):
             (SANITYCHECK_STEP, 'sanity checking', [lambda x: x.sanity_check_step()], False),
             (CLEANUP_STEP, 'cleaning up', [lambda x: x.cleanup_step()], False),
             (MODULE_STEP, 'creating module', [lambda x: x.make_module_step()], False),
+            (FINALIZE_STEP, 'finalizing', [lambda x: x.finalize_step()], False),
         ]
 
         # full list of steps, included iterated steps
@@ -1986,6 +1993,9 @@ def build_and_install_one(ecdict, init_env):
                 new_log_dir = os.path.dirname(app.logfile)
         else:
             new_log_dir = os.path.join(app.installdir, config.log_path())
+            if build_option('read_only_installdir'):
+                # temporarily re-enable write permissions for copying log/easyconfig to install dir
+                adjust_permissions(new_log_dir, stat.S_IWUSR, add=True, recursive=False)
 
             # collect build stats
             _log.info("Collecting build stats...")
@@ -2027,6 +2037,10 @@ def build_and_install_one(ecdict, init_env):
         except (IOError, OSError), err:
             print_error("Failed to copy easyconfig %s to %s: %s" % (spec, newspec, err))
 
+        if build_option('read_only_installdir'):
+            # take away user write permissions (again)
+            adjust_permissions(new_log_dir, stat.S_IWUSR, add=False, recursive=False)
+
     # build failed
     else:
         success = False
diff --git a/easybuild/main.py b/easybuild/main.py
index 0c42cd6a2e..7d1a5b627b 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -37,6 +37,7 @@
 """
 import copy
 import os
+import stat
 import sys
 import traceback
 
@@ -52,7 +53,7 @@
 from easybuild.framework.easyconfig.tools import get_paths_for, parse_easyconfigs, skip_available
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak
 from easybuild.tools.config import get_repository, get_repositorypath, set_tmpdir
-from easybuild.tools.filetools import cleanup, write_file
+from easybuild.tools.filetools import adjust_permissions, cleanup, write_file
 from easybuild.tools.options import process_software_build_specs
 from easybuild.tools.robot import det_robot_path, dry_run, resolve_dependencies, search_easyconfigs
 from easybuild.tools.parallelbuild import submit_jobs
@@ -128,7 +129,14 @@ def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
         test_report_txt = create_test_report(test_msg, [(ec, ec_res)], init_session_state)
         if 'log_file' in ec_res:
             test_report_fp = "%s_test_report.md" % '.'.join(ec_res['log_file'].split('.')[:-1])
-            write_file(test_report_fp, test_report_txt)
+            parent_dir = os.path.dirname(test_report_fp)
+            # parent dir for test report may not be writeable at this time, e.g. when --read-only-installdir is used
+            if os.stat(parent_dir).st_mode & 0200:
+                write_file(test_report_fp, test_report_txt)
+            else:
+                adjust_permissions(parent_dir, stat.S_IWUSR, add=True, recursive=False)
+                write_file(test_report_fp, test_report_txt)
+                adjust_permissions(parent_dir, stat.S_IWUSR, add=False, recursive=False)
 
         if not ec_res['success'] and exit_on_failure:
             if 'traceback' in ec_res:
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 46797db2d1..31c454e0a0 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -44,7 +44,7 @@
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import get_module_syntax
-from easybuild.tools.filetools import mkdir, read_file, which, write_file
+from easybuild.tools.filetools import adjust_permissions, mkdir, read_file, which, write_file
 from easybuild.tools.modules import modules_tool
 
 
@@ -480,6 +480,31 @@ def test_toy_permissions(self):
         # restore original umask
         os.umask(orig_umask)
 
+    def test_toy_permissions_installdir(self):
+        """Test --read-only-installdir and --group-write-installdir."""
+        # set umask hard to verify default reliably
+        orig_umask = os.umask(0022)
+
+        self.test_toy_build()
+        installdir_perms = os.stat(os.path.join(self.test_installpath, 'software', 'toy', '0.0')).st_mode & 0777
+        self.assertEqual(installdir_perms, 0755, "%s has default permissions" % self.test_installpath)
+        shutil.rmtree(self.test_installpath)
+
+        self.test_toy_build(extra_args=['--read-only-installdir'])
+        installdir_perms = os.stat(os.path.join(self.test_installpath, 'software', 'toy', '0.0')).st_mode & 0777
+        self.assertEqual(installdir_perms, 0555, "%s has read-only permissions" % self.test_installpath)
+        installdir_perms = os.stat(os.path.join(self.test_installpath, 'software', 'toy')).st_mode & 0777
+        self.assertEqual(installdir_perms, 0755, "%s has default permissions" % self.test_installpath)
+        adjust_permissions(os.path.join(self.test_installpath, 'software', 'toy', '0.0'), stat.S_IWUSR, add=True)
+        shutil.rmtree(self.test_installpath)
+
+        self.test_toy_build(extra_args=['--group-writable-installdir'])
+        installdir_perms = os.stat(os.path.join(self.test_installpath, 'software', 'toy', '0.0')).st_mode & 0777
+        self.assertEqual(installdir_perms, 0775, "%s has group write permissions" % self.test_installpath)
+
+        # restore original umask
+        os.umask(orig_umask)
+
     def test_toy_gid_sticky_bits(self):
         """Test setting gid and sticky bits."""
         subdirs = [

From ef6b3bd4048265549f76276fbc43471a262a71af Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 10 Jul 2015 23:59:49 +0200
Subject: [PATCH 1147/1356] fix typo

---
 easybuild/main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index 7d1a5b627b..4b542b4b1b 100644
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -130,7 +130,7 @@ def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
         if 'log_file' in ec_res:
             test_report_fp = "%s_test_report.md" % '.'.join(ec_res['log_file'].split('.')[:-1])
             parent_dir = os.path.dirname(test_report_fp)
-            # parent dir for test report may not be writeable at this time, e.g. when --read-only-installdir is used
+            # parent dir for test report may not be writable at this time, e.g. when --read-only-installdir is used
             if os.stat(parent_dir).st_mode & 0200:
                 write_file(test_report_fp, test_report_txt)
             else:

From a7ce2c18d7a4dbebaf6135478b83cae0bb271edf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 11 Jul 2015 00:15:17 +0200
Subject: [PATCH 1148/1356] dev -> ~dev

---
 .../tools/package/package_naming_scheme/easybuild_pns.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/package/package_naming_scheme/easybuild_pns.py b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
index d1990de6d9..d6698b551e 100644
--- a/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
+++ b/easybuild/tools/package/package_naming_scheme/easybuild_pns.py
@@ -43,4 +43,11 @@ def name(self, ec):
 
     def version(self, ec):
         """Determine package version: EasyBuild version used to build & install."""
-        return 'eb-%s' % EASYBUILD_VERSION
+        ebver = str(EASYBUILD_VERSION)
+        if ebver.endswith('dev'):
+            # try and make sure that 'dev' EasyBuild version is not considered newer just because it's longer
+            # (e.g., 2.2.0 vs 2.2.0dev)
+            # cfr. http://rpm.org/ticket/56,
+            # https://debian-handbook.info/browse/stable/sect.manipulating-packages-with-dpkg.html (see box in 5.4.3)
+            ebver.replace('dev', '~dev')
+        return 'eb-%s' % ebver

From 79955a914ca98a12e15465ae813faea3828a2f43 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 11 Jul 2015 00:23:55 +0200
Subject: [PATCH 1149/1356] drop empty test

---
 test/framework/options.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 0f6f7ce693..20bf8ca55a 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1815,8 +1815,6 @@ def test_include_toolchains(self):
         logtxt = read_file(self.logfile)
         self.assertTrue(tc_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (tc_regex.pattern, logtxt))
 
-    def test_package(self):
-        """Test use of --package."""
 
 def suite():
     """ returns all the testcases in this module """

From 7ee1bad2f7deb29260587fbd1bf209c34b74a300 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 11 Jul 2015 00:37:30 +0200
Subject: [PATCH 1150/1356] rename to permissions_step

---
 easybuild/framework/easyblock.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 31ba2040c8..ef13e0e83b 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -83,10 +83,10 @@
 CONFIGURE_STEP = 'configure'
 EXTENSIONS_STEP = 'extensions'
 FETCH_STEP = 'fetch'
-FINALIZE_STEP = 'finalize'
 MODULE_STEP = 'module'
 PACKAGE_STEP = 'package'
 PATCH_STEP = 'patch'
+PERMISSIONS_STEP = 'permissions'
 POSTPROC_STEP = 'postproc'
 PREPARE_STEP = 'prepare'
 READY_STEP = 'ready'
@@ -1693,7 +1693,7 @@ def make_module_step(self, fake=False):
 
         return modpath
 
-    def finalize_step(self):
+    def permissions_step(self):
         """
         Finalize installation procedure: adjust permissions as configured, change group ownership (if requested).
         Installing user must be member of the group that it is changed to.
@@ -1879,7 +1879,7 @@ def prepare_step_spec(initial):
             (SANITYCHECK_STEP, 'sanity checking', [lambda x: x.sanity_check_step()], False),
             (CLEANUP_STEP, 'cleaning up', [lambda x: x.cleanup_step()], False),
             (MODULE_STEP, 'creating module', [lambda x: x.make_module_step()], False),
-            (FINALIZE_STEP, 'finalizing', [lambda x: x.finalize_step()], False),
+            (PERMISSIONS_STEP, 'permissions', [lambda x: x.permissions_step()], False),
         ]
 
         # full list of steps, included iterated steps

From e622c2c0f30198136fe5a7b251306871b330ecd7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 11 Jul 2015 01:20:39 +0200
Subject: [PATCH 1151/1356] include tools.package packages in setup.py

---
 setup.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index edf1ff7655..cb9af5cc78 100644
--- a/setup.py
+++ b/setup.py
@@ -73,8 +73,9 @@ def find_rel_test():
     "easybuild", "easybuild.framework", "easybuild.framework.easyconfig", "easybuild.framework.easyconfig.format",
     "easybuild.toolchains", "easybuild.toolchains.compiler", "easybuild.toolchains.mpi",
     "easybuild.toolchains.fft", "easybuild.toolchains.linalg", "easybuild.tools", "easybuild.tools.deprecated",
-    "easybuild.tools.job", "easybuild.tools.toolchain", "easybuild.tools.module_naming_scheme", "easybuild.tools.repository",
-    "test.framework", "test",
+    "easybuild.tools.job", "easybuild.tools.toolchain", "easybuild.tools.module_naming_scheme",
+    "easybuild.tools.package", "easybuild.tools.package.package_naming_scheme",
+    "easybuild.tools.repository", "test.framework", "test",
 ]
 
 setup(

From 9cf1d2ee9b6637b96aa9e1b80ef1c4d9c2691a73 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 11 Jul 2015 10:41:54 +0200
Subject: [PATCH 1152/1356] final style tweaks to packaging support

---
 easybuild/framework/easyblock.py                   |  2 +-
 easybuild/main.py                                  |  2 +-
 easybuild/tools/config.py                          | 14 +++++++++++---
 easybuild/tools/options.py                         | 10 +++++-----
 .../tools/package/package_naming_scheme/pns.py     |  3 ++-
 easybuild/tools/package/utilities.py               |  9 ++-------
 6 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index bd5f4cdc0b..8a7d06535c 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -71,7 +71,7 @@
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
 from easybuild.tools.modules import ROOT_ENV_VAR_NAME_PREFIX, VERSION_ENV_VAR_NAME_PREFIX, DEVEL_ENV_VAR_NAME_PREFIX
 from easybuild.tools.modules import get_software_root, modules_tool
-from easybuild.tools.package.utilities import PKG_TOOL_FPM, package
+from easybuild.tools.package.utilities import package
 from easybuild.tools.repository.repository import init_repository
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
 from easybuild.tools.systemtools import det_parallelism, use_group
diff --git a/easybuild/main.py b/easybuild/main.py
index a5307a8c97..67aefd0f4c 100755
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -215,7 +215,7 @@ def main(testing_data=(None, None, None)):
     if options.package:
         check_pkg_support()
     else:
-        _log.debug("Packaging not enabled, so not check for packaging support.")
+        _log.debug("Packaging not enabled, so not checking for packaging support.")
 
     # update session state
     eb_config = eb_go.generate_cmd_line(add_default=True)
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 1dd1e16b5f..63986efe59 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -52,6 +52,10 @@
 _log = fancylogger.getLogger('config', fname=False)
 
 
+PKG_TOOL_FPM = 'fpm'
+PKG_TYPE_RPM = 'rpm'
+
+
 DEFAULT_JOB_BACKEND = 'PbsPython'
 DEFAULT_LOGFILE_FORMAT = ("easybuild", "easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log")
 DEFAULT_MNS = 'EasyBuildMNS'
@@ -66,6 +70,10 @@
     'subdir_modules': 'modules',
     'subdir_software': 'software',
 }
+DEFAULT_PKG_RELEASE = '1'
+DEFAULT_PKG_TOOL = PKG_TOOL_FPM
+DEFAULT_PKG_TYPE = PKG_TYPE_RPM
+DEFAULT_PNS = 'EasyBuildPNS'
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
 DEFAULT_STRICT = run.WARN
@@ -132,13 +140,13 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
     DEFAULT_STRICT: [
         'strict',
     ],
-    '1': [
+    DEFAULT_PKG_RELEASE: [
         'package_release',
     ],
-    'fpm': [
+    DEFAULT_PKG_TOOL: [
         'package_tool',
     ],
-    'rpm': [
+    DEFAULT_PKG_TYPE: [
         'package_type',
     ],
 }
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 7dbfd59dd2..c585ae103e 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -52,7 +52,8 @@
 from easybuild.tools import build_log, run  # build_log should always stay there, to ensure EasyBuildLog
 from easybuild.tools.build_log import EasyBuildError, raise_easybuilderror
 from easybuild.tools.config import DEFAULT_JOB_BACKEND, DEFAULT_LOGFILE_FORMAT, DEFAULT_MNS, DEFAULT_MODULE_SYNTAX
-from easybuild.tools.config import DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PREFIX
+from easybuild.tools.config import DEFAULT_MODULES_TOOL, DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS
+from easybuild.tools.config import DEFAULT_PKG_RELEASE, DEFAULT_PKG_TOOL, DEFAULT_PKG_TYPE, DEFAULT_PNS, DEFAULT_PREFIX
 from easybuild.tools.config import DEFAULT_REPOSITORY, DEFAULT_STRICT
 from easybuild.tools.config import get_pretend_installpath, mk_full_default_path, set_tmpdir
 from easybuild.tools.configobj import ConfigObj, ConfigObjError
@@ -66,7 +67,6 @@
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes
 from easybuild.tools.modules import Lmod
 from easybuild.tools.ordereddict import OrderedDict
-from easybuild.tools.package.utilities import DEFAULT_PNS, PKG_TOOL_FPM, PKG_TYPE_RPM
 from easybuild.tools.package.utilities import avail_package_naming_schemes
 from easybuild.tools.toolchain.utilities import search_toolchain
 from easybuild.tools.repository.repository import avail_repositories
@@ -369,9 +369,9 @@ def package_options(self):
 
         opts = OrderedDict({
             'package': ("Enabling packaging", None, 'store_true', False),
-            'package-tool': ("Packaging tool to use", None, 'store', PKG_TOOL_FPM),
-            'package-type': ("Type of package to generate", None, 'store', PKG_TYPE_RPM),
-            'package-release': ("Package release iteration number", None, 'store', '1'),
+            'package-tool': ("Packaging tool to use", None, 'store', DEFAULT_PKG_TOOL),
+            'package-type': ("Type of package to generate", None, 'store', DEFAULT_PKG_TYPE),
+            'package-release': ("Package release iteration number", None, 'store', DEFAULT_PKG_RELEASE),
         })
 
         self.log.debug("package_options: descr %s opts %s" % (descr, opts))
diff --git a/easybuild/tools/package/package_naming_scheme/pns.py b/easybuild/tools/package/package_naming_scheme/pns.py
index deb81c3909..d66bce2262 100644
--- a/easybuild/tools/package/package_naming_scheme/pns.py
+++ b/easybuild/tools/package/package_naming_scheme/pns.py
@@ -48,9 +48,10 @@ def name(self, ec):
         """Determine package name"""
         pass
 
+    @abstractmethod
     def version(self, ec):
         """Determine package version."""
-        return ec['version']
+        pass
 
     def release(self, ec=None):
         """Determine package release"""
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index 3e70c1c776..a3d559bcc8 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -26,7 +26,7 @@
 """
 Various utilities related to packaging support.
 
-@author: Marc Litherland
+@author: Marc Litherland (Novartis)
 @author: Gianluca Santarossa (Novartis)
 @author: Robert Schmidt (Ottawa Hospital Research Institute)
 @author: Fotis Georgatos (Uni.Lu, NTUA)
@@ -40,7 +40,7 @@
 from vsc.utils.missing import get_subclasses
 from vsc.utils.patterns import Singleton
 
-from easybuild.tools.config import build_option, get_package_naming_scheme
+from easybuild.tools.config import PKG_TOOL_FPM, PKG_TYPE_RPM, build_option, get_package_naming_scheme
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import which
 from easybuild.tools.package.package_naming_scheme.pns import PackageNamingScheme
@@ -49,11 +49,6 @@
 from easybuild.tools.utilities import import_available_modules
 
 
-DEFAULT_PNS = 'EasyBuildPNS'
-PKG_TOOL_FPM = 'fpm'
-PKG_TYPE_RPM = 'rpm'
-
-
 _log = fancylogger.getLogger('tools.package')
 
 

From 50936ff7fcbaaa0c3afa4b76b9960383b917fdd5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 11 Jul 2015 14:47:06 +0200
Subject: [PATCH 1153/1356] bump version to 2.2.0 and update release notes

---
 RELEASE_NOTES              | 29 +++++++++++++++++++++++++++++
 easybuild/tools/version.py |  2 +-
 2 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 241f8b3d8c..d148a8ffa2 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,6 +3,35 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
+v2.2.0 (July 14th 2015)
+-----------------------
+
+feature + bugfix release
+- add support for using GC3Pie as a backend for --job (#1008)
+    - see also http://easybuild.readthedocs.org/en/latest/Submitting_jobs.html
+- add support for --include-* configuration options to include additional easyblocks, toolchains, etc. (#1301)
+    - see http://easybuild.readthedocs.org/en/latest/Including_additional_Python_modules.html
+- add (experimental) support for packaging installed software using FPM (#1224)
+- various other enhancements, including:
+    - use https for PyPI URL templates (#1286)
+    - add GNU toolchain definition (#1287)
+    - make bootstrap script more robust:
+        - exclude 'easyblocks' pkg from sys.path to avoid that setup.py for easybuild-easyblocks picks up wrong version
+        - undefine $EASYBUILD_BOOTSTRAP* environment variables, since they do not correspond with known config options
+    - improve error reporting/robustness in fix_broken_easyconfigs.py script (#1290)
+    - reset keep toolchain component class 'constants' every time (#1294)
+    - make --strict also a build option (#1295)
+    - fix purging of loaded modules in unit tests' setup method (#1297)
+    - promote MigrateFromEBToHMNS to a 'production' MNS (#1302)
+    - add support for --read-only-installdir and --group-writable-installdir configuration options (#1304)
+    - add support for *not* expanding relative paths in prepend_paths (#1310)
+- various bug fixes, including:
+    - fix issue with cleaning up (no) logfile if --logtostdout/-l is used (#1298)
+    - stop making ModulesTool class a singleton since it causes problems when multilple toolchains are in play (#1299)
+    - don't modify values of 'paths' list passed as argument to prepend_paths (#1300)
+    - fix issue with EasyConfig.dump + cleanup (#1308, #1311)
+    - reenable (and fix) accidentally disabled test (#1316)
+
 v2.1.1 (May 18th 2015)
 ----------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 2efb989a88..042c1f7796 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.2.0dev')
+VERSION = LooseVersion('2.2.0')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From a57c4cd2bad64334cca0e4b38f0d74c64fbebe8e Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 13 Jul 2015 09:42:44 +0200
Subject: [PATCH 1154/1356] Fixed more remarks

---
 easybuild/framework/easyconfig/easyconfig.py | 14 +++++++-------
 test/framework/easyconfig.py                 | 18 +++++++++++++-----
 2 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index f0b105e0b7..a62826e14f 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -76,7 +76,7 @@
 ITERATE_OPTIONS = ['preconfigopts', 'configopts', 'prebuildopts', 'buildopts', 'preinstallopts', 'installopts']
 
 # values for these keys will not be templated in dump()
-EXCLUDED_KEYS_REPLACE_TEMPLATES = ['name', 'version', 'description', 'homepage', 'toolchain']
+EXCLUDED_KEYS_REPLACE_TEMPLATES = ['easyblock', 'name', 'version', 'description', 'homepage', 'toolchain']
 
 _easyconfig_files_cache = {}
 _easyconfigs_cache = {}
@@ -505,9 +505,8 @@ def dump(self, fp):
         self.generate_template_values()
         templ_const = dict([(const[1], const[0]) for const in TEMPLATE_CONSTANTS])
         # reverse map of templates longer than 2 characters, to inject template values where possible, sorted on length
-        templ_val = OrderedDict([(self.template_values[k], k)
-                        for k in sorted(self.template_values, key=lambda k:len(self.template_values[k]), reverse=True)
-                        if len(self.template_values[k]) > 2])
+        keys = sorted(self.template_values, key=lambda k:len(self.template_values[k]), reverse=True)
+        templ_val = OrderedDict([(self.template_values[k], k) for k in keys if len(self.template_values[k]) > 2])
 
         def include_defined_parameters(keyset):
             """
@@ -954,8 +953,9 @@ def replace_templates(value, templ_const, templ_val):
                 value = templ_const[value]
             else:
                 # check for template values
-                for k, v in templ_val.items():
-                    value = re.sub(r"\b" + re.escape(k) + r"\b", r'%(' + v + ')s', value)
+                for temp_val, temp_name in templ_val.items():
+                    # only replace full words with templates, not substrings, by using \b in regex
+                    value = re.sub(r"\b" + re.escape(temp_val) + r"\b", r'%(' + temp_name + ')s', value)
 
     else:
         if isinstance(value, list):
@@ -963,7 +963,7 @@ def replace_templates(value, templ_const, templ_val):
         elif isinstance(value, tuple):
             value = tuple(replace_templates(list(value), templ_const, templ_val))
         elif isinstance(value, dict):
-            value = dict([(key, replace_templates(v, templ_const, templ_val)) for key, v in value.items()])
+            value = dict([(k, replace_templates(v, templ_const, templ_val)) for k, v in value.items()])
     return value
 
 
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 7ffe603137..a916c9f65b 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1206,7 +1206,7 @@ def test_dump_extra(self):
     def test_dump_template(self):
         """ Test EasyConfig's dump() method for files containing templates"""
         rawtxt = '\n'.join([
-            'easyblock = "EB_toy"',
+            'easyblock = "EB_foo"',
             '',
             'name = "Foo"',
             'version = "0.0.1"',
@@ -1221,7 +1221,9 @@ def test_dump_template(self):
             'preconfigopts = "--opt1=%s" % name',
             'configopts = "--opt2=0.0.1"',
             '',
-            "sanity_check_paths = {'files': ['files/foo/bar'], 'dirs':[] }",
+            "sanity_check_paths = {'files': ['files/foo/foobar'], 'dirs':[] }",
+            '',
+            'foo_extra1 = "foobar"'
         ])
 
         handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')
@@ -1232,20 +1234,26 @@ def test_dump_template(self):
         ec.dump(testec)
         ectxt = read_file(testec)
 
-        self.assertTrue(ec.enable_templating)
+        self.assertTrue(ec.enable_templating)  # templating should still be enabled after calling dump()
 
         patterns = [
-            r"sources = \['SOURCELOWER_TAR_GZ'\]",
+            r'easyblock = "EB_foo"',
+            r'name = "Foo"',
+            r'version = "0.0.1"',
+            r'homepage = "http://foo.com/"',
             r'description = "foo description"',  # no templating for description
-            r"sanity_check_paths = {'files': \['files/%\(namelower\)s/bar'\]",
+            r"sources = \['SOURCELOWER_TAR_GZ'\]",
             r'preconfigopts = "--opt1=%\(name\)s"',
             r'configopts = "--opt2=%\(version\)s"',
+            r"sanity_check_paths = {'files': \['files/%\(namelower\)s/foobar'\]",
         ]
 
         for pattern in patterns:
             regex = re.compile(pattern, re.M)
             self.assertTrue(regex.search(ectxt), "Pattern '%s' found in: %s" % (regex.pattern, ectxt))
 
+        # reparsing the dumped easyconfig file should work
+        ecbis = EasyConfig(testec)
 
 def suite():
     """ returns all the testcases in this module """

From 7a36365c4cfab08cb3ec8cfe25bde4bb59bbd3a6 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 13 Jul 2015 10:42:58 +0200
Subject: [PATCH 1155/1356] sorted imports

---
 easybuild/tools/docs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index a46d3b1ed8..85f06ae304 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -39,9 +39,9 @@
 
 from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, HIDDEN, sorted_categories
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
-from easybuild.tools.ordereddict import OrderedDict
-from easybuild.tools.utilities import quote_str, import_available_modules
 from easybuild.tools.filetools import read_file
+from easybuild.tools.ordereddict import OrderedDict
+from easybuild.tools.utilities import import_available_modules, quote_str
 
 
 FORMAT_RST = 'rst'

From 9204337da20074ec5d1a1393f1fe6d949870fc09 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 13 Jul 2015 11:15:51 +0200
Subject: [PATCH 1156/1356] Fixed remarks

---
 easybuild/tools/docs.py | 43 +++++++++++++++++++++++++++--------------
 test/framework/docs.py  | 26 ++++++++++++-------------
 2 files changed, 42 insertions(+), 27 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 85f06ae304..433f62bea4 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -73,7 +73,7 @@ def avail_easyconfig_params_rst(title, grouped_params):
         values = [
             ['``' + name + '``' for name in grouped_params[grpname].keys()],  # parameter name
             [x[0] for x in grouped_params[grpname].values()],  # description
-            [str(quote_str(x[1])) for x in grouped_params[grpname].values()]  #default value
+            [str(quote_str(x[1])) for x in grouped_params[grpname].values()]  # default value
         ]
 
         lines.extend(mk_rst_table(titles, values))
@@ -81,6 +81,7 @@ def avail_easyconfig_params_rst(title, grouped_params):
 
     return '\n'.join(lines)
 
+
 def avail_easyconfig_params_txt(title, grouped_params):
     """
     Compose overview of available easyconfig parameters, in plain text format.
@@ -106,6 +107,7 @@ def avail_easyconfig_params_txt(title, grouped_params):
 
     return '\n'.join(lines)
 
+
 def avail_easyconfig_params(easyblock, output_format):
     """
     Compose overview of available easyconfig parameters, in specified format.
@@ -160,20 +162,30 @@ def gen_easyblocks_overview_rst(package_name, path_to_examples, common_params={}
     all_blocks = []
 
     # get all blocks
-    for m in modules:
-        for name,obj in inspect.getmembers(m, inspect.isclass):
-            eb_class = getattr(m, name)
+    for mod in modules:
+        for name,obj in inspect.getmembers(mod, inspect.isclass):
+            eb_class = getattr(mod, name)
             # skip imported classes that are not easyblocks
             if eb_class.__module__.startswith(package_name) and eb_class not in all_blocks:
                 all_blocks.append(eb_class)
 
-    for eb_class in all_blocks:
+    for eb_class in sorted(all_blocks):
         docs.append(gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc_functions, all_blocks))
 
     title = 'Overview of generic easyblocks'
 
-    heading = ['=' * len(title), title, '=' * len(title), '', '.. contents::', '    :depth: 2', '']
-    return heading + sorted(docs)
+    heading = [
+        '=' * len(title),
+        title,
+        '=' * len(title),
+        '',
+        '.. contents::',
+        '    :depth: 2',
+        '',
+    ]
+
+    return heading + docs
+
 
 def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc_functions, all_blocks):
     """
@@ -220,20 +232,23 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
         commonly_used = 'Commonly used easyconfig parameters with ``' + classname + '`` easyblock'
         lines.extend([commonly_used, '-' * len(commonly_used)])
 
-        for opt in common_params[classname]:
-            param = '* ``' + opt + '`` - ' + DEFAULT_CONFIG[opt][1]
-            lines.append(param)
-    lines.append('')
+        titles = ['easyconfig parameter', 'description']
+        values = [
+            [common_params[classname]],
+            [DEFAULT_CONFIG[opt][1] for opt in common_params],
+        ]
+
+        lines.extend(mk_rst_table(titles, values))
+
+        lines.append('')
 
     # Add docstring for custom steps
     custom = []
     inh = ''
+    f = None
     for func in doc_functions:
         if func in eb_class.__dict__:
             f = eb_class.__dict__[func]
-        elif func in eb_class.__bases__[0].__dict__:
-            f = eb_class.__bases__[0].__dict__[func]
-            inh = ' (inherited)'
 
         if f.__doc__:
             custom.append('* ``' + func + '`` - ' + f.__doc__.strip() + inh)
diff --git a/test/framework/docs.py b/test/framework/docs.py
index 36f0d997f0..f05e68f3a1 100644
--- a/test/framework/docs.py
+++ b/test/framework/docs.py
@@ -34,24 +34,24 @@ class DocsTest(EnhancedTestCase):
 
     def test_rst_table(self):
         """ Test mk_rst_table function """
-        entries_1 = [['one', 'two', 'three']]
-        t1 = 'This title is long'
-        titles_1 = [t1]
+        entries = [['one', 'two', 'three']]
+        t = 'This title is longer than the entries in the column'
+        titles = [t]
 
         # small table
-        table_1 = '\n'.join(mk_rst_table(titles_1, entries_1))
-        check_1 = '\n'.join([
-            '=' * len(t1),
-            t1,
-            '=' * len(t1),
-            'one' + ' ' * (len(t1) - 3),
-            'two' + ' ' * (len(t1) -3),
-            'three' + ' ' * (len(t1) - 5),
-            '=' * len(t1),
+        table = '\n'.join(mk_rst_table(titles, entries))
+        check = '\n'.join([
+            '=' * len(t),
+            t,
+            '=' * len(t),
+            'one' + ' ' * (len(t) - 3),
+            'two' + ' ' * (len(t) -3),
+            'three' + ' ' * (len(t) - 5),
+            '=' * len(t),
             '',
         ])
 
-        self.assertEqual(table_1, check_1)
+        self.assertEqual(table, check)
 
 
 def suite():

From 8a4ec13b44f5bf3997c560e3a8935b8abd7970ef Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 13 Jul 2015 11:38:04 +0200
Subject: [PATCH 1157/1356] sort easyblocks

---
 easybuild/tools/docs.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 433f62bea4..7495e7baa5 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -169,7 +169,8 @@ def gen_easyblocks_overview_rst(package_name, path_to_examples, common_params={}
             if eb_class.__module__.startswith(package_name) and eb_class not in all_blocks:
                 all_blocks.append(eb_class)
 
-    for eb_class in sorted(all_blocks):
+    for eb_class in sorted(all_blocks, key=lambda c: c.__name__):
+        print eb_class
         docs.append(gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc_functions, all_blocks))
 
     title = 'Overview of generic easyblocks'

From a48c80beeded792f6425830925fd15e1ed4a6517 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 13 Jul 2015 11:47:24 +0200
Subject: [PATCH 1158/1356] remove debug print

---
 easybuild/tools/docs.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 7495e7baa5..5e45cf1f08 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -170,7 +170,6 @@ def gen_easyblocks_overview_rst(package_name, path_to_examples, common_params={}
                 all_blocks.append(eb_class)
 
     for eb_class in sorted(all_blocks, key=lambda c: c.__name__):
-        print eb_class
         docs.append(gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc_functions, all_blocks))
 
     title = 'Overview of generic easyblocks'
@@ -182,6 +181,8 @@ def gen_easyblocks_overview_rst(package_name, path_to_examples, common_params={}
         '',
         '.. contents::',
         '    :depth: 2',
+        '    :local',
+        '    :backlinks: top',
         '',
     ]
 

From b48bf8c76fbd13fa9c47657c46c1688e5a59cb07 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 13 Jul 2015 11:49:41 +0200
Subject: [PATCH 1159/1356] forgot a ':'

---
 easybuild/tools/docs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 5e45cf1f08..4374f6e53b 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -181,7 +181,7 @@ def gen_easyblocks_overview_rst(package_name, path_to_examples, common_params={}
         '',
         '.. contents::',
         '    :depth: 2',
-        '    :local',
+        '    :local:',
         '    :backlinks: top',
         '',
     ]

From f02c539fb6ec875fb9c8b99e75bed985a10b2b97 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 13 Jul 2015 15:46:48 +0200
Subject: [PATCH 1160/1356] Dump templates bugfix

---
 easybuild/framework/easyconfig/easyconfig.py | 27 +++++++----
 easybuild/tools/utilities.py                 | 24 ++++++----
 test/framework/easyconfig.py                 | 47 +++++++++++---------
 3 files changed, 59 insertions(+), 39 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index a62826e14f..46a3c9e5e5 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1,4 +1,4 @@
-# #
+
 # Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,
@@ -503,7 +503,8 @@ def dump(self, fp):
         default_values.update(dict([(key, self.extra_options[key][0]) for key in self.extra_options]))
 
         self.generate_template_values()
-        templ_const = dict([(const[1], const[0]) for const in TEMPLATE_CONSTANTS])
+        templ_const = dict([(quote_str(const[1], escape_newline=True, prefer_single_quotes=True), const[0]) for const in TEMPLATE_CONSTANTS])
+
         # reverse map of templates longer than 2 characters, to inject template values where possible, sorted on length
         keys = sorted(self.template_values, key=lambda k:len(self.template_values[k]), reverse=True)
         templ_val = OrderedDict([(self.template_values[k], k) for k in keys if len(self.template_values[k]) > 2])
@@ -519,9 +520,11 @@ def include_defined_parameters(keyset):
                     if val != default_values[key]:
                         if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
                             self.log.debug("Original value before replacing matching template values: %s", val)
-                            val = replace_templates(val, templ_const, templ_val)
+                            val = to_template_str(val, templ_const, templ_val)
                             self.log.debug("New value after replacing matching template values: %s", val)
-                        ebtxt.append("%s = %s" % (key, quote_str(val, escape_newline=True)))
+                        else:
+                            val = quote_str(val, escape_newline=True, prefer_single_quotes=True)
+                        ebtxt.append("%s = %s" % (key, val))
                         printed_keys.append(key)
                         printed = True
                 if printed:
@@ -536,7 +539,7 @@ def include_defined_parameters(keyset):
         keys_to_ignore = printed_keys + last_keys
         for key in default_values:
             if key not in keys_to_ignore and self[key] != default_values[key]:
-                ebtxt.append("%s = %s" % (key, quote_str(self[key], escape_newline=True)))
+                ebtxt.append("%s = %s" % (key, quote_str(self[key], escape_newline=True, prefer_single_quotes=True)))
         ebtxt.append("")
 
         # print last two parameters
@@ -938,7 +941,7 @@ def resolve_template(value, tmpl_dict):
 
     return value
 
-def replace_templates(value, templ_const, templ_val):
+def to_template_str(value, templ_const, templ_val):
     """
     Given a value, try to substitute template strings where possible.
         - value can be a string, list, tuple, dict or combination thereof
@@ -946,6 +949,9 @@ def replace_templates(value, templ_const, templ_val):
         - templ_val is an ordered dictionary of template strings specific for this easyconfig file
     """
     if isinstance(value, basestring):
+        if value not in templ_const.values():
+            value = quote_str(value, escape_newline=True, prefer_single_quotes=True)
+
         old_value = None
         while value != old_value:
             old_value = value
@@ -959,11 +965,14 @@ def replace_templates(value, templ_const, templ_val):
 
     else:
         if isinstance(value, list):
-            value = [replace_templates(v, templ_const, templ_val) for v in value]
+            value = '[' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ']'
         elif isinstance(value, tuple):
-            value = tuple(replace_templates(list(value), templ_const, templ_val))
+            value = '(' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ')'
         elif isinstance(value, dict):
-            value = dict([(k, replace_templates(v, templ_const, templ_val)) for k, v in value.items()])
+            value = '{' + ', '.join(["%s: %s" % (quote_str(k, escape_newline=True, prefer_single_quotes=True), to_template_str(v, templ_const, templ_val))
+            for k, v in value.items()]) + '}'
+        else:
+            value = str(value)
     return value
 
 
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index add8dbc57f..f05dfa856e 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -56,12 +56,12 @@ def flatten(lst):
     return res
 
 
-def quote_str(x, escape_newline=False):
+def quote_str(val, escape_newline=False, prefer_single_quotes=False):
     """
     Obtain a new value to be used in string replacement context.
 
     For non-string values, it just returns the exact same value.
- 
+
     For string values, it tries to escape the string in quotes, e.g.,
     foo becomes 'foo', foo'bar becomes "foo'bar",
     foo'bar"baz becomes \"\"\"foo'bar"baz\"\"\", etc.
@@ -69,15 +69,21 @@ def quote_str(x, escape_newline=False):
     @param escape_newline: wrap strings that include a newline in triple quotes
     """
 
-    if isinstance(x, basestring):
-        if ("'" in x and '"' in x) or (escape_newline and '\n' in x):
-            return '"""%s"""' % x
-        elif '"' in x:
-            return "'%s'" % x
+    if isinstance(val, basestring):
+        # forced triple double quotes
+        if ("'" in val and '"' in val) or (escape_newline and '\n' in val):
+            return '"""%s"""' % val
+        # single quotes to escape double quote used in strings
+        elif '"' in val:
+            return "'%s'" % val
+        # if single quotes are preferred, use single quotes
+        elif prefer_single_quotes and ' ' not in val:
+            return "'%s'" % val
+        # fallback on double quotes (required in tcl syntax)
         else:
-            return '"%s"' % x
+            return '"%s"' % val
     else:
-        return x
+        return val
 
 
 def remove_unwanted_chars(inputstring):
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index a916c9f65b..730a35da9a 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1140,7 +1140,8 @@ def test_quote_str(self):
             'foo\'bar' : '"foo\'bar"',
             'foo\'bar"baz' : '"""foo\'bar"baz"""',
             "foo'bar\"baz" : '"""foo\'bar"baz"""',
-            "foo\nbar" : '"foo\nbar"'
+            "foo\nbar" : '"foo\nbar"',
+            'foo bar' : '"foo bar"'
         }
 
         for t in teststrings:
@@ -1150,6 +1151,10 @@ def test_quote_str(self):
         self.assertEqual(quote_str("foo\nbar", escape_newline=False), '"foo\nbar"')
         self.assertEqual(quote_str("foo\nbar", escape_newline=True), '"""foo\nbar"""')
 
+        # test prefer_single_quotes
+        self.assertEqual(quote_str("foo", prefer_single_quotes=True), "'foo'")
+        self.assertEqual(quote_str('foo bar', prefer_single_quotes=True), '"foo bar"')
+
         # non-string values
         n = 42
         self.assertEqual(quote_str(n), 42)
@@ -1168,7 +1173,7 @@ def test_dump(self):
             ec.dump(test_ec)
             ectxt = read_file(test_ec)
 
-            patterns = [r'^name = ["\']', r'^version = ["0-9\.]', r'^description = ["\']']
+            patterns = [r"^name = ['\"]", r"^version = ['0-9\.]", r'^description = ["\']']
             for pattern in patterns:
                 regex = re.compile(pattern, re.M)
                 self.assertTrue(regex.search(ectxt), "Pattern '%s' found in: %s" % (regex.pattern, ectxt))
@@ -1180,17 +1185,17 @@ def test_dump_extra(self):
         """Test EasyConfig's dump() method for files containing extra values"""
 
         rawtxt = '\n'.join([
-            'easyblock = "EB_foo"',
+            "easyblock = 'EB_foo'",
             '',
-            'name = "foo"',
-            'version = "0.0.1"',
+            "name = 'foo'",
+            "version = '0.0.1'",
             '',
-            'homepage = "http://foo.com/"',
+            "homepage = 'http://foo.com/'",
             'description = "foo description"',
             '',
             "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
-            'foo_extra1 = "foobar"',
+            "foo_extra1 = 'foobar'",
         ])
 
         handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')
@@ -1206,24 +1211,24 @@ def test_dump_extra(self):
     def test_dump_template(self):
         """ Test EasyConfig's dump() method for files containing templates"""
         rawtxt = '\n'.join([
-            'easyblock = "EB_foo"',
+            "easyblock = 'EB_foo'",
             '',
-            'name = "Foo"',
-            'version = "0.0.1"',
+            "name = 'Foo'",
+            "version = '0.0.1'",
             '',
-            'homepage = "http://foo.com/"',
+            "homepage = 'http://foo.com/'",
             'description = "foo description"',
             '',
             "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
             "sources = ['foo-0.0.1.tar.gz']",
             '',
-            'preconfigopts = "--opt1=%s" % name',
-            'configopts = "--opt2=0.0.1"',
+            "preconfigopts = '--opt1=%s' % name",
+            "configopts = '--opt2=0.0.1'",
             '',
             "sanity_check_paths = {'files': ['files/foo/foobar'], 'dirs':[] }",
             '',
-            'foo_extra1 = "foobar"'
+            "foo_extra1 = 'foobar'"
         ])
 
         handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')
@@ -1237,14 +1242,14 @@ def test_dump_template(self):
         self.assertTrue(ec.enable_templating)  # templating should still be enabled after calling dump()
 
         patterns = [
-            r'easyblock = "EB_foo"',
-            r'name = "Foo"',
-            r'version = "0.0.1"',
-            r'homepage = "http://foo.com/"',
+            r"easyblock = 'EB_foo'",
+            r"name = 'Foo'",
+            r"version = '0.0.1'",
+            r"homepage = 'http://foo.com/'",
             r'description = "foo description"',  # no templating for description
-            r"sources = \['SOURCELOWER_TAR_GZ'\]",
-            r'preconfigopts = "--opt1=%\(name\)s"',
-            r'configopts = "--opt2=%\(version\)s"',
+            r"sources = \[SOURCELOWER_TAR_GZ\]",
+            r"preconfigopts = '--opt1=%\(name\)s'",
+            r"configopts = '--opt2=%\(version\)s'",
             r"sanity_check_paths = {'files': \['files/%\(namelower\)s/foobar'\]",
         ]
 

From 1c81f21a9f892ebc78bd4cef06cfa34981905c04 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 13 Jul 2015 16:05:59 +0200
Subject: [PATCH 1161/1356] typo

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 46a3c9e5e5..56b9d8df15 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1,4 +1,4 @@
-
+# #
 # Copyright 2009-2015 Ghent University
 #
 # This file is part of EasyBuild,

From 20452539e0b8f2c58902ab722e46de678491fd9e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 13 Jul 2015 16:12:23 +0200
Subject: [PATCH 1162/1356] fix style issues

---
 easybuild/framework/easyconfig/easyconfig.py | 28 +++++++++++++-------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 56b9d8df15..63a21ed9eb 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -475,7 +475,7 @@ def dump(self, fp):
         """
         Dump this easyconfig to file, with the given filename.
         """
-        eb_file = file(fp, "w")
+        eb_file = file(fp, 'w')
 
         # ordered groups of keys to obtain a nice looking easyconfig file
         grouped_keys = [
@@ -503,7 +503,7 @@ def dump(self, fp):
         default_values.update(dict([(key, self.extra_options[key][0]) for key in self.extra_options]))
 
         self.generate_template_values()
-        templ_const = dict([(quote_str(const[1], escape_newline=True, prefer_single_quotes=True), const[0]) for const in TEMPLATE_CONSTANTS])
+        templ_const = dict([(quote_py_str(const[1]), const[0]) for const in TEMPLATE_CONSTANTS])
 
         # reverse map of templates longer than 2 characters, to inject template values where possible, sorted on length
         keys = sorted(self.template_values, key=lambda k:len(self.template_values[k]), reverse=True)
@@ -523,12 +523,12 @@ def include_defined_parameters(keyset):
                             val = to_template_str(val, templ_const, templ_val)
                             self.log.debug("New value after replacing matching template values: %s", val)
                         else:
-                            val = quote_str(val, escape_newline=True, prefer_single_quotes=True)
+                            val = quote_py_str(val)
                         ebtxt.append("%s = %s" % (key, val))
                         printed_keys.append(key)
                         printed = True
                 if printed:
-                    ebtxt.append("")
+                    ebtxt.append('')
 
         # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
@@ -539,8 +539,8 @@ def include_defined_parameters(keyset):
         keys_to_ignore = printed_keys + last_keys
         for key in default_values:
             if key not in keys_to_ignore and self[key] != default_values[key]:
-                ebtxt.append("%s = %s" % (key, quote_str(self[key], escape_newline=True, prefer_single_quotes=True)))
-        ebtxt.append("")
+                ebtxt.append("%s = %s" % (key, quote_py_str(self[key])))
+        ebtxt.append('')
 
         # print last two parameters
         include_defined_parameters([[k] for k in last_keys])
@@ -941,16 +941,24 @@ def resolve_template(value, tmpl_dict):
 
     return value
 
+
+def quote_py_str(val):
+    """Version of quote_str specific for generating use in Python context (e.g., easyconfig parameters)."""
+    return quote_str(val, escape_newline=True, prefer_single_quotes=True)
+
+
 def to_template_str(value, templ_const, templ_val):
     """
-    Given a value, try to substitute template strings where possible.
+    Create string representation of provided value, using template values where possible.
         - value can be a string, list, tuple, dict or combination thereof
         - templ_const is a dictionary of template strings (constants)
         - templ_val is an ordered dictionary of template strings specific for this easyconfig file
     """
     if isinstance(value, basestring):
+
+        # wrap string into quotes, except if it matches a template constant
         if value not in templ_const.values():
-            value = quote_str(value, escape_newline=True, prefer_single_quotes=True)
+            value = quote_py_str(value)
 
         old_value = None
         while value != old_value:
@@ -962,17 +970,17 @@ def to_template_str(value, templ_const, templ_val):
                 for temp_val, temp_name in templ_val.items():
                     # only replace full words with templates, not substrings, by using \b in regex
                     value = re.sub(r"\b" + re.escape(temp_val) + r"\b", r'%(' + temp_name + ')s', value)
-
     else:
         if isinstance(value, list):
             value = '[' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ']'
         elif isinstance(value, tuple):
             value = '(' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ')'
         elif isinstance(value, dict):
-            value = '{' + ', '.join(["%s: %s" % (quote_str(k, escape_newline=True, prefer_single_quotes=True), to_template_str(v, templ_const, templ_val))
+            value = '{' + ', '.join(["%s: %s" % (quote_py_str(k), to_template_str(v, templ_const, templ_val))
             for k, v in value.items()]) + '}'
         else:
             value = str(value)
+
     return value
 
 

From 09f6db74ecd9264912858e2125b068a9c23478b8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 13 Jul 2015 20:00:58 +0200
Subject: [PATCH 1163/1356] don't wrap string containing single quotes with
 single quotes in quote_str function

---
 easybuild/tools/utilities.py | 5 +++--
 test/framework/easyconfig.py | 1 +
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 7ab1743d8a..cc8fe2185b 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -79,8 +79,9 @@ def quote_str(val, escape_newline=False, prefer_single_quotes=False):
         # single quotes to escape double quote used in strings
         elif '"' in val:
             return "'%s'" % val
-        # if single quotes are preferred, use single quotes
-        elif prefer_single_quotes and ' ' not in val:
+        # if single quotes are preferred, use single quotes;
+        # unless a space or a single quote are in the string
+        elif prefer_single_quotes and "'" not in val and ' ' not in val:
             return "'%s'" % val
         # fallback on double quotes (required in tcl syntax)
         else:
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 730a35da9a..3fafc3e39c 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1154,6 +1154,7 @@ def test_quote_str(self):
         # test prefer_single_quotes
         self.assertEqual(quote_str("foo", prefer_single_quotes=True), "'foo'")
         self.assertEqual(quote_str('foo bar', prefer_single_quotes=True), '"foo bar"')
+        self.assertEqual(quote_str("foo'bar", prefer_single_quotes=True), '"foo\'bar"')
 
         # non-string values
         n = 42

From 1bdb3f737ecf186e4312d202dc049c3f2e24e7e9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 13 Jul 2015 20:48:34 +0200
Subject: [PATCH 1164/1356] fix dumping of dependencies, avoid template values
 that refer to the key they're defining

---
 easybuild/framework/easyconfig/easyconfig.py | 42 ++++++++++++++++----
 test/framework/easyconfig.py                 | 10 ++++-
 2 files changed, 43 insertions(+), 9 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index d0d7e9ae15..53a25533c0 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -506,7 +506,7 @@ def dump(self, fp):
         templ_const = dict([(quote_py_str(const[1]), const[0]) for const in TEMPLATE_CONSTANTS])
 
         # reverse map of templates longer than 2 characters, to inject template values where possible, sorted on length
-        keys = sorted(self.template_values, key=lambda k:len(self.template_values[k]), reverse=True)
+        keys = sorted(self.template_values, key=lambda k: len(self.template_values[k]), reverse=True)
         templ_val = OrderedDict([(self.template_values[k], k) for k in keys if len(self.template_values[k]) > 2])
 
         def include_defined_parameters(keyset):
@@ -518,12 +518,24 @@ def include_defined_parameters(keyset):
                 for key in group:
                     val = self[key]
                     if val != default_values[key]:
-                        if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
+                        # dependency easyconfig parameters were parsed, so these need special care to 'unparse' them
+                        if key in ['builddependencies', 'dependencies', 'hiddendependencies']:
+                            newval = to_template_str([self._dump_dependency(d) for d in val], templ_const, templ_val)
+
+                        elif key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
                             self.log.debug("Original value before replacing matching template values: %s", val)
-                            val = to_template_str(val, templ_const, templ_val)
-                            self.log.debug("New value after replacing matching template values: %s", val)
+                            newval = to_template_str(val, templ_const, templ_val)
+                            self.log.debug("New value after replacing matching template values: %s", newval)
+
+                        else:
+                            newval = quote_py_str(val)
+
+                        # quote string, but avoid that templated value refers to parameter that it defines
+                        if (r'%(' + key) not in newval:
+                            val = newval
                         else:
                             val = quote_py_str(val)
+
                         ebtxt.append("%s = %s" % (key, val))
                         printed_keys.append(key)
                         printed = True
@@ -684,6 +696,22 @@ def _parse_dependency(self, dep, hidden=False):
 
         return dependency
 
+    def _dump_dependency(self, dep):
+        """Dump parsed dependency in tuple format"""
+        # mininal spec: (name, version)
+        tup = (dep['name'], dep['version'])
+
+        if dep['toolchain'] != self['toolchain']:
+            if dep['dummy']:
+                tup += (dep['versionsuffix'], True)
+            else:
+                tup += (dep['versionsuffix'], (dep['toolchain']['name'], dep['toolchain']['version']))
+
+        elif dep['versionsuffix']:
+            tup += (dep['versionsuffix'],)
+
+        return tup
+
     def generate_template_values(self):
         """Try to generate all template values."""
         # TODO proper recursive code https://github.com/hpcugent/easybuild-framework/issues/474
@@ -966,10 +994,10 @@ def to_template_str(value, templ_const, templ_val):
             if value in templ_const:
                 value = templ_const[value]
             else:
-                # check for template values
-                for temp_val, temp_name in templ_val.items():
+                # check for template values (note: templ_val dict is 'upside-down')
+                for tval, tname in templ_val.items():
                     # only replace full words with templates, not substrings, by using \b in regex
-                    value = re.sub(r"\b" + re.escape(temp_val) + r"\b", r'%(' + temp_name + ')s', value)
+                    value = re.sub(r"\b" + re.escape(tval) + r"\b", r'%(' + tname + ')s', value)
     else:
         if isinstance(value, list):
             value = '[' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ']'
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 3fafc3e39c..d064aae7ae 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -332,7 +332,7 @@ def test_tweaking(self):
             'homepage = "http://www.example.com"',
             'description = "dummy description"',
             'version = "3.14"',
-            'toolchain = {"name":"GCC", "version": "4.6.3"}',
+            'toolchain = {"name":"GCC","version":"4.6.3"}',
             'patches = %s',
         ]) % str(patches)
         self.prep()
@@ -1190,12 +1190,15 @@ def test_dump_extra(self):
             '',
             "name = 'foo'",
             "version = '0.0.1'",
+            "versionsuffix = '_bar'",
             '',
             "homepage = 'http://foo.com/'",
             'description = "foo description"',
             '',
             "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
+            "dependencies = [('GCC', '4.6.4', '-test'), ('MPICH', '1.8', '', ('GCC', '4.6.4')), ('bar', '1.0')]",
+            '',
             "foo_extra1 = 'foobar'",
         ])
 
@@ -1216,6 +1219,7 @@ def test_dump_template(self):
             '',
             "name = 'Foo'",
             "version = '0.0.1'",
+            "versionsuffix = '-test'",
             '',
             "homepage = 'http://foo.com/'",
             'description = "foo description"',
@@ -1224,6 +1228,8 @@ def test_dump_template(self):
             '',
             "sources = ['foo-0.0.1.tar.gz']",
             '',
+            "dependencies = [('bar', '1.2.3', '-test')]",
+            '',
             "preconfigopts = '--opt1=%s' % name",
             "configopts = '--opt2=0.0.1'",
             '',
@@ -1236,7 +1242,6 @@ def test_dump_template(self):
         os.close(handle)
 
         ec = EasyConfig(None, rawtxt=rawtxt)
-        ec.enable_templating = True
         ec.dump(testec)
         ectxt = read_file(testec)
 
@@ -1246,6 +1251,7 @@ def test_dump_template(self):
             r"easyblock = 'EB_foo'",
             r"name = 'Foo'",
             r"version = '0.0.1'",
+            r"versionsuffix = '-test'",
             r"homepage = 'http://foo.com/'",
             r'description = "foo description"',  # no templating for description
             r"sources = \[SOURCELOWER_TAR_GZ\]",

From 7fda48b08407a7d26b4e33e4640efb017e0982c8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 13 Jul 2015 22:13:28 +0200
Subject: [PATCH 1165/1356] deal with dependencies marked as external module in
 EasyConfig.dump()

---
 easybuild/framework/easyconfig/easyconfig.py | 39 ++++++++++++--------
 test/framework/easyconfig.py                 |  4 +-
 2 files changed, 25 insertions(+), 18 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 53a25533c0..9d76c49d47 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -520,7 +520,8 @@ def include_defined_parameters(keyset):
                     if val != default_values[key]:
                         # dependency easyconfig parameters were parsed, so these need special care to 'unparse' them
                         if key in ['builddependencies', 'dependencies', 'hiddendependencies']:
-                            newval = to_template_str([self._dump_dependency(d) for d in val], templ_const, templ_val)
+                            dumped_deps = [self._dump_dependency(d, templ_const, templ_val) for d in val]
+                            newval = '[' + ', '.join(dumped_deps) + ']'
 
                         elif key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
                             self.log.debug("Original value before replacing matching template values: %s", val)
@@ -530,11 +531,11 @@ def include_defined_parameters(keyset):
                         else:
                             newval = quote_py_str(val)
 
-                        # quote string, but avoid that templated value refers to parameter that it defines
-                        if (r'%(' + key) not in newval:
-                            val = newval
-                        else:
+                        # avoid that templated value refers to parameter that it defines
+                        if r'%(' + key in newval:
                             val = quote_py_str(val)
+                        else:
+                            val = newval
 
                         ebtxt.append("%s = %s" % (key, val))
                         printed_keys.append(key)
@@ -696,21 +697,27 @@ def _parse_dependency(self, dep, hidden=False):
 
         return dependency
 
-    def _dump_dependency(self, dep):
+    def _dump_dependency(self, dep, templ_const, templ_val):
         """Dump parsed dependency in tuple format"""
-        # mininal spec: (name, version)
-        tup = (dep['name'], dep['version'])
 
-        if dep['toolchain'] != self['toolchain']:
-            if dep['dummy']:
-                tup += (dep['versionsuffix'], True)
-            else:
-                tup += (dep['versionsuffix'], (dep['toolchain']['name'], dep['toolchain']['version']))
+        if dep['external_module']:
+            res = "(%s, EXTERNAL_MODULE)" % quote_py_str(dep['name'])
 
-        elif dep['versionsuffix']:
-            tup += (dep['versionsuffix'],)
+        else:
+            # mininal spec: (name, version)
+            tup = (dep['name'], dep['version'])
+            if dep['toolchain'] != self['toolchain']:
+                if dep['dummy']:
+                    tup += (dep['versionsuffix'], True)
+                else:
+                    tup += (dep['versionsuffix'], (dep['toolchain']['name'], dep['toolchain']['version']))
+
+            elif dep['versionsuffix']:
+                tup += (dep['versionsuffix'],)
 
-        return tup
+            res = to_template_str(tup, templ_const, templ_val)
+
+        return res
 
     def generate_template_values(self):
         """Try to generate all template values."""
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index d064aae7ae..b8ff89ae3f 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -332,7 +332,7 @@ def test_tweaking(self):
             'homepage = "http://www.example.com"',
             'description = "dummy description"',
             'version = "3.14"',
-            'toolchain = {"name":"GCC","version":"4.6.3"}',
+            'toolchain = {"name": "GCC", "version": "4.6.3"}',
             'patches = %s',
         ]) % str(patches)
         self.prep()
@@ -1162,7 +1162,6 @@ def test_quote_str(self):
         self.assertEqual(quote_str(["foo", "bar"]), ["foo", "bar"])
         self.assertEqual(quote_str(('foo', 'bar')), ('foo', 'bar'))
 
-
     def test_dump(self):
         """Test EasyConfig's dump() method."""
         test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
@@ -1267,6 +1266,7 @@ def test_dump_template(self):
         # reparsing the dumped easyconfig file should work
         ecbis = EasyConfig(testec)
 
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(EasyConfigTest)

From ccb70a71eae74990d58bb49a688446394974be51 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 13 Jul 2015 23:47:12 +0200
Subject: [PATCH 1166/1356] also check dump() with dependencies marked as
 external module

---
 test/framework/easyconfig.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index b8ff89ae3f..b5f2bbc442 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1183,6 +1183,11 @@ def test_dump(self):
 
     def test_dump_extra(self):
         """Test EasyConfig's dump() method for files containing extra values"""
+        build_options = {
+            'valid_module_classes': module_classes(),
+            'external_modules_metadata': ConfigObj(),
+        }
+        init_config(build_options=build_options)
 
         rawtxt = '\n'.join([
             "easyblock = 'EB_foo'",
@@ -1196,7 +1201,8 @@ def test_dump_extra(self):
             '',
             "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
-            "dependencies = [('GCC', '4.6.4', '-test'), ('MPICH', '1.8', '', ('GCC', '4.6.4')), ('bar', '1.0')]",
+            "dependencies = [('GCC', '4.6.4', '-test'), ('MPICH', '1.8', '', ('GCC', '4.6.4')), " +
+                "('bar', '1.0'), ('foobar/1.2.3', EXTERNAL_MODULE)]",
             '',
             "foo_extra1 = 'foobar'",
         ])

From 44295255f94eb5f24a59b1d41a91d0c7c9eb82db Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 13 Jul 2015 23:50:05 +0200
Subject: [PATCH 1167/1356] fix dumping of dependencies marked as external
 module

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 9d76c49d47..7c21b4a5dc 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -701,7 +701,7 @@ def _dump_dependency(self, dep, templ_const, templ_val):
         """Dump parsed dependency in tuple format"""
 
         if dep['external_module']:
-            res = "(%s, EXTERNAL_MODULE)" % quote_py_str(dep['name'])
+            res = "(%s, EXTERNAL_MODULE)" % quote_py_str(dep['full_mod_name'])
 
         else:
             # mininal spec: (name, version)

From d1519a7958578cc072d062f476d83648e9c8d161 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Jul 2015 00:35:51 +0200
Subject: [PATCH 1168/1356] include enhancements to EasyConfig.dump() in
 release notes

---
 RELEASE_NOTES | 1 +
 1 file changed, 1 insertion(+)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index d148a8ffa2..2bc39d681e 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -25,6 +25,7 @@ feature + bugfix release
     - promote MigrateFromEBToHMNS to a 'production' MNS (#1302)
     - add support for --read-only-installdir and --group-writable-installdir configuration options (#1304)
     - add support for *not* expanding relative paths in prepend_paths (#1310)
+    - enhance EasyConfig.dump() method to use easyconfig templates where possible (#1314, #1319, #1320, #1321)
 - various bug fixes, including:
     - fix issue with cleaning up (no) logfile if --logtostdout/-l is used (#1298)
     - stop making ModulesTool class a singleton since it causes problems when multilple toolchains are in play (#1299)

From 4fc4c24412c004098cdb7aac3e46e4ff23a7846f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Jul 2015 01:01:00 +0200
Subject: [PATCH 1169/1356] small clarification in release notes

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 2bc39d681e..971789fb20 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -29,7 +29,7 @@ feature + bugfix release
 - various bug fixes, including:
     - fix issue with cleaning up (no) logfile if --logtostdout/-l is used (#1298)
     - stop making ModulesTool class a singleton since it causes problems when multilple toolchains are in play (#1299)
-    - don't modify values of 'paths' list passed as argument to prepend_paths (#1300)
+    - don't modify values of 'paths' list passed as argument to prepend_paths in ModuleGenerator (#1300)
     - fix issue with EasyConfig.dump + cleanup (#1308, #1311)
     - reenable (and fix) accidentally disabled test (#1316)
 

From 5d08e010c57003ec7e61db007a867e963f72b491 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 14 Jul 2015 13:30:06 +0200
Subject: [PATCH 1170/1356] fix bug with special characters in templates for
 dump function

---
 easybuild/framework/easyconfig/easyconfig.py | 6 ++++--
 test/framework/easyconfig.py                 | 5 +++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 9d76c49d47..2b7d0ff5ea 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1003,8 +1003,10 @@ def to_template_str(value, templ_const, templ_val):
             else:
                 # check for template values (note: templ_val dict is 'upside-down')
                 for tval, tname in templ_val.items():
-                    # only replace full words with templates, not substrings, by using \b in regex
-                    value = re.sub(r"\b" + re.escape(tval) + r"\b", r'%(' + tname + ')s', value)
+                    # only replace full words with templates: word to replace should be at the beginning of a line
+                    # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
+                    # by another non-alphanumeric.
+                    value = re.sub(r"(^|\W)" + re.escape(tval) + r"(^|\W)", r'\1%(' + tname + r')s\2', value)
     else:
         if isinstance(value, list):
             value = '[' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ']'
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index b8ff89ae3f..8803880ef0 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1232,7 +1232,7 @@ def test_dump_template(self):
             "preconfigopts = '--opt1=%s' % name",
             "configopts = '--opt2=0.0.1'",
             '',
-            "sanity_check_paths = {'files': ['files/foo/foobar'], 'dirs':[] }",
+            "sanity_check_paths = {'files': ['files/foo/foobar', 'files/x-test'], 'dirs':[] }",
             '',
             "foo_extra1 = 'foobar'"
         ])
@@ -1254,9 +1254,10 @@ def test_dump_template(self):
             r"homepage = 'http://foo.com/'",
             r'description = "foo description"',  # no templating for description
             r"sources = \[SOURCELOWER_TAR_GZ\]",
+            r"dependencies = \[\('bar', '1.2.3', '%\(versionsuffix\)s'\)\]",
             r"preconfigopts = '--opt1=%\(name\)s'",
             r"configopts = '--opt2=%\(version\)s'",
-            r"sanity_check_paths = {'files': \['files/%\(namelower\)s/foobar'\]",
+            r"sanity_check_paths = {'files': \['files/%\(namelower\)s/foobar', 'files/x-test'\]",
         ]
 
         for pattern in patterns:

From 8342e6e7ea880892934deb75a0eb34af715cea03 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 14 Jul 2015 13:34:28 +0200
Subject: [PATCH 1171/1356] consistency in quotes

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 2b7d0ff5ea..be1349f096 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1006,7 +1006,7 @@ def to_template_str(value, templ_const, templ_val):
                     # only replace full words with templates: word to replace should be at the beginning of a line
                     # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
                     # by another non-alphanumeric.
-                    value = re.sub(r"(^|\W)" + re.escape(tval) + r"(^|\W)", r'\1%(' + tname + r')s\2', value)
+                    value = re.sub(r'(^|\W)' + re.escape(tval) + r'(^|\W)', r'\1%(' + tname + r')s\2', value)
     else:
         if isinstance(value, list):
             value = '[' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ']'

From 7000904efb318341cc23da7fada709f6c0b2292d Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 14 Jul 2015 13:45:29 +0200
Subject: [PATCH 1172/1356] lookahead in templating regex instead of working
 with backreferences

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index be1349f096..1a1f5652f6 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1006,7 +1006,7 @@ def to_template_str(value, templ_const, templ_val):
                     # only replace full words with templates: word to replace should be at the beginning of a line
                     # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
                     # by another non-alphanumeric.
-                    value = re.sub(r'(^|\W)' + re.escape(tval) + r'(^|\W)', r'\1%(' + tname + r')s\2', value)
+                    value = re.sub(r'(^|(?<=\W))' + re.escape(tval) + r'((?=\W)|$)', r'%(' + tname + r')s', value)
     else:
         if isinstance(value, list):
             value = '[' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ']'

From e0511f3314e871a03d513dc109bb123f968d95d7 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 14 Jul 2015 14:59:48 +0200
Subject: [PATCH 1173/1356] fix typo + unit test for to_template_str

---
 easybuild/framework/easyconfig/easyconfig.py |  3 +--
 test/framework/easyconfig.py                 | 22 +++++++++++++++++++-
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 1a1f5652f6..116d6077d3 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -990,7 +990,6 @@ def to_template_str(value, templ_const, templ_val):
         - templ_val is an ordered dictionary of template strings specific for this easyconfig file
     """
     if isinstance(value, basestring):
-
         # wrap string into quotes, except if it matches a template constant
         if value not in templ_const.values():
             value = quote_py_str(value)
@@ -1006,7 +1005,7 @@ def to_template_str(value, templ_const, templ_val):
                     # only replace full words with templates: word to replace should be at the beginning of a line
                     # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
                     # by another non-alphanumeric.
-                    value = re.sub(r'(^|(?<=\W))' + re.escape(tval) + r'((?=\W)|$)', r'%(' + tname + r')s', value)
+                    value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1%(' + tname + r')s\2', value)
     else:
         if isinstance(value, list):
             value = '[' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ']'
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 8803880ef0..f48d78f05c 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -45,7 +45,7 @@
 from easybuild.framework.easyconfig.constants import EXTERNAL_MODULE_MARKER
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.framework.easyconfig.easyconfig import create_paths
-from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
+from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, quote_py_str, to_template_str
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak_one
 from easybuild.tools.build_log import EasyBuildError
@@ -1267,6 +1267,26 @@ def test_dump_template(self):
         # reparsing the dumped easyconfig file should work
         ecbis = EasyConfig(testec)
 
+    def test_to_template_str(self):
+        """ Test for to_template_str method """
+        templ_const = {
+            quote_py_str('template'):'TEMPLATE_VALUE',
+            quote_py_str('%(name)s-%(version)s'): 'NAME_VERSION',
+        }
+
+        templ_val = {
+            'foo':'name',
+            '0.0.1':'version',
+            '-test':'special_char',
+        }
+
+        self.assertEqual(to_template_str("template", templ_const, templ_val), 'TEMPLATE_VALUE')
+        self.assertEqual(to_template_str("foo/bar/0.0.1/", templ_const, templ_val), "'%(name)s/bar/%(version)s/'")
+        self.assertEqual(to_template_str("foo-0.0.1", templ_const, templ_val), 'NAME_VERSION')
+        self.assertEqual(to_template_str(['-test', 'dontreplacenamehere'], templ_const, templ_val), "['%(special_char)s', 'dontreplacenamehere']")
+        self.assertEqual(to_template_str({'a':'foo', 'b':'notemplate'}, templ_const, templ_val), "{'a': '%(name)s', 'b': 'notemplate'}")
+        self.assertEqual(to_template_str(('foo', '0.0.1'), templ_const, templ_val), "('%(name)s', '%(version)s')")
+
 
 def suite():
     """ returns all the testcases in this module """

From 307ae84cebce4fee72627450fc8fd069e0579aaa Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 14 Jul 2015 16:48:54 +0200
Subject: [PATCH 1174/1356] rst documentation for generic easyblocks unit test

---
 easybuild/tools/docs.py |  8 +++---
 test/framework/docs.py  | 62 ++++++++++++++++++++++++++++++++++++++++-
 2 files changed, 65 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 5e45cf1f08..078488bd72 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -180,8 +180,8 @@ def gen_easyblocks_overview_rst(package_name, path_to_examples, common_params={}
         '=' * len(title),
         '',
         '.. contents::',
-        '    :depth: 2',
-        '    :local',
+        '    :depth: 1',
+        '    :local:',
         '    :backlinks: top',
         '',
     ]
@@ -236,8 +236,8 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
 
         titles = ['easyconfig parameter', 'description']
         values = [
-            [common_params[classname]],
-            [DEFAULT_CONFIG[opt][1] for opt in common_params],
+            [opt for opt in common_params[classname]],
+            [DEFAULT_CONFIG[opt][1] for opt in common_params[classname]],
         ]
 
         lines.extend(mk_rst_table(titles, values))
diff --git a/test/framework/docs.py b/test/framework/docs.py
index f05e68f3a1..26eb9f07a2 100644
--- a/test/framework/docs.py
+++ b/test/framework/docs.py
@@ -26,9 +26,15 @@
 Unit tests for docs.py.
 """
 
+import os
+import re
+import sys
+import inspect
+
+from easybuild.tools.docs import gen_easyblocks_overview_rst, mk_rst_table
+from easybuild.tools.utilities import import_available_modules
 from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader, main
-from easybuild.tools.docs import mk_rst_table
 
 class DocsTest(EnhancedTestCase):
 
@@ -53,6 +59,60 @@ def test_rst_table(self):
 
         self.assertEqual(table, check)
 
+    def test_gen_easyblocks(self):
+        """ Test gen_easyblocks_overview_rst function """
+        module = 'easybuild.easyblocks.generic'
+        modules = import_available_modules(module)
+        common_params = {
+            'ConfigureMake' : ['configopts', 'buildopts', 'installopts'],
+        }
+        doc_functions = ['build_step', 'configure_step', 'test_step']
+
+        eb_overview = gen_easyblocks_overview_rst(module, 'easyconfigs', common_params, doc_functions)
+        ebdoc = '\n'.join(eb_overview)
+
+        # extensive check for ConfigureMake easyblock
+        check_configuremake = '\n'.join([
+            ".. _ConfigureMake:",
+            '',
+            "``ConfigureMake``",
+            "=================",
+            '',
+            "(derives from EasyBlock)",
+            '',
+            "Dummy support for building and installing applications with configure/make/make install.",
+            '',
+            "Commonly used easyconfig parameters with ``ConfigureMake`` easyblock",
+            "--------------------------------------------------------------------",
+            "====================   ================================================================",
+            "easyconfig parameter   description                                                     ",
+            "====================   ================================================================",
+            "configopts             Extra options passed to configure (default already has --prefix)",
+            "buildopts              Extra options passed to make step (default already has -j X)    ",
+            "installopts            Extra options for installation                                  ",
+            "====================   ================================================================",
+        ])
+
+        self.assertTrue(check_configuremake in ebdoc)
+
+        for mod in modules:
+            for name, obj in inspect.getmembers(mod, inspect.isclass):
+                eb_class = getattr(mod, name)
+                # skip imported classes that are not easyblocks
+                if eb_class.__module__.startswith(module):
+                    self.assertTrue(name in ebdoc)
+
+        patterns = [
+            r'..contents::',
+            r'    :depth: 1',
+            r'    :local:',
+            r'    :backlinks: top'
+        ]
+
+        for pattern in patterns:
+            regex = re.compile(pattern)
+            self.assertTrue(re.search(regex, ebdoc), "Pattern %s found in %s" % (regex.pattern, ebdoc))
+
 
 def suite():
     """ returns all test cases in this module """

From 66962bf2afa19027085879f406b6a2fd933bbd76 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Jul 2015 16:53:35 +0200
Subject: [PATCH 1175/1356] unset $EASYBUILD_BOOTSTRAP_* env vars before
 copying environment in bootstrap script

---
 easybuild/scripts/bootstrap_eb.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 17a6055513..c8a14b9ff0 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -66,6 +66,9 @@
 # clean PYTHONPATH to avoid finding readily installed stuff
 os.environ['PYTHONPATH'] = ''
 
+EASYBUILD_BOOTSTRAP_SOURCEPATH = os.environ.pop('EASYBUILD_BOOTSTRAP_SOURCEPATH', None)
+EASYBUILD_BOOTSTRAP_SKIP_STAGE0 = os.environ.pop('EASYBUILD_BOOTSTRAP_SKIP_STAGE0', False)
+
 # keep track of original environment (after clearing PYTHONPATH)
 orig_os_environ = copy.deepcopy(os.environ)
 
@@ -439,12 +442,10 @@ def main():
         error("Usage: %s <install path>" % sys.argv[0])
     install_path = os.path.abspath(sys.argv[1])
 
-    sourcepath = os.environ.pop('EASYBUILD_BOOTSTRAP_SOURCEPATH', None)
+    sourcepath = EASYBUILD_BOOTSTRAP_SOURCEPATH
     if sourcepath is not None:
         info("Fetching sources from %s..." % sourcepath)
 
-    skip_stage0 = os.environ.pop('EASYBUILD_BOOTSTRAP_SKIP_STAGE0', False)
-
     # create temporary dir for temporary installations
     tmpdir = tempfile.mkdtemp()
     debug("Going to use %s as temporary directory" % tmpdir)
@@ -478,7 +479,7 @@ def main():
     # install EasyBuild in stages
 
     # STAGE 0: install distribute, which delivers easy_install
-    if skip_stage0:
+    if EASYBUILD_BOOTSTRAP_SKIP_STAGE0:
         distribute_egg_dir = None
         info("Skipping stage0, using local distribute/setuptools providing easy_install")
     else:

From 3953477887711c328b3da486972a6a24ea5a0e53 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Jul 2015 16:55:37 +0200
Subject: [PATCH 1176/1356] include #1325

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 971789fb20..f50580033a 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -15,7 +15,7 @@ feature + bugfix release
 - various other enhancements, including:
     - use https for PyPI URL templates (#1286)
     - add GNU toolchain definition (#1287)
-    - make bootstrap script more robust:
+    - make bootstrap script more robust (#1289, #1325):
         - exclude 'easyblocks' pkg from sys.path to avoid that setup.py for easybuild-easyblocks picks up wrong version
         - undefine $EASYBUILD_BOOTSTRAP* environment variables, since they do not correspond with known config options
     - improve error reporting/robustness in fix_broken_easyconfigs.py script (#1290)

From 05f76e501aaeb703bb7ce5b3f4017710d7a4536b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 14 Jul 2015 20:16:57 +0200
Subject: [PATCH 1177/1356] bump release date

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index f50580033a..f06a6b004c 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,7 +3,7 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-v2.2.0 (July 14th 2015)
+v2.2.0 (July 15th 2015)
 -----------------------
 
 feature + bugfix release

From 6d7f123f768fcb85f35172230fbdb12b3fb4600b Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 15 Jul 2015 15:36:26 +0200
Subject: [PATCH 1178/1356] fix remarks

---
 test/framework/easyconfig.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index f48d78f05c..a615b44fe2 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1269,9 +1269,11 @@ def test_dump_template(self):
 
     def test_to_template_str(self):
         """ Test for to_template_str method """
+
+        # reverse dict of known template constants; template values (which are keys here) must be 'string-in-string
         templ_const = {
-            quote_py_str('template'):'TEMPLATE_VALUE',
-            quote_py_str('%(name)s-%(version)s'): 'NAME_VERSION',
+            "'template'":'TEMPLATE_VALUE',
+            "'%(name)s-%(version)s'": 'NAME_VERSION',
         }
 
         templ_val = {
@@ -1283,8 +1285,10 @@ def test_to_template_str(self):
         self.assertEqual(to_template_str("template", templ_const, templ_val), 'TEMPLATE_VALUE')
         self.assertEqual(to_template_str("foo/bar/0.0.1/", templ_const, templ_val), "'%(name)s/bar/%(version)s/'")
         self.assertEqual(to_template_str("foo-0.0.1", templ_const, templ_val), 'NAME_VERSION')
-        self.assertEqual(to_template_str(['-test', 'dontreplacenamehere'], templ_const, templ_val), "['%(special_char)s', 'dontreplacenamehere']")
-        self.assertEqual(to_template_str({'a':'foo', 'b':'notemplate'}, templ_const, templ_val), "{'a': '%(name)s', 'b': 'notemplate'}")
+        templ_list = to_template_str(['-test', 'dontreplacenamehere'], templ_const, templ_val)
+        self.assertEqual(templ_list, "['%(special_char)s', 'dontreplacenamehere']")
+        templ_dict = to_template_str({'a':'foo', 'b':'notemplate'}, templ_const, templ_val)
+        self.assertEqual(templ_dict, "{'a': '%(name)s', 'b': 'notemplate'}")
         self.assertEqual(to_template_str(('foo', '0.0.1'), templ_const, templ_val), "('%(name)s', '%(version)s')")
 
 

From 74c3216ef892ad3886d96d543249942a745a76de Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Jul 2015 15:45:13 +0200
Subject: [PATCH 1179/1356] bump version to 2.3.0dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 042c1f7796..5117cffb7d 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.2.0')
+VERSION = LooseVersion('2.3.0dev')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From cb4bd0f032675a066263f702c3803e3afcad968e Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 15 Jul 2015 16:40:31 +0200
Subject: [PATCH 1180/1356] table of contents as list

---
 easybuild/tools/docs.py | 10 ++++++----
 test/framework/docs.py  | 15 ++++++---------
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 078488bd72..6e28ab18f8 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -179,13 +179,15 @@ def gen_easyblocks_overview_rst(package_name, path_to_examples, common_params={}
         title,
         '=' * len(title),
         '',
-        '.. contents::',
-        '    :depth: 1',
-        '    :local:',
-        '    :backlinks: top',
+        '*(this page was generated automatically using* ``easybuild.tools.docs.gen_easyblocks_overview_rst()`` *)*',
         '',
     ]
 
+    contents = [":ref:`" + b.__name__ + "`" for b in sorted(all_blocks, key=lambda b: b.__name__)]
+    toc = ' - '.join(contents)
+    heading.append(toc)
+    heading.append('')
+
     return heading + docs
 
 
diff --git a/test/framework/docs.py b/test/framework/docs.py
index 26eb9f07a2..50c8e1c3bb 100644
--- a/test/framework/docs.py
+++ b/test/framework/docs.py
@@ -94,6 +94,7 @@ def test_gen_easyblocks(self):
         ])
 
         self.assertTrue(check_configuremake in ebdoc)
+        names = []
 
         for mod in modules:
             for name, obj in inspect.getmembers(mod, inspect.isclass):
@@ -101,17 +102,13 @@ def test_gen_easyblocks(self):
                 # skip imported classes that are not easyblocks
                 if eb_class.__module__.startswith(module):
                     self.assertTrue(name in ebdoc)
+                    names.append(name)
 
-        patterns = [
-            r'..contents::',
-            r'    :depth: 1',
-            r'    :local:',
-            r'    :backlinks: top'
-        ]
+        toc = [":ref:`" + n + "`" for n in sorted(names)]
+        pattern = " - ".join(toc)
 
-        for pattern in patterns:
-            regex = re.compile(pattern)
-            self.assertTrue(re.search(regex, ebdoc), "Pattern %s found in %s" % (regex.pattern, ebdoc))
+        regex = re.compile(pattern)
+        self.assertTrue(re.search(regex, ebdoc), "Pattern %s found in %s" % (regex.pattern, ebdoc))
 
 
 def suite():

From 3c394ae9bc9aad447c4e1240b5e03fc4f28f7572 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 15 Jul 2015 16:58:43 +0200
Subject: [PATCH 1181/1356] remark above title

---
 easybuild/tools/docs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 6e28ab18f8..17a43636b5 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -175,12 +175,12 @@ def gen_easyblocks_overview_rst(package_name, path_to_examples, common_params={}
     title = 'Overview of generic easyblocks'
 
     heading = [
+        '*(this page was generated automatically using* ``easybuild.tools.docs.gen_easyblocks_overview_rst()`` *)*',
+        '',
         '=' * len(title),
         title,
         '=' * len(title),
         '',
-        '*(this page was generated automatically using* ``easybuild.tools.docs.gen_easyblocks_overview_rst()`` *)*',
-        '',
     ]
 
     contents = [":ref:`" + b.__name__ + "`" for b in sorted(all_blocks, key=lambda b: b.__name__)]

From 3b7554e833c5e1417e44bb9c69f62134b1ebca24 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Jul 2015 18:38:53 +0200
Subject: [PATCH 1182/1356] include link to packaging support docs in EB v2.2.0
 release notes

---
 RELEASE_NOTES | 1 +
 1 file changed, 1 insertion(+)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index f06a6b004c..4103cb3c8d 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -12,6 +12,7 @@ feature + bugfix release
 - add support for --include-* configuration options to include additional easyblocks, toolchains, etc. (#1301)
     - see http://easybuild.readthedocs.org/en/latest/Including_additional_Python_modules.html
 - add (experimental) support for packaging installed software using FPM (#1224)
+    - see http://easybuild.readthedocs.org/en/latest/Packaging_support.html
 - various other enhancements, including:
     - use https for PyPI URL templates (#1286)
     - add GNU toolchain definition (#1287)

From 8b83451a27fdac3035a4d9c537e1ba62444e0940 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Jul 2015 18:38:53 +0200
Subject: [PATCH 1183/1356] include link to packaging support docs in EB v2.2.0
 release notes

---
 RELEASE_NOTES | 1 +
 1 file changed, 1 insertion(+)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index f06a6b004c..4103cb3c8d 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -12,6 +12,7 @@ feature + bugfix release
 - add support for --include-* configuration options to include additional easyblocks, toolchains, etc. (#1301)
     - see http://easybuild.readthedocs.org/en/latest/Including_additional_Python_modules.html
 - add (experimental) support for packaging installed software using FPM (#1224)
+    - see http://easybuild.readthedocs.org/en/latest/Packaging_support.html
 - various other enhancements, including:
     - use https for PyPI URL templates (#1286)
     - add GNU toolchain definition (#1287)

From 74ce11dad3b12d17ab15cd68d93e945980397823 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 16 Jul 2015 09:11:27 +0200
Subject: [PATCH 1184/1356] bump version to 2.2.1dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 042c1f7796..f486e317f2 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.2.0')
+VERSION = LooseVersion('2.2.1dev')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From 84dde4553591a32773e1f631da13449cdc3eae45 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 17 Jul 2015 14:09:54 +0200
Subject: [PATCH 1185/1356] take comments into account in dump() method

---
 easybuild/framework/easyconfig/easyconfig.py | 27 +++++++++---
 easybuild/framework/easyconfig/parser.py     | 45 ++++++++++++++++++++
 test/framework/easyconfig.py                 | 45 ++++++++++++++++++++
 3 files changed, 111 insertions(+), 6 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 7c21b4a5dc..4738df0ad2 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -46,7 +46,7 @@
 import easybuild.tools.environment as env
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_module_naming_scheme
-from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file
+from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file, write_file
 from easybuild.tools.module_naming_scheme import DEVEL_MODULE_SUFFIX
 from easybuild.tools.module_naming_scheme.utilities import avail_module_naming_schemes, det_full_ec_version
 from easybuild.tools.module_naming_scheme.utilities import det_hidden_modname, is_valid_module_name
@@ -246,6 +246,8 @@ def parse(self):
         local_vars = parser.get_config_dict()
         self.log.debug("Parsed easyconfig as a dictionary: %s" % local_vars)
 
+        self.comments = parser.get_comments()
+
         # make sure all mandatory parameters are defined
         # this includes both generic mandatory parameters and software-specific parameters defined via extra_options
         missing_mandatory_keys = [key for key in self.mandatory if key not in local_vars]
@@ -475,7 +477,6 @@ def dump(self, fp):
         """
         Dump this easyconfig to file, with the given filename.
         """
-        eb_file = file(fp, 'w')
 
         # ordered groups of keys to obtain a nice looking easyconfig file
         grouped_keys = [
@@ -537,29 +538,43 @@ def include_defined_parameters(keyset):
                         else:
                             val = newval
 
-                        ebtxt.append("%s = %s" % (key, val))
+                        add_key_and_comments(key, val)
+
                         printed_keys.append(key)
                         printed = True
                 if printed:
                     ebtxt.append('')
 
+        def add_key_and_comments(key, val):
+            """ Adds key, value pair and comments (if there are any) to the dump file """
+            if key in self.comments['inline']:
+                ebtxt.append("%s = %s  %s" % (key, val, self.comments['inline'][key]))
+            else:
+                if key in self.comments['above']:
+                    ebtxt.extend(self.comments['above'][key])
+
+                ebtxt.append("%s = %s" % (key, val))
+
         # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
         printed_keys = []
+
+        # add header comments
+        ebtxt.extend(self.comments['header'])
+
         include_defined_parameters(grouped_keys)
 
         # print other easyconfig parameters at the end
         keys_to_ignore = printed_keys + last_keys
         for key in default_values:
             if key not in keys_to_ignore and self[key] != default_values[key]:
-                ebtxt.append("%s = %s" % (key, quote_py_str(self[key])))
+                add_key_and_comments(key, quote_py_str(self[key]))
         ebtxt.append('')
 
         # print last two parameters
         include_defined_parameters([[k] for k in last_keys])
 
-        eb_file.write(('\n'.join(ebtxt)).strip()) # strip for newlines at the end
-        eb_file.close()
+        write_file(fp, ('\n'.join(ebtxt)).strip()) # strip for newlines at the end
 
         self.enable_templating = orig_enable_templating
 
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 3937ad1833..c10fd8d03f 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -29,6 +29,7 @@
 
 @author: Stijn De Weirdt (Ghent University)
 """
+import copy
 import os
 import re
 from vsc.utils import fancylogger
@@ -84,6 +85,9 @@ def __init__(self, filename=None, format_version=None, rawcontent=None):
 
         self.rawcontent = None  # the actual unparsed content
 
+        # comments in the easyconfig file
+        self.comments = None
+
         self.get_fn = None  # read method and args
         self.set_fn = None  # write method and args
 
@@ -99,6 +103,8 @@ def __init__(self, filename=None, format_version=None, rawcontent=None):
         else:
             raise EasyBuildError("Neither filename nor rawcontent provided to EasyConfigParser")
 
+        self._extract_comments()
+
     def process(self, filename=None):
         """Create an instance"""
         self._read(filename=filename)
@@ -131,6 +137,41 @@ def _read(self, filename=None):
             msg = 'rawcontent is not basestring: type %s, content %s' % (type(self.rawcontent), self.rawcontent)
             raise EasyBuildError("Unexpected result for raw content: %s", msg)
 
+    def _extract_comments(self):
+        """Extract comments from raw content."""
+        # Keep track of comments and their location (top of easyconfig, key they are intended for, line they are on
+        # discriminate between header comments (top of easyconfig file), single-line comments (at end of line) and other
+
+        self.comments = {
+            'header' : [],
+            'inline' : dict(),
+            'above' : dict(),
+         }
+
+        raw = self.rawcontent.split('\n')
+        header = True
+
+        i = 0
+        while i<len(raw):
+            if raw[i].startswith('#') and header:
+                self.comments['header'].append(raw[i])
+            else:
+                header = False
+                if raw[i].startswith('#'):
+                    comment = []
+                    # comment could be multi-line
+                    while raw[i].startswith('#') or not raw[i]:
+                        comment.append(raw[i])
+                        i += 1
+                    key = raw[i].partition('=')[0].strip()
+                    self.comments['above'][key] = comment
+
+                elif '#' in raw[i]:  # inline comment
+                    comment = '# ' + raw[i].partition('#')[2].strip()
+                    key = raw[i].partition('=')[0].strip()
+                    self.comments['inline'][key] = comment
+            i += 1
+
     def _det_format_version(self):
         """Extract the format version from the raw content"""
         if self.format_version is None:
@@ -184,3 +225,7 @@ def get_config_dict(self, validate=True):
         if validate:
             self._formatter.validate()
         return self._formatter.get_config_dict()
+
+    def get_comments(self):
+        """Return comments, and their location info"""
+        return copy.deepcopy(self.comments)
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index b5f2bbc442..ff4f0857aa 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1272,6 +1272,51 @@ def test_dump_template(self):
         # reparsing the dumped easyconfig file should work
         ecbis = EasyConfig(testec)
 
+    def test_dump_comments(self):
+        """ Test dump() method for files containing comments """
+        rawtxt = '\n'.join([
+            "# #",
+            "# some header comment",
+            "# #",
+            "easyblock = 'EB_foo'",
+            '',
+            "name = 'Foo'  # name comment",
+            "version = '0.0.1'",
+            "versionsuffix = '-test'",
+            '',
+            "# comment on the homepage",
+            "homepage = 'http://foo.com/'",
+            'description = "foo description"',
+            '',
+            "# toolchain comment with newline",
+            '',
+            "toolchain = {'version': 'dummy', 'name': 'dummy'}",
+            '',
+            "sanity_check_paths = {'files': ['files/foo/foobar'], 'dirs':[] }",
+            '',
+            "foo_extra1 = 'foobar'",
+        ])
+
+        handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')
+        os.close(handle)
+
+        ec = EasyConfig(None, rawtxt=rawtxt)
+        ec.dump(testec)
+        ectxt = read_file(testec)
+
+        patterns = [
+            r"# #\n# some header comment\n# #",
+            r"name = 'Foo'  # name comment",
+            r"# comment on the homepage\nhomepage = 'http://foo.com/'",
+            r"# toolchain comment with newline\n\ntoolchain = {'version': 'dummy', 'name': 'dummy'}"
+        ]
+
+        for pattern in patterns:
+            regex = re.compile(pattern, re.M)
+            self.assertTrue(regex.search(ectxt), "Pattern '%s' found in: %s" % (regex.pattern, ectxt))
+
+        # reparsing the dumped easyconfig file should work
+        ecbis = EasyConfig(testec)
 
 def suite():
     """ returns all the testcases in this module """

From ad8a9e7fd00092028dbcea7981ff832ee006f190 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 17 Jul 2015 14:50:39 +0200
Subject: [PATCH 1186/1356] hashes in values that are not comments

---
 easybuild/framework/easyconfig/parser.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index c10fd8d03f..f62bfdc490 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -163,13 +163,16 @@ def _extract_comments(self):
                     while raw[i].startswith('#') or not raw[i]:
                         comment.append(raw[i])
                         i += 1
-                    key = raw[i].partition('=')[0].strip()
+                    key = raw[i].split('=', 1)[0].strip()
                     self.comments['above'][key] = comment
 
                 elif '#' in raw[i]:  # inline comment
-                    comment = '# ' + raw[i].partition('#')[2].strip()
-                    key = raw[i].partition('=')[0].strip()
-                    self.comments['inline'][key] = comment
+                    comment = raw[i].rsplit('#', 1)[1].strip()
+                    key = raw[i].split('=', 1)[0].strip()
+
+                    # check if hash actually indicated a comment; or is part of the value
+                    if comment.replace("'", "").replace('"', '') not in self.get_config_dict()[key]:
+                        self.comments['inline'][key] = '# ' + comment
             i += 1
 
     def _det_format_version(self):

From 718c8efdd562447f6ebe32de0706a2664c6dc55c Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 17 Jul 2015 14:54:55 +0200
Subject: [PATCH 1187/1356] complete documentation

---
 easybuild/framework/easyconfig/parser.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index f62bfdc490..ceb7e0648b 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -141,6 +141,7 @@ def _extract_comments(self):
         """Extract comments from raw content."""
         # Keep track of comments and their location (top of easyconfig, key they are intended for, line they are on
         # discriminate between header comments (top of easyconfig file), single-line comments (at end of line) and other
+        # At the moment there is no support for inline comments on lines that don't contain the key value
 
         self.comments = {
             'header' : [],

From 2e8b55bf0dd73cad23f8b96f3c81afe360fa87b5 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 17 Jul 2015 15:05:32 +0200
Subject: [PATCH 1188/1356] fix merge

---
 test/framework/easyconfig.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 4de25bb037..38b11ca9b8 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1343,7 +1343,6 @@ def test_to_template_str(self):
         self.assertEqual(templ_dict, "{'a': '%(name)s', 'b': 'notemplate'}")
         self.assertEqual(to_template_str(('foo', '0.0.1'), templ_const, templ_val), "('%(name)s', '%(version)s')")
 
->>>>>>> develop
 
 def suite():
     """ returns all the testcases in this module """

From 4f7750d463471c5b35ba4efb36c2fb023f811528 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 17 Jul 2015 15:20:41 +0200
Subject: [PATCH 1189/1356] fix keyerror

---
 easybuild/framework/easyconfig/parser.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index ceb7e0648b..e7a40075c4 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -172,8 +172,9 @@ def _extract_comments(self):
                     key = raw[i].split('=', 1)[0].strip()
 
                     # check if hash actually indicated a comment; or is part of the value
-                    if comment.replace("'", "").replace('"', '') not in self.get_config_dict()[key]:
-                        self.comments['inline'][key] = '# ' + comment
+                    if key in self.get_config_dict():
+                        if comment.replace("'", "").replace('"', '') not in self.get_config_dict()[key]:
+                            self.comments['inline'][key] = '# ' + comment
             i += 1
 
     def _det_format_version(self):

From e7d810f5ef2cceb7678b487270d2c267ec443f62 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Fri, 17 Jul 2015 15:43:47 +0200
Subject: [PATCH 1190/1356] precompute len(raw)

---
 easybuild/framework/easyconfig/parser.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index e7a40075c4..767ceb950a 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -153,7 +153,8 @@ def _extract_comments(self):
         header = True
 
         i = 0
-        while i<len(raw):
+        num_lines = len(raw)
+        while i<num_lines:
             if raw[i].startswith('#') and header:
                 self.comments['header'].append(raw[i])
             else:

From 97743508ce8f5cc83b2a61f17604921fb3ee4c0e Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 27 Jul 2015 11:36:44 +0200
Subject: [PATCH 1191/1356] small bugfix

---
 easybuild/framework/easyconfig/parser.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 767ceb950a..ee83230dbf 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -174,7 +174,7 @@ def _extract_comments(self):
 
                     # check if hash actually indicated a comment; or is part of the value
                     if key in self.get_config_dict():
-                        if comment.replace("'", "").replace('"', '') not in self.get_config_dict()[key]:
+                        if comment.replace("'", "").replace('"', '') not in str(self.get_config_dict()[key]):
                             self.comments['inline'][key] = '# ' + comment
             i += 1
 

From bd575d4f0121ba875e015b71f5b1cca1de18fc75 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Mon, 27 Jul 2015 16:58:26 +0200
Subject: [PATCH 1192/1356] begin dump formatting

---
 easybuild/framework/easyconfig/easyconfig.py | 26 ++++++++++++-
 easybuild/framework/easyconfig/parser.py     | 24 +++++++++++-
 out.eb                                       | 35 +++++++++++++++++
 test.eb                                      | 41 ++++++++++++++++++++
 4 files changed, 122 insertions(+), 4 deletions(-)
 create mode 100644 out.eb
 create mode 100644 test.eb

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 4fce3b3330..8526d2cf58 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -35,6 +35,7 @@
 @author: Ward Poelmans (Ghent University)
 """
 
+import ast
 import copy
 import difflib
 import os
@@ -477,7 +478,6 @@ def dump(self, fp):
         """
         Dump this easyconfig to file, with the given filename.
         """
-
         # ordered groups of keys to obtain a nice looking easyconfig file
         grouped_keys = [
             ['easyblock'],
@@ -547,14 +547,36 @@ def include_defined_parameters(keyset):
 
         def add_key_and_comments(key, val):
             """ Adds key, value pair and comments (if there are any) to the dump file """
+            val = insert_indents(str(val), True)
             if key in self.comments['inline']:
-                ebtxt.append("%s = %s  %s" % (key, val, self.comments['inline'][key]))
+                ebtxt.append("%s = %s%s" % (key, val, self.comments['inline'][key]))
             else:
                 if key in self.comments['above']:
                     ebtxt.extend(self.comments['above'][key])
 
                 ebtxt.append("%s = %s" % (key, val))
 
+        def insert_indents(val, outer):
+            if val.startswith('(') or val.startswith('{') or val.startswith('['):
+                if outer:
+                    val = ast.literal_eval(val)
+                    if len(val) > 1:
+                        if isinstance(val, list):
+                            val = '[\n' + ',\n'.join([insert_indents(str(v), False) for v in val]) + '\n]'
+                        elif isinstance(val, tuple):
+                            val = '(\n' + ',\n'.join([insert_indents(str(v), False) for v in val]) + '\n)'
+                        elif isinstance(val, dict):
+                            val = '{\n' + ',\n'.join(["%s: %s" % (quote_py_str(k), insert_indents(str(v), False))
+                            for k, v in val.items()]) + '\n'
+                # else:
+                    # if self.comments['list_value'].get(key):
+                      #  val = val + self.comments['list_value'][key].get(val, '')
+            else:
+                if not outer:
+                    val = quote_py_str(val)
+
+            return val
+
         # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
         printed_keys = []
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index ee83230dbf..c493c2b529 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -29,6 +29,8 @@
 
 @author: Stijn De Weirdt (Ghent University)
 """
+
+import ast
 import copy
 import os
 import re
@@ -147,6 +149,7 @@ def _extract_comments(self):
             'header' : [],
             'inline' : dict(),
             'above' : dict(),
+       #     'list_value' : dict(),
          }
 
         raw = self.rawcontent.split('\n')
@@ -170,12 +173,29 @@ def _extract_comments(self):
 
                 elif '#' in raw[i]:  # inline comment
                     comment = raw[i].rsplit('#', 1)[1].strip()
-                    key = raw[i].split('=', 1)[0].strip()
+                    key = None
+                    comment_value = None
+                    if '=' in raw[i]:
+                        key = raw[i].split('=', 1)[0].strip()
+                    # else:
+                        # search for key and index of comment in config dict
+                      #   for k, v in self.get_config_dict().items():
+                        #     val = re.sub(r',$', r'', raw[i].rsplit('#', 1)[0].strip())
+                          #   if not isinstance(v, basestring) and val in str(v):
+                            #     key = k
+                              #   comment_value = val
+                                # if not self.comments['list_value'].get(key):
+                                  #   self.comments['list_value'][key] = dict()
 
                     # check if hash actually indicated a comment; or is part of the value
                     if key in self.get_config_dict():
                         if comment.replace("'", "").replace('"', '') not in str(self.get_config_dict()[key]):
-                            self.comments['inline'][key] = '# ' + comment
+                      #      if comment_value:
+                      #          self.comments['list_value'][key][comment_value] = '  # ' + comment
+                      #      else:
+                                self.comments['inline'][key] = '  # ' + comment
+
+
             i += 1
 
     def _det_format_version(self):
diff --git a/out.eb b/out.eb
new file mode 100644
index 0000000000..170d6b6233
--- /dev/null
+++ b/out.eb
@@ -0,0 +1,35 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+easyblock = 'ConfigureMake'
+
+name = 'AMOS'
+version = '3.1.0'
+
+homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS'
+description = "The AMOS consortium is committed to the development of open-source whole genome assembly software"
+
+toolchain = {'version': '1.4.10', 'name': 'goolf'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [('http://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s', 'download')]
+
+patches = ['%(name)s-%(version_major_minor)s.0_GCC-4.7.patch']
+
+dependencies = [('expat', '2.1.0'), ('MUMmer', '3.23')]
+
+parallel = 1  # make crashes otherwise
+
+
+sanity_check_paths = {'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], 'dirs': []}
+
+moduleclass = 'bio'
\ No newline at end of file
diff --git a/test.eb b/test.eb
new file mode 100644
index 0000000000..67f7c8c305
--- /dev/null
+++ b/test.eb
@@ -0,0 +1,41 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'AMOS'
+version = '3.1.0'
+
+homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS'
+description = """The AMOS consortium is committed to the development of open-source whole genome assembly software"""
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')]
+
+patches = ['AMOS-3.1.0_GCC-4.7.patch']
+
+dependencies = [
+                ('expat', '2.1.0'),
+                ('MUMmer', '3.23'),
+               ]
+
+sanity_check_paths = {
+                      'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed' ],
+                      'dirs': []
+                     }
+
+parallel = 1  # make crashes otherwise
+
+moduleclass = 'bio'

From 6be0295639df1dca85b04e1653a13914a6e5a018 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 28 Jul 2015 10:33:19 +0200
Subject: [PATCH 1193/1356] dump formatting and inline comments

---
 easybuild/framework/easyconfig/easyconfig.py |  132 +-
 easybuild/framework/easyconfig/parser.py     |   24 +-
 easybuild/tools/autopep8.py                  | 3648 ++++++++++++++++++
 out.eb                                       |   35 -
 test.eb                                      |   41 -
 test/framework/easyconfig.py                 |   50 +-
 6 files changed, 3760 insertions(+), 170 deletions(-)
 create mode 100644 easybuild/tools/autopep8.py
 delete mode 100644 out.eb
 delete mode 100644 test.eb

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 8526d2cf58..f6b8ca6dbe 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -35,7 +35,6 @@
 @author: Ward Poelmans (Ghent University)
 """
 
-import ast
 import copy
 import difflib
 import os
@@ -45,6 +44,7 @@
 from vsc.utils.patterns import Singleton
 
 import easybuild.tools.environment as env
+from easybuild.tools.autopep8 import fix_code
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_module_naming_scheme
 from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file, write_file
@@ -521,22 +521,10 @@ def include_defined_parameters(keyset):
                     if val != default_values[key]:
                         # dependency easyconfig parameters were parsed, so these need special care to 'unparse' them
                         if key in ['builddependencies', 'dependencies', 'hiddendependencies']:
-                            dumped_deps = [self._dump_dependency(d, templ_const, templ_val) for d in val]
-                            newval = '[' + ', '.join(dumped_deps) + ']'
-
-                        elif key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
-                            self.log.debug("Original value before replacing matching template values: %s", val)
-                            newval = to_template_str(val, templ_const, templ_val)
-                            self.log.debug("New value after replacing matching template values: %s", newval)
-
+                            dumped_deps = [self._dump_dependency(d) for d in val]
+                            val = dumped_deps
                         else:
-                            newval = quote_py_str(val)
-
-                        # avoid that templated value refers to parameter that it defines
-                        if r'%(' + key in newval:
                             val = quote_py_str(val)
-                        else:
-                            val = newval
 
                         add_key_and_comments(key, val)
 
@@ -546,8 +534,8 @@ def include_defined_parameters(keyset):
                     ebtxt.append('')
 
         def add_key_and_comments(key, val):
-            """ Adds key, value pair and comments (if there are any) to the dump file """
-            val = insert_indents(str(val), True)
+            """ Add key, value pair and comments (if there are any) to the dump file """
+            val = format_and_template(key, val, True)
             if key in self.comments['inline']:
                 ebtxt.append("%s = %s%s" % (key, val, self.comments['inline'][key]))
             else:
@@ -556,26 +544,47 @@ def add_key_and_comments(key, val):
 
                 ebtxt.append("%s = %s" % (key, val))
 
-        def insert_indents(val, outer):
-            if val.startswith('(') or val.startswith('{') or val.startswith('['):
-                if outer:
-                    val = ast.literal_eval(val)
-                    if len(val) > 1:
-                        if isinstance(val, list):
-                            val = '[\n' + ',\n'.join([insert_indents(str(v), False) for v in val]) + '\n]'
-                        elif isinstance(val, tuple):
-                            val = '(\n' + ',\n'.join([insert_indents(str(v), False) for v in val]) + '\n)'
-                        elif isinstance(val, dict):
-                            val = '{\n' + ',\n'.join(["%s: %s" % (quote_py_str(k), insert_indents(str(v), False))
-                            for k, v in val.items()]) + '\n'
-                # else:
-                    # if self.comments['list_value'].get(key):
-                      #  val = val + self.comments['list_value'][key].get(val, '')
+        def format_and_template(key, value, outer, comment = dict()):
+            """ Returns string version of the value, including comments and newlines in lists, tuples and dicts """
+            str_value = ''
+
+            for k, v in self.comments['list_value'].get(key, {}).items():
+                if str(value) in k:
+                    comment[str(value)] = v
+
+            if outer:
+                if isinstance(value, list):
+                    str_value += '[\n'
+                    for el in value:
+                        str_value += format_and_template(key, el, False, comment) + ',' + comment.get(str(el), '') + '\n'
+                    str_value += ']'
+                elif isinstance(value, tuple):
+                    str_value += '(\n'
+                    for el in value:
+                        str_value += format_and_template(key, el, False, comment) + ',' + comment.get(str(el), '') + '\n'
+                    str_value += ')'
+                elif isinstance(value, dict):
+                    str_value += '{\n'
+                    for k, v in value.items():
+                        str_value += quote_py_str(k) + ': ' + format_and_template(key, v, False, comment) + ',' + comment.get(str(v), '') + '\n'
+                    str_value += '}'
+
+                value = str_value or value
+
             else:
-                if not outer:
-                    val = quote_py_str(val)
+                # dependencies are already dumped as strings, so they do not need to be quoted again
+                if isinstance(value, basestring) and key not in ['builddependencies', 'dependencies', 'hiddendependencies']:
+                    value = quote_py_str(value)
+                else:
+                    value = str(value)
+
+            # templates
+            if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
+                new_value = to_template_str(value, templ_const, templ_val)
+                if not r'%(' + key in new_value:
+                    value = new_value
 
-            return val
+            return value
 
         # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
@@ -596,8 +605,8 @@ def insert_indents(val, outer):
         # print last two parameters
         include_defined_parameters([[k] for k in last_keys])
 
-        write_file(fp, ('\n'.join(ebtxt)).strip()) # strip for newlines at the end
-
+        dumped_text = ('\n'.join(ebtxt))
+        write_file(fp, (fix_code(dumped_text, options={'aggressive': 1, 'max_line_length':120})).strip())
         self.enable_templating = orig_enable_templating
 
     def _validate(self, attr, values):  # private method
@@ -734,12 +743,11 @@ def _parse_dependency(self, dep, hidden=False):
 
         return dependency
 
-    def _dump_dependency(self, dep, templ_const, templ_val):
+    def _dump_dependency(self, dep):
         """Dump parsed dependency in tuple format"""
 
         if dep['external_module']:
-            res = "(%s, EXTERNAL_MODULE)" % quote_py_str(dep['full_mod_name'])
-
+            res = "('" + dep['full_mod_name']+ "', EXTERNAL_MODULE)"
         else:
             # mininal spec: (name, version)
             tup = (dep['name'], dep['version'])
@@ -752,8 +760,7 @@ def _dump_dependency(self, dep, templ_const, templ_val):
             elif dep['versionsuffix']:
                 tup += (dep['versionsuffix'],)
 
-            res = to_template_str(tup, templ_const, templ_val)
-
+            res = str(tup)
         return res
 
     def generate_template_values(self):
@@ -1021,39 +1028,26 @@ def quote_py_str(val):
 
 def to_template_str(value, templ_const, templ_val):
     """
-    Create string representation of provided value, using template values where possible.
-        - value can be a string, list, tuple, dict or combination thereof
+    Insert template values where possible
+        - value is a string
         - templ_const is a dictionary of template strings (constants)
         - templ_val is an ordered dictionary of template strings specific for this easyconfig file
     """
-    if isinstance(value, basestring):
-        # wrap string into quotes, except if it matches a template constant
-        if value not in templ_const.values():
-            value = quote_py_str(value)
-
+    if value not in templ_const.values():
         old_value = None
         while value != old_value:
             old_value = value
-            if value in templ_const:
-                value = templ_const[value]
-            else:
-                # check for template values (note: templ_val dict is 'upside-down')
-                for tval, tname in templ_val.items():
-                    # only replace full words with templates: word to replace should be at the beginning of a line
-                    # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
-                    # by another non-alphanumeric.
-                    value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1%(' + tname + r')s\2', value)
-    else:
-        if isinstance(value, list):
-            value = '[' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ']'
-        elif isinstance(value, tuple):
-            value = '(' + ', '.join([to_template_str(v, templ_const, templ_val) for v in value]) + ')'
-        elif isinstance(value, dict):
-            value = '{' + ', '.join(["%s: %s" % (quote_py_str(k), to_template_str(v, templ_const, templ_val))
-            for k, v in value.items()]) + '}'
-        else:
-            value = str(value)
-
+            # check for constant values
+            for const in templ_const:
+                if const in value:
+                    value = value.replace(const, templ_const[const])
+
+            # check for template values (note: templ_val dict is 'upside-down')
+            for tval, tname in templ_val.items():
+                # only replace full words with templates: word to replace should be at the beginning of a line
+                # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
+                # by another non-alphanumeric.
+                value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1%(' + tname + r')s\2', value)
     return value
 
 
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index c493c2b529..e88684ea35 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -149,7 +149,7 @@ def _extract_comments(self):
             'header' : [],
             'inline' : dict(),
             'above' : dict(),
-       #     'list_value' : dict(),
+            'list_value' : dict(),
          }
 
         raw = self.rawcontent.split('\n')
@@ -177,22 +177,22 @@ def _extract_comments(self):
                     comment_value = None
                     if '=' in raw[i]:
                         key = raw[i].split('=', 1)[0].strip()
-                    # else:
+                    else:
                         # search for key and index of comment in config dict
-                      #   for k, v in self.get_config_dict().items():
-                        #     val = re.sub(r',$', r'', raw[i].rsplit('#', 1)[0].strip())
-                          #   if not isinstance(v, basestring) and val in str(v):
-                            #     key = k
-                              #   comment_value = val
-                                # if not self.comments['list_value'].get(key):
-                                  #   self.comments['list_value'][key] = dict()
+                        for k, v in self.get_config_dict().items():
+                            val = re.sub(r',$', r'', raw[i].rsplit('#', 1)[0].strip())
+                            if not isinstance(v, basestring) and val in str(v):
+                                key = k
+                                comment_value = val
+                                if not self.comments['list_value'].get(key):
+                                    self.comments['list_value'][key] = dict()
 
                     # check if hash actually indicated a comment; or is part of the value
                     if key in self.get_config_dict():
                         if comment.replace("'", "").replace('"', '') not in str(self.get_config_dict()[key]):
-                      #      if comment_value:
-                      #          self.comments['list_value'][key][comment_value] = '  # ' + comment
-                      #      else:
+                            if comment_value:
+                                self.comments['list_value'][key][comment_value] = '  # ' + comment
+                            else:
                                 self.comments['inline'][key] = '  # ' + comment
 
 
diff --git a/easybuild/tools/autopep8.py b/easybuild/tools/autopep8.py
new file mode 100644
index 0000000000..c5b57ee9eb
--- /dev/null
+++ b/easybuild/tools/autopep8.py
@@ -0,0 +1,3648 @@
+# Copyright (C) 2010-2011 Hideo Hattori
+# Copyright (C) 2011-2013 Hideo Hattori, Steven Myint
+# Copyright (C) 2013-2015 Hideo Hattori, Steven Myint, Bill Wendling
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+"""Automatically formats Python code to conform to the PEP 8 style guide.
+
+Fixes that only need be done once can be added by adding a function of the form
+"fix_<code>(source)" to this module. They should return the fixed source code.
+These fixes are picked up by apply_global_fixes().
+
+Fixes that depend on pep8 should be added as methods to FixPEP8. See the class
+documentation for more information.
+
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+import codecs
+import collections
+import copy
+import difflib
+import fnmatch
+import inspect
+import io
+import keyword
+import locale
+import os
+import re
+import signal
+import sys
+import textwrap
+import token
+import tokenize
+
+import pep8
+
+
+try:
+    unicode
+except NameError:
+    unicode = str
+
+
+__version__ = '1.2.1a0'
+
+
+CR = '\r'
+LF = '\n'
+CRLF = '\r\n'
+
+
+PYTHON_SHEBANG_REGEX = re.compile(r'^#!.*\bpython[23]?\b\s*$')
+
+
+# For generating line shortening candidates.
+SHORTEN_OPERATOR_GROUPS = frozenset([
+    frozenset([',']),
+    frozenset(['%']),
+    frozenset([',', '(', '[', '{']),
+    frozenset(['%', '(', '[', '{']),
+    frozenset([',', '(', '[', '{', '%', '+', '-', '*', '/', '//']),
+    frozenset(['%', '+', '-', '*', '/', '//']),
+])
+
+
+DEFAULT_IGNORE = 'E24'
+DEFAULT_INDENT_SIZE = 4
+
+
+# W602 is handled separately due to the need to avoid "with_traceback".
+CODE_TO_2TO3 = {
+    'E231': ['ws_comma'],
+    'E721': ['idioms'],
+    'W601': ['has_key'],
+    'W603': ['ne'],
+    'W604': ['repr'],
+    'W690': ['apply',
+             'except',
+             'exitfunc',
+             'numliterals',
+             'operator',
+             'paren',
+             'reduce',
+             'renames',
+             'standarderror',
+             'sys_exc',
+             'throw',
+             'tuple_params',
+             'xreadlines']}
+
+
+if sys.platform == 'win32':  # pragma: no cover
+    DEFAULT_CONFIG = os.path.expanduser(r'~\.pep8')
+else:
+    DEFAULT_CONFIG = os.path.join(os.getenv('XDG_CONFIG_HOME') or
+                                  os.path.expanduser('~/.config'), 'pep8')
+PROJECT_CONFIG = ('setup.cfg', 'tox.ini', '.pep8')
+
+
+def open_with_encoding(filename, encoding=None, mode='r'):
+    """Return opened file with a specific encoding."""
+    if not encoding:
+        encoding = detect_encoding(filename)
+
+    return io.open(filename, mode=mode, encoding=encoding,
+                   newline='')  # Preserve line endings
+
+
+def detect_encoding(filename):
+    """Return file encoding."""
+    try:
+        with open(filename, 'rb') as input_file:
+            from lib2to3.pgen2 import tokenize as lib2to3_tokenize
+            encoding = lib2to3_tokenize.detect_encoding(input_file.readline)[0]
+
+        # Check for correctness of encoding
+        with open_with_encoding(filename, encoding) as test_file:
+            test_file.read()
+
+        return encoding
+    except (LookupError, SyntaxError, UnicodeDecodeError):
+        return 'latin-1'
+
+
+def readlines_from_file(filename):
+    """Return contents of file."""
+    with open_with_encoding(filename) as input_file:
+        return input_file.readlines()
+
+
+def extended_blank_lines(logical_line,
+                         blank_lines,
+                         blank_before,
+                         indent_level,
+                         previous_logical):
+    """Check for missing blank lines after class declaration."""
+    if previous_logical.startswith('class '):
+        if logical_line.startswith(('def ', 'class ', '@')):
+            if indent_level and not blank_lines and not blank_before:
+                yield (0, 'E309 expected 1 blank line after class declaration')
+    elif previous_logical.startswith('def '):
+        if blank_lines and pep8.DOCSTRING_REGEX.match(logical_line):
+            yield (0, 'E303 too many blank lines ({0})'.format(blank_lines))
+    elif pep8.DOCSTRING_REGEX.match(previous_logical):
+        # Missing blank line between class docstring and method declaration.
+        if (
+            indent_level and
+            not blank_lines and
+            not blank_before and
+            logical_line.startswith(('def ')) and
+            '(self' in logical_line
+        ):
+            yield (0, 'E301 expected 1 blank line, found 0')
+pep8.register_check(extended_blank_lines)
+
+
+def continued_indentation(logical_line, tokens, indent_level, indent_char,
+                          noqa):
+    """Override pep8's function to provide indentation information."""
+    first_row = tokens[0][2][0]
+    nrows = 1 + tokens[-1][2][0] - first_row
+    if noqa or nrows == 1:
+        return
+
+    # indent_next tells us whether the next block is indented. Assuming
+    # that it is indented by 4 spaces, then we should not allow 4-space
+    # indents on the final continuation line. In turn, some other
+    # indents are allowed to have an extra 4 spaces.
+    indent_next = logical_line.endswith(':')
+
+    row = depth = 0
+    valid_hangs = (
+        (DEFAULT_INDENT_SIZE,)
+        if indent_char != '\t' else (DEFAULT_INDENT_SIZE,
+                                     2 * DEFAULT_INDENT_SIZE)
+    )
+
+    # Remember how many brackets were opened on each line.
+    parens = [0] * nrows
+
+    # Relative indents of physical lines.
+    rel_indent = [0] * nrows
+
+    # For each depth, collect a list of opening rows.
+    open_rows = [[0]]
+    # For each depth, memorize the hanging indentation.
+    hangs = [None]
+
+    # Visual indents.
+    indent_chances = {}
+    last_indent = tokens[0][2]
+    indent = [last_indent[1]]
+
+    last_token_multiline = None
+    line = None
+    last_line = ''
+    last_line_begins_with_multiline = False
+    for token_type, text, start, end, line in tokens:
+
+        newline = row < start[0] - first_row
+        if newline:
+            row = start[0] - first_row
+            newline = (not last_token_multiline and
+                       token_type not in (tokenize.NL, tokenize.NEWLINE))
+            last_line_begins_with_multiline = last_token_multiline
+
+        if newline:
+            # This is the beginning of a continuation line.
+            last_indent = start
+
+            # Record the initial indent.
+            rel_indent[row] = pep8.expand_indent(line) - indent_level
+
+            # Identify closing bracket.
+            close_bracket = (token_type == tokenize.OP and text in ']})')
+
+            # Is the indent relative to an opening bracket line?
+            for open_row in reversed(open_rows[depth]):
+                hang = rel_indent[row] - rel_indent[open_row]
+                hanging_indent = hang in valid_hangs
+                if hanging_indent:
+                    break
+            if hangs[depth]:
+                hanging_indent = (hang == hangs[depth])
+
+            visual_indent = (not close_bracket and hang > 0 and
+                             indent_chances.get(start[1]))
+
+            if close_bracket and indent[depth]:
+                # Closing bracket for visual indent.
+                if start[1] != indent[depth]:
+                    yield (start, 'E124 {0}'.format(indent[depth]))
+            elif close_bracket and not hang:
+                pass
+            elif indent[depth] and start[1] < indent[depth]:
+                # Visual indent is broken.
+                yield (start, 'E128 {0}'.format(indent[depth]))
+            elif (hanging_indent or
+                  (indent_next and
+                   rel_indent[row] == 2 * DEFAULT_INDENT_SIZE)):
+                # Hanging indent is verified.
+                if close_bracket:
+                    yield (start, 'E123 {0}'.format(indent_level +
+                                                    rel_indent[open_row]))
+                hangs[depth] = hang
+            elif visual_indent is True:
+                # Visual indent is verified.
+                indent[depth] = start[1]
+            elif visual_indent in (text, unicode):
+                # Ignore token lined up with matching one from a previous line.
+                pass
+            else:
+                one_indented = (indent_level + rel_indent[open_row] +
+                                DEFAULT_INDENT_SIZE)
+                # Indent is broken.
+                if hang <= 0:
+                    error = ('E122', one_indented)
+                elif indent[depth]:
+                    error = ('E127', indent[depth])
+                elif hang > DEFAULT_INDENT_SIZE:
+                    error = ('E126', one_indented)
+                else:
+                    hangs[depth] = hang
+                    error = ('E121', one_indented)
+
+                yield (start, '{0} {1}'.format(*error))
+
+        # Look for visual indenting.
+        if (
+            parens[row] and
+            token_type not in (tokenize.NL, tokenize.COMMENT) and
+            not indent[depth]
+        ):
+            indent[depth] = start[1]
+            indent_chances[start[1]] = True
+        # Deal with implicit string concatenation.
+        elif (token_type in (tokenize.STRING, tokenize.COMMENT) or
+              text in ('u', 'ur', 'b', 'br')):
+            indent_chances[start[1]] = unicode
+        # Special case for the "if" statement because len("if (") is equal to
+        # 4.
+        elif not indent_chances and not row and not depth and text == 'if':
+            indent_chances[end[1] + 1] = True
+        elif text == ':' and line[end[1]:].isspace():
+            open_rows[depth].append(row)
+
+        # Keep track of bracket depth.
+        if token_type == tokenize.OP:
+            if text in '([{':
+                depth += 1
+                indent.append(0)
+                hangs.append(None)
+                if len(open_rows) == depth:
+                    open_rows.append([])
+                open_rows[depth].append(row)
+                parens[row] += 1
+            elif text in ')]}' and depth > 0:
+                # Parent indents should not be more than this one.
+                prev_indent = indent.pop() or last_indent[1]
+                hangs.pop()
+                for d in range(depth):
+                    if indent[d] > prev_indent:
+                        indent[d] = 0
+                for ind in list(indent_chances):
+                    if ind >= prev_indent:
+                        del indent_chances[ind]
+                del open_rows[depth + 1:]
+                depth -= 1
+                if depth:
+                    indent_chances[indent[depth]] = True
+                for idx in range(row, -1, -1):
+                    if parens[idx]:
+                        parens[idx] -= 1
+                        break
+            assert len(indent) == depth + 1
+            if (
+                start[1] not in indent_chances and
+                # This is for purposes of speeding up E121 (GitHub #90).
+                not last_line.rstrip().endswith(',')
+            ):
+                # Allow to line up tokens.
+                indent_chances[start[1]] = text
+
+        last_token_multiline = (start[0] != end[0])
+        if last_token_multiline:
+            rel_indent[end[0] - first_row] = rel_indent[row]
+
+        last_line = line
+
+    if (
+        indent_next and
+        not last_line_begins_with_multiline and
+        pep8.expand_indent(line) == indent_level + DEFAULT_INDENT_SIZE
+    ):
+        pos = (start[0], indent[0] + 4)
+        yield (pos, 'E125 {0}'.format(indent_level +
+                                      2 * DEFAULT_INDENT_SIZE))
+del pep8._checks['logical_line'][pep8.continued_indentation]
+pep8.register_check(continued_indentation)
+
+
+class FixPEP8(object):
+
+    """Fix invalid code.
+
+    Fixer methods are prefixed "fix_". The _fix_source() method looks for these
+    automatically.
+
+    The fixer method can take either one or two arguments (in addition to
+    self). The first argument is "result", which is the error information from
+    pep8. The second argument, "logical", is required only for logical-line
+    fixes.
+
+    The fixer method can return the list of modified lines or None. An empty
+    list would mean that no changes were made. None would mean that only the
+    line reported in the pep8 error was modified. Note that the modified line
+    numbers that are returned are indexed at 1. This typically would correspond
+    with the line number reported in the pep8 error information.
+
+    [fixed method list]
+        - e121,e122,e123,e124,e125,e126,e127,e128,e129
+        - e201,e202,e203
+        - e211
+        - e221,e222,e223,e224,e225
+        - e231
+        - e251
+        - e261,e262
+        - e271,e272,e273,e274
+        - e301,e302,e303
+        - e401
+        - e502
+        - e701,e702
+        - e711
+        - w291
+
+    """
+
+    def __init__(self, filename,
+                 options,
+                 contents=None,
+                 long_line_ignore_cache=None):
+        self.filename = filename
+        if contents is None:
+            self.source = readlines_from_file(filename)
+        else:
+            sio = io.StringIO(contents)
+            self.source = sio.readlines()
+        self.options = options
+        self.indent_word = _get_indentword(''.join(self.source))
+
+        self.long_line_ignore_cache = (
+            set() if long_line_ignore_cache is None
+            else long_line_ignore_cache)
+
+        # Many fixers are the same even though pep8 categorizes them
+        # differently.
+        self.fix_e115 = self.fix_e112
+        self.fix_e116 = self.fix_e113
+        self.fix_e121 = self._fix_reindent
+        self.fix_e122 = self._fix_reindent
+        self.fix_e123 = self._fix_reindent
+        self.fix_e124 = self._fix_reindent
+        self.fix_e126 = self._fix_reindent
+        self.fix_e127 = self._fix_reindent
+        self.fix_e128 = self._fix_reindent
+        self.fix_e129 = self._fix_reindent
+        self.fix_e202 = self.fix_e201
+        self.fix_e203 = self.fix_e201
+        self.fix_e211 = self.fix_e201
+        self.fix_e221 = self.fix_e271
+        self.fix_e222 = self.fix_e271
+        self.fix_e223 = self.fix_e271
+        self.fix_e226 = self.fix_e225
+        self.fix_e227 = self.fix_e225
+        self.fix_e228 = self.fix_e225
+        self.fix_e241 = self.fix_e271
+        self.fix_e242 = self.fix_e224
+        self.fix_e261 = self.fix_e262
+        self.fix_e272 = self.fix_e271
+        self.fix_e273 = self.fix_e271
+        self.fix_e274 = self.fix_e271
+        self.fix_e309 = self.fix_e301
+        self.fix_e501 = (
+            self.fix_long_line_logically if
+            options and (options.aggressive >= 2 or options.experimental) else
+            self.fix_long_line_physically)
+        self.fix_e703 = self.fix_e702
+        self.fix_w293 = self.fix_w291
+
+    def _fix_source(self, results):
+        try:
+            (logical_start, logical_end) = _find_logical(self.source)
+            logical_support = True
+        except (SyntaxError, tokenize.TokenError):  # pragma: no cover
+            logical_support = False
+
+        completed_lines = set()
+        for result in sorted(results, key=_priority_key):
+            if result['line'] in completed_lines:
+                continue
+
+            fixed_methodname = 'fix_' + result['id'].lower()
+            if hasattr(self, fixed_methodname):
+                fix = getattr(self, fixed_methodname)
+
+                line_index = result['line'] - 1
+                original_line = self.source[line_index]
+
+                is_logical_fix = len(inspect.getargspec(fix).args) > 2
+                if is_logical_fix:
+                    logical = None
+                    if logical_support:
+                        logical = _get_logical(self.source,
+                                               result,
+                                               logical_start,
+                                               logical_end)
+                        if logical and set(range(
+                            logical[0][0] + 1,
+                            logical[1][0] + 1)).intersection(
+                                completed_lines):
+                            continue
+
+                    modified_lines = fix(result, logical)
+                else:
+                    modified_lines = fix(result)
+
+                if modified_lines is None:
+                    # Force logical fixes to report what they modified.
+                    assert not is_logical_fix
+
+                    if self.source[line_index] == original_line:
+                        modified_lines = []
+
+                if modified_lines:
+                    completed_lines.update(modified_lines)
+                elif modified_lines == []:  # Empty list means no fix
+                    if self.options.verbose >= 2:
+                        print(
+                            '--->  Not fixing {f} on line {l}'.format(
+                                f=result['id'], l=result['line']),
+                            file=sys.stderr)
+                else:  # We assume one-line fix when None.
+                    completed_lines.add(result['line'])
+            else:
+                if self.options.verbose >= 3:
+                    print(
+                        "--->  '{0}' is not defined.".format(fixed_methodname),
+                        file=sys.stderr)
+
+                    info = result['info'].strip()
+                    print('--->  {0}:{1}:{2}:{3}'.format(self.filename,
+                                                         result['line'],
+                                                         result['column'],
+                                                         info),
+                          file=sys.stderr)
+
+    def fix(self):
+        """Return a version of the source code with PEP 8 violations fixed."""
+        pep8_options = {
+            'ignore': self.options.ignore,
+            'select': self.options.select,
+            'max_line_length': self.options.max_line_length,
+        }
+        results = _execute_pep8(pep8_options, self.source)
+
+        if self.options.verbose:
+            progress = {}
+            for r in results:
+                if r['id'] not in progress:
+                    progress[r['id']] = set()
+                progress[r['id']].add(r['line'])
+            print('--->  {n} issue(s) to fix {progress}'.format(
+                n=len(results), progress=progress), file=sys.stderr)
+
+        if self.options.line_range:
+            start, end = self.options.line_range
+            results = [r for r in results
+                       if start <= r['line'] <= end]
+
+        self._fix_source(filter_results(source=''.join(self.source),
+                                        results=results,
+                                        aggressive=self.options.aggressive))
+
+        if self.options.line_range:
+            # If number of lines has changed then change line_range.
+            count = sum(sline.count('\n')
+                        for sline in self.source[start - 1:end])
+            self.options.line_range[1] = start + count - 1
+
+        return ''.join(self.source)
+
+    def _fix_reindent(self, result):
+        """Fix a badly indented line.
+
+        This is done by adding or removing from its initial indent only.
+
+        """
+        num_indent_spaces = int(result['info'].split()[1])
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+
+        self.source[line_index] = ' ' * num_indent_spaces + target.lstrip()
+
+    def fix_e112(self, result):
+        """Fix under-indented comments."""
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+
+        if not target.lstrip().startswith('#'):
+            # Don't screw with invalid syntax.
+            return []
+
+        self.source[line_index] = self.indent_word + target
+
+    def fix_e113(self, result):
+        """Fix over-indented comments."""
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+
+        indent = _get_indentation(target)
+        stripped = target.lstrip()
+
+        if not stripped.startswith('#'):
+            # Don't screw with invalid syntax.
+            return []
+
+        self.source[line_index] = indent[1:] + stripped
+
+    def fix_e125(self, result):
+        """Fix indentation undistinguish from the next logical line."""
+        num_indent_spaces = int(result['info'].split()[1])
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+
+        spaces_to_add = num_indent_spaces - len(_get_indentation(target))
+        indent = len(_get_indentation(target))
+        modified_lines = []
+
+        while len(_get_indentation(self.source[line_index])) >= indent:
+            self.source[line_index] = (' ' * spaces_to_add +
+                                       self.source[line_index])
+            modified_lines.append(1 + line_index)  # Line indexed at 1.
+            line_index -= 1
+
+        return modified_lines
+
+    def fix_e201(self, result):
+        """Remove extraneous whitespace."""
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+        offset = result['column'] - 1
+
+        if is_probably_part_of_multiline(target):
+            return []
+
+        fixed = fix_whitespace(target,
+                               offset=offset,
+                               replacement='')
+
+        self.source[line_index] = fixed
+
+    def fix_e224(self, result):
+        """Remove extraneous whitespace around operator."""
+        target = self.source[result['line'] - 1]
+        offset = result['column'] - 1
+        fixed = target[:offset] + target[offset:].replace('\t', ' ')
+        self.source[result['line'] - 1] = fixed
+
+    def fix_e225(self, result):
+        """Fix missing whitespace around operator."""
+        target = self.source[result['line'] - 1]
+        offset = result['column'] - 1
+        fixed = target[:offset] + ' ' + target[offset:]
+
+        # Only proceed if non-whitespace characters match.
+        # And make sure we don't break the indentation.
+        if (
+            fixed.replace(' ', '') == target.replace(' ', '') and
+            _get_indentation(fixed) == _get_indentation(target)
+        ):
+            self.source[result['line'] - 1] = fixed
+        else:
+            return []
+
+    def fix_e231(self, result):
+        """Add missing whitespace."""
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+        offset = result['column']
+        fixed = target[:offset] + ' ' + target[offset:]
+        self.source[line_index] = fixed
+
+    def fix_e251(self, result):
+        """Remove whitespace around parameter '=' sign."""
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+
+        # This is necessary since pep8 sometimes reports columns that goes
+        # past the end of the physical line. This happens in cases like,
+        # foo(bar\n=None)
+        c = min(result['column'] - 1,
+                len(target) - 1)
+
+        if target[c].strip():
+            fixed = target
+        else:
+            fixed = target[:c].rstrip() + target[c:].lstrip()
+
+        # There could be an escaped newline
+        #
+        #     def foo(a=\
+        #             1)
+        if fixed.endswith(('=\\\n', '=\\\r\n', '=\\\r')):
+            self.source[line_index] = fixed.rstrip('\n\r \t\\')
+            self.source[line_index + 1] = self.source[line_index + 1].lstrip()
+            return [line_index + 1, line_index + 2]  # Line indexed at 1
+
+        self.source[result['line'] - 1] = fixed
+
+    def fix_e262(self, result):
+        """Fix spacing after comment hash."""
+        target = self.source[result['line'] - 1]
+        offset = result['column']
+
+        code = target[:offset].rstrip(' \t#')
+        comment = target[offset:].lstrip(' \t#')
+
+        fixed = code + ('  # ' + comment if comment.strip() else '\n')
+
+        self.source[result['line'] - 1] = fixed
+
+    def fix_e271(self, result):
+        """Fix extraneous whitespace around keywords."""
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+        offset = result['column'] - 1
+
+        if is_probably_part_of_multiline(target):
+            return []
+
+        fixed = fix_whitespace(target,
+                               offset=offset,
+                               replacement=' ')
+
+        if fixed == target:
+            return []
+        else:
+            self.source[line_index] = fixed
+
+    def fix_e301(self, result):
+        """Add missing blank line."""
+        cr = '\n'
+        self.source[result['line'] - 1] = cr + self.source[result['line'] - 1]
+
+    def fix_e302(self, result):
+        """Add missing 2 blank lines."""
+        add_linenum = 2 - int(result['info'].split()[-1])
+        cr = '\n' * add_linenum
+        self.source[result['line'] - 1] = cr + self.source[result['line'] - 1]
+
+    def fix_e303(self, result):
+        """Remove extra blank lines."""
+        delete_linenum = int(result['info'].split('(')[1].split(')')[0]) - 2
+        delete_linenum = max(1, delete_linenum)
+
+        # We need to count because pep8 reports an offset line number if there
+        # are comments.
+        cnt = 0
+        line = result['line'] - 2
+        modified_lines = []
+        while cnt < delete_linenum and line >= 0:
+            if not self.source[line].strip():
+                self.source[line] = ''
+                modified_lines.append(1 + line)  # Line indexed at 1
+                cnt += 1
+            line -= 1
+
+        return modified_lines
+
+    def fix_e304(self, result):
+        """Remove blank line following function decorator."""
+        line = result['line'] - 2
+        if not self.source[line].strip():
+            self.source[line] = ''
+
+    def fix_e401(self, result):
+        """Put imports on separate lines."""
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+        offset = result['column'] - 1
+
+        if not target.lstrip().startswith('import'):
+            return []
+
+        indentation = re.split(pattern=r'\bimport\b',
+                               string=target, maxsplit=1)[0]
+        fixed = (target[:offset].rstrip('\t ,') + '\n' +
+                 indentation + 'import ' + target[offset:].lstrip('\t ,'))
+        self.source[line_index] = fixed
+
+    def fix_long_line_logically(self, result, logical):
+        """Try to make lines fit within --max-line-length characters."""
+        if (
+            not logical or
+            len(logical[2]) == 1 or
+            self.source[result['line'] - 1].lstrip().startswith('#')
+        ):
+            return self.fix_long_line_physically(result)
+
+        start_line_index = logical[0][0]
+        end_line_index = logical[1][0]
+        logical_lines = logical[2]
+
+        previous_line = get_item(self.source, start_line_index - 1, default='')
+        next_line = get_item(self.source, end_line_index + 1, default='')
+
+        single_line = join_logical_line(''.join(logical_lines))
+
+        try:
+            fixed = self.fix_long_line(
+                target=single_line,
+                previous_line=previous_line,
+                next_line=next_line,
+                original=''.join(logical_lines))
+        except (SyntaxError, tokenize.TokenError):
+            return self.fix_long_line_physically(result)
+
+        if fixed:
+            for line_index in range(start_line_index, end_line_index + 1):
+                self.source[line_index] = ''
+            self.source[start_line_index] = fixed
+            return range(start_line_index + 1, end_line_index + 1)
+        else:
+            return []
+
+    def fix_long_line_physically(self, result):
+        """Try to make lines fit within --max-line-length characters."""
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+
+        previous_line = get_item(self.source, line_index - 1, default='')
+        next_line = get_item(self.source, line_index + 1, default='')
+
+        try:
+            fixed = self.fix_long_line(
+                target=target,
+                previous_line=previous_line,
+                next_line=next_line,
+                original=target)
+        except (SyntaxError, tokenize.TokenError):
+            return []
+
+        if fixed:
+            self.source[line_index] = fixed
+            return [line_index + 1]
+        else:
+            return []
+
+    def fix_long_line(self, target, previous_line,
+                      next_line, original):
+        cache_entry = (target, previous_line, next_line)
+        if cache_entry in self.long_line_ignore_cache:
+            return []
+
+        if target.lstrip().startswith('#'):
+            # Wrap commented lines.
+            return shorten_comment(
+                line=target,
+                max_line_length=self.options.max_line_length,
+                last_comment=not next_line.lstrip().startswith('#'))
+
+        fixed = get_fixed_long_line(
+            target=target,
+            previous_line=previous_line,
+            original=original,
+            indent_word=self.indent_word,
+            max_line_length=self.options.max_line_length,
+            aggressive=self.options.aggressive,
+            experimental=self.options.experimental,
+            verbose=self.options.verbose)
+        if fixed and not code_almost_equal(original, fixed):
+            return fixed
+        else:
+            self.long_line_ignore_cache.add(cache_entry)
+            return None
+
+    def fix_e502(self, result):
+        """Remove extraneous escape of newline."""
+        (line_index, _, target) = get_index_offset_contents(result,
+                                                            self.source)
+        self.source[line_index] = target.rstrip('\n\r \t\\') + '\n'
+
+    def fix_e701(self, result):
+        """Put colon-separated compound statement on separate lines."""
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+        c = result['column']
+
+        fixed_source = (target[:c] + '\n' +
+                        _get_indentation(target) + self.indent_word +
+                        target[c:].lstrip('\n\r \t\\'))
+        self.source[result['line'] - 1] = fixed_source
+        return [result['line'], result['line'] + 1]
+
+    def fix_e702(self, result, logical):
+        """Put semicolon-separated compound statement on separate lines."""
+        if not logical:
+            return []  # pragma: no cover
+        logical_lines = logical[2]
+
+        line_index = result['line'] - 1
+        target = self.source[line_index]
+
+        if target.rstrip().endswith('\\'):
+            # Normalize '1; \\\n2' into '1; 2'.
+            self.source[line_index] = target.rstrip('\n \r\t\\')
+            self.source[line_index + 1] = self.source[line_index + 1].lstrip()
+            return [line_index + 1, line_index + 2]
+
+        if target.rstrip().endswith(';'):
+            self.source[line_index] = target.rstrip('\n \r\t;') + '\n'
+            return [line_index + 1]
+
+        offset = result['column'] - 1
+        first = target[:offset].rstrip(';').rstrip()
+        second = (_get_indentation(logical_lines[0]) +
+                  target[offset:].lstrip(';').lstrip())
+
+        # find inline commnet
+        inline_comment = None
+        if '# ' == target[offset:].lstrip(';').lstrip()[:2]:
+            inline_comment = target[offset:].lstrip(';')
+
+        if inline_comment:
+            self.source[line_index] = first + inline_comment
+        else:
+            self.source[line_index] = first + '\n' + second
+        return [line_index + 1]
+
+    def fix_e711(self, result):
+        """Fix comparison with None."""
+        (line_index, offset, target) = get_index_offset_contents(result,
+                                                                 self.source)
+
+        right_offset = offset + 2
+        if right_offset >= len(target):
+            return []
+
+        left = target[:offset].rstrip()
+        center = target[offset:right_offset]
+        right = target[right_offset:].lstrip()
+
+        if not right.startswith('None'):
+            return []
+
+        if center.strip() == '==':
+            new_center = 'is'
+        elif center.strip() == '!=':
+            new_center = 'is not'
+        else:
+            return []
+
+        self.source[line_index] = ' '.join([left, new_center, right])
+
+    def fix_e712(self, result):
+        """Fix (trivial case of) comparison with boolean."""
+        (line_index, offset, target) = get_index_offset_contents(result,
+                                                                 self.source)
+
+        # Handle very easy "not" special cases.
+        if re.match(r'^\s*if [\w.]+ == False:$', target):
+            self.source[line_index] = re.sub(r'if ([\w.]+) == False:',
+                                             r'if not \1:', target, count=1)
+        elif re.match(r'^\s*if [\w.]+ != True:$', target):
+            self.source[line_index] = re.sub(r'if ([\w.]+) != True:',
+                                             r'if not \1:', target, count=1)
+        else:
+            right_offset = offset + 2
+            if right_offset >= len(target):
+                return []
+
+            left = target[:offset].rstrip()
+            center = target[offset:right_offset]
+            right = target[right_offset:].lstrip()
+
+            # Handle simple cases only.
+            new_right = None
+            if center.strip() == '==':
+                if re.match(r'\bTrue\b', right):
+                    new_right = re.sub(r'\bTrue\b *', '', right, count=1)
+            elif center.strip() == '!=':
+                if re.match(r'\bFalse\b', right):
+                    new_right = re.sub(r'\bFalse\b *', '', right, count=1)
+
+            if new_right is None:
+                return []
+
+            if new_right[0].isalnum():
+                new_right = ' ' + new_right
+
+            self.source[line_index] = left + new_right
+
+    def fix_e713(self, result):
+        """Fix (trivial case of) non-membership check."""
+        (line_index, _, target) = get_index_offset_contents(result,
+                                                            self.source)
+
+        # Handle very easy case only.
+        if re.match(r'^\s*if not [\w.]+ in [\w.]+:$', target):
+            self.source[line_index] = re.sub(r'if not ([\w.]+) in ([\w.]+):',
+                                             r'if \1 not in \2:',
+                                             target,
+                                             count=1)
+
+    def fix_w291(self, result):
+        """Remove trailing whitespace."""
+        fixed_line = self.source[result['line'] - 1].rstrip()
+        self.source[result['line'] - 1] = fixed_line + '\n'
+
+    def fix_w391(self, _):
+        """Remove trailing blank lines."""
+        blank_count = 0
+        for line in reversed(self.source):
+            line = line.rstrip()
+            if line:
+                break
+            else:
+                blank_count += 1
+
+        original_length = len(self.source)
+        self.source = self.source[:original_length - blank_count]
+        return range(1, 1 + original_length)
+
+
+def get_index_offset_contents(result, source):
+    """Return (line_index, column_offset, line_contents)."""
+    line_index = result['line'] - 1
+    return (line_index,
+            result['column'] - 1,
+            source[line_index])
+
+
+def get_fixed_long_line(target, previous_line, original,
+                        indent_word='    ', max_line_length=79,
+                        aggressive=False, experimental=False, verbose=False):
+    """Break up long line and return result.
+
+    Do this by generating multiple reformatted candidates and then
+    ranking the candidates to heuristically select the best option.
+
+    """
+    indent = _get_indentation(target)
+    source = target[len(indent):]
+    assert source.lstrip() == source
+
+    # Check for partial multiline.
+    tokens = list(generate_tokens(source))
+
+    candidates = shorten_line(
+        tokens, source, indent,
+        indent_word,
+        max_line_length,
+        aggressive=aggressive,
+        experimental=experimental,
+        previous_line=previous_line)
+
+    # Also sort alphabetically as a tie breaker (for determinism).
+    candidates = sorted(
+        sorted(set(candidates).union([target, original])),
+        key=lambda x: line_shortening_rank(
+            x,
+            indent_word,
+            max_line_length,
+            experimental=experimental))
+
+    if verbose >= 4:
+        print(('-' * 79 + '\n').join([''] + candidates + ['']),
+              file=wrap_output(sys.stderr, 'utf-8'))
+
+    if candidates:
+        best_candidate = candidates[0]
+        # Don't allow things to get longer.
+        if longest_line_length(best_candidate) > longest_line_length(original):
+            return None
+        else:
+            return best_candidate
+
+
+def longest_line_length(code):
+    """Return length of longest line."""
+    return max(len(line) for line in code.splitlines())
+
+
+def join_logical_line(logical_line):
+    """Return single line based on logical line input."""
+    indentation = _get_indentation(logical_line)
+
+    return indentation + untokenize_without_newlines(
+        generate_tokens(logical_line.lstrip())) + '\n'
+
+
+def untokenize_without_newlines(tokens):
+    """Return source code based on tokens."""
+    text = ''
+    last_row = 0
+    last_column = -1
+
+    for t in tokens:
+        token_string = t[1]
+        (start_row, start_column) = t[2]
+        (end_row, end_column) = t[3]
+
+        if start_row > last_row:
+            last_column = 0
+        if (
+            (start_column > last_column or token_string == '\n') and
+            not text.endswith(' ')
+        ):
+            text += ' '
+
+        if token_string != '\n':
+            text += token_string
+
+        last_row = end_row
+        last_column = end_column
+
+    return text.rstrip()
+
+
+def _find_logical(source_lines):
+    # Make a variable which is the index of all the starts of lines.
+    logical_start = []
+    logical_end = []
+    last_newline = True
+    parens = 0
+    for t in generate_tokens(''.join(source_lines)):
+        if t[0] in [tokenize.COMMENT, tokenize.DEDENT,
+                    tokenize.INDENT, tokenize.NL,
+                    tokenize.ENDMARKER]:
+            continue
+        if not parens and t[0] in [tokenize.NEWLINE, tokenize.SEMI]:
+            last_newline = True
+            logical_end.append((t[3][0] - 1, t[2][1]))
+            continue
+        if last_newline and not parens:
+            logical_start.append((t[2][0] - 1, t[2][1]))
+            last_newline = False
+        if t[0] == tokenize.OP:
+            if t[1] in '([{':
+                parens += 1
+            elif t[1] in '}])':
+                parens -= 1
+    return (logical_start, logical_end)
+
+
+def _get_logical(source_lines, result, logical_start, logical_end):
+    """Return the logical line corresponding to the result.
+
+    Assumes input is already E702-clean.
+
+    """
+    row = result['line'] - 1
+    col = result['column'] - 1
+    ls = None
+    le = None
+    for i in range(0, len(logical_start), 1):
+        assert logical_end
+        x = logical_end[i]
+        if x[0] > row or (x[0] == row and x[1] > col):
+            le = x
+            ls = logical_start[i]
+            break
+    if ls is None:
+        return None
+    original = source_lines[ls[0]:le[0] + 1]
+    return ls, le, original
+
+
+def get_item(items, index, default=None):
+    if 0 <= index < len(items):
+        return items[index]
+    else:
+        return default
+
+
+def reindent(source, indent_size):
+    """Reindent all lines."""
+    reindenter = Reindenter(source)
+    return reindenter.run(indent_size)
+
+
+def code_almost_equal(a, b):
+    """Return True if code is similar.
+
+    Ignore whitespace when comparing specific line.
+
+    """
+    split_a = split_and_strip_non_empty_lines(a)
+    split_b = split_and_strip_non_empty_lines(b)
+
+    if len(split_a) != len(split_b):
+        return False
+
+    for index in range(len(split_a)):
+        if ''.join(split_a[index].split()) != ''.join(split_b[index].split()):
+            return False
+
+    return True
+
+
+def split_and_strip_non_empty_lines(text):
+    """Return lines split by newline.
+
+    Ignore empty lines.
+
+    """
+    return [line.strip() for line in text.splitlines() if line.strip()]
+
+
+def fix_e265(source, aggressive=False):  # pylint: disable=unused-argument
+    """Format block comments."""
+    if '#' not in source:
+        # Optimization.
+        return source
+
+    ignored_line_numbers = multiline_string_lines(
+        source,
+        include_docstrings=True) | set(commented_out_code_lines(source))
+
+    fixed_lines = []
+    sio = io.StringIO(source)
+    for (line_number, line) in enumerate(sio.readlines(), start=1):
+        if (
+            line.lstrip().startswith('#') and
+            line_number not in ignored_line_numbers
+        ):
+            indentation = _get_indentation(line)
+            line = line.lstrip()
+
+            # Normalize beginning if not a shebang.
+            if len(line) > 1:
+                pos = next((index for index, c in enumerate(line)
+                            if c != '#'))
+                if (
+                    # Leave multiple spaces like '#    ' alone.
+                    (line[:pos].count('#') > 1 or line[1].isalnum()) and
+                    # Leave stylistic outlined blocks alone.
+                    not line.rstrip().endswith('#')
+                ):
+                    line = '# ' + line.lstrip('# \t')
+
+            fixed_lines.append(indentation + line)
+        else:
+            fixed_lines.append(line)
+
+    return ''.join(fixed_lines)
+
+
+def refactor(source, fixer_names, ignore=None, filename=''):
+    """Return refactored code using lib2to3.
+
+    Skip if ignore string is produced in the refactored code.
+
+    """
+    from lib2to3 import pgen2
+    try:
+        new_text = refactor_with_2to3(source,
+                                      fixer_names=fixer_names,
+                                      filename=filename)
+    except (pgen2.parse.ParseError,
+            SyntaxError,
+            UnicodeDecodeError,
+            UnicodeEncodeError):
+        return source
+
+    if ignore:
+        if ignore in new_text and ignore not in source:
+            return source
+
+    return new_text
+
+
+def code_to_2to3(select, ignore):
+    fixes = set()
+    for code, fix in CODE_TO_2TO3.items():
+        if code_match(code, select=select, ignore=ignore):
+            fixes |= set(fix)
+    return fixes
+
+
+def fix_2to3(source,
+             aggressive=True, select=None, ignore=None, filename=''):
+    """Fix various deprecated code (via lib2to3)."""
+    if not aggressive:
+        return source
+
+    select = select or []
+    ignore = ignore or []
+
+    return refactor(source,
+                    code_to_2to3(select=select,
+                                 ignore=ignore),
+                    filename=filename)
+
+
+def fix_w602(source, aggressive=True):
+    """Fix deprecated form of raising exception."""
+    if not aggressive:
+        return source
+
+    return refactor(source, ['raise'],
+                    ignore='with_traceback')
+
+
+def find_newline(source):
+    """Return type of newline used in source.
+
+    Input is a list of lines.
+
+    """
+    assert not isinstance(source, unicode)
+
+    counter = collections.defaultdict(int)
+    for line in source:
+        if line.endswith(CRLF):
+            counter[CRLF] += 1
+        elif line.endswith(CR):
+            counter[CR] += 1
+        elif line.endswith(LF):
+            counter[LF] += 1
+
+    return (sorted(counter, key=counter.get, reverse=True) or [LF])[0]
+
+
+def _get_indentword(source):
+    """Return indentation type."""
+    indent_word = '    '  # Default in case source has no indentation
+    try:
+        for t in generate_tokens(source):
+            if t[0] == token.INDENT:
+                indent_word = t[1]
+                break
+    except (SyntaxError, tokenize.TokenError):
+        pass
+    return indent_word
+
+
+def _get_indentation(line):
+    """Return leading whitespace."""
+    if line.strip():
+        non_whitespace_index = len(line) - len(line.lstrip())
+        return line[:non_whitespace_index]
+    else:
+        return ''
+
+
+def get_diff_text(old, new, filename):
+    """Return text of unified diff between old and new."""
+    newline = '\n'
+    diff = difflib.unified_diff(
+        old, new,
+        'original/' + filename,
+        'fixed/' + filename,
+        lineterm=newline)
+
+    text = ''
+    for line in diff:
+        text += line
+
+        # Work around missing newline (http://bugs.python.org/issue2142).
+        if text and not line.endswith(newline):
+            text += newline + r'\ No newline at end of file' + newline
+
+    return text
+
+
+def _priority_key(pep8_result):
+    """Key for sorting PEP8 results.
+
+    Global fixes should be done first. This is important for things like
+    indentation.
+
+    """
+    priority = [
+        # Fix multiline colon-based before semicolon based.
+        'e701',
+        # Break multiline statements early.
+        'e702',
+        # Things that make lines longer.
+        'e225', 'e231',
+        # Remove extraneous whitespace before breaking lines.
+        'e201',
+        # Shorten whitespace in comment before resorting to wrapping.
+        'e262'
+    ]
+    middle_index = 10000
+    lowest_priority = [
+        # We need to shorten lines last since the logical fixer can get in a
+        # loop, which causes us to exit early.
+        'e501'
+    ]
+    key = pep8_result['id'].lower()
+    try:
+        return priority.index(key)
+    except ValueError:
+        try:
+            return middle_index + lowest_priority.index(key) + 1
+        except ValueError:
+            return middle_index
+
+
+def shorten_line(tokens, source, indentation, indent_word, max_line_length,
+                 aggressive=False, experimental=False, previous_line=''):
+    """Separate line at OPERATOR.
+
+    Multiple candidates will be yielded.
+
+    """
+    for candidate in _shorten_line(tokens=tokens,
+                                   source=source,
+                                   indentation=indentation,
+                                   indent_word=indent_word,
+                                   aggressive=aggressive,
+                                   previous_line=previous_line):
+        yield candidate
+
+    if aggressive:
+        for key_token_strings in SHORTEN_OPERATOR_GROUPS:
+            shortened = _shorten_line_at_tokens(
+                tokens=tokens,
+                source=source,
+                indentation=indentation,
+                indent_word=indent_word,
+                key_token_strings=key_token_strings,
+                aggressive=aggressive)
+
+            if shortened is not None and shortened != source:
+                yield shortened
+
+    if experimental:
+        for shortened in _shorten_line_at_tokens_new(
+                tokens=tokens,
+                source=source,
+                indentation=indentation,
+                max_line_length=max_line_length):
+
+            yield shortened
+
+
+def _shorten_line(tokens, source, indentation, indent_word,
+                  aggressive=False, previous_line=''):
+    """Separate line at OPERATOR.
+
+    The input is expected to be free of newlines except for inside multiline
+    strings and at the end.
+
+    Multiple candidates will be yielded.
+
+    """
+    for (token_type,
+         token_string,
+         start_offset,
+         end_offset) in token_offsets(tokens):
+
+        if (
+            token_type == tokenize.COMMENT and
+            not is_probably_part_of_multiline(previous_line) and
+            not is_probably_part_of_multiline(source) and
+            not source[start_offset + 1:].strip().lower().startswith(
+                ('noqa', 'pragma:', 'pylint:'))
+        ):
+            # Move inline comments to previous line.
+            first = source[:start_offset]
+            second = source[start_offset:]
+            yield (indentation + second.strip() + '\n' +
+                   indentation + first.strip() + '\n')
+        elif token_type == token.OP and token_string != '=':
+            # Don't break on '=' after keyword as this violates PEP 8.
+
+            assert token_type != token.INDENT
+
+            first = source[:end_offset]
+
+            second_indent = indentation
+            if first.rstrip().endswith('('):
+                second_indent += indent_word
+            elif '(' in first:
+                second_indent += ' ' * (1 + first.find('('))
+            else:
+                second_indent += indent_word
+
+            second = (second_indent + source[end_offset:].lstrip())
+            if (
+                not second.strip() or
+                second.lstrip().startswith('#')
+            ):
+                continue
+
+            # Do not begin a line with a comma
+            if second.lstrip().startswith(','):
+                continue
+            # Do end a line with a dot
+            if first.rstrip().endswith('.'):
+                continue
+            if token_string in '+-*/':
+                fixed = first + ' \\' + '\n' + second
+            else:
+                fixed = first + '\n' + second
+
+            # Only fix if syntax is okay.
+            if check_syntax(normalize_multiline(fixed)
+                            if aggressive else fixed):
+                yield indentation + fixed
+
+
+# A convenient way to handle tokens.
+Token = collections.namedtuple('Token', ['token_type', 'token_string',
+                                         'spos', 'epos', 'line'])
+
+
+class ReformattedLines(object):
+
+    """The reflowed lines of atoms.
+
+    Each part of the line is represented as an "atom." They can be moved
+    around when need be to get the optimal formatting.
+
+    """
+
+    ###########################################################################
+    # Private Classes
+
+    class _Indent(object):
+
+        """Represent an indentation in the atom stream."""
+
+        def __init__(self, indent_amt):
+            self._indent_amt = indent_amt
+
+        def emit(self):
+            return ' ' * self._indent_amt
+
+        @property
+        def size(self):
+            return self._indent_amt
+
+    class _Space(object):
+
+        """Represent a space in the atom stream."""
+
+        def emit(self):
+            return ' '
+
+        @property
+        def size(self):
+            return 1
+
+    class _LineBreak(object):
+
+        """Represent a line break in the atom stream."""
+
+        def emit(self):
+            return '\n'
+
+        @property
+        def size(self):
+            return 0
+
+    def __init__(self, max_line_length):
+        self._max_line_length = max_line_length
+        self._lines = []
+        self._bracket_depth = 0
+        self._prev_item = None
+        self._prev_prev_item = None
+
+    def __repr__(self):
+        return self.emit()
+
+    ###########################################################################
+    # Public Methods
+
+    def add(self, obj, indent_amt, break_after_open_bracket):
+        if isinstance(obj, Atom):
+            self._add_item(obj, indent_amt)
+            return
+
+        self._add_container(obj, indent_amt, break_after_open_bracket)
+
+    def add_comment(self, item):
+        num_spaces = 2
+        if len(self._lines) > 1:
+            if isinstance(self._lines[-1], self._Space):
+                num_spaces -= 1
+            if len(self._lines) > 2:
+                if isinstance(self._lines[-2], self._Space):
+                    num_spaces -= 1
+
+        while num_spaces > 0:
+            self._lines.append(self._Space())
+            num_spaces -= 1
+        self._lines.append(item)
+
+    def add_indent(self, indent_amt):
+        self._lines.append(self._Indent(indent_amt))
+
+    def add_line_break(self, indent):
+        self._lines.append(self._LineBreak())
+        self.add_indent(len(indent))
+
+    def add_line_break_at(self, index, indent_amt):
+        self._lines.insert(index, self._LineBreak())
+        self._lines.insert(index + 1, self._Indent(indent_amt))
+
+    def add_space_if_needed(self, curr_text, equal=False):
+        if (
+            not self._lines or isinstance(
+                self._lines[-1], (self._LineBreak, self._Indent, self._Space))
+        ):
+            return
+
+        prev_text = unicode(self._prev_item)
+        prev_prev_text = (
+            unicode(self._prev_prev_item) if self._prev_prev_item else '')
+
+        if (
+            # The previous item was a keyword or identifier and the current
+            # item isn't an operator that doesn't require a space.
+            ((self._prev_item.is_keyword or self._prev_item.is_string or
+              self._prev_item.is_name or self._prev_item.is_number) and
+             (curr_text[0] not in '([{.,:}])' or
+              (curr_text[0] == '=' and equal))) or
+
+            # Don't place spaces around a '.', unless it's in an 'import'
+            # statement.
+            ((prev_prev_text != 'from' and prev_text[-1] != '.' and
+              curr_text != 'import') and
+
+             # Don't place a space before a colon.
+             curr_text[0] != ':' and
+
+             # Don't split up ending brackets by spaces.
+             ((prev_text[-1] in '}])' and curr_text[0] not in '.,}])') or
+
+              # Put a space after a colon or comma.
+              prev_text[-1] in ':,' or
+
+              # Put space around '=' if asked to.
+              (equal and prev_text == '=') or
+
+              # Put spaces around non-unary arithmetic operators.
+              ((self._prev_prev_item and
+                (prev_text not in '+-' and
+                 (self._prev_prev_item.is_name or
+                  self._prev_prev_item.is_number or
+                  self._prev_prev_item.is_string)) and
+                prev_text in ('+', '-', '%', '*', '/', '//', '**', 'in')))))
+        ):
+            self._lines.append(self._Space())
+
+    def previous_item(self):
+        """Return the previous non-whitespace item."""
+        return self._prev_item
+
+    def fits_on_current_line(self, item_extent):
+        return self.current_size() + item_extent <= self._max_line_length
+
+    def current_size(self):
+        """The size of the current line minus the indentation."""
+        size = 0
+        for item in reversed(self._lines):
+            size += item.size
+            if isinstance(item, self._LineBreak):
+                break
+
+        return size
+
+    def line_empty(self):
+        return (self._lines and
+                isinstance(self._lines[-1],
+                           (self._LineBreak, self._Indent)))
+
+    def emit(self):
+        string = ''
+        for item in self._lines:
+            if isinstance(item, self._LineBreak):
+                string = string.rstrip()
+            string += item.emit()
+
+        return string.rstrip() + '\n'
+
+    ###########################################################################
+    # Private Methods
+
+    def _add_item(self, item, indent_amt):
+        """Add an item to the line.
+
+        Reflow the line to get the best formatting after the item is
+        inserted. The bracket depth indicates if the item is being
+        inserted inside of a container or not.
+
+        """
+        if self._prev_item and self._prev_item.is_string and item.is_string:
+            # Place consecutive string literals on separate lines.
+            self._lines.append(self._LineBreak())
+            self._lines.append(self._Indent(indent_amt))
+
+        item_text = unicode(item)
+        if self._lines and self._bracket_depth:
+            # Adding the item into a container.
+            self._prevent_default_initializer_splitting(item, indent_amt)
+
+            if item_text in '.,)]}':
+                self._split_after_delimiter(item, indent_amt)
+
+        elif self._lines and not self.line_empty():
+            # Adding the item outside of a container.
+            if self.fits_on_current_line(len(item_text)):
+                self._enforce_space(item)
+
+            else:
+                # Line break for the new item.
+                self._lines.append(self._LineBreak())
+                self._lines.append(self._Indent(indent_amt))
+
+        self._lines.append(item)
+        self._prev_item, self._prev_prev_item = item, self._prev_item
+
+        if item_text in '([{':
+            self._bracket_depth += 1
+
+        elif item_text in '}])':
+            self._bracket_depth -= 1
+            assert self._bracket_depth >= 0
+
+    def _add_container(self, container, indent_amt, break_after_open_bracket):
+        actual_indent = indent_amt + 1
+
+        if (
+            unicode(self._prev_item) != '=' and
+            not self.line_empty() and
+            not self.fits_on_current_line(
+                container.size + self._bracket_depth + 2)
+        ):
+
+            if unicode(container)[0] == '(' and self._prev_item.is_name:
+                # Don't split before the opening bracket of a call.
+                break_after_open_bracket = True
+                actual_indent = indent_amt + 4
+            elif (
+                break_after_open_bracket or
+                unicode(self._prev_item) not in '([{'
+            ):
+                # If the container doesn't fit on the current line and the
+                # current line isn't empty, place the container on the next
+                # line.
+                self._lines.append(self._LineBreak())
+                self._lines.append(self._Indent(indent_amt))
+                break_after_open_bracket = False
+        else:
+            actual_indent = self.current_size() + 1
+            break_after_open_bracket = False
+
+        if isinstance(container, (ListComprehension, IfExpression)):
+            actual_indent = indent_amt
+
+        # Increase the continued indentation only if recursing on a
+        # container.
+        container.reflow(self, ' ' * actual_indent,
+                         break_after_open_bracket=break_after_open_bracket)
+
+    def _prevent_default_initializer_splitting(self, item, indent_amt):
+        """Prevent splitting between a default initializer.
+
+        When there is a default initializer, it's best to keep it all on
+        the same line. It's nicer and more readable, even if it goes
+        over the maximum allowable line length. This goes back along the
+        current line to determine if we have a default initializer, and,
+        if so, to remove extraneous whitespaces and add a line
+        break/indent before it if needed.
+
+        """
+        if unicode(item) == '=':
+            # This is the assignment in the initializer. Just remove spaces for
+            # now.
+            self._delete_whitespace()
+            return
+
+        if (not self._prev_item or not self._prev_prev_item or
+                unicode(self._prev_item) != '='):
+            return
+
+        self._delete_whitespace()
+        prev_prev_index = self._lines.index(self._prev_prev_item)
+
+        if (
+            isinstance(self._lines[prev_prev_index - 1], self._Indent) or
+            self.fits_on_current_line(item.size + 1)
+        ):
+            # The default initializer is already the only item on this line.
+            # Don't insert a newline here.
+            return
+
+        # Replace the space with a newline/indent combo.
+        if isinstance(self._lines[prev_prev_index - 1], self._Space):
+            del self._lines[prev_prev_index - 1]
+
+        self.add_line_break_at(self._lines.index(self._prev_prev_item),
+                               indent_amt)
+
+    def _split_after_delimiter(self, item, indent_amt):
+        """Split the line only after a delimiter."""
+        self._delete_whitespace()
+
+        if self.fits_on_current_line(item.size):
+            return
+
+        last_space = None
+        for item in reversed(self._lines):
+            if (
+                last_space and
+                (not isinstance(item, Atom) or not item.is_colon)
+            ):
+                break
+            else:
+                last_space = None
+            if isinstance(item, self._Space):
+                last_space = item
+            if isinstance(item, (self._LineBreak, self._Indent)):
+                return
+
+        if not last_space:
+            return
+
+        self.add_line_break_at(self._lines.index(last_space), indent_amt)
+
+    def _enforce_space(self, item):
+        """Enforce a space in certain situations.
+
+        There are cases where we will want a space where normally we
+        wouldn't put one. This just enforces the addition of a space.
+
+        """
+        if isinstance(self._lines[-1],
+                      (self._Space, self._LineBreak, self._Indent)):
+            return
+
+        if not self._prev_item:
+            return
+
+        item_text = unicode(item)
+        prev_text = unicode(self._prev_item)
+
+        # Prefer a space around a '.' in an import statement, and between the
+        # 'import' and '('.
+        if (
+            (item_text == '.' and prev_text == 'from') or
+            (item_text == 'import' and prev_text == '.') or
+            (item_text == '(' and prev_text == 'import')
+        ):
+            self._lines.append(self._Space())
+
+    def _delete_whitespace(self):
+        """Delete all whitespace from the end of the line."""
+        while isinstance(self._lines[-1], (self._Space, self._LineBreak,
+                                           self._Indent)):
+            del self._lines[-1]
+
+
+class Atom(object):
+
+    """The smallest unbreakable unit that can be reflowed."""
+
+    def __init__(self, atom):
+        self._atom = atom
+
+    def __repr__(self):
+        return self._atom.token_string
+
+    def __len__(self):
+        return self.size
+
+    def reflow(
+        self, reflowed_lines, continued_indent, extent,
+        break_after_open_bracket=False,
+        is_list_comp_or_if_expr=False,
+        next_is_dot=False
+    ):
+        if self._atom.token_type == tokenize.COMMENT:
+            reflowed_lines.add_comment(self)
+            return
+
+        total_size = extent if extent else self.size
+
+        if self._atom.token_string not in ',:([{}])':
+            # Some atoms will need an extra 1-sized space token after them.
+            total_size += 1
+
+        prev_item = reflowed_lines.previous_item()
+        if (
+            not is_list_comp_or_if_expr and
+            not reflowed_lines.fits_on_current_line(total_size) and
+            not (next_is_dot and
+                 reflowed_lines.fits_on_current_line(self.size + 1)) and
+            not reflowed_lines.line_empty() and
+            not self.is_colon and
+            not (prev_item and prev_item.is_name and
+                 unicode(self) == '(')
+        ):
+            # Start a new line if there is already something on the line and
+            # adding this atom would make it go over the max line length.
+            reflowed_lines.add_line_break(continued_indent)
+        else:
+            reflowed_lines.add_space_if_needed(unicode(self))
+
+        reflowed_lines.add(self, len(continued_indent),
+                           break_after_open_bracket)
+
+    def emit(self):
+        return self.__repr__()
+
+    @property
+    def is_keyword(self):
+        return keyword.iskeyword(self._atom.token_string)
+
+    @property
+    def is_string(self):
+        return self._atom.token_type == tokenize.STRING
+
+    @property
+    def is_name(self):
+        return self._atom.token_type == tokenize.NAME
+
+    @property
+    def is_number(self):
+        return self._atom.token_type == tokenize.NUMBER
+
+    @property
+    def is_comma(self):
+        return self._atom.token_string == ','
+
+    @property
+    def is_colon(self):
+        return self._atom.token_string == ':'
+
+    @property
+    def size(self):
+        return len(self._atom.token_string)
+
+
+class Container(object):
+
+    """Base class for all container types."""
+
+    def __init__(self, items):
+        self._items = items
+
+    def __repr__(self):
+        string = ''
+        last_was_keyword = False
+
+        for item in self._items:
+            if item.is_comma:
+                string += ', '
+            elif item.is_colon:
+                string += ': '
+            else:
+                item_string = unicode(item)
+                if (
+                    string and
+                    (last_was_keyword or
+                     (not string.endswith(tuple('([{,.:}]) ')) and
+                      not item_string.startswith(tuple('([{,.:}])'))))
+                ):
+                    string += ' '
+                string += item_string
+
+            last_was_keyword = item.is_keyword
+        return string
+
+    def __iter__(self):
+        for element in self._items:
+            yield element
+
+    def __getitem__(self, idx):
+        return self._items[idx]
+
+    def reflow(self, reflowed_lines, continued_indent,
+               break_after_open_bracket=False):
+        last_was_container = False
+        for (index, item) in enumerate(self._items):
+            next_item = get_item(self._items, index + 1)
+
+            if isinstance(item, Atom):
+                is_list_comp_or_if_expr = (
+                    isinstance(self, (ListComprehension, IfExpression)))
+                item.reflow(reflowed_lines, continued_indent,
+                            self._get_extent(index),
+                            is_list_comp_or_if_expr=is_list_comp_or_if_expr,
+                            next_is_dot=(next_item and
+                                         unicode(next_item) == '.'))
+                if last_was_container and item.is_comma:
+                    reflowed_lines.add_line_break(continued_indent)
+                last_was_container = False
+            else:  # isinstance(item, Container)
+                reflowed_lines.add(item, len(continued_indent),
+                                   break_after_open_bracket)
+                last_was_container = not isinstance(item, (ListComprehension,
+                                                           IfExpression))
+
+            if (
+                break_after_open_bracket and index == 0 and
+                # Prefer to keep empty containers together instead of
+                # separating them.
+                unicode(item) == self.open_bracket and
+                (not next_item or unicode(next_item) != self.close_bracket) and
+                (len(self._items) != 3 or not isinstance(next_item, Atom))
+            ):
+                reflowed_lines.add_line_break(continued_indent)
+                break_after_open_bracket = False
+            else:
+                next_next_item = get_item(self._items, index + 2)
+                if (
+                    unicode(item) not in ['.', '%', 'in'] and
+                    next_item and not isinstance(next_item, Container) and
+                    unicode(next_item) != ':' and
+                    next_next_item and (not isinstance(next_next_item, Atom) or
+                                        unicode(next_item) == 'not') and
+                    not reflowed_lines.line_empty() and
+                    not reflowed_lines.fits_on_current_line(
+                        self._get_extent(index + 1) + 2)
+                ):
+                    reflowed_lines.add_line_break(continued_indent)
+
+    def _get_extent(self, index):
+        """The extent of the full element.
+
+        E.g., the length of a function call or keyword.
+
+        """
+        extent = 0
+        prev_item = get_item(self._items, index - 1)
+        seen_dot = prev_item and unicode(prev_item) == '.'
+        while index < len(self._items):
+            item = get_item(self._items, index)
+            index += 1
+
+            if isinstance(item, (ListComprehension, IfExpression)):
+                break
+
+            if isinstance(item, Container):
+                if prev_item and prev_item.is_name:
+                    if seen_dot:
+                        extent += 1
+                    else:
+                        extent += item.size
+
+                    prev_item = item
+                    continue
+            elif (unicode(item) not in ['.', '=', ':', 'not'] and
+                  not item.is_name and not item.is_string):
+                break
+
+            if unicode(item) == '.':
+                seen_dot = True
+
+            extent += item.size
+            prev_item = item
+
+        return extent
+
+    @property
+    def is_string(self):
+        return False
+
+    @property
+    def size(self):
+        return len(self.__repr__())
+
+    @property
+    def is_keyword(self):
+        return False
+
+    @property
+    def is_name(self):
+        return False
+
+    @property
+    def is_comma(self):
+        return False
+
+    @property
+    def is_colon(self):
+        return False
+
+    @property
+    def open_bracket(self):
+        return None
+
+    @property
+    def close_bracket(self):
+        return None
+
+
+class Tuple(Container):
+
+    """A high-level representation of a tuple."""
+
+    @property
+    def open_bracket(self):
+        return '('
+
+    @property
+    def close_bracket(self):
+        return ')'
+
+
+class List(Container):
+
+    """A high-level representation of a list."""
+
+    @property
+    def open_bracket(self):
+        return '['
+
+    @property
+    def close_bracket(self):
+        return ']'
+
+
+class DictOrSet(Container):
+
+    """A high-level representation of a dictionary or set."""
+
+    @property
+    def open_bracket(self):
+        return '{'
+
+    @property
+    def close_bracket(self):
+        return '}'
+
+
+class ListComprehension(Container):
+
+    """A high-level representation of a list comprehension."""
+
+    @property
+    def size(self):
+        length = 0
+        for item in self._items:
+            if isinstance(item, IfExpression):
+                break
+            length += item.size
+        return length
+
+
+class IfExpression(Container):
+
+    """A high-level representation of an if-expression."""
+
+
+def _parse_container(tokens, index, for_or_if=None):
+    """Parse a high-level container, such as a list, tuple, etc."""
+
+    # Store the opening bracket.
+    items = [Atom(Token(*tokens[index]))]
+    index += 1
+
+    num_tokens = len(tokens)
+    while index < num_tokens:
+        tok = Token(*tokens[index])
+
+        if tok.token_string in ',)]}':
+            # First check if we're at the end of a list comprehension or
+            # if-expression. Don't add the ending token as part of the list
+            # comprehension or if-expression, because they aren't part of those
+            # constructs.
+            if for_or_if == 'for':
+                return (ListComprehension(items), index - 1)
+
+            elif for_or_if == 'if':
+                return (IfExpression(items), index - 1)
+
+            # We've reached the end of a container.
+            items.append(Atom(tok))
+
+            # If not, then we are at the end of a container.
+            if tok.token_string == ')':
+                # The end of a tuple.
+                return (Tuple(items), index)
+
+            elif tok.token_string == ']':
+                # The end of a list.
+                return (List(items), index)
+
+            elif tok.token_string == '}':
+                # The end of a dictionary or set.
+                return (DictOrSet(items), index)
+
+        elif tok.token_string in '([{':
+            # A sub-container is being defined.
+            (container, index) = _parse_container(tokens, index)
+            items.append(container)
+
+        elif tok.token_string == 'for':
+            (container, index) = _parse_container(tokens, index, 'for')
+            items.append(container)
+
+        elif tok.token_string == 'if':
+            (container, index) = _parse_container(tokens, index, 'if')
+            items.append(container)
+
+        else:
+            items.append(Atom(tok))
+
+        index += 1
+
+    return (None, None)
+
+
+def _parse_tokens(tokens):
+    """Parse the tokens.
+
+    This converts the tokens into a form where we can manipulate them
+    more easily.
+
+    """
+
+    index = 0
+    parsed_tokens = []
+
+    num_tokens = len(tokens)
+    while index < num_tokens:
+        tok = Token(*tokens[index])
+
+        assert tok.token_type != token.INDENT
+        if tok.token_type == tokenize.NEWLINE:
+            # There's only one newline and it's at the end.
+            break
+
+        if tok.token_string in '([{':
+            (container, index) = _parse_container(tokens, index)
+            if not container:
+                return None
+            parsed_tokens.append(container)
+        else:
+            parsed_tokens.append(Atom(tok))
+
+        index += 1
+
+    return parsed_tokens
+
+
+def _reflow_lines(parsed_tokens, indentation, max_line_length,
+                  start_on_prefix_line):
+    """Reflow the lines so that it looks nice."""
+
+    if unicode(parsed_tokens[0]) == 'def':
+        # A function definition gets indented a bit more.
+        continued_indent = indentation + ' ' * 2 * DEFAULT_INDENT_SIZE
+    else:
+        continued_indent = indentation + ' ' * DEFAULT_INDENT_SIZE
+
+    break_after_open_bracket = not start_on_prefix_line
+
+    lines = ReformattedLines(max_line_length)
+    lines.add_indent(len(indentation.lstrip('\r\n')))
+
+    if not start_on_prefix_line:
+        # If splitting after the opening bracket will cause the first element
+        # to be aligned weirdly, don't try it.
+        first_token = get_item(parsed_tokens, 0)
+        second_token = get_item(parsed_tokens, 1)
+
+        if (
+            first_token and second_token and
+            unicode(second_token)[0] == '(' and
+            len(indentation) + len(first_token) + 1 == len(continued_indent)
+        ):
+            return None
+
+    for item in parsed_tokens:
+        lines.add_space_if_needed(unicode(item), equal=True)
+
+        save_continued_indent = continued_indent
+        if start_on_prefix_line and isinstance(item, Container):
+            start_on_prefix_line = False
+            continued_indent = ' ' * (lines.current_size() + 1)
+
+        item.reflow(lines, continued_indent, break_after_open_bracket)
+        continued_indent = save_continued_indent
+
+    return lines.emit()
+
+
+def _shorten_line_at_tokens_new(tokens, source, indentation,
+                                max_line_length):
+    """Shorten the line taking its length into account.
+
+    The input is expected to be free of newlines except for inside
+    multiline strings and at the end.
+
+    """
+    # Yield the original source so to see if it's a better choice than the
+    # shortened candidate lines we generate here.
+    yield indentation + source
+
+    parsed_tokens = _parse_tokens(tokens)
+
+    if parsed_tokens:
+        # Perform two reflows. The first one starts on the same line as the
+        # prefix. The second starts on the line after the prefix.
+        fixed = _reflow_lines(parsed_tokens, indentation, max_line_length,
+                              start_on_prefix_line=True)
+        if fixed and check_syntax(normalize_multiline(fixed.lstrip())):
+            yield fixed
+
+        fixed = _reflow_lines(parsed_tokens, indentation, max_line_length,
+                              start_on_prefix_line=False)
+        if fixed and check_syntax(normalize_multiline(fixed.lstrip())):
+            yield fixed
+
+
+def _shorten_line_at_tokens(tokens, source, indentation, indent_word,
+                            key_token_strings, aggressive):
+    """Separate line by breaking at tokens in key_token_strings.
+
+    The input is expected to be free of newlines except for inside
+    multiline strings and at the end.
+
+    """
+    offsets = []
+    for (index, _t) in enumerate(token_offsets(tokens)):
+        (token_type,
+         token_string,
+         start_offset,
+         end_offset) = _t
+
+        assert token_type != token.INDENT
+
+        if token_string in key_token_strings:
+            # Do not break in containers with zero or one items.
+            unwanted_next_token = {
+                '(': ')',
+                '[': ']',
+                '{': '}'}.get(token_string)
+            if unwanted_next_token:
+                if (
+                    get_item(tokens,
+                             index + 1,
+                             default=[None, None])[1] == unwanted_next_token or
+                    get_item(tokens,
+                             index + 2,
+                             default=[None, None])[1] == unwanted_next_token
+                ):
+                    continue
+
+            if (
+                index > 2 and token_string == '(' and
+                tokens[index - 1][1] in ',(%['
+            ):
+                # Don't split after a tuple start, or before a tuple start if
+                # the tuple is in a list.
+                continue
+
+            if end_offset < len(source) - 1:
+                # Don't split right before newline.
+                offsets.append(end_offset)
+        else:
+            # Break at adjacent strings. These were probably meant to be on
+            # separate lines in the first place.
+            previous_token = get_item(tokens, index - 1)
+            if (
+                token_type == tokenize.STRING and
+                previous_token and previous_token[0] == tokenize.STRING
+            ):
+                offsets.append(start_offset)
+
+    current_indent = None
+    fixed = None
+    for line in split_at_offsets(source, offsets):
+        if fixed:
+            fixed += '\n' + current_indent + line
+
+            for symbol in '([{':
+                if line.endswith(symbol):
+                    current_indent += indent_word
+        else:
+            # First line.
+            fixed = line
+            assert not current_indent
+            current_indent = indent_word
+
+    assert fixed is not None
+
+    if check_syntax(normalize_multiline(fixed)
+                    if aggressive > 1 else fixed):
+        return indentation + fixed
+    else:
+        return None
+
+
+def token_offsets(tokens):
+    """Yield tokens and offsets."""
+    end_offset = 0
+    previous_end_row = 0
+    previous_end_column = 0
+    for t in tokens:
+        token_type = t[0]
+        token_string = t[1]
+        (start_row, start_column) = t[2]
+        (end_row, end_column) = t[3]
+
+        # Account for the whitespace between tokens.
+        end_offset += start_column
+        if previous_end_row == start_row:
+            end_offset -= previous_end_column
+
+        # Record the start offset of the token.
+        start_offset = end_offset
+
+        # Account for the length of the token itself.
+        end_offset += len(token_string)
+
+        yield (token_type,
+               token_string,
+               start_offset,
+               end_offset)
+
+        previous_end_row = end_row
+        previous_end_column = end_column
+
+
+def normalize_multiline(line):
+    """Normalize multiline-related code that will cause syntax error.
+
+    This is for purposes of checking syntax.
+
+    """
+    if line.startswith('def ') and line.rstrip().endswith(':'):
+        return line + ' pass'
+    elif line.startswith('return '):
+        return 'def _(): ' + line
+    elif line.startswith('@'):
+        return line + 'def _(): pass'
+    elif line.startswith('class '):
+        return line + ' pass'
+    elif line.startswith(('if ', 'elif ', 'for ', 'while ')):
+        return line + ' pass'
+    else:
+        return line
+
+
+def fix_whitespace(line, offset, replacement):
+    """Replace whitespace at offset and return fixed line."""
+    # Replace escaped newlines too
+    left = line[:offset].rstrip('\n\r \t\\')
+    right = line[offset:].lstrip('\n\r \t\\')
+    if right.startswith('#'):
+        return line
+    else:
+        return left + replacement + right
+
+
+def _execute_pep8(pep8_options, source):
+    """Execute pep8 via python method calls."""
+    class QuietReport(pep8.BaseReport):
+
+        """Version of checker that does not print."""
+
+        def __init__(self, options):
+            super(QuietReport, self).__init__(options)
+            self.__full_error_results = []
+
+        def error(self, line_number, offset, text, check):
+            """Collect errors."""
+            code = super(QuietReport, self).error(line_number,
+                                                  offset,
+                                                  text,
+                                                  check)
+            if code:
+                self.__full_error_results.append(
+                    {'id': code,
+                     'line': line_number,
+                     'column': offset + 1,
+                     'info': text})
+
+        def full_error_results(self):
+            """Return error results in detail.
+
+            Results are in the form of a list of dictionaries. Each
+            dictionary contains 'id', 'line', 'column', and 'info'.
+
+            """
+            return self.__full_error_results
+
+    checker = pep8.Checker('', lines=source,
+                           reporter=QuietReport, **pep8_options)
+    checker.check_all()
+    return checker.report.full_error_results()
+
+
+def _remove_leading_and_normalize(line):
+    return line.lstrip().rstrip(CR + LF) + '\n'
+
+
+class Reindenter(object):
+
+    """Reindents badly-indented code to uniformly use four-space indentation.
+
+    Released to the public domain, by Tim Peters, 03 October 2000.
+
+    """
+
+    def __init__(self, input_text):
+        sio = io.StringIO(input_text)
+        source_lines = sio.readlines()
+
+        self.string_content_line_numbers = multiline_string_lines(input_text)
+
+        # File lines, rstripped & tab-expanded. Dummy at start is so
+        # that we can use tokenize's 1-based line numbering easily.
+        # Note that a line is all-blank iff it is a newline.
+        self.lines = []
+        for line_number, line in enumerate(source_lines, start=1):
+            # Do not modify if inside a multiline string.
+            if line_number in self.string_content_line_numbers:
+                self.lines.append(line)
+            else:
+                # Only expand leading tabs.
+                self.lines.append(_get_indentation(line).expandtabs() +
+                                  _remove_leading_and_normalize(line))
+
+        self.lines.insert(0, None)
+        self.index = 1  # index into self.lines of next line
+        self.input_text = input_text
+
+    def run(self, indent_size=DEFAULT_INDENT_SIZE):
+        """Fix indentation and return modified line numbers.
+
+        Line numbers are indexed at 1.
+
+        """
+        if indent_size < 1:
+            return self.input_text
+
+        try:
+            stats = _reindent_stats(tokenize.generate_tokens(self.getline))
+        except (SyntaxError, tokenize.TokenError):
+            return self.input_text
+        # Remove trailing empty lines.
+        lines = self.lines
+        # Sentinel.
+        stats.append((len(lines), 0))
+        # Map count of leading spaces to # we want.
+        have2want = {}
+        # Program after transformation.
+        after = []
+        # Copy over initial empty lines -- there's nothing to do until
+        # we see a line with *something* on it.
+        i = stats[0][0]
+        after.extend(lines[1:i])
+        for i in range(len(stats) - 1):
+            thisstmt, thislevel = stats[i]
+            nextstmt = stats[i + 1][0]
+            have = _leading_space_count(lines[thisstmt])
+            want = thislevel * indent_size
+            if want < 0:
+                # A comment line.
+                if have:
+                    # An indented comment line. If we saw the same
+                    # indentation before, reuse what it most recently
+                    # mapped to.
+                    want = have2want.get(have, -1)
+                    if want < 0:
+                        # Then it probably belongs to the next real stmt.
+                        for j in range(i + 1, len(stats) - 1):
+                            jline, jlevel = stats[j]
+                            if jlevel >= 0:
+                                if have == _leading_space_count(lines[jline]):
+                                    want = jlevel * indent_size
+                                break
+                    if want < 0:            # Maybe it's a hanging
+                                            # comment like this one,
+                        # in which case we should shift it like its base
+                        # line got shifted.
+                        for j in range(i - 1, -1, -1):
+                            jline, jlevel = stats[j]
+                            if jlevel >= 0:
+                                want = (have + _leading_space_count(
+                                        after[jline - 1]) -
+                                        _leading_space_count(lines[jline]))
+                                break
+                    if want < 0:
+                        # Still no luck -- leave it alone.
+                        want = have
+                else:
+                    want = 0
+            assert want >= 0
+            have2want[have] = want
+            diff = want - have
+            if diff == 0 or have == 0:
+                after.extend(lines[thisstmt:nextstmt])
+            else:
+                for line_number, line in enumerate(lines[thisstmt:nextstmt],
+                                                   start=thisstmt):
+                    if line_number in self.string_content_line_numbers:
+                        after.append(line)
+                    elif diff > 0:
+                        if line == '\n':
+                            after.append(line)
+                        else:
+                            after.append(' ' * diff + line)
+                    else:
+                        remove = min(_leading_space_count(line), -diff)
+                        after.append(line[remove:])
+
+        return ''.join(after)
+
+    def getline(self):
+        """Line-getter for tokenize."""
+        if self.index >= len(self.lines):
+            line = ''
+        else:
+            line = self.lines[self.index]
+            self.index += 1
+        return line
+
+
+def _reindent_stats(tokens):
+    """Return list of (lineno, indentlevel) pairs.
+
+    One for each stmt and comment line. indentlevel is -1 for comment lines, as
+    a signal that tokenize doesn't know what to do about them; indeed, they're
+    our headache!
+
+    """
+    find_stmt = 1  # Next token begins a fresh stmt?
+    level = 0  # Current indent level.
+    stats = []
+
+    for t in tokens:
+        token_type = t[0]
+        sline = t[2][0]
+        line = t[4]
+
+        if token_type == tokenize.NEWLINE:
+            # A program statement, or ENDMARKER, will eventually follow,
+            # after some (possibly empty) run of tokens of the form
+            #     (NL | COMMENT)* (INDENT | DEDENT+)?
+            find_stmt = 1
+
+        elif token_type == tokenize.INDENT:
+            find_stmt = 1
+            level += 1
+
+        elif token_type == tokenize.DEDENT:
+            find_stmt = 1
+            level -= 1
+
+        elif token_type == tokenize.COMMENT:
+            if find_stmt:
+                stats.append((sline, -1))
+                # But we're still looking for a new stmt, so leave
+                # find_stmt alone.
+
+        elif token_type == tokenize.NL:
+            pass
+
+        elif find_stmt:
+            # This is the first "real token" following a NEWLINE, so it
+            # must be the first token of the next program statement, or an
+            # ENDMARKER.
+            find_stmt = 0
+            if line:   # Not endmarker.
+                stats.append((sline, level))
+
+    return stats
+
+
+def _leading_space_count(line):
+    """Return number of leading spaces in line."""
+    i = 0
+    while i < len(line) and line[i] == ' ':
+        i += 1
+    return i
+
+
+def refactor_with_2to3(source_text, fixer_names, filename=''):
+    """Use lib2to3 to refactor the source.
+
+    Return the refactored source code.
+
+    """
+    from lib2to3.refactor import RefactoringTool
+    fixers = ['lib2to3.fixes.fix_' + name for name in fixer_names]
+    tool = RefactoringTool(fixer_names=fixers, explicit=fixers)
+
+    from lib2to3.pgen2 import tokenize as lib2to3_tokenize
+    try:
+        # The name parameter is necessary particularly for the "import" fixer.
+        return unicode(tool.refactor_string(source_text, name=filename))
+    except lib2to3_tokenize.TokenError:
+        return source_text
+
+
+def check_syntax(code):
+    """Return True if syntax is okay."""
+    try:
+        return compile(code, '<string>', 'exec')
+    except (SyntaxError, TypeError, UnicodeDecodeError):
+        return False
+
+
+def filter_results(source, results, aggressive):
+    """Filter out spurious reports from pep8.
+
+    If aggressive is True, we allow possibly unsafe fixes (E711, E712).
+
+    """
+    non_docstring_string_line_numbers = multiline_string_lines(
+        source, include_docstrings=False)
+    all_string_line_numbers = multiline_string_lines(
+        source, include_docstrings=True)
+
+    commented_out_code_line_numbers = commented_out_code_lines(source)
+
+    has_e901 = any(result['id'].lower() == 'e901' for result in results)
+
+    for r in results:
+        issue_id = r['id'].lower()
+
+        if r['line'] in non_docstring_string_line_numbers:
+            if issue_id.startswith(('e1', 'e501', 'w191')):
+                continue
+
+        if r['line'] in all_string_line_numbers:
+            if issue_id in ['e501']:
+                continue
+
+        # We must offset by 1 for lines that contain the trailing contents of
+        # multiline strings.
+        if not aggressive and (r['line'] + 1) in all_string_line_numbers:
+            # Do not modify multiline strings in non-aggressive mode. Remove
+            # trailing whitespace could break doctests.
+            if issue_id.startswith(('w29', 'w39')):
+                continue
+
+        if aggressive <= 0:
+            if issue_id.startswith(('e711', 'w6')):
+                continue
+
+        if aggressive <= 1:
+            if issue_id.startswith(('e712', 'e713')):
+                continue
+
+        if r['line'] in commented_out_code_line_numbers:
+            if issue_id.startswith(('e26', 'e501')):
+                continue
+
+        # Do not touch indentation if there is a token error caused by
+        # incomplete multi-line statement. Otherwise, we risk screwing up the
+        # indentation.
+        if has_e901:
+            if issue_id.startswith(('e1', 'e7')):
+                continue
+
+        yield r
+
+
+def multiline_string_lines(source, include_docstrings=False):
+    """Return line numbers that are within multiline strings.
+
+    The line numbers are indexed at 1.
+
+    Docstrings are ignored.
+
+    """
+    line_numbers = set()
+    previous_token_type = ''
+    try:
+        for t in generate_tokens(source):
+            token_type = t[0]
+            start_row = t[2][0]
+            end_row = t[3][0]
+
+            if token_type == tokenize.STRING and start_row != end_row:
+                if (
+                    include_docstrings or
+                    previous_token_type != tokenize.INDENT
+                ):
+                    # We increment by one since we want the contents of the
+                    # string.
+                    line_numbers |= set(range(1 + start_row, 1 + end_row))
+
+            previous_token_type = token_type
+    except (SyntaxError, tokenize.TokenError):
+        pass
+
+    return line_numbers
+
+
+def commented_out_code_lines(source):
+    """Return line numbers of comments that are likely code.
+
+    Commented-out code is bad practice, but modifying it just adds even more
+    clutter.
+
+    """
+    line_numbers = []
+    try:
+        for t in generate_tokens(source):
+            token_type = t[0]
+            token_string = t[1]
+            start_row = t[2][0]
+            line = t[4]
+
+            # Ignore inline comments.
+            if not line.lstrip().startswith('#'):
+                continue
+
+            if token_type == tokenize.COMMENT:
+                stripped_line = token_string.lstrip('#').strip()
+                if (
+                    ' ' in stripped_line and
+                    '#' not in stripped_line and
+                    check_syntax(stripped_line)
+                ):
+                    line_numbers.append(start_row)
+    except (SyntaxError, tokenize.TokenError):
+        pass
+
+    return line_numbers
+
+
+def shorten_comment(line, max_line_length, last_comment=False):
+    """Return trimmed or split long comment line.
+
+    If there are no comments immediately following it, do a text wrap.
+    Doing this wrapping on all comments in general would lead to jagged
+    comment text.
+
+    """
+    assert len(line) > max_line_length
+    line = line.rstrip()
+
+    # PEP 8 recommends 72 characters for comment text.
+    indentation = _get_indentation(line) + '# '
+    max_line_length = min(max_line_length,
+                          len(indentation) + 72)
+
+    MIN_CHARACTER_REPEAT = 5
+    if (
+        len(line) - len(line.rstrip(line[-1])) >= MIN_CHARACTER_REPEAT and
+        not line[-1].isalnum()
+    ):
+        # Trim comments that end with things like ---------
+        return line[:max_line_length] + '\n'
+    elif last_comment and re.match(r'\s*#+\s*\w+', line):
+        split_lines = textwrap.wrap(line.lstrip(' \t#'),
+                                    initial_indent=indentation,
+                                    subsequent_indent=indentation,
+                                    width=max_line_length,
+                                    break_long_words=False,
+                                    break_on_hyphens=False)
+        return '\n'.join(split_lines) + '\n'
+    else:
+        return line + '\n'
+
+
+def normalize_line_endings(lines, newline):
+    """Return fixed line endings.
+
+    All lines will be modified to use the most common line ending.
+
+    """
+    return [line.rstrip('\n\r') + newline for line in lines]
+
+
+def mutual_startswith(a, b):
+    return b.startswith(a) or a.startswith(b)
+
+
+def code_match(code, select, ignore):
+    if ignore:
+        assert not isinstance(ignore, unicode)
+        for ignored_code in [c.strip() for c in ignore]:
+            if mutual_startswith(code.lower(), ignored_code.lower()):
+                return False
+
+    if select:
+        assert not isinstance(select, unicode)
+        for selected_code in [c.strip() for c in select]:
+            if mutual_startswith(code.lower(), selected_code.lower()):
+                return True
+        return False
+
+    return True
+
+
+def fix_code(source, options=None, encoding=None, apply_config=False):
+    """Return fixed source code.
+
+    "encoding" will be used to decode "source" if it is a byte string.
+
+    """
+    options = _get_options(options, apply_config)
+
+    if not isinstance(source, unicode):
+        source = source.decode(encoding or get_encoding())
+
+    sio = io.StringIO(source)
+    return fix_lines(sio.readlines(), options=options)
+
+
+def _get_options(raw_options, apply_config):
+    """Return parsed options."""
+    if not raw_options:
+        return parse_args([''], apply_config=apply_config)
+
+    if isinstance(raw_options, dict):
+        options = parse_args([''], apply_config=apply_config)
+        for name, value in raw_options.items():
+            if not hasattr(options, name):
+                raise ValueError("No such option '{}'".format(name))
+
+            # Check for very basic type errors.
+            expected_type = type(getattr(options, name))
+            if not isinstance(expected_type, (str, unicode)):
+                if isinstance(value, (str, unicode)):
+                    raise ValueError(
+                        "Option '{}' should not be a string".format(name))
+            setattr(options, name, value)
+    else:
+        options = raw_options
+
+    return options
+
+
+def fix_lines(source_lines, options, filename=''):
+    """Return fixed source code."""
+    # Transform everything to line feed. Then change them back to original
+    # before returning fixed source code.
+    original_newline = find_newline(source_lines)
+    tmp_source = ''.join(normalize_line_endings(source_lines, '\n'))
+
+    # Keep a history to break out of cycles.
+    previous_hashes = set()
+
+    if options.line_range:
+        # Disable "apply_local_fixes()" for now due to issue #175.
+        fixed_source = tmp_source
+    else:
+        # Apply global fixes only once (for efficiency).
+        fixed_source = apply_global_fixes(tmp_source,
+                                          options,
+                                          filename=filename)
+
+    passes = 0
+    long_line_ignore_cache = set()
+    while hash(fixed_source) not in previous_hashes:
+        if options.pep8_passes >= 0 and passes > options.pep8_passes:
+            break
+        passes += 1
+
+        previous_hashes.add(hash(fixed_source))
+
+        tmp_source = copy.copy(fixed_source)
+
+        fix = FixPEP8(
+            filename,
+            options,
+            contents=tmp_source,
+            long_line_ignore_cache=long_line_ignore_cache)
+
+        fixed_source = fix.fix()
+
+    sio = io.StringIO(fixed_source)
+    return ''.join(normalize_line_endings(sio.readlines(), original_newline))
+
+
+def fix_file(filename, options=None, output=None, apply_config=False):
+    if not options:
+        options = parse_args([filename], apply_config=apply_config)
+
+    original_source = readlines_from_file(filename)
+
+    fixed_source = original_source
+
+    if options.in_place or output:
+        encoding = detect_encoding(filename)
+
+    if output:
+        output = LineEndingWrapper(wrap_output(output, encoding=encoding))
+
+    fixed_source = fix_lines(fixed_source, options, filename=filename)
+
+    if options.diff:
+        new = io.StringIO(fixed_source)
+        new = new.readlines()
+        diff = get_diff_text(original_source, new, filename)
+        if output:
+            output.write(diff)
+            output.flush()
+        else:
+            return diff
+    elif options.in_place:
+        fp = open_with_encoding(filename, encoding=encoding,
+                                mode='w')
+        fp.write(fixed_source)
+        fp.close()
+    else:
+        if output:
+            output.write(fixed_source)
+            output.flush()
+        else:
+            return fixed_source
+
+
+def global_fixes():
+    """Yield multiple (code, function) tuples."""
+    for function in globals().values():
+        if inspect.isfunction(function):
+            arguments = inspect.getargspec(function)[0]
+            if arguments[:1] != ['source']:
+                continue
+
+            code = extract_code_from_function(function)
+            if code:
+                yield (code, function)
+
+
+def apply_global_fixes(source, options, where='global', filename=''):
+    """Run global fixes on source code.
+
+    These are fixes that only need be done once (unlike those in
+    FixPEP8, which are dependent on pep8).
+
+    """
+    if any(code_match(code, select=options.select, ignore=options.ignore)
+           for code in ['E101', 'E111']):
+        source = reindent(source,
+                          indent_size=options.indent_size)
+
+    for (code, function) in global_fixes():
+        if code_match(code, select=options.select, ignore=options.ignore):
+            if options.verbose:
+                print('--->  Applying {0} fix for {1}'.format(where,
+                                                              code.upper()),
+                      file=sys.stderr)
+            source = function(source,
+                              aggressive=options.aggressive)
+
+    source = fix_2to3(source,
+                      aggressive=options.aggressive,
+                      select=options.select,
+                      ignore=options.ignore,
+                      filename=filename)
+
+    return source
+
+
+def extract_code_from_function(function):
+    """Return code handled by function."""
+    if not function.__name__.startswith('fix_'):
+        return None
+
+    code = re.sub('^fix_', '', function.__name__)
+    if not code:
+        return None
+
+    try:
+        int(code[1:])
+    except ValueError:
+        return None
+
+    return code
+
+
+def create_parser():
+    """Return command-line parser."""
+    # Do import locally to be friendly to those who use autopep8 as a library
+    # and are supporting Python 2.6.
+    import argparse
+
+    parser = argparse.ArgumentParser(description=docstring_summary(__doc__),
+                                     prog='autopep8')
+    parser.add_argument('--version', action='version',
+                        version='%(prog)s ' + __version__)
+    parser.add_argument('-v', '--verbose', action='count',
+                        default=0,
+                        help='print verbose messages; '
+                             'multiple -v result in more verbose messages')
+    parser.add_argument('-d', '--diff', action='store_true',
+                        help='print the diff for the fixed source')
+    parser.add_argument('-i', '--in-place', action='store_true',
+                        help='make changes to files in place')
+    parser.add_argument('--global-config', metavar='filename',
+                        default=DEFAULT_CONFIG,
+                        help='path to a global pep8 config file; if this file '
+                             'does not exist then this is ignored '
+                             '(default: {0})'.format(DEFAULT_CONFIG))
+    parser.add_argument('--ignore-local-config', action='store_true',
+                        help="don't look for and apply local config files; "
+                             'if not passed, defaults are updated with any '
+                             "config files in the project's root directory")
+    parser.add_argument('-r', '--recursive', action='store_true',
+                        help='run recursively over directories; '
+                             'must be used with --in-place or --diff')
+    parser.add_argument('-j', '--jobs', type=int, metavar='n', default=1,
+                        help='number of parallel jobs; '
+                             'match CPU count if value is less than 1')
+    parser.add_argument('-p', '--pep8-passes', metavar='n',
+                        default=-1, type=int,
+                        help='maximum number of additional pep8 passes '
+                             '(default: infinite)')
+    parser.add_argument('-a', '--aggressive', action='count', default=0,
+                        help='enable non-whitespace changes; '
+                             'multiple -a result in more aggressive changes')
+    parser.add_argument('--experimental', action='store_true',
+                        help='enable experimental fixes')
+    parser.add_argument('--exclude', metavar='globs',
+                        help='exclude file/directory names that match these '
+                             'comma-separated globs')
+    parser.add_argument('--list-fixes', action='store_true',
+                        help='list codes for fixes; '
+                        'used by --ignore and --select')
+    parser.add_argument('--ignore', metavar='errors', default='',
+                        help='do not fix these errors/warnings '
+                             '(default: {0})'.format(DEFAULT_IGNORE))
+    parser.add_argument('--select', metavar='errors', default='',
+                        help='fix only these errors/warnings (e.g. E4,W)')
+    parser.add_argument('--max-line-length', metavar='n', default=79, type=int,
+                        help='set maximum allowed line length '
+                             '(default: %(default)s)')
+    parser.add_argument('--line-range', '--range', metavar='line',
+                        default=None, type=int, nargs=2,
+                        help='only fix errors found within this inclusive '
+                             'range of line numbers (e.g. 1 99); '
+                             'line numbers are indexed at 1')
+    parser.add_argument('--indent-size', default=DEFAULT_INDENT_SIZE,
+                        type=int, metavar='n',
+                        help='number of spaces per indent level '
+                             '(default %(default)s)')
+    parser.add_argument('files', nargs='*',
+                        help="files to format or '-' for standard in")
+
+    return parser
+
+
+def parse_args(arguments, apply_config=False):
+    """Parse command-line options."""
+    parser = create_parser()
+    args = parser.parse_args(arguments)
+
+    if not args.files and not args.list_fixes:
+        parser.error('incorrect number of arguments')
+
+    args.files = [decode_filename(name) for name in args.files]
+
+    if apply_config:
+        parser = read_config(args, parser)
+        args = parser.parse_args(arguments)
+        args.files = [decode_filename(name) for name in args.files]
+
+    if '-' in args.files:
+        if len(args.files) > 1:
+            parser.error('cannot mix stdin and regular files')
+
+        if args.diff:
+            parser.error('--diff cannot be used with standard input')
+
+        if args.in_place:
+            parser.error('--in-place cannot be used with standard input')
+
+        if args.recursive:
+            parser.error('--recursive cannot be used with standard input')
+
+    if len(args.files) > 1 and not (args.in_place or args.diff):
+        parser.error('autopep8 only takes one filename as argument '
+                     'unless the "--in-place" or "--diff" args are '
+                     'used')
+
+    if args.recursive and not (args.in_place or args.diff):
+        parser.error('--recursive must be used with --in-place or --diff')
+
+    if args.in_place and args.diff:
+        parser.error('--in-place and --diff are mutually exclusive')
+
+    if args.max_line_length <= 0:
+        parser.error('--max-line-length must be greater than 0')
+
+    if args.select:
+        args.select = _split_comma_separated(args.select)
+
+    if args.ignore:
+        args.ignore = _split_comma_separated(args.ignore)
+    elif not args.select:
+        if args.aggressive:
+            # Enable everything by default if aggressive.
+            args.select = ['E', 'W']
+        else:
+            args.ignore = _split_comma_separated(DEFAULT_IGNORE)
+
+    if args.exclude:
+        args.exclude = _split_comma_separated(args.exclude)
+    else:
+        args.exclude = []
+
+    if args.jobs < 1:
+        # Do not import multiprocessing globally in case it is not supported
+        # on the platform.
+        import multiprocessing
+        args.jobs = multiprocessing.cpu_count()
+
+    if args.jobs > 1 and not args.in_place:
+        parser.error('parallel jobs requires --in-place')
+
+    if args.line_range:
+        if args.line_range[0] <= 0:
+            parser.error('--range must be positive numbers')
+        if args.line_range[0] > args.line_range[1]:
+            parser.error('First value of --range should be less than or equal '
+                         'to the second')
+
+    return args
+
+
+def read_config(args, parser):
+    """Read both user configuration and local configuration."""
+    try:
+        from configparser import ConfigParser as SafeConfigParser
+        from configparser import Error
+    except ImportError:
+        from ConfigParser import SafeConfigParser
+        from ConfigParser import Error
+
+    config = SafeConfigParser()
+
+    try:
+        config.read(args.global_config)
+
+        if not args.ignore_local_config:
+            parent = tail = args.files and os.path.abspath(
+                os.path.commonprefix(args.files))
+            while tail:
+                if config.read([os.path.join(parent, fn)
+                                for fn in PROJECT_CONFIG]):
+                    break
+                (parent, tail) = os.path.split(parent)
+
+        defaults = dict((k.lstrip('-').replace('-', '_'), v)
+                        for k, v in config.items('pep8'))
+        parser.set_defaults(**defaults)
+    except Error:
+        # Ignore for now.
+        pass
+
+    return parser
+
+
+def _split_comma_separated(string):
+    """Return a set of strings."""
+    return set(text.strip() for text in string.split(',') if text.strip())
+
+
+def decode_filename(filename):
+    """Return Unicode filename."""
+    if isinstance(filename, unicode):
+        return filename
+    else:
+        return filename.decode(sys.getfilesystemencoding())
+
+
+def supported_fixes():
+    """Yield pep8 error codes that autopep8 fixes.
+
+    Each item we yield is a tuple of the code followed by its
+    description.
+
+    """
+    yield ('E101', docstring_summary(reindent.__doc__))
+
+    instance = FixPEP8(filename=None, options=None, contents='')
+    for attribute in dir(instance):
+        code = re.match('fix_([ew][0-9][0-9][0-9])', attribute)
+        if code:
+            yield (
+                code.group(1).upper(),
+                re.sub(r'\s+', ' ',
+                       docstring_summary(getattr(instance, attribute).__doc__))
+            )
+
+    for (code, function) in sorted(global_fixes()):
+        yield (code.upper() + (4 - len(code)) * ' ',
+               re.sub(r'\s+', ' ', docstring_summary(function.__doc__)))
+
+    for code in sorted(CODE_TO_2TO3):
+        yield (code.upper() + (4 - len(code)) * ' ',
+               re.sub(r'\s+', ' ', docstring_summary(fix_2to3.__doc__)))
+
+
+def docstring_summary(docstring):
+    """Return summary of docstring."""
+    return docstring.split('\n')[0]
+
+
+def line_shortening_rank(candidate, indent_word, max_line_length,
+                         experimental=False):
+    """Return rank of candidate.
+
+    This is for sorting candidates.
+
+    """
+    if not candidate.strip():
+        return 0
+
+    rank = 0
+    lines = candidate.rstrip().split('\n')
+
+    offset = 0
+    if (
+        not lines[0].lstrip().startswith('#') and
+        lines[0].rstrip()[-1] not in '([{'
+    ):
+        for (opening, closing) in ('()', '[]', '{}'):
+            # Don't penalize empty containers that aren't split up. Things like
+            # this "foo(\n    )" aren't particularly good.
+            opening_loc = lines[0].find(opening)
+            closing_loc = lines[0].find(closing)
+            if opening_loc >= 0:
+                if closing_loc < 0 or closing_loc != opening_loc + 1:
+                    offset = max(offset, 1 + opening_loc)
+
+    current_longest = max(offset + len(x.strip()) for x in lines)
+
+    rank += 4 * max(0, current_longest - max_line_length)
+
+    rank += len(lines)
+
+    # Too much variation in line length is ugly.
+    rank += 2 * standard_deviation(len(line) for line in lines)
+
+    bad_staring_symbol = {
+        '(': ')',
+        '[': ']',
+        '{': '}'}.get(lines[0][-1])
+
+    if len(lines) > 1:
+        if (
+            bad_staring_symbol and
+            lines[1].lstrip().startswith(bad_staring_symbol)
+        ):
+            rank += 20
+
+    for lineno, current_line in enumerate(lines):
+        current_line = current_line.strip()
+
+        if current_line.startswith('#'):
+            continue
+
+        for bad_start in ['.', '%', '+', '-', '/']:
+            if current_line.startswith(bad_start):
+                rank += 100
+
+            # Do not tolerate operators on their own line.
+            if current_line == bad_start:
+                rank += 1000
+
+        if (
+            current_line.endswith(('.', '%', '+', '-', '/')) and
+            "': " in current_line
+        ):
+            rank += 1000
+
+        if current_line.endswith(('(', '[', '{', '.')):
+            # Avoid lonely opening. They result in longer lines.
+            if len(current_line) <= len(indent_word):
+                rank += 100
+
+            # Avoid the ugliness of ", (\n".
+            if (
+                current_line.endswith('(') and
+                current_line[:-1].rstrip().endswith(',')
+            ):
+                rank += 100
+
+            # Also avoid the ugliness of "foo.\nbar"
+            if current_line.endswith('.'):
+                rank += 100
+
+            if has_arithmetic_operator(current_line):
+                rank += 100
+
+        # Avoid breaking at unary operators.
+        if re.match(r'.*[(\[{]\s*[\-\+~]$', current_line.rstrip('\\ ')):
+            rank += 1000
+
+        if re.match(r'.*lambda\s*\*$', current_line.rstrip('\\ ')):
+            rank += 1000
+
+        if current_line.endswith(('%', '(', '[', '{')):
+            rank -= 20
+
+        # Try to break list comprehensions at the "for".
+        if current_line.startswith('for '):
+            rank -= 50
+
+        if current_line.endswith('\\'):
+            # If a line ends in \-newline, it may be part of a
+            # multiline string. In that case, we would like to know
+            # how long that line is without the \-newline. If it's
+            # longer than the maximum, or has comments, then we assume
+            # that the \-newline is an okay candidate and only
+            # penalize it a bit.
+            total_len = len(current_line)
+            lineno += 1
+            while lineno < len(lines):
+                total_len += len(lines[lineno])
+
+                if lines[lineno].lstrip().startswith('#'):
+                    total_len = max_line_length
+                    break
+
+                if not lines[lineno].endswith('\\'):
+                    break
+
+                lineno += 1
+
+            if total_len < max_line_length:
+                rank += 10
+            else:
+                rank += 100 if experimental else 1
+
+        # Prefer breaking at commas rather than colon.
+        if ',' in current_line and current_line.endswith(':'):
+            rank += 10
+
+        # Avoid splitting dictionaries between key and value.
+        if current_line.endswith(':'):
+            rank += 100
+
+        rank += 10 * count_unbalanced_brackets(current_line)
+
+    return max(0, rank)
+
+
+def standard_deviation(numbers):
+    """Return standard devation."""
+    numbers = list(numbers)
+    if not numbers:
+        return 0
+    mean = sum(numbers) / len(numbers)
+    return (sum((n - mean) ** 2 for n in numbers) /
+            len(numbers)) ** .5
+
+
+def has_arithmetic_operator(line):
+    """Return True if line contains any arithmetic operators."""
+    for operator in pep8.ARITHMETIC_OP:
+        if operator in line:
+            return True
+
+    return False
+
+
+def count_unbalanced_brackets(line):
+    """Return number of unmatched open/close brackets."""
+    count = 0
+    for opening, closing in ['()', '[]', '{}']:
+        count += abs(line.count(opening) - line.count(closing))
+
+    return count
+
+
+def split_at_offsets(line, offsets):
+    """Split line at offsets.
+
+    Return list of strings.
+
+    """
+    result = []
+
+    previous_offset = 0
+    current_offset = 0
+    for current_offset in sorted(offsets):
+        if current_offset < len(line) and previous_offset != current_offset:
+            result.append(line[previous_offset:current_offset].strip())
+        previous_offset = current_offset
+
+    result.append(line[current_offset:])
+
+    return result
+
+
+class LineEndingWrapper(object):
+
+    r"""Replace line endings to work with sys.stdout.
+
+    It seems that sys.stdout expects only '\n' as the line ending, no matter
+    the platform. Otherwise, we get repeated line endings.
+
+    """
+
+    def __init__(self, output):
+        self.__output = output
+
+    def write(self, s):
+        self.__output.write(s.replace('\r\n', '\n').replace('\r', '\n'))
+
+    def flush(self):
+        self.__output.flush()
+
+
+def match_file(filename, exclude):
+    """Return True if file is okay for modifying/recursing."""
+    base_name = os.path.basename(filename)
+
+    if base_name.startswith('.'):
+        return False
+
+    for pattern in exclude:
+        if fnmatch.fnmatch(base_name, pattern):
+            return False
+        if fnmatch.fnmatch(filename, pattern):
+            return False
+
+    if not os.path.isdir(filename) and not is_python_file(filename):
+        return False
+
+    return True
+
+
+def find_files(filenames, recursive, exclude):
+    """Yield filenames."""
+    while filenames:
+        name = filenames.pop(0)
+        if recursive and os.path.isdir(name):
+            for root, directories, children in os.walk(name):
+                filenames += [os.path.join(root, f) for f in children
+                              if match_file(os.path.join(root, f),
+                                            exclude)]
+                directories[:] = [d for d in directories
+                                  if match_file(os.path.join(root, d),
+                                                exclude)]
+        else:
+            yield name
+
+
+def _fix_file(parameters):
+    """Helper function for optionally running fix_file() in parallel."""
+    if parameters[1].verbose:
+        print('[file:{0}]'.format(parameters[0]), file=sys.stderr)
+    try:
+        fix_file(*parameters)
+    except IOError as error:
+        print(unicode(error), file=sys.stderr)
+
+
+def fix_multiple_files(filenames, options, output=None):
+    """Fix list of files.
+
+    Optionally fix files recursively.
+
+    """
+    filenames = find_files(filenames, options.recursive, options.exclude)
+    if options.jobs > 1:
+        import multiprocessing
+        pool = multiprocessing.Pool(options.jobs)
+        pool.map(_fix_file,
+                 [(name, options) for name in filenames])
+    else:
+        for name in filenames:
+            _fix_file((name, options, output))
+
+
+def is_python_file(filename):
+    """Return True if filename is Python file."""
+    if filename.endswith('.py'):
+        return True
+
+    try:
+        with open_with_encoding(filename) as f:
+            first_line = f.readlines(1)[0]
+    except (IOError, IndexError):
+        return False
+
+    if not PYTHON_SHEBANG_REGEX.match(first_line):
+        return False
+
+    return True
+
+
+def is_probably_part_of_multiline(line):
+    """Return True if line is likely part of a multiline string.
+
+    When multiline strings are involved, pep8 reports the error as being
+    at the start of the multiline string, which doesn't work for us.
+
+    """
+    return (
+        '"""' in line or
+        "'''" in line or
+        line.rstrip().endswith('\\')
+    )
+
+
+def wrap_output(output, encoding):
+    """Return output with specified encoding."""
+    return codecs.getwriter(encoding)(output.buffer
+                                      if hasattr(output, 'buffer')
+                                      else output)
+
+
+def get_encoding():
+    """Return preferred encoding."""
+    return locale.getpreferredencoding() or sys.getdefaultencoding()
+
+
+def main(argv=None, apply_config=True):
+    """Command-line entry."""
+    if argv is None:
+        argv = sys.argv
+
+    try:
+        # Exit on broken pipe.
+        signal.signal(signal.SIGPIPE, signal.SIG_DFL)
+    except AttributeError:  # pragma: no cover
+        # SIGPIPE is not available on Windows.
+        pass
+
+    try:
+        args = parse_args(argv[1:], apply_config=apply_config)
+
+        if args.list_fixes:
+            for code, description in sorted(supported_fixes()):
+                print('{code} - {description}'.format(
+                    code=code, description=description))
+            return 0
+
+        if args.files == ['-']:
+            assert not args.in_place
+
+            encoding = sys.stdin.encoding or get_encoding()
+
+            # LineEndingWrapper is unnecessary here due to the symmetry between
+            # standard in and standard out.
+            wrap_output(sys.stdout, encoding=encoding).write(
+                fix_code(sys.stdin.read(), args, encoding=encoding))
+        else:
+            if args.in_place or args.diff:
+                args.files = list(set(args.files))
+            else:
+                assert len(args.files) == 1
+                assert not args.recursive
+
+            fix_multiple_files(args.files, args, sys.stdout)
+    except KeyboardInterrupt:
+        return 1  # pragma: no cover
+
+
+class CachedTokenizer(object):
+
+    """A one-element cache around tokenize.generate_tokens().
+
+    Original code written by Ned Batchelder, in coverage.py.
+
+    """
+
+    def __init__(self):
+        self.last_text = None
+        self.last_tokens = None
+
+    def generate_tokens(self, text):
+        """A stand-in for tokenize.generate_tokens()."""
+        if text != self.last_text:
+            string_io = io.StringIO(text)
+            self.last_tokens = list(
+                tokenize.generate_tokens(string_io.readline)
+            )
+            self.last_text = text
+        return self.last_tokens
+
+_cached_tokenizer = CachedTokenizer()
+generate_tokens = _cached_tokenizer.generate_tokens
diff --git a/out.eb b/out.eb
deleted file mode 100644
index 170d6b6233..0000000000
--- a/out.eb
+++ /dev/null
@@ -1,35 +0,0 @@
-##
-# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
-#
-# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
-# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
-# License::   MIT/GPL
-# $Id$
-#
-# This work implements a part of the HPCBIOS project and is a component of the policy:
-# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
-##
-easyblock = 'ConfigureMake'
-
-name = 'AMOS'
-version = '3.1.0'
-
-homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS'
-description = "The AMOS consortium is committed to the development of open-source whole genome assembly software"
-
-toolchain = {'version': '1.4.10', 'name': 'goolf'}
-toolchainopts = {'optarch': True, 'pic': True}
-
-sources = [SOURCELOWER_TAR_GZ]
-source_urls = [('http://sourceforge.net/projects/%(namelower)s/files/%(namelower)s/%(version)s', 'download')]
-
-patches = ['%(name)s-%(version_major_minor)s.0_GCC-4.7.patch']
-
-dependencies = [('expat', '2.1.0'), ('MUMmer', '3.23')]
-
-parallel = 1  # make crashes otherwise
-
-
-sanity_check_paths = {'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], 'dirs': []}
-
-moduleclass = 'bio'
\ No newline at end of file
diff --git a/test.eb b/test.eb
deleted file mode 100644
index 67f7c8c305..0000000000
--- a/test.eb
+++ /dev/null
@@ -1,41 +0,0 @@
-##
-# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
-#
-# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
-# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
-# License::   MIT/GPL
-# $Id$
-#
-# This work implements a part of the HPCBIOS project and is a component of the policy:
-# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
-##
-
-easyblock = 'ConfigureMake'
-
-name = 'AMOS'
-version = '3.1.0'
-
-homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS'
-description = """The AMOS consortium is committed to the development of open-source whole genome assembly software"""
-
-toolchain = {'name': 'goolf', 'version': '1.4.10'}
-toolchainopts = {'optarch': True, 'pic': True}
-
-sources = [SOURCELOWER_TAR_GZ]
-source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')]
-
-patches = ['AMOS-3.1.0_GCC-4.7.patch']
-
-dependencies = [
-                ('expat', '2.1.0'),
-                ('MUMmer', '3.23'),
-               ]
-
-sanity_check_paths = {
-                      'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed' ],
-                      'dirs': []
-                     }
-
-parallel = 1  # make crashes otherwise
-
-moduleclass = 'bio'
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 38b11ca9b8..9fe934f18f 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1199,10 +1199,17 @@ def test_dump_extra(self):
             "homepage = 'http://foo.com/'",
             'description = "foo description"',
             '',
-            "toolchain = {'version': 'dummy', 'name': 'dummy'}",
+            "toolchain = {",
+            "    'version': 'dummy',",
+            "    'name': 'dummy'",
+            "}",
             '',
-            "dependencies = [('GCC', '4.6.4', '-test'), ('MPICH', '1.8', '', ('GCC', '4.6.4')), " +
-                "('bar', '1.0'), ('foobar/1.2.3', EXTERNAL_MODULE)]",
+            "dependencies = [",
+            "    ('GCC', '4.6.4', '-test'),",
+            "    ('MPICH', '1.8', '', ('GCC', '4.6.4')),",
+            "    ('bar', '1.0'),",
+            "    ('foobar/1.2.3', EXTERNAL_MODULE)",
+            "]",
             '',
             "foo_extra1 = 'foobar'",
         ])
@@ -1229,16 +1236,26 @@ def test_dump_template(self):
             "homepage = 'http://foo.com/'",
             'description = "foo description"',
             '',
-            "toolchain = {'version': 'dummy', 'name': 'dummy'}",
+            "toolchain = {",
+            "    'version': 'dummy',",
+            "    'name': 'dummy'",
+            '}',
             '',
-            "sources = ['foo-0.0.1.tar.gz']",
+            "sources = [",
+            "    'foo-0.0.1.tar.gz'",
+            ']',
             '',
-            "dependencies = [('bar', '1.2.3', '-test')]",
+            "dependencies = [",
+            "    ('bar', '1.2.3', '-test')",
+            ']',
             '',
             "preconfigopts = '--opt1=%s' % name",
             "configopts = '--opt2=0.0.1'",
             '',
-            "sanity_check_paths = {'files': ['files/foo/foobar', 'files/x-test'], 'dirs':[] }",
+            "sanity_check_paths = {",
+            "    'files': ['files/foo/foobar', 'files/x-test'],",
+            "    'dirs':[]",
+            '}',
             '',
             "foo_extra1 = 'foobar'"
         ])
@@ -1259,11 +1276,11 @@ def test_dump_template(self):
             r"versionsuffix = '-test'",
             r"homepage = 'http://foo.com/'",
             r'description = "foo description"',  # no templating for description
-            r"sources = \[SOURCELOWER_TAR_GZ\]",
-            r"dependencies = \[\('bar', '1.2.3', '%\(versionsuffix\)s'\)\]",
+            r"sources = \[\n    SOURCELOWER_TAR_GZ\n\]",
+            r"dependencies = \[\n    \('bar', '1.2.3', '%\(versionsuffix\)s'\)\n\]",
             r"preconfigopts = '--opt1=%\(name\)s'",
             r"configopts = '--opt2=%\(version\)s'",
-            r"sanity_check_paths = {'files': \['files/%\(namelower\)s/foobar', 'files/x-test'\]",
+            r"sanity_check_paths = {\n    'files': \['files/%\(namelower\)s/foobar', 'files/x-test'\]",
         ]
 
         for pattern in patterns:
@@ -1291,9 +1308,15 @@ def test_dump_comments(self):
             '',
             "# toolchain comment with newline",
             '',
-            "toolchain = {'version': 'dummy', 'name': 'dummy'}",
+            "toolchain = {",
+            "    'version': 'dummy',",
+            "    'name': 'dummy'",
+            '}',
             '',
-            "sanity_check_paths = {'files': ['files/foo/foobar'], 'dirs':[] }",
+            "sanity_check_paths = {",
+            "    'files': ['files/foobar'],  # comment on files",
+            "    'dirs':[]",
+            '}',
             '',
             "foo_extra1 = 'foobar'",
         ])
@@ -1309,7 +1332,8 @@ def test_dump_comments(self):
             r"# #\n# some header comment\n# #",
             r"name = 'Foo'  # name comment",
             r"# comment on the homepage\nhomepage = 'http://foo.com/'",
-            r"# toolchain comment with newline\n\ntoolchain = {'version': 'dummy', 'name': 'dummy'}"
+            r"# toolchain comment with newline\n\ntoolchain = {",
+            r"'files': \['files/foobar'\],  # comment on files",
         ]
 
         for pattern in patterns:

From 2ebee7ad2ecb0feca07538ea6a44cba0186e2f52 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Tue, 28 Jul 2015 15:24:15 +0200
Subject: [PATCH 1194/1356] style fixes

---
 easybuild/framework/easyconfig/easyconfig.py |  4 ++--
 easybuild/framework/easyconfig/parser.py     |  2 +-
 test/framework/easyconfig.py                 | 16 ++++++++--------
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index f6b8ca6dbe..1e79fa881c 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -544,7 +544,7 @@ def add_key_and_comments(key, val):
 
                 ebtxt.append("%s = %s" % (key, val))
 
-        def format_and_template(key, value, outer, comment = dict()):
+        def format_and_template(key, value, outer, comment=dict()):
             """ Returns string version of the value, including comments and newlines in lists, tuples and dicts """
             str_value = ''
 
@@ -747,7 +747,7 @@ def _dump_dependency(self, dep):
         """Dump parsed dependency in tuple format"""
 
         if dep['external_module']:
-            res = "('" + dep['full_mod_name']+ "', EXTERNAL_MODULE)"
+            res = "(%s, EXTERNAL_MODULE)" % quote_py_str(dep['full_mod_name'])
         else:
             # mininal spec: (name, version)
             tup = (dep['name'], dep['version'])
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index e88684ea35..6a023ff6d1 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -157,7 +157,7 @@ def _extract_comments(self):
 
         i = 0
         num_lines = len(raw)
-        while i<num_lines:
+        while i < num_lines:
             if raw[i].startswith('#') and header:
                 self.comments['header'].append(raw[i])
             else:
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 9fe934f18f..eb0c27af9b 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1201,14 +1201,14 @@ def test_dump_extra(self):
             '',
             "toolchain = {",
             "    'version': 'dummy',",
-            "    'name': 'dummy'",
+            "    'name': 'dummy',",
             "}",
             '',
             "dependencies = [",
             "    ('GCC', '4.6.4', '-test'),",
             "    ('MPICH', '1.8', '', ('GCC', '4.6.4')),",
             "    ('bar', '1.0'),",
-            "    ('foobar/1.2.3', EXTERNAL_MODULE)",
+            "    ('foobar/1.2.3', EXTERNAL_MODULE),",
             "]",
             '',
             "foo_extra1 = 'foobar'",
@@ -1238,15 +1238,15 @@ def test_dump_template(self):
             '',
             "toolchain = {",
             "    'version': 'dummy',",
-            "    'name': 'dummy'",
+            "    'name': 'dummy',",
             '}',
             '',
             "sources = [",
-            "    'foo-0.0.1.tar.gz'",
+            "    'foo-0.0.1.tar.gz',",
             ']',
             '',
             "dependencies = [",
-            "    ('bar', '1.2.3', '-test')",
+            "    ('bar', '1.2.3', '-test'),",
             ']',
             '',
             "preconfigopts = '--opt1=%s' % name",
@@ -1254,7 +1254,7 @@ def test_dump_template(self):
             '',
             "sanity_check_paths = {",
             "    'files': ['files/foo/foobar', 'files/x-test'],",
-            "    'dirs':[]",
+            "    'dirs':[],",
             '}',
             '',
             "foo_extra1 = 'foobar'"
@@ -1276,8 +1276,8 @@ def test_dump_template(self):
             r"versionsuffix = '-test'",
             r"homepage = 'http://foo.com/'",
             r'description = "foo description"',  # no templating for description
-            r"sources = \[\n    SOURCELOWER_TAR_GZ\n\]",
-            r"dependencies = \[\n    \('bar', '1.2.3', '%\(versionsuffix\)s'\)\n\]",
+            r"sources = \[\n    SOURCELOWER_TAR_GZ,\n\]",
+            r"dependencies = \[\n    \('bar', '1.2.3', '%\(versionsuffix\)s'\),\n\]",
             r"preconfigopts = '--opt1=%\(name\)s'",
             r"configopts = '--opt2=%\(version\)s'",
             r"sanity_check_paths = {\n    'files': \['files/%\(namelower\)s/foobar', 'files/x-test'\]",

From de35868b97dd4a35b44c44792912181435e53794 Mon Sep 17 00:00:00 2001
From: Caroline De Brouwer <debrouwercaroline@gmail.com>
Date: Wed, 29 Jul 2015 11:42:38 +0200
Subject: [PATCH 1195/1356] private methods + split formatting and templating

---
 easybuild/framework/easyconfig/easyconfig.py | 155 ++++++++++---------
 test/framework/easyconfig.py                 |  14 +-
 2 files changed, 87 insertions(+), 82 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 1e79fa881c..14717d1f7b 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -474,7 +474,7 @@ def toolchain(self):
             self.log.debug("Initialized toolchain: %s (opts: %s)" % (tc_dict, self['toolchainopts']))
         return self._toolchain
 
-    def dump(self, fp):
+    def dump(self, fp, formatting=True):
         """
         Dump this easyconfig to file, with the given filename.
         """
@@ -495,7 +495,6 @@ def dump(self, fp):
         ]
 
         last_keys = ['sanity_check_paths', 'moduleclass']
-
         orig_enable_templating = self.enable_templating
         self.enable_templating = False # templated values should be dumped unresolved
 
@@ -510,7 +509,7 @@ def dump(self, fp):
         keys = sorted(self.template_values, key=lambda k: len(self.template_values[k]), reverse=True)
         templ_val = OrderedDict([(self.template_values[k], k) for k in keys if len(self.template_values[k]) > 2])
 
-        def include_defined_parameters(keyset):
+        def include_defined_parameters(ebtxt, keyset):
             """
             Internal function to include parameters in the dumped easyconfig file which have a non-default value.
             """
@@ -526,66 +525,13 @@ def include_defined_parameters(keyset):
                         else:
                             val = quote_py_str(val)
 
-                        add_key_and_comments(key, val)
+                        ebtxt = self._add_key_and_comments(ebtxt, key, val, templ_const, templ_val, formatting)
 
                         printed_keys.append(key)
                         printed = True
                 if printed:
                     ebtxt.append('')
 
-        def add_key_and_comments(key, val):
-            """ Add key, value pair and comments (if there are any) to the dump file """
-            val = format_and_template(key, val, True)
-            if key in self.comments['inline']:
-                ebtxt.append("%s = %s%s" % (key, val, self.comments['inline'][key]))
-            else:
-                if key in self.comments['above']:
-                    ebtxt.extend(self.comments['above'][key])
-
-                ebtxt.append("%s = %s" % (key, val))
-
-        def format_and_template(key, value, outer, comment=dict()):
-            """ Returns string version of the value, including comments and newlines in lists, tuples and dicts """
-            str_value = ''
-
-            for k, v in self.comments['list_value'].get(key, {}).items():
-                if str(value) in k:
-                    comment[str(value)] = v
-
-            if outer:
-                if isinstance(value, list):
-                    str_value += '[\n'
-                    for el in value:
-                        str_value += format_and_template(key, el, False, comment) + ',' + comment.get(str(el), '') + '\n'
-                    str_value += ']'
-                elif isinstance(value, tuple):
-                    str_value += '(\n'
-                    for el in value:
-                        str_value += format_and_template(key, el, False, comment) + ',' + comment.get(str(el), '') + '\n'
-                    str_value += ')'
-                elif isinstance(value, dict):
-                    str_value += '{\n'
-                    for k, v in value.items():
-                        str_value += quote_py_str(k) + ': ' + format_and_template(key, v, False, comment) + ',' + comment.get(str(v), '') + '\n'
-                    str_value += '}'
-
-                value = str_value or value
-
-            else:
-                # dependencies are already dumped as strings, so they do not need to be quoted again
-                if isinstance(value, basestring) and key not in ['builddependencies', 'dependencies', 'hiddendependencies']:
-                    value = quote_py_str(value)
-                else:
-                    value = str(value)
-
-            # templates
-            if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
-                new_value = to_template_str(value, templ_const, templ_val)
-                if not r'%(' + key in new_value:
-                    value = new_value
-
-            return value
-
         # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
         printed_keys = []
@@ -593,22 +539,83 @@ def format_and_template(key, value, outer, comment=dict()):
         # add header comments
         ebtxt.extend(self.comments['header'])
 
-        include_defined_parameters(grouped_keys)
+        include_defined_parameters(ebtxt, grouped_keys)
 
         # print other easyconfig parameters at the end
         keys_to_ignore = printed_keys + last_keys
         for key in default_values:
             if key not in keys_to_ignore and self[key] != default_values[key]:
-                add_key_and_comments(key, quote_py_str(self[key]))
+                ebtxt = self._add_key_and_comments(ebtxt, key, quote_py_str(self[key]), templ_const, templ_val, formatting)
         ebtxt.append('')
 
         # print last two parameters
-        include_defined_parameters([[k] for k in last_keys])
+        include_defined_parameters(ebtxt, [[k] for k in last_keys])
 
         dumped_text = ('\n'.join(ebtxt))
         write_file(fp, (fix_code(dumped_text, options={'aggressive': 1, 'max_line_length':120})).strip())
         self.enable_templating = orig_enable_templating
 
+    def _add_key_and_comments(self, ebtxt, key, val, templ_const, templ_val, formatting):
+        """ Add key, value pair and comments (if there are any) to the dump file (helper method for dump()) """
+        if formatting:
+            val = self._format(key, val, True, dict())
+        else:
+            val = str(val)
+
+        # templates
+        if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
+            new_val = to_template_str(val, templ_const, templ_val)
+            if not r'%(' + key in new_val:
+                val = new_val
+
+        if key in self.comments['inline']:
+            ebtxt.append("%s = %s%s" % (key, val, self.comments['inline'][key]))
+        else:
+            if key in self.comments['above']:
+                ebtxt.extend(self.comments['above'][key])
+            ebtxt.append("%s = %s" % (key, val))
+
+        return ebtxt
+
+    def _format(self, key, value, outer, comment):
+        """ Returns string version of the value, including comments and newlines in lists, tuples and dicts """
+        str_value = ''
+
+        for k, v in self.comments['list_value'].get(key, {}).items():
+            if str(value) in k:
+                comment[str(value)] = v
+
+        if outer:
+            if isinstance(value, list):
+                str_value += '[\n'
+                for el in value:
+                    str_value += self._format(key, el, False, comment)
+                    str_value += ',' + comment.get(str(el), '') + '\n'
+                str_value += ']'
+            elif isinstance(value, tuple):
+                str_value += '(\n'
+                for el in value:
+                    str_value += self._format(key, el, False, comment)
+                    str_value += ',' + comment.get(str(el), '') + '\n'
+                str_value += ')'
+            elif isinstance(value, dict):
+                str_value += '{\n'
+                for k, v in value.items():
+                    str_value += quote_py_str(k) + ': ' + self._format(key, v, False, comment)
+                    str_value += ',' + comment.get(str(v), '') + '\n'
+                str_value += '}'
+
+            value = str_value or str(value)
+
+        else:
+            # dependencies are already dumped as strings, so they do not need to be quoted again
+            if isinstance(value, basestring) and key not in ['builddependencies', 'dependencies', 'hiddendependencies']:
+                value = quote_py_str(value)
+            else:
+                value = str(value)
+
+        return value
+
     def _validate(self, attr, values):  # private method
         """
         validation helper method. attr is the attribute it will check, values are the possible values.
@@ -1033,21 +1040,19 @@ def to_template_str(value, templ_const, templ_val):
         - templ_const is a dictionary of template strings (constants)
         - templ_val is an ordered dictionary of template strings specific for this easyconfig file
     """
-    if value not in templ_const.values():
-        old_value = None
-        while value != old_value:
-            old_value = value
-            # check for constant values
-            for const in templ_const:
-                if const in value:
-                    value = value.replace(const, templ_const[const])
-
-            # check for template values (note: templ_val dict is 'upside-down')
-            for tval, tname in templ_val.items():
-                # only replace full words with templates: word to replace should be at the beginning of a line
-                # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
-                # by another non-alphanumeric.
-                value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1%(' + tname + r')s\2', value)
+    old_value = None
+    while value != old_value:
+        old_value = value
+        # check for constant values
+        for tval, tname in templ_const.items():
+            value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1' + tname + r'\2', value)
+
+        for tval, tname in templ_val.items():
+            # only replace full words with templates: word to replace should be at the beginning of a line
+            # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
+            # by another non-alphanumeric.
+            value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1%(' + tname + r')s\2', value)
+
     return value
 
 
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index eb0c27af9b..4184af199f 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -367,7 +367,7 @@ def test_tweaking(self):
         eb['version'] = ver
         eb['toolchain']['version'] = tcver
         eb.enable_templating = True
-        eb.dump(self.eb_file)
+        eb.dump(self.eb_file, formatting=False)
 
         tweaks = {
             'toolchain_name': tcname,
@@ -1348,8 +1348,8 @@ def test_to_template_str(self):
 
         # reverse dict of known template constants; template values (which are keys here) must be 'string-in-string
         templ_const = {
-            "'template'":'TEMPLATE_VALUE',
-            "'%(name)s-%(version)s'": 'NAME_VERSION',
+            "template":'TEMPLATE_VALUE',
+            "%(name)s-%(version)s": 'NAME_VERSION',
         }
 
         templ_val = {
@@ -1359,13 +1359,13 @@ def test_to_template_str(self):
         }
 
         self.assertEqual(to_template_str("template", templ_const, templ_val), 'TEMPLATE_VALUE')
-        self.assertEqual(to_template_str("foo/bar/0.0.1/", templ_const, templ_val), "'%(name)s/bar/%(version)s/'")
+        self.assertEqual(to_template_str("foo/bar/0.0.1/", templ_const, templ_val), "%(name)s/bar/%(version)s/")
         self.assertEqual(to_template_str("foo-0.0.1", templ_const, templ_val), 'NAME_VERSION')
-        templ_list = to_template_str(['-test', 'dontreplacenamehere'], templ_const, templ_val)
+        templ_list = to_template_str("['-test', 'dontreplacenamehere']", templ_const, templ_val)
         self.assertEqual(templ_list, "['%(special_char)s', 'dontreplacenamehere']")
-        templ_dict = to_template_str({'a':'foo', 'b':'notemplate'}, templ_const, templ_val)
+        templ_dict = to_template_str("{'a': 'foo', 'b': 'notemplate'}", templ_const, templ_val)
         self.assertEqual(templ_dict, "{'a': '%(name)s', 'b': 'notemplate'}")
-        self.assertEqual(to_template_str(('foo', '0.0.1'), templ_const, templ_val), "('%(name)s', '%(version)s')")
+        self.assertEqual(to_template_str("('foo', '0.0.1')", templ_const, templ_val), "('%(name)s', '%(version)s')")
 
 
 def suite():

From 0eb05c6534a038ebaf4b967c349a93ea851efa89 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 5 Aug 2015 10:06:46 +0200
Subject: [PATCH 1196/1356] fix remarks

---
 easybuild/framework/easyconfig/easyconfig.py | 67 ++++++++++----------
 easybuild/framework/easyconfig/parser.py     | 61 +++++++++---------
 test/framework/easyconfig.py                 |  7 +-
 3 files changed, 69 insertions(+), 66 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 4fce3b3330..8d51fbf122 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -78,6 +78,24 @@
 # values for these keys will not be templated in dump()
 EXCLUDED_KEYS_REPLACE_TEMPLATES = ['easyblock', 'name', 'version', 'description', 'homepage', 'toolchain']
 
+
+# ordered groups of keys to obtain a nice looking easyconfig file
+GROUPED_PARAMS = [
+    ['easyblock'],
+    ['name', 'version', 'versionprefix', 'versionsuffix'],
+    ['homepage', 'description'],
+    ['toolchain', 'toolchainopts'],
+    ['sources', 'source_urls'],
+    ['patches'],
+    ['builddependencies', 'dependencies', 'hiddendependencies'],
+    ['osdependencies'],
+    ['preconfigopts', 'configopts'],
+    ['prebuildopts', 'buildopts'],
+    ['preinstallopts', 'installopts'],
+    ['parallel', 'maxparallel'],
+]
+LAST_PARAMS = ['sanity_check_paths', 'moduleclass']
+
 _easyconfig_files_cache = {}
 _easyconfigs_cache = {}
 
@@ -478,24 +496,6 @@ def dump(self, fp):
         Dump this easyconfig to file, with the given filename.
         """
 
-        # ordered groups of keys to obtain a nice looking easyconfig file
-        grouped_keys = [
-            ['easyblock'],
-            ['name', 'version', 'versionprefix', 'versionsuffix'],
-            ['homepage', 'description'],
-            ['toolchain', 'toolchainopts'],
-            ['sources', 'source_urls'],
-            ['patches'],
-            ['builddependencies', 'dependencies', 'hiddendependencies'],
-            ['osdependencies'],
-            ['preconfigopts', 'configopts'],
-            ['prebuildopts', 'buildopts'],
-            ['preinstallopts', 'installopts'],
-            ['parallel', 'maxparallel'],
-        ]
-
-        last_keys = ['sanity_check_paths', 'moduleclass']
-
         orig_enable_templating = self.enable_templating
         self.enable_templating = False # templated values should be dumped unresolved
 
@@ -510,6 +510,17 @@ def dump(self, fp):
         keys = sorted(self.template_values, key=lambda k: len(self.template_values[k]), reverse=True)
         templ_val = OrderedDict([(self.template_values[k], k) for k in keys if len(self.template_values[k]) > 2])
 
+        def add_key_and_comments(key, val):
+            """
+            Add key + value and comments (if any) to txt to be dumped.
+            """
+            if key in self.comments['inline']:
+                ebtxt.append("%s = %s  %s" % (key, val, self.comments['inline'][key]))
+            else:
+                if key in self.comments['above']:
+                    ebtxt.extend(self.comments['above'][key])
+                ebtxt.append("%s = %s" % (key, val))
+
         def include_defined_parameters(keyset):
             """
             Internal function to include parameters in the dumped easyconfig file which have a non-default value.
@@ -545,34 +556,24 @@ def include_defined_parameters(keyset):
                 if printed:
                     ebtxt.append('')
 
-        def add_key_and_comments(key, val):
-            """ Adds key, value pair and comments (if there are any) to the dump file """
-            if key in self.comments['inline']:
-                ebtxt.append("%s = %s  %s" % (key, val, self.comments['inline'][key]))
-            else:
-                if key in self.comments['above']:
-                    ebtxt.extend(self.comments['above'][key])
-
-                ebtxt.append("%s = %s" % (key, val))
-
-        # print easyconfig parameters ordered and in groups specified above
         ebtxt = []
         printed_keys = []
 
         # add header comments
         ebtxt.extend(self.comments['header'])
 
-        include_defined_parameters(grouped_keys)
+        # print easyconfig parameters ordered and in groups specified above
+        include_defined_parameters(GROUPED_PARAMS)
 
         # print other easyconfig parameters at the end
-        keys_to_ignore = printed_keys + last_keys
+        keys_to_ignore = printed_keys + LAST_PARAMS
         for key in default_values:
             if key not in keys_to_ignore and self[key] != default_values[key]:
                 add_key_and_comments(key, quote_py_str(self[key]))
         ebtxt.append('')
 
-        # print last two parameters
-        include_defined_parameters([[k] for k in last_keys])
+        # print last parameters
+        include_defined_parameters([[k] for k in LAST_PARAMS])
 
         write_file(fp, ('\n'.join(ebtxt)).strip()) # strip for newlines at the end
 
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index ee83230dbf..f78ba3a0e0 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -144,39 +144,40 @@ def _extract_comments(self):
         # At the moment there is no support for inline comments on lines that don't contain the key value
 
         self.comments = {
+            'above' : {},
             'header' : [],
-            'inline' : dict(),
-            'above' : dict(),
+            'inline' : {},
          }
 
-        raw = self.rawcontent.split('\n')
-        header = True
-
-        i = 0
-        num_lines = len(raw)
-        while i<num_lines:
-            if raw[i].startswith('#') and header:
-                self.comments['header'].append(raw[i])
-            else:
-                header = False
-                if raw[i].startswith('#'):
-                    comment = []
-                    # comment could be multi-line
-                    while raw[i].startswith('#') or not raw[i]:
-                        comment.append(raw[i])
-                        i += 1
-                    key = raw[i].split('=', 1)[0].strip()
-                    self.comments['above'][key] = comment
-
-                elif '#' in raw[i]:  # inline comment
-                    comment = raw[i].rsplit('#', 1)[1].strip()
-                    key = raw[i].split('=', 1)[0].strip()
-
-                    # check if hash actually indicated a comment; or is part of the value
-                    if key in self.get_config_dict():
-                        if comment.replace("'", "").replace('"', '') not in str(self.get_config_dict()[key]):
-                            self.comments['inline'][key] = '# ' + comment
-            i += 1
+        rawlines = self.rawcontent.split('\n')
+
+        # extract header first
+        while rawlines[0].startswith('#'):
+            self.comments['header'].append(rawlines.pop(0))
+
+        parsed_ec = self.get_config_dict()
+
+        while rawlines:
+            rawline = rawlines.pop(0)
+            if rawline.startswith('#'):
+                comment = []
+                # comment could be multi-line
+                while rawline.startswith('#') or not rawline:
+                    # drop empty lines (that don't even include a #)
+                    if rawline:
+                        comment.append(rawline)
+                    rawline = rawlines.pop(0)
+                key = rawline.split('=', 1)[0].strip()
+                self.comments['above'][key] = comment
+
+            elif '#' in rawline:  # inline comment
+                key = rawline.split('=', 1)[0].strip()
+                comment = rawline.rsplit('#', 1)[1].strip()
+
+                # check if hash actually indicated a comment, or if it is part of the value
+                if key in parsed_ec:
+                    if comment.replace("'", "").replace('"', '') not in str(parsed_ec[key]):
+                        self.comments['inline'][key] = '# ' + comment
 
     def _det_format_version(self):
         """Extract the format version from the raw content"""
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 38b11ca9b8..8f785250c7 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1287,9 +1287,9 @@ def test_dump_comments(self):
             '',
             "# comment on the homepage",
             "homepage = 'http://foo.com/'",
-            'description = "foo description"',
+            'description = "foo description with a # in it"  # test',
             '',
-            "# toolchain comment with newline",
+            "# toolchain comment",
             '',
             "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
@@ -1309,7 +1309,8 @@ def test_dump_comments(self):
             r"# #\n# some header comment\n# #",
             r"name = 'Foo'  # name comment",
             r"# comment on the homepage\nhomepage = 'http://foo.com/'",
-            r"# toolchain comment with newline\n\ntoolchain = {'version': 'dummy', 'name': 'dummy'}"
+            r'description = "foo description with a # in it"  # test',
+            r"# toolchain comment\ntoolchain = {'version': 'dummy', 'name': 'dummy'}"
         ]
 
         for pattern in patterns:

From a60754cf4b24442c33a32c5c849a333c637020a2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 5 Aug 2015 12:01:41 +0200
Subject: [PATCH 1197/1356] dance around issue with get_config_dict triggering
 a (re)parse, which may be a problem for format v2 easyconfigs

---
 easybuild/framework/easyconfig/parser.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index f78ba3a0e0..6e49a59232 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -155,8 +155,7 @@ def _extract_comments(self):
         while rawlines[0].startswith('#'):
             self.comments['header'].append(rawlines.pop(0))
 
-        parsed_ec = self.get_config_dict()
-
+        parsed_ec = None
         while rawlines:
             rawline = rawlines.pop(0)
             if rawline.startswith('#'):
@@ -171,6 +170,11 @@ def _extract_comments(self):
                 self.comments['above'][key] = comment
 
             elif '#' in rawline:  # inline comment
+                if parsed_ec is None:
+                    # obtain parsed easyconfig as a dict, if it wasn't already
+                    # note: this currently trigger a reparse
+                    parsed_ec = self.get_config_dict()
+
                 key = rawline.split('=', 1)[0].strip()
                 comment = rawline.rsplit('#', 1)[1].strip()
 

From b0ced05fa293ba0cdd17404176b58d9ce5273a5b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Aug 2015 12:13:58 +0200
Subject: [PATCH 1198/1356] move support for dumping easyconfig in format v1 to
 easyconfig/format/one.py + some refactoring

---
 easybuild/framework/easyconfig/easyconfig.py  | 202 +-----------------
 .../framework/easyconfig/format/format.py     |  23 +-
 easybuild/framework/easyconfig/format/one.py  | 141 +++++++++++-
 easybuild/framework/easyconfig/parser.py      |  19 +-
 easybuild/framework/easyconfig/templates.py   |  25 ++-
 easybuild/framework/easyconfig/tweak.py       |   5 +-
 easybuild/tools/utilities.py                  |   5 +
 test/framework/easyconfig.py                  |  10 +-
 8 files changed, 218 insertions(+), 212 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 6c24852792..d523ced2b0 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -44,7 +44,7 @@
 from vsc.utils.patterns import Singleton
 
 import easybuild.tools.environment as env
-from easybuild.tools.autopep8 import fix_code
+#from easybuild.tools.autopep8 import fix_code
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_module_naming_scheme
 from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file, write_file
@@ -56,7 +56,7 @@
 from easybuild.tools.systemtools import check_os_dependency
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME, DUMMY_TOOLCHAIN_VERSION
 from easybuild.tools.toolchain.utilities import get_toolchain
-from easybuild.tools.utilities import remove_unwanted_chars, quote_str
+from easybuild.tools.utilities import quote_py_str, quote_str, remove_unwanted_chars
 from easybuild.framework.easyconfig import MANDATORY
 from easybuild.framework.easyconfig.constants import EXTERNAL_MODULE_MARKER
 from easybuild.framework.easyconfig.default import DEFAULT_CONFIG
@@ -76,26 +76,6 @@
 # set of configure/build/install options that can be provided as lists for an iterated build
 ITERATE_OPTIONS = ['preconfigopts', 'configopts', 'prebuildopts', 'buildopts', 'preinstallopts', 'installopts']
 
-# values for these keys will not be templated in dump()
-EXCLUDED_KEYS_REPLACE_TEMPLATES = ['easyblock', 'name', 'version', 'description', 'homepage', 'toolchain']
-
-
-# ordered groups of keys to obtain a nice looking easyconfig file
-GROUPED_PARAMS = [
-    ['easyblock'],
-    ['name', 'version', 'versionprefix', 'versionsuffix'],
-    ['homepage', 'description'],
-    ['toolchain', 'toolchainopts'],
-    ['sources', 'source_urls'],
-    ['patches'],
-    ['builddependencies', 'dependencies', 'hiddendependencies'],
-    ['osdependencies'],
-    ['preconfigopts', 'configopts'],
-    ['prebuildopts', 'buildopts'],
-    ['preinstallopts', 'installopts'],
-    ['parallel', 'maxparallel'],
-]
-LAST_PARAMS = ['sanity_check_paths', 'moduleclass']
 
 _easyconfig_files_cache = {}
 _easyconfigs_cache = {}
@@ -197,6 +177,7 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
 
         # parse easyconfig file
         self.build_specs = build_specs
+        self.parser = EasyConfigParser(filename=self.path, rawcontent=self.rawtxt)
         self.parse()
 
         # handle allowed system dependencies
@@ -260,13 +241,10 @@ def parse(self):
         self.log.debug("Obtained specs dict %s" % arg_specs)
 
         self.log.info("Parsing easyconfig file %s with rawcontent: %s" % (self.path, self.rawtxt))
-        parser = EasyConfigParser(filename=self.path, rawcontent=self.rawtxt)
-        parser.set_specifications(arg_specs)
-        local_vars = parser.get_config_dict()
+        self.parser.set_specifications(arg_specs)
+        local_vars = self.parser.get_config_dict()
         self.log.debug("Parsed easyconfig as a dictionary: %s" % local_vars)
 
-        self.comments = parser.get_comments()
-
         # make sure all mandatory parameters are defined
         # this includes both generic mandatory parameters and software-specific parameters defined via extra_options
         missing_mandatory_keys = [key for key in self.mandatory if key not in local_vars]
@@ -492,7 +470,7 @@ def toolchain(self):
             self.log.debug("Initialized toolchain: %s (opts: %s)" % (tc_dict, self['toolchainopts']))
         return self._toolchain
 
-    def dump(self, fp, formatting=True):
+    def dump(self, fp):
         """
         Dump this easyconfig to file, with the given filename.
         """
@@ -510,125 +488,13 @@ def dump(self, fp, formatting=True):
         keys = sorted(self.template_values, key=lambda k: len(self.template_values[k]), reverse=True)
         templ_val = OrderedDict([(self.template_values[k], k) for k in keys if len(self.template_values[k]) > 2])
 
-        def add_key_and_comments(key, val):
-            """
-            Add key + value and comments (if any) to txt to be dumped.
-            """
-            if key in self.comments['inline']:
-                ebtxt.append("%s = %s  %s" % (key, val, self.comments['inline'][key]))
-            else:
-                if key in self.comments['above']:
-                    ebtxt.extend(self.comments['above'][key])
-                ebtxt.append("%s = %s" % (key, val))
-
-        def include_defined_parameters(ebtxt, keyset):
-            """
-            Internal function to include parameters in the dumped easyconfig file which have a non-default value.
-            """
-            for group in keyset:
-                printed = False
-                for key in group:
-                    val = self[key]
-                    if val != default_values[key]:
-                        # dependency easyconfig parameters were parsed, so these need special care to 'unparse' them
-                        if key in ['builddependencies', 'dependencies', 'hiddendependencies']:
-                            dumped_deps = [self._dump_dependency(d) for d in val]
-                            val = dumped_deps
-                        else:
-                            val = quote_py_str(val)
-
-                        ebtxt = self._add_key_and_comments(ebtxt, key, val, templ_const, templ_val, formatting)
-
-                        printed_keys.append(key)
-                        printed = True
-                if printed:
-                    ebtxt.append('')
-
-        ebtxt = []
-        printed_keys = []
-
-        # add header comments
-        ebtxt.extend(self.comments['header'])
-
-        # print easyconfig parameters ordered and in groups specified above
-        include_defined_parameters(ebtxt, GROUPED_PARAMS)
-
-        # print other easyconfig parameters at the end
-        keys_to_ignore = printed_keys + LAST_PARAMS
-        for key in default_values:
-            if key not in keys_to_ignore and self[key] != default_values[key]:
-                ebtxt = self._add_key_and_comments(ebtxt, key, quote_py_str(self[key]), templ_const, templ_val, formatting)
-        ebtxt.append('')
-
-        # print last parameters
-        include_defined_parameters(ebtxt, [[k] for k in LAST_PARAMS])
-
-        write_file(fp, ('\n'.join(ebtxt)).strip()) # strip for newlines at the end
-
-        dumped_text = ('\n'.join(ebtxt))
-        write_file(fp, (fix_code(dumped_text, options={'aggressive': 1, 'max_line_length':120})).strip())
-        self.enable_templating = orig_enable_templating
+        ectxt = self.parser.dump(self, default_values, templ_const, templ_val)
 
-    def _add_key_and_comments(self, ebtxt, key, val, templ_const, templ_val, formatting):
-        """ Add key, value pair and comments (if there are any) to the dump file (helper method for dump()) """
-        if formatting:
-            val = self._format(key, val, True, dict())
-        else:
-            val = str(val)
+        #ectxt = fix_code(ectxt, options={'aggressive': 1, 'max_line_length': 120})
 
-        # templates
-        if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
-            new_val = to_template_str(val, templ_const, templ_val)
-            if not r'%(' + key in new_val:
-                val = new_val
+        write_file(fp, ectxt.strip())
 
-        if key in self.comments['inline']:
-            ebtxt.append("%s = %s%s" % (key, val, self.comments['inline'][key]))
-        else:
-            if key in self.comments['above']:
-                ebtxt.extend(self.comments['above'][key])
-            ebtxt.append("%s = %s" % (key, val))
-
-        return ebtxt
-
-    def _format(self, key, value, outer, comment):
-        """ Returns string version of the value, including comments and newlines in lists, tuples and dicts """
-        str_value = ''
-
-        for k, v in self.comments['list_value'].get(key, {}).items():
-            if str(value) in k:
-                comment[str(value)] = v
-
-        if outer:
-            if isinstance(value, list):
-                str_value += '[\n'
-                for el in value:
-                    str_value += self._format(key, el, False, comment)
-                    str_value += ',' + comment.get(str(el), '') + '\n'
-                str_value += ']'
-            elif isinstance(value, tuple):
-                str_value += '(\n'
-                for el in value:
-                    str_value += self._format(key, el, False, comment)
-                    str_value += ',' + comment.get(str(el), '') + '\n'
-                str_value += ')'
-            elif isinstance(value, dict):
-                str_value += '{\n'
-                for k, v in value.items():
-                    str_value += quote_py_str(k) + ': ' + self._format(key, v, False, comment)
-                    str_value += ',' + comment.get(str(v), '') + '\n'
-                str_value += '}'
-
-            value = str_value or str(value)
-
-        else:
-            # dependencies are already dumped as strings, so they do not need to be quoted again
-            if isinstance(value, basestring) and key not in ['builddependencies', 'dependencies', 'hiddendependencies']:
-                value = quote_py_str(value)
-            else:
-                value = str(value)
-
-        return value
+        self.enable_templating = orig_enable_templating
 
     def _validate(self, attr, values):  # private method
         """
@@ -764,26 +630,6 @@ def _parse_dependency(self, dep, hidden=False):
 
         return dependency
 
-    def _dump_dependency(self, dep):
-        """Dump parsed dependency in tuple format"""
-
-        if dep['external_module']:
-            res = "(%s, EXTERNAL_MODULE)" % quote_py_str(dep['full_mod_name'])
-        else:
-            # mininal spec: (name, version)
-            tup = (dep['name'], dep['version'])
-            if dep['toolchain'] != self['toolchain']:
-                if dep['dummy']:
-                    tup += (dep['versionsuffix'], True)
-                else:
-                    tup += (dep['versionsuffix'], (dep['toolchain']['name'], dep['toolchain']['version']))
-
-            elif dep['versionsuffix']:
-                tup += (dep['versionsuffix'],)
-
-            res = str(tup)
-        return res
-
     def generate_template_values(self):
         """Try to generate all template values."""
         # TODO proper recursive code https://github.com/hpcugent/easybuild-framework/issues/474
@@ -1042,34 +888,6 @@ def resolve_template(value, tmpl_dict):
     return value
 
 
-def quote_py_str(val):
-    """Version of quote_str specific for generating use in Python context (e.g., easyconfig parameters)."""
-    return quote_str(val, escape_newline=True, prefer_single_quotes=True)
-
-
-def to_template_str(value, templ_const, templ_val):
-    """
-    Insert template values where possible
-        - value is a string
-        - templ_const is a dictionary of template strings (constants)
-        - templ_val is an ordered dictionary of template strings specific for this easyconfig file
-    """
-    old_value = None
-    while value != old_value:
-        old_value = value
-        # check for constant values
-        for tval, tname in templ_const.items():
-            value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1' + tname + r'\2', value)
-
-        for tval, tname in templ_val.items():
-            # only replace full words with templates: word to replace should be at the beginning of a line
-            # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
-            # by another non-alphanumeric.
-            value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1%(' + tname + r')s\2', value)
-
-    return value
-
-
 def process_easyconfig(path, build_specs=None, validate=True, parse_only=False, hidden=None):
     """
     Process easyconfig, returning some information for each block
diff --git a/easybuild/framework/easyconfig/format/format.py b/easybuild/framework/easyconfig/format/format.py
index 01bc6a4268..ec388d845d 100644
--- a/easybuild/framework/easyconfig/format/format.py
+++ b/easybuild/framework/easyconfig/format/format.py
@@ -48,6 +48,27 @@
 FORMAT_VERSION_REGEXP = re.compile(r'^#\s+%s\s*(?P<major>\d+)\.(?P<minor>\d+)\s*$' % FORMAT_VERSION_KEYWORD, re.M)
 FORMAT_DEFAULT_VERSION = EasyVersion('1.0')
 
+# values for these keys will not be templated in dump()
+EXCLUDED_KEYS_REPLACE_TEMPLATES = ['easyblock', 'name', 'version', 'description', 'homepage', 'toolchain']
+
+# ordered groups of keys to obtain a nice looking easyconfig file
+GROUPED_PARAMS = [
+    ['easyblock'],
+    ['name', 'version', 'versionprefix', 'versionsuffix'],
+    ['homepage', 'description'],
+    ['toolchain', 'toolchainopts'],
+    ['sources', 'source_urls'],
+    ['patches'],
+    ['builddependencies', 'dependencies', 'hiddendependencies'],
+    ['osdependencies'],
+    ['preconfigopts', 'configopts'],
+    ['prebuildopts', 'buildopts'],
+    ['preinstallopts', 'installopts'],
+    ['parallel', 'maxparallel'],
+]
+LAST_PARAMS = ['sanity_check_paths', 'moduleclass']
+
+
 _log = fancylogger.getLogger('easyconfig.format.format', fname=False)
 
 
@@ -602,7 +623,7 @@ def parse(self, txt, **kwargs):
         """Parse the txt according to this format. This is highly version specific"""
         raise NotImplementedError
 
-    def dump(self):
+    def dump(self, ecfg, default_values, comments, templ_const, templ_val):
         """Dump easyconfig according to this format. This is higly version specific"""
         raise NotImplementedError
 
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index da8277b175..6d33786be3 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -36,16 +36,40 @@
 import tempfile
 from vsc.utils import fancylogger
 
-from easybuild.framework.easyconfig.format.format import FORMAT_DEFAULT_VERSION, get_format_version
+from easybuild.framework.easyconfig.format.format import EXCLUDED_KEYS_REPLACE_TEMPLATES, FORMAT_DEFAULT_VERSION
+from easybuild.framework.easyconfig.format.format import GROUPED_PARAMS, LAST_PARAMS, get_format_version
 from easybuild.framework.easyconfig.format.pyheaderconfigobj import EasyConfigFormatConfigObj
 from easybuild.framework.easyconfig.format.version import EasyVersion
+from easybuild.framework.easyconfig.templates import to_template_str
 from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.filetools import write_file
+from easybuild.tools.utilities import quote_py_str
 
 
 _log = fancylogger.getLogger('easyconfig.format.one', fname=False)
 
 
+def dump_dependency(dep, toolchain):
+    """Dump parsed dependency in tuple format"""
+
+    if dep['external_module']:
+        res = "(%s, EXTERNAL_MODULE)" % quote_py_str(dep['full_mod_name'])
+    else:
+        # mininal spec: (name, version)
+        tup = (dep['name'], dep['version'])
+        if dep['toolchain'] != toolchain:
+            if dep['dummy']:
+                tup += (dep['versionsuffix'], True)
+            else:
+                tup += (dep['versionsuffix'], (dep['toolchain']['name'], dep['toolchain']['version']))
+
+        elif dep['versionsuffix']:
+            tup += (dep['versionsuffix'],)
+
+        res = str(tup)
+    return res
+
+
 class FormatOneZero(EasyConfigFormatConfigObj):
     """Support for easyconfig format 1.x"""
     VERSION = EasyVersion('1.0')
@@ -88,6 +112,121 @@ def parse(self, txt):
         """
         super(FormatOneZero, self).parse(txt, strict_section_markers=True)
 
+    def _format(self, key, value, item_comments, comments, outer=False):
+        """ Returns string version of the value, including comments and newlines in lists, tuples and dicts """
+        res = ''
+
+        for k, v in comments['iter'].get(key, {}).items():
+            if str(value) in k:
+                item_comments[str(value)] = v
+
+        if outer:
+            if isinstance(value, list):
+                res += '[\n'
+                for el in value:
+                    res += '    ' + self._format(key, el, item_comments, comments)
+                    res += ',' + item_comments.get(str(el), '') + '\n'
+                res += ']'
+            elif isinstance(value, tuple):
+                res += '(\n'
+                for el in value:
+                    res += '    ' + self._format(key, el, item_comments, comments)
+                    res += ',' + item_comments.get(str(el), '') + '\n'
+                res += ')'
+            elif isinstance(value, dict) and key not in ['toolchain']:  # FIXME
+                res += '{\n'
+                for k, v in sorted(value.items())[::-1]:  # FIXME
+                    res += '    ' + quote_py_str(k) + ': ' + self._format(key, v, item_comments, comments)
+                    res += ',' + item_comments.get(str(v), '') + '\n'
+                res += '}'
+
+            res = res or str(value)
+
+        else:
+            # dependencies are already dumped as strings, so they do not need to be quoted again
+            if isinstance(value, basestring) and key not in ['builddependencies', 'dependencies', 'hiddendependencies']:
+                res = quote_py_str(value)
+            else:
+                res = str(value)
+
+        return res
+
+    def _add_key_and_comments(self, key, val, comments, templ_const, templ_val):
+        """ Add key, value pair and comments (if there are any) to the dump file (helper method for dump()) """
+        res = []
+        val = self._format(key, val, {}, comments, outer=True)
+
+        # templates
+        if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
+            new_val = to_template_str(val, templ_const, templ_val)
+            if not r'%(' + key in new_val:
+                val = new_val
+
+        if key in comments['inline']:
+            res.append("%s = %s%s" % (key, val, comments['inline'][key]))
+        else:
+            if key in comments['above']:
+                res.extend(comments['above'][key])
+            res.append("%s = %s" % (key, val))
+
+        return res
+
+    def _include_defined_parameters(self, ecfg, keyset, default_values, comments, templ_const, templ_val):
+        """
+        Internal function to include parameters in the dumped easyconfig file which have a non-default value.
+        """
+        eclines = []
+        printed_keys = []
+        for group in keyset:
+            printed = False
+            for key in group:
+                if ecfg[key] != default_values[key]:
+                    # dependency easyconfig parameters were parsed, so these need special care to 'unparse' them
+                    if key in ['builddependencies', 'dependencies', 'hiddendependencies']:
+                        dumped_deps = [dump_dependency(d, ecfg['toolchain']) for d in ecfg[key]]
+                        val = dumped_deps
+                    else:
+                        val = quote_py_str(ecfg[key])
+
+                    eclines.extend(self._add_key_and_comments(key, val, comments, templ_const, templ_val))
+
+                    printed_keys.append(key)
+                    printed = True
+            if printed:
+                eclines.append('')
+
+        return eclines, printed_keys
+
+    def dump(self, ecfg, default_values, comments, templ_const, templ_val):
+        """
+        Dump easyconfig in format v1.
+
+        @param ecfg: EasyConfig instance
+        @param default_values: default values for easyconfig parameters
+        @param comments: comments extracted from easyconfig file
+        @param templ_const: known template constants
+        @param templ_val: known template values
+        """
+        # include header comments first
+        eclines = comments['header'][:]
+
+        # print easyconfig parameters ordered and in groups specified above
+        more_eclines, printed_keys = self._include_defined_parameters(ecfg, GROUPED_PARAMS, default_values, comments, templ_const, templ_val)
+        eclines.extend(more_eclines)
+
+        # print other easyconfig parameters at the end
+        keys_to_ignore = printed_keys + LAST_PARAMS
+        for key in default_values:
+            if key not in keys_to_ignore and ecfg[key] != default_values[key]:
+                eclines.extend(self._add_key_and_comments(key, quote_py_str(ecfg[key]), comments, templ_const, templ_val))
+        eclines.append('')
+
+        # print last parameters
+        more_eclines, _ = self._include_defined_parameters(ecfg, [[k] for k in LAST_PARAMS], default_values, comments, templ_const, templ_val)
+        eclines.extend(more_eclines)
+
+        return '\n'.join(eclines)
+
 
 def retrieve_blocks_in_spec(spec, only_blocks, silent=False):
     """
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 25cc500199..703ff9983c 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -146,9 +146,10 @@ def _extract_comments(self):
         # At the moment there is no support for inline comments on lines that don't contain the key value
 
         self.comments = {
-            'above' : {},
-            'header' : [],
-            'inline' : {},
+            'above' : {},  # comments for a particular parameter definition
+            'header' : [],  # header comment lines
+            'inline' : {},  # inline comments
+            'iter': {},  # (inline) comments on elements of iterable values
          }
 
         rawlines = self.rawcontent.split('\n')
@@ -189,14 +190,14 @@ def _extract_comments(self):
                         if not isinstance(v, basestring) and val in str(v):
                             key = k
                             comment_value = val
-                            if not self.comments['list_value'].get(key):
-                                self.comments['list_value'][key] = {}
+                            if not self.comments['iter'].get(key):
+                                self.comments['iter'][key] = {}
 
                 # check if hash actually indicated a comment; or is part of the value
                 if key in parsed_ec:
                     if comment.replace("'", "").replace('"', '') not in str(parsed_ec[key]):
                         if comment_value:
-                            self.comments['list_value'][key][comment_value] = '  # ' + comment
+                            self.comments['iter'][key][comment_value] = '  # ' + comment
                         else:
                             self.comments['inline'][key] = '  # ' + comment
 
@@ -254,6 +255,6 @@ def get_config_dict(self, validate=True):
             self._formatter.validate()
         return self._formatter.get_config_dict()
 
-    def get_comments(self):
-        """Return comments, and their location info"""
-        return copy.deepcopy(self.comments)
+    def dump(self, ecfg, default_values, templ_const, templ_val):
+        """Dump easyconfig in format it was parsed from."""
+        return self._formatter.dump(ecfg, default_values, self.comments, templ_const, templ_val)
diff --git a/easybuild/framework/easyconfig/templates.py b/easybuild/framework/easyconfig/templates.py
index 7608aeece5..93dd3d9844 100644
--- a/easybuild/framework/easyconfig/templates.py
+++ b/easybuild/framework/easyconfig/templates.py
@@ -30,7 +30,7 @@
 @author: Stijn De Weirdt (Ghent University)
 @author: Fotis Georgatos (Uni.Lu, NTUA)
 """
-
+import re
 from vsc.utils import fancylogger
 from distutils.version import LooseVersion
 
@@ -203,6 +203,29 @@ def template_constant_dict(config, ignore=None, skip_lower=True):
     return template_values
 
 
+def to_template_str(value, templ_const, templ_val):
+    """
+    Insert template values where possible
+        - value is a string
+        - templ_const is a dictionary of template strings (constants)
+        - templ_val is an ordered dictionary of template strings specific for this easyconfig file
+    """
+    old_value = None
+    while value != old_value:
+        old_value = value
+        # check for constant values
+        for tval, tname in templ_const.items():
+            value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1' + tname + r'\2', value)
+
+        for tval, tname in templ_val.items():
+            # only replace full words with templates: word to replace should be at the beginning of a line
+            # or be preceded by a non-alphanumeric (\W). It should end at the end of a line or be succeeded
+            # by another non-alphanumeric.
+            value = re.sub(r'(^|\W)' + re.escape(tval) + r'(\W|$)', r'\1%(' + tname + r')s\2', value)
+
+    return value
+
+
 def template_documentation():
     """Generate the templating documentation"""
     # This has to reflect the methods/steps used in easyconfig _generate_template_values
diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index aeca7e2a2e..3c79b7205e 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -143,10 +143,11 @@ def tweak_one(src_fn, target_fn, tweaks, targetdir=None):
     # determine new toolchain if it's being changed
     keys = tweaks.keys()
     if 'toolchain_name' in keys or 'toolchain_version' in keys:
-        tc_regexp = re.compile(r"^\s*toolchain\s*=\s*(.*)$", re.M)
+        # note: this assumes that the toolchain spec is single-line
+        tc_regexp = re.compile(r"^\s*toolchain\s*=\s*({[^}\n]+})\s*$", re.M)
         res = tc_regexp.search(ectxt)
         if not res:
-            raise EasyBuildError("No toolchain found in easyconfig file %s?", src_fn)
+            raise EasyBuildError("No toolchain found in easyconfig file %s: %s", src_fn, ectxt)
 
         toolchain = eval(res.group(1))
         for key in ['name', 'version']:
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index cc8fe2185b..555081d60e 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -90,6 +90,11 @@ def quote_str(val, escape_newline=False, prefer_single_quotes=False):
         return val
 
 
+def quote_py_str(val):
+    """Version of quote_str specific for generating use in Python context (e.g., easyconfig parameters)."""
+    return quote_str(val, escape_newline=True, prefer_single_quotes=True)
+
+
 def remove_unwanted_chars(inputstring):
     """Remove unwanted characters from the given string and return a copy
 
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 74c60f46af..8d7fd4bb0b 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -45,8 +45,9 @@
 from easybuild.framework.easyconfig.constants import EXTERNAL_MODULE_MARKER
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.framework.easyconfig.easyconfig import create_paths
-from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, quote_py_str, to_template_str
+from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, quote_py_str
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
+from easybuild.framework.easyconfig.templates import to_template_str
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak_one
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import module_classes
@@ -367,7 +368,7 @@ def test_tweaking(self):
         eb['version'] = ver
         eb['toolchain']['version'] = tcver
         eb.enable_templating = True
-        eb.dump(self.eb_file, formatting=False)
+        eb.dump(self.eb_file)
 
         tweaks = {
             'toolchain_name': tcname,
@@ -1199,10 +1200,7 @@ def test_dump_extra(self):
             "homepage = 'http://foo.com/'",
             'description = "foo description"',
             '',
-            "toolchain = {",
-            "    'version': 'dummy',",
-            "    'name': 'dummy',",
-            "}",
+            "toolchain = {'version': 'dummy', 'name': 'dummy'}",
             '',
             "dependencies = [",
             "    ('GCC', '4.6.4', '-test'),",

From 38361401dd36985c2045f62e19df1dd93319c36e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Aug 2015 15:02:03 +0200
Subject: [PATCH 1199/1356] use copy() method rather than copy.deepcopy on
 EasyConfig instances

---
 easybuild/framework/easyconfig/easyconfig.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index d523ced2b0..509fde7ecd 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -906,7 +906,7 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False,
     if build_specs is None:
         cache_key = (path, validate, hidden, parse_only)
         if cache_key in _easyconfigs_cache:
-            return copy.deepcopy(_easyconfigs_cache[cache_key])
+            return [e.copy() for e in _easyconfigs_cache[cache_key]]
 
     easyconfigs = []
     for spec in blocks:
@@ -965,7 +965,7 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False,
             easyconfig['unresolved_deps'] = copy.deepcopy(easyconfig['dependencies'])
 
     if cache_key is not None:
-        _easyconfigs_cache[cache_key] = copy.deepcopy(easyconfigs)
+        _easyconfigs_cache[cache_key] = [e.copy() for e in easyconfigs]
 
     return easyconfigs
 

From 702a9235421ddb639eeeb3745e2f4282e534c54d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Aug 2015 15:53:38 +0200
Subject: [PATCH 1200/1356] make reformatting of dumped easyconfigs with
 autopep8 optional, add unit test

---
 easybuild/framework/easyconfig/easyconfig.py | 24 ++++++++++++++++----
 easybuild/tools/config.py                    |  1 +
 easybuild/tools/options.py                   |  1 +
 test/framework/easyconfig.py                 | 11 +++++++++
 4 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 509fde7ecd..0bfb6c55d7 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -44,7 +44,6 @@
 from vsc.utils.patterns import Singleton
 
 import easybuild.tools.environment as env
-#from easybuild.tools.autopep8 import fix_code
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option, get_module_naming_scheme
 from easybuild.tools.filetools import decode_class_name, encode_class_name, read_file, write_file
@@ -77,6 +76,12 @@
 ITERATE_OPTIONS = ['preconfigopts', 'configopts', 'prebuildopts', 'buildopts', 'preinstallopts', 'installopts']
 
 
+try:
+    import autopep8
+except ImportError as err:
+    _log.warning("Failed to import autopep8, dumping easyconfigs with reformatting enabled will not work: %s", err)
+
+
 _easyconfig_files_cache = {}
 _easyconfigs_cache = {}
 
@@ -475,7 +480,9 @@ def dump(self, fp):
         Dump this easyconfig to file, with the given filename.
         """
         orig_enable_templating = self.enable_templating
-        self.enable_templating = False # templated values should be dumped unresolved
+
+        # templated values should be dumped unresolved
+        self.enable_templating = False
 
         # build dict of default values
         default_values = dict([(key, DEFAULT_CONFIG[key][0]) for key in DEFAULT_CONFIG])
@@ -489,8 +496,17 @@ def dump(self, fp):
         templ_val = OrderedDict([(self.template_values[k], k) for k in keys if len(self.template_values[k]) > 2])
 
         ectxt = self.parser.dump(self, default_values, templ_const, templ_val)
-
-        #ectxt = fix_code(ectxt, options={'aggressive': 1, 'max_line_length': 120})
+        self.log.debug("Dumped easyconfig: %s", ectxt)
+
+        if build_option('dump_autopep8'):
+            autopep8_opts = {
+                'aggressive': 1,  # enable non-whitespace changes, but don't be too aggressive
+                'max_line_length': 120,
+            }
+            self.log.info("Reformatting dumped easyconfig using autopep8 (options: %s)", autopep8_opts)
+            print("Reformatting dumped easyconfig using autopep8 (options: %s)", autopep8_opts)
+            ectxt = autopep8.fix_code(ectxt, options=autopep8_opts)
+            self.log.debug("Dumped easyconfig after autopep8 reformatting: %s", ectxt)
 
         write_file(fp, ectxt.strip())
 
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index ad30ff312c..9a7bd38be1 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -121,6 +121,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
     False: [
         'allow_modules_tool_mismatch',
         'debug',
+        'dump_autopep8',
         'experimental',
         'force',
         'group_writable_installdir',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 832ef5eca7..a7dc99e2ef 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -200,6 +200,7 @@ def override_options(self):
             'deprecated': ("Run pretending to be (future) version, to test removal of deprecated code.",
                            None, 'store', None),
             'download-timeout': ("Timeout for initiating downloads (in seconds)", float, 'store', None),
+            'dump-autopep8': ("Reformat easyconfigs using autopep8 when dumping them", None, 'store_true', False),
             'easyblock': ("easyblock to use for processing the spec file or dumping the options",
                           None, 'store', None, 'e', {'metavar': 'CLASS'}),
             'experimental': ("Allow experimental code (with behaviour that can be changed/removed at any given time).",
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 8d7fd4bb0b..49086fb0c3 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1182,6 +1182,17 @@ def test_dump(self):
             # parse result again
             dumped_ec = EasyConfig(test_ec)
 
+    def test_dump_autopep8(self):
+        """Test dump() with autopep8 usage enabled (only if autopep8 is available)."""
+        try:
+            import autopep8
+            os.environ['EASYBUILD_DUMP_AUTOPEP8'] = '1'
+            init_config()
+            self.test_dump()
+            del os.environ['EASYBUILD_DUMP_AUTOPEP8']
+        except ImportError:
+            print "Skipping test_dump_autopep8, since autopep8 is not available"
+
     def test_dump_extra(self):
         """Test EasyConfig's dump() method for files containing extra values"""
         build_options = {

From dc8ee7a4844958656777554573c06f9f56639268 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Aug 2015 17:20:55 +0200
Subject: [PATCH 1201/1356] move extract_comments to format/one.py

---
 .../framework/easyconfig/format/format.py     |   7 +-
 easybuild/framework/easyconfig/format/one.py  | 101 ++++++++++++++----
 easybuild/framework/easyconfig/format/two.py  |   5 +
 easybuild/framework/easyconfig/parser.py      |  69 +-----------
 4 files changed, 92 insertions(+), 90 deletions(-)

diff --git a/easybuild/framework/easyconfig/format/format.py b/easybuild/framework/easyconfig/format/format.py
index ec388d845d..21b680abc9 100644
--- a/easybuild/framework/easyconfig/format/format.py
+++ b/easybuild/framework/easyconfig/format/format.py
@@ -601,6 +601,7 @@ def __init__(self):
             raise EasyBuildError('Invalid version number %s (incorrect length)', self.VERSION)
 
         self.rawtext = None  # text version of the easyconfig
+        self.comments = {}  # comments in easyconfig file
         self.header = None  # easyconfig header (e.g., format version, license, ...)
         self.docstring = None  # easyconfig docstring (e.g., author, maintainer, ...)
 
@@ -623,10 +624,14 @@ def parse(self, txt, **kwargs):
         """Parse the txt according to this format. This is highly version specific"""
         raise NotImplementedError
 
-    def dump(self, ecfg, default_values, comments, templ_const, templ_val):
+    def dump(self, ecfg, default_values, templ_const, templ_val):
         """Dump easyconfig according to this format. This is higly version specific"""
         raise NotImplementedError
 
+    def extract_comments(self, rawtxt):
+        """Extract comments from raw content."""
+        raise NotImplementedError
+
 
 def get_format_version_classes(version=None):
     """Return the (usable) subclasses from EasyConfigFormat that have a matching version."""
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 6d33786be3..a568c040f1 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -97,8 +97,8 @@ def get_config_dict(self):
         if spec_version is not None and not spec_version == cfg['version']:
             raise EasyBuildError('Requested version %s not available, only %s', spec_version, cfg['version'])
 
-        tc_name = cfg['toolchain']['name']
-        tc_version = cfg['toolchain']['version']
+        tc_name = cfg.get('toolchain', {}).get('name', None)
+        tc_version = cfg.get('toolchain', {}).get('version', None)
         if spec_tc_name is not None and not spec_tc_name == tc_name:
             raise EasyBuildError('Requested toolchain name %s not available, only %s', spec_tc_name, tc_name)
         if spec_tc_version is not None and not spec_tc_version == tc_version:
@@ -151,29 +151,30 @@ def _format(self, key, value, item_comments, comments, outer=False):
 
         return res
 
-    def _add_key_and_comments(self, key, val, comments, templ_const, templ_val):
-        """ Add key, value pair and comments (if there are any) to the dump file (helper method for dump()) """
+    def _find_param_with_comments(self, key, val, templ_const, templ_val):
+        """Find parameter definition and accompanying comments, to include in dumped easyconfig file."""
         res = []
-        val = self._format(key, val, {}, comments, outer=True)
+        val = self._format(key, val, {}, self.comments, outer=True)
 
         # templates
         if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
             new_val = to_template_str(val, templ_const, templ_val)
+            # avoid self-referencing templated parameter definitions
             if not r'%(' + key in new_val:
                 val = new_val
 
-        if key in comments['inline']:
-            res.append("%s = %s%s" % (key, val, comments['inline'][key]))
+        if key in self.comments['inline']:
+            res.append("%s = %s%s" % (key, val, self.comments['inline'][key]))
         else:
-            if key in comments['above']:
-                res.extend(comments['above'][key])
+            if key in self.comments['above']:
+                res.extend(self.comments['above'][key])
             res.append("%s = %s" % (key, val))
 
         return res
 
-    def _include_defined_parameters(self, ecfg, keyset, default_values, comments, templ_const, templ_val):
+    def _find_defined_params(self, ecfg, keyset, default_values, templ_const, templ_val):
         """
-        Internal function to include parameters in the dumped easyconfig file which have a non-default value.
+        Determine parameters in the dumped easyconfig file which have a non-default value.
         """
         eclines = []
         printed_keys = []
@@ -188,7 +189,7 @@ def _include_defined_parameters(self, ecfg, keyset, default_values, comments, te
                     else:
                         val = quote_py_str(ecfg[key])
 
-                    eclines.extend(self._add_key_and_comments(key, val, comments, templ_const, templ_val))
+                    eclines.extend(self._find_param_with_comments(key, val, templ_const, templ_val))
 
                     printed_keys.append(key)
                     printed = True
@@ -197,35 +198,91 @@ def _include_defined_parameters(self, ecfg, keyset, default_values, comments, te
 
         return eclines, printed_keys
 
-    def dump(self, ecfg, default_values, comments, templ_const, templ_val):
+    def dump(self, ecfg, default_values, templ_const, templ_val):
         """
         Dump easyconfig in format v1.
 
         @param ecfg: EasyConfig instance
         @param default_values: default values for easyconfig parameters
-        @param comments: comments extracted from easyconfig file
         @param templ_const: known template constants
         @param templ_val: known template values
         """
         # include header comments first
-        eclines = comments['header'][:]
+        dump = self.comments['header'][:]
 
         # print easyconfig parameters ordered and in groups specified above
-        more_eclines, printed_keys = self._include_defined_parameters(ecfg, GROUPED_PARAMS, default_values, comments, templ_const, templ_val)
-        eclines.extend(more_eclines)
+        params, printed_keys = self._find_defined_params(ecfg, GROUPED_PARAMS, default_values, templ_const, templ_val)
+        dump.extend(params)
 
         # print other easyconfig parameters at the end
         keys_to_ignore = printed_keys + LAST_PARAMS
         for key in default_values:
             if key not in keys_to_ignore and ecfg[key] != default_values[key]:
-                eclines.extend(self._add_key_and_comments(key, quote_py_str(ecfg[key]), comments, templ_const, templ_val))
-        eclines.append('')
+                dump.extend(self._find_param_with_comments(key, quote_py_str(ecfg[key]), templ_const, templ_val))
+        dump.append('')
 
         # print last parameters
-        more_eclines, _ = self._include_defined_parameters(ecfg, [[k] for k in LAST_PARAMS], default_values, comments, templ_const, templ_val)
-        eclines.extend(more_eclines)
+        params, _ = self._find_defined_params(ecfg, [[k] for k in LAST_PARAMS], default_values, templ_const, templ_val)
+        dump.extend(params)
+
+        return '\n'.join(dump)
+
+    def extract_comments(self, rawtxt):
+        """Extract comments from raw content."""
+        # Keep track of comments and their location (top of easyconfig, key they are intended for, line they are on
+        # discriminate between header comments (top of easyconfig file), single-line comments (at end of line) and other
+        # At the moment there is no support for inline comments on lines that don't contain the key value
+
+        self.comments = {
+            'above' : {},  # comments for a particular parameter definition
+            'header' : [],  # header comment lines
+            'inline' : {},  # inline comments
+            'iter': {},  # (inline) comments on elements of iterable values
+         }
+
+        rawlines = rawtxt.split('\n')
+
+        # extract header first
+        while rawlines[0].startswith('#'):
+            self.comments['header'].append(rawlines.pop(0))
+
+        parsed_ec = self.get_config_dict()
+
+        while rawlines:
+            rawline = rawlines.pop(0)
+            if rawline.startswith('#'):
+                comment = []
+                # comment could be multi-line
+                while rawline.startswith('#') or not rawline:
+                    # drop empty lines (that don't even include a #)
+                    if rawline:
+                        comment.append(rawline)
+                    rawline = rawlines.pop(0)
+                key = rawline.split('=', 1)[0].strip()
+                self.comments['above'][key] = comment
+
+            elif '#' in rawline:  # inline comment
+                comment = rawline.rsplit('#', 1)[1].strip()
+                comment_key, comment_val = None, None
+                if '=' in rawline:
+                    comment_key = rawline.split('=', 1)[0].strip()
+                else:
+                    # search for key and index of comment in config dict
+                    for key, val in parsed_ec.items():
+                        item_val = re.sub(r',$', r'', rawline.rsplit('#', 1)[0].strip())
+                        if not isinstance(val, basestring) and item_val in str(val):
+                            comment_key, comment_val = key, item_val
+                            if not self.comments['iter'].get(comment_key):
+                                self.comments['iter'][comment_key] = {}
+
+                # check if hash actually indicated a comment; or is part of the value
+                if comment_key in parsed_ec:
+                    if comment.replace("'", '').replace('"', '') not in str(parsed_ec[comment_key]):
+                        if comment_val:
+                            self.comments['iter'][comment_key][comment_val] = '  # ' + comment
+                        else:
+                            self.comments['inline'][comment_key] = '  # ' + comment
 
-        return '\n'.join(eclines)
 
 
 def retrieve_blocks_in_spec(spec, only_blocks, silent=False):
diff --git a/easybuild/framework/easyconfig/format/two.py b/easybuild/framework/easyconfig/format/two.py
index 2c6618cb85..7e67ba0da2 100644
--- a/easybuild/framework/easyconfig/format/two.py
+++ b/easybuild/framework/easyconfig/format/two.py
@@ -132,3 +132,8 @@ def get_config_dict(self):
 
         self.log.debug("Final config dict (including correct version/toolchain): %s" % cfg)
         return cfg
+
+    def extract_comments(self, rawtxt):
+        """Extract comments from raw content."""
+        # this is fine-ish, it only implies that comments will be lost for format v2 easyconfig files that are dumped
+        self.log.warning("Extraction of comments not supported yet for easyconfig format v2")
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 703ff9983c..fdf431138d 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -87,9 +87,6 @@ def __init__(self, filename=None, format_version=None, rawcontent=None):
 
         self.rawcontent = None  # the actual unparsed content
 
-        # comments in the easyconfig file
-        self.comments = None
-
         self.get_fn = None  # read method and args
         self.set_fn = None  # write method and args
 
@@ -105,7 +102,7 @@ def __init__(self, filename=None, format_version=None, rawcontent=None):
         else:
             raise EasyBuildError("Neither filename nor rawcontent provided to EasyConfigParser")
 
-        self._extract_comments()
+        self._formatter.extract_comments(self.rawcontent)
 
     def process(self, filename=None):
         """Create an instance"""
@@ -139,68 +136,6 @@ def _read(self, filename=None):
             msg = 'rawcontent is not basestring: type %s, content %s' % (type(self.rawcontent), self.rawcontent)
             raise EasyBuildError("Unexpected result for raw content: %s", msg)
 
-    def _extract_comments(self):
-        """Extract comments from raw content."""
-        # Keep track of comments and their location (top of easyconfig, key they are intended for, line they are on
-        # discriminate between header comments (top of easyconfig file), single-line comments (at end of line) and other
-        # At the moment there is no support for inline comments on lines that don't contain the key value
-
-        self.comments = {
-            'above' : {},  # comments for a particular parameter definition
-            'header' : [],  # header comment lines
-            'inline' : {},  # inline comments
-            'iter': {},  # (inline) comments on elements of iterable values
-         }
-
-        rawlines = self.rawcontent.split('\n')
-
-        # extract header first
-        while rawlines[0].startswith('#'):
-            self.comments['header'].append(rawlines.pop(0))
-
-        parsed_ec = None
-        while rawlines:
-            rawline = rawlines.pop(0)
-            if rawline.startswith('#'):
-                comment = []
-                # comment could be multi-line
-                while rawline.startswith('#') or not rawline:
-                    # drop empty lines (that don't even include a #)
-                    if rawline:
-                        comment.append(rawline)
-                    rawline = rawlines.pop(0)
-                key = rawline.split('=', 1)[0].strip()
-                self.comments['above'][key] = comment
-
-            elif '#' in rawline:  # inline comment
-                if parsed_ec is None:
-                    # obtain parsed easyconfig as a dict, if it wasn't already
-                    # note: this currently trigger a reparse
-                    parsed_ec = self.get_config_dict()
-
-                comment = rawline.rsplit('#', 1)[1].strip()
-                key = None
-                comment_value = None
-                if '=' in rawline:
-                    key = rawline.split('=', 1)[0].strip()
-                else:
-                    # search for key and index of comment in config dict
-                    for k, v in parsed_ec.items():
-                        val = re.sub(r',$', r'', rawline.rsplit('#', 1)[0].strip())
-                        if not isinstance(v, basestring) and val in str(v):
-                            key = k
-                            comment_value = val
-                            if not self.comments['iter'].get(key):
-                                self.comments['iter'][key] = {}
-
-                # check if hash actually indicated a comment; or is part of the value
-                if key in parsed_ec:
-                    if comment.replace("'", "").replace('"', '') not in str(parsed_ec[key]):
-                        if comment_value:
-                            self.comments['iter'][key][comment_value] = '  # ' + comment
-                        else:
-                            self.comments['inline'][key] = '  # ' + comment
-
     def _det_format_version(self):
         """Extract the format version from the raw content"""
         if self.format_version is None:
@@ -257,4 +192,4 @@ def get_config_dict(self, validate=True):
 
     def dump(self, ecfg, default_values, templ_const, templ_val):
         """Dump easyconfig in format it was parsed from."""
-        return self._formatter.dump(ecfg, default_values, self.comments, templ_const, templ_val)
+        return self._formatter.dump(ecfg, default_values, templ_const, templ_val)

From 89d2c78ca5977d7953967263be02d92f859aadb1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Aug 2015 21:13:22 +0200
Subject: [PATCH 1202/1356] rework _reformat_line method (was _format)

---
 .../framework/easyconfig/format/format.py     |   2 +
 easybuild/framework/easyconfig/format/one.py  | 102 +++++++++++-------
 2 files changed, 68 insertions(+), 36 deletions(-)

diff --git a/easybuild/framework/easyconfig/format/format.py b/easybuild/framework/easyconfig/format/format.py
index 21b680abc9..d1d95b9613 100644
--- a/easybuild/framework/easyconfig/format/format.py
+++ b/easybuild/framework/easyconfig/format/format.py
@@ -41,6 +41,8 @@
 from easybuild.tools.configobj import Section
 
 
+INDENT_4SPACES = ' ' * 4
+
 # format is mandatory major.minor
 FORMAT_VERSION_KEYWORD = "EASYCONFIGFORMAT"
 FORMAT_VERSION_TEMPLATE = "%(major)s.%(minor)s"
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index a568c040f1..93c715b483 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -37,7 +37,7 @@
 from vsc.utils import fancylogger
 
 from easybuild.framework.easyconfig.format.format import EXCLUDED_KEYS_REPLACE_TEMPLATES, FORMAT_DEFAULT_VERSION
-from easybuild.framework.easyconfig.format.format import GROUPED_PARAMS, LAST_PARAMS, get_format_version
+from easybuild.framework.easyconfig.format.format import GROUPED_PARAMS, INDENT_4SPACES, LAST_PARAMS, get_format_version
 from easybuild.framework.easyconfig.format.pyheaderconfigobj import EasyConfigFormatConfigObj
 from easybuild.framework.easyconfig.format.version import EasyVersion
 from easybuild.framework.easyconfig.templates import to_template_str
@@ -46,6 +46,15 @@
 from easybuild.tools.utilities import quote_py_str
 
 
+DEPENDENCY_PARAMETERS = ['builddependencies', 'dependencies', 'hiddendependencies']
+REFORMAT_FORCED_PARAMS = ['sanity_check_paths']
+REFORMAT_SKIPPED_PARAMS = ['toolchain', 'toolchainopts']
+REFORMAT_THRESHOLD_LENGTH = 100  # only reformat lines that would be longer than this amount of characters
+REFORMAT_ORDERED_ITEM_KEYS = {
+    'sanity_check_paths': ['files', 'dirs'],
+}
+
+
 _log = fancylogger.getLogger('easyconfig.format.one', fname=False)
 
 
@@ -112,49 +121,70 @@ def parse(self, txt):
         """
         super(FormatOneZero, self).parse(txt, strict_section_markers=True)
 
-    def _format(self, key, value, item_comments, comments, outer=False):
-        """ Returns string version of the value, including comments and newlines in lists, tuples and dicts """
-        res = ''
-
-        for k, v in comments['iter'].get(key, {}).items():
-            if str(value) in k:
-                item_comments[str(value)] = v
-
-        if outer:
-            if isinstance(value, list):
-                res += '[\n'
-                for el in value:
-                    res += '    ' + self._format(key, el, item_comments, comments)
-                    res += ',' + item_comments.get(str(el), '') + '\n'
-                res += ']'
-            elif isinstance(value, tuple):
-                res += '(\n'
-                for el in value:
-                    res += '    ' + self._format(key, el, item_comments, comments)
-                    res += ',' + item_comments.get(str(el), '') + '\n'
-                res += ')'
-            elif isinstance(value, dict) and key not in ['toolchain']:  # FIXME
-                res += '{\n'
-                for k, v in sorted(value.items())[::-1]:  # FIXME
-                    res += '    ' + quote_py_str(k) + ': ' + self._format(key, v, item_comments, comments)
-                    res += ',' + item_comments.get(str(v), '') + '\n'
-                res += '}'
-
-            res = res or str(value)
+    def _reformat_line(self, param_name, param_val, item_comments=None, outer=False):
+        """Construct formatted string representation of iterable parameter (list/tuple/dict), including comments."""
+        param_strval = str(param_val)
+        res = param_strval
+
+        if param_name in REFORMAT_SKIPPED_PARAMS:
+            self.log.info("Skipping reformatting value for parameter '%s'", param_name)
+
+        #elif len(param_strval) >= REFORMAT_THRESHOLD_LENGTH or key in REFORMAT_FORCED_PARAMS:  # FIXME
+
+        elif outer:
+            res = None
+            if isinstance(param_val, (list, tuple, dict)):
+
+                item_tmpl = INDENT_4SPACES + '%(item)s,%(comment)s\n'
+
+                # start with opening character: [, (, {
+                res = '%s\n' % param_strval[0]
+
+                # add items one-by-one, special care for dict values (order of keys, different format for elements)
+                if isinstance(param_val, dict):
+                    ordered_item_keys = REFORMAT_ORDERED_ITEM_KEYS.get(param_name, sorted(param_val.keys()))
+                    for item_key in ordered_item_keys:
+                        item_val = param_val[item_key]
+                        new_item_comments = self._get_item_comments(param_name, item_val)
+                        formatted_item = self._reformat_line(param_name, item_val, item_comments=new_item_comments)
+                        res += item_tmpl % {
+                            'comment': new_item_comments.get(str(item_val), ''),
+                            'item': quote_py_str(item_key) + ': ' + formatted_item,
+                        }
+                else:  # list, tuple
+                    for item in param_val:
+                        new_item_comments = self._get_item_comments(param_name, item)
+                        res += item_tmpl % {
+                            'comment': new_item_comments.get(str(item), ''),
+                            'item': self._reformat_line(param_name, item, item_comments=new_item_comments),
+                        }
+
+                # end with closing character: ], ), }
+                res += param_strval[-1]
+
+            res = res or param_strval
 
         else:
             # dependencies are already dumped as strings, so they do not need to be quoted again
-            if isinstance(value, basestring) and key not in ['builddependencies', 'dependencies', 'hiddendependencies']:
-                res = quote_py_str(value)
-            else:
-                res = str(value)
+            if isinstance(param_val, basestring) and param_name not in DEPENDENCY_PARAMETERS:
+                res = quote_py_str(param_val)
 
         return res
 
+    def _get_item_comments(self, key, val):
+        """Get per-item comments for specified parameter name/value."""
+        item_comments = {}
+        for comment_key, comment_val in self.comments['iter'].get(key, {}).items():
+            if str(val) in comment_key:
+                item_comments[str(val)] = comment_val
+
+        return item_comments
+
     def _find_param_with_comments(self, key, val, templ_const, templ_val):
         """Find parameter definition and accompanying comments, to include in dumped easyconfig file."""
         res = []
-        val = self._format(key, val, {}, self.comments, outer=True)
+
+        val = self._reformat_line(key, val, item_comments=self._get_item_comments(key, val), outer=True)
 
         # templates
         if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
@@ -264,7 +294,7 @@ def extract_comments(self, rawtxt):
             elif '#' in rawline:  # inline comment
                 comment = rawline.rsplit('#', 1)[1].strip()
                 comment_key, comment_val = None, None
-                if '=' in rawline:
+                if '=' in rawline:   # FIXME
                     comment_key = rawline.split('=', 1)[0].strip()
                 else:
                     # search for key and index of comment in config dict

From 1a5be3c5728e9df6b4846c2c6349899cdaddaeca Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Aug 2015 21:29:14 +0200
Subject: [PATCH 1203/1356] simplify _reformat_line, fix FIXME w.r.t.
 recognizing parameter definition line

---
 easybuild/framework/easyconfig/format/one.py | 32 ++++++++++++--------
 1 file changed, 20 insertions(+), 12 deletions(-)

diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 93c715b483..623522474f 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -121,8 +121,14 @@ def parse(self, txt):
         """
         super(FormatOneZero, self).parse(txt, strict_section_markers=True)
 
-    def _reformat_line(self, param_name, param_val, item_comments=None, outer=False):
-        """Construct formatted string representation of iterable parameter (list/tuple/dict), including comments."""
+    def _reformat_line(self, param_name, param_val, outer=False):
+        """
+        Construct formatted string representation of iterable parameter (list/tuple/dict), including comments.
+
+        @param param_name: parameter name
+        @param param_val: parameter value
+        @param outer: reformat for top-level parameter, or not
+        """
         param_strval = str(param_val)
         res = param_strval
 
@@ -145,18 +151,18 @@ def _reformat_line(self, param_name, param_val, item_comments=None, outer=False)
                     ordered_item_keys = REFORMAT_ORDERED_ITEM_KEYS.get(param_name, sorted(param_val.keys()))
                     for item_key in ordered_item_keys:
                         item_val = param_val[item_key]
-                        new_item_comments = self._get_item_comments(param_name, item_val)
-                        formatted_item = self._reformat_line(param_name, item_val, item_comments=new_item_comments)
+                        comments = self._get_item_comments(param_name, item_val)
+                        formatted_item = self._reformat_line(param_name, item_val)
                         res += item_tmpl % {
-                            'comment': new_item_comments.get(str(item_val), ''),
+                            'comment': comments.get(str(item_val), ''),
                             'item': quote_py_str(item_key) + ': ' + formatted_item,
                         }
                 else:  # list, tuple
                     for item in param_val:
-                        new_item_comments = self._get_item_comments(param_name, item)
+                        comments = self._get_item_comments(param_name, item)
                         res += item_tmpl % {
-                            'comment': new_item_comments.get(str(item), ''),
-                            'item': self._reformat_line(param_name, item, item_comments=new_item_comments),
+                            'comment': comments.get(str(item), ''),
+                            'item': self._reformat_line(param_name, item)
                         }
 
                 # end with closing character: ], ), }
@@ -184,7 +190,7 @@ def _find_param_with_comments(self, key, val, templ_const, templ_val):
         """Find parameter definition and accompanying comments, to include in dumped easyconfig file."""
         res = []
 
-        val = self._reformat_line(key, val, item_comments=self._get_item_comments(key, val), outer=True)
+        val = self._reformat_line(key, val, outer=True)
 
         # templates
         if key not in EXCLUDED_KEYS_REPLACE_TEMPLATES:
@@ -292,12 +298,14 @@ def extract_comments(self, rawtxt):
                 self.comments['above'][key] = comment
 
             elif '#' in rawline:  # inline comment
-                comment = rawline.rsplit('#', 1)[1].strip()
                 comment_key, comment_val = None, None
-                if '=' in rawline:   # FIXME
+                comment = rawline.rsplit('#', 1)[1].strip()
+                # check whether this line is parameter definition;
+                # if not, assume it's a continuation of a multi-line value
+                if re.match(r'^[a-z_]+\s*=', rawline):
                     comment_key = rawline.split('=', 1)[0].strip()
                 else:
-                    # search for key and index of comment in config dict
+                    # determine parameter value where the item value on this line is a part of
                     for key, val in parsed_ec.items():
                         item_val = re.sub(r',$', r'', rawline.rsplit('#', 1)[0].strip())
                         if not isinstance(val, basestring) and item_val in str(val):

From b04d9ade2b74de507fbc5f86b3e9f9de70aa0afc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Aug 2015 22:41:46 +0200
Subject: [PATCH 1204/1356] only reformat long lines

---
 easybuild/framework/easyconfig/format/one.py | 37 +++++++++++---------
 test/framework/easyconfig.py                 |  2 +-
 2 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 623522474f..61b13d8394 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -47,7 +47,8 @@
 
 
 DEPENDENCY_PARAMETERS = ['builddependencies', 'dependencies', 'hiddendependencies']
-REFORMAT_FORCED_PARAMS = ['sanity_check_paths']
+# dependency parameters always need to be reformatted, to correctly deal with dumping parsed dependencies
+REFORMAT_FORCED_PARAMS = ['sanity_check_paths'] + DEPENDENCY_PARAMETERS
 REFORMAT_SKIPPED_PARAMS = ['toolchain', 'toolchainopts']
 REFORMAT_THRESHOLD_LENGTH = 100  # only reformat lines that would be longer than this amount of characters
 REFORMAT_ORDERED_ITEM_KEYS = {
@@ -121,25 +122,29 @@ def parse(self, txt):
         """
         super(FormatOneZero, self).parse(txt, strict_section_markers=True)
 
-    def _reformat_line(self, param_name, param_val, outer=False):
+    def _reformat_line(self, param_name, param_val, outer=False, addlen=0):
         """
         Construct formatted string representation of iterable parameter (list/tuple/dict), including comments.
 
         @param param_name: parameter name
         @param param_val: parameter value
         @param outer: reformat for top-level parameter, or not
+        @param addlen: # characters to add to line length
         """
         param_strval = str(param_val)
         res = param_strval
 
+        # determine whether line would be too long
+        # note: this does not take into account the parameter name + '=', only the value
+        line_too_long = len(param_strval) + addlen > REFORMAT_THRESHOLD_LENGTH
+        forced = param_name in REFORMAT_FORCED_PARAMS
+
         if param_name in REFORMAT_SKIPPED_PARAMS:
             self.log.info("Skipping reformatting value for parameter '%s'", param_name)
 
-        #elif len(param_strval) >= REFORMAT_THRESHOLD_LENGTH or key in REFORMAT_FORCED_PARAMS:  # FIXME
-
         elif outer:
-            res = None
-            if isinstance(param_val, (list, tuple, dict)):
+            # only reformat outer (iterable) values for (too) long lines (or for select parameters)
+            if isinstance(param_val, (list, tuple, dict)) and ((len(param_val) > 1 and line_too_long) or forced):
 
                 item_tmpl = INDENT_4SPACES + '%(item)s,%(comment)s\n'
 
@@ -151,25 +156,26 @@ def _reformat_line(self, param_name, param_val, outer=False):
                     ordered_item_keys = REFORMAT_ORDERED_ITEM_KEYS.get(param_name, sorted(param_val.keys()))
                     for item_key in ordered_item_keys:
                         item_val = param_val[item_key]
-                        comments = self._get_item_comments(param_name, item_val)
-                        formatted_item = self._reformat_line(param_name, item_val)
+                        comment = self._get_item_comments(param_name, item_val).get(str(item_val), '')
+                        key_pref = quote_py_str(item_key) + ': '
+                        addlen = addlen + len(INDENT_4SPACES) + len(key_pref) + len(comment)
+                        formatted_item_val = self._reformat_line(param_name, item_val, addlen=addlen)
                         res += item_tmpl % {
-                            'comment': comments.get(str(item_val), ''),
-                            'item': quote_py_str(item_key) + ': ' + formatted_item,
+                            'comment': comment,
+                            'item': key_pref + formatted_item_val,
                         }
                 else:  # list, tuple
                     for item in param_val:
-                        comments = self._get_item_comments(param_name, item)
+                        comment = self._get_item_comments(param_name, item).get(str(item), '')
+                        addlen = addlen + len(INDENT_4SPACES) + len(comment)
                         res += item_tmpl % {
-                            'comment': comments.get(str(item), ''),
-                            'item': self._reformat_line(param_name, item)
+                            'comment': comment,
+                            'item': self._reformat_line(param_name, item, addlen=addlen)
                         }
 
                 # end with closing character: ], ), }
                 res += param_strval[-1]
 
-            res = res or param_strval
-
         else:
             # dependencies are already dumped as strings, so they do not need to be quoted again
             if isinstance(param_val, basestring) and param_name not in DEPENDENCY_PARAMETERS:
@@ -322,7 +328,6 @@ def extract_comments(self, rawtxt):
                             self.comments['inline'][comment_key] = '  # ' + comment
 
 
-
 def retrieve_blocks_in_spec(spec, only_blocks, silent=False):
     """
     Easyconfigs can contain blocks (headed by a [Title]-line)
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 49086fb0c3..98802be6e5 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1285,7 +1285,7 @@ def test_dump_template(self):
             r"versionsuffix = '-test'",
             r"homepage = 'http://foo.com/'",
             r'description = "foo description"',  # no templating for description
-            r"sources = \[\n    SOURCELOWER_TAR_GZ,\n\]",
+            r"sources = \[SOURCELOWER_TAR_GZ\]",
             r"dependencies = \[\n    \('bar', '1.2.3', '%\(versionsuffix\)s'\),\n\]",
             r"preconfigopts = '--opt1=%\(name\)s'",
             r"configopts = '--opt2=%\(version\)s'",

From 6afadc04803091541b346a4f8ed98ead39b0d56d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Aug 2015 22:48:18 +0200
Subject: [PATCH 1205/1356] restore toolchain regexin tweak_one

---
 easybuild/framework/easyconfig/tweak.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/tweak.py b/easybuild/framework/easyconfig/tweak.py
index 3c79b7205e..339e349d71 100644
--- a/easybuild/framework/easyconfig/tweak.py
+++ b/easybuild/framework/easyconfig/tweak.py
@@ -144,7 +144,7 @@ def tweak_one(src_fn, target_fn, tweaks, targetdir=None):
     keys = tweaks.keys()
     if 'toolchain_name' in keys or 'toolchain_version' in keys:
         # note: this assumes that the toolchain spec is single-line
-        tc_regexp = re.compile(r"^\s*toolchain\s*=\s*({[^}\n]+})\s*$", re.M)
+        tc_regexp = re.compile(r"^\s*toolchain\s*=\s*(.*)$", re.M)
         res = tc_regexp.search(ectxt)
         if not res:
             raise EasyBuildError("No toolchain found in easyconfig file %s: %s", src_fn, ectxt)

From df611f1f6519b937d48d081bc4eefa9468a576ca Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Aug 2015 14:18:44 +0200
Subject: [PATCH 1206/1356] hotfix for minor change in help output for --help
 in vsc-base + import mk_rst_table from vsc.utils.docs

---
 easybuild/tools/docs.py   | 34 +---------------------------------
 setup.py                  |  2 +-
 test/framework/docs.py    | 14 +++++++-------
 test/framework/options.py |  2 +-
 4 files changed, 10 insertions(+), 42 deletions(-)

diff --git a/easybuild/tools/docs.py b/easybuild/tools/docs.py
index 17a43636b5..dead250516 100644
--- a/easybuild/tools/docs.py
+++ b/easybuild/tools/docs.py
@@ -36,6 +36,7 @@
 import copy
 import inspect
 import os
+from vsc.utils.docs import mk_rst_table
 
 from easybuild.framework.easyconfig.default import DEFAULT_CONFIG, HIDDEN, sorted_categories
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
@@ -271,36 +272,3 @@ def gen_easyblock_doc_section_rst(eb_class, path_to_examples, common_params, doc
         lines.append('') # empty line after literal block
 
     return '\n'.join(lines)
-
-
-def mk_rst_table(titles, values):
-    """
-    Returns an rst table with given titles and values (a nested list of string values for each column)
-    """
-    num_col = len(titles)
-    table = []
-    col_widths = []
-    tmpl = []
-    line= []
-
-    # figure out column widths
-    for i in range(0, num_col):
-        col_widths.append(det_col_width(values[i], titles[i]))
-
-        # make line template
-        tmpl.append('{' + str(i) + ':{c}<' + str(col_widths[i]) + '}')
-        line.append('') # needed for table line
-
-    line_tmpl = '   '.join(tmpl)
-    table_line = line_tmpl.format(*line, c="=")
-
-    table.append(table_line)
-    table.append(line_tmpl.format(*titles, c=' '))
-    table.append(table_line)
-
-    for i in range(0, len(values[0])):
-        table.append(line_tmpl.format(*[v[i] for v in values], c=' '))
-
-    table.extend([table_line, ''])
-
-    return table
diff --git a/setup.py b/setup.py
index cb9af5cc78..7da6baecdf 100644
--- a/setup.py
+++ b/setup.py
@@ -107,5 +107,5 @@ def find_rel_test():
     provides=["eb"] + easybuild_packages,
     test_suite="test.framework.suite",
     zip_safe=False,
-    install_requires=["vsc-base >= 2.2.0"],
+    install_requires=["vsc-base >= 2.2.4"],
 )
diff --git a/test/framework/docs.py b/test/framework/docs.py
index 50c8e1c3bb..1051a121b1 100644
--- a/test/framework/docs.py
+++ b/test/framework/docs.py
@@ -84,13 +84,13 @@ def test_gen_easyblocks(self):
             '',
             "Commonly used easyconfig parameters with ``ConfigureMake`` easyblock",
             "--------------------------------------------------------------------",
-            "====================   ================================================================",
-            "easyconfig parameter   description                                                     ",
-            "====================   ================================================================",
-            "configopts             Extra options passed to configure (default already has --prefix)",
-            "buildopts              Extra options passed to make step (default already has -j X)    ",
-            "installopts            Extra options for installation                                  ",
-            "====================   ================================================================",
+            "====================    ================================================================",
+            "easyconfig parameter    description                                                     ",
+            "====================    ================================================================",
+            "configopts              Extra options passed to configure (default already has --prefix)",
+            "buildopts               Extra options passed to make step (default already has -j X)    ",
+            "installopts             Extra options for installation                                  ",
+            "====================    ================================================================",
         ])
 
         self.assertTrue(check_configuremake in ebdoc)
diff --git a/test/framework/options.py b/test/framework/options.py
index 20bf8ca55a..91f170eda3 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -103,7 +103,7 @@ def test_help_long(self):
                                )
         outtxt = topt.parser.help_to_file.getvalue()
 
-        self.assertTrue(re.search("-H, --help", outtxt), "Long documentation expanded in long help")
+        self.assertTrue(re.search("-H OUTPUT_FORMAT, --help=OUTPUT_FORMAT", outtxt), "Long documentation expanded in long help")
         self.assertTrue(re.search("show short help message and exit", outtxt), "Documentation included in long help")
         self.assertTrue(re.search("Software search and build options", outtxt), "Not all option groups included in short help (1)")
         self.assertTrue(re.search("Regression test options", outtxt), "Not all option groups included in short help (2)")

From 3885967ce17e4c69936be5c87b857b83a3445ea7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Aug 2015 14:31:05 +0200
Subject: [PATCH 1207/1356] remove test for mk_rst_table, since it's tested in
 vsc-base

---
 test/framework/docs.py | 23 +----------------------
 1 file changed, 1 insertion(+), 22 deletions(-)

diff --git a/test/framework/docs.py b/test/framework/docs.py
index 1051a121b1..dbb1d257cb 100644
--- a/test/framework/docs.py
+++ b/test/framework/docs.py
@@ -31,34 +31,13 @@
 import sys
 import inspect
 
-from easybuild.tools.docs import gen_easyblocks_overview_rst, mk_rst_table
+from easybuild.tools.docs import gen_easyblocks_overview_rst
 from easybuild.tools.utilities import import_available_modules
 from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader, main
 
 class DocsTest(EnhancedTestCase):
 
-    def test_rst_table(self):
-        """ Test mk_rst_table function """
-        entries = [['one', 'two', 'three']]
-        t = 'This title is longer than the entries in the column'
-        titles = [t]
-
-        # small table
-        table = '\n'.join(mk_rst_table(titles, entries))
-        check = '\n'.join([
-            '=' * len(t),
-            t,
-            '=' * len(t),
-            'one' + ' ' * (len(t) - 3),
-            'two' + ' ' * (len(t) -3),
-            'three' + ' ' * (len(t) - 5),
-            '=' * len(t),
-            '',
-        ])
-
-        self.assertEqual(table, check)
-
     def test_gen_easyblocks(self):
         """ Test gen_easyblocks_overview_rst function """
         module = 'easybuild.easyblocks.generic'

From f4d671b2a1de8bc8db784fc2b507600ff56bf737 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Aug 2015 14:59:29 +0200
Subject: [PATCH 1208/1356] moar minor style fixes

---
 easybuild/framework/easyconfig/easyconfig.py    | 3 ++-
 easybuild/framework/easyconfig/format/format.py | 6 ++++--
 easybuild/framework/easyconfig/format/one.py    | 8 ++++----
 easybuild/framework/easyconfig/parser.py        | 3 ---
 easybuild/tools/options.py                      | 6 ++++++
 test/framework/easyconfig.py                    | 3 ++-
 6 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 0bfb6c55d7..12b41dcb8c 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -78,8 +78,10 @@
 
 try:
     import autopep8
+    HAVE_AUTOPEP8 = True
 except ImportError as err:
     _log.warning("Failed to import autopep8, dumping easyconfigs with reformatting enabled will not work: %s", err)
+    HAVE_AUTOPEP8 = False
 
 
 _easyconfig_files_cache = {}
@@ -504,7 +506,6 @@ def dump(self, fp):
                 'max_line_length': 120,
             }
             self.log.info("Reformatting dumped easyconfig using autopep8 (options: %s)", autopep8_opts)
-            print("Reformatting dumped easyconfig using autopep8 (options: %s)", autopep8_opts)
             ectxt = autopep8.fix_code(ectxt, options=autopep8_opts)
             self.log.debug("Dumped easyconfig after autopep8 reformatting: %s", ectxt)
 
diff --git a/easybuild/framework/easyconfig/format/format.py b/easybuild/framework/easyconfig/format/format.py
index d1d95b9613..648af65c05 100644
--- a/easybuild/framework/easyconfig/format/format.py
+++ b/easybuild/framework/easyconfig/format/format.py
@@ -50,8 +50,10 @@
 FORMAT_VERSION_REGEXP = re.compile(r'^#\s+%s\s*(?P<major>\d+)\.(?P<minor>\d+)\s*$' % FORMAT_VERSION_KEYWORD, re.M)
 FORMAT_DEFAULT_VERSION = EasyVersion('1.0')
 
+DEPENDENCY_PARAMETERS = ['builddependencies', 'dependencies', 'hiddendependencies']
+
 # values for these keys will not be templated in dump()
-EXCLUDED_KEYS_REPLACE_TEMPLATES = ['easyblock', 'name', 'version', 'description', 'homepage', 'toolchain']
+EXCLUDED_KEYS_REPLACE_TEMPLATES = ['description', 'easyblock', 'homepage', 'name', 'toolchain', 'version']
 
 # ordered groups of keys to obtain a nice looking easyconfig file
 GROUPED_PARAMS = [
@@ -61,7 +63,7 @@
     ['toolchain', 'toolchainopts'],
     ['sources', 'source_urls'],
     ['patches'],
-    ['builddependencies', 'dependencies', 'hiddendependencies'],
+    DEPENDENCY_PARAMETERS,
     ['osdependencies'],
     ['preconfigopts', 'configopts'],
     ['prebuildopts', 'buildopts'],
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 61b13d8394..e4caa92a7b 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -36,8 +36,9 @@
 import tempfile
 from vsc.utils import fancylogger
 
-from easybuild.framework.easyconfig.format.format import EXCLUDED_KEYS_REPLACE_TEMPLATES, FORMAT_DEFAULT_VERSION
-from easybuild.framework.easyconfig.format.format import GROUPED_PARAMS, INDENT_4SPACES, LAST_PARAMS, get_format_version
+from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS, EXCLUDED_KEYS_REPLACE_TEMPLATES
+from easybuild.framework.easyconfig.format.format import FORMAT_DEFAULT_VERSION, GROUPED_PARAMS, INDENT_4SPACES
+from easybuild.framework.easyconfig.format.format import LAST_PARAMS, get_format_version
 from easybuild.framework.easyconfig.format.pyheaderconfigobj import EasyConfigFormatConfigObj
 from easybuild.framework.easyconfig.format.version import EasyVersion
 from easybuild.framework.easyconfig.templates import to_template_str
@@ -46,7 +47,6 @@
 from easybuild.tools.utilities import quote_py_str
 
 
-DEPENDENCY_PARAMETERS = ['builddependencies', 'dependencies', 'hiddendependencies']
 # dependency parameters always need to be reformatted, to correctly deal with dumping parsed dependencies
 REFORMAT_FORCED_PARAMS = ['sanity_check_paths'] + DEPENDENCY_PARAMETERS
 REFORMAT_SKIPPED_PARAMS = ['toolchain', 'toolchainopts']
@@ -225,7 +225,7 @@ def _find_defined_params(self, ecfg, keyset, default_values, templ_const, templ_
             for key in group:
                 if ecfg[key] != default_values[key]:
                     # dependency easyconfig parameters were parsed, so these need special care to 'unparse' them
-                    if key in ['builddependencies', 'dependencies', 'hiddendependencies']:
+                    if key in DEPENDENCY_PARAMETERS:
                         dumped_deps = [dump_dependency(d, ecfg['toolchain']) for d in ecfg[key]]
                         val = dumped_deps
                     else:
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index fdf431138d..36173d35a1 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -29,9 +29,6 @@
 
 @author: Stijn De Weirdt (Ghent University)
 """
-
-import ast
-import copy
 import os
 import re
 from vsc.utils import fancylogger
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index a7dc99e2ef..33661c2c2b 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -44,6 +44,7 @@
 from easybuild.framework.easyblock import MODULE_ONLY_STEPS, SOURCE_STEP, EasyBlock
 from easybuild.framework.easyconfig import EASYCONFIGS_PKG_SUBDIR
 from easybuild.framework.easyconfig.constants import constant_documentation
+from easybuild.framework.easyconfig.easyconfig import HAVE_AUTOPEP8
 from easybuild.framework.easyconfig.format.pyheaderconfigobj import build_easyconfig_constants_dict
 from easybuild.framework.easyconfig.licenses import license_documentation
 from easybuild.framework.easyconfig.templates import template_documentation
@@ -504,6 +505,11 @@ def postprocess(self):
             if token is None:
                 raise EasyBuildError("Failed to obtain required GitHub token for user '%s'", self.options.github_user)
 
+        # make sure autopep8 is available when it needs to be
+        if self.options.dump_autopep8:
+            if not HAVE_AUTOPEP8:
+                raise EasyBuildError("Python 'autopep8' module required to reformat dumped easyconfigs as requested")
+
         self._postprocess_external_modules_metadata()
 
         self._postprocess_config()
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 98802be6e5..6b994d5326 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1343,7 +1343,8 @@ def test_dump_comments(self):
             r"# comment on the homepage\nhomepage = 'http://foo.com/'",
             r'description = "foo description with a # in it"  # test',
             r"# toolchain comment\ntoolchain = {",
-            r"'files': \['files/foobar'\],  # comment on files",
+            r"    'files': \['files/foobar'\],  # comment on files",
+            r"    'dirs': \[\],",
         ]
 
         for pattern in patterns:

From 460a07a6552bae6da2acba83669a27dcb7b14404 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Aug 2015 19:59:31 +0200
Subject: [PATCH 1209/1356] extend docstring for extract_comments + use
 setdefault where applicable

---
 easybuild/framework/easyconfig/format/one.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index e4caa92a7b..7028013c2e 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -270,11 +270,12 @@ def dump(self, ecfg, default_values, templ_const, templ_val):
         return '\n'.join(dump)
 
     def extract_comments(self, rawtxt):
-        """Extract comments from raw content."""
-        # Keep track of comments and their location (top of easyconfig, key they are intended for, line they are on
-        # discriminate between header comments (top of easyconfig file), single-line comments (at end of line) and other
-        # At the moment there is no support for inline comments on lines that don't contain the key value
+        """
+        Extract comments from raw content.
 
+        Discriminates between comment header, comments above a line (parameter definition), and inline comments.
+        Inline comments on items of iterable values are also extracted.
+        """
         self.comments = {
             'above' : {},  # comments for a particular parameter definition
             'header' : [],  # header comment lines
@@ -316,14 +317,13 @@ def extract_comments(self, rawtxt):
                         item_val = re.sub(r',$', r'', rawline.rsplit('#', 1)[0].strip())
                         if not isinstance(val, basestring) and item_val in str(val):
                             comment_key, comment_val = key, item_val
-                            if not self.comments['iter'].get(comment_key):
-                                self.comments['iter'][comment_key] = {}
+                            break
 
                 # check if hash actually indicated a comment; or is part of the value
                 if comment_key in parsed_ec:
                     if comment.replace("'", '').replace('"', '') not in str(parsed_ec[comment_key]):
                         if comment_val:
-                            self.comments['iter'][comment_key][comment_val] = '  # ' + comment
+                            self.comments['iter'].setdefault(comment_key, {})[comment_val] = '  # ' + comment
                         else:
                             self.comments['inline'][comment_key] = '  # ' + comment
 

From e7663ad0fc8c36dc229f5f94a3405758ee152c73 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Aug 2015 21:45:42 +0200
Subject: [PATCH 1210/1356] remove autopep8.py, it's simply being imported (as
 it should be)

---
 easybuild/tools/autopep8.py | 3648 -----------------------------------
 1 file changed, 3648 deletions(-)
 delete mode 100644 easybuild/tools/autopep8.py

diff --git a/easybuild/tools/autopep8.py b/easybuild/tools/autopep8.py
deleted file mode 100644
index c5b57ee9eb..0000000000
--- a/easybuild/tools/autopep8.py
+++ /dev/null
@@ -1,3648 +0,0 @@
-# Copyright (C) 2010-2011 Hideo Hattori
-# Copyright (C) 2011-2013 Hideo Hattori, Steven Myint
-# Copyright (C) 2013-2015 Hideo Hattori, Steven Myint, Bill Wendling
-#
-# Permission is hereby granted, free of charge, to any person obtaining
-# a copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to
-# permit persons to whom the Software is furnished to do so, subject to
-# the following conditions:
-#
-# The above copyright notice and this permission notice shall be
-# included in all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
-# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
-# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-
-"""Automatically formats Python code to conform to the PEP 8 style guide.
-
-Fixes that only need be done once can be added by adding a function of the form
-"fix_<code>(source)" to this module. They should return the fixed source code.
-These fixes are picked up by apply_global_fixes().
-
-Fixes that depend on pep8 should be added as methods to FixPEP8. See the class
-documentation for more information.
-
-"""
-
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
-from __future__ import unicode_literals
-
-import codecs
-import collections
-import copy
-import difflib
-import fnmatch
-import inspect
-import io
-import keyword
-import locale
-import os
-import re
-import signal
-import sys
-import textwrap
-import token
-import tokenize
-
-import pep8
-
-
-try:
-    unicode
-except NameError:
-    unicode = str
-
-
-__version__ = '1.2.1a0'
-
-
-CR = '\r'
-LF = '\n'
-CRLF = '\r\n'
-
-
-PYTHON_SHEBANG_REGEX = re.compile(r'^#!.*\bpython[23]?\b\s*$')
-
-
-# For generating line shortening candidates.
-SHORTEN_OPERATOR_GROUPS = frozenset([
-    frozenset([',']),
-    frozenset(['%']),
-    frozenset([',', '(', '[', '{']),
-    frozenset(['%', '(', '[', '{']),
-    frozenset([',', '(', '[', '{', '%', '+', '-', '*', '/', '//']),
-    frozenset(['%', '+', '-', '*', '/', '//']),
-])
-
-
-DEFAULT_IGNORE = 'E24'
-DEFAULT_INDENT_SIZE = 4
-
-
-# W602 is handled separately due to the need to avoid "with_traceback".
-CODE_TO_2TO3 = {
-    'E231': ['ws_comma'],
-    'E721': ['idioms'],
-    'W601': ['has_key'],
-    'W603': ['ne'],
-    'W604': ['repr'],
-    'W690': ['apply',
-             'except',
-             'exitfunc',
-             'numliterals',
-             'operator',
-             'paren',
-             'reduce',
-             'renames',
-             'standarderror',
-             'sys_exc',
-             'throw',
-             'tuple_params',
-             'xreadlines']}
-
-
-if sys.platform == 'win32':  # pragma: no cover
-    DEFAULT_CONFIG = os.path.expanduser(r'~\.pep8')
-else:
-    DEFAULT_CONFIG = os.path.join(os.getenv('XDG_CONFIG_HOME') or
-                                  os.path.expanduser('~/.config'), 'pep8')
-PROJECT_CONFIG = ('setup.cfg', 'tox.ini', '.pep8')
-
-
-def open_with_encoding(filename, encoding=None, mode='r'):
-    """Return opened file with a specific encoding."""
-    if not encoding:
-        encoding = detect_encoding(filename)
-
-    return io.open(filename, mode=mode, encoding=encoding,
-                   newline='')  # Preserve line endings
-
-
-def detect_encoding(filename):
-    """Return file encoding."""
-    try:
-        with open(filename, 'rb') as input_file:
-            from lib2to3.pgen2 import tokenize as lib2to3_tokenize
-            encoding = lib2to3_tokenize.detect_encoding(input_file.readline)[0]
-
-        # Check for correctness of encoding
-        with open_with_encoding(filename, encoding) as test_file:
-            test_file.read()
-
-        return encoding
-    except (LookupError, SyntaxError, UnicodeDecodeError):
-        return 'latin-1'
-
-
-def readlines_from_file(filename):
-    """Return contents of file."""
-    with open_with_encoding(filename) as input_file:
-        return input_file.readlines()
-
-
-def extended_blank_lines(logical_line,
-                         blank_lines,
-                         blank_before,
-                         indent_level,
-                         previous_logical):
-    """Check for missing blank lines after class declaration."""
-    if previous_logical.startswith('class '):
-        if logical_line.startswith(('def ', 'class ', '@')):
-            if indent_level and not blank_lines and not blank_before:
-                yield (0, 'E309 expected 1 blank line after class declaration')
-    elif previous_logical.startswith('def '):
-        if blank_lines and pep8.DOCSTRING_REGEX.match(logical_line):
-            yield (0, 'E303 too many blank lines ({0})'.format(blank_lines))
-    elif pep8.DOCSTRING_REGEX.match(previous_logical):
-        # Missing blank line between class docstring and method declaration.
-        if (
-            indent_level and
-            not blank_lines and
-            not blank_before and
-            logical_line.startswith(('def ')) and
-            '(self' in logical_line
-        ):
-            yield (0, 'E301 expected 1 blank line, found 0')
-pep8.register_check(extended_blank_lines)
-
-
-def continued_indentation(logical_line, tokens, indent_level, indent_char,
-                          noqa):
-    """Override pep8's function to provide indentation information."""
-    first_row = tokens[0][2][0]
-    nrows = 1 + tokens[-1][2][0] - first_row
-    if noqa or nrows == 1:
-        return
-
-    # indent_next tells us whether the next block is indented. Assuming
-    # that it is indented by 4 spaces, then we should not allow 4-space
-    # indents on the final continuation line. In turn, some other
-    # indents are allowed to have an extra 4 spaces.
-    indent_next = logical_line.endswith(':')
-
-    row = depth = 0
-    valid_hangs = (
-        (DEFAULT_INDENT_SIZE,)
-        if indent_char != '\t' else (DEFAULT_INDENT_SIZE,
-                                     2 * DEFAULT_INDENT_SIZE)
-    )
-
-    # Remember how many brackets were opened on each line.
-    parens = [0] * nrows
-
-    # Relative indents of physical lines.
-    rel_indent = [0] * nrows
-
-    # For each depth, collect a list of opening rows.
-    open_rows = [[0]]
-    # For each depth, memorize the hanging indentation.
-    hangs = [None]
-
-    # Visual indents.
-    indent_chances = {}
-    last_indent = tokens[0][2]
-    indent = [last_indent[1]]
-
-    last_token_multiline = None
-    line = None
-    last_line = ''
-    last_line_begins_with_multiline = False
-    for token_type, text, start, end, line in tokens:
-
-        newline = row < start[0] - first_row
-        if newline:
-            row = start[0] - first_row
-            newline = (not last_token_multiline and
-                       token_type not in (tokenize.NL, tokenize.NEWLINE))
-            last_line_begins_with_multiline = last_token_multiline
-
-        if newline:
-            # This is the beginning of a continuation line.
-            last_indent = start
-
-            # Record the initial indent.
-            rel_indent[row] = pep8.expand_indent(line) - indent_level
-
-            # Identify closing bracket.
-            close_bracket = (token_type == tokenize.OP and text in ']})')
-
-            # Is the indent relative to an opening bracket line?
-            for open_row in reversed(open_rows[depth]):
-                hang = rel_indent[row] - rel_indent[open_row]
-                hanging_indent = hang in valid_hangs
-                if hanging_indent:
-                    break
-            if hangs[depth]:
-                hanging_indent = (hang == hangs[depth])
-
-            visual_indent = (not close_bracket and hang > 0 and
-                             indent_chances.get(start[1]))
-
-            if close_bracket and indent[depth]:
-                # Closing bracket for visual indent.
-                if start[1] != indent[depth]:
-                    yield (start, 'E124 {0}'.format(indent[depth]))
-            elif close_bracket and not hang:
-                pass
-            elif indent[depth] and start[1] < indent[depth]:
-                # Visual indent is broken.
-                yield (start, 'E128 {0}'.format(indent[depth]))
-            elif (hanging_indent or
-                  (indent_next and
-                   rel_indent[row] == 2 * DEFAULT_INDENT_SIZE)):
-                # Hanging indent is verified.
-                if close_bracket:
-                    yield (start, 'E123 {0}'.format(indent_level +
-                                                    rel_indent[open_row]))
-                hangs[depth] = hang
-            elif visual_indent is True:
-                # Visual indent is verified.
-                indent[depth] = start[1]
-            elif visual_indent in (text, unicode):
-                # Ignore token lined up with matching one from a previous line.
-                pass
-            else:
-                one_indented = (indent_level + rel_indent[open_row] +
-                                DEFAULT_INDENT_SIZE)
-                # Indent is broken.
-                if hang <= 0:
-                    error = ('E122', one_indented)
-                elif indent[depth]:
-                    error = ('E127', indent[depth])
-                elif hang > DEFAULT_INDENT_SIZE:
-                    error = ('E126', one_indented)
-                else:
-                    hangs[depth] = hang
-                    error = ('E121', one_indented)
-
-                yield (start, '{0} {1}'.format(*error))
-
-        # Look for visual indenting.
-        if (
-            parens[row] and
-            token_type not in (tokenize.NL, tokenize.COMMENT) and
-            not indent[depth]
-        ):
-            indent[depth] = start[1]
-            indent_chances[start[1]] = True
-        # Deal with implicit string concatenation.
-        elif (token_type in (tokenize.STRING, tokenize.COMMENT) or
-              text in ('u', 'ur', 'b', 'br')):
-            indent_chances[start[1]] = unicode
-        # Special case for the "if" statement because len("if (") is equal to
-        # 4.
-        elif not indent_chances and not row and not depth and text == 'if':
-            indent_chances[end[1] + 1] = True
-        elif text == ':' and line[end[1]:].isspace():
-            open_rows[depth].append(row)
-
-        # Keep track of bracket depth.
-        if token_type == tokenize.OP:
-            if text in '([{':
-                depth += 1
-                indent.append(0)
-                hangs.append(None)
-                if len(open_rows) == depth:
-                    open_rows.append([])
-                open_rows[depth].append(row)
-                parens[row] += 1
-            elif text in ')]}' and depth > 0:
-                # Parent indents should not be more than this one.
-                prev_indent = indent.pop() or last_indent[1]
-                hangs.pop()
-                for d in range(depth):
-                    if indent[d] > prev_indent:
-                        indent[d] = 0
-                for ind in list(indent_chances):
-                    if ind >= prev_indent:
-                        del indent_chances[ind]
-                del open_rows[depth + 1:]
-                depth -= 1
-                if depth:
-                    indent_chances[indent[depth]] = True
-                for idx in range(row, -1, -1):
-                    if parens[idx]:
-                        parens[idx] -= 1
-                        break
-            assert len(indent) == depth + 1
-            if (
-                start[1] not in indent_chances and
-                # This is for purposes of speeding up E121 (GitHub #90).
-                not last_line.rstrip().endswith(',')
-            ):
-                # Allow to line up tokens.
-                indent_chances[start[1]] = text
-
-        last_token_multiline = (start[0] != end[0])
-        if last_token_multiline:
-            rel_indent[end[0] - first_row] = rel_indent[row]
-
-        last_line = line
-
-    if (
-        indent_next and
-        not last_line_begins_with_multiline and
-        pep8.expand_indent(line) == indent_level + DEFAULT_INDENT_SIZE
-    ):
-        pos = (start[0], indent[0] + 4)
-        yield (pos, 'E125 {0}'.format(indent_level +
-                                      2 * DEFAULT_INDENT_SIZE))
-del pep8._checks['logical_line'][pep8.continued_indentation]
-pep8.register_check(continued_indentation)
-
-
-class FixPEP8(object):
-
-    """Fix invalid code.
-
-    Fixer methods are prefixed "fix_". The _fix_source() method looks for these
-    automatically.
-
-    The fixer method can take either one or two arguments (in addition to
-    self). The first argument is "result", which is the error information from
-    pep8. The second argument, "logical", is required only for logical-line
-    fixes.
-
-    The fixer method can return the list of modified lines or None. An empty
-    list would mean that no changes were made. None would mean that only the
-    line reported in the pep8 error was modified. Note that the modified line
-    numbers that are returned are indexed at 1. This typically would correspond
-    with the line number reported in the pep8 error information.
-
-    [fixed method list]
-        - e121,e122,e123,e124,e125,e126,e127,e128,e129
-        - e201,e202,e203
-        - e211
-        - e221,e222,e223,e224,e225
-        - e231
-        - e251
-        - e261,e262
-        - e271,e272,e273,e274
-        - e301,e302,e303
-        - e401
-        - e502
-        - e701,e702
-        - e711
-        - w291
-
-    """
-
-    def __init__(self, filename,
-                 options,
-                 contents=None,
-                 long_line_ignore_cache=None):
-        self.filename = filename
-        if contents is None:
-            self.source = readlines_from_file(filename)
-        else:
-            sio = io.StringIO(contents)
-            self.source = sio.readlines()
-        self.options = options
-        self.indent_word = _get_indentword(''.join(self.source))
-
-        self.long_line_ignore_cache = (
-            set() if long_line_ignore_cache is None
-            else long_line_ignore_cache)
-
-        # Many fixers are the same even though pep8 categorizes them
-        # differently.
-        self.fix_e115 = self.fix_e112
-        self.fix_e116 = self.fix_e113
-        self.fix_e121 = self._fix_reindent
-        self.fix_e122 = self._fix_reindent
-        self.fix_e123 = self._fix_reindent
-        self.fix_e124 = self._fix_reindent
-        self.fix_e126 = self._fix_reindent
-        self.fix_e127 = self._fix_reindent
-        self.fix_e128 = self._fix_reindent
-        self.fix_e129 = self._fix_reindent
-        self.fix_e202 = self.fix_e201
-        self.fix_e203 = self.fix_e201
-        self.fix_e211 = self.fix_e201
-        self.fix_e221 = self.fix_e271
-        self.fix_e222 = self.fix_e271
-        self.fix_e223 = self.fix_e271
-        self.fix_e226 = self.fix_e225
-        self.fix_e227 = self.fix_e225
-        self.fix_e228 = self.fix_e225
-        self.fix_e241 = self.fix_e271
-        self.fix_e242 = self.fix_e224
-        self.fix_e261 = self.fix_e262
-        self.fix_e272 = self.fix_e271
-        self.fix_e273 = self.fix_e271
-        self.fix_e274 = self.fix_e271
-        self.fix_e309 = self.fix_e301
-        self.fix_e501 = (
-            self.fix_long_line_logically if
-            options and (options.aggressive >= 2 or options.experimental) else
-            self.fix_long_line_physically)
-        self.fix_e703 = self.fix_e702
-        self.fix_w293 = self.fix_w291
-
-    def _fix_source(self, results):
-        try:
-            (logical_start, logical_end) = _find_logical(self.source)
-            logical_support = True
-        except (SyntaxError, tokenize.TokenError):  # pragma: no cover
-            logical_support = False
-
-        completed_lines = set()
-        for result in sorted(results, key=_priority_key):
-            if result['line'] in completed_lines:
-                continue
-
-            fixed_methodname = 'fix_' + result['id'].lower()
-            if hasattr(self, fixed_methodname):
-                fix = getattr(self, fixed_methodname)
-
-                line_index = result['line'] - 1
-                original_line = self.source[line_index]
-
-                is_logical_fix = len(inspect.getargspec(fix).args) > 2
-                if is_logical_fix:
-                    logical = None
-                    if logical_support:
-                        logical = _get_logical(self.source,
-                                               result,
-                                               logical_start,
-                                               logical_end)
-                        if logical and set(range(
-                            logical[0][0] + 1,
-                            logical[1][0] + 1)).intersection(
-                                completed_lines):
-                            continue
-
-                    modified_lines = fix(result, logical)
-                else:
-                    modified_lines = fix(result)
-
-                if modified_lines is None:
-                    # Force logical fixes to report what they modified.
-                    assert not is_logical_fix
-
-                    if self.source[line_index] == original_line:
-                        modified_lines = []
-
-                if modified_lines:
-                    completed_lines.update(modified_lines)
-                elif modified_lines == []:  # Empty list means no fix
-                    if self.options.verbose >= 2:
-                        print(
-                            '--->  Not fixing {f} on line {l}'.format(
-                                f=result['id'], l=result['line']),
-                            file=sys.stderr)
-                else:  # We assume one-line fix when None.
-                    completed_lines.add(result['line'])
-            else:
-                if self.options.verbose >= 3:
-                    print(
-                        "--->  '{0}' is not defined.".format(fixed_methodname),
-                        file=sys.stderr)
-
-                    info = result['info'].strip()
-                    print('--->  {0}:{1}:{2}:{3}'.format(self.filename,
-                                                         result['line'],
-                                                         result['column'],
-                                                         info),
-                          file=sys.stderr)
-
-    def fix(self):
-        """Return a version of the source code with PEP 8 violations fixed."""
-        pep8_options = {
-            'ignore': self.options.ignore,
-            'select': self.options.select,
-            'max_line_length': self.options.max_line_length,
-        }
-        results = _execute_pep8(pep8_options, self.source)
-
-        if self.options.verbose:
-            progress = {}
-            for r in results:
-                if r['id'] not in progress:
-                    progress[r['id']] = set()
-                progress[r['id']].add(r['line'])
-            print('--->  {n} issue(s) to fix {progress}'.format(
-                n=len(results), progress=progress), file=sys.stderr)
-
-        if self.options.line_range:
-            start, end = self.options.line_range
-            results = [r for r in results
-                       if start <= r['line'] <= end]
-
-        self._fix_source(filter_results(source=''.join(self.source),
-                                        results=results,
-                                        aggressive=self.options.aggressive))
-
-        if self.options.line_range:
-            # If number of lines has changed then change line_range.
-            count = sum(sline.count('\n')
-                        for sline in self.source[start - 1:end])
-            self.options.line_range[1] = start + count - 1
-
-        return ''.join(self.source)
-
-    def _fix_reindent(self, result):
-        """Fix a badly indented line.
-
-        This is done by adding or removing from its initial indent only.
-
-        """
-        num_indent_spaces = int(result['info'].split()[1])
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-
-        self.source[line_index] = ' ' * num_indent_spaces + target.lstrip()
-
-    def fix_e112(self, result):
-        """Fix under-indented comments."""
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-
-        if not target.lstrip().startswith('#'):
-            # Don't screw with invalid syntax.
-            return []
-
-        self.source[line_index] = self.indent_word + target
-
-    def fix_e113(self, result):
-        """Fix over-indented comments."""
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-
-        indent = _get_indentation(target)
-        stripped = target.lstrip()
-
-        if not stripped.startswith('#'):
-            # Don't screw with invalid syntax.
-            return []
-
-        self.source[line_index] = indent[1:] + stripped
-
-    def fix_e125(self, result):
-        """Fix indentation undistinguish from the next logical line."""
-        num_indent_spaces = int(result['info'].split()[1])
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-
-        spaces_to_add = num_indent_spaces - len(_get_indentation(target))
-        indent = len(_get_indentation(target))
-        modified_lines = []
-
-        while len(_get_indentation(self.source[line_index])) >= indent:
-            self.source[line_index] = (' ' * spaces_to_add +
-                                       self.source[line_index])
-            modified_lines.append(1 + line_index)  # Line indexed at 1.
-            line_index -= 1
-
-        return modified_lines
-
-    def fix_e201(self, result):
-        """Remove extraneous whitespace."""
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-        offset = result['column'] - 1
-
-        if is_probably_part_of_multiline(target):
-            return []
-
-        fixed = fix_whitespace(target,
-                               offset=offset,
-                               replacement='')
-
-        self.source[line_index] = fixed
-
-    def fix_e224(self, result):
-        """Remove extraneous whitespace around operator."""
-        target = self.source[result['line'] - 1]
-        offset = result['column'] - 1
-        fixed = target[:offset] + target[offset:].replace('\t', ' ')
-        self.source[result['line'] - 1] = fixed
-
-    def fix_e225(self, result):
-        """Fix missing whitespace around operator."""
-        target = self.source[result['line'] - 1]
-        offset = result['column'] - 1
-        fixed = target[:offset] + ' ' + target[offset:]
-
-        # Only proceed if non-whitespace characters match.
-        # And make sure we don't break the indentation.
-        if (
-            fixed.replace(' ', '') == target.replace(' ', '') and
-            _get_indentation(fixed) == _get_indentation(target)
-        ):
-            self.source[result['line'] - 1] = fixed
-        else:
-            return []
-
-    def fix_e231(self, result):
-        """Add missing whitespace."""
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-        offset = result['column']
-        fixed = target[:offset] + ' ' + target[offset:]
-        self.source[line_index] = fixed
-
-    def fix_e251(self, result):
-        """Remove whitespace around parameter '=' sign."""
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-
-        # This is necessary since pep8 sometimes reports columns that goes
-        # past the end of the physical line. This happens in cases like,
-        # foo(bar\n=None)
-        c = min(result['column'] - 1,
-                len(target) - 1)
-
-        if target[c].strip():
-            fixed = target
-        else:
-            fixed = target[:c].rstrip() + target[c:].lstrip()
-
-        # There could be an escaped newline
-        #
-        #     def foo(a=\
-        #             1)
-        if fixed.endswith(('=\\\n', '=\\\r\n', '=\\\r')):
-            self.source[line_index] = fixed.rstrip('\n\r \t\\')
-            self.source[line_index + 1] = self.source[line_index + 1].lstrip()
-            return [line_index + 1, line_index + 2]  # Line indexed at 1
-
-        self.source[result['line'] - 1] = fixed
-
-    def fix_e262(self, result):
-        """Fix spacing after comment hash."""
-        target = self.source[result['line'] - 1]
-        offset = result['column']
-
-        code = target[:offset].rstrip(' \t#')
-        comment = target[offset:].lstrip(' \t#')
-
-        fixed = code + ('  # ' + comment if comment.strip() else '\n')
-
-        self.source[result['line'] - 1] = fixed
-
-    def fix_e271(self, result):
-        """Fix extraneous whitespace around keywords."""
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-        offset = result['column'] - 1
-
-        if is_probably_part_of_multiline(target):
-            return []
-
-        fixed = fix_whitespace(target,
-                               offset=offset,
-                               replacement=' ')
-
-        if fixed == target:
-            return []
-        else:
-            self.source[line_index] = fixed
-
-    def fix_e301(self, result):
-        """Add missing blank line."""
-        cr = '\n'
-        self.source[result['line'] - 1] = cr + self.source[result['line'] - 1]
-
-    def fix_e302(self, result):
-        """Add missing 2 blank lines."""
-        add_linenum = 2 - int(result['info'].split()[-1])
-        cr = '\n' * add_linenum
-        self.source[result['line'] - 1] = cr + self.source[result['line'] - 1]
-
-    def fix_e303(self, result):
-        """Remove extra blank lines."""
-        delete_linenum = int(result['info'].split('(')[1].split(')')[0]) - 2
-        delete_linenum = max(1, delete_linenum)
-
-        # We need to count because pep8 reports an offset line number if there
-        # are comments.
-        cnt = 0
-        line = result['line'] - 2
-        modified_lines = []
-        while cnt < delete_linenum and line >= 0:
-            if not self.source[line].strip():
-                self.source[line] = ''
-                modified_lines.append(1 + line)  # Line indexed at 1
-                cnt += 1
-            line -= 1
-
-        return modified_lines
-
-    def fix_e304(self, result):
-        """Remove blank line following function decorator."""
-        line = result['line'] - 2
-        if not self.source[line].strip():
-            self.source[line] = ''
-
-    def fix_e401(self, result):
-        """Put imports on separate lines."""
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-        offset = result['column'] - 1
-
-        if not target.lstrip().startswith('import'):
-            return []
-
-        indentation = re.split(pattern=r'\bimport\b',
-                               string=target, maxsplit=1)[0]
-        fixed = (target[:offset].rstrip('\t ,') + '\n' +
-                 indentation + 'import ' + target[offset:].lstrip('\t ,'))
-        self.source[line_index] = fixed
-
-    def fix_long_line_logically(self, result, logical):
-        """Try to make lines fit within --max-line-length characters."""
-        if (
-            not logical or
-            len(logical[2]) == 1 or
-            self.source[result['line'] - 1].lstrip().startswith('#')
-        ):
-            return self.fix_long_line_physically(result)
-
-        start_line_index = logical[0][0]
-        end_line_index = logical[1][0]
-        logical_lines = logical[2]
-
-        previous_line = get_item(self.source, start_line_index - 1, default='')
-        next_line = get_item(self.source, end_line_index + 1, default='')
-
-        single_line = join_logical_line(''.join(logical_lines))
-
-        try:
-            fixed = self.fix_long_line(
-                target=single_line,
-                previous_line=previous_line,
-                next_line=next_line,
-                original=''.join(logical_lines))
-        except (SyntaxError, tokenize.TokenError):
-            return self.fix_long_line_physically(result)
-
-        if fixed:
-            for line_index in range(start_line_index, end_line_index + 1):
-                self.source[line_index] = ''
-            self.source[start_line_index] = fixed
-            return range(start_line_index + 1, end_line_index + 1)
-        else:
-            return []
-
-    def fix_long_line_physically(self, result):
-        """Try to make lines fit within --max-line-length characters."""
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-
-        previous_line = get_item(self.source, line_index - 1, default='')
-        next_line = get_item(self.source, line_index + 1, default='')
-
-        try:
-            fixed = self.fix_long_line(
-                target=target,
-                previous_line=previous_line,
-                next_line=next_line,
-                original=target)
-        except (SyntaxError, tokenize.TokenError):
-            return []
-
-        if fixed:
-            self.source[line_index] = fixed
-            return [line_index + 1]
-        else:
-            return []
-
-    def fix_long_line(self, target, previous_line,
-                      next_line, original):
-        cache_entry = (target, previous_line, next_line)
-        if cache_entry in self.long_line_ignore_cache:
-            return []
-
-        if target.lstrip().startswith('#'):
-            # Wrap commented lines.
-            return shorten_comment(
-                line=target,
-                max_line_length=self.options.max_line_length,
-                last_comment=not next_line.lstrip().startswith('#'))
-
-        fixed = get_fixed_long_line(
-            target=target,
-            previous_line=previous_line,
-            original=original,
-            indent_word=self.indent_word,
-            max_line_length=self.options.max_line_length,
-            aggressive=self.options.aggressive,
-            experimental=self.options.experimental,
-            verbose=self.options.verbose)
-        if fixed and not code_almost_equal(original, fixed):
-            return fixed
-        else:
-            self.long_line_ignore_cache.add(cache_entry)
-            return None
-
-    def fix_e502(self, result):
-        """Remove extraneous escape of newline."""
-        (line_index, _, target) = get_index_offset_contents(result,
-                                                            self.source)
-        self.source[line_index] = target.rstrip('\n\r \t\\') + '\n'
-
-    def fix_e701(self, result):
-        """Put colon-separated compound statement on separate lines."""
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-        c = result['column']
-
-        fixed_source = (target[:c] + '\n' +
-                        _get_indentation(target) + self.indent_word +
-                        target[c:].lstrip('\n\r \t\\'))
-        self.source[result['line'] - 1] = fixed_source
-        return [result['line'], result['line'] + 1]
-
-    def fix_e702(self, result, logical):
-        """Put semicolon-separated compound statement on separate lines."""
-        if not logical:
-            return []  # pragma: no cover
-        logical_lines = logical[2]
-
-        line_index = result['line'] - 1
-        target = self.source[line_index]
-
-        if target.rstrip().endswith('\\'):
-            # Normalize '1; \\\n2' into '1; 2'.
-            self.source[line_index] = target.rstrip('\n \r\t\\')
-            self.source[line_index + 1] = self.source[line_index + 1].lstrip()
-            return [line_index + 1, line_index + 2]
-
-        if target.rstrip().endswith(';'):
-            self.source[line_index] = target.rstrip('\n \r\t;') + '\n'
-            return [line_index + 1]
-
-        offset = result['column'] - 1
-        first = target[:offset].rstrip(';').rstrip()
-        second = (_get_indentation(logical_lines[0]) +
-                  target[offset:].lstrip(';').lstrip())
-
-        # find inline commnet
-        inline_comment = None
-        if '# ' == target[offset:].lstrip(';').lstrip()[:2]:
-            inline_comment = target[offset:].lstrip(';')
-
-        if inline_comment:
-            self.source[line_index] = first + inline_comment
-        else:
-            self.source[line_index] = first + '\n' + second
-        return [line_index + 1]
-
-    def fix_e711(self, result):
-        """Fix comparison with None."""
-        (line_index, offset, target) = get_index_offset_contents(result,
-                                                                 self.source)
-
-        right_offset = offset + 2
-        if right_offset >= len(target):
-            return []
-
-        left = target[:offset].rstrip()
-        center = target[offset:right_offset]
-        right = target[right_offset:].lstrip()
-
-        if not right.startswith('None'):
-            return []
-
-        if center.strip() == '==':
-            new_center = 'is'
-        elif center.strip() == '!=':
-            new_center = 'is not'
-        else:
-            return []
-
-        self.source[line_index] = ' '.join([left, new_center, right])
-
-    def fix_e712(self, result):
-        """Fix (trivial case of) comparison with boolean."""
-        (line_index, offset, target) = get_index_offset_contents(result,
-                                                                 self.source)
-
-        # Handle very easy "not" special cases.
-        if re.match(r'^\s*if [\w.]+ == False:$', target):
-            self.source[line_index] = re.sub(r'if ([\w.]+) == False:',
-                                             r'if not \1:', target, count=1)
-        elif re.match(r'^\s*if [\w.]+ != True:$', target):
-            self.source[line_index] = re.sub(r'if ([\w.]+) != True:',
-                                             r'if not \1:', target, count=1)
-        else:
-            right_offset = offset + 2
-            if right_offset >= len(target):
-                return []
-
-            left = target[:offset].rstrip()
-            center = target[offset:right_offset]
-            right = target[right_offset:].lstrip()
-
-            # Handle simple cases only.
-            new_right = None
-            if center.strip() == '==':
-                if re.match(r'\bTrue\b', right):
-                    new_right = re.sub(r'\bTrue\b *', '', right, count=1)
-            elif center.strip() == '!=':
-                if re.match(r'\bFalse\b', right):
-                    new_right = re.sub(r'\bFalse\b *', '', right, count=1)
-
-            if new_right is None:
-                return []
-
-            if new_right[0].isalnum():
-                new_right = ' ' + new_right
-
-            self.source[line_index] = left + new_right
-
-    def fix_e713(self, result):
-        """Fix (trivial case of) non-membership check."""
-        (line_index, _, target) = get_index_offset_contents(result,
-                                                            self.source)
-
-        # Handle very easy case only.
-        if re.match(r'^\s*if not [\w.]+ in [\w.]+:$', target):
-            self.source[line_index] = re.sub(r'if not ([\w.]+) in ([\w.]+):',
-                                             r'if \1 not in \2:',
-                                             target,
-                                             count=1)
-
-    def fix_w291(self, result):
-        """Remove trailing whitespace."""
-        fixed_line = self.source[result['line'] - 1].rstrip()
-        self.source[result['line'] - 1] = fixed_line + '\n'
-
-    def fix_w391(self, _):
-        """Remove trailing blank lines."""
-        blank_count = 0
-        for line in reversed(self.source):
-            line = line.rstrip()
-            if line:
-                break
-            else:
-                blank_count += 1
-
-        original_length = len(self.source)
-        self.source = self.source[:original_length - blank_count]
-        return range(1, 1 + original_length)
-
-
-def get_index_offset_contents(result, source):
-    """Return (line_index, column_offset, line_contents)."""
-    line_index = result['line'] - 1
-    return (line_index,
-            result['column'] - 1,
-            source[line_index])
-
-
-def get_fixed_long_line(target, previous_line, original,
-                        indent_word='    ', max_line_length=79,
-                        aggressive=False, experimental=False, verbose=False):
-    """Break up long line and return result.
-
-    Do this by generating multiple reformatted candidates and then
-    ranking the candidates to heuristically select the best option.
-
-    """
-    indent = _get_indentation(target)
-    source = target[len(indent):]
-    assert source.lstrip() == source
-
-    # Check for partial multiline.
-    tokens = list(generate_tokens(source))
-
-    candidates = shorten_line(
-        tokens, source, indent,
-        indent_word,
-        max_line_length,
-        aggressive=aggressive,
-        experimental=experimental,
-        previous_line=previous_line)
-
-    # Also sort alphabetically as a tie breaker (for determinism).
-    candidates = sorted(
-        sorted(set(candidates).union([target, original])),
-        key=lambda x: line_shortening_rank(
-            x,
-            indent_word,
-            max_line_length,
-            experimental=experimental))
-
-    if verbose >= 4:
-        print(('-' * 79 + '\n').join([''] + candidates + ['']),
-              file=wrap_output(sys.stderr, 'utf-8'))
-
-    if candidates:
-        best_candidate = candidates[0]
-        # Don't allow things to get longer.
-        if longest_line_length(best_candidate) > longest_line_length(original):
-            return None
-        else:
-            return best_candidate
-
-
-def longest_line_length(code):
-    """Return length of longest line."""
-    return max(len(line) for line in code.splitlines())
-
-
-def join_logical_line(logical_line):
-    """Return single line based on logical line input."""
-    indentation = _get_indentation(logical_line)
-
-    return indentation + untokenize_without_newlines(
-        generate_tokens(logical_line.lstrip())) + '\n'
-
-
-def untokenize_without_newlines(tokens):
-    """Return source code based on tokens."""
-    text = ''
-    last_row = 0
-    last_column = -1
-
-    for t in tokens:
-        token_string = t[1]
-        (start_row, start_column) = t[2]
-        (end_row, end_column) = t[3]
-
-        if start_row > last_row:
-            last_column = 0
-        if (
-            (start_column > last_column or token_string == '\n') and
-            not text.endswith(' ')
-        ):
-            text += ' '
-
-        if token_string != '\n':
-            text += token_string
-
-        last_row = end_row
-        last_column = end_column
-
-    return text.rstrip()
-
-
-def _find_logical(source_lines):
-    # Make a variable which is the index of all the starts of lines.
-    logical_start = []
-    logical_end = []
-    last_newline = True
-    parens = 0
-    for t in generate_tokens(''.join(source_lines)):
-        if t[0] in [tokenize.COMMENT, tokenize.DEDENT,
-                    tokenize.INDENT, tokenize.NL,
-                    tokenize.ENDMARKER]:
-            continue
-        if not parens and t[0] in [tokenize.NEWLINE, tokenize.SEMI]:
-            last_newline = True
-            logical_end.append((t[3][0] - 1, t[2][1]))
-            continue
-        if last_newline and not parens:
-            logical_start.append((t[2][0] - 1, t[2][1]))
-            last_newline = False
-        if t[0] == tokenize.OP:
-            if t[1] in '([{':
-                parens += 1
-            elif t[1] in '}])':
-                parens -= 1
-    return (logical_start, logical_end)
-
-
-def _get_logical(source_lines, result, logical_start, logical_end):
-    """Return the logical line corresponding to the result.
-
-    Assumes input is already E702-clean.
-
-    """
-    row = result['line'] - 1
-    col = result['column'] - 1
-    ls = None
-    le = None
-    for i in range(0, len(logical_start), 1):
-        assert logical_end
-        x = logical_end[i]
-        if x[0] > row or (x[0] == row and x[1] > col):
-            le = x
-            ls = logical_start[i]
-            break
-    if ls is None:
-        return None
-    original = source_lines[ls[0]:le[0] + 1]
-    return ls, le, original
-
-
-def get_item(items, index, default=None):
-    if 0 <= index < len(items):
-        return items[index]
-    else:
-        return default
-
-
-def reindent(source, indent_size):
-    """Reindent all lines."""
-    reindenter = Reindenter(source)
-    return reindenter.run(indent_size)
-
-
-def code_almost_equal(a, b):
-    """Return True if code is similar.
-
-    Ignore whitespace when comparing specific line.
-
-    """
-    split_a = split_and_strip_non_empty_lines(a)
-    split_b = split_and_strip_non_empty_lines(b)
-
-    if len(split_a) != len(split_b):
-        return False
-
-    for index in range(len(split_a)):
-        if ''.join(split_a[index].split()) != ''.join(split_b[index].split()):
-            return False
-
-    return True
-
-
-def split_and_strip_non_empty_lines(text):
-    """Return lines split by newline.
-
-    Ignore empty lines.
-
-    """
-    return [line.strip() for line in text.splitlines() if line.strip()]
-
-
-def fix_e265(source, aggressive=False):  # pylint: disable=unused-argument
-    """Format block comments."""
-    if '#' not in source:
-        # Optimization.
-        return source
-
-    ignored_line_numbers = multiline_string_lines(
-        source,
-        include_docstrings=True) | set(commented_out_code_lines(source))
-
-    fixed_lines = []
-    sio = io.StringIO(source)
-    for (line_number, line) in enumerate(sio.readlines(), start=1):
-        if (
-            line.lstrip().startswith('#') and
-            line_number not in ignored_line_numbers
-        ):
-            indentation = _get_indentation(line)
-            line = line.lstrip()
-
-            # Normalize beginning if not a shebang.
-            if len(line) > 1:
-                pos = next((index for index, c in enumerate(line)
-                            if c != '#'))
-                if (
-                    # Leave multiple spaces like '#    ' alone.
-                    (line[:pos].count('#') > 1 or line[1].isalnum()) and
-                    # Leave stylistic outlined blocks alone.
-                    not line.rstrip().endswith('#')
-                ):
-                    line = '# ' + line.lstrip('# \t')
-
-            fixed_lines.append(indentation + line)
-        else:
-            fixed_lines.append(line)
-
-    return ''.join(fixed_lines)
-
-
-def refactor(source, fixer_names, ignore=None, filename=''):
-    """Return refactored code using lib2to3.
-
-    Skip if ignore string is produced in the refactored code.
-
-    """
-    from lib2to3 import pgen2
-    try:
-        new_text = refactor_with_2to3(source,
-                                      fixer_names=fixer_names,
-                                      filename=filename)
-    except (pgen2.parse.ParseError,
-            SyntaxError,
-            UnicodeDecodeError,
-            UnicodeEncodeError):
-        return source
-
-    if ignore:
-        if ignore in new_text and ignore not in source:
-            return source
-
-    return new_text
-
-
-def code_to_2to3(select, ignore):
-    fixes = set()
-    for code, fix in CODE_TO_2TO3.items():
-        if code_match(code, select=select, ignore=ignore):
-            fixes |= set(fix)
-    return fixes
-
-
-def fix_2to3(source,
-             aggressive=True, select=None, ignore=None, filename=''):
-    """Fix various deprecated code (via lib2to3)."""
-    if not aggressive:
-        return source
-
-    select = select or []
-    ignore = ignore or []
-
-    return refactor(source,
-                    code_to_2to3(select=select,
-                                 ignore=ignore),
-                    filename=filename)
-
-
-def fix_w602(source, aggressive=True):
-    """Fix deprecated form of raising exception."""
-    if not aggressive:
-        return source
-
-    return refactor(source, ['raise'],
-                    ignore='with_traceback')
-
-
-def find_newline(source):
-    """Return type of newline used in source.
-
-    Input is a list of lines.
-
-    """
-    assert not isinstance(source, unicode)
-
-    counter = collections.defaultdict(int)
-    for line in source:
-        if line.endswith(CRLF):
-            counter[CRLF] += 1
-        elif line.endswith(CR):
-            counter[CR] += 1
-        elif line.endswith(LF):
-            counter[LF] += 1
-
-    return (sorted(counter, key=counter.get, reverse=True) or [LF])[0]
-
-
-def _get_indentword(source):
-    """Return indentation type."""
-    indent_word = '    '  # Default in case source has no indentation
-    try:
-        for t in generate_tokens(source):
-            if t[0] == token.INDENT:
-                indent_word = t[1]
-                break
-    except (SyntaxError, tokenize.TokenError):
-        pass
-    return indent_word
-
-
-def _get_indentation(line):
-    """Return leading whitespace."""
-    if line.strip():
-        non_whitespace_index = len(line) - len(line.lstrip())
-        return line[:non_whitespace_index]
-    else:
-        return ''
-
-
-def get_diff_text(old, new, filename):
-    """Return text of unified diff between old and new."""
-    newline = '\n'
-    diff = difflib.unified_diff(
-        old, new,
-        'original/' + filename,
-        'fixed/' + filename,
-        lineterm=newline)
-
-    text = ''
-    for line in diff:
-        text += line
-
-        # Work around missing newline (http://bugs.python.org/issue2142).
-        if text and not line.endswith(newline):
-            text += newline + r'\ No newline at end of file' + newline
-
-    return text
-
-
-def _priority_key(pep8_result):
-    """Key for sorting PEP8 results.
-
-    Global fixes should be done first. This is important for things like
-    indentation.
-
-    """
-    priority = [
-        # Fix multiline colon-based before semicolon based.
-        'e701',
-        # Break multiline statements early.
-        'e702',
-        # Things that make lines longer.
-        'e225', 'e231',
-        # Remove extraneous whitespace before breaking lines.
-        'e201',
-        # Shorten whitespace in comment before resorting to wrapping.
-        'e262'
-    ]
-    middle_index = 10000
-    lowest_priority = [
-        # We need to shorten lines last since the logical fixer can get in a
-        # loop, which causes us to exit early.
-        'e501'
-    ]
-    key = pep8_result['id'].lower()
-    try:
-        return priority.index(key)
-    except ValueError:
-        try:
-            return middle_index + lowest_priority.index(key) + 1
-        except ValueError:
-            return middle_index
-
-
-def shorten_line(tokens, source, indentation, indent_word, max_line_length,
-                 aggressive=False, experimental=False, previous_line=''):
-    """Separate line at OPERATOR.
-
-    Multiple candidates will be yielded.
-
-    """
-    for candidate in _shorten_line(tokens=tokens,
-                                   source=source,
-                                   indentation=indentation,
-                                   indent_word=indent_word,
-                                   aggressive=aggressive,
-                                   previous_line=previous_line):
-        yield candidate
-
-    if aggressive:
-        for key_token_strings in SHORTEN_OPERATOR_GROUPS:
-            shortened = _shorten_line_at_tokens(
-                tokens=tokens,
-                source=source,
-                indentation=indentation,
-                indent_word=indent_word,
-                key_token_strings=key_token_strings,
-                aggressive=aggressive)
-
-            if shortened is not None and shortened != source:
-                yield shortened
-
-    if experimental:
-        for shortened in _shorten_line_at_tokens_new(
-                tokens=tokens,
-                source=source,
-                indentation=indentation,
-                max_line_length=max_line_length):
-
-            yield shortened
-
-
-def _shorten_line(tokens, source, indentation, indent_word,
-                  aggressive=False, previous_line=''):
-    """Separate line at OPERATOR.
-
-    The input is expected to be free of newlines except for inside multiline
-    strings and at the end.
-
-    Multiple candidates will be yielded.
-
-    """
-    for (token_type,
-         token_string,
-         start_offset,
-         end_offset) in token_offsets(tokens):
-
-        if (
-            token_type == tokenize.COMMENT and
-            not is_probably_part_of_multiline(previous_line) and
-            not is_probably_part_of_multiline(source) and
-            not source[start_offset + 1:].strip().lower().startswith(
-                ('noqa', 'pragma:', 'pylint:'))
-        ):
-            # Move inline comments to previous line.
-            first = source[:start_offset]
-            second = source[start_offset:]
-            yield (indentation + second.strip() + '\n' +
-                   indentation + first.strip() + '\n')
-        elif token_type == token.OP and token_string != '=':
-            # Don't break on '=' after keyword as this violates PEP 8.
-
-            assert token_type != token.INDENT
-
-            first = source[:end_offset]
-
-            second_indent = indentation
-            if first.rstrip().endswith('('):
-                second_indent += indent_word
-            elif '(' in first:
-                second_indent += ' ' * (1 + first.find('('))
-            else:
-                second_indent += indent_word
-
-            second = (second_indent + source[end_offset:].lstrip())
-            if (
-                not second.strip() or
-                second.lstrip().startswith('#')
-            ):
-                continue
-
-            # Do not begin a line with a comma
-            if second.lstrip().startswith(','):
-                continue
-            # Do end a line with a dot
-            if first.rstrip().endswith('.'):
-                continue
-            if token_string in '+-*/':
-                fixed = first + ' \\' + '\n' + second
-            else:
-                fixed = first + '\n' + second
-
-            # Only fix if syntax is okay.
-            if check_syntax(normalize_multiline(fixed)
-                            if aggressive else fixed):
-                yield indentation + fixed
-
-
-# A convenient way to handle tokens.
-Token = collections.namedtuple('Token', ['token_type', 'token_string',
-                                         'spos', 'epos', 'line'])
-
-
-class ReformattedLines(object):
-
-    """The reflowed lines of atoms.
-
-    Each part of the line is represented as an "atom." They can be moved
-    around when need be to get the optimal formatting.
-
-    """
-
-    ###########################################################################
-    # Private Classes
-
-    class _Indent(object):
-
-        """Represent an indentation in the atom stream."""
-
-        def __init__(self, indent_amt):
-            self._indent_amt = indent_amt
-
-        def emit(self):
-            return ' ' * self._indent_amt
-
-        @property
-        def size(self):
-            return self._indent_amt
-
-    class _Space(object):
-
-        """Represent a space in the atom stream."""
-
-        def emit(self):
-            return ' '
-
-        @property
-        def size(self):
-            return 1
-
-    class _LineBreak(object):
-
-        """Represent a line break in the atom stream."""
-
-        def emit(self):
-            return '\n'
-
-        @property
-        def size(self):
-            return 0
-
-    def __init__(self, max_line_length):
-        self._max_line_length = max_line_length
-        self._lines = []
-        self._bracket_depth = 0
-        self._prev_item = None
-        self._prev_prev_item = None
-
-    def __repr__(self):
-        return self.emit()
-
-    ###########################################################################
-    # Public Methods
-
-    def add(self, obj, indent_amt, break_after_open_bracket):
-        if isinstance(obj, Atom):
-            self._add_item(obj, indent_amt)
-            return
-
-        self._add_container(obj, indent_amt, break_after_open_bracket)
-
-    def add_comment(self, item):
-        num_spaces = 2
-        if len(self._lines) > 1:
-            if isinstance(self._lines[-1], self._Space):
-                num_spaces -= 1
-            if len(self._lines) > 2:
-                if isinstance(self._lines[-2], self._Space):
-                    num_spaces -= 1
-
-        while num_spaces > 0:
-            self._lines.append(self._Space())
-            num_spaces -= 1
-        self._lines.append(item)
-
-    def add_indent(self, indent_amt):
-        self._lines.append(self._Indent(indent_amt))
-
-    def add_line_break(self, indent):
-        self._lines.append(self._LineBreak())
-        self.add_indent(len(indent))
-
-    def add_line_break_at(self, index, indent_amt):
-        self._lines.insert(index, self._LineBreak())
-        self._lines.insert(index + 1, self._Indent(indent_amt))
-
-    def add_space_if_needed(self, curr_text, equal=False):
-        if (
-            not self._lines or isinstance(
-                self._lines[-1], (self._LineBreak, self._Indent, self._Space))
-        ):
-            return
-
-        prev_text = unicode(self._prev_item)
-        prev_prev_text = (
-            unicode(self._prev_prev_item) if self._prev_prev_item else '')
-
-        if (
-            # The previous item was a keyword or identifier and the current
-            # item isn't an operator that doesn't require a space.
-            ((self._prev_item.is_keyword or self._prev_item.is_string or
-              self._prev_item.is_name or self._prev_item.is_number) and
-             (curr_text[0] not in '([{.,:}])' or
-              (curr_text[0] == '=' and equal))) or
-
-            # Don't place spaces around a '.', unless it's in an 'import'
-            # statement.
-            ((prev_prev_text != 'from' and prev_text[-1] != '.' and
-              curr_text != 'import') and
-
-             # Don't place a space before a colon.
-             curr_text[0] != ':' and
-
-             # Don't split up ending brackets by spaces.
-             ((prev_text[-1] in '}])' and curr_text[0] not in '.,}])') or
-
-              # Put a space after a colon or comma.
-              prev_text[-1] in ':,' or
-
-              # Put space around '=' if asked to.
-              (equal and prev_text == '=') or
-
-              # Put spaces around non-unary arithmetic operators.
-              ((self._prev_prev_item and
-                (prev_text not in '+-' and
-                 (self._prev_prev_item.is_name or
-                  self._prev_prev_item.is_number or
-                  self._prev_prev_item.is_string)) and
-                prev_text in ('+', '-', '%', '*', '/', '//', '**', 'in')))))
-        ):
-            self._lines.append(self._Space())
-
-    def previous_item(self):
-        """Return the previous non-whitespace item."""
-        return self._prev_item
-
-    def fits_on_current_line(self, item_extent):
-        return self.current_size() + item_extent <= self._max_line_length
-
-    def current_size(self):
-        """The size of the current line minus the indentation."""
-        size = 0
-        for item in reversed(self._lines):
-            size += item.size
-            if isinstance(item, self._LineBreak):
-                break
-
-        return size
-
-    def line_empty(self):
-        return (self._lines and
-                isinstance(self._lines[-1],
-                           (self._LineBreak, self._Indent)))
-
-    def emit(self):
-        string = ''
-        for item in self._lines:
-            if isinstance(item, self._LineBreak):
-                string = string.rstrip()
-            string += item.emit()
-
-        return string.rstrip() + '\n'
-
-    ###########################################################################
-    # Private Methods
-
-    def _add_item(self, item, indent_amt):
-        """Add an item to the line.
-
-        Reflow the line to get the best formatting after the item is
-        inserted. The bracket depth indicates if the item is being
-        inserted inside of a container or not.
-
-        """
-        if self._prev_item and self._prev_item.is_string and item.is_string:
-            # Place consecutive string literals on separate lines.
-            self._lines.append(self._LineBreak())
-            self._lines.append(self._Indent(indent_amt))
-
-        item_text = unicode(item)
-        if self._lines and self._bracket_depth:
-            # Adding the item into a container.
-            self._prevent_default_initializer_splitting(item, indent_amt)
-
-            if item_text in '.,)]}':
-                self._split_after_delimiter(item, indent_amt)
-
-        elif self._lines and not self.line_empty():
-            # Adding the item outside of a container.
-            if self.fits_on_current_line(len(item_text)):
-                self._enforce_space(item)
-
-            else:
-                # Line break for the new item.
-                self._lines.append(self._LineBreak())
-                self._lines.append(self._Indent(indent_amt))
-
-        self._lines.append(item)
-        self._prev_item, self._prev_prev_item = item, self._prev_item
-
-        if item_text in '([{':
-            self._bracket_depth += 1
-
-        elif item_text in '}])':
-            self._bracket_depth -= 1
-            assert self._bracket_depth >= 0
-
-    def _add_container(self, container, indent_amt, break_after_open_bracket):
-        actual_indent = indent_amt + 1
-
-        if (
-            unicode(self._prev_item) != '=' and
-            not self.line_empty() and
-            not self.fits_on_current_line(
-                container.size + self._bracket_depth + 2)
-        ):
-
-            if unicode(container)[0] == '(' and self._prev_item.is_name:
-                # Don't split before the opening bracket of a call.
-                break_after_open_bracket = True
-                actual_indent = indent_amt + 4
-            elif (
-                break_after_open_bracket or
-                unicode(self._prev_item) not in '([{'
-            ):
-                # If the container doesn't fit on the current line and the
-                # current line isn't empty, place the container on the next
-                # line.
-                self._lines.append(self._LineBreak())
-                self._lines.append(self._Indent(indent_amt))
-                break_after_open_bracket = False
-        else:
-            actual_indent = self.current_size() + 1
-            break_after_open_bracket = False
-
-        if isinstance(container, (ListComprehension, IfExpression)):
-            actual_indent = indent_amt
-
-        # Increase the continued indentation only if recursing on a
-        # container.
-        container.reflow(self, ' ' * actual_indent,
-                         break_after_open_bracket=break_after_open_bracket)
-
-    def _prevent_default_initializer_splitting(self, item, indent_amt):
-        """Prevent splitting between a default initializer.
-
-        When there is a default initializer, it's best to keep it all on
-        the same line. It's nicer and more readable, even if it goes
-        over the maximum allowable line length. This goes back along the
-        current line to determine if we have a default initializer, and,
-        if so, to remove extraneous whitespaces and add a line
-        break/indent before it if needed.
-
-        """
-        if unicode(item) == '=':
-            # This is the assignment in the initializer. Just remove spaces for
-            # now.
-            self._delete_whitespace()
-            return
-
-        if (not self._prev_item or not self._prev_prev_item or
-                unicode(self._prev_item) != '='):
-            return
-
-        self._delete_whitespace()
-        prev_prev_index = self._lines.index(self._prev_prev_item)
-
-        if (
-            isinstance(self._lines[prev_prev_index - 1], self._Indent) or
-            self.fits_on_current_line(item.size + 1)
-        ):
-            # The default initializer is already the only item on this line.
-            # Don't insert a newline here.
-            return
-
-        # Replace the space with a newline/indent combo.
-        if isinstance(self._lines[prev_prev_index - 1], self._Space):
-            del self._lines[prev_prev_index - 1]
-
-        self.add_line_break_at(self._lines.index(self._prev_prev_item),
-                               indent_amt)
-
-    def _split_after_delimiter(self, item, indent_amt):
-        """Split the line only after a delimiter."""
-        self._delete_whitespace()
-
-        if self.fits_on_current_line(item.size):
-            return
-
-        last_space = None
-        for item in reversed(self._lines):
-            if (
-                last_space and
-                (not isinstance(item, Atom) or not item.is_colon)
-            ):
-                break
-            else:
-                last_space = None
-            if isinstance(item, self._Space):
-                last_space = item
-            if isinstance(item, (self._LineBreak, self._Indent)):
-                return
-
-        if not last_space:
-            return
-
-        self.add_line_break_at(self._lines.index(last_space), indent_amt)
-
-    def _enforce_space(self, item):
-        """Enforce a space in certain situations.
-
-        There are cases where we will want a space where normally we
-        wouldn't put one. This just enforces the addition of a space.
-
-        """
-        if isinstance(self._lines[-1],
-                      (self._Space, self._LineBreak, self._Indent)):
-            return
-
-        if not self._prev_item:
-            return
-
-        item_text = unicode(item)
-        prev_text = unicode(self._prev_item)
-
-        # Prefer a space around a '.' in an import statement, and between the
-        # 'import' and '('.
-        if (
-            (item_text == '.' and prev_text == 'from') or
-            (item_text == 'import' and prev_text == '.') or
-            (item_text == '(' and prev_text == 'import')
-        ):
-            self._lines.append(self._Space())
-
-    def _delete_whitespace(self):
-        """Delete all whitespace from the end of the line."""
-        while isinstance(self._lines[-1], (self._Space, self._LineBreak,
-                                           self._Indent)):
-            del self._lines[-1]
-
-
-class Atom(object):
-
-    """The smallest unbreakable unit that can be reflowed."""
-
-    def __init__(self, atom):
-        self._atom = atom
-
-    def __repr__(self):
-        return self._atom.token_string
-
-    def __len__(self):
-        return self.size
-
-    def reflow(
-        self, reflowed_lines, continued_indent, extent,
-        break_after_open_bracket=False,
-        is_list_comp_or_if_expr=False,
-        next_is_dot=False
-    ):
-        if self._atom.token_type == tokenize.COMMENT:
-            reflowed_lines.add_comment(self)
-            return
-
-        total_size = extent if extent else self.size
-
-        if self._atom.token_string not in ',:([{}])':
-            # Some atoms will need an extra 1-sized space token after them.
-            total_size += 1
-
-        prev_item = reflowed_lines.previous_item()
-        if (
-            not is_list_comp_or_if_expr and
-            not reflowed_lines.fits_on_current_line(total_size) and
-            not (next_is_dot and
-                 reflowed_lines.fits_on_current_line(self.size + 1)) and
-            not reflowed_lines.line_empty() and
-            not self.is_colon and
-            not (prev_item and prev_item.is_name and
-                 unicode(self) == '(')
-        ):
-            # Start a new line if there is already something on the line and
-            # adding this atom would make it go over the max line length.
-            reflowed_lines.add_line_break(continued_indent)
-        else:
-            reflowed_lines.add_space_if_needed(unicode(self))
-
-        reflowed_lines.add(self, len(continued_indent),
-                           break_after_open_bracket)
-
-    def emit(self):
-        return self.__repr__()
-
-    @property
-    def is_keyword(self):
-        return keyword.iskeyword(self._atom.token_string)
-
-    @property
-    def is_string(self):
-        return self._atom.token_type == tokenize.STRING
-
-    @property
-    def is_name(self):
-        return self._atom.token_type == tokenize.NAME
-
-    @property
-    def is_number(self):
-        return self._atom.token_type == tokenize.NUMBER
-
-    @property
-    def is_comma(self):
-        return self._atom.token_string == ','
-
-    @property
-    def is_colon(self):
-        return self._atom.token_string == ':'
-
-    @property
-    def size(self):
-        return len(self._atom.token_string)
-
-
-class Container(object):
-
-    """Base class for all container types."""
-
-    def __init__(self, items):
-        self._items = items
-
-    def __repr__(self):
-        string = ''
-        last_was_keyword = False
-
-        for item in self._items:
-            if item.is_comma:
-                string += ', '
-            elif item.is_colon:
-                string += ': '
-            else:
-                item_string = unicode(item)
-                if (
-                    string and
-                    (last_was_keyword or
-                     (not string.endswith(tuple('([{,.:}]) ')) and
-                      not item_string.startswith(tuple('([{,.:}])'))))
-                ):
-                    string += ' '
-                string += item_string
-
-            last_was_keyword = item.is_keyword
-        return string
-
-    def __iter__(self):
-        for element in self._items:
-            yield element
-
-    def __getitem__(self, idx):
-        return self._items[idx]
-
-    def reflow(self, reflowed_lines, continued_indent,
-               break_after_open_bracket=False):
-        last_was_container = False
-        for (index, item) in enumerate(self._items):
-            next_item = get_item(self._items, index + 1)
-
-            if isinstance(item, Atom):
-                is_list_comp_or_if_expr = (
-                    isinstance(self, (ListComprehension, IfExpression)))
-                item.reflow(reflowed_lines, continued_indent,
-                            self._get_extent(index),
-                            is_list_comp_or_if_expr=is_list_comp_or_if_expr,
-                            next_is_dot=(next_item and
-                                         unicode(next_item) == '.'))
-                if last_was_container and item.is_comma:
-                    reflowed_lines.add_line_break(continued_indent)
-                last_was_container = False
-            else:  # isinstance(item, Container)
-                reflowed_lines.add(item, len(continued_indent),
-                                   break_after_open_bracket)
-                last_was_container = not isinstance(item, (ListComprehension,
-                                                           IfExpression))
-
-            if (
-                break_after_open_bracket and index == 0 and
-                # Prefer to keep empty containers together instead of
-                # separating them.
-                unicode(item) == self.open_bracket and
-                (not next_item or unicode(next_item) != self.close_bracket) and
-                (len(self._items) != 3 or not isinstance(next_item, Atom))
-            ):
-                reflowed_lines.add_line_break(continued_indent)
-                break_after_open_bracket = False
-            else:
-                next_next_item = get_item(self._items, index + 2)
-                if (
-                    unicode(item) not in ['.', '%', 'in'] and
-                    next_item and not isinstance(next_item, Container) and
-                    unicode(next_item) != ':' and
-                    next_next_item and (not isinstance(next_next_item, Atom) or
-                                        unicode(next_item) == 'not') and
-                    not reflowed_lines.line_empty() and
-                    not reflowed_lines.fits_on_current_line(
-                        self._get_extent(index + 1) + 2)
-                ):
-                    reflowed_lines.add_line_break(continued_indent)
-
-    def _get_extent(self, index):
-        """The extent of the full element.
-
-        E.g., the length of a function call or keyword.
-
-        """
-        extent = 0
-        prev_item = get_item(self._items, index - 1)
-        seen_dot = prev_item and unicode(prev_item) == '.'
-        while index < len(self._items):
-            item = get_item(self._items, index)
-            index += 1
-
-            if isinstance(item, (ListComprehension, IfExpression)):
-                break
-
-            if isinstance(item, Container):
-                if prev_item and prev_item.is_name:
-                    if seen_dot:
-                        extent += 1
-                    else:
-                        extent += item.size
-
-                    prev_item = item
-                    continue
-            elif (unicode(item) not in ['.', '=', ':', 'not'] and
-                  not item.is_name and not item.is_string):
-                break
-
-            if unicode(item) == '.':
-                seen_dot = True
-
-            extent += item.size
-            prev_item = item
-
-        return extent
-
-    @property
-    def is_string(self):
-        return False
-
-    @property
-    def size(self):
-        return len(self.__repr__())
-
-    @property
-    def is_keyword(self):
-        return False
-
-    @property
-    def is_name(self):
-        return False
-
-    @property
-    def is_comma(self):
-        return False
-
-    @property
-    def is_colon(self):
-        return False
-
-    @property
-    def open_bracket(self):
-        return None
-
-    @property
-    def close_bracket(self):
-        return None
-
-
-class Tuple(Container):
-
-    """A high-level representation of a tuple."""
-
-    @property
-    def open_bracket(self):
-        return '('
-
-    @property
-    def close_bracket(self):
-        return ')'
-
-
-class List(Container):
-
-    """A high-level representation of a list."""
-
-    @property
-    def open_bracket(self):
-        return '['
-
-    @property
-    def close_bracket(self):
-        return ']'
-
-
-class DictOrSet(Container):
-
-    """A high-level representation of a dictionary or set."""
-
-    @property
-    def open_bracket(self):
-        return '{'
-
-    @property
-    def close_bracket(self):
-        return '}'
-
-
-class ListComprehension(Container):
-
-    """A high-level representation of a list comprehension."""
-
-    @property
-    def size(self):
-        length = 0
-        for item in self._items:
-            if isinstance(item, IfExpression):
-                break
-            length += item.size
-        return length
-
-
-class IfExpression(Container):
-
-    """A high-level representation of an if-expression."""
-
-
-def _parse_container(tokens, index, for_or_if=None):
-    """Parse a high-level container, such as a list, tuple, etc."""
-
-    # Store the opening bracket.
-    items = [Atom(Token(*tokens[index]))]
-    index += 1
-
-    num_tokens = len(tokens)
-    while index < num_tokens:
-        tok = Token(*tokens[index])
-
-        if tok.token_string in ',)]}':
-            # First check if we're at the end of a list comprehension or
-            # if-expression. Don't add the ending token as part of the list
-            # comprehension or if-expression, because they aren't part of those
-            # constructs.
-            if for_or_if == 'for':
-                return (ListComprehension(items), index - 1)
-
-            elif for_or_if == 'if':
-                return (IfExpression(items), index - 1)
-
-            # We've reached the end of a container.
-            items.append(Atom(tok))
-
-            # If not, then we are at the end of a container.
-            if tok.token_string == ')':
-                # The end of a tuple.
-                return (Tuple(items), index)
-
-            elif tok.token_string == ']':
-                # The end of a list.
-                return (List(items), index)
-
-            elif tok.token_string == '}':
-                # The end of a dictionary or set.
-                return (DictOrSet(items), index)
-
-        elif tok.token_string in '([{':
-            # A sub-container is being defined.
-            (container, index) = _parse_container(tokens, index)
-            items.append(container)
-
-        elif tok.token_string == 'for':
-            (container, index) = _parse_container(tokens, index, 'for')
-            items.append(container)
-
-        elif tok.token_string == 'if':
-            (container, index) = _parse_container(tokens, index, 'if')
-            items.append(container)
-
-        else:
-            items.append(Atom(tok))
-
-        index += 1
-
-    return (None, None)
-
-
-def _parse_tokens(tokens):
-    """Parse the tokens.
-
-    This converts the tokens into a form where we can manipulate them
-    more easily.
-
-    """
-
-    index = 0
-    parsed_tokens = []
-
-    num_tokens = len(tokens)
-    while index < num_tokens:
-        tok = Token(*tokens[index])
-
-        assert tok.token_type != token.INDENT
-        if tok.token_type == tokenize.NEWLINE:
-            # There's only one newline and it's at the end.
-            break
-
-        if tok.token_string in '([{':
-            (container, index) = _parse_container(tokens, index)
-            if not container:
-                return None
-            parsed_tokens.append(container)
-        else:
-            parsed_tokens.append(Atom(tok))
-
-        index += 1
-
-    return parsed_tokens
-
-
-def _reflow_lines(parsed_tokens, indentation, max_line_length,
-                  start_on_prefix_line):
-    """Reflow the lines so that it looks nice."""
-
-    if unicode(parsed_tokens[0]) == 'def':
-        # A function definition gets indented a bit more.
-        continued_indent = indentation + ' ' * 2 * DEFAULT_INDENT_SIZE
-    else:
-        continued_indent = indentation + ' ' * DEFAULT_INDENT_SIZE
-
-    break_after_open_bracket = not start_on_prefix_line
-
-    lines = ReformattedLines(max_line_length)
-    lines.add_indent(len(indentation.lstrip('\r\n')))
-
-    if not start_on_prefix_line:
-        # If splitting after the opening bracket will cause the first element
-        # to be aligned weirdly, don't try it.
-        first_token = get_item(parsed_tokens, 0)
-        second_token = get_item(parsed_tokens, 1)
-
-        if (
-            first_token and second_token and
-            unicode(second_token)[0] == '(' and
-            len(indentation) + len(first_token) + 1 == len(continued_indent)
-        ):
-            return None
-
-    for item in parsed_tokens:
-        lines.add_space_if_needed(unicode(item), equal=True)
-
-        save_continued_indent = continued_indent
-        if start_on_prefix_line and isinstance(item, Container):
-            start_on_prefix_line = False
-            continued_indent = ' ' * (lines.current_size() + 1)
-
-        item.reflow(lines, continued_indent, break_after_open_bracket)
-        continued_indent = save_continued_indent
-
-    return lines.emit()
-
-
-def _shorten_line_at_tokens_new(tokens, source, indentation,
-                                max_line_length):
-    """Shorten the line taking its length into account.
-
-    The input is expected to be free of newlines except for inside
-    multiline strings and at the end.
-
-    """
-    # Yield the original source so to see if it's a better choice than the
-    # shortened candidate lines we generate here.
-    yield indentation + source
-
-    parsed_tokens = _parse_tokens(tokens)
-
-    if parsed_tokens:
-        # Perform two reflows. The first one starts on the same line as the
-        # prefix. The second starts on the line after the prefix.
-        fixed = _reflow_lines(parsed_tokens, indentation, max_line_length,
-                              start_on_prefix_line=True)
-        if fixed and check_syntax(normalize_multiline(fixed.lstrip())):
-            yield fixed
-
-        fixed = _reflow_lines(parsed_tokens, indentation, max_line_length,
-                              start_on_prefix_line=False)
-        if fixed and check_syntax(normalize_multiline(fixed.lstrip())):
-            yield fixed
-
-
-def _shorten_line_at_tokens(tokens, source, indentation, indent_word,
-                            key_token_strings, aggressive):
-    """Separate line by breaking at tokens in key_token_strings.
-
-    The input is expected to be free of newlines except for inside
-    multiline strings and at the end.
-
-    """
-    offsets = []
-    for (index, _t) in enumerate(token_offsets(tokens)):
-        (token_type,
-         token_string,
-         start_offset,
-         end_offset) = _t
-
-        assert token_type != token.INDENT
-
-        if token_string in key_token_strings:
-            # Do not break in containers with zero or one items.
-            unwanted_next_token = {
-                '(': ')',
-                '[': ']',
-                '{': '}'}.get(token_string)
-            if unwanted_next_token:
-                if (
-                    get_item(tokens,
-                             index + 1,
-                             default=[None, None])[1] == unwanted_next_token or
-                    get_item(tokens,
-                             index + 2,
-                             default=[None, None])[1] == unwanted_next_token
-                ):
-                    continue
-
-            if (
-                index > 2 and token_string == '(' and
-                tokens[index - 1][1] in ',(%['
-            ):
-                # Don't split after a tuple start, or before a tuple start if
-                # the tuple is in a list.
-                continue
-
-            if end_offset < len(source) - 1:
-                # Don't split right before newline.
-                offsets.append(end_offset)
-        else:
-            # Break at adjacent strings. These were probably meant to be on
-            # separate lines in the first place.
-            previous_token = get_item(tokens, index - 1)
-            if (
-                token_type == tokenize.STRING and
-                previous_token and previous_token[0] == tokenize.STRING
-            ):
-                offsets.append(start_offset)
-
-    current_indent = None
-    fixed = None
-    for line in split_at_offsets(source, offsets):
-        if fixed:
-            fixed += '\n' + current_indent + line
-
-            for symbol in '([{':
-                if line.endswith(symbol):
-                    current_indent += indent_word
-        else:
-            # First line.
-            fixed = line
-            assert not current_indent
-            current_indent = indent_word
-
-    assert fixed is not None
-
-    if check_syntax(normalize_multiline(fixed)
-                    if aggressive > 1 else fixed):
-        return indentation + fixed
-    else:
-        return None
-
-
-def token_offsets(tokens):
-    """Yield tokens and offsets."""
-    end_offset = 0
-    previous_end_row = 0
-    previous_end_column = 0
-    for t in tokens:
-        token_type = t[0]
-        token_string = t[1]
-        (start_row, start_column) = t[2]
-        (end_row, end_column) = t[3]
-
-        # Account for the whitespace between tokens.
-        end_offset += start_column
-        if previous_end_row == start_row:
-            end_offset -= previous_end_column
-
-        # Record the start offset of the token.
-        start_offset = end_offset
-
-        # Account for the length of the token itself.
-        end_offset += len(token_string)
-
-        yield (token_type,
-               token_string,
-               start_offset,
-               end_offset)
-
-        previous_end_row = end_row
-        previous_end_column = end_column
-
-
-def normalize_multiline(line):
-    """Normalize multiline-related code that will cause syntax error.
-
-    This is for purposes of checking syntax.
-
-    """
-    if line.startswith('def ') and line.rstrip().endswith(':'):
-        return line + ' pass'
-    elif line.startswith('return '):
-        return 'def _(): ' + line
-    elif line.startswith('@'):
-        return line + 'def _(): pass'
-    elif line.startswith('class '):
-        return line + ' pass'
-    elif line.startswith(('if ', 'elif ', 'for ', 'while ')):
-        return line + ' pass'
-    else:
-        return line
-
-
-def fix_whitespace(line, offset, replacement):
-    """Replace whitespace at offset and return fixed line."""
-    # Replace escaped newlines too
-    left = line[:offset].rstrip('\n\r \t\\')
-    right = line[offset:].lstrip('\n\r \t\\')
-    if right.startswith('#'):
-        return line
-    else:
-        return left + replacement + right
-
-
-def _execute_pep8(pep8_options, source):
-    """Execute pep8 via python method calls."""
-    class QuietReport(pep8.BaseReport):
-
-        """Version of checker that does not print."""
-
-        def __init__(self, options):
-            super(QuietReport, self).__init__(options)
-            self.__full_error_results = []
-
-        def error(self, line_number, offset, text, check):
-            """Collect errors."""
-            code = super(QuietReport, self).error(line_number,
-                                                  offset,
-                                                  text,
-                                                  check)
-            if code:
-                self.__full_error_results.append(
-                    {'id': code,
-                     'line': line_number,
-                     'column': offset + 1,
-                     'info': text})
-
-        def full_error_results(self):
-            """Return error results in detail.
-
-            Results are in the form of a list of dictionaries. Each
-            dictionary contains 'id', 'line', 'column', and 'info'.
-
-            """
-            return self.__full_error_results
-
-    checker = pep8.Checker('', lines=source,
-                           reporter=QuietReport, **pep8_options)
-    checker.check_all()
-    return checker.report.full_error_results()
-
-
-def _remove_leading_and_normalize(line):
-    return line.lstrip().rstrip(CR + LF) + '\n'
-
-
-class Reindenter(object):
-
-    """Reindents badly-indented code to uniformly use four-space indentation.
-
-    Released to the public domain, by Tim Peters, 03 October 2000.
-
-    """
-
-    def __init__(self, input_text):
-        sio = io.StringIO(input_text)
-        source_lines = sio.readlines()
-
-        self.string_content_line_numbers = multiline_string_lines(input_text)
-
-        # File lines, rstripped & tab-expanded. Dummy at start is so
-        # that we can use tokenize's 1-based line numbering easily.
-        # Note that a line is all-blank iff it is a newline.
-        self.lines = []
-        for line_number, line in enumerate(source_lines, start=1):
-            # Do not modify if inside a multiline string.
-            if line_number in self.string_content_line_numbers:
-                self.lines.append(line)
-            else:
-                # Only expand leading tabs.
-                self.lines.append(_get_indentation(line).expandtabs() +
-                                  _remove_leading_and_normalize(line))
-
-        self.lines.insert(0, None)
-        self.index = 1  # index into self.lines of next line
-        self.input_text = input_text
-
-    def run(self, indent_size=DEFAULT_INDENT_SIZE):
-        """Fix indentation and return modified line numbers.
-
-        Line numbers are indexed at 1.
-
-        """
-        if indent_size < 1:
-            return self.input_text
-
-        try:
-            stats = _reindent_stats(tokenize.generate_tokens(self.getline))
-        except (SyntaxError, tokenize.TokenError):
-            return self.input_text
-        # Remove trailing empty lines.
-        lines = self.lines
-        # Sentinel.
-        stats.append((len(lines), 0))
-        # Map count of leading spaces to # we want.
-        have2want = {}
-        # Program after transformation.
-        after = []
-        # Copy over initial empty lines -- there's nothing to do until
-        # we see a line with *something* on it.
-        i = stats[0][0]
-        after.extend(lines[1:i])
-        for i in range(len(stats) - 1):
-            thisstmt, thislevel = stats[i]
-            nextstmt = stats[i + 1][0]
-            have = _leading_space_count(lines[thisstmt])
-            want = thislevel * indent_size
-            if want < 0:
-                # A comment line.
-                if have:
-                    # An indented comment line. If we saw the same
-                    # indentation before, reuse what it most recently
-                    # mapped to.
-                    want = have2want.get(have, -1)
-                    if want < 0:
-                        # Then it probably belongs to the next real stmt.
-                        for j in range(i + 1, len(stats) - 1):
-                            jline, jlevel = stats[j]
-                            if jlevel >= 0:
-                                if have == _leading_space_count(lines[jline]):
-                                    want = jlevel * indent_size
-                                break
-                    if want < 0:            # Maybe it's a hanging
-                                            # comment like this one,
-                        # in which case we should shift it like its base
-                        # line got shifted.
-                        for j in range(i - 1, -1, -1):
-                            jline, jlevel = stats[j]
-                            if jlevel >= 0:
-                                want = (have + _leading_space_count(
-                                        after[jline - 1]) -
-                                        _leading_space_count(lines[jline]))
-                                break
-                    if want < 0:
-                        # Still no luck -- leave it alone.
-                        want = have
-                else:
-                    want = 0
-            assert want >= 0
-            have2want[have] = want
-            diff = want - have
-            if diff == 0 or have == 0:
-                after.extend(lines[thisstmt:nextstmt])
-            else:
-                for line_number, line in enumerate(lines[thisstmt:nextstmt],
-                                                   start=thisstmt):
-                    if line_number in self.string_content_line_numbers:
-                        after.append(line)
-                    elif diff > 0:
-                        if line == '\n':
-                            after.append(line)
-                        else:
-                            after.append(' ' * diff + line)
-                    else:
-                        remove = min(_leading_space_count(line), -diff)
-                        after.append(line[remove:])
-
-        return ''.join(after)
-
-    def getline(self):
-        """Line-getter for tokenize."""
-        if self.index >= len(self.lines):
-            line = ''
-        else:
-            line = self.lines[self.index]
-            self.index += 1
-        return line
-
-
-def _reindent_stats(tokens):
-    """Return list of (lineno, indentlevel) pairs.
-
-    One for each stmt and comment line. indentlevel is -1 for comment lines, as
-    a signal that tokenize doesn't know what to do about them; indeed, they're
-    our headache!
-
-    """
-    find_stmt = 1  # Next token begins a fresh stmt?
-    level = 0  # Current indent level.
-    stats = []
-
-    for t in tokens:
-        token_type = t[0]
-        sline = t[2][0]
-        line = t[4]
-
-        if token_type == tokenize.NEWLINE:
-            # A program statement, or ENDMARKER, will eventually follow,
-            # after some (possibly empty) run of tokens of the form
-            #     (NL | COMMENT)* (INDENT | DEDENT+)?
-            find_stmt = 1
-
-        elif token_type == tokenize.INDENT:
-            find_stmt = 1
-            level += 1
-
-        elif token_type == tokenize.DEDENT:
-            find_stmt = 1
-            level -= 1
-
-        elif token_type == tokenize.COMMENT:
-            if find_stmt:
-                stats.append((sline, -1))
-                # But we're still looking for a new stmt, so leave
-                # find_stmt alone.
-
-        elif token_type == tokenize.NL:
-            pass
-
-        elif find_stmt:
-            # This is the first "real token" following a NEWLINE, so it
-            # must be the first token of the next program statement, or an
-            # ENDMARKER.
-            find_stmt = 0
-            if line:   # Not endmarker.
-                stats.append((sline, level))
-
-    return stats
-
-
-def _leading_space_count(line):
-    """Return number of leading spaces in line."""
-    i = 0
-    while i < len(line) and line[i] == ' ':
-        i += 1
-    return i
-
-
-def refactor_with_2to3(source_text, fixer_names, filename=''):
-    """Use lib2to3 to refactor the source.
-
-    Return the refactored source code.
-
-    """
-    from lib2to3.refactor import RefactoringTool
-    fixers = ['lib2to3.fixes.fix_' + name for name in fixer_names]
-    tool = RefactoringTool(fixer_names=fixers, explicit=fixers)
-
-    from lib2to3.pgen2 import tokenize as lib2to3_tokenize
-    try:
-        # The name parameter is necessary particularly for the "import" fixer.
-        return unicode(tool.refactor_string(source_text, name=filename))
-    except lib2to3_tokenize.TokenError:
-        return source_text
-
-
-def check_syntax(code):
-    """Return True if syntax is okay."""
-    try:
-        return compile(code, '<string>', 'exec')
-    except (SyntaxError, TypeError, UnicodeDecodeError):
-        return False
-
-
-def filter_results(source, results, aggressive):
-    """Filter out spurious reports from pep8.
-
-    If aggressive is True, we allow possibly unsafe fixes (E711, E712).
-
-    """
-    non_docstring_string_line_numbers = multiline_string_lines(
-        source, include_docstrings=False)
-    all_string_line_numbers = multiline_string_lines(
-        source, include_docstrings=True)
-
-    commented_out_code_line_numbers = commented_out_code_lines(source)
-
-    has_e901 = any(result['id'].lower() == 'e901' for result in results)
-
-    for r in results:
-        issue_id = r['id'].lower()
-
-        if r['line'] in non_docstring_string_line_numbers:
-            if issue_id.startswith(('e1', 'e501', 'w191')):
-                continue
-
-        if r['line'] in all_string_line_numbers:
-            if issue_id in ['e501']:
-                continue
-
-        # We must offset by 1 for lines that contain the trailing contents of
-        # multiline strings.
-        if not aggressive and (r['line'] + 1) in all_string_line_numbers:
-            # Do not modify multiline strings in non-aggressive mode. Remove
-            # trailing whitespace could break doctests.
-            if issue_id.startswith(('w29', 'w39')):
-                continue
-
-        if aggressive <= 0:
-            if issue_id.startswith(('e711', 'w6')):
-                continue
-
-        if aggressive <= 1:
-            if issue_id.startswith(('e712', 'e713')):
-                continue
-
-        if r['line'] in commented_out_code_line_numbers:
-            if issue_id.startswith(('e26', 'e501')):
-                continue
-
-        # Do not touch indentation if there is a token error caused by
-        # incomplete multi-line statement. Otherwise, we risk screwing up the
-        # indentation.
-        if has_e901:
-            if issue_id.startswith(('e1', 'e7')):
-                continue
-
-        yield r
-
-
-def multiline_string_lines(source, include_docstrings=False):
-    """Return line numbers that are within multiline strings.
-
-    The line numbers are indexed at 1.
-
-    Docstrings are ignored.
-
-    """
-    line_numbers = set()
-    previous_token_type = ''
-    try:
-        for t in generate_tokens(source):
-            token_type = t[0]
-            start_row = t[2][0]
-            end_row = t[3][0]
-
-            if token_type == tokenize.STRING and start_row != end_row:
-                if (
-                    include_docstrings or
-                    previous_token_type != tokenize.INDENT
-                ):
-                    # We increment by one since we want the contents of the
-                    # string.
-                    line_numbers |= set(range(1 + start_row, 1 + end_row))
-
-            previous_token_type = token_type
-    except (SyntaxError, tokenize.TokenError):
-        pass
-
-    return line_numbers
-
-
-def commented_out_code_lines(source):
-    """Return line numbers of comments that are likely code.
-
-    Commented-out code is bad practice, but modifying it just adds even more
-    clutter.
-
-    """
-    line_numbers = []
-    try:
-        for t in generate_tokens(source):
-            token_type = t[0]
-            token_string = t[1]
-            start_row = t[2][0]
-            line = t[4]
-
-            # Ignore inline comments.
-            if not line.lstrip().startswith('#'):
-                continue
-
-            if token_type == tokenize.COMMENT:
-                stripped_line = token_string.lstrip('#').strip()
-                if (
-                    ' ' in stripped_line and
-                    '#' not in stripped_line and
-                    check_syntax(stripped_line)
-                ):
-                    line_numbers.append(start_row)
-    except (SyntaxError, tokenize.TokenError):
-        pass
-
-    return line_numbers
-
-
-def shorten_comment(line, max_line_length, last_comment=False):
-    """Return trimmed or split long comment line.
-
-    If there are no comments immediately following it, do a text wrap.
-    Doing this wrapping on all comments in general would lead to jagged
-    comment text.
-
-    """
-    assert len(line) > max_line_length
-    line = line.rstrip()
-
-    # PEP 8 recommends 72 characters for comment text.
-    indentation = _get_indentation(line) + '# '
-    max_line_length = min(max_line_length,
-                          len(indentation) + 72)
-
-    MIN_CHARACTER_REPEAT = 5
-    if (
-        len(line) - len(line.rstrip(line[-1])) >= MIN_CHARACTER_REPEAT and
-        not line[-1].isalnum()
-    ):
-        # Trim comments that end with things like ---------
-        return line[:max_line_length] + '\n'
-    elif last_comment and re.match(r'\s*#+\s*\w+', line):
-        split_lines = textwrap.wrap(line.lstrip(' \t#'),
-                                    initial_indent=indentation,
-                                    subsequent_indent=indentation,
-                                    width=max_line_length,
-                                    break_long_words=False,
-                                    break_on_hyphens=False)
-        return '\n'.join(split_lines) + '\n'
-    else:
-        return line + '\n'
-
-
-def normalize_line_endings(lines, newline):
-    """Return fixed line endings.
-
-    All lines will be modified to use the most common line ending.
-
-    """
-    return [line.rstrip('\n\r') + newline for line in lines]
-
-
-def mutual_startswith(a, b):
-    return b.startswith(a) or a.startswith(b)
-
-
-def code_match(code, select, ignore):
-    if ignore:
-        assert not isinstance(ignore, unicode)
-        for ignored_code in [c.strip() for c in ignore]:
-            if mutual_startswith(code.lower(), ignored_code.lower()):
-                return False
-
-    if select:
-        assert not isinstance(select, unicode)
-        for selected_code in [c.strip() for c in select]:
-            if mutual_startswith(code.lower(), selected_code.lower()):
-                return True
-        return False
-
-    return True
-
-
-def fix_code(source, options=None, encoding=None, apply_config=False):
-    """Return fixed source code.
-
-    "encoding" will be used to decode "source" if it is a byte string.
-
-    """
-    options = _get_options(options, apply_config)
-
-    if not isinstance(source, unicode):
-        source = source.decode(encoding or get_encoding())
-
-    sio = io.StringIO(source)
-    return fix_lines(sio.readlines(), options=options)
-
-
-def _get_options(raw_options, apply_config):
-    """Return parsed options."""
-    if not raw_options:
-        return parse_args([''], apply_config=apply_config)
-
-    if isinstance(raw_options, dict):
-        options = parse_args([''], apply_config=apply_config)
-        for name, value in raw_options.items():
-            if not hasattr(options, name):
-                raise ValueError("No such option '{}'".format(name))
-
-            # Check for very basic type errors.
-            expected_type = type(getattr(options, name))
-            if not isinstance(expected_type, (str, unicode)):
-                if isinstance(value, (str, unicode)):
-                    raise ValueError(
-                        "Option '{}' should not be a string".format(name))
-            setattr(options, name, value)
-    else:
-        options = raw_options
-
-    return options
-
-
-def fix_lines(source_lines, options, filename=''):
-    """Return fixed source code."""
-    # Transform everything to line feed. Then change them back to original
-    # before returning fixed source code.
-    original_newline = find_newline(source_lines)
-    tmp_source = ''.join(normalize_line_endings(source_lines, '\n'))
-
-    # Keep a history to break out of cycles.
-    previous_hashes = set()
-
-    if options.line_range:
-        # Disable "apply_local_fixes()" for now due to issue #175.
-        fixed_source = tmp_source
-    else:
-        # Apply global fixes only once (for efficiency).
-        fixed_source = apply_global_fixes(tmp_source,
-                                          options,
-                                          filename=filename)
-
-    passes = 0
-    long_line_ignore_cache = set()
-    while hash(fixed_source) not in previous_hashes:
-        if options.pep8_passes >= 0 and passes > options.pep8_passes:
-            break
-        passes += 1
-
-        previous_hashes.add(hash(fixed_source))
-
-        tmp_source = copy.copy(fixed_source)
-
-        fix = FixPEP8(
-            filename,
-            options,
-            contents=tmp_source,
-            long_line_ignore_cache=long_line_ignore_cache)
-
-        fixed_source = fix.fix()
-
-    sio = io.StringIO(fixed_source)
-    return ''.join(normalize_line_endings(sio.readlines(), original_newline))
-
-
-def fix_file(filename, options=None, output=None, apply_config=False):
-    if not options:
-        options = parse_args([filename], apply_config=apply_config)
-
-    original_source = readlines_from_file(filename)
-
-    fixed_source = original_source
-
-    if options.in_place or output:
-        encoding = detect_encoding(filename)
-
-    if output:
-        output = LineEndingWrapper(wrap_output(output, encoding=encoding))
-
-    fixed_source = fix_lines(fixed_source, options, filename=filename)
-
-    if options.diff:
-        new = io.StringIO(fixed_source)
-        new = new.readlines()
-        diff = get_diff_text(original_source, new, filename)
-        if output:
-            output.write(diff)
-            output.flush()
-        else:
-            return diff
-    elif options.in_place:
-        fp = open_with_encoding(filename, encoding=encoding,
-                                mode='w')
-        fp.write(fixed_source)
-        fp.close()
-    else:
-        if output:
-            output.write(fixed_source)
-            output.flush()
-        else:
-            return fixed_source
-
-
-def global_fixes():
-    """Yield multiple (code, function) tuples."""
-    for function in globals().values():
-        if inspect.isfunction(function):
-            arguments = inspect.getargspec(function)[0]
-            if arguments[:1] != ['source']:
-                continue
-
-            code = extract_code_from_function(function)
-            if code:
-                yield (code, function)
-
-
-def apply_global_fixes(source, options, where='global', filename=''):
-    """Run global fixes on source code.
-
-    These are fixes that only need be done once (unlike those in
-    FixPEP8, which are dependent on pep8).
-
-    """
-    if any(code_match(code, select=options.select, ignore=options.ignore)
-           for code in ['E101', 'E111']):
-        source = reindent(source,
-                          indent_size=options.indent_size)
-
-    for (code, function) in global_fixes():
-        if code_match(code, select=options.select, ignore=options.ignore):
-            if options.verbose:
-                print('--->  Applying {0} fix for {1}'.format(where,
-                                                              code.upper()),
-                      file=sys.stderr)
-            source = function(source,
-                              aggressive=options.aggressive)
-
-    source = fix_2to3(source,
-                      aggressive=options.aggressive,
-                      select=options.select,
-                      ignore=options.ignore,
-                      filename=filename)
-
-    return source
-
-
-def extract_code_from_function(function):
-    """Return code handled by function."""
-    if not function.__name__.startswith('fix_'):
-        return None
-
-    code = re.sub('^fix_', '', function.__name__)
-    if not code:
-        return None
-
-    try:
-        int(code[1:])
-    except ValueError:
-        return None
-
-    return code
-
-
-def create_parser():
-    """Return command-line parser."""
-    # Do import locally to be friendly to those who use autopep8 as a library
-    # and are supporting Python 2.6.
-    import argparse
-
-    parser = argparse.ArgumentParser(description=docstring_summary(__doc__),
-                                     prog='autopep8')
-    parser.add_argument('--version', action='version',
-                        version='%(prog)s ' + __version__)
-    parser.add_argument('-v', '--verbose', action='count',
-                        default=0,
-                        help='print verbose messages; '
-                             'multiple -v result in more verbose messages')
-    parser.add_argument('-d', '--diff', action='store_true',
-                        help='print the diff for the fixed source')
-    parser.add_argument('-i', '--in-place', action='store_true',
-                        help='make changes to files in place')
-    parser.add_argument('--global-config', metavar='filename',
-                        default=DEFAULT_CONFIG,
-                        help='path to a global pep8 config file; if this file '
-                             'does not exist then this is ignored '
-                             '(default: {0})'.format(DEFAULT_CONFIG))
-    parser.add_argument('--ignore-local-config', action='store_true',
-                        help="don't look for and apply local config files; "
-                             'if not passed, defaults are updated with any '
-                             "config files in the project's root directory")
-    parser.add_argument('-r', '--recursive', action='store_true',
-                        help='run recursively over directories; '
-                             'must be used with --in-place or --diff')
-    parser.add_argument('-j', '--jobs', type=int, metavar='n', default=1,
-                        help='number of parallel jobs; '
-                             'match CPU count if value is less than 1')
-    parser.add_argument('-p', '--pep8-passes', metavar='n',
-                        default=-1, type=int,
-                        help='maximum number of additional pep8 passes '
-                             '(default: infinite)')
-    parser.add_argument('-a', '--aggressive', action='count', default=0,
-                        help='enable non-whitespace changes; '
-                             'multiple -a result in more aggressive changes')
-    parser.add_argument('--experimental', action='store_true',
-                        help='enable experimental fixes')
-    parser.add_argument('--exclude', metavar='globs',
-                        help='exclude file/directory names that match these '
-                             'comma-separated globs')
-    parser.add_argument('--list-fixes', action='store_true',
-                        help='list codes for fixes; '
-                        'used by --ignore and --select')
-    parser.add_argument('--ignore', metavar='errors', default='',
-                        help='do not fix these errors/warnings '
-                             '(default: {0})'.format(DEFAULT_IGNORE))
-    parser.add_argument('--select', metavar='errors', default='',
-                        help='fix only these errors/warnings (e.g. E4,W)')
-    parser.add_argument('--max-line-length', metavar='n', default=79, type=int,
-                        help='set maximum allowed line length '
-                             '(default: %(default)s)')
-    parser.add_argument('--line-range', '--range', metavar='line',
-                        default=None, type=int, nargs=2,
-                        help='only fix errors found within this inclusive '
-                             'range of line numbers (e.g. 1 99); '
-                             'line numbers are indexed at 1')
-    parser.add_argument('--indent-size', default=DEFAULT_INDENT_SIZE,
-                        type=int, metavar='n',
-                        help='number of spaces per indent level '
-                             '(default %(default)s)')
-    parser.add_argument('files', nargs='*',
-                        help="files to format or '-' for standard in")
-
-    return parser
-
-
-def parse_args(arguments, apply_config=False):
-    """Parse command-line options."""
-    parser = create_parser()
-    args = parser.parse_args(arguments)
-
-    if not args.files and not args.list_fixes:
-        parser.error('incorrect number of arguments')
-
-    args.files = [decode_filename(name) for name in args.files]
-
-    if apply_config:
-        parser = read_config(args, parser)
-        args = parser.parse_args(arguments)
-        args.files = [decode_filename(name) for name in args.files]
-
-    if '-' in args.files:
-        if len(args.files) > 1:
-            parser.error('cannot mix stdin and regular files')
-
-        if args.diff:
-            parser.error('--diff cannot be used with standard input')
-
-        if args.in_place:
-            parser.error('--in-place cannot be used with standard input')
-
-        if args.recursive:
-            parser.error('--recursive cannot be used with standard input')
-
-    if len(args.files) > 1 and not (args.in_place or args.diff):
-        parser.error('autopep8 only takes one filename as argument '
-                     'unless the "--in-place" or "--diff" args are '
-                     'used')
-
-    if args.recursive and not (args.in_place or args.diff):
-        parser.error('--recursive must be used with --in-place or --diff')
-
-    if args.in_place and args.diff:
-        parser.error('--in-place and --diff are mutually exclusive')
-
-    if args.max_line_length <= 0:
-        parser.error('--max-line-length must be greater than 0')
-
-    if args.select:
-        args.select = _split_comma_separated(args.select)
-
-    if args.ignore:
-        args.ignore = _split_comma_separated(args.ignore)
-    elif not args.select:
-        if args.aggressive:
-            # Enable everything by default if aggressive.
-            args.select = ['E', 'W']
-        else:
-            args.ignore = _split_comma_separated(DEFAULT_IGNORE)
-
-    if args.exclude:
-        args.exclude = _split_comma_separated(args.exclude)
-    else:
-        args.exclude = []
-
-    if args.jobs < 1:
-        # Do not import multiprocessing globally in case it is not supported
-        # on the platform.
-        import multiprocessing
-        args.jobs = multiprocessing.cpu_count()
-
-    if args.jobs > 1 and not args.in_place:
-        parser.error('parallel jobs requires --in-place')
-
-    if args.line_range:
-        if args.line_range[0] <= 0:
-            parser.error('--range must be positive numbers')
-        if args.line_range[0] > args.line_range[1]:
-            parser.error('First value of --range should be less than or equal '
-                         'to the second')
-
-    return args
-
-
-def read_config(args, parser):
-    """Read both user configuration and local configuration."""
-    try:
-        from configparser import ConfigParser as SafeConfigParser
-        from configparser import Error
-    except ImportError:
-        from ConfigParser import SafeConfigParser
-        from ConfigParser import Error
-
-    config = SafeConfigParser()
-
-    try:
-        config.read(args.global_config)
-
-        if not args.ignore_local_config:
-            parent = tail = args.files and os.path.abspath(
-                os.path.commonprefix(args.files))
-            while tail:
-                if config.read([os.path.join(parent, fn)
-                                for fn in PROJECT_CONFIG]):
-                    break
-                (parent, tail) = os.path.split(parent)
-
-        defaults = dict((k.lstrip('-').replace('-', '_'), v)
-                        for k, v in config.items('pep8'))
-        parser.set_defaults(**defaults)
-    except Error:
-        # Ignore for now.
-        pass
-
-    return parser
-
-
-def _split_comma_separated(string):
-    """Return a set of strings."""
-    return set(text.strip() for text in string.split(',') if text.strip())
-
-
-def decode_filename(filename):
-    """Return Unicode filename."""
-    if isinstance(filename, unicode):
-        return filename
-    else:
-        return filename.decode(sys.getfilesystemencoding())
-
-
-def supported_fixes():
-    """Yield pep8 error codes that autopep8 fixes.
-
-    Each item we yield is a tuple of the code followed by its
-    description.
-
-    """
-    yield ('E101', docstring_summary(reindent.__doc__))
-
-    instance = FixPEP8(filename=None, options=None, contents='')
-    for attribute in dir(instance):
-        code = re.match('fix_([ew][0-9][0-9][0-9])', attribute)
-        if code:
-            yield (
-                code.group(1).upper(),
-                re.sub(r'\s+', ' ',
-                       docstring_summary(getattr(instance, attribute).__doc__))
-            )
-
-    for (code, function) in sorted(global_fixes()):
-        yield (code.upper() + (4 - len(code)) * ' ',
-               re.sub(r'\s+', ' ', docstring_summary(function.__doc__)))
-
-    for code in sorted(CODE_TO_2TO3):
-        yield (code.upper() + (4 - len(code)) * ' ',
-               re.sub(r'\s+', ' ', docstring_summary(fix_2to3.__doc__)))
-
-
-def docstring_summary(docstring):
-    """Return summary of docstring."""
-    return docstring.split('\n')[0]
-
-
-def line_shortening_rank(candidate, indent_word, max_line_length,
-                         experimental=False):
-    """Return rank of candidate.
-
-    This is for sorting candidates.
-
-    """
-    if not candidate.strip():
-        return 0
-
-    rank = 0
-    lines = candidate.rstrip().split('\n')
-
-    offset = 0
-    if (
-        not lines[0].lstrip().startswith('#') and
-        lines[0].rstrip()[-1] not in '([{'
-    ):
-        for (opening, closing) in ('()', '[]', '{}'):
-            # Don't penalize empty containers that aren't split up. Things like
-            # this "foo(\n    )" aren't particularly good.
-            opening_loc = lines[0].find(opening)
-            closing_loc = lines[0].find(closing)
-            if opening_loc >= 0:
-                if closing_loc < 0 or closing_loc != opening_loc + 1:
-                    offset = max(offset, 1 + opening_loc)
-
-    current_longest = max(offset + len(x.strip()) for x in lines)
-
-    rank += 4 * max(0, current_longest - max_line_length)
-
-    rank += len(lines)
-
-    # Too much variation in line length is ugly.
-    rank += 2 * standard_deviation(len(line) for line in lines)
-
-    bad_staring_symbol = {
-        '(': ')',
-        '[': ']',
-        '{': '}'}.get(lines[0][-1])
-
-    if len(lines) > 1:
-        if (
-            bad_staring_symbol and
-            lines[1].lstrip().startswith(bad_staring_symbol)
-        ):
-            rank += 20
-
-    for lineno, current_line in enumerate(lines):
-        current_line = current_line.strip()
-
-        if current_line.startswith('#'):
-            continue
-
-        for bad_start in ['.', '%', '+', '-', '/']:
-            if current_line.startswith(bad_start):
-                rank += 100
-
-            # Do not tolerate operators on their own line.
-            if current_line == bad_start:
-                rank += 1000
-
-        if (
-            current_line.endswith(('.', '%', '+', '-', '/')) and
-            "': " in current_line
-        ):
-            rank += 1000
-
-        if current_line.endswith(('(', '[', '{', '.')):
-            # Avoid lonely opening. They result in longer lines.
-            if len(current_line) <= len(indent_word):
-                rank += 100
-
-            # Avoid the ugliness of ", (\n".
-            if (
-                current_line.endswith('(') and
-                current_line[:-1].rstrip().endswith(',')
-            ):
-                rank += 100
-
-            # Also avoid the ugliness of "foo.\nbar"
-            if current_line.endswith('.'):
-                rank += 100
-
-            if has_arithmetic_operator(current_line):
-                rank += 100
-
-        # Avoid breaking at unary operators.
-        if re.match(r'.*[(\[{]\s*[\-\+~]$', current_line.rstrip('\\ ')):
-            rank += 1000
-
-        if re.match(r'.*lambda\s*\*$', current_line.rstrip('\\ ')):
-            rank += 1000
-
-        if current_line.endswith(('%', '(', '[', '{')):
-            rank -= 20
-
-        # Try to break list comprehensions at the "for".
-        if current_line.startswith('for '):
-            rank -= 50
-
-        if current_line.endswith('\\'):
-            # If a line ends in \-newline, it may be part of a
-            # multiline string. In that case, we would like to know
-            # how long that line is without the \-newline. If it's
-            # longer than the maximum, or has comments, then we assume
-            # that the \-newline is an okay candidate and only
-            # penalize it a bit.
-            total_len = len(current_line)
-            lineno += 1
-            while lineno < len(lines):
-                total_len += len(lines[lineno])
-
-                if lines[lineno].lstrip().startswith('#'):
-                    total_len = max_line_length
-                    break
-
-                if not lines[lineno].endswith('\\'):
-                    break
-
-                lineno += 1
-
-            if total_len < max_line_length:
-                rank += 10
-            else:
-                rank += 100 if experimental else 1
-
-        # Prefer breaking at commas rather than colon.
-        if ',' in current_line and current_line.endswith(':'):
-            rank += 10
-
-        # Avoid splitting dictionaries between key and value.
-        if current_line.endswith(':'):
-            rank += 100
-
-        rank += 10 * count_unbalanced_brackets(current_line)
-
-    return max(0, rank)
-
-
-def standard_deviation(numbers):
-    """Return standard devation."""
-    numbers = list(numbers)
-    if not numbers:
-        return 0
-    mean = sum(numbers) / len(numbers)
-    return (sum((n - mean) ** 2 for n in numbers) /
-            len(numbers)) ** .5
-
-
-def has_arithmetic_operator(line):
-    """Return True if line contains any arithmetic operators."""
-    for operator in pep8.ARITHMETIC_OP:
-        if operator in line:
-            return True
-
-    return False
-
-
-def count_unbalanced_brackets(line):
-    """Return number of unmatched open/close brackets."""
-    count = 0
-    for opening, closing in ['()', '[]', '{}']:
-        count += abs(line.count(opening) - line.count(closing))
-
-    return count
-
-
-def split_at_offsets(line, offsets):
-    """Split line at offsets.
-
-    Return list of strings.
-
-    """
-    result = []
-
-    previous_offset = 0
-    current_offset = 0
-    for current_offset in sorted(offsets):
-        if current_offset < len(line) and previous_offset != current_offset:
-            result.append(line[previous_offset:current_offset].strip())
-        previous_offset = current_offset
-
-    result.append(line[current_offset:])
-
-    return result
-
-
-class LineEndingWrapper(object):
-
-    r"""Replace line endings to work with sys.stdout.
-
-    It seems that sys.stdout expects only '\n' as the line ending, no matter
-    the platform. Otherwise, we get repeated line endings.
-
-    """
-
-    def __init__(self, output):
-        self.__output = output
-
-    def write(self, s):
-        self.__output.write(s.replace('\r\n', '\n').replace('\r', '\n'))
-
-    def flush(self):
-        self.__output.flush()
-
-
-def match_file(filename, exclude):
-    """Return True if file is okay for modifying/recursing."""
-    base_name = os.path.basename(filename)
-
-    if base_name.startswith('.'):
-        return False
-
-    for pattern in exclude:
-        if fnmatch.fnmatch(base_name, pattern):
-            return False
-        if fnmatch.fnmatch(filename, pattern):
-            return False
-
-    if not os.path.isdir(filename) and not is_python_file(filename):
-        return False
-
-    return True
-
-
-def find_files(filenames, recursive, exclude):
-    """Yield filenames."""
-    while filenames:
-        name = filenames.pop(0)
-        if recursive and os.path.isdir(name):
-            for root, directories, children in os.walk(name):
-                filenames += [os.path.join(root, f) for f in children
-                              if match_file(os.path.join(root, f),
-                                            exclude)]
-                directories[:] = [d for d in directories
-                                  if match_file(os.path.join(root, d),
-                                                exclude)]
-        else:
-            yield name
-
-
-def _fix_file(parameters):
-    """Helper function for optionally running fix_file() in parallel."""
-    if parameters[1].verbose:
-        print('[file:{0}]'.format(parameters[0]), file=sys.stderr)
-    try:
-        fix_file(*parameters)
-    except IOError as error:
-        print(unicode(error), file=sys.stderr)
-
-
-def fix_multiple_files(filenames, options, output=None):
-    """Fix list of files.
-
-    Optionally fix files recursively.
-
-    """
-    filenames = find_files(filenames, options.recursive, options.exclude)
-    if options.jobs > 1:
-        import multiprocessing
-        pool = multiprocessing.Pool(options.jobs)
-        pool.map(_fix_file,
-                 [(name, options) for name in filenames])
-    else:
-        for name in filenames:
-            _fix_file((name, options, output))
-
-
-def is_python_file(filename):
-    """Return True if filename is Python file."""
-    if filename.endswith('.py'):
-        return True
-
-    try:
-        with open_with_encoding(filename) as f:
-            first_line = f.readlines(1)[0]
-    except (IOError, IndexError):
-        return False
-
-    if not PYTHON_SHEBANG_REGEX.match(first_line):
-        return False
-
-    return True
-
-
-def is_probably_part_of_multiline(line):
-    """Return True if line is likely part of a multiline string.
-
-    When multiline strings are involved, pep8 reports the error as being
-    at the start of the multiline string, which doesn't work for us.
-
-    """
-    return (
-        '"""' in line or
-        "'''" in line or
-        line.rstrip().endswith('\\')
-    )
-
-
-def wrap_output(output, encoding):
-    """Return output with specified encoding."""
-    return codecs.getwriter(encoding)(output.buffer
-                                      if hasattr(output, 'buffer')
-                                      else output)
-
-
-def get_encoding():
-    """Return preferred encoding."""
-    return locale.getpreferredencoding() or sys.getdefaultencoding()
-
-
-def main(argv=None, apply_config=True):
-    """Command-line entry."""
-    if argv is None:
-        argv = sys.argv
-
-    try:
-        # Exit on broken pipe.
-        signal.signal(signal.SIGPIPE, signal.SIG_DFL)
-    except AttributeError:  # pragma: no cover
-        # SIGPIPE is not available on Windows.
-        pass
-
-    try:
-        args = parse_args(argv[1:], apply_config=apply_config)
-
-        if args.list_fixes:
-            for code, description in sorted(supported_fixes()):
-                print('{code} - {description}'.format(
-                    code=code, description=description))
-            return 0
-
-        if args.files == ['-']:
-            assert not args.in_place
-
-            encoding = sys.stdin.encoding or get_encoding()
-
-            # LineEndingWrapper is unnecessary here due to the symmetry between
-            # standard in and standard out.
-            wrap_output(sys.stdout, encoding=encoding).write(
-                fix_code(sys.stdin.read(), args, encoding=encoding))
-        else:
-            if args.in_place or args.diff:
-                args.files = list(set(args.files))
-            else:
-                assert len(args.files) == 1
-                assert not args.recursive
-
-            fix_multiple_files(args.files, args, sys.stdout)
-    except KeyboardInterrupt:
-        return 1  # pragma: no cover
-
-
-class CachedTokenizer(object):
-
-    """A one-element cache around tokenize.generate_tokens().
-
-    Original code written by Ned Batchelder, in coverage.py.
-
-    """
-
-    def __init__(self):
-        self.last_text = None
-        self.last_tokens = None
-
-    def generate_tokens(self, text):
-        """A stand-in for tokenize.generate_tokens()."""
-        if text != self.last_text:
-            string_io = io.StringIO(text)
-            self.last_tokens = list(
-                tokenize.generate_tokens(string_io.readline)
-            )
-            self.last_text = text
-        return self.last_tokens
-
-_cached_tokenizer = CachedTokenizer()
-generate_tokens = _cached_tokenizer.generate_tokens

From f421a227d0af3f08e34b2e57c1788e9067e9117f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Aug 2015 22:42:14 +0200
Subject: [PATCH 1211/1356] enhance test for --package, to trigger bug with
 path of module file being passed

---
 test/framework/package.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/test/framework/package.py b/test/framework/package.py
index 53feaf504f..2ce61a5ce2 100644
--- a/test/framework/package.py
+++ b/test/framework/package.py
@@ -28,6 +28,7 @@
 @author: Kenneth Hoste (Ghent University)
 """
 import os
+import re
 import stat
 
 from test.framework.utilities import EnhancedTestCase, init_config
@@ -37,7 +38,7 @@
 import easybuild.tools.build_log
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import adjust_permissions, write_file
+from easybuild.tools.filetools import adjust_permissions, read_file, write_file
 from easybuild.tools.package.utilities import ActivePNS, avail_package_naming_schemes, check_pkg_support, package
 from easybuild.tools.version import VERSION as EASYBUILD_VERSION
 
@@ -50,7 +51,17 @@
 iteration=`echo $@ | sed 's/.*--iteration \([^ ]*\).*/\\1/g'`
 target=`echo $@ | sed 's/.*-t \([^ ]*\).*/\\1/g'`
 
-echo "thisisan$target" > ${workdir}/${name}-${version}.${iteration}.${target}
+args=`echo $@ | sed 's/-[^ ]* [^ ]* //g'`
+installdir=`echo $args | cut -d' ' -f1`
+modulefile=`echo $args | cut -d' ' -f2`
+
+pkgfile=${workdir}/${name}-${version}.${iteration}.${target}
+echo "thisisan$target" > $pkgfile
+echo $@ >> $pkgfile
+echo "Contents of installdir $installdir:" >> $pkgfile
+ls $installdir >> $pkgfile
+echo "Contents of module file $modulefile:" >> $pkgfile
+cat $modulefile >> $pkgfile
 """
 
 
@@ -133,6 +144,9 @@ def test_package(self):
         pkgfile = os.path.join(pkgdir, 'toy-0.0-gompi-1.3.12-test-eb-%s.1.rpm' % EASYBUILD_VERSION)
         self.assertTrue(os.path.isfile(pkgfile), "Found %s" % pkgfile)
 
+        pkgtxt = read_file(pkgfile)
+        pkgtxt_regex = re.compile("Contents of installdir %s" % easyblock.installdir)
+        self.assertTrue(pkgtxt_regex.search(pkgtxt), "Pattern '%s' found in: %s" % (pkgtxt_regex.pattern, pkgtxt))
 
 def suite():
     """ returns all the testcases in this module """

From af0ecc7296ddfefe141c69bae6ffed4ecf51099e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Aug 2015 22:46:50 +0200
Subject: [PATCH 1212/1356] rework module_generator to avoid keeping state
 w.r.t. fake modules that bites us in the ass later

---
 easybuild/framework/easyblock.py     | 15 +++--
 easybuild/tools/module_generator.py  | 83 ++++++++++++++--------------
 easybuild/tools/package/utilities.py |  2 +-
 3 files changed, 49 insertions(+), 51 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index a9a338794e..76ca7992d6 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1028,7 +1028,7 @@ def load_fake_module(self, purge=False):
         env = copy.deepcopy(os.environ)
 
         # create fake module
-        fake_mod_path = self.make_module_step(True)
+        fake_mod_path = self.make_module_step(fake=True)
 
         # load fake module
         self.modules_tool.prepend_module_path(fake_mod_path)
@@ -1688,10 +1688,7 @@ def make_module_step(self, fake=False):
         """
         Generate a module file.
         """
-        self.module_generator.set_fake(fake)
-
-        mod_symlink_paths = ActiveMNS().det_module_symlink_paths(self.cfg)
-        modpath = self.module_generator.prepare(mod_symlink_paths)
+        modpath = self.module_generator.prepare(fake=fake)
 
         txt = self.make_module_description()
         txt += self.make_module_dep()
@@ -1700,15 +1697,17 @@ def make_module_step(self, fake=False):
         txt += self.make_module_extra()
         txt += self.make_module_footer()
 
-        write_file(self.module_generator.filename, txt)
+        mod_filepath = self.module_generator.get_module_filepath(fake=fake)
+        write_file(mod_filepath, txt)
 
-        self.log.info("Module file %s written: %s", self.module_generator.filename, txt)
+        self.log.info("Module file %s written: %s", mod_filepath, txt)
 
          # only update after generating final module file
         if not fake:
             self.modules_tool.update()
 
-        self.module_generator.create_symlinks()
+        mod_symlink_paths = ActiveMNS().det_module_symlink_paths(self.cfg)
+        self.module_generator.create_symlinks(mod_symlink_paths, fake=fake)
 
         if not fake:
             self.make_devel_module()
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index a63dfada92..be31a6b044 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -64,64 +64,63 @@ class ModuleGenerator(object):
     def __init__(self, application, fake=False):
         """ModuleGenerator constructor."""
         self.app = application
-        self.fake = fake
-        self.tmpdir = None
-        self.filename = None
-        self.class_mod_file = None
-        self.module_path = None
-        self.class_mod_files = None
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
+        self.fake_mod_path = tempfile.mkdtemp()
 
-    def prepare(self, mod_symlink_paths):
+    def get_modules_path(self, fake=False, mod_path_suffix=None):
+        """Return path to directory where module files should be generated in."""
+        mod_path = install_path('mod')
+        if fake:
+            self.log.debug("Fake mode: using %s (instead of %s)" % (self.fake_mod_path, mod_path))
+            mod_path = self.fake_mod_path
+
+        if mod_path_suffix is None:
+            mod_path_suffix = build_option('suffix_modules_path')
+
+        return os.path.join(mod_path, mod_path_suffix)
+
+    def get_module_filepath(self, fake=False, mod_path_suffix=None):
+        """Return path to module file."""
+        mod_path = self.get_modules_path(fake=fake, mod_path_suffix=mod_path_suffix)
+        full_mod_name = self.app.full_mod_name + self.MODULE_FILE_EXTENSION
+        return os.path.join(mod_path, full_mod_name)
+
+    def prepare(self, fake=False):
         """
-        Creates the absolute filename for the module.
+        Prepare for generating module file: Creates the absolute filename for the module.
         """
-        mod_path_suffix = build_option('suffix_modules_path')
-        full_mod_name = self.app.full_mod_name + self.MODULE_FILE_EXTENSION
+        mod_path = self.get_modules_path(fake=fake)
         # module file goes in general moduleclass category
-        self.filename = os.path.join(self.module_path, mod_path_suffix, full_mod_name)
         # make symlink in moduleclass category
-        self.class_mod_files = [os.path.join(self.module_path, p, full_mod_name) for p in mod_symlink_paths]
 
-        # create directories and links
-        for path in [os.path.dirname(x) for x in [self.filename] + self.class_mod_files]:
-            mkdir(path, parents=True)
+        mod_filepath = self.get_module_filepath(fake=fake)
+        mkdir(os.path.dirname(mod_filepath), parents=True)
 
-        # remove module file if it's there (it'll be recreated), see Application.make_module
-        if os.path.exists(self.filename):
-            os.remove(self.filename)
+        # remove module file if it's there (it'll be recreated), see EasyBlock.make_module
+        if os.path.exists(mod_filepath):
+            self.log.debug("Removing existing module file %s", mod_filepath)
+            os.remove(mod_filepath)
 
-        return os.path.join(self.module_path, mod_path_suffix)
+        return mod_path
 
-    def create_symlinks(self):
+    def create_symlinks(self, mod_symlink_paths, fake=False):
         """Create moduleclass symlink(s) to actual module file."""
+        mod_filepath = self.get_module_filepath(fake=fake)
+        class_mod_files = [self.get_module_filepath(fake=fake, mod_path_suffix=p) for p in mod_symlink_paths]
         try:
-            # remove symlink if its there (even if it's broken)
-            for class_mod_file in self.class_mod_files:
+            for class_mod_file in class_mod_files:
+                # remove symlink if its there (even if it's broken)
                 if os.path.lexists(class_mod_file):
+                    self.log.debug("Removing existing symlink %s", class_mod_file)
                     os.remove(class_mod_file)
-                os.symlink(self.filename, class_mod_file)
+
+                mkdir(os.path.dirname(class_mod_file), parents=True)
+                os.symlink(mod_filepath, class_mod_file)
+
         except OSError, err:
-            raise EasyBuildError("Failed to create symlinks from %s to %s: %s",
-                                 self.class_mod_files, self.filename, err)
-
-    def is_fake(self):
-        """Return whether this ModuleGenerator instance generates fake modules or not."""
-        return self.fake
-
-    def set_fake(self, fake):
-        """Determine whether this ModuleGenerator instance should generate fake modules."""
-        self.log.debug("Updating fake for this ModuleGenerator instance to %s (was %s)" % (fake, self.fake))
-        self.fake = fake
-        # fake mode: set installpath to temporary dir
-        if self.fake:
-            self.tmpdir = tempfile.mkdtemp()
-            self.log.debug("Fake mode: using %s (instead of %s)" % (self.tmpdir, self.module_path))
-            self.module_path = self.tmpdir
-        else:
-            self.module_path = install_path('mod')
+            raise EasyBuildError("Failed to create symlinks from %s to %s: %s", class_mod_files, mod_filepath, err)
 
-    def comment(self, str):
+    def comment(self, msg):
         """Return given string formatted as a comment."""
         raise NotImplementedError
 
diff --git a/easybuild/tools/package/utilities.py b/easybuild/tools/package/utilities.py
index a3d559bcc8..2e6977b160 100644
--- a/easybuild/tools/package/utilities.py
+++ b/easybuild/tools/package/utilities.py
@@ -121,7 +121,7 @@ def package_with_fpm(easyblock):
         '--iteration', pkgrel,
         depstring,
         easyblock.installdir,
-        easyblock.module_generator.filename,
+        easyblock.module_generator.get_module_filepath(),
     ]
     cmd = ' '.join(cmdlist)
     _log.debug("The flattened cmdlist looks like: %s", cmd)

From 3a52f0bfd1c24a6ea5d806e7ffeed0c98baa7c6c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 13 Aug 2015 20:18:02 +0200
Subject: [PATCH 1213/1356] fix dumping of hidden deps

---
 easybuild/framework/easyconfig/easyconfig.py |  5 +++++
 easybuild/framework/easyconfig/format/one.py | 15 ++++++++++-----
 test/framework/easyconfig.py                 | 20 +++++++++++++++++---
 3 files changed, 32 insertions(+), 8 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 12b41dcb8c..11ca071273 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -196,6 +196,7 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
             self.validate(check_osdeps=build_option('check_osdeps'))
 
         # filter hidden dependencies from list of dependencies
+        self.orig_dependencies = None
         self.filter_hidden_deps()
 
         # keep track of whether the generated module file should be hidden
@@ -209,6 +210,7 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         self.short_mod_name = mns.det_short_module_name(self)
         self.mod_subdir = mns.det_module_subdir(self)
 
+
     def copy(self):
         """
         Return a copy of this EasyConfig instance.
@@ -399,6 +401,9 @@ def filter_hidden_deps(self):
         """
         Filter hidden dependencies from list of dependencies.
         """
+        # keep a copy of the original list of dependencies, since it may be modified below
+        self.orig_dependencies = self['dependencies'][:]
+
         dep_mod_names = [dep['full_mod_name'] for dep in self['dependencies']]
 
         faulty_deps = []
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 7028013c2e..22bb440536 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -223,15 +223,20 @@ def _find_defined_params(self, ecfg, keyset, default_values, templ_const, templ_
         for group in keyset:
             printed = False
             for key in group:
-                if ecfg[key] != default_values[key]:
+                # the value for 'dependencies' may have been modified after parsing via filter_hidden_deps
+                if key == 'dependencies':
+                    val = ecfg.orig_dependencies
+                else:
+                    val = ecfg[key]
+
+                if val != default_values[key]:
                     # dependency easyconfig parameters were parsed, so these need special care to 'unparse' them
                     if key in DEPENDENCY_PARAMETERS:
-                        dumped_deps = [dump_dependency(d, ecfg['toolchain']) for d in ecfg[key]]
-                        val = dumped_deps
+                        valstr = [dump_dependency(d, ecfg['toolchain']) for d in val]
                     else:
-                        val = quote_py_str(ecfg[key])
+                        valstr = quote_py_str(ecfg[key])
 
-                    eclines.extend(self._find_param_with_comments(key, val, templ_const, templ_val))
+                    eclines.extend(self._find_param_with_comments(key, valstr, templ_const, templ_val))
 
                     printed_keys.append(key)
                     printed = True
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 6b994d5326..3356d67780 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1166,11 +1166,16 @@ def test_quote_str(self):
     def test_dump(self):
         """Test EasyConfig's dump() method."""
         test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
-
-        for f in ['toy-0.0.eb', 'goolf-1.4.10.eb', 'ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb']:
+        ecfiles = [
+            #'toy-0.0.eb',
+            #'goolf-1.4.10.eb',
+            #'ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb',
+            'gzip-1.4-GCC-4.6.3.eb',
+        ]
+        for ecfile in ecfiles:
             test_ec = os.path.join(self.test_prefix, 'test.eb')
 
-            ec = EasyConfig(os.path.join(test_ecs_dir, f))
+            ec = EasyConfig(os.path.join(test_ecs_dir, ecfile))
             ec.dump(test_ec)
             ectxt = read_file(test_ec)
 
@@ -1182,6 +1187,15 @@ def test_dump(self):
             # parse result again
             dumped_ec = EasyConfig(test_ec)
 
+            # check that selected parameters still have the same value
+            params = [
+                'name',
+                'toolchain',
+                'dependencies',  # checking this is important w.r.t. filtered hidden dependencies being restored in dump
+            ]
+            for param in params:
+                self.assertEqual(ec[param], dumped_ec[param])
+
     def test_dump_autopep8(self):
         """Test dump() with autopep8 usage enabled (only if autopep8 is available)."""
         try:

From d5de8fdcf2fd17063bbef7d6edccd58cbf20e7ed Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 13 Aug 2015 20:51:14 +0200
Subject: [PATCH 1214/1356] undo commenting out of easyconfig files in test

---
 test/framework/easyconfig.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 3356d67780..7811e9e9e7 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1167,9 +1167,9 @@ def test_dump(self):
         """Test EasyConfig's dump() method."""
         test_ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
         ecfiles = [
-            #'toy-0.0.eb',
-            #'goolf-1.4.10.eb',
-            #'ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb',
+            'toy-0.0.eb',
+            'goolf-1.4.10.eb',
+            'ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb',
             'gzip-1.4-GCC-4.6.3.eb',
         ]
         for ecfile in ecfiles:

From 151c0cbfde171c2f87f71f811fae40043a7065de Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Aug 2015 08:22:11 +0200
Subject: [PATCH 1215/1356] rename orig_dependencies to all_dependencies

---
 easybuild/framework/easyconfig/easyconfig.py | 4 ++--
 easybuild/framework/easyconfig/format/one.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 11ca071273..53cebe0544 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -196,7 +196,7 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
             self.validate(check_osdeps=build_option('check_osdeps'))
 
         # filter hidden dependencies from list of dependencies
-        self.orig_dependencies = None
+        self.all_dependencies = None
         self.filter_hidden_deps()
 
         # keep track of whether the generated module file should be hidden
@@ -402,7 +402,7 @@ def filter_hidden_deps(self):
         Filter hidden dependencies from list of dependencies.
         """
         # keep a copy of the original list of dependencies, since it may be modified below
-        self.orig_dependencies = self['dependencies'][:]
+        self.all_dependencies = self['dependencies'][:]
 
         dep_mod_names = [dep['full_mod_name'] for dep in self['dependencies']]
 
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 22bb440536..a44595b2dd 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -225,7 +225,7 @@ def _find_defined_params(self, ecfg, keyset, default_values, templ_const, templ_
             for key in group:
                 # the value for 'dependencies' may have been modified after parsing via filter_hidden_deps
                 if key == 'dependencies':
-                    val = ecfg.orig_dependencies
+                    val = ecfg.all_dependencies
                 else:
                     val = ecfg[key]
 

From e0f074011551a01e13b8a8a73e892e76f60fba5d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Aug 2015 08:38:36 +0200
Subject: [PATCH 1216/1356] enhance test for --job to check whether --hidden is
 used for hidden dependencies

---
 test/framework/parallelbuild.py | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 22f29bcb92..03d50a704d 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -28,6 +28,7 @@
 @author: Kenneth Hoste (Ghent University)
 """
 import os
+import re
 import stat
 from test.framework.utilities import EnhancedTestCase, init_config
 from unittest import TestLoader, main
@@ -38,7 +39,7 @@
 from easybuild.tools.filetools import adjust_permissions, mkdir, which, write_file
 from easybuild.tools.job import pbs_python
 from easybuild.tools.job.pbs_python import PbsPython
-from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel
+from easybuild.tools.parallelbuild import build_easyconfigs_in_parallel, submit_jobs
 from easybuild.tools.robot import resolve_dependencies
 
 
@@ -71,6 +72,7 @@ def __init__(self, *args, **kwargs):
         self.deps = []
         self.jobid = None
         self.clean_conn = None
+        self.script = args[1]
 
     def add_dependencies(self, *args, **kwargs):
         pass
@@ -106,6 +108,7 @@ def test_build_easyconfigs_in_parallel_pbs_python(self):
         pbs_python.PbsJob = MockPbsJob
 
         build_options = {
+            'external_modules_metadata': {},
             'robot_path': os.path.join(os.path.dirname(__file__), 'easyconfigs'),
             'valid_module_classes': config.module_classes(),
             'validate': False,
@@ -115,8 +118,22 @@ def test_build_easyconfigs_in_parallel_pbs_python(self):
         ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'gzip-1.5-goolf-1.4.10.eb')
         easyconfigs = process_easyconfig(ec_file)
         ordered_ecs = resolve_dependencies(easyconfigs)
-        jobs = build_easyconfigs_in_parallel("echo %(spec)s", ordered_ecs, prepare_first=False)
+        jobs = build_easyconfigs_in_parallel("echo '%(spec)s'", ordered_ecs, prepare_first=False)
         self.assertEqual(len(jobs), 8)
+        regex = re.compile("echo '.*/gzip-1.5-goolf-1.4.10.eb'")
+        self.assertTrue(regex.search(jobs[-1].script), "Pattern '%s' found in: %s" % (regex.pattern, jobs[-1].script))
+
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'gzip-1.4-GCC-4.6.3.eb')
+        ordered_ecs = resolve_dependencies(process_easyconfig(ec_file), retain_all_deps=True)
+        jobs = submit_jobs(ordered_ecs, '', testing=False, prepare_first=False)
+
+        # make sure command is correct, and that --hidden is there when it needs to be
+        for i, ec in enumerate(ordered_ecs):
+            if ec['hidden']:
+                regex = re.compile("eb %s.* --hidden" % ec['spec'])
+            else:
+                regex = re.compile("eb %s" % ec['spec'])
+            self.assertTrue(regex.search(jobs[i].script), "Pattern '%s' found in: %s" % (regex.pattern, jobs[i].script))
 
         # restore mocked stuff
         PbsPython.__init__ = PbsPython__init__

From b05c14bcf0470d4925eecc19f4239153675b4e07 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Aug 2015 08:38:46 +0200
Subject: [PATCH 1217/1356] include --hidden in job script when needed, filter
 external modules when determining job deps

---
 easybuild/tools/parallelbuild.py | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index a34968772d..29fde76041 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -96,8 +96,10 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybu
         _log.info("creating job for ec: %s" % str(ec))
         new_job = create_job(active_job_backend, build_command, ec, output_dir=output_dir)
 
-        # sometimes unresolved_deps will contain things, not needed to be build
-        dep_mod_names = map(ActiveMNS().det_full_module_name, ec['unresolved_deps'])
+        # filter out dependencies marked as external modules
+        deps = [d for d in ec['dependencies'] if not d['external_module']]
+
+        dep_mod_names = map(ActiveMNS().det_full_module_name, deps)
         job_deps = [module_to_job[dep] for dep in dep_mod_names if dep in module_to_job]
 
         # actually (try to) submit job
@@ -113,7 +115,7 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybu
     return jobs
 
 
-def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
+def submit_jobs(ordered_ecs, cmd_line_opts, testing=False, prepare_first=True):
     """
     Submit jobs.
     @param ordered_ecs: list of easyconfigs, in the order they should be processed
@@ -131,13 +133,13 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False):
     # compose string with command line options, properly quoted and with '%' characters escaped
     opts_str = subprocess.list2cmdline(opts).replace('%', '%%')
 
-    command = "unset TMPDIR && cd %s && eb %%(spec)s %s --testoutput=%%(output_dir)s" % (curdir, opts_str)
+    command = "unset TMPDIR && cd %s && eb %%(spec)s %s %%(add_opts)s--testoutput=%%(output_dir)s" % (curdir, opts_str)
     _log.info("Command template for jobs: %s" % command)
     job_info_lines = []
     if testing:
         _log.debug("Skipping actual submission of jobs since testing mode is enabled")
     else:
-        build_easyconfigs_in_parallel(command, ordered_ecs)
+        return build_easyconfigs_in_parallel(command, ordered_ecs, prepare_first=prepare_first)
 
 
 def create_job(job_backend, build_command, easyconfig, output_dir='easybuild-build'):
@@ -167,10 +169,16 @@ def create_job(job_backend, build_command, easyconfig, output_dir='easybuild-bui
     ec_tuple = (easyconfig['ec']['name'], det_full_ec_version(easyconfig['ec']))
     name = '-'.join(ec_tuple)
 
+    # determine whether additional options need to be passed to the 'eb' command
+    add_opts = ''
+    if easyconfig['hidden']:
+        add_opts += ' --hidden'
+
     # create command based on build_command template
     command = build_command % {
-        'spec': easyconfig['spec'],
+        'add_opts': add_opts,
         'output_dir': os.path.join(os.path.abspath(output_dir), name),
+        'spec': easyconfig['spec'],
     }
 
     # just use latest build stats

From 1aa881f934f8fef70e178c9b67e8a4910fa2d5fc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Aug 2015 08:46:23 +0200
Subject: [PATCH 1218/1356] remove 'unresolved_deps' key in processed
 easyconfigs, since it's identical to 'dependencies'

---
 easybuild/framework/easyconfig/easyconfig.py | 3 ---
 easybuild/framework/easyconfig/tools.py      | 6 +++---
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 12b41dcb8c..b34db8ff09 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -978,9 +978,6 @@ def process_easyconfig(path, build_specs=None, validate=True, parse_only=False,
                 _log.debug("Adding toolchain %s as dependency for app %s." % (dep, name))
                 easyconfig['dependencies'].append(dep)
 
-            # this is used by the parallel builder
-            easyconfig['unresolved_deps'] = copy.deepcopy(easyconfig['dependencies'])
-
     if cache_key is not None:
         _easyconfigs_cache[cache_key] = [e.copy() for e in easyconfigs]
 
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index ed7b118571..d8a57bdba1 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -169,14 +169,14 @@ def mk_node_name(spec):
     for spec in specs:
         spec['module'] = mk_node_name(spec['ec'])
         all_nodes.add(spec['module'])
-        spec['unresolved_deps'] = [mk_node_name(s) for s in spec['unresolved_deps']]
-        all_nodes.update(spec['unresolved_deps'])
+        spec['dependencies'] = [mk_node_name(s) for s in spec['dependencies']]
+        all_nodes.update(spec['dependencies'])
 
     # build directed graph
     dgr = digraph()
     dgr.add_nodes(all_nodes)
     for spec in specs:
-        for dep in spec['unresolved_deps']:
+        for dep in spec['dependencies']:
             dgr.add_edge((spec['module'], dep))
 
     # write to file

From f5b252168d89ab910c889349e69394022c9812e6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Aug 2015 23:10:11 +0200
Subject: [PATCH 1219/1356] fix remarks

---
 easybuild/tools/parallelbuild.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index 29fde76041..b7451f2da4 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -121,6 +121,7 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False, prepare_first=True):
     @param ordered_ecs: list of easyconfigs, in the order they should be processed
     @param cmd_line_opts: list of command line options (in 'longopt=value' form)
     @param testing: If `True`, skip actual job submission
+    @param prepare_first: prepare by runnning fetch step first for each easyconfig
     """
     curdir = os.getcwd()
 
@@ -133,7 +134,7 @@ def submit_jobs(ordered_ecs, cmd_line_opts, testing=False, prepare_first=True):
     # compose string with command line options, properly quoted and with '%' characters escaped
     opts_str = subprocess.list2cmdline(opts).replace('%', '%%')
 
-    command = "unset TMPDIR && cd %s && eb %%(spec)s %s %%(add_opts)s--testoutput=%%(output_dir)s" % (curdir, opts_str)
+    command = "unset TMPDIR && cd %s && eb %%(spec)s %s %%(add_opts)s --testoutput=%%(output_dir)s" % (curdir, opts_str)
     _log.info("Command template for jobs: %s" % command)
     job_info_lines = []
     if testing:

From d2a86ff1caddaf6add69cd7fff36944934682225 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 15 Aug 2015 11:03:47 +0200
Subject: [PATCH 1220/1356] fix dep graph, use all_dependencies EasyConfig
 class variable rather than the 'dependencies' parameter

---
 easybuild/framework/easyconfig/easyconfig.py | 2 +-
 easybuild/framework/easyconfig/tools.py      | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 79e68d26b8..a1f58fb0f1 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -402,7 +402,7 @@ def filter_hidden_deps(self):
         Filter hidden dependencies from list of dependencies.
         """
         # keep a copy of the original list of dependencies, since it may be modified below
-        self.all_dependencies = self['dependencies'][:]
+        self.all_dependencies = copy.deepcopy(self['dependencies'])
 
         dep_mod_names = [dep['full_mod_name'] for dep in self['dependencies']]
 
diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index d8a57bdba1..2b114a5e88 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -169,14 +169,14 @@ def mk_node_name(spec):
     for spec in specs:
         spec['module'] = mk_node_name(spec['ec'])
         all_nodes.add(spec['module'])
-        spec['dependencies'] = [mk_node_name(s) for s in spec['dependencies']]
-        all_nodes.update(spec['dependencies'])
+        spec['ec'].all_dependencies = [mk_node_name(s) for s in spec['ec'].all_dependencies]
+        all_nodes.update(spec['ec'].all_dependencies)
 
     # build directed graph
     dgr = digraph()
     dgr.add_nodes(all_nodes)
     for spec in specs:
-        for dep in spec['dependencies']:
+        for dep in spec['ec'].all_dependencies:
             dgr.add_edge((spec['module'], dep))
 
     # write to file

From 646b0919a860719ab2082ddbff1688550dc71fd7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 15 Aug 2015 17:46:34 +0200
Subject: [PATCH 1221/1356] fix ActiveMNS.det_full_module_name for external
 modules

---
 easybuild/framework/easyconfig/easyconfig.py |  9 ++++++--
 test/framework/easyconfig.py                 | 23 +++++++++++++++++++-
 2 files changed, 29 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 79e68d26b8..59c20c974d 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1105,8 +1105,13 @@ def _det_module_name_with(self, mns_method, ec, force_visible=False):
     def det_full_module_name(self, ec, force_visible=False):
         """Determine full module name by selected module naming scheme, based on supplied easyconfig."""
         self.log.debug("Determining full module name for %s (force_visible: %s)" % (ec, force_visible))
-        mod_name = self._det_module_name_with(self.mns.det_full_module_name, ec, force_visible=force_visible)
-        self.log.debug("Obtained valid full module name %s" % mod_name)
+        if ec.get('external_module', False):
+            # external modules have the module name readily available, and may lack the info required by the MNS
+            mod_name = ec['full_mod_name']
+            self.log.debug("Full module name for external module: %s", mod_name)
+        else:
+            mod_name = self._det_module_name_with(self.mns.det_full_module_name, ec, force_visible=force_visible)
+            self.log.debug("Obtained valid full module name %s", mod_name)
         return mod_name
 
     def det_install_subdir(self, ec):
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 7811e9e9e7..168b7a47aa 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -43,7 +43,7 @@
 import easybuild.framework.easyconfig as easyconfig
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig.constants import EXTERNAL_MODULE_MARKER
-from easybuild.framework.easyconfig.easyconfig import EasyConfig
+from easybuild.framework.easyconfig.easyconfig import ActiveMNS, EasyConfig
 from easybuild.framework.easyconfig.easyconfig import create_paths
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, quote_py_str
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
@@ -1392,6 +1392,27 @@ def test_to_template_str(self):
         self.assertEqual(templ_dict, "{'a': '%(name)s', 'b': 'notemplate'}")
         self.assertEqual(to_template_str("('foo', '0.0.1')", templ_const, templ_val), "('%(name)s', '%(version)s')")
 
+    def test_ActiveMNS_det_full_module_name(self):
+        """Test det_full_module_name method of ActiveMNS."""
+        build_options = {
+            'valid_module_classes': module_classes(),
+            'external_modules_metadata': ConfigObj(),
+        }
+
+        init_config(build_options=build_options)
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0-deps.eb')
+        ec = EasyConfig(ec_file)
+
+        self.assertEqual(ActiveMNS().det_full_module_name(ec), 'toy/0.0-deps')
+        self.assertEqual(ActiveMNS().det_full_module_name(ec['dependencies'][0]), 'ictce/4.1.13')
+        self.assertEqual(ActiveMNS().det_full_module_name(ec['dependencies'][1]), 'GCC/4.7.2')
+
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'gzip-1.4-GCC-4.6.3.eb')
+        ec = EasyConfig(ec_file)
+        hiddendep = ec['hiddendependencies'][0]
+        self.assertEqual(ActiveMNS().det_full_module_name(hiddendep), 'toy/.0.0-deps')
+        self.assertEqual(ActiveMNS().det_full_module_name(hiddendep, force_visible=True), 'toy/0.0-deps')
+
 
 def suite():
     """ returns all the testcases in this module """

From 8c8e4883fad01554b8fce31cf137033a98908eb8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 15 Aug 2015 19:52:52 +0200
Subject: [PATCH 1222/1356] include empty external_modules_metadata in default
 build options for unit tests

---
 test/framework/utilities.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 5e6e204e9e..85fc642abb 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -47,6 +47,7 @@
 from easybuild.main import main
 from easybuild.tools import config
 from easybuild.tools.config import module_classes, set_tmpdir
+from easybuild.tools.configobj import ConfigObj
 from easybuild.tools.environment import modify_env
 from easybuild.tools.filetools import mkdir, read_file
 from easybuild.tools.module_naming_scheme import GENERAL_CLASS
@@ -327,6 +328,7 @@ def init_config(args=None, build_options=None):
     # initialize build options
     if build_options is None:
         build_options = {
+            'external_modules_metadata': ConfigObj(),
             'valid_module_classes': module_classes(),
             'valid_stops': [x[0] for x in EasyBlock.get_steps()],
         }

From ed52df06a10a25343b0dc073b2a3e1ed59f8df50 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 15 Aug 2015 19:53:49 +0200
Subject: [PATCH 1223/1356] add unit test for dep_graph that catches bug that
 was fixed in d2a86ff

---
 test/framework/easyconfig.py | 56 ++++++++++++++++++++++++++++--------
 1 file changed, 44 insertions(+), 12 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 7811e9e9e7..eb01985c03 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -45,9 +45,10 @@
 from easybuild.framework.easyconfig.constants import EXTERNAL_MODULE_MARKER
 from easybuild.framework.easyconfig.easyconfig import EasyConfig
 from easybuild.framework.easyconfig.easyconfig import create_paths
-from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, quote_py_str
+from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.templates import to_template_str
+from easybuild.framework.easyconfig.tools import dep_graph, parse_easyconfigs
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak_one
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import module_classes
@@ -55,11 +56,22 @@
 from easybuild.tools.filetools import read_file, write_file
 from easybuild.tools.module_naming_scheme.toolchain import det_toolchain_compilers, det_toolchain_mpi
 from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version
+from easybuild.tools.robot import resolve_dependencies
 from easybuild.tools.systemtools import get_shared_lib_ext
 from easybuild.tools.utilities import quote_str
 from test.framework.utilities import find_full_path
 
 
+EXPECTED_DOTTXT_TOY_DEPS = """digraph graphname {
+"GCC/4.7.2 (EXT)";
+toy;
+ictce;
+toy -> ictce;
+toy -> "GCC/4.7.2 (EXT)";
+}
+"""
+
+
 class EasyConfigTest(EnhancedTestCase):
     """ easyconfig tests """
     contents = None
@@ -1057,11 +1069,6 @@ def test_external_dependencies(self):
         ectxt += "\nbuilddependencies = [('somebuilddep/0.1', EXTERNAL_MODULE)]"
         write_file(toy_ec, ectxt)
 
-        build_options = {
-            'valid_module_classes': module_classes(),
-            'external_modules_metadata': ConfigObj(),
-        }
-        init_config(build_options=build_options)
         ec = EasyConfig(toy_ec)
 
         builddeps = ec.builddependencies()
@@ -1209,12 +1216,6 @@ def test_dump_autopep8(self):
 
     def test_dump_extra(self):
         """Test EasyConfig's dump() method for files containing extra values"""
-        build_options = {
-            'valid_module_classes': module_classes(),
-            'external_modules_metadata': ConfigObj(),
-        }
-        init_config(build_options=build_options)
-
         rawtxt = '\n'.join([
             "easyblock = 'EB_foo'",
             '',
@@ -1392,6 +1393,37 @@ def test_to_template_str(self):
         self.assertEqual(templ_dict, "{'a': '%(name)s', 'b': 'notemplate'}")
         self.assertEqual(to_template_str("('foo', '0.0.1')", templ_const, templ_val), "('%(name)s', '%(version)s')")
 
+    def test_dep_graph(self):
+        """Test for dep_graph."""
+        try:
+            import pygraph
+
+            test_easyconfigs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+            build_options = {
+                'external_modules_metadata': ConfigObj(),
+                'valid_module_classes': module_classes(),
+                'robot_path': [test_easyconfigs],
+                'silent': True,
+            }
+            init_config(build_options=build_options)
+
+            ec_file = os.path.join(test_easyconfigs, 'toy-0.0-deps.eb')
+            ec_files = [(ec_file, False)]
+            ecs, _ = parse_easyconfigs(ec_files)
+
+            dot_file = os.path.join(self.test_prefix, 'test.dot')
+            ordered_ecs = resolve_dependencies(ecs, retain_all_deps=True)
+            dep_graph(dot_file, ordered_ecs)
+
+            # hard check for expect .dot file contents
+            # 3 nodes should be there: 'GCC/4.7.2 (EXT)', 'toy', and 'ictce/4.1.13'
+            # and 2 edges: 'toy -> ictce' and 'toy -> "GCC/4.7.2 (EXT)"'
+            dottxt = read_file(dot_file)
+            self.assertEqual(dottxt, EXPECTED_DOTTXT_TOY_DEPS)
+
+        except ImportError:
+            print "Skipping test_dep_graph, since pygraph is not available"
+
 
 def suite():
     """ returns all the testcases in this module """

From 6273d35e9efa89b092024ea87e02df2c35a88025 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 15 Aug 2015 19:59:09 +0200
Subject: [PATCH 1224/1356] check 'silent' build option in dep_graph rather
 than have an (unused) named argument for that purpose

---
 easybuild/framework/easyconfig/tools.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 2b114a5e88..90bbef873d 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -142,11 +142,10 @@ def find_resolved_modules(unprocessed, avail_modules, retain_all_deps=False):
     return ordered_ecs, new_unprocessed, new_avail_modules
 
 
-def _dep_graph(fn, specs, silent=False):
+def _dep_graph(fn, specs):
     """
     Create a dependency graph for the given easyconfigs.
     """
-
     # check whether module names are unique
     # if so, we can omit versions in the graph
     names = set()
@@ -190,7 +189,7 @@ def mk_node_name(spec):
         gv.layout(gvv, 'dot')
         gv.render(gvv, fn.split('.')[-1], fn)
 
-    if not silent:
+    if not build_option('silent'):
         print "Wrote dependency graph for %d easyconfigs to %s" % (len(specs), fn)
 
 

From c3180e058c7147d1b8c40adee7c9424ae646033a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 16 Aug 2015 12:44:09 +0200
Subject: [PATCH 1225/1356] fix keeping track of list of *all* dependencies

---
 .../framework/easyconfig/.easyconfig.py.swo     | Bin 0 -> 77824 bytes
 easybuild/framework/easyconfig/easyconfig.py    |   8 ++++----
 easybuild/framework/easyconfig/format/one.py    |   2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)
 create mode 100644 easybuild/framework/easyconfig/.easyconfig.py.swo

diff --git a/easybuild/framework/easyconfig/.easyconfig.py.swo b/easybuild/framework/easyconfig/.easyconfig.py.swo
new file mode 100644
index 0000000000000000000000000000000000000000..b03e2400240963c1a0e4ceb058dafd1137e28f12
GIT binary patch
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HcmV?d00001

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 59c20c974d..90baacb724 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -196,9 +196,12 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
             self.validate(check_osdeps=build_option('check_osdeps'))
 
         # filter hidden dependencies from list of dependencies
-        self.all_dependencies = None
         self.filter_hidden_deps()
 
+        # list of *all* dependencies, including hidden/build deps & toolchain, but excluding filtered deps
+        self.all_dependencies = copy.deepcopy(self.dependencies())
+        self.all_dependencies.append(self.toolchain.as_dict())
+
         # keep track of whether the generated module file should be hidden
         if hidden is None:
             hidden = build_option('hidden')
@@ -401,9 +404,6 @@ def filter_hidden_deps(self):
         """
         Filter hidden dependencies from list of dependencies.
         """
-        # keep a copy of the original list of dependencies, since it may be modified below
-        self.all_dependencies = self['dependencies'][:]
-
         dep_mod_names = [dep['full_mod_name'] for dep in self['dependencies']]
 
         faulty_deps = []
diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index a44595b2dd..4aa3adc768 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -225,7 +225,7 @@ def _find_defined_params(self, ecfg, keyset, default_values, templ_const, templ_
             for key in group:
                 # the value for 'dependencies' may have been modified after parsing via filter_hidden_deps
                 if key == 'dependencies':
-                    val = ecfg.all_dependencies
+                    val = ecfg[key] + ecfg['hiddendependencies']
                 else:
                     val = ecfg[key]
 

From b2db588a6ed97bfe405a0ccba22d6a2ff6cfb22c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 16 Aug 2015 12:50:52 +0200
Subject: [PATCH 1226/1356] fix tracking of job dependencies + enhance unit
 test to check them

---
 easybuild/tools/parallelbuild.py | 10 +++++-----
 test/framework/parallelbuild.py  | 20 ++++++++++++++++++--
 2 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/easybuild/tools/parallelbuild.py b/easybuild/tools/parallelbuild.py
index b7451f2da4..e30b9203d2 100644
--- a/easybuild/tools/parallelbuild.py
+++ b/easybuild/tools/parallelbuild.py
@@ -85,19 +85,19 @@ def build_easyconfigs_in_parallel(build_command, easyconfigs, output_dir='easybu
     # keep track of which job builds which module
     module_to_job = {}
 
-    for ec in easyconfigs:
+    for easyconfig in easyconfigs:
         # this is very important, otherwise we might have race conditions
         # e.g. GCC-4.5.3 finds cloog.tar.gz but it was incorrectly downloaded by GCC-4.6.3
         # running this step here, prevents this
         if prepare_first:
-            prepare_easyconfig(ec)
+            prepare_easyconfig(easyconfig)
 
         # the new job will only depend on already submitted jobs
-        _log.info("creating job for ec: %s" % str(ec))
-        new_job = create_job(active_job_backend, build_command, ec, output_dir=output_dir)
+        _log.info("creating job for ec: %s" % easyconfig['ec'])
+        new_job = create_job(active_job_backend, build_command, easyconfig, output_dir=output_dir)
 
         # filter out dependencies marked as external modules
-        deps = [d for d in ec['dependencies'] if not d['external_module']]
+        deps = [d for d in easyconfig['ec'].all_dependencies if not d.get('external_module', False)]
 
         dep_mod_names = map(ActiveMNS().det_full_module_name, deps)
         job_deps = [module_to_job[dep] for dep in dep_mod_names if dep in module_to_job]
diff --git a/test/framework/parallelbuild.py b/test/framework/parallelbuild.py
index 03d50a704d..e679347c20 100644
--- a/test/framework/parallelbuild.py
+++ b/test/framework/parallelbuild.py
@@ -74,8 +74,8 @@ def __init__(self, *args, **kwargs):
         self.clean_conn = None
         self.script = args[1]
 
-    def add_dependencies(self, *args, **kwargs):
-        pass
+    def add_dependencies(self, jobs):
+        self.deps.extend(jobs)
 
     def cleanup(self, *args, **kwargs):
         pass
@@ -135,6 +135,22 @@ def test_build_easyconfigs_in_parallel_pbs_python(self):
                 regex = re.compile("eb %s" % ec['spec'])
             self.assertTrue(regex.search(jobs[i].script), "Pattern '%s' found in: %s" % (regex.pattern, jobs[i].script))
 
+        # no deps for GCC/4.6.3 (toolchain) and ictce/4.1.13 (test easyconfig with 'fake' deps)
+        self.assertEqual(len(jobs[0].deps), 0)
+        self.assertEqual(len(jobs[1].deps), 0)
+
+        # only dependency for toy/0.0-deps is ictce/4.1.13 (dep marked as external module is filtered out)
+        self.assertTrue('toy-0.0-deps.eb' in jobs[2].script)
+        self.assertEqual(len(jobs[2].deps), 1)
+        self.assertTrue('ictce-4.1.13.eb' in jobs[2].deps[0].script)
+
+        # dependencies for gzip/1.4-GCC-4.6.3: GCC/4.6.3 (toolchain) + toy/.0.0-deps
+        self.assertTrue('gzip-1.4-GCC-4.6.3.eb' in jobs[3].script)
+        self.assertEqual(len(jobs[3].deps), 2)
+        regex = re.compile('toy-0.0-deps.eb\s* --hidden')
+        self.assertTrue(regex.search(jobs[3].deps[0].script))
+        self.assertTrue('GCC-4.6.3.eb' in jobs[3].deps[1].script)
+
         # restore mocked stuff
         PbsPython.__init__ = PbsPython__init__
         PbsPython._check_version = PbsPython_check_version

From 19cdfab1b6efa64bea31dad4062b2fea6e6bd501 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 16 Aug 2015 14:23:19 +0200
Subject: [PATCH 1227/1356] only include toolchain as dependency if it's a
 non-dummy toolchain

---
 easybuild/framework/easyconfig/easyconfig.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 90baacb724..0cd9c6ad0b 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -200,7 +200,8 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
 
         # list of *all* dependencies, including hidden/build deps & toolchain, but excluding filtered deps
         self.all_dependencies = copy.deepcopy(self.dependencies())
-        self.all_dependencies.append(self.toolchain.as_dict())
+        if self.toolchain.name != DUMMY_TOOLCHAIN_NAME:
+            self.all_dependencies.append(self.toolchain.as_dict())
 
         # keep track of whether the generated module file should be hidden
         if hidden is None:

From 2eb13a45835718a5b5226ffebc3d96f8e84e58be Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 16 Aug 2015 14:26:45 +0200
Subject: [PATCH 1228/1356] don't use non-existing toolchain in unit tests

---
 .../framework/easyconfig/.easyconfig.py.swo     | Bin 77824 -> 0 bytes
 test/framework/easyconfig.py                    |   4 ++--
 test/framework/scripts.py                       |   4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)
 delete mode 100644 easybuild/framework/easyconfig/.easyconfig.py.swo

diff --git a/easybuild/framework/easyconfig/.easyconfig.py.swo b/easybuild/framework/easyconfig/.easyconfig.py.swo
deleted file mode 100644
index b03e2400240963c1a0e4ceb058dafd1137e28f12..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 168b7a47aa..b578dd0415 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -341,8 +341,8 @@ def test_tweaking(self):
         ver = "1.2.3"
         verpref = "myprefix"
         versuff = "mysuffix"
-        tcname = "mytc"
-        tcver = "4.1.2"
+        tcname = "gompi"
+        tcver = "1.4.10"
         new_patches = ['t5.patch', 't6.patch']
         homepage = "http://www.justatest.com"
 
diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index f406640da0..8c5e84e215 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -121,7 +121,7 @@ def test_fix_broken_easyconfig(self):
             "description = 'foo'",
             "homepage = 'http://example.com'",
             '',
-            "toolchain = {'name': 'bar', 'version': '3.2.1'}",
+            "toolchain = {'name': 'GCC', 'version': '4.8.2'}",
             '',
             "premakeopts = 'FOO=libfoo.%%s' %% shared_lib_ext",
             "makeopts = 'CC=gcc'",
@@ -136,7 +136,7 @@ def test_fix_broken_easyconfig(self):
             "description = 'foo'",
             "homepage = 'http://example.com'",
             '',
-            "toolchain = {'name': 'bar', 'version': '3.2.1'}",
+            "toolchain = {'name': 'GCC', 'version': '4.8.2'}",
             '',
             "prebuildopts = 'FOO=libfoo.%%s' %% SHLIB_EXT",
             "buildopts = 'CC=gcc'",

From f8ba3d050452039ae468b99152be3357e3585edb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 16 Aug 2015 19:07:16 +0200
Subject: [PATCH 1229/1356] fix breaking generate_software_list.py script
 because of suffix_modules_path build option incorrectly being set to None

---
 easybuild/tools/config.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 9a7bd38be1..d7fcfb3ede 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -46,6 +46,7 @@
 import easybuild.tools.environment as env
 from easybuild.tools import run
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.module_naming_scheme import GENERAL_CLASS
 from easybuild.tools.run import run_cmd
 
 
@@ -113,7 +114,6 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'regtest_output_dir',
         'skip',
         'stop',
-        'suffix_modules_path',
         'test_report_env_filter',
         'testoutput',
         'umask',
@@ -152,6 +152,9 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
     DEFAULT_PKG_TYPE: [
         'package_type',
     ],
+    GENERAL_CLASS: [
+        'suffix_modules_path',
+    ],
 }
 # build option that do not have a perfectly matching command line option
 BUILD_OPTIONS_OTHER = {

From 6c9392088d2c72dbe7876e6e82d1cb64868e84c2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Aug 2015 11:45:31 +0200
Subject: [PATCH 1230/1356] fix 'exist' method of ModulesTool classes for
 checking of hidden modules in Lua syntax

---
 easybuild/tools/modules.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 17e366bae9..8710f25df4 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -355,7 +355,7 @@ def available(self, mod_name=None, extra_args=None):
         self.log.debug("'module available %s' gave %d answers: %s" % (mod_name, len(ans), ans))
         return ans
 
-    def exist(self, mod_names):
+    def _exist(self, mod_names, mod_exists_regex_template):
         """
         Check if modules with specified names exists.
         """
@@ -372,8 +372,8 @@ def exist(self, mod_names):
                 modtype = ('hidden', 'visible (not hidden)')[visible]
                 self.log.debug("checking whether %s module %s exists via 'show'..." % (modtype, mod_name))
                 txt = self.show(mod_name)
-                mods_exist_re = re.compile('^\s*\S*/%s:\s*$' % re.escape(mod_name), re.M)
-                mods_exist.append(bool(mods_exist_re.search(txt)))
+                mod_exists_regex = re.compile(mod_exists_regex_template % re.escape(mod_name), re.M)
+                mods_exist.append(bool(mod_exists_regex.search(txt)))
 
         return mods_exist
 
@@ -703,6 +703,10 @@ def update(self):
         """Update after new modules were added."""
         pass
 
+    def exist(self, mod_names):
+        """Check if modules with specified names exists."""
+        return super(EnvironmentModulesC, self)._exist(mod_names, r'^\s*\S*/%s:\s*$')
+
 
 class EnvironmentModulesTcl(EnvironmentModulesC):
     """Interface to (Tcl) environment modules (modulecmd.tcl)."""
@@ -852,6 +856,13 @@ def prepend_module_path(self, path):
         self.use(path)
         self.set_mod_paths()
 
+    def exist(self, mod_names):
+        """Check if modules with specified names exists."""
+        # module file may be either in Tcl syntax (no file extension) or Lua sytax (.lua extension);
+        # the current configuration for matters little, since the module may have been installed with a different cfg;
+        # Lmod may pick up both Tcl and Lua module files, regardless of the EasyBuild configuration
+        return super(Lmod, self)._exist(mod_names, r'^\s*\S*/%s(.lua)?:\s*$')
+
 
 def get_software_root_env_var_name(name):
     """Return name of environment variable for software root."""

From 8647c4042d032bdfcbc39f7041840ef79a655b3e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Aug 2015 11:46:19 +0200
Subject: [PATCH 1231/1356] add check in test_exist unit test for hidden Lua
 module file

---
 test/framework/modules.py               |  9 +++++++++
 test/framework/modules/bzip2/.1.0.6.lua | 24 ++++++++++++++++++++++++
 2 files changed, 33 insertions(+)
 create mode 100644 test/framework/modules/bzip2/.1.0.6.lua

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 737e780375..387d74826f 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -117,6 +117,15 @@ def test_exists(self):
         # exists works on hidden modules
         self.assertEqual(self.testmods.exist(['toy/.0.0-deps']), [True])
 
+        # exists works on hidden modules in Lua syntax (only with Lmod)
+        modtool = modules_tool()
+        if isinstance(modtool, Lmod):
+            test_modules_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'modules'))
+            # make sure only the .lua module file is there, otherwise this test doesn't work as intended
+            self.assertTrue(os.path.exists(os.path.join(test_modules_path, 'bzip2', '.1.0.6.lua')))
+            self.assertFalse(os.path.exists(os.path.join(test_modules_path, 'bzip2', '.1.0.6')))
+            self.assertEqual(self.testmods.exist(['bzip2/.1.0.6']), [True])
+
         # exists also works on lists of module names
         # list should be sufficiently long, since for short lists 'show' is always used
         mod_names = ['OpenMPI/1.6.4-GCC-4.6.4', 'foo/1.2.3', 'GCC',
diff --git a/test/framework/modules/bzip2/.1.0.6.lua b/test/framework/modules/bzip2/.1.0.6.lua
new file mode 100644
index 0000000000..cad0e55a36
--- /dev/null
+++ b/test/framework/modules/bzip2/.1.0.6.lua
@@ -0,0 +1,24 @@
+help([[bzip2 is a freely available, patent free, high-quality data compressor. It typically
+compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical
+compressors), whilst being around twice as fast at compression and six times faster at decompression. - Homepage: http://www.bzip.org/]])
+whatis([[Name: bzip2]])
+whatis([[Version: 1.0.6]])
+whatis([[Description: bzip2 is a freely available, patent free, high-quality data compressor. It typically
+compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical
+compressors), whilst being around twice as fast at compression and six times faster at decompression. - Homepage: http://www.bzip.org/]])
+whatis([[Homepage: http://www.bzip.org/]])
+
+local root = "/Users/example/.local/easybuild/software/bzip2/1.0.6"
+
+conflict("bzip2")
+
+prepend_path("CPATH", pathJoin(root, "include"))
+prepend_path("LD_LIBRARY_PATH", pathJoin(root, "lib"))
+prepend_path("LIBRARY_PATH", pathJoin(root, "lib"))
+prepend_path("MANPATH", pathJoin(root, "man"))
+prepend_path("PATH", pathJoin(root, "bin"))
+setenv("EBROOTBZIP2", root)
+setenv("EBVERSIONBZIP2", "1.0.6")
+setenv("EBDEVELBZIP2", pathJoin(root, "easybuild/bzip2-1.0.6-easybuild-devel"))
+
+-- Built with EasyBuild version 2.1.1

From 26272582af6ea46456473479628e74ef1491c663 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Tue, 18 Aug 2015 12:21:32 +0200
Subject: [PATCH 1232/1356] Added --cleanup-tmpdir option

Disable this option to not delete the temporarily directory and log file
at the end of a successful run.
---
 easybuild/tools/config.py    | 4 +++-
 easybuild/tools/filetools.py | 4 ++++
 easybuild/tools/options.py   | 3 ++-
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index d7fcfb3ede..75ff8e5a14 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -79,6 +79,7 @@
 DEFAULT_REPOSITORY = 'FileRepository'
 DEFAULT_STRICT = run.WARN
 
+
 # utility function for obtaining default paths
 def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
     """Create full path, avoid '/' at the end."""
@@ -139,6 +140,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
     ],
     True: [
         'cleanup_builddir',
+        'cleanup_tmpdir',
     ],
     DEFAULT_STRICT: [
         'strict',
@@ -244,7 +246,7 @@ def get_items_check_required(self):
         For all known/required keys, check if exists and return all key/value pairs.
             no_missing: boolean, when True, will throw error message for missing values
         """
-        missing = [x for x in self.KNOWN_KEYS if not x in self]
+        missing = [x for x in self.KNOWN_KEYS if x not in self]
         if len(missing) > 0:
             raise EasyBuildError("Cannot determine value for configuration variables %s. Please specify it.", missing)
 
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 99dfb1a317..4b56ec6a28 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -930,6 +930,10 @@ def move_logs(src_logfile, target_logfile):
 
 def cleanup(logfile, tempdir, testing):
     """Cleanup the specified log file and the tmp directory"""
+    if not build_option('cleanup_tmpdir'):
+        print_msg('Keeping temporary log file(s) and directory.', log=None, silent=testing)
+        return
+
     if not testing and logfile is not None:
         try:
             for log in glob.glob('%s*' % logfile):
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 33661c2c2b..8931cbbf6e 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -198,6 +198,7 @@ def override_options(self):
             'allow-modules-tool-mismatch': ("Allow mismatch of modules tool and definition of 'module' function",
                                             None, 'store_true', False),
             'cleanup-builddir': ("Cleanup build dir after successful installation.", None, 'store_true', True),
+            'cleanup-tmpdir': ("Cleanup tmp dir after successful run.", None, 'store_true', True),
             'deprecated': ("Run pretending to be (future) version, to test removal of deprecated code.",
                            None, 'store', None),
             'download-timeout': ("Timeout for initiating downloads (in seconds)", float, 'store', None),
@@ -281,7 +282,7 @@ def config_options(self):
                              'choice', 'store', DEFAULT_MODULES_TOOL, sorted(avail_modules_tools().keys())),
             'packagepath': ("The destination path for the packages built by package-tool",
                              None, 'store', mk_full_default_path('packagepath')),
-            'package-naming-scheme': ("Packaging naming scheme choice", 
+            'package-naming-scheme': ("Packaging naming scheme choice",
                                       'choice', 'store', DEFAULT_PNS, sorted(avail_package_naming_schemes().keys())),
             'prefix': (("Change prefix for buildpath, installpath, sourcepath and repositorypath "
                         "(used prefix for defaults %s)" % DEFAULT_PREFIX),

From b041fd442b4a63d8675eeac4db0e2ac395190f71 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Aug 2015 13:51:07 +0200
Subject: [PATCH 1233/1356] style cleanup in exist unit test

---
 test/framework/modules.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/test/framework/modules.py b/test/framework/modules.py
index 387d74826f..3da4f62272 100644
--- a/test/framework/modules.py
+++ b/test/framework/modules.py
@@ -118,8 +118,7 @@ def test_exists(self):
         self.assertEqual(self.testmods.exist(['toy/.0.0-deps']), [True])
 
         # exists works on hidden modules in Lua syntax (only with Lmod)
-        modtool = modules_tool()
-        if isinstance(modtool, Lmod):
+        if isinstance(self.testmods, Lmod):
             test_modules_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'modules'))
             # make sure only the .lua module file is there, otherwise this test doesn't work as intended
             self.assertTrue(os.path.exists(os.path.join(test_modules_path, 'bzip2', '.1.0.6.lua')))

From de1cab674e35438dbe3e904bd7b80dedd7138088 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Aug 2015 21:48:49 +0200
Subject: [PATCH 1234/1356] avoid (only) defining exist() in classes that
 derive from ModulesTool

---
 easybuild/tools/modules.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 8710f25df4..57a0add671 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -355,7 +355,7 @@ def available(self, mod_name=None, extra_args=None):
         self.log.debug("'module available %s' gave %d answers: %s" % (mod_name, len(ans), ans))
         return ans
 
-    def _exist(self, mod_names, mod_exists_regex_template):
+    def exist(self, mod_names, mod_exists_regex_template=r'^\s*\S*/%s:\s*$'):
         """
         Check if modules with specified names exists.
         """
@@ -703,10 +703,6 @@ def update(self):
         """Update after new modules were added."""
         pass
 
-    def exist(self, mod_names):
-        """Check if modules with specified names exists."""
-        return super(EnvironmentModulesC, self)._exist(mod_names, r'^\s*\S*/%s:\s*$')
-
 
 class EnvironmentModulesTcl(EnvironmentModulesC):
     """Interface to (Tcl) environment modules (modulecmd.tcl)."""

From ac1ebef2f92416b38ea26f2f388764040dbbcceb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Aug 2015 22:08:00 +0200
Subject: [PATCH 1235/1356] fix super call in Lmod.exist

---
 easybuild/tools/modules.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/modules.py b/easybuild/tools/modules.py
index 57a0add671..b670a4078f 100644
--- a/easybuild/tools/modules.py
+++ b/easybuild/tools/modules.py
@@ -857,7 +857,7 @@ def exist(self, mod_names):
         # module file may be either in Tcl syntax (no file extension) or Lua sytax (.lua extension);
         # the current configuration for matters little, since the module may have been installed with a different cfg;
         # Lmod may pick up both Tcl and Lua module files, regardless of the EasyBuild configuration
-        return super(Lmod, self)._exist(mod_names, r'^\s*\S*/%s(.lua)?:\s*$')
+        return super(Lmod, self).exist(mod_names, r'^\s*\S*/%s(.lua)?:\s*$')
 
 
 def get_software_root_env_var_name(name):

From 889b313be1c0c522472be7da6bf1fc004a14d0d7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 18 Aug 2015 23:23:23 +0200
Subject: [PATCH 1236/1356] only call EasyBlock.sanity_check_step for
 non-extensions

---
 easybuild/framework/extensioneasyblock.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/extensioneasyblock.py b/easybuild/framework/extensioneasyblock.py
index 7f9523f3f0..49b9a5e3e6 100644
--- a/easybuild/framework/extensioneasyblock.py
+++ b/easybuild/framework/extensioneasyblock.py
@@ -119,9 +119,9 @@ def sanity_check_step(self, exts_filter=None, custom_paths=None, custom_commands
             # unload fake module and clean up
             self.clean_up_fake_module(fake_mod_data)
 
-        if custom_paths or self.cfg['sanity_check_paths'] or custom_commands or self.cfg['sanity_check_commands']:
-            EasyBlock.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands,
-                extension=self.is_extension)
+            if custom_paths or self.cfg['sanity_check_paths'] or custom_commands or self.cfg['sanity_check_commands']:
+                EasyBlock.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands,
+                                            extension=self.is_extension)
 
         # pass or fail sanity check
         if not sanity_check_ok:

From e2f29a9f7de480e8b870aa12f522775049430cb3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 19 Aug 2015 10:04:49 +0200
Subject: [PATCH 1237/1356] add unit test to check for sanity check behavior
 for extensions

---
 test/framework/easyblock.py                     |  16 ++++++++++++++++
 .../easyconfigs/toy-0.0-gompi-1.3.12-test.eb    |   1 +
 .../sandbox/easybuild/easyblocks/t/toy.py       |   2 +-
 .../sources/toy/extensions/barbar-0.0.tar.gz    | Bin 0 -> 279 bytes
 4 files changed, 18 insertions(+), 1 deletion(-)
 create mode 100644 test/framework/sandbox/sources/toy/extensions/barbar-0.0.tar.gz

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 5382068066..e7c25f568e 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -635,6 +635,22 @@ def test_patch_step(self):
         eb.extract_step()
         eb.patch_step()
 
+    def test_extensions_sanity_check(self):
+        """Test sanity check aspect of extensions."""
+        test_ecs_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
+        toy_ec = EasyConfig(os.path.join(test_ecs_dir, 'toy-0.0-gompi-1.3.12-test.eb'))
+
+        # purposely put sanity check command in place that breaks the build,
+        # to check whether sanity check is only run once;
+        # sanity check commands are checked after checking sanity check paths, so this should work
+        toy_ec.update('sanity_check_commands', [("%(installdir)s/bin/toy && rm %(installdir)s/bin/toy", '')])
+
+        # this import only works here, since EB_toy is a test easyblock
+        from easybuild.easyblocks.toy import EB_toy
+        eb = EB_toy(toy_ec)
+        eb.silent = True
+        eb.run_all_steps(True)
+
 
 def suite():
     """ return all the tests in this file """
diff --git a/test/framework/easyconfigs/toy-0.0-gompi-1.3.12-test.eb b/test/framework/easyconfigs/toy-0.0-gompi-1.3.12-test.eb
index b866a7ee1c..d4de1ae5fb 100644
--- a/test/framework/easyconfigs/toy-0.0-gompi-1.3.12-test.eb
+++ b/test/framework/easyconfigs/toy-0.0-gompi-1.3.12-test.eb
@@ -21,6 +21,7 @@ patches = ['toy-0.0_typo.patch']
 
 exts_list = [
     ('bar', '0.0'),
+    ('barbar', '0.0'),
 ]
 
 sanity_check_paths = {
diff --git a/test/framework/sandbox/easybuild/easyblocks/t/toy.py b/test/framework/sandbox/easybuild/easyblocks/t/toy.py
index 43d9eebe1c..f0c02aa99f 100644
--- a/test/framework/sandbox/easybuild/easyblocks/t/toy.py
+++ b/test/framework/sandbox/easybuild/easyblocks/t/toy.py
@@ -57,7 +57,7 @@ def configure_step(self, name=None):
         # make sure Python system dep is handled correctly when specified
         if self.cfg['allow_system_deps']:
             if get_software_root('Python') != 'Python' or get_software_version('Python') != platform.python_version():
-                raise EasyBlock("Sanity check on allowed Python system dep failed.")
+                raise EasyBuildError("Sanity check on allowed Python system dep failed.")
         os.rename('%s.source' % name, '%s.c' % name)
 
     def build_step(self, name=None):
diff --git a/test/framework/sandbox/sources/toy/extensions/barbar-0.0.tar.gz b/test/framework/sandbox/sources/toy/extensions/barbar-0.0.tar.gz
new file mode 100644
index 0000000000000000000000000000000000000000..d6659164153e297c1313f9c72782ccea40b70f93
GIT binary patch
literal 279
zcmV+y0qFi8iwFRhE!0&21MShjPQx$|2Jp;&ic=YAQ3;pCc84N%o&gw~e<XrB$Z?Pm
z;@xqZ3RuE`s1We|mODA8=<F{yE;sI!V?K)xg_&1M(XQ&Taw^BVM@g!*;#6za#7QQT
zRYdAw8+|bJ-ng*JUDb5GuO{chSY3bepZz`F>MxPM=RdY_-wm#qeupmz@1dof&OgyI
z<e#xlvNV$%^4F|XMEspgO!?>eAGNl)AIgf(dtbI)+*}CJT2C9(+WEFI?zUJ`(HM8K
z?H{jh7SBRZ@ZiGtdOo{6-jE^RJuS)DG8}h9NnK5?kFV`)vEB{4$`8&Guf>b_={o}e
d0000000000000000002|6|a>IAzT0`008Ehg}VR%

literal 0
HcmV?d00001


From e4f8fc528235b03d3bf7f74b4568de6674ba5f97 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 19 Aug 2015 10:13:11 +0200
Subject: [PATCH 1238/1356] switch to calling sanity_check_step of super (i.e.,
 an EasyBlock class) for non-extensions or if custom paths/commands are
 defined

---
 easybuild/framework/extensioneasyblock.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/extensioneasyblock.py b/easybuild/framework/extensioneasyblock.py
index 49b9a5e3e6..52e3e11783 100644
--- a/easybuild/framework/extensioneasyblock.py
+++ b/easybuild/framework/extensioneasyblock.py
@@ -119,9 +119,10 @@ def sanity_check_step(self, exts_filter=None, custom_paths=None, custom_commands
             # unload fake module and clean up
             self.clean_up_fake_module(fake_mod_data)
 
-            if custom_paths or self.cfg['sanity_check_paths'] or custom_commands or self.cfg['sanity_check_commands']:
-                EasyBlock.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands,
-                                            extension=self.is_extension)
+        if custom_paths or custom_commands or not self.is_extension:
+            super(ExtensionEasyBlock, self).sanity_check_step(custom_paths=custom_paths,
+                                                              custom_commands=custom_commands,
+                                                              extension=self.is_extension)
 
         # pass or fail sanity check
         if not sanity_check_ok:

From ab32f3382c889407ae7a5f559f1a835926508f0b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 19 Aug 2015 21:43:06 +0200
Subject: [PATCH 1239/1356] delay check for specified MNS until after
 processing options to take --include-module-naming-schemes into account

---
 easybuild/tools/options.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index 33661c2c2b..ba1fa8c1ad 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -268,8 +268,7 @@ def config_options(self):
             # purposely take a copy for the default logfile format
             'logfile-format': ("Directory name and format of the log file",
                                'strtuple', 'store', DEFAULT_LOGFILE_FORMAT[:], {'metavar': 'DIR,FORMAT'}),
-            'module-naming-scheme': ("Module naming scheme",
-                                     'choice', 'store', DEFAULT_MNS, sorted(avail_module_naming_schemes().keys())),
+            'module-naming-scheme': ("Module naming scheme to use", None, 'store', DEFAULT_MNS),
             'module-syntax': ("Syntax to be used for module files", 'choice', 'store', DEFAULT_MODULE_SYNTAX,
                               sorted(avail_module_generators().keys())),
             'moduleclasses': (("Extend supported module classes "
@@ -451,6 +450,12 @@ def validate(self):
                 msg = msg % (subdir_opt, typ, val)
                 error_msgs.append(msg)
 
+        # specified module naming scheme must be a known one
+        avail_mnss = avail_module_naming_schemes()
+        if self.options.module_naming_scheme and self.options.module_naming_scheme not in avail_mnss:
+            msg = "Selected module naming scheme '%s' is unknown: %s" % (self.options.module_naming_scheme, avail_mnss)
+            error_msgs.append(msg)
+
         if error_msgs:
             raise EasyBuildError("Found problems validating the options: %s", '\n'.join(error_msgs))
 

From 192b22420ed14a1a96adab902dfe03121e40a90b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 19 Aug 2015 21:43:33 +0200
Subject: [PATCH 1240/1356] enhance tests to catch problem with
 --module-naming-scheme vs --include-module-naming-schemes

---
 test/framework/options.py   | 55 ++++++++++++++++++++++++++++++++-----
 test/framework/utilities.py |  9 +++---
 2 files changed, 53 insertions(+), 11 deletions(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 91f170eda3..6247fa21f5 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -202,7 +202,7 @@ def test_skip(self):
         """Test skipping installation of module (--skip, -k)."""
 
         # use toy-0.0.eb easyconfig file that comes with the tests
-        eb_file = os.path.join(os.path.dirname(__file__), 'easyconfigs', 'toy-0.0.eb')
+        eb_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb')
 
         # check log message with --skip for existing module
         args = [
@@ -1739,14 +1739,14 @@ def test_include_module_naming_schemes(self):
 
         mns_regex = re.compile(r'^\s*TestIncludedMNS', re.M)
 
-        # TestIncludeMNS module naming scheme is not available by default
+        # TestIncludedMNS module naming scheme is not available by default
         args = [
             '--avail-module-naming-schemes',
             '--unittest-file=%s' % self.logfile,
         ]
         self.eb_main(args, logfile=dummylogfn, raise_error=True)
         logtxt = read_file(self.logfile)
-        self.assertFalse(mns_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (mns_regex.pattern, logtxt))
+        self.assertFalse(mns_regex.search(logtxt), "Unexpected pattern '%s' found in: %s" % (mns_regex.pattern, logtxt))
 
         # include extra test MNS
         mns_txt = '\n'.join([
@@ -1768,6 +1768,43 @@ def test_include_module_naming_schemes(self):
         logtxt = read_file(self.logfile)
         self.assertTrue(mns_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (mns_regex.pattern, logtxt))
 
+        # undo successful import
+        del sys.modules['easybuild.tools.module_naming_scheme.test_mns']
+
+    def test_use_included_module_naming_scheme(self):
+        """Test using an included module naming scheme."""
+        # try selecting the added module naming scheme
+        fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
+        os.close(fd)
+
+        # include extra test MNS
+        mns_txt = '\n'.join([
+            'import os',
+            'from easybuild.tools.module_naming_scheme import ModuleNamingScheme',
+            'class AnotherTestIncludedMNS(ModuleNamingScheme):',
+            '   def det_full_module_name(self, ec):',
+            "       return os.path.join(ec['name'], ec['version'])",
+        ])
+        write_file(os.path.join(self.test_prefix, 'test_mns.py'), mns_txt)
+
+        eb_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb')
+        args = [
+            '--unittest-file=%s' % self.logfile,
+            '--module-naming-scheme=AnotherTestIncludedMNS',
+            '--force',
+            eb_file,
+        ]
+
+        # selecting a module naming scheme that doesn't exist leads to 'invalid choice'
+        error_regex = "Selected module naming scheme \'AnotherTestIncludedMNS\' is unknown"
+        self.assertErrorRegex(EasyBuildError, error_regex, self.eb_main, args, logfile=dummylogfn,
+                              raise_error=True, raise_systemexit=True)
+
+        args.append('--include-module-naming-schemes=%s/*.py' % self.test_prefix)
+        self.eb_main(args, logfile=dummylogfn, do_build=True, raise_error=True, raise_systemexit=True, verbose=True)
+        toy_mod = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0')
+        self.assertTrue(os.path.exists(toy_mod), "Found %s" % toy_mod)
+
     def test_include_toolchains(self):
         """Test --include-toolchains."""
         fd, dummylogfn = tempfile.mkstemp(prefix='easybuild-dummy', suffix='.log')
@@ -1781,14 +1818,14 @@ def test_include_toolchains(self):
 
         tc_regex = re.compile(r'^\s*test_included_toolchain: TestIncludedCompiler', re.M)
 
-        # TestIncludeMNS module naming scheme is not available by default
+        # TestIncludedCompiler is not available by default
         args = [
             '--list-toolchains',
             '--unittest-file=%s' % self.logfile,
         ]
-        #self.eb_main(args, logfile=dummylogfn, raise_error=True)
-        #logtxt = read_file(self.logfile)
-        #self.assertFalse(tc_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (tc_regex.pattern, logtxt))
+        self.eb_main(args, logfile=dummylogfn, raise_error=True)
+        logtxt = read_file(self.logfile)
+        self.assertFalse(tc_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (tc_regex.pattern, logtxt))
 
         # include extra test toolchain
         comp_txt = '\n'.join([
@@ -1815,6 +1852,10 @@ def test_include_toolchains(self):
         logtxt = read_file(self.logfile)
         self.assertTrue(tc_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (tc_regex.pattern, logtxt))
 
+        # undo successful import
+        del sys.modules['easybuild.toolchains.compiler.test_comp']
+        del sys.modules['easybuild.toolchains.test_tc']
+
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 85fc642abb..fc722ea143 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -189,7 +189,7 @@ def reset_modulepath(self, modpaths):
             modtool.add_module_path(modpath)
 
     def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbose=False, raise_error=False,
-                reset_env=True):
+                reset_env=True, raise_systemexit=False):
         """Helper method to call EasyBuild main function."""
         cleanup()
 
@@ -206,9 +206,10 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
 
         try:
             main((args, logfile, do_build))
-        except SystemExit:
-            pass
-        except Exception, err:
+        except SystemExit as err:
+            if raise_systemexit:
+                raise err
+        except Exception as err:
             myerr = err
             if verbose:
                 print "err: %s" % err

From 738f1291f3ccf2321c26ad18e47fab4642ba96b9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 20 Aug 2015 07:59:23 +0200
Subject: [PATCH 1241/1356] take .lua into account in
 test_use_included_module_naming_scheme

---
 test/framework/options.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 6247fa21f5..1f030cb828 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1803,6 +1803,8 @@ def test_use_included_module_naming_scheme(self):
         args.append('--include-module-naming-schemes=%s/*.py' % self.test_prefix)
         self.eb_main(args, logfile=dummylogfn, do_build=True, raise_error=True, raise_systemexit=True, verbose=True)
         toy_mod = os.path.join(self.test_installpath, 'modules', 'all', 'toy', '0.0')
+        if get_module_syntax() == 'Lua':
+            toy_mod += '.lua'
         self.assertTrue(os.path.exists(toy_mod), "Found %s" % toy_mod)
 
     def test_include_toolchains(self):

From e439378ad5087b55b14db08842612e29a328a702 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 21 Aug 2015 10:15:56 +0200
Subject: [PATCH 1242/1356] clean up passing options to main()

---
 easybuild/main.py           | 11 +++++------
 test/framework/utilities.py |  6 +++---
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/easybuild/main.py b/easybuild/main.py
index bfa223975c..ecd146cc7c 100755
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -151,18 +151,17 @@ def build_and_install_software(ecs, init_session_state, exit_on_failure=True):
     return res
 
 
-def main(testing_data=(None, None, None)):
+def main(args=None, logfile=None, do_build=None, testing=False):
     """
     Main function: parse command line options, and act accordingly.
-    @param testing_data: tuple with command line arguments, log file and boolean indicating whether or not to build
+    @param args: command line arguments to use
+    @param logfile: log file to use
+    @param do_build: whether or not to actually perform the build
+    @param testing: enable testing mode
     """
     # purposely session state very early, to avoid modules loaded by EasyBuild meddling in
     init_session_state = session_state()
 
-    # steer behavior when testing main
-    testing = testing_data[0] is not None
-    args, logfile, do_build = testing_data
-
     # initialise options
     eb_go = eboptions.parse_options(args=args)
     options = eb_go.options
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 85fc642abb..0f6b125fde 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -189,7 +189,7 @@ def reset_modulepath(self, modpaths):
             modtool.add_module_path(modpath)
 
     def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbose=False, raise_error=False,
-                reset_env=True):
+                reset_env=True, testing=True):
         """Helper method to call EasyBuild main function."""
         cleanup()
 
@@ -205,7 +205,7 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
         env_before = copy.deepcopy(os.environ)
 
         try:
-            main((args, logfile, do_build))
+            main(args=args, logfile=logfile, do_build=do_build, testing=testing)
         except SystemExit:
             pass
         except Exception, err:
@@ -213,7 +213,7 @@ def eb_main(self, args, do_build=False, return_error=False, logfile=None, verbos
             if verbose:
                 print "err: %s" % err
 
-        if logfile:
+        if logfile and os.path.exists(logfile):
             logtxt = read_file(logfile)
         else:
             logtxt = None

From 799f578c8b3124c325ad2acf8794d9a30da461c6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 21 Aug 2015 10:16:26 +0200
Subject: [PATCH 1243/1356] reorganize cleanup()

---
 easybuild/tools/filetools.py | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 4b56ec6a28..e33ce3708d 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -929,25 +929,26 @@ def move_logs(src_logfile, target_logfile):
 
 
 def cleanup(logfile, tempdir, testing):
-    """Cleanup the specified log file and the tmp directory"""
-    if not build_option('cleanup_tmpdir'):
-        print_msg('Keeping temporary log file(s) and directory.', log=None, silent=testing)
-        return
+    """Cleanup the specified log file and the tmp directory, if desired."""
 
-    if not testing and logfile is not None:
-        try:
-            for log in glob.glob('%s*' % logfile):
-                os.remove(log)
-        except OSError, err:
-            raise EasyBuildError("Failed to remove log file(s) %s*: %s", logfile, err)
-        print_msg('temporary log file(s) %s* have been removed.' % (logfile), log=None, silent=testing)
+    if build_option('cleanup_tmpdir') and not testing:
+        if logfile is not None:
+            try:
+                for log in glob.glob('%s*' % logfile):
+                    os.remove(log)
+            except OSError, err:
+                raise EasyBuildError("Failed to remove log file(s) %s*: %s", logfile, err)
+            print_msg("Tmporary log file(s) %s* have been removed." % (logfile), log=None, silent=testing)
 
-    if not testing and tempdir is not None:
-        try:
-            shutil.rmtree(tempdir, ignore_errors=True)
-        except OSError, err:
-            raise EasyBuildError("Failed to remove temporary directory %s: %s", tempdir, err)
-        print_msg('temporary directory %s has been removed.' % (tempdir), log=None, silent=testing)
+        if tempdir is not None:
+            try:
+                shutil.rmtree(tempdir, ignore_errors=True)
+            except OSError, err:
+                raise EasyBuildError("Failed to remove temporary directory %s: %s", tempdir, err)
+            print_msg("Temporary directory %s has been removed." % tempdir, log=None, silent=testing)
+
+    else:
+        print_msg("Keeping temporary log file(s) %s* and directory %s." % (logfile, tempdir), log=None, silent=testing)
 
 
 def copytree(src, dst, symlinks=False, ignore=None):

From 3ac156e3637f19c451eac2cdeafaa5190ab3de6c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 21 Aug 2015 10:16:38 +0200
Subject: [PATCH 1244/1356] add unit test for --cleanup-tmpdir

---
 test/framework/options.py | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/test/framework/options.py b/test/framework/options.py
index 91f170eda3..837ccdfd07 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1815,6 +1815,38 @@ def test_include_toolchains(self):
         logtxt = read_file(self.logfile)
         self.assertTrue(tc_regex.search(logtxt), "Pattern '%s' *not* found in: %s" % (tc_regex.pattern, logtxt))
 
+    def test_cleanup_tmpdir(self):
+        """Test --cleanup-tmpdir."""
+
+        args = [
+            os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0.eb'),
+            '--dry-run',
+            '--try-software-version=1.0',  # so we get a tweaked easyconfig
+        ]
+
+        tmpdir = tempfile.gettempdir()
+        # just making sure this is empty before we get started
+        self.assertEqual(os.listdir(tmpdir), [])
+
+        # force silence (since we're not using testing mode)
+        self.mock_stdout(True)
+
+        # default: cleanup tmpdir & logfile
+        self.eb_main(args, raise_error=True, testing=False)
+        self.assertEqual(os.listdir(tmpdir), [])
+        self.assertFalse(os.path.exists(self.logfile))
+
+        # disable cleaning up tmpdir
+        args.append('--disable-cleanup-tmpdir')
+        self.eb_main(args, raise_error=True, testing=False)
+        tmpdir_files = os.listdir(tmpdir)
+        # tmpdir and logfile are still there \o/
+        self.assertTrue(len(tmpdir_files) == 1)
+        self.assertTrue(os.path.exists(self.logfile))
+        # tweaked easyconfigs is still there \o/
+        tweaked_dir = os.path.join(tmpdir, tmpdir_files[0], 'tweaked_easyconfigs')
+        self.assertTrue(os.path.exists(os.path.join(tweaked_dir, 'toy-1.0.eb')))
+
 
 def suite():
     """ returns all the testcases in this module """

From 09c4ea78a0f8059246dfecddcb073397f26333f4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 21 Aug 2015 12:44:24 +0200
Subject: [PATCH 1245/1356] fix remark

---
 easybuild/tools/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index e33ce3708d..ffc77b7458 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -934,7 +934,7 @@ def cleanup(logfile, tempdir, testing):
     if build_option('cleanup_tmpdir') and not testing:
         if logfile is not None:
             try:
-                for log in glob.glob('%s*' % logfile):
+                for log in [logfile] + glob.glob('%s.[0-9]*' % logfile):
                     os.remove(log)
             except OSError, err:
                 raise EasyBuildError("Failed to remove log file(s) %s*: %s", logfile, err)

From 5e9688c20e97f20b9e734adec83acd31ac54a247 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 31 Aug 2015 17:19:13 +0200
Subject: [PATCH 1246/1356] add support for extracting .iso files using 7z
 (p7zip)

---
 easybuild/tools/filetools.py | 3 +++
 test/framework/filetools.py  | 1 +
 2 files changed, 4 insertions(+)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index ffc77b7458..78aa8699d5 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -554,6 +554,9 @@ def extract_cmd(filepath, overwrite=False):
         else:
             cmd_tmpl = "unzip -qq %(filepath)s"
 
+    elif exts[-1] in ['iso']:
+        cmd_tmpl = "7z x %(filepath)s"
+
     if cmd_tmpl is None:
         raise EasyBuildError('Unknown file type for file %s (%s)', filepath, exts)
 
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index afedd291aa..59fbbd1b52 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -70,6 +70,7 @@ def test_extract_cmd(self):
             ('test.xz', "unxz test.xz"),
             ('test.tar.xz', "unxz test.tar.xz --stdout | tar x"),
             ('test.txz', "unxz test.txz --stdout | tar x"),
+            ('test.iso', "7z x test.iso"),
         ]
         for (fn, expected_cmd) in tests:
             cmd = ft.extract_cmd(fn)

From c98711b04cc55c21287f99917a88c5cdf8f94524 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 1 Sep 2015 21:33:35 +0200
Subject: [PATCH 1247/1356] bump version to 2.3.0 and update release notes

---
 RELEASE_NOTES              | 26 ++++++++++++++++++++++++++
 easybuild/tools/version.py |  2 +-
 2 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 4103cb3c8d..f2a1ab6d7b 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,6 +3,32 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
+v2.3.0 (September 2nd 2015)
+---------------------------
+
+feature + bugfix release
+- requires vsc-base v2.2.4 or more recent (#1343)
+    - required for mk_rst_table function in vsc.utils.docs
+- various other enhancements, including:
+    - add support for generating documentation for (generic) easyblocks in .rst format (#1317)
+    - preserve comments in easyconfig file in EasyConfig.dump() method (#1327)
+    - add --cleanup-tmpdir option (#1365)
+        - enables to preserve the used temporary directory via --disable-cleanup-tmpdir
+    - enhance EasyConfig.dump() to reformat dumped easyconfig according to style guidelines (#1345)
+    - add support for extracting .iso files using 7z (p7zip) (#1375)
+- various bug fixes, including:
+    - correctly deal with special characters in template strings in EasyConfig.dump() method (#1323)
+    - rework easybuild.tools.module_generator module to avoid keeping state w.r.t. fake modules (#1348)
+    - fix dumping of hidden deps (#1354)
+    - fix use of --job with hidden dependencies: include --hidden in submitted job script when needed (#1356)
+    - fix ActiveMNS.det_full_module_name() for external modules (#1360)
+    - fix EasyConfig.all_dependencies definition, fix tracking of job dependencies (#1359, #1361)
+    - fix 'ModulesTool.exist' for hidden Lua module files (#1364)
+    - only call EasyBlock.sanity_check_step for non-extensions (#1366)
+        - this results is significant speedup when installing easyconfigs with lots of extensions, but also
+          fixes checking the default sanity check paths if none were defined for extensions installed as a module
+    - fix using module naming schemes that were included via --include-module-naming-schemes (#1370)
+
 v2.2.0 (July 15th 2015)
 -----------------------
 
diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 5117cffb7d..8fbbb94ba9 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.3.0dev')
+VERSION = LooseVersion('2.3.0')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From 3f61602ecaef3e43fcc8c70eb8ed68614997dced Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 2 Sep 2015 07:32:30 +0200
Subject: [PATCH 1248/1356] fix typo

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index f2a1ab6d7b..d2650f96b1 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -25,7 +25,7 @@ feature + bugfix release
     - fix EasyConfig.all_dependencies definition, fix tracking of job dependencies (#1359, #1361)
     - fix 'ModulesTool.exist' for hidden Lua module files (#1364)
     - only call EasyBlock.sanity_check_step for non-extensions (#1366)
-        - this results is significant speedup when installing easyconfigs with lots of extensions, but also
+        - this results in significant speedup when installing easyconfigs with lots of extensions, but also
           fixes checking the default sanity check paths if none were defined for extensions installed as a module
     - fix using module naming schemes that were included via --include-module-naming-schemes (#1370)
 

From 1f897e777f74b8678934acea9e2c095d0e1b5b72 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 2 Sep 2015 08:40:29 +0200
Subject: [PATCH 1249/1356] minor rewording in release notes

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index d2650f96b1..6ce9d9ce17 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -26,7 +26,7 @@ feature + bugfix release
     - fix 'ModulesTool.exist' for hidden Lua module files (#1364)
     - only call EasyBlock.sanity_check_step for non-extensions (#1366)
         - this results in significant speedup when installing easyconfigs with lots of extensions, but also
-          fixes checking the default sanity check paths if none were defined for extensions installed as a module
+          results in checking the default sanity check paths if none were defined for extensions installed as a module
     - fix using module naming schemes that were included via --include-module-naming-schemes (#1370)
 
 v2.2.0 (July 15th 2015)

From c407580288fbd6a74179894cb59e82abd17345d4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 2 Sep 2015 12:54:50 +0200
Subject: [PATCH 1250/1356] bump version to 2.3.1dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 8fbbb94ba9..0b760216c4 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.3.0')
+VERSION = LooseVersion('2.3.1dev')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From 7f45f71554c681b8aecf55edd02770c0b3fd9ec2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 2 Sep 2015 12:55:29 +0200
Subject: [PATCH 1251/1356] bump version to 2.4.0dev

---
 easybuild/tools/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 0b760216c4..24b139d960 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,7 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.3.1dev')
+VERSION = LooseVersion('2.4.0dev')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From 87eb36781f6dc6b92caeb0fdf7e62b18b9d07331 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 3 Sep 2015 22:08:21 +0200
Subject: [PATCH 1252/1356] fix extracting of comments from an easyconfig file
 that includes 'tail' comments

---
 easybuild/framework/easyconfig/format/one.py | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/format/one.py b/easybuild/framework/easyconfig/format/one.py
index 4aa3adc768..cce947f3f8 100644
--- a/easybuild/framework/easyconfig/format/one.py
+++ b/easybuild/framework/easyconfig/format/one.py
@@ -272,6 +272,8 @@ def dump(self, ecfg, default_values, templ_const, templ_val):
         params, _ = self._find_defined_params(ecfg, [[k] for k in LAST_PARAMS], default_values, templ_const, templ_val)
         dump.extend(params)
 
+        dump.extend(self.comments['tail'])
+
         return '\n'.join(dump)
 
     def extract_comments(self, rawtxt):
@@ -286,6 +288,7 @@ def extract_comments(self, rawtxt):
             'header' : [],  # header comment lines
             'inline' : {},  # inline comments
             'iter': {},  # (inline) comments on elements of iterable values
+            'tail': [],
          }
 
         rawlines = rawtxt.split('\n')
@@ -301,13 +304,21 @@ def extract_comments(self, rawtxt):
             if rawline.startswith('#'):
                 comment = []
                 # comment could be multi-line
-                while rawline.startswith('#') or not rawline:
+                while rawline is not None and (rawline.startswith('#') or not rawline):
                     # drop empty lines (that don't even include a #)
                     if rawline:
                         comment.append(rawline)
-                    rawline = rawlines.pop(0)
-                key = rawline.split('=', 1)[0].strip()
-                self.comments['above'][key] = comment
+                    # grab next line (if more lines are left)
+                    if rawlines:
+                        rawline = rawlines.pop(0)
+                    else:
+                        rawline = None
+
+                if rawline is None:
+                    self.comments['tail'] = comment
+                else:
+                    key = rawline.split('=', 1)[0].strip()
+                    self.comments['above'][key] = comment
 
             elif '#' in rawline:  # inline comment
                 comment_key, comment_val = None, None

From 2def3b1f204019ee16ac12de42c9a861af35be40 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 4 Sep 2015 00:17:58 +0200
Subject: [PATCH 1253/1356] add tail comment in test easyconfig

---
 test/framework/easyconfig.py          | 2 +-
 test/framework/easyconfigs/toy-0.0.eb | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 5f304efaf4..a619224707 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -303,7 +303,7 @@ def test_exts_list(self):
             '       "patches": ["toy-0.0.eb"],',  # dummy patch to avoid downloading fail
             '       "checksums": [',
             '           "787393bfc465c85607a5b24486e861c5",',  # MD5 checksum for source (gzip-1.4.eb)
-            '           "ddd5161154f5db67701525123129ff09",',  # MD5 checksum for patch (toy-0.0.eb)
+            '           "44893c3ed46a7c7ab2e72fea7d19925d",',  # MD5 checksum for patch (toy-0.0.eb)
             '       ],',
             '   }),',
             ']',
diff --git a/test/framework/easyconfigs/toy-0.0.eb b/test/framework/easyconfigs/toy-0.0.eb
index 08f6303826..d3b5717f96 100644
--- a/test/framework/easyconfigs/toy-0.0.eb
+++ b/test/framework/easyconfigs/toy-0.0.eb
@@ -25,3 +25,4 @@ sanity_check_paths = {
 postinstallcmds = ["echo TOY > %(installdir)s/README"]
 
 moduleclass = 'tools'
+# trailing comment, leave this here, it may trigger bugs with extract_comments()

From 688ce45afaa6b4b86b5364f24af8703b4fd12733 Mon Sep 17 00:00:00 2001
From: sfranky <sfranky@gmail.com>
Date: Fri, 4 Sep 2015 02:31:51 +0300
Subject: [PATCH 1254/1356] refactored extract_cmd with switch and regex
 matching, for both single and double extensions (.gz vs .tar.gz)

---
 easybuild/tools/filetools.py | 87 ++++++++++++++----------------------
 1 file changed, 34 insertions(+), 53 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 78aa8699d5..d37626b9ba 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -33,6 +33,7 @@
 @author: Toon Willems (Ghent University)
 @author: Ward Poelmans (Ghent University)
 @author: Fotis Georgatos (Uni.Lu, NTUA)
+@author: Sotiris Fragkiskos (NTUA, CERN)
 """
 import glob
 import os
@@ -503,62 +504,42 @@ def get_local_dirs_purged():
 
 def extract_cmd(filepath, overwrite=False):
     """
-    Determines the file type of file fn, returns extract cmd
-    - based on file suffix
-    - better to use Python magic?
+    Determines the file type of file at filepath, returns extract cmd based on file suffix
     """
     filename = os.path.basename(filepath)
-    exts = [x.lower() for x in filename.split('.')]
-    target = '.'.join(exts[:-1])
-    cmd_tmpl = None
-
-    # gzipped or gzipped tarball
-    if exts[-1] in ['gz']:
-        if exts[-2] in ['tar']:
-            # unzip .tar.gz in one go
-            cmd_tmpl = "tar xzf %(filepath)s"
-        else:
-            cmd_tmpl = "gunzip -c %(filepath)s > %(target)s"
-
-    elif exts[-1] in ['tgz', 'gtgz']:
-        cmd_tmpl = "tar xzf %(filepath)s"
-
-    # bzipped or bzipped tarball
-    elif exts[-1] in ['bz2']:
-        if exts[-2] in ['tar']:
-            cmd_tmpl = 'tar xjf %(filepath)s'
-        else:
-            cmd_tmpl = "bunzip2 %(filepath)s"
-
-    elif exts[-1] in ['tbz', 'tbz2', 'tb2']:
-        cmd_tmpl = "tar xjf %(filepath)s"
-
-    # xzipped or xzipped tarball
-    elif exts[-1] in ['xz']:
-        if exts[-2] in ['tar']:
-            cmd_tmpl = "unxz %(filepath)s --stdout | tar x"
-        else:
-            cmd_tmpl = "unxz %(filepath)s"
-
-    elif exts[-1] in ['txz']:
-        cmd_tmpl = "unxz %(filepath)s --stdout | tar x"
-
-    # tarball
-    elif exts[-1] in ['tar']:
-        cmd_tmpl = "tar xf %(filepath)s"
-
-    # zip file
-    elif exts[-1] in ['zip']:
-        if overwrite:
-            cmd_tmpl = "unzip -qq -o %(filepath)s"
-        else:
-            cmd_tmpl = "unzip -qq %(filepath)s"
-
-    elif exts[-1] in ['iso']:
-        cmd_tmpl = "7z x %(filepath)s"
+    pat = r'\.(?P<ext>tar\.gz|gz|tgz|gtgz|tar.bz2|bz2|tbz|tbz2|tb2|tar.xz|xz|txz|tar|zip|iso)$'
+    try:
+        ext = '.' + re.search(pat, filename, flags=re.IGNORECASE).group('ext')
+    except AttributeError:
+        raise EasyBuildError('Unknown file type for file %s (%s)', filepath, ext)
+
+    target = filename.rstrip(ext)
+
+    extract_cmds = {
+        # gzipped or gzipped tarball
+        '.tar.gz':  "tar xzf %(filepath)s",
+        '.gz':      "gunzip -c %(filepath)s > %(target)s",
+        '.tgz':     "tar xzf %(filepath)s",
+        '.gtgz':    "tar xzf %(filepath)s",
+        # bzipped or bzipped tarball
+        '.tar.bz2': "tar xjf %(filepath)s",
+        '.bz2':     "bunzip2 %(filepath)s",
+        '.tbz':     "tar xjf %(filepath)s",
+        '.tbz2':    "tar xjf %(filepath)s",
+        '.tb2':     "tar xjf %(filepath)s",
+        # xzipped or xzipped tarball
+        '.tar.xz':  "unxz %(filepath)s --stdout | tar x",
+        '.xz':      "unxz %(filepath)s",
+        '.txz':     "unxz %(filepath)s --stdout | tar x",
+        # tarball
+        '.tar':     "tar xf %(filepath)s",
+        # zip file
+        '.zip':     "unzip -qq -o %(filepath)s" if overwrite else "unzip -qq %(filepath)s",
+        # iso file
+        '.iso':     "7z x %(filepath)s"
+    }
 
-    if cmd_tmpl is None:
-        raise EasyBuildError('Unknown file type for file %s (%s)', filepath, exts)
+    cmd_tmpl = extract_cmds[ext.lower()]
 
     return cmd_tmpl % {'filepath': filepath, 'target': target}
 

From be2c25af0bd32927a65a30866acf2ac242bb8db2 Mon Sep 17 00:00:00 2001
From: sfranky <sfranky@gmail.com>
Date: Fri, 4 Sep 2015 02:32:03 +0300
Subject: [PATCH 1255/1356] added test for capitalised extensions

---
 test/framework/filetools.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 59fbbd1b52..b887fc95a0 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -58,6 +58,7 @@ def test_extract_cmd(self):
             ('test.zip', "unzip -qq test.zip"),
             ('/some/path/test.tar', "tar xf /some/path/test.tar"),
             ('test.tar.gz', "tar xzf test.tar.gz"),
+            ('test.TAR.GZ', "tar xzf test.TAR.GZ"),
             ('test.tgz', "tar xzf test.tgz"),
             ('test.gtgz', "tar xzf test.gtgz"),
             ('test.bz2', "bunzip2 test.bz2"),
@@ -76,6 +77,8 @@ def test_extract_cmd(self):
             cmd = ft.extract_cmd(fn)
             self.assertEqual(expected_cmd, cmd)
 
+        self.assertEqual("unzip -qq -o test.zip", ft.extract_cmd('test.zip', True))
+
     def test_convert_name(self):
         """Test convert_name function."""
         name = ft.convert_name("test+test-test")

From 07989fe4da6a02a01498dcd00284a28f01df23f9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 4 Sep 2015 10:42:30 +0200
Subject: [PATCH 1256/1356] enhance test_dump_comments with trailing comment

---
 test/framework/easyconfig.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index a619224707..c4e2276635 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1343,6 +1343,7 @@ def test_dump_comments(self):
             '}',
             '',
             "foo_extra1 = 'foobar'",
+            "# trailing comment",
         ])
 
         handle, testec = tempfile.mkstemp(prefix=self.test_prefix, suffix='.eb')
@@ -1366,6 +1367,8 @@ def test_dump_comments(self):
             regex = re.compile(pattern, re.M)
             self.assertTrue(regex.search(ectxt), "Pattern '%s' found in: %s" % (regex.pattern, ectxt))
 
+        self.assertTrue(ectxt.endswith("# trailing comment"))
+
         # reparsing the dumped easyconfig file should work
         ecbis = EasyConfig(testec)
 

From 3ba70c1f65fa663ba3ab1083ceaff54070701505 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 5 Sep 2015 13:32:48 +0200
Subject: [PATCH 1257/1356] fix typo

---
 easybuild/tools/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 78aa8699d5..74c3a458b9 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -941,7 +941,7 @@ def cleanup(logfile, tempdir, testing):
                     os.remove(log)
             except OSError, err:
                 raise EasyBuildError("Failed to remove log file(s) %s*: %s", logfile, err)
-            print_msg("Tmporary log file(s) %s* have been removed." % (logfile), log=None, silent=testing)
+            print_msg("Temporary log file(s) %s* have been removed." % (logfile), log=None, silent=testing)
 
         if tempdir is not None:
             try:

From 2def9847bbc928a9c0b44c6b8b5937af7d27c996 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 7 Sep 2015 09:30:43 +0200
Subject: [PATCH 1258/1356] fix remarks

---
 easybuild/framework/easyconfig/tools.py | 57 +++++++++++--------------
 easybuild/main.py                       |  2 +-
 easybuild/tools/github.py               |  3 +-
 easybuild/tools/utilities.py            |  1 +
 4 files changed, 29 insertions(+), 34 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 1f90311952..13d3397cbb 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -373,24 +373,15 @@ def find_related_easyconfigs(path, ec):
     A list of easyconfigs for the same software (name) is returned,
     matching the 1st criterion that yields a non-empty list.
 
-    Software version is considered more important than toolchain.
+    The following criteria are considered (in this order) next to common software version criterion, i.e.
+    exact version match, a major/minor version match, a major version match, or no version match (in that order).
 
-    Toolchain is considered with exact same version prior to without version (only name).
-
-    Matching versionsuffix is considered prior to any versionsuffix.
-
-    Exact software version is considered prior to matching major/minor version numbers,
-    and only matching major version number. Any software version is considered last.
-
-    The following criteria are considered, in order (with 'version criterion' being either an
-    exact version match, a major/minor version match, a major version match, or no version match).
-
-    (i)   software version criterion, matching versionsuffix and toolchain name/version
-    (ii)  software version criterion, matching versionsuffix and toolchain name (any toolchain version)
-    (iii) software version criterion, matching versionsuffix (any toolchain name/version)
-    (iv)  software version criterion, matching toolchain name/version (any versionsuffix)
-    (v)   software version criterion, matching toolchain name (any versionsuffix, toolchain version)
-    (vi)  software version criterion (any versionsuffix, toolchain name/version)
+    (i)   matching versionsuffix and toolchain name/version
+    (ii)  matching versionsuffix and toolchain name (any toolchain version)
+    (iii) matching versionsuffix (any toolchain name/version)
+    (iv)  matching toolchain name/version (any versionsuffix)
+    (v)   matching toolchain name (any versionsuffix, toolchain version)
+    (vi)  no extra requirements (any versionsuffix, toolchain name/version)
 
     If no related easyconfigs with a matching software name are found, an empty list is returned.
     """
@@ -407,29 +398,30 @@ def find_related_easyconfigs(path, ec):
 
     potential_paths = [glob.glob(ec_path) for ec_path in create_paths(path, name, '*')]
     potential_paths = sum(potential_paths, [])  # flatten
+    _log.debug("found these potential paths: %s" % potential_paths)
 
     parsed_version = LooseVersion(version).version
     version_patterns = [version]  # exact version match
     if len(parsed_version) >= 2:
-        version_patterns.append(r'%s\.%s\.[0-9_A-Za-z]+' % tuple(parsed_version[:2]))  # major/minor version match
+        version_patterns.append(r'%s\.%s\.\w+' % tuple(parsed_version[:2]))  # major/minor version match
     if parsed_version != parsed_version[0]:
-        version_patterns.append(r'%s\.[0-9-]+\.[0-9_A-Za-z]+' % parsed_version[0])  # major version match
-    version_patterns.append(r'[0-9._A-Za-z-]+')  # any version
+        version_patterns.append(r'%s\.[\d-]+\.\w+' % parsed_version[0])  # major version match
+    version_patterns.append(r'[\w.]+')  # any version
 
     regexes = []
     for version_pattern in version_patterns:
+        common_pattern = r'^\S+/%s-%s%%s\.eb$' % (name, version_pattern)
         regexes.extend([
-            re.compile((r"^\S+/%s-%s%s%s.eb$" % (name, version_pattern, toolchain_pattern, versionsuffix))),
-            re.compile((r"^\S+/%s-%s%s%s.eb$" % (name, version_pattern, toolchain_name_pattern, versionsuffix))),
-            re.compile((r"^\S+/%s-%s-\S+%s.eb$" % (name, version_pattern, versionsuffix))),
-            re.compile((r"^\S+/%s-%s%s.eb$" % (name, version_pattern, toolchain_pattern))),
-            re.compile((r"^\S+/%s-%s%s.eb$" % (name, version_pattern, toolchain_name_pattern))),
-            re.compile((r"^\S+/%s-%s-\S+.eb$" % (name, version_pattern))),
+            common_pattern % (toolchain_pattern + versionsuffix),
+            common_pattern % (toolchain_name_pattern + versionsuffix),
+            common_pattern % (r'-\S+%s' % versionsuffix),
+            common_pattern % toolchain_pattern,
+            common_pattern % toolchain_name_pattern,
+            common_pattern % r'-\S+',
         ])
-    _log.debug("found these potential paths: %s" % potential_paths)
 
     for regex in regexes:
-        res = [p for p in potential_paths if regex.match(p)]
+        res = [p for p in potential_paths if re.match(regex, p)]
         if res:
             _log.debug("Related easyconfigs found using '%s': %s" % (regex.pattern, res))
             break
@@ -451,13 +443,14 @@ def review_pr(pr, colored=True, branch='develop'):
     repo_path = os.path.join(download_repo_path, 'easybuild', 'easyconfigs')
     pr_files = [path for path in fetch_easyconfigs_from_pr(pr) if path.endswith('.eb')]
 
+    lines = []
     ecs, _ = parse_easyconfigs([(fp, False) for fp in pr_files], validate=False)
     for ec in ecs:
         files = find_related_easyconfigs(repo_path, ec['ec'])
         _log.debug("File in PR#%s %s has these related easyconfigs: %s" % (pr, ec['spec'], files))
         if files:
-            diff = multidiff(ec['spec'], files, colored=colored)
-            msg = diff
+            lines.append(multidiff(ec['spec'], files, colored=colored))
         else:
-            msg = "\n(no related easyconfigs found for %s)\n" % os.path.basename(ec['spec'])
-        print(msg)
+            lines.extend(['', "(no related easyconfigs found for %s)\n" % os.path.basename(ec['spec'])])
+
+    return '\n'.join(lines)
diff --git a/easybuild/main.py b/easybuild/main.py
index e20028fb0a..68ccea97a4 100755
--- a/easybuild/main.py
+++ b/easybuild/main.py
@@ -233,7 +233,7 @@ def main(args=None, logfile=None, do_build=None, testing=False):
 
     # review specified PR
     if options.review_pr:
-        review_pr(options.review_pr, colored=options.color)
+        print review_pr(options.review_pr, colored=options.color)
 
     # search for easyconfigs, if a query is specified
     query = options.search or options.search_short
diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 6c6ea845d7..1d784bad79 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -176,7 +176,7 @@ def read(self, path, api=True):
         # https://raw.github.com/hpcugent/easybuild/master/README.rst
         if not api:
             outfile = tempfile.mkstemp()[1]
-            url = ("%s/%s/%s/%s/%s" % (GITHUB_RAW, self.githubuser, self.reponame, self.branchname, path))
+            url = '/'.join([GITHUB_RAW, self.githubuser, self.reponame, self.branchname, path])
             download_file(os.path.basename(path), url, outfile)
             return outfile
         else:
@@ -231,6 +231,7 @@ def fetch_latest_commit_sha(repo, account, branch='master'):
     for entry in data:
         if entry[u'name'] == branch:
             res = entry['commit']['sha']
+            break
 
     if res is None:
         raise EasyBuildError("No branch with name %s found in repo %s/%s (%s)", branch, account, repo, data)
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 28bd19f278..a9314fe592 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -132,5 +132,6 @@ def det_terminal_size():
     Determine the current size of the terminal window.
     @return: tuple with terminal width and height
     """
+    # see http://bytes.com/topic/python/answers/607757-getting-terminal-display-size
     height, width, _, _ = struct.unpack('HHHH', fcntl.ioctl(0, termios.TIOCGWINSZ, struct.pack('HHHH', 0, 0, 0, 0)))
     return width, height

From a787f6e6ce8decc6bad931d51966928504ff7ae2 Mon Sep 17 00:00:00 2001
From: sfranky <sfranky@gmail.com>
Date: Tue, 8 Sep 2015 01:10:25 +0300
Subject: [PATCH 1259/1356] fixed remarks, also added a best guess extension
 just before raising EasyBuildError, and removed '.' from '.' +
 res.group('ext') and from the beginning of the regex

---
 easybuild/tools/filetools.py | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index d37626b9ba..fd335414a5 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -507,30 +507,23 @@ def extract_cmd(filepath, overwrite=False):
     Determines the file type of file at filepath, returns extract cmd based on file suffix
     """
     filename = os.path.basename(filepath)
-    pat = r'\.(?P<ext>tar\.gz|gz|tgz|gtgz|tar.bz2|bz2|tbz|tbz2|tb2|tar.xz|xz|txz|tar|zip|iso)$'
-    try:
-        ext = '.' + re.search(pat, filename, flags=re.IGNORECASE).group('ext')
-    except AttributeError:
-        raise EasyBuildError('Unknown file type for file %s (%s)', filepath, ext)
-
-    target = filename.rstrip(ext)
 
     extract_cmds = {
         # gzipped or gzipped tarball
-        '.tar.gz':  "tar xzf %(filepath)s",
         '.gz':      "gunzip -c %(filepath)s > %(target)s",
-        '.tgz':     "tar xzf %(filepath)s",
         '.gtgz':    "tar xzf %(filepath)s",
+        '.tar.gz':  "tar xzf %(filepath)s",
+        '.tgz':     "tar xzf %(filepath)s",
         # bzipped or bzipped tarball
-        '.tar.bz2': "tar xjf %(filepath)s",
         '.bz2':     "bunzip2 %(filepath)s",
+        '.tar.bz2': "tar xjf %(filepath)s",
+        '.tb2':     "tar xjf %(filepath)s",
         '.tbz':     "tar xjf %(filepath)s",
         '.tbz2':    "tar xjf %(filepath)s",
-        '.tb2':     "tar xjf %(filepath)s",
         # xzipped or xzipped tarball
         '.tar.xz':  "unxz %(filepath)s --stdout | tar x",
-        '.xz':      "unxz %(filepath)s",
         '.txz':     "unxz %(filepath)s --stdout | tar x",
+        '.xz':      "unxz %(filepath)s",
         # tarball
         '.tar':     "tar xf %(filepath)s",
         # zip file
@@ -538,6 +531,15 @@ def extract_cmd(filepath, overwrite=False):
         # iso file
         '.iso':     "7z x %(filepath)s"
     }
+    pat = r'(?P<ext>%s)$' % '|'.join([ext.replace('.', '\\.') for ext in sorted(extract_cmds.keys(), key=len, reverse=True)])
+    res = re.search(pat, filename, flags=re.IGNORECASE)
+    if res:
+        ext = res.group('ext')
+    else:
+        ext = filename.split('.')[-1]  # best guess?
+        raise EasyBuildError('Unknown file type for file %s (%s)', filepath, ext)
+
+    target = filename.rstrip(ext)
 
     cmd_tmpl = extract_cmds[ext.lower()]
 

From 0f56a13deb59e09552a31e5a48e3c66bb955f264 Mon Sep 17 00:00:00 2001
From: sfranky <sfranky@gmail.com>
Date: Wed, 9 Sep 2015 02:26:44 +0300
Subject: [PATCH 1260/1356] addressed fgeorgatos comments in #1382

---
 easybuild/tools/filetools.py | 4 +++-
 test/framework/filetools.py  | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index fd335414a5..abb37d5b21 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -531,7 +531,9 @@ def extract_cmd(filepath, overwrite=False):
         # iso file
         '.iso':     "7z x %(filepath)s"
     }
-    pat = r'(?P<ext>%s)$' % '|'.join([ext.replace('.', '\\.') for ext in sorted(extract_cmds.keys(), key=len, reverse=True)])
+
+    suffixes = sorted(extract_cmds.keys(), key=len, reverse=True)
+    pat = r'(?P<ext>%s)$' % '|'.join([ext.replace('.', '\\.') for ext in suffixes])
     res = re.search(pat, filename, flags=re.IGNORECASE)
     if res:
         ext = res.group('ext')
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index b887fc95a0..74fd071a10 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -67,6 +67,7 @@ def test_extract_cmd(self):
             ('test.tb2', "tar xjf test.tb2"),
             ('test.tar.bz2', "tar xjf test.tar.bz2"),
             ('test.gz', "gunzip -c test.gz > test"),
+            ('untar.gz', "gunzip -c untar.gz > untar"),
             ("/some/path/test.gz", "gunzip -c /some/path/test.gz > test"),
             ('test.xz', "unxz test.xz"),
             ('test.tar.xz', "unxz test.tar.xz --stdout | tar x"),

From 70de7fe97dab2d5a634bd2b187c76deb80063eef Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Sep 2015 14:43:55 +0200
Subject: [PATCH 1261/1356] fix debug log statements w.r.t. regex

---
 easybuild/framework/easyconfig/tools.py |  4 +--
 easybuild/toolchains/intel-taito.py     | 36 +++++++++++++++++++++++++
 2 files changed, 38 insertions(+), 2 deletions(-)
 create mode 100644 easybuild/toolchains/intel-taito.py

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 13d3397cbb..b4a56f1e92 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -423,10 +423,10 @@ def find_related_easyconfigs(path, ec):
     for regex in regexes:
         res = [p for p in potential_paths if re.match(regex, p)]
         if res:
-            _log.debug("Related easyconfigs found using '%s': %s" % (regex.pattern, res))
+            _log.debug("Related easyconfigs found using '%s': %s" % (regex, res))
             break
         else:
-            _log.debug("No related easyconfigs in potential paths using '%s'" % regex.pattern)
+            _log.debug("No related easyconfigs in potential paths using '%s'" % regex)
     return res
 
 
diff --git a/easybuild/toolchains/intel-taito.py b/easybuild/toolchains/intel-taito.py
new file mode 100644
index 0000000000..64ffd5d411
--- /dev/null
+++ b/easybuild/toolchains/intel-taito.py
@@ -0,0 +1,36 @@
+from easybuild.toolchains.intel import Intel
+
+METADATA_BY_VERSION = {
+    '15.0.2': {
+        'prefixes': {
+            'GCC': '/appl/opt/gcc/4.9.2',
+            'icc': '/appl/opt/cluster_studio_xe2015/composer_xe_2015.2.164',
+            'ifort': '/appl/opt/cluster_studio_xe2015/composer_xe_2015.2.164',
+            'imkl': '/appl/opt/cluster_studio_xe2015/composer_xe_2015.2.164',
+            'impi': '/appl/opt/cluster_studio_xe2015/composer_xe_2015.2.164',
+        },
+        'versions': {
+            'GCC': '4.9.2',
+            'icc': '2015.2.164',
+            'ifort': '2015.2.164',
+            'imkl': '11.2.2.164',
+            'impi': '???',  # FIXME
+        }
+    }
+}
+
+class IntelTaito(Intel):
+    NAME = 'intel'
+    COMPILER_MODULE_NAME = []
+    MPI_MODULE_NAME = []
+    BLAS_MODULE_NAME = []
+    LAPACK_MODULE_NAME = []
+    SCALAPACK_MODULE_NAME = []
+
+    def _get_software_root(self, name):
+        """Get install prefix for specified software name"""
+        # TODO
+
+    def _get_software_version(self, name):
+        """Get install prefix for specified software name"""
+        # TODO

From 58e1aeb3b4b897363074e2b5d892fd7f9bf27e59 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Sep 2015 16:28:31 +0200
Subject: [PATCH 1262/1356] fix patterns without toolchain name/version
 (exclude '-', use *)

---
 easybuild/framework/easyconfig/tools.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index b4a56f1e92..7d833cf747 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -390,8 +390,7 @@ def find_related_easyconfigs(path, ec):
     versionsuffix = ec['versionsuffix']
     toolchain_name = ec['toolchain']['name']
     toolchain_name_pattern = r'-%s-\S+' % toolchain_name
-    toolchain = "%s-%s" % (toolchain_name, ec['toolchain']['version'])
-    toolchain_pattern = '-%s' % toolchain
+    toolchain_pattern = '-%s-%s' % (toolchain_name, ec['toolchain']['version'])
     if toolchain_name == DUMMY_TOOLCHAIN_NAME:
         toolchain_name_pattern = ''
         toolchain_pattern = ''
@@ -414,10 +413,10 @@ def find_related_easyconfigs(path, ec):
         regexes.extend([
             common_pattern % (toolchain_pattern + versionsuffix),
             common_pattern % (toolchain_name_pattern + versionsuffix),
-            common_pattern % (r'-\S+%s' % versionsuffix),
+            common_pattern % (r'\S*%s' % versionsuffix),
             common_pattern % toolchain_pattern,
             common_pattern % toolchain_name_pattern,
-            common_pattern % r'-\S+',
+            common_pattern % r'\S*',
         ])
 
     for regex in regexes:
@@ -427,6 +426,7 @@ def find_related_easyconfigs(path, ec):
             break
         else:
             _log.debug("No related easyconfigs in potential paths using '%s'" % regex)
+
     return res
 
 

From 47e2e1ccbcc9c7203296d29fd4727d63172f5175 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Sep 2015 16:28:53 +0200
Subject: [PATCH 1263/1356] add unit test for find_related_easyconfigs

---
 test/framework/easyconfig.py | 45 +++++++++++++++++++++++++++++++++++-
 1 file changed, 44 insertions(+), 1 deletion(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index c4e2276635..1a6e5f3885 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -48,7 +48,7 @@
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.templates import to_template_str
-from easybuild.framework.easyconfig.tools import dep_graph, parse_easyconfigs
+from easybuild.framework.easyconfig.tools import dep_graph, find_related_easyconfigs, parse_easyconfigs
 from easybuild.framework.easyconfig.tweak import obtain_ec_for, tweak_one
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import module_classes
@@ -1448,6 +1448,49 @@ def test_ActiveMNS_det_full_module_name(self):
         self.assertEqual(ActiveMNS().det_full_module_name(hiddendep), 'toy/.0.0-deps')
         self.assertEqual(ActiveMNS().det_full_module_name(hiddendep, force_visible=True), 'toy/0.0-deps')
 
+    def test_find_related_easyconfigs(self):
+        """Test find_related_easyconfigs function."""
+        test_easyconfigs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        ec_file = os.path.join(test_easyconfigs, 'GCC-4.6.3.eb')
+        ec = EasyConfig(ec_file)
+
+        # exact match: GCC-4.6.3.eb
+        res = [os.path.basename(x) for x in find_related_easyconfigs(test_easyconfigs, ec)]
+        self.assertEqual(res, ['GCC-4.6.3.eb'])
+
+        # tweak version to 4.6.1, GCC/4.6.x easyconfigs are found as closest match
+        ec['version'] = '4.6.1'
+        res = [os.path.basename(x) for x in find_related_easyconfigs(test_easyconfigs, ec)]
+        self.assertEqual(res, ['GCC-4.6.3.eb', 'GCC-4.6.4.eb'])
+
+        # tweak version to 4.5.0, GCC/4.x easyconfigs are found as closest match
+        ec['version'] = '4.5.0'
+        res = [os.path.basename(x) for x in find_related_easyconfigs(test_easyconfigs, ec)]
+        expected = ['GCC-4.6.3.eb', 'GCC-4.6.4.eb', 'GCC-4.7.2.eb', 'GCC-4.8.2.eb', 'GCC-4.8.3.eb', 'GCC-4.9.2.eb']
+        self.assertEqual(res, expected)
+
+        ec_file = os.path.join(test_easyconfigs, 'toy-0.0-deps.eb')
+        ec = EasyConfig(ec_file)
+
+        # exact match
+        res = [os.path.basename(x) for x in find_related_easyconfigs(test_easyconfigs, ec)]
+        self.assertEqual(res, ['toy-0.0-deps.eb'])
+
+        # tweak toolchain name/version and versionsuffix => closest match with same toolchain name is found
+        ec['toolchain'] = {'name': 'gompi', 'version': '1.5.16'}
+        ec['versionsuffix'] = '-foobar'
+        res = [os.path.basename(x) for x in find_related_easyconfigs(test_easyconfigs, ec)]
+        self.assertEqual(res, ['toy-0.0-gompi-1.3.12-test.eb'])
+
+        # restore original versionsuffix => matching versionsuffix wins over matching toolchain (name)
+        ec['versionsuffix'] = '-deps'
+        res = [os.path.basename(x) for x in find_related_easyconfigs(test_easyconfigs, ec)]
+        self.assertEqual(res, ['toy-0.0-deps.eb'])
+
+        # no matches for unknown software name
+        ec['name'] = 'nosuchsoftware'
+        self.assertEqual(find_related_easyconfigs(test_easyconfigs, ec), [])
+
 
 def suite():
     """ returns all the testcases in this module """

From 945dd2e0b4bd6afe211ce09d9568b3c5da8290f1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Sep 2015 17:18:06 +0200
Subject: [PATCH 1264/1356] move det_terminal_size to systemtools.py

---
 easybuild/tools/multidiff.py   |  2 +-
 easybuild/tools/systemtools.py | 13 +++++++++++++
 easybuild/tools/utilities.py   | 13 -------------
 3 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/easybuild/tools/multidiff.py b/easybuild/tools/multidiff.py
index e145d6bb39..fd46ff44c1 100644
--- a/easybuild/tools/multidiff.py
+++ b/easybuild/tools/multidiff.py
@@ -36,7 +36,7 @@
 
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import read_file
-from easybuild.tools.utilities import det_terminal_size
+from easybuild.tools.systemtools import det_terminal_size
 
 
 SEP_WIDTH = 5
diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index e3bd6316e9..d3b9987e7b 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -28,12 +28,15 @@
 @author: Jens Timmerman (Ghent University)
 @auther: Ward Poelmans (Ghent University)
 """
+import fcntl
 import grp  # @UnresolvedImport
 import os
 import platform
 import pwd
 import re
+import struct
 import sys
+import termios
 from socket import gethostname
 from vsc.utils import fancylogger
 from vsc.utils.affinity import sched_getaffinity
@@ -499,3 +502,13 @@ def det_parallelism(par, maxpar):
         par = min(par, maxpar)
 
     return par
+
+
+def det_terminal_size():
+    """
+    Determine the current size of the terminal window.
+    @return: tuple with terminal width and height
+    """
+    # see http://bytes.com/topic/python/answers/607757-getting-terminal-display-size
+    height, width, _, _ = struct.unpack('HHHH', fcntl.ioctl(0, termios.TIOCGWINSZ, struct.pack('HHHH', 0, 0, 0, 0)))
+    return width, height
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index a9314fe592..555081d60e 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -27,13 +27,10 @@
 
 @author: Kenneth Hoste (Ghent University)
 """
-import fcntl
 import glob
 import os
 import string
-import struct
 import sys
-import termios
 from vsc.utils import fancylogger
 
 import easybuild.tools.environment as env
@@ -125,13 +122,3 @@ def import_available_modules(namespace):
                     raise EasyBuildError("import_available_modules: Failed to import %s: %s", modpath, err)
                 modules.append(mod)
     return modules
-
-
-def det_terminal_size():
-    """
-    Determine the current size of the terminal window.
-    @return: tuple with terminal width and height
-    """
-    # see http://bytes.com/topic/python/answers/607757-getting-terminal-display-size
-    height, width, _, _ = struct.unpack('HHHH', fcntl.ioctl(0, termios.TIOCGWINSZ, struct.pack('HHHH', 0, 0, 0, 0)))
-    return width, height

From 669f63bf866e158a1975e2ca2170ae14157b8152 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Sep 2015 17:20:52 +0200
Subject: [PATCH 1265/1356] add unit test for det_terminal_size

---
 test/framework/systemtools.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index 0bda1e2e2c..4b6558cc49 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -427,6 +427,13 @@ def test_det_parallelism_mocked(self):
 
         st.get_avail_core_count = orig_get_avail_core_count
 
+    def test_det_terminal_size(self):
+        """Test det_terminal_size function."""
+        (width, height) = st.det_terminal_size()
+        self.assertTrue(isinstance(width, int) and width > 0)
+        self.assertTrue(isinstance(height, int) and height > 0)
+
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(SystemToolsTest)

From 082cfc808361352817a329adbb3332e97d1e4ffa Mon Sep 17 00:00:00 2001
From: sfranky <sfranky@gmail.com>
Date: Wed, 9 Sep 2015 19:59:28 +0300
Subject: [PATCH 1266/1356] addressed fgeorgatos comments in #1382

---
 easybuild/tools/filetools.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index abb37d5b21..592d25face 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -510,8 +510,8 @@ def extract_cmd(filepath, overwrite=False):
 
     extract_cmds = {
         # gzipped or gzipped tarball
-        '.gz':      "gunzip -c %(filepath)s > %(target)s",
         '.gtgz':    "tar xzf %(filepath)s",
+        '.gz':      "gunzip -c %(filepath)s > %(target)s",
         '.tar.gz':  "tar xzf %(filepath)s",
         '.tgz':     "tar xzf %(filepath)s",
         # bzipped or bzipped tarball
@@ -538,8 +538,7 @@ def extract_cmd(filepath, overwrite=False):
     if res:
         ext = res.group('ext')
     else:
-        ext = filename.split('.')[-1]  # best guess?
-        raise EasyBuildError('Unknown file type for file %s (%s)', filepath, ext)
+        raise EasyBuildError('Unknown file type for file %s', filename)
 
     target = filename.rstrip(ext)
 

From 60fdae0015c8cd05d61884f4c270fa2e29af713e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Sep 2015 19:48:35 +0200
Subject: [PATCH 1267/1356] add unit test for multidiff function

---
 test/framework/filetools.py | 69 +++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 59fbbd1b52..718db81fc3 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -39,6 +39,7 @@
 
 import easybuild.tools.filetools as ft
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.multidiff import multidiff
 
 
 class FileToolsTest(EnhancedTestCase):
@@ -350,6 +351,74 @@ def test_move_logs(self):
         self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log')), 'moarbar')
         self.assertEqual(ft.read_file(os.path.join(self.test_prefix, 'bar.log.1')), 'evenmoarbar')
 
+    def test_multidiff(self):
+        """Test multidiff function."""
+        test_easyconfigs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
+        other_toy_ecs = [
+            os.path.join(test_easyconfigs, 'toy-0.0-deps.eb'),
+            os.path.join(test_easyconfigs, 'toy-0.0-gompi-1.3.12-test.eb'),
+        ]
+
+        # default (colored)
+        lines = multidiff(os.path.join(test_easyconfigs, 'toy-0.0.eb'), other_toy_ecs).split('\n')
+        expected = "Comparing \x1b[0;35mtoy-0.0.eb\x1b[0m with toy-0.0-deps.eb, toy-0.0-gompi-1.3.12-test.eb"
+
+        red = "\x1b[0;41m"
+        green = "\x1b[0;42m"
+        endcol = "\x1b[0m"
+
+        self.assertEqual(lines[0], expected)
+        self.assertEqual(lines[1], "=====")
+
+        # different versionsuffix
+        self.assertEqual(lines[2], "3 %s- versionsuffix = '-test'%s (1/2) toy-0.0-gompi-1.3.12-test.eb" % (red, endcol))
+        self.assertEqual(lines[3], "3 %s- versionsuffix = '-deps'%s (1/2) toy-0.0-deps.eb" % (red, endcol))
+
+        # different toolchain in toy-0.0-gompi-1.3.12-test: '+' line (removed chars in toolchain name/version, in red)
+        expected = "7 %(endcol)s-%(endcol)s toolchain = {"
+        expected += "'name': '%(endcol)s%(red)sgo%(endcol)sm\x1b[0m%(red)spi%(endcol)s', "
+        expected += "'version': '%(endcol)s%(red)s1.3.12%(endcol)s'} (1/2) toy-0.0-gompi-1.3.12-test.eb"
+        expected = expected % {'endcol': endcol, 'green': green, 'red': red}
+        self.assertEqual(lines[7], expected)
+        # different toolchain in toy-0.0-gompi-1.3.12-test: '+' line (added chars in toolchain name/version, in green)
+        expected = "7 %(endcol)s+%(endcol)s toolchain = {"
+        expected += "'name': '%(endcol)s%(green)sdu%(endcol)sm\x1b[0m%(green)smy%(endcol)s', "
+        expected += "'version': '%(endcol)s%(green)sdummy%(endcol)s'} (1/2) toy-0.0-gompi-1.3.12-test.eb"
+        expected = expected % {'endcol': endcol, 'green': green, 'red': red}
+        self.assertEqual(lines[8], expected)
+
+        # no postinstallcmds in toy-0.0-deps.eb
+        expected = "25 %s+ postinstallcmds = [\"echo TOY > %%(installdir)s/README\"]%s" % (green, endcol)
+        expected += " (1/2) toy-0.0-deps.eb"
+        self.assertTrue(expected in lines)
+        self.assertTrue("26 %s+%s (1/2) toy-0.0-deps.eb" % (green, endcol) in lines)
+        self.assertEqual(lines[-1], "=====")
+
+        lines = multidiff(os.path.join(test_easyconfigs, 'toy-0.0.eb'), other_toy_ecs, colored=False).split('\n')
+        self.assertEqual(lines[0], "Comparing toy-0.0.eb with toy-0.0-deps.eb, toy-0.0-gompi-1.3.12-test.eb")
+        self.assertEqual(lines[1], "=====")
+
+        # different versionsuffix
+        self.assertEqual(lines[2], "3 - versionsuffix = '-test' (1/2) toy-0.0-gompi-1.3.12-test.eb")
+        self.assertEqual(lines[3], "3 - versionsuffix = '-deps' (1/2) toy-0.0-deps.eb")
+
+        # different toolchain in toy-0.0-gompi-1.3.12-test: '+' line with squigly line underneath to mark removed chars
+        expected = "7 - toolchain = {'name': 'gompi', 'version': '1.3.12'} (1/2) toy-0.0-gompi-1.3.12-test.eb"
+        self.assertEqual(lines[7], expected)
+        expected = "  ?                       ^^ ^^               ^^^^^^"
+        self.assertEqual(lines[8], expected)
+        # different toolchain in toy-0.0-gompi-1.3.12-test: '-' line with squigly line underneath to mark added chars
+        expected = "7 + toolchain = {'name': 'dummy', 'version': 'dummy'} (1/2) toy-0.0-gompi-1.3.12-test.eb"
+        self.assertEqual(lines[9], expected)
+        expected = "  ?                       ^^ ^^               ^^^^^"
+        self.assertEqual(lines[10], expected)
+
+        # no postinstallcmds in toy-0.0-deps.eb
+        self.assertTrue("25 + postinstallcmds = [\"echo TOY > %(installdir)s/README\"] (1/2) toy-0.0-deps.eb" in lines)
+        self.assertTrue("26 + (1/2) toy-0.0-deps.eb" in lines)
+
+        self.assertEqual(lines[-1], "=====")
+
 
 def suite():
     """ returns all the testcases in this module """

From b12c7e6272b9905bf58b8694e793901315b8d7fe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Sep 2015 20:03:59 +0200
Subject: [PATCH 1268/1356] fix bugs in download_repo

---
 easybuild/tools/github.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/github.py b/easybuild/tools/github.py
index 1d784bad79..f6d0705b42 100644
--- a/easybuild/tools/github.py
+++ b/easybuild/tools/github.py
@@ -255,15 +255,15 @@ def download_repo(repo=GITHUB_EASYCONFIGS_REPO, branch='master', account=GITHUB_
     path = os.path.join(path, account)
     mkdir(path, parents=True)
 
-    extracted_dir_name = '%s-%s' % (GITHUB_EASYCONFIGS_REPO, branch)
+    extracted_dir_name = '%s-%s' % (repo, branch)
     base_name = '%s.tar.gz' % branch
     latest_commit_sha = fetch_latest_commit_sha(repo, account, branch)
 
     expected_path = os.path.join(path, extracted_dir_name)
     latest_sha_path = os.path.join(expected_path, 'latest-sha')
 
-    # check if directory already exists, don't download if it does
-    if os.path.isdir(expected_path):
+    # check if directory already exists, don't download if 'latest-sha' file indicates that it's up to date
+    if os.path.exists(latest_sha_path):
         sha = read_file(latest_sha_path).split('\n')[0].rstrip()
         if latest_commit_sha == sha:
             _log.debug("Not redownloading %s/%s as it already exists: %s" % (account, repo, expected_path))

From f9bd146a42c2fd4dcaafd9b8dd2417e828fc4d43 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Sep 2015 20:04:32 +0200
Subject: [PATCH 1269/1356] add tests for fetch_latest_commit_sha and
 download_repo functions in github.py

---
 test/framework/github.py | 51 ++++++++++++++++++++++++++++++++++++----
 1 file changed, 46 insertions(+), 5 deletions(-)

diff --git a/test/framework/github.py b/test/framework/github.py
index 819b1d9a6e..2d6b8ca347 100644
--- a/test/framework/github.py
+++ b/test/framework/github.py
@@ -29,6 +29,7 @@
 """
 
 import os
+import re
 import shutil
 import tempfile
 from test.framework.utilities import EnhancedTestCase
@@ -36,7 +37,8 @@
 from urllib2 import URLError
 
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.github import Githubfs, fetch_github_token, fetch_easyconfigs_from_pr
+from easybuild.tools.filetools import read_file, write_file
+import easybuild.tools.github as gh
 
 
 # test account, for which a token is available
@@ -56,11 +58,11 @@ class GithubTest(EnhancedTestCase):
     def setUp(self):
         """setup"""
         super(GithubTest, self).setUp()
-        self.github_token = fetch_github_token(GITHUB_TEST_ACCOUNT)
+        self.github_token = gh.fetch_github_token(GITHUB_TEST_ACCOUNT)
         if self.github_token is None:
             self.ghfs = None
         else:
-            self.ghfs = Githubfs(GITHUB_USER, GITHUB_REPO, GITHUB_BRANCH, GITHUB_TEST_ACCOUNT, None, self.github_token)
+            self.ghfs = gh.Githubfs(GITHUB_USER, GITHUB_REPO, GITHUB_BRANCH, GITHUB_TEST_ACCOUNT, None, self.github_token)
 
     def test_walk(self):
         """test the gitubfs walk function"""
@@ -111,19 +113,58 @@ def test_fetch_easyconfigs_from_pr(self):
         all_ecs = ['gzip-1.6-ictce-6.2.5.eb', 'icc-2013_sp1.2.144.eb', 'ictce-6.2.5.eb', 'ifort-2013_sp1.2.144.eb',
                    'imkl-11.1.2.144.eb', 'impi-4.1.3.049.eb']
         try:
-            ec_files = fetch_easyconfigs_from_pr(726, path=tmpdir, github_user=GITHUB_TEST_ACCOUNT)
+            ec_files = gh.fetch_easyconfigs_from_pr(726, path=tmpdir, github_user=GITHUB_TEST_ACCOUNT)
             self.assertEqual(all_ecs, sorted([os.path.basename(f) for f in ec_files]))
             self.assertEqual(all_ecs, sorted(os.listdir(tmpdir)))
 
             # PR for EasyBuild v1.13.0 release (250+ commits, 218 files changed)
             err_msg = "PR #897 contains more than .* commits, can't obtain last commit"
-            self.assertErrorRegex(EasyBuildError, err_msg, fetch_easyconfigs_from_pr, 897, github_user=GITHUB_TEST_ACCOUNT)
+            self.assertErrorRegex(EasyBuildError, err_msg, gh.fetch_easyconfigs_from_pr, 897,
+                                  github_user=GITHUB_TEST_ACCOUNT)
 
         except URLError, err:
             print "Ignoring URLError '%s' in test_fetch_easyconfigs_from_pr" % err
 
         shutil.rmtree(tmpdir)
 
+    def test_fetch_latest_commit_sha(self):
+        """Test fetch_latest_commit_sha function."""
+        sha = gh.fetch_latest_commit_sha('easybuild-framework', 'hpcugent')
+        self.assertTrue(re.match('^[0-9a-f]{40}$', sha))
+        sha = gh.fetch_latest_commit_sha('easybuild-easyblocks', 'hpcugent', branch='develop')
+        self.assertTrue(re.match('^[0-9a-f]{40}$', sha))
+
+    def test_download_repo(self):
+        """Test download_repo function."""
+        # default: download tarball for master branch of hpcugent/easybuild-easyconfigs repo
+        path = gh.download_repo(path=self.test_prefix)
+        repodir = os.path.join(self.test_prefix, 'hpcugent', 'easybuild-easyconfigs-master')
+        self.assertTrue(os.path.samefile(path, repodir))
+        self.assertTrue(os.path.exists(repodir))
+        shafile = os.path.join(repodir, 'latest-sha')
+        self.assertTrue(re.match('^[0-9a-f]{40}$', read_file(shafile)))
+        self.assertTrue(os.path.exists(os.path.join(repodir, 'easybuild', 'easyconfigs', 'f', 'foss', 'foss-2015a.eb')))
+
+        # existing downloaded repo is not reperformed, except if SHA is different
+        account, repo, branch = 'boegel', 'easybuild-easyblocks', 'develop'
+        repodir = os.path.join(self.test_prefix, account, '%s-%s' % (repo, branch))
+        latest_sha = gh.fetch_latest_commit_sha(repo, account, branch=branch)
+
+        # put 'latest-sha' fail in place, check whether repo was (re)downloaded (should not)
+        shafile = os.path.join(repodir, 'latest-sha')
+        write_file(shafile, latest_sha)
+        path = gh.download_repo(repo=repo, branch=branch, account=account, path=self.test_prefix)
+        self.assertTrue(os.path.samefile(path, repodir))
+        self.assertEqual(os.listdir(repodir), ['latest-sha'])
+
+        # remove 'latest-sha' file and verify that download was performed
+        os.remove(shafile)
+        path = gh.download_repo(repo=repo, branch=branch, account=account, path=self.test_prefix)
+        self.assertTrue(os.path.samefile(path, repodir))
+        self.assertTrue('easybuild' in os.listdir(repodir))
+        self.assertTrue(re.match('^[0-9a-f]{40}$', read_file(shafile)))
+        self.assertTrue(os.path.exists(os.path.join(repodir, 'easybuild', 'easyblocks', '__init__.py')))
+
 
 def suite():
     """ returns all the testcases in this module """

From d88c3c2a826513a9b9a3700dbc2211fe9651de53 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 9 Sep 2015 20:24:10 +0200
Subject: [PATCH 1270/1356] add unit test for --review-pr

---
 test/framework/options.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 05f0df6ef9..64b8644d02 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -1860,7 +1860,6 @@ def test_include_toolchains(self):
 
     def test_cleanup_tmpdir(self):
         """Test --cleanup-tmpdir."""
-
         args = [
             os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0.eb'),
             '--dry-run',
@@ -1890,6 +1889,15 @@ def test_cleanup_tmpdir(self):
         tweaked_dir = os.path.join(tmpdir, tmpdir_files[0], 'tweaked_easyconfigs')
         self.assertTrue(os.path.exists(os.path.join(tweaked_dir, 'toy-1.0.eb')))
 
+    def test_review_pr(self):
+        """Test --review-pr."""
+        self.mock_stdout(True)
+        # PR for zlib 1.2.8 easyconfig, see https://github.com/hpcugent/easybuild-easyconfigs/pull/1484
+        self.eb_main(['--review-pr=1484', '--disable-color'], raise_error=True)
+        txt = self.get_stdout()
+        self.mock_stdout(False)
+        self.assertTrue(re.search(r"^Comparing zlib-1.2.8\S* with zlib-1.2.8", txt))
+
 
 def suite():
     """ returns all the testcases in this module """

From d73130068ce84a34f6b96a40a83e7c00e64b6f5a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 10 Sep 2015 10:26:42 +0200
Subject: [PATCH 1271/1356] sort result of find_related_easyconfigs

---
 easybuild/framework/easyconfig/tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 7d833cf747..611de90bbf 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -427,7 +427,7 @@ def find_related_easyconfigs(path, ec):
         else:
             _log.debug("No related easyconfigs in potential paths using '%s'" % regex)
 
-    return res
+    return sorted(res)
 
 
 def review_pr(pr, colored=True, branch='develop'):

From 32edb877623f24a6e336cb2e4876d76c06da4eed Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 10 Sep 2015 10:27:06 +0200
Subject: [PATCH 1272/1356] make det_terminal_size more robust, fix order of
 values in result

---
 easybuild/tools/multidiff.py   |  2 +-
 easybuild/tools/systemtools.py | 13 +++++++++++--
 test/framework/systemtools.py  |  4 ++--
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/easybuild/tools/multidiff.py b/easybuild/tools/multidiff.py
index fd46ff44c1..925fac805a 100644
--- a/easybuild/tools/multidiff.py
+++ b/easybuild/tools/multidiff.py
@@ -213,7 +213,7 @@ def limit(text, length):
             else:
                 return text
 
-        term_width, _ = det_terminal_size()
+        _, term_width = det_terminal_size()
 
         base = self.color_line(self.base_fn, PURPLE)
         filenames = ', '.join(map(os.path.basename, self.files))
diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index d3b9987e7b..2738e07043 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -509,6 +509,15 @@ def det_terminal_size():
     Determine the current size of the terminal window.
     @return: tuple with terminal width and height
     """
-    # see http://bytes.com/topic/python/answers/607757-getting-terminal-display-size
-    height, width, _, _ = struct.unpack('HHHH', fcntl.ioctl(0, termios.TIOCGWINSZ, struct.pack('HHHH', 0, 0, 0, 0)))
+    # see http://stackoverflow.com/questions/566746/how-to-get-console-window-width-in-python
+    try:
+        height, width, _, _ = struct.unpack('HHHH', fcntl.ioctl(0, termios.TIOCGWINSZ, struct.pack('HHHH', 0, 0, 0, 0)))
+    except Exception as err:
+        _log.warning("First attempt to determine terminal size failed: %s", err)
+        try:
+            height, width = [int(x) for x in os.popen("stty size").read().strip().split()]
+        except Exception as err:
+            _log.warning("Second attempt to determine terminal size failed, going to return defaults: %s", err)
+            height, width = 25, 80
+
     return width, height
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index 4b6558cc49..c5d60fcf76 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -429,9 +429,9 @@ def test_det_parallelism_mocked(self):
 
     def test_det_terminal_size(self):
         """Test det_terminal_size function."""
-        (width, height) = st.det_terminal_size()
-        self.assertTrue(isinstance(width, int) and width > 0)
+        (height, width) = st.det_terminal_size()
         self.assertTrue(isinstance(height, int) and height > 0)
+        self.assertTrue(isinstance(width, int) and width > 0)
 
 
 def suite():

From f5357fd24a6651e48ce3609308078097c7e5221d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 10 Sep 2015 10:56:55 +0200
Subject: [PATCH 1273/1356] fix height/width order in det_terminal_size

---
 easybuild/tools/systemtools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 2738e07043..3665cc5fc4 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -520,4 +520,4 @@ def det_terminal_size():
             _log.warning("Second attempt to determine terminal size failed, going to return defaults: %s", err)
             height, width = 25, 80
 
-    return width, height
+    return height, width

From 5ff93903a11deb49e6b8b394421c3d515d29e45e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 10 Sep 2015 11:30:45 +0200
Subject: [PATCH 1274/1356] fix multidiff unit test w.r.t. small terminal width

---
 test/framework/filetools.py | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 718db81fc3..57b40659eb 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -377,20 +377,17 @@ def test_multidiff(self):
         # different toolchain in toy-0.0-gompi-1.3.12-test: '+' line (removed chars in toolchain name/version, in red)
         expected = "7 %(endcol)s-%(endcol)s toolchain = {"
         expected += "'name': '%(endcol)s%(red)sgo%(endcol)sm\x1b[0m%(red)spi%(endcol)s', "
-        expected += "'version': '%(endcol)s%(red)s1.3.12%(endcol)s'} (1/2) toy-0.0-gompi-1.3.12-test.eb"
         expected = expected % {'endcol': endcol, 'green': green, 'red': red}
-        self.assertEqual(lines[7], expected)
+        self.assertTrue(lines[7].startswith(expected))
         # different toolchain in toy-0.0-gompi-1.3.12-test: '+' line (added chars in toolchain name/version, in green)
         expected = "7 %(endcol)s+%(endcol)s toolchain = {"
         expected += "'name': '%(endcol)s%(green)sdu%(endcol)sm\x1b[0m%(green)smy%(endcol)s', "
-        expected += "'version': '%(endcol)s%(green)sdummy%(endcol)s'} (1/2) toy-0.0-gompi-1.3.12-test.eb"
         expected = expected % {'endcol': endcol, 'green': green, 'red': red}
-        self.assertEqual(lines[8], expected)
+        self.assertTrue(lines[8].startswith(expected))
 
         # no postinstallcmds in toy-0.0-deps.eb
-        expected = "25 %s+ postinstallcmds = [\"echo TOY > %%(installdir)s/README\"]%s" % (green, endcol)
-        expected += " (1/2) toy-0.0-deps.eb"
-        self.assertTrue(expected in lines)
+        expected = "25 %s+ postinstallcmds = " % green
+        self.assertTrue(any([line.startswith(expected) for line in lines]))
         self.assertTrue("26 %s+%s (1/2) toy-0.0-deps.eb" % (green, endcol) in lines)
         self.assertEqual(lines[-1], "=====")
 
@@ -403,18 +400,19 @@ def test_multidiff(self):
         self.assertEqual(lines[3], "3 - versionsuffix = '-deps' (1/2) toy-0.0-deps.eb")
 
         # different toolchain in toy-0.0-gompi-1.3.12-test: '+' line with squigly line underneath to mark removed chars
-        expected = "7 - toolchain = {'name': 'gompi', 'version': '1.3.12'} (1/2) toy-0.0-gompi-1.3.12-test.eb"
-        self.assertEqual(lines[7], expected)
+        expected = "7 - toolchain = {'name': 'gompi', 'version': '1.3.12'} (1/2) toy"
+        self.assertTrue(lines[7].startswith(expected))
         expected = "  ?                       ^^ ^^               ^^^^^^"
         self.assertEqual(lines[8], expected)
         # different toolchain in toy-0.0-gompi-1.3.12-test: '-' line with squigly line underneath to mark added chars
-        expected = "7 + toolchain = {'name': 'dummy', 'version': 'dummy'} (1/2) toy-0.0-gompi-1.3.12-test.eb"
-        self.assertEqual(lines[9], expected)
+        expected = "7 + toolchain = {'name': 'dummy', 'version': 'dummy'} (1/2) toy"
+        self.assertTrue(lines[9].startswith(expected))
         expected = "  ?                       ^^ ^^               ^^^^^"
         self.assertEqual(lines[10], expected)
 
         # no postinstallcmds in toy-0.0-deps.eb
-        self.assertTrue("25 + postinstallcmds = [\"echo TOY > %(installdir)s/README\"] (1/2) toy-0.0-deps.eb" in lines)
+        expected = "25 + postinstallcmds = "
+        self.assertTrue(any([line.startswith(expected) for line in lines]))
         self.assertTrue("26 + (1/2) toy-0.0-deps.eb" in lines)
 
         self.assertEqual(lines[-1], "=====")

From f9912824898d404fc070c59dbc47254ebb4ae16e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 10 Sep 2015 12:45:28 +0200
Subject: [PATCH 1275/1356] remove intel-taito.py toolchain definition that
 slipped in

---
 easybuild/toolchains/intel-taito.py | 36 -----------------------------
 1 file changed, 36 deletions(-)
 delete mode 100644 easybuild/toolchains/intel-taito.py

diff --git a/easybuild/toolchains/intel-taito.py b/easybuild/toolchains/intel-taito.py
deleted file mode 100644
index 64ffd5d411..0000000000
--- a/easybuild/toolchains/intel-taito.py
+++ /dev/null
@@ -1,36 +0,0 @@
-from easybuild.toolchains.intel import Intel
-
-METADATA_BY_VERSION = {
-    '15.0.2': {
-        'prefixes': {
-            'GCC': '/appl/opt/gcc/4.9.2',
-            'icc': '/appl/opt/cluster_studio_xe2015/composer_xe_2015.2.164',
-            'ifort': '/appl/opt/cluster_studio_xe2015/composer_xe_2015.2.164',
-            'imkl': '/appl/opt/cluster_studio_xe2015/composer_xe_2015.2.164',
-            'impi': '/appl/opt/cluster_studio_xe2015/composer_xe_2015.2.164',
-        },
-        'versions': {
-            'GCC': '4.9.2',
-            'icc': '2015.2.164',
-            'ifort': '2015.2.164',
-            'imkl': '11.2.2.164',
-            'impi': '???',  # FIXME
-        }
-    }
-}
-
-class IntelTaito(Intel):
-    NAME = 'intel'
-    COMPILER_MODULE_NAME = []
-    MPI_MODULE_NAME = []
-    BLAS_MODULE_NAME = []
-    LAPACK_MODULE_NAME = []
-    SCALAPACK_MODULE_NAME = []
-
-    def _get_software_root(self, name):
-        """Get install prefix for specified software name"""
-        # TODO
-
-    def _get_software_version(self, name):
-        """Get install prefix for specified software name"""
-        # TODO

From e94e5c5642906941d723ec9be4870ccb3a1d558f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 14 Sep 2015 22:58:45 +0200
Subject: [PATCH 1276/1356] add support for specifying alternate name to be
 part of generated module name

---
 easybuild/framework/easyconfig/default.py    |  3 ++-
 easybuild/framework/easyconfig/easyconfig.py | 15 ++++++++++++++-
 test/framework/easyconfig.py                 | 11 +++++++++++
 3 files changed, 27 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 64cf46be16..858aa377b7 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -155,12 +155,13 @@
     'exts_list': [[], 'List with extensions added to the base installation', EXTENSIONS],
 
     # MODULES easyconfig parameters
+    'modaliases': [{}, "Aliases to be defined in module file", MODULES],
     'modextrapaths': [{}, "Extra paths to be prepended in module file", MODULES],
     'modextravars': [{}, "Extra environment variables to be added to module file", MODULES],
     'modloadmsg': [{}, "Message that should be printed when generated module is loaded", MODULES],
     'modluafooter': ["", "Footer to include in generated module file (Lua syntax)", MODULES],
+    'modname': [None, "Module name to use (rather than using software name", MODULES],
     'modtclfooter': ["", "Footer to include in generated module file (Tcl syntax)", MODULES],
-    'modaliases': [{}, "Aliases to be defined in module file", MODULES],
     'moduleclass': ['base', 'Module class to be used for this software', MODULES],
     'moduleforceunload': [False, 'Force unload of all modules when loading the extension', MODULES],
     'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", MODULES],
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 0cd9c6ad0b..16ea027151 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1091,8 +1091,21 @@ def _det_module_name_with(self, mns_method, ec, force_visible=False):
             - string representing module name has length > 0
             - module name only contains printable characters (string.printable, except carriage-control chars)
         """
+        ec = self.check_ec_type(ec)
+
+        # replace software name with desired replacement (if specified)
+        orig_name = None
+        if ec.get('modname', None):
+            orig_name = ec['name']
+            ec['name'] = ec['modname']
+            self.log.info("Replaced software name '%s' with '%s' when determining module name", orig_name, ec['name'])
+
         mod_name = mns_method(self.check_ec_type(ec))
 
+        # restore original software name if it was tampered with
+        if orig_name is not None:
+            ec['name'] = orig_name
+
         if not is_valid_module_name(mod_name):
             raise EasyBuildError("%s is not a valid module name", str(mod_name))
 
@@ -1134,7 +1147,7 @@ def det_short_module_name(self, ec, force_visible=False):
         self.log.debug("Obtained valid short module name %s" % mod_name)
 
         # sanity check: obtained module name should pass the 'is_short_modname_for' check
-        if not self.is_short_modname_for(mod_name, ec['name']):
+        if not self.is_short_modname_for(mod_name, ec.get('modname', None) or ec['name']):
             raise EasyBuildError("is_short_modname_for('%s', '%s') for active module naming scheme returns False",
                                  mod_name, ec['name'])
         return mod_name
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 1a6e5f3885..7bbc6b8661 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1491,6 +1491,17 @@ def test_find_related_easyconfigs(self):
         ec['name'] = 'nosuchsoftware'
         self.assertEqual(find_related_easyconfigs(test_easyconfigs, ec), [])
 
+    def test_alt_name(self):
+        """Test specifying an alternative name for the software name, to use when determining module name."""
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0-deps.eb')
+        ectxt = read_file(ec_file)
+        modified_ec_file = os.path.join(self.test_prefix, os.path.basename(ec_file))
+        write_file(modified_ec_file, ectxt + "\nmodname = 'notreallyatoy'")
+        ec = EasyConfig(modified_ec_file)
+        self.assertEqual(ec.full_mod_name, 'notreallyatoy/0.0-deps')
+        self.assertEqual(ec.short_mod_name, 'notreallyatoy/0.0-deps')
+        self.assertEqual(ec['name'], 'toy')
+
 
 def suite():
     """ returns all the testcases in this module """

From b36af8f4c9a751d3d76fab0ada50d98fde4bb68c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 18 Sep 2015 15:28:30 +0200
Subject: [PATCH 1277/1356] support overriding # used cores via --parallel

---
 easybuild/framework/easyblock.py | 19 +++++++++++---
 easybuild/tools/config.py        |  1 +
 easybuild/tools/options.py       |  2 ++
 easybuild/tools/systemtools.py   |  2 +-
 test/framework/easyblock.py      | 44 ++++++++++++++++++++++++++++++++
 test/framework/systemtools.py    | 18 ++++++-------
 6 files changed, 72 insertions(+), 14 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 76ca7992d6..2708438a37 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1194,6 +1194,21 @@ def check_readiness_step(self):
         """
         Verify if all is ok to start build.
         """
+        # set level of parallelism for build
+        par = build_option('parallel')
+
+        if self.cfg['parallel']:
+            if par is None:
+                par = self.cfg['parallel']
+                self.log.debug("Desired parallelism specified via 'parallel' easyconfig parameter: %s", par)
+            else:
+                par = min(int(par), int(self.cfg['parallel']))
+                self.log.debug("Desired parallelism: minimum of 'parallel' build option/easyconfig parameter: %s", par)
+        else:
+            self.log.debug("Desired parallelism specified via 'parallel' build option: %s", par)
+        self.cfg['parallel'] = det_parallelism(par=par, maxpar=self.cfg['maxparallel'])
+        self.log.info("Setting parallelism: %s" % self.cfg['parallel'])
+
         # check whether modules are loaded
         loadedmods = self.modules_tool.loaded_modules()
         if len(loadedmods) > 0:
@@ -1267,10 +1282,6 @@ def fetch_step(self, skip_checksums=False):
                 fil[DEFAULT_CHECKSUM] = check_sum
                 self.log.info("%s checksum for %s: %s" % (DEFAULT_CHECKSUM, fil['path'], fil[DEFAULT_CHECKSUM]))
 
-        # set level of parallelism for build
-        self.cfg['parallel'] = det_parallelism(self.cfg['parallel'], self.cfg['maxparallel'])
-        self.log.info("Setting parallelism: %s" % self.cfg['parallel'])
-
         # create parent dirs in install and modules path already
         # this is required when building in parallel
         mod_path_suffix = build_option('suffix_modules_path')
diff --git a/easybuild/tools/config.py b/easybuild/tools/config.py
index 75ff8e5a14..309268f618 100644
--- a/easybuild/tools/config.py
+++ b/easybuild/tools/config.py
@@ -112,6 +112,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'modules_footer',
         'only_blocks',
         'optarch',
+        'parallel',
         'regtest_output_dir',
         'skip',
         'stop',
diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index a8310a9146..b4b729ab0c 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -222,6 +222,8 @@ def override_options(self):
                             None, 'store_true', False),
             'optarch': ("Set architecture optimization, overriding native architecture optimizations",
                         None, 'store', None),
+            'parallel': ("Specify (maximum) level of parallellism used during build procedure",
+                         'int', 'store', None),
             'pretend': (("Does the build/installation in a test directory located in $HOME/easybuildinstall"),
                         None, 'store_true', False, 'p'),
             'read-only-installdir': ("Set read-only permissions on installation directory after installation",
diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index 3665cc5fc4..b8c899b1c5 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -470,7 +470,7 @@ def use_group(group_name):
     return group
 
 
-def det_parallelism(par, maxpar):
+def det_parallelism(par=None, maxpar=None):
     """
     Determine level of parallelism that should be used.
     Default: educated guess based on # cores and 'ulimit -u' setting: min(# cores, ((ulimit -u) - 15) / 6)
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index e7c25f568e..5561e46d7f 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -651,6 +651,50 @@ def test_extensions_sanity_check(self):
         eb.silent = True
         eb.run_all_steps(True)
 
+    def test_parallel(self):
+        """Test defining of parallellism."""
+        toy_ec = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb')
+        toytxt = read_file(toy_ec)
+
+        handle, toy_ec1 = tempfile.mkstemp(prefix='easyblock_test_file_', suffix='.eb')
+        os.close(handle)
+        write_file(toy_ec1, toytxt + "\nparallel = 123")
+
+        handle, toy_ec2 = tempfile.mkstemp(prefix='easyblock_test_file_', suffix='.eb')
+        os.close(handle)
+        write_file(toy_ec2, toytxt + "\nparallel = 123\nmaxparallel = 67")
+
+        # default: parallellism is derived from # available cores + ulimit
+        test_eb = EasyBlock(EasyConfig(toy_ec))
+        test_eb.check_readiness_step()
+        self.assertTrue(isinstance(test_eb.cfg['parallel'], int) and test_eb.cfg['parallel'] > 0)
+
+        # only 'parallel' easyconfig parameter specified (no 'parallel' build option)
+        test_eb = EasyBlock(EasyConfig(toy_ec1))
+        test_eb.check_readiness_step()
+        self.assertEqual(test_eb.cfg['parallel'], 123)
+
+        # both 'parallel' and 'maxparallel' easyconfig parameters specified (no 'parallel' build option)
+        test_eb = EasyBlock(EasyConfig(toy_ec2))
+        test_eb.check_readiness_step()
+        self.assertEqual(test_eb.cfg['parallel'], 67)
+
+        # only 'parallel' build option specified
+        init_config(build_options={'parallel': '97', 'validate': False})
+        test_eb = EasyBlock(EasyConfig(toy_ec))
+        test_eb.check_readiness_step()
+        self.assertEqual(test_eb.cfg['parallel'], 97)
+
+        # both 'parallel' build option and easyconfig parameter specified (no 'maxparallel')
+        test_eb = EasyBlock(EasyConfig(toy_ec1))
+        test_eb.check_readiness_step()
+        self.assertEqual(test_eb.cfg['parallel'], 97)
+
+        # both 'parallel' and 'maxparallel' easyconfig parameters specified + 'parallel' build option
+        test_eb = EasyBlock(EasyConfig(toy_ec2))
+        test_eb.check_readiness_step()
+        self.assertEqual(test_eb.cfg['parallel'], 67)
+
 
 def suite():
     """ return all the tests in this file """
diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index c5d60fcf76..ee5cf4f2b5 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -403,14 +403,14 @@ def test_system_info(self):
 
     def test_det_parallelism_native(self):
         """Test det_parallelism function (native calls)."""
-        self.assertTrue(det_parallelism(None, None) > 0)
+        self.assertTrue(det_parallelism() > 0)
         # specified parallellism
-        self.assertEqual(det_parallelism(5, None), 5)
+        self.assertEqual(det_parallelism(par=5), 5)
         # max parallellism caps
-        self.assertEqual(det_parallelism(None, 1), 1)
+        self.assertEqual(det_parallelism(maxpar=1), 1)
         self.assertEqual(det_parallelism(16, 1), 1)
-        self.assertEqual(det_parallelism(5, 2), 2)
-        self.assertEqual(det_parallelism(5, 10), 5)
+        self.assertEqual(det_parallelism(par=5, maxpar=2), 2)
+        self.assertEqual(det_parallelism(par=5, maxpar=10), 5)
 
     def test_det_parallelism_mocked(self):
         """Test det_parallelism function (with mocked ulimit/get_avail_core_count)."""
@@ -418,12 +418,12 @@ def test_det_parallelism_mocked(self):
 
         # mock number of available cores to 8
         st.get_avail_core_count = lambda: 8
-        self.assertTrue(det_parallelism(None, None), 8)
+        self.assertTrue(det_parallelism(), 8)
         # make 'ulimit -u' return '40', which should result in default (max) parallelism of 4 ((40-15)/6)
         st.run_cmd = mocked_run_cmd
-        self.assertTrue(det_parallelism(None, None), 4)
-        self.assertTrue(det_parallelism(6, None), 4)
-        self.assertTrue(det_parallelism(2, None), 2)
+        self.assertTrue(det_parallelism(), 4)
+        self.assertTrue(det_parallelism(par=6), 4)
+        self.assertTrue(det_parallelism(maxpar=2), 2)
 
         st.get_avail_core_count = orig_get_avail_core_count
 

From 448eaa5a1790e50c84fd91a3bf3a1f0e38792dc0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 18 Sep 2015 17:40:21 +0200
Subject: [PATCH 1278/1356] also define $FC in build environment

---
 easybuild/toolchains/compiler/craype.py       |   1 +
 .../toolchains/compiler/dummycompiler.py      |   1 +
 easybuild/toolchains/compiler/gcc.py          |   1 +
 .../toolchains/compiler/inteliccifort.py      |   1 +
 easybuild/toolchains/mpi/craympich.py         |   2 +
 easybuild/toolchains/mpi/intelmpi.py          |   7 +-
 easybuild/toolchains/mpi/mpich.py             |  16 +--
 easybuild/toolchains/mpi/mpich2.py            |  24 +---
 easybuild/toolchains/mpi/openmpi.py           |  37 ++++--
 easybuild/tools/toolchain/compiler.py         |  25 ++--
 easybuild/tools/toolchain/constants.py        |   4 +
 easybuild/tools/toolchain/mpi.py              |  12 +-
 test/framework/toolchain.py                   | 120 ++++++++----------
 13 files changed, 120 insertions(+), 131 deletions(-)

diff --git a/easybuild/toolchains/compiler/craype.py b/easybuild/toolchains/compiler/craype.py
index 8250c2b9f5..0383f13121 100644
--- a/easybuild/toolchains/compiler/craype.py
+++ b/easybuild/toolchains/compiler/craype.py
@@ -80,6 +80,7 @@ class CrayPECompiler(Compiler):
 
     COMPILER_F77 = 'ftn'
     COMPILER_F90 = 'ftn'
+    COMPILER_FC = 'ftn'
 
     # suffix for PrgEnv module that matches this toolchain
     # e.g. 'gnu' => 'PrgEnv-gnu/<version>'
diff --git a/easybuild/toolchains/compiler/dummycompiler.py b/easybuild/toolchains/compiler/dummycompiler.py
index 9296ac85d5..cc1dea94ea 100644
--- a/easybuild/toolchains/compiler/dummycompiler.py
+++ b/easybuild/toolchains/compiler/dummycompiler.py
@@ -46,3 +46,4 @@ class DummyCompiler(Compiler):
 
     COMPILER_F77 = '%sF77' % TC_CONSTANT_DUMMY
     COMPILER_F90 = '%sF90' % TC_CONSTANT_DUMMY
+    COMPILER_FC = '%sFC' % TC_CONSTANT_DUMMY
diff --git a/easybuild/toolchains/compiler/gcc.py b/easybuild/toolchains/compiler/gcc.py
index bdd4fb7001..cc1eb80e2a 100644
--- a/easybuild/toolchains/compiler/gcc.py
+++ b/easybuild/toolchains/compiler/gcc.py
@@ -75,6 +75,7 @@ class Gcc(Compiler):
 
     COMPILER_F77 = 'gfortran'
     COMPILER_F90 = 'gfortran'
+    COMPILER_FC = 'gfortran'
     COMPILER_F_UNIQUE_FLAGS = ['f2c']
 
     LIB_MULTITHREAD = ['pthread']
diff --git a/easybuild/toolchains/compiler/inteliccifort.py b/easybuild/toolchains/compiler/inteliccifort.py
index e9af5dc722..58e33b9d41 100644
--- a/easybuild/toolchains/compiler/inteliccifort.py
+++ b/easybuild/toolchains/compiler/inteliccifort.py
@@ -80,6 +80,7 @@ class IntelIccIfort(Compiler):
 
     COMPILER_F77 = 'ifort'
     COMPILER_F90 = 'ifort'
+    COMPILER_FC = 'ifort'
     COMPILER_F_UNIQUE_FLAGS = ['intel-static']
 
     LINKER_TOGGLE_STATIC_DYNAMIC = {
diff --git a/easybuild/toolchains/mpi/craympich.py b/easybuild/toolchains/mpi/craympich.py
index e2ec238008..b940bfbd9f 100644
--- a/easybuild/toolchains/mpi/craympich.py
+++ b/easybuild/toolchains/mpi/craympich.py
@@ -47,6 +47,7 @@ class CrayMPICH(Mpi):
     MPI_COMPILER_MPICXX = CrayPECompiler.COMPILER_CXX
     MPI_COMPILER_MPIF77 = CrayPECompiler.COMPILER_F77
     MPI_COMPILER_MPIF90 = CrayPECompiler.COMPILER_F90
+    MPI_COMPILER_MPIFC = CrayPECompiler.COMPILER_FC
 
     # no MPI wrappers, so no need to specify serial compiler
     MPI_SHARED_OPTION_MAP = {
@@ -54,6 +55,7 @@ class CrayMPICH(Mpi):
         '_opt_MPICXX': '',
         '_opt_MPIF77': '',
         '_opt_MPIF90': '',
+        '_opt_MPIFC': '',
     }
 
     def _set_mpi_compiler_variables(self):
diff --git a/easybuild/toolchains/mpi/intelmpi.py b/easybuild/toolchains/mpi/intelmpi.py
index a8fb512964..06d842d784 100644
--- a/easybuild/toolchains/mpi/intelmpi.py
+++ b/easybuild/toolchains/mpi/intelmpi.py
@@ -30,6 +30,7 @@
 """
 
 from easybuild.toolchains.mpi.mpich2 import Mpich2
+from easybuild.tools.toolchain.constants import COMPILER_FLAGS, COMPILER_VARIABLES
 from easybuild.tools.toolchain.variables import CommandFlagList
 
 
@@ -53,8 +54,8 @@ def _set_mpi_compiler_variables(self):
         """Add I_MPI_XXX variables to set."""
 
         # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
-        for var in ["CC", "CXX", "F77", "F90"]:
-            self.variables.nappend("I_MPI_%s" % var, str(self.variables[var].get_first()), var_class=CommandFlagList)
+        for var in COMPILER_VARIABLES:
+            self.variables.nappend('I_MPI_%s' % var, str(self.variables[var].get_first()), var_class=CommandFlagList)
 
         super(IntelMPI, self)._set_mpi_compiler_variables()
 
@@ -66,5 +67,5 @@ def set_variables(self):
         # add -mt_mpi flag to ensure linking against thread-safe MPI library when OpenMP is enabled
         if self.options.get('openmp', None) and self.options.get('usempi', None):
             mt_mpi_option = ['mt_mpi']
-            for flags_var in ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']:
+            for flags_var in COMPILER_FLAGS:
                 self.variables.nappend(flags_var, mt_mpi_option)
diff --git a/easybuild/toolchains/mpi/mpich.py b/easybuild/toolchains/mpi/mpich.py
index b173148137..43bf527667 100644
--- a/easybuild/toolchains/mpi/mpich.py
+++ b/easybuild/toolchains/mpi/mpich.py
@@ -31,6 +31,7 @@
 @author: Dmitri Gribenko (National Technical University of Ukraine "KPI")
 """
 
+from easybuild.tools.toolchain.constants import COMPILER_VARIABLES, MPI_COMPILER_VARIABLES
 from easybuild.tools.toolchain.mpi import Mpi
 from easybuild.tools.toolchain.variables import CommandFlagList
 
@@ -46,19 +47,18 @@ class Mpich(Mpi):
 
     MPI_LIBRARY_NAME = 'mpich'
 
+    # FIXME version-dependent? see http://www.mpich.org/static/docs/v3.1.4/www1/mpifort.html
+    MPI_COMPILER_MPIFC = 'mpif90'
+    #MPI_COMPILER_MPIFC = 'mpifort'
+
     # clear MPI wrapper command options
-    MPI_SHARED_OPTION_MAP = {
-                             '_opt_MPICC': '',
-                             '_opt_MPICXX': '',
-                             '_opt_MPIF77': '',
-                             '_opt_MPIF90': '',
-                             }
+    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var, '') for var in MPI_COMPILER_VARIABLES])
 
     def _set_mpi_compiler_variables(self):
-        """Set the MPICH_{CC, CXX, F77, F90} variables."""
+        """Set the MPICH_{CC, CXX, F77, F90, FC} variables."""
 
         # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
-        for var in ["CC", "CXX", "F77", "F90"]:
+        for var in COMPILER_VARIABLES:
             self.variables.nappend("MPICH_%s" % var, str(self.variables[var].get_first()), var_class=CommandFlagList)
 
         super(Mpich, self)._set_mpi_compiler_variables()
diff --git a/easybuild/toolchains/mpi/mpich2.py b/easybuild/toolchains/mpi/mpich2.py
index d68b7917d9..8aacc85081 100644
--- a/easybuild/toolchains/mpi/mpich2.py
+++ b/easybuild/toolchains/mpi/mpich2.py
@@ -30,34 +30,14 @@
 @author: Jens Timmerman (Ghent University)
 """
 
-from easybuild.tools.toolchain.mpi import Mpi
-from easybuild.tools.toolchain.variables import CommandFlagList
+from easybuild.toolchains.mpi.mpich import Mpich
 
 TC_CONSTANT_MPICH2 = "MPICH2"
 TC_CONSTANT_MPI_TYPE_MPICH = "MPI_TYPE_MPICH"
 
 
-class Mpich2(Mpi):
+class Mpich2(Mpich):
     """MPICH2 MPI class"""
     MPI_MODULE_NAME = ["MPICH2"]
     MPI_FAMILY = TC_CONSTANT_MPICH2
     MPI_TYPE = TC_CONSTANT_MPI_TYPE_MPICH
-
-    MPI_LIBRARY_NAME = 'mpich'
-
-    # clear MPI wrapper command options
-    MPI_SHARED_OPTION_MAP = {
-                             '_opt_MPICC': '',
-                             '_opt_MPICXX': '',
-                             '_opt_MPIF77': '',
-                             '_opt_MPIF90': '',
-                             }
-
-    def _set_mpi_compiler_variables(self):
-        """Set the MPICH_{CC, CXX, F77, F90} variables."""
-
-        # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
-        for var in ["CC", "CXX", "F77", "F90"]:
-            self.variables.nappend("MPICH_%s" % var, str(self.variables[var].get_first()), var_class=CommandFlagList)
-
-        super(Mpich2, self)._set_mpi_compiler_variables()
diff --git a/easybuild/toolchains/mpi/openmpi.py b/easybuild/toolchains/mpi/openmpi.py
index 8a2137e0f1..2f9f5a2ab9 100644
--- a/easybuild/toolchains/mpi/openmpi.py
+++ b/easybuild/toolchains/mpi/openmpi.py
@@ -28,7 +28,9 @@
 @author: Stijn De Weirdt (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 """
+from distutils.version import LooseVersion
 
+from easybuild.tools.toolchain.constants import COMPILER_VARIABLES, MPI_COMPILER_VARIABLES
 from easybuild.tools.toolchain.mpi import Mpi
 from easybuild.tools.toolchain.variables import CommandFlagList
 
@@ -45,27 +47,42 @@ class OpenMPI(Mpi):
 
     MPI_LIBRARY_NAME = 'mpi'
 
-    ## OpenMPI reads from CC etc env variables
-    MPI_SHARED_OPTION_MAP = {
-                             '_opt_MPICC': '',
-                             '_opt_MPICXX':'',
-                             '_opt_MPICF77':'',
-                             '_opt_MPICF90':'',
-                             }
+    # version-dependent, see http://www.open-mpi.org/faq/?category=mpi-apps#override-wrappers-after-v1.0
+    MPI_COMPILER_MPIF77 = 'mpif77'
+    MPI_COMPILER_MPIF90 = 'mpif90'
+    MPI_COMPILER_MPIFC = 'mpifc'
+
+    # OpenMPI reads from CC etc env variables
+    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var, '') for var in MPI_COMPILER_VARIABLES])
 
     MPI_LINK_INFO_OPTION = '-showme:link'
 
+    def __init__(self, *args, **kwargs):
+        """Toolchain constructor."""
+        super(OpenMPI, self).__init__(*args, **kwargs)
+
+        ompi_ver = self.get_software_version(self.MPI_MODULE_NAME)
+        if LooseVersion(ompi_ver) >= LooseVersion('1.7'):
+            self.MPI_COMPILER_MPIF77 = 'mpifort'
+            self.MPI_COMPILER_MPIF90 = 'mpifort'
+            self.MPI_COMPILER_MPIFC = 'mpifort'
+        else:
+            self.MPI_COMPILER_MPIF77 = 'mpif77'
+            self.MPI_COMPILER_MPIF90 = 'mpif90'
+            self.MPI_COMPILER_MPIFC = 'mpif90'
+
     def _set_mpi_compiler_variables(self):
-        """Add OMPI_XXX variables to set."""
+        """Add OMPI_* variables to set."""
 
         # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
-        for var in ["CC", "CXX", "F77", ("F90", "FC")]:
+        for var in COMPILER_VARIABLES:
             if isinstance(var, basestring):
                 source_var = var
                 target_var = var
             else:
                 source_var = var[0]
                 target_var = var[1]
-            self.variables.nappend("OMPI_%s" % target_var, str(self.variables[source_var].get_first()), var_class=CommandFlagList)
+            var = 'OMPI_%s' % target_var
+            self.variables.nappend(var, str(self.variables[source_var].get_first()), var_class=CommandFlagList)
 
         super(OpenMPI, self)._set_mpi_compiler_variables()
diff --git a/easybuild/tools/toolchain/compiler.py b/easybuild/tools/toolchain/compiler.py
index 45de8f34f7..80df84ba51 100644
--- a/easybuild/tools/toolchain/compiler.py
+++ b/easybuild/tools/toolchain/compiler.py
@@ -108,6 +108,7 @@ class Compiler(Toolchain):
 
     COMPILER_F77 = None
     COMPILER_F90 = None
+    COMPILER_FC = None
     COMPILER_F_FLAGS = ['i8', 'r8']
     COMPILER_F_UNIQUE_FLAGS = []
 
@@ -237,21 +238,15 @@ def _set_compiler_flags(self):
         self.variables.nextend('PRECFLAGS', precflags[:1])
 
         # precflags last
-        self.variables.nappend('CFLAGS', flags)
-        self.variables.nappend('CFLAGS', cflags)
-        self.variables.join('CFLAGS', 'OPTFLAGS', 'PRECFLAGS')
-
-        self.variables.nappend('CXXFLAGS', flags)
-        self.variables.nappend('CXXFLAGS', cflags)
-        self.variables.join('CXXFLAGS', 'OPTFLAGS', 'PRECFLAGS')
-
-        self.variables.nappend('FFLAGS', flags)
-        self.variables.nappend('FFLAGS', fflags)
-        self.variables.join('FFLAGS', 'OPTFLAGS', 'PRECFLAGS')
-
-        self.variables.nappend('F90FLAGS', flags)
-        self.variables.nappend('F90FLAGS', fflags)
-        self.variables.join('F90FLAGS', 'OPTFLAGS', 'PRECFLAGS')
+        for var in ['CFLAGS', 'CXXFLAGS']:
+            self.variables.nappend(var, flags)
+            self.variables.nappend(var, cflags)
+            self.variables.join(var, 'OPTFLAGS', 'PRECFLAGS')
+
+        for var in ['FFLAGS', 'F90FLAGS']:  # FIXME F77FLAGS?
+            self.variables.nappend(var, flags)
+            self.variables.nappend(var, fflags)
+            self.variables.join(var, 'OPTFLAGS', 'PRECFLAGS')
 
     def _set_optimal_architecture(self):
         """ Get options for the current architecture """
diff --git a/easybuild/tools/toolchain/constants.py b/easybuild/tools/toolchain/constants.py
index 7c9cbf30d1..eea842d663 100644
--- a/easybuild/tools/toolchain/constants.py
+++ b/easybuild/tools/toolchain/constants.py
@@ -39,6 +39,7 @@
     ('CXX', 'C++ compiler'),
     ('F77', 'Fortran 77 compiler'),
     ('F90', 'Fortran 90 compiler'),
+    ('FC', 'Fortran compiler'),
 ]
 
 COMPILER_FLAGS = [
@@ -46,6 +47,7 @@
     ('CXXFLAGS', 'C++ compiler flags'),
     ('FFLAGS', 'Fortran compiler flags'),
     ('F90FLAGS', 'Fortran 90 compiler flags'),
+    # FIXME F77FLAGS?
 ]
 
 COMPILER_MAP_CLASS = {
@@ -72,12 +74,14 @@
         ('CUDA_CXX', 'CUDA C++ compiler command'),
         ('CUDA_F77', 'CUDA Fortran77 compiler command'),
         ('CUDA_F90', 'CUDA Fortran90 compiler command'),
+        ('CUDA_FC', 'CUDA Fortran compiler command'),
     ],
     FlagList: [
         ('CUDA_CFLAGS', 'CUDA C compiler flags'),
         ('CUDA_CXXFLAGS', 'CUDA C++ compiler flags'),
         ('CUDA_FFLAGS', 'CUDA Fortran compiler flags'),
         ('CUDA_F90FLAGS', 'CUDA Fortran 90 compiler flags'),
+        # FIXME CUDA_F77FLAGS?
     ],
 }
 
diff --git a/easybuild/tools/toolchain/mpi.py b/easybuild/tools/toolchain/mpi.py
index 74da9d5ff6..1f2d5bd924 100644
--- a/easybuild/tools/toolchain/mpi.py
+++ b/easybuild/tools/toolchain/mpi.py
@@ -57,17 +57,19 @@ class Mpi(Toolchain):
 
     MPI_UNIQUE_OPTION_MAP = None
     MPI_SHARED_OPTION_MAP = {
-                             '_opt_MPICC': 'cc=%(CC_base)s',
-                             '_opt_MPICXX':'cxx=%(CXX_base)s',
-                             '_opt_MPIF77':'fc=%(F77_base)s',
-                             '_opt_MPIF90':'f90=%(F90_base)s',
-                             }
+        '_opt_MPICC': 'cc=%(CC_base)s',
+        '_opt_MPICXX':'cxx=%(CXX_base)s',
+        '_opt_MPIF77':'fc=%(F77_base)s',
+        '_opt_MPIF90':'f90=%(F90_base)s',
+        '_opt_MPIFC':'fc=%(FC_base)s',
+    }
 
     MPI_COMPILER_MPICC = 'mpicc'
     MPI_COMPILER_MPICXX = 'mpicxx'
 
     MPI_COMPILER_MPIF77 = 'mpif77'
     MPI_COMPILER_MPIF90 = 'mpif90'
+    MPI_COMPILER_MPIFC = 'mpifc'
 
     MPI_LINK_INFO_OPTION = None
 
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index faf64fface..4c196eafa7 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -79,31 +79,22 @@ def test_get_variable_compilers(self):
         tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
         tc.prepare()
 
-        cc = tc.get_variable('CC')
-        self.assertEqual(cc, "gcc")
-        cxx = tc.get_variable('CXX')
-        self.assertEqual(cxx, "g++")
-        f77 = tc.get_variable('F77')
-        self.assertEqual(f77, "gfortran")
-        f90 = tc.get_variable('F90')
-        self.assertEqual(f90, "gfortran")
-        mpicc = tc.get_variable('MPICC')
-        self.assertEqual(mpicc, "mpicc")
-        mpicxx = tc.get_variable('MPICXX')
-        self.assertEqual(mpicxx, "mpicxx")
-        mpif77 = tc.get_variable('MPIF77')
-        self.assertEqual(mpif77, "mpif77")
-        mpif90 = tc.get_variable('MPIF90')
-        self.assertEqual(mpif90, "mpif90")
-
-        ompi_cc = tc.get_variable('OMPI_CC')
-        self.assertEqual(ompi_cc, "gcc")
-        ompi_cxx = tc.get_variable('OMPI_CXX')
-        self.assertEqual(ompi_cxx, "g++")
-        ompi_f77 = tc.get_variable('OMPI_F77')
-        self.assertEqual(ompi_f77, "gfortran")
-        ompi_fc = tc.get_variable('OMPI_FC')
-        self.assertEqual(ompi_fc, "gfortran")
+        self.assertEqual(tc.get_variable('CC'), 'gcc')
+        self.assertEqual(tc.get_variable('CXX'), 'g++')
+        self.assertEqual(tc.get_variable('F77'), 'gfortran')
+        self.assertEqual(tc.get_variable('F90'), 'gfortran')
+        self.assertEqual(tc.get_variable('FC'), 'gfortran')
+
+        self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
+        self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
+        self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
+        self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpif90')
+
+        self.assertEqual(tc.get_variable('OMPI_CC'), 'gcc')
+        self.assertEqual(tc.get_variable('OMPI_CXX'), 'g++')
+        self.assertEqual(tc.get_variable('OMPI_F77'), 'gfortran')
+        self.assertEqual(tc.get_variable('OMPI_FC'), 'gfortran')
 
     def test_get_variable_mpi_compilers(self):
         """Test get_variable function to obtain compiler variables."""
@@ -111,32 +102,22 @@ def test_get_variable_mpi_compilers(self):
         tc.set_options({'usempi': True})
         tc.prepare()
 
-        cc = tc.get_variable('CC')
-        self.assertEqual(cc, "mpicc")
-        cxx = tc.get_variable('CXX')
-        self.assertEqual(cxx, "mpicxx")
-        f77 = tc.get_variable('F77')
-        self.assertEqual(f77, "mpif77")
-        f90 = tc.get_variable('F90')
-        self.assertEqual(f90, "mpif90")
-
-        mpicc = tc.get_variable('MPICC')
-        self.assertEqual(mpicc, "mpicc")
-        mpicxx = tc.get_variable('MPICXX')
-        self.assertEqual(mpicxx, "mpicxx")
-        mpif77 = tc.get_variable('MPIF77')
-        self.assertEqual(mpif77, "mpif77")
-        mpif90 = tc.get_variable('MPIF90')
-        self.assertEqual(mpif90, "mpif90")
-
-        ompi_cc = tc.get_variable('OMPI_CC')
-        self.assertEqual(ompi_cc, "gcc")
-        ompi_cxx = tc.get_variable('OMPI_CXX')
-        self.assertEqual(ompi_cxx, "g++")
-        ompi_f77 = tc.get_variable('OMPI_F77')
-        self.assertEqual(ompi_f77, "gfortran")
-        ompi_fc = tc.get_variable('OMPI_FC')
-        self.assertEqual(ompi_fc, "gfortran")
+        self.assertEqual(tc.get_variable('CC'), 'mpicc')
+        self.assertEqual(tc.get_variable('CXX'), 'mpicxx')
+        self.assertEqual(tc.get_variable('F77'), 'mpif77')
+        self.assertEqual(tc.get_variable('F90'), 'mpif90')
+        self.assertEqual(tc.get_variable('FC'), 'mpif90')
+
+        self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
+        self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
+        self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
+        self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpif90')
+
+        self.assertEqual(tc.get_variable('OMPI_CC'), 'gcc')
+        self.assertEqual(tc.get_variable('OMPI_CXX'), 'g++')
+        self.assertEqual(tc.get_variable('OMPI_F77'), 'gfortran')
+        self.assertEqual(tc.get_variable('OMPI_FC'), 'gfortran')
 
     def test_get_variable_seq_compilers(self):
         """Test get_variable function to obtain compiler variables."""
@@ -144,14 +125,11 @@ def test_get_variable_seq_compilers(self):
         tc.set_options({'usempi': True})
         tc.prepare()
 
-        cc_seq = tc.get_variable('CC_SEQ')
-        self.assertEqual(cc_seq, "gcc")
-        cxx_seq = tc.get_variable('CXX_SEQ')
-        self.assertEqual(cxx_seq, "g++")
-        f77_seq = tc.get_variable('F77_SEQ')
-        self.assertEqual(f77_seq, "gfortran")
-        f90_seq = tc.get_variable('F90_SEQ')
-        self.assertEqual(f90_seq, "gfortran")
+        self.assertEqual(tc.get_variable('CC_SEQ'), 'gcc')
+        self.assertEqual(tc.get_variable('CXX_SEQ'), 'g++')
+        self.assertEqual(tc.get_variable('F77_SEQ'), 'gfortran')
+        self.assertEqual(tc.get_variable('F90_SEQ'), 'gfortran')
+        self.assertEqual(tc.get_variable('FC_SEQ'), 'gfortran')
 
     def test_get_variable_libs_list(self):
         """Test get_variable function to obtain list of libraries."""
@@ -189,7 +167,7 @@ def test_validate_pass_by_value(self):
     def test_optimization_flags(self):
         """Test whether optimization flags are being set correctly."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
 
         # check default optimization flag (e.g. -O2)
         tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
@@ -216,7 +194,7 @@ def test_optimization_flags(self):
     def test_optimization_flags_combos(self):
         """Test whether combining optimization levels works as expected."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
 
         # check combining of optimization flags (doesn't make much sense)
         # lowest optimization should always be picked
@@ -249,7 +227,7 @@ def test_optimization_flags_combos(self):
     def test_misc_flags_shared(self):
         """Test whether shared compiler flags are set correctly."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
 
         # setting option should result in corresponding flag to be set (shared options)
         for opt in ['pic', 'verbose', 'debug', 'static', 'shared']:
@@ -270,7 +248,7 @@ def test_misc_flags_shared(self):
     def test_misc_flags_unique(self):
         """Test whether unique compiler flags are set correctly."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
 
         # setting option should result in corresponding flag to be set (unique options)
         for opt in ['unroll', 'optarch', 'openmp']:
@@ -292,7 +270,7 @@ def test_misc_flags_unique(self):
 
     def test_override_optarch(self):
         """Test whether overriding the optarch flag works."""
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
         for optarch_var in ['march=lovelylovelysandybridge', None]:
             build_options = {'optarch': optarch_var}
             init_config(build_options=build_options)
@@ -318,7 +296,7 @@ def test_override_optarch(self):
     def test_misc_flags_unique_fortran(self):
         """Test whether unique Fortran compiler flags are set correctly."""
 
-        flag_vars = ['FFLAGS', 'F90FLAGS']
+        flag_vars = ['FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
 
         # setting option should result in corresponding flag to be set (Fortran unique options)
         for opt in ['i8', 'r8']:
@@ -338,7 +316,7 @@ def test_misc_flags_unique_fortran(self):
     def test_precision_flags(self):
         """Test whether precision flags are being set correctly."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
 
         # check default precision flag
         tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
@@ -372,6 +350,7 @@ def test_cgoolf_toolchain(self):
         self.assertEqual(tc.get_variable('CXX'), 'clang++')
         self.assertEqual(tc.get_variable('F77'), 'gfortran')
         self.assertEqual(tc.get_variable('F90'), 'gfortran')
+        self.assertEqual(tc.get_variable('FC'), 'gfortran')
 
     def test_comp_family(self):
         """Test determining compiler family."""
@@ -464,6 +443,7 @@ def test_ictce_toolchain(self):
         self.assertEqual(tc.get_variable('CXX'), 'icpc')
         self.assertEqual(tc.get_variable('F77'), 'ifort')
         self.assertEqual(tc.get_variable('F90'), 'ifort')
+        self.assertEqual(tc.get_variable('FC'), 'ifort')
         modules.modules_tool().purge()
 
         tc = self.get_toolchain("ictce", version="4.1.13")
@@ -474,11 +454,13 @@ def test_ictce_toolchain(self):
         self.assertEqual(tc.get_variable('CC'), 'mpicc')
         self.assertEqual(tc.get_variable('CXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('F77'), 'mpif77')
-        self.assertEqual(tc.get_variable('F90'), 'mpif90')
+        self.assertEqual(tc.get_variable('F90'), 'mpifc')
+        self.assertEqual(tc.get_variable('FC'), 'mpif90')
         self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
         self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpifc')
         modules.modules_tool().purge()
 
         tc = self.get_toolchain("ictce", version="4.1.13")
@@ -489,15 +471,17 @@ def test_ictce_toolchain(self):
         self.assertTrue('-mt_mpi' in tc.get_variable('CFLAGS'))
         self.assertTrue('-mt_mpi' in tc.get_variable('CXXFLAGS'))
         self.assertTrue('-mt_mpi' in tc.get_variable('FFLAGS'))
-        self.assertTrue('-mt_mpi' in tc.get_variable('F90FLAGS'))
+        self.assertTrue('-mt_mpi' in tc.get_variable('F90FLAGS'))  # FIXME F77FLAGS?
         self.assertEqual(tc.get_variable('CC'), 'mpicc')
         self.assertEqual(tc.get_variable('CXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('F77'), 'mpif77')
         self.assertEqual(tc.get_variable('F90'), 'mpif90')
+        self.assertEqual(tc.get_variable('FC'), 'mpifc')
         self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
         self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpifc')
 
         # cleanup
         shutil.rmtree(tmpdir)

From 888cbbef362c27931a58a05ad35d35338fed408b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 18 Sep 2015 17:45:37 +0200
Subject: [PATCH 1279/1356] trivial whitespace change

---
 easybuild/framework/easyblock.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 2708438a37..557e439fd8 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1196,7 +1196,6 @@ def check_readiness_step(self):
         """
         # set level of parallelism for build
         par = build_option('parallel')
-
         if self.cfg['parallel']:
             if par is None:
                 par = self.cfg['parallel']

From b8d17bd775306a4b52a04247b8c20f5f5d62a594 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Mon, 21 Sep 2015 18:06:20 +0200
Subject: [PATCH 1280/1356] Add support for .tar.Z files

---
 easybuild/framework/easyconfig/templates.py | 5 +++--
 easybuild/tools/filetools.py                | 4 +++-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/templates.py b/easybuild/framework/easyconfig/templates.py
index 93dd3d9844..7cdfcfc9b4 100644
--- a/easybuild/framework/easyconfig/templates.py
+++ b/easybuild/framework/easyconfig/templates.py
@@ -114,7 +114,7 @@
     ('SHLIB_EXT', get_shared_lib_ext(), 'extension for shared libraries'),
 ]
 
-extensions = ['tar.gz', 'tar.xz', 'tar.bz2', 'tgz', 'txz', 'tbz2', 'tb2', 'gtgz', 'zip', 'tar', 'xz']
+extensions = ['tar.gz', 'tar.xz', 'tar.bz2', 'tgz', 'txz', 'tbz2', 'tb2', 'gtgz', 'zip', 'tar', 'xz', 'tar.Z']
 for ext in extensions:
     suffix = ext.replace('.', '_').upper()
     TEMPLATE_CONSTANTS += [
@@ -125,6 +125,7 @@
 # TODO derived config templates
 # versionmajor, versionminor, versionmajorminor (eg '.'.join(version.split('.')[:2])) )
 
+
 def template_constant_dict(config, ignore=None, skip_lower=True):
     """Create a dict for templating the values in the easyconfigs.
         - config is a dict with the structure of EasyConfig._config
@@ -195,7 +196,7 @@ def template_constant_dict(config, ignore=None, skip_lower=True):
             if t_v is None:
                 continue
             try:
-                template_values[TEMPLATE_NAMES_LOWER_TEMPLATE % {'name':name}] = t_v.lower()
+                template_values[TEMPLATE_NAMES_LOWER_TEMPLATE % {'name': name}] = t_v.lower()
             except:
                 _log.debug("_getitem_string: can't get .lower() for name %s value %s (type %s)" %
                            (name, t_v, type(t_v)))
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index c5665289a2..882ff7278b 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -529,7 +529,9 @@ def extract_cmd(filepath, overwrite=False):
         # zip file
         '.zip':     "unzip -qq -o %(filepath)s" if overwrite else "unzip -qq %(filepath)s",
         # iso file
-        '.iso':     "7z x %(filepath)s"
+        '.iso':     "7z x %(filepath)s",
+        # tar.Z: using compress (LZW)
+        '.tar.Z':   "tar xZf %(filepath)s",
     }
 
     suffixes = sorted(extract_cmds.keys(), key=len, reverse=True)

From e2433529090f93ae772a7bc1b1db1e266a8f9995 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Mon, 21 Sep 2015 18:17:21 +0200
Subject: [PATCH 1281/1356] Added test for tar.Z

---
 test/framework/filetools.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 2f489957fd..e3d75002c9 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -74,6 +74,7 @@ def test_extract_cmd(self):
             ('test.tar.xz', "unxz test.tar.xz --stdout | tar x"),
             ('test.txz', "unxz test.txz --stdout | tar x"),
             ('test.iso', "7z x test.iso"),
+            ('test.tar.Z', "tar xZf test.tar.Z"),
         ]
         for (fn, expected_cmd) in tests:
             cmd = ft.extract_cmd(fn)
@@ -273,7 +274,7 @@ def test_path_matches(self):
         tmpdir = tempfile.mkdtemp()
         path1 = os.path.join(tmpdir, 'path1')
         ft.mkdir(path1)
-        path2 = os.path.join(tmpdir, 'path2') 
+        path2 = os.path.join(tmpdir, 'path2')
         ft.mkdir(path1)
         symlink = os.path.join(tmpdir, 'symlink')
         os.symlink(path1, symlink)

From 692961c10b4225d2ebbd0b80dc4fddb7bb7fa7da Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Mon, 21 Sep 2015 20:38:22 +0200
Subject: [PATCH 1282/1356] Fixes case dependency for tar.Z

---
 easybuild/tools/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 882ff7278b..1199f31933 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -531,7 +531,7 @@ def extract_cmd(filepath, overwrite=False):
         # iso file
         '.iso':     "7z x %(filepath)s",
         # tar.Z: using compress (LZW)
-        '.tar.Z':   "tar xZf %(filepath)s",
+        '.tar.z':   "tar xZf %(filepath)s",
     }
 
     suffixes = sorted(extract_cmds.keys(), key=len, reverse=True)

From f21b1a938cb136e310651fd16d60de11b165d6ee Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 22 Sep 2015 09:33:22 +0200
Subject: [PATCH 1283/1356] also install scripts (fixes #1386)

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 7da6baecdf..13800b9f51 100644
--- a/setup.py
+++ b/setup.py
@@ -30,7 +30,7 @@
 
 @author: Kenneth Hoste (Ghent University)
 """
-
+import glob
 import os
 from distutils import log
 
@@ -92,7 +92,7 @@ def find_rel_test():
     package_dir={'test.framework': "test/framework"},
     package_data={"test.framework": find_rel_test()},
     scripts=["eb", "optcomplete.bash", "minimal_bash_completion.bash"],
-    data_files=[],
+    data_files=[('easybuild/scripts', glob.glob('easybuild/scripts/*'))],
     long_description=read('README.rst'),
     classifiers=[
         "Development Status :: 5 - Production/Stable",

From 8e18877d94e4b9899516276e5e3891f146947626 Mon Sep 17 00:00:00 2001
From: Alan <a.ocais@fz-juelich.de>
Date: Tue, 22 Sep 2015 11:50:35 +0200
Subject: [PATCH 1284/1356] removing files from version control

---
 .../module_naming_scheme/toolchain_mns.py     | 73 -------------------
 1 file changed, 73 deletions(-)
 delete mode 100644 easybuild/tools/module_naming_scheme/toolchain_mns.py

diff --git a/easybuild/tools/module_naming_scheme/toolchain_mns.py b/easybuild/tools/module_naming_scheme/toolchain_mns.py
deleted file mode 100644
index 03397c52eb..0000000000
--- a/easybuild/tools/module_naming_scheme/toolchain_mns.py
+++ /dev/null
@@ -1,73 +0,0 @@
-##
-# Copyright 2013-2014 Ghent University
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
-# the Hercules foundation (http://www.herculesstichting.be/in_English)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# http://github.com/hpcugent/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-Implementation of an example hierarchical module naming scheme.
-
-@author: Alan O'Cais (Forschungszentrum Juelich GmbH)
-@author: Eric "The Knife" Gregory (Forschungszentrum Juelich GmbH)
-"""
-
-from easybuild.tools.module_naming_scheme.hierarchical_mns import HierarchicalMNS
-from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
-
-TOOLCHAIN = 'Toolchain'
-MODULECLASS_TC = 'toolchain'
-
-class ToolchainMNS(HierarchicalMNS):
-    """Class implementing a toolchain-based hierarchical module naming scheme."""
-
-    def det_module_subdir(self, ec):
-        """
-        Determine module subdirectory, relative to the top of the module path.
-        This determines the separation between module names exposed to users, and what's part of the $MODULEPATH.
-        Examples: Core, Toolchain/gpsolf/2015.02
-        """
-        if ec.toolchain.name == DUMMY_TOOLCHAIN_NAME:
-            # toolchain is dummy/dummy, put in Core
-            subdir = CORE
-        else:
-            subdir = os.path.join(TOOLCHAIN,ec.toolchain.name,ec.toolchain.version)
-        return subdir
-
-    def det_modpath_extensions(self, ec):
-        """
-        Determine module path extensions, if any.
-        Examples: Toolchain/intel/2014.12 (for intel/2014.12 module)
-        """
-        modclass = ec['moduleclass']
-        paths = []
-	# Take care of the corner cases, such as GCC, where it is both a compiler and a toolchain
-        if modclass == MODULECLASS_TC or ec['name'] in ['GCC']:
-            fullver = self.det_full_version(ec)
-            paths.append(os.path.join(TOOLCHAIN,  ec['name'], fullver))
-        return paths
-
-    def expand_toolchain_load(self):
-        """
-        Determine whether load statements for a toolchain should be expanded to load statements for its dependencies.
-        This is useful when toolchains are not exposed to users.
-        """
-	# In our case we still have to load the toolchains because they are explicitly exposed when extending the module path
-        return True

From 3a6252fe62866797dd60b1ddba3366dedf87f7e4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 25 Sep 2015 16:09:48 +0200
Subject: [PATCH 1285/1356] fix dev version to follow PEP-440, which setuptools
 basically jams down our throat

---
 easybuild/tools/version.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/easybuild/tools/version.py b/easybuild/tools/version.py
index 24b139d960..6b90246ba7 100644
--- a/easybuild/tools/version.py
+++ b/easybuild/tools/version.py
@@ -37,7 +37,13 @@
 
 # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1"
 # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware!
-VERSION = LooseVersion('2.4.0dev')
+#
+# important note: dev versions should follow the 'X.Y.Z.dev0' format
+# see https://www.python.org/dev/peps/pep-0440/#developmental-releases
+# recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
+#   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
+# This causes problems further up the dependency chain...
+VERSION = LooseVersion('2.4.0.dev0')
 UNKNOWN = 'UNKNOWN'
 
 def get_git_revision():

From fd46bfd3d5205dd87b015269fb552483067a34ac Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 7 Oct 2015 10:34:16 +0200
Subject: [PATCH 1286/1356] Ignore hidden directories when returning the
 finaldir

---
 easybuild/tools/filetools.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 1199f31933..525cf3ff66 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -472,12 +472,11 @@ def find_base_dir():
     """
     def get_local_dirs_purged():
         # e.g. always purge the log directory
+        # and hidden directories
         ignoreDirs = ["easybuild"]
 
         lst = os.listdir(os.getcwd())
-        for ignDir in ignoreDirs:
-            if ignDir in lst:
-                lst.remove(ignDir)
+        lst = [Dir for Dir in lst if not Dir.startswith('.') or Dir in ignoreDirs]
         return lst
 
     lst = get_local_dirs_purged()

From 012a967db64cdf497f023b83fa146a38525a6550 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 7 Oct 2015 10:48:23 +0200
Subject: [PATCH 1287/1356] Fix remarks

---
 easybuild/tools/filetools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 525cf3ff66..d11097cfa3 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -473,10 +473,10 @@ def find_base_dir():
     def get_local_dirs_purged():
         # e.g. always purge the log directory
         # and hidden directories
-        ignoreDirs = ["easybuild"]
+        ignoredirs = ["easybuild"]
 
         lst = os.listdir(os.getcwd())
-        lst = [Dir for Dir in lst if not Dir.startswith('.') or Dir in ignoreDirs]
+        lst = [d for d in lst if not d.startswith('.') or d in ignoredirs]
         return lst
 
     lst = get_local_dirs_purged()

From e82b4032e10ad22dc2e985cc2ff676e021bf578b Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 7 Oct 2015 11:51:39 +0200
Subject: [PATCH 1288/1356] Bugfix in find_base_dir

---
 easybuild/tools/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index d11097cfa3..21998b2512 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -476,7 +476,7 @@ def get_local_dirs_purged():
         ignoredirs = ["easybuild"]
 
         lst = os.listdir(os.getcwd())
-        lst = [d for d in lst if not d.startswith('.') or d in ignoredirs]
+        lst = [d for d in lst if not d.startswith('.') and d not in ignoredirs]
         return lst
 
     lst = get_local_dirs_purged()

From 67603f4fb6c14a7bcbbc5fc2a3c316fa8fbf2016 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 7 Oct 2015 11:52:13 +0200
Subject: [PATCH 1289/1356] Added test for find_base_dir

---
 test/framework/filetools.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index e3d75002c9..7086add22c 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -28,6 +28,7 @@
 @author: Toon Willems (Ghent University)
 @author: Kenneth Hoste (Ghent University)
 @author: Stijn De Weirdt (Ghent University)
+@author: Ward Poelmans (Ghent University)
 """
 import os
 import shutil
@@ -94,6 +95,18 @@ def test_cwd(self):
         # used to be part of test_parse_log_error
         self.assertEqual(os.getcwd(), ft.find_base_dir())
 
+    def test_find_base_dir(self):
+        """test if we find the correct base dir"""
+        tmpdir = tempfile.mkdtemp()
+
+        foodir = os.path.join(tmpdir, 'foo')
+        os.mkdir(foodir)
+        os.mkdir(os.path.join(tmpdir, '.bar'))
+        os.mkdir(os.path.join(tmpdir, 'easybuild'))
+
+        os.chdir(tmpdir)
+        self.assertEqual(foodir, ft.find_base_dir())
+
     def test_encode_class_name(self):
         """Test encoding of class names."""
         for (class_name, encoded_class_name) in self.class_names:

From 6d39f7e7c5fe300b51acfe98a983943b9dc854c6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 7 Oct 2015 13:57:28 +0200
Subject: [PATCH 1290/1356] fix guess_start_dir in case we're already in
 start_dir

---
 easybuild/framework/easyblock.py | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 557e439fd8..475454b77c 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1136,19 +1136,28 @@ def guess_start_dir(self):
         -- if abspath: use that
         -- else, treat it as subdir for regular procedure
         """
-        tmpdir = ''
+        start_dir = ''
         if self.cfg['start_dir']:
-            tmpdir = self.cfg['start_dir']
+            start_dir = self.cfg['start_dir']
 
-        if not os.path.isabs(tmpdir):
+        if not os.path.isabs(start_dir):
             if len(self.src) > 0 and not self.skip and self.src[0]['finalpath']:
-                self.cfg['start_dir'] = os.path.join(self.src[0]['finalpath'], tmpdir)
+                topdir = self.src[0]['finalpath']
             else:
-                self.cfg['start_dir'] = os.path.join(self.builddir, tmpdir)
+                topdir = self.builddir
+
+            abs_start_dir = os.path.join(topdir, start_dir)
+            if topdir.endswith(start_dir) and not os.path.exists(abs_start_dir):
+                self.cfg['start_dir'] = topdir
+            else:
+                if os.path.exists(abs_start_dir):
+                    self.cfg['start_dir'] = abs_start_dir
+                else:
+                    raise EasyBuildError("Specified start dir %s does not exist", abs_start_dir)
 
         try:
             os.chdir(self.cfg['start_dir'])
-            self.log.debug("Changed to real build directory %s" % (self.cfg['start_dir']))
+            self.log.debug("Changed to real build directory %s (start_dir)" % self.cfg['start_dir'])
         except OSError, err:
             raise EasyBuildError("Can't change to real build directory %s: %s", self.cfg['start_dir'], err)
 

From 051687a9a626d97370c5d559068828f9061b3ec1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 7 Oct 2015 15:45:13 +0200
Subject: [PATCH 1291/1356] add and use only_if_module_is_available decorator
 function

---
 easybuild/framework/easyconfig/tools.py | 65 ++++++++++++-------------
 easybuild/tools/filetools.py            | 14 ++----
 easybuild/tools/job/gc3pie.py           | 28 +++--------
 easybuild/tools/job/pbs_python.py       | 33 +++++--------
 easybuild/tools/repository/gitrepo.py   | 10 ++--
 easybuild/tools/repository/svnrepo.py   | 12 ++---
 easybuild/tools/utilities.py            | 24 +++++++++
 7 files changed, 87 insertions(+), 99 deletions(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index 611de90bbf..ed054b6c8a 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -55,34 +55,28 @@
 from easybuild.tools.ordereddict import OrderedDict
 from easybuild.tools.run import run_cmd
 from easybuild.tools.toolchain import DUMMY_TOOLCHAIN_NAME
-from easybuild.tools.utilities import quote_str
+from easybuild.tools.utilities import only_if_module_is_available, quote_str
 
 # optional Python packages, these might be missing
 # failing imports are just ignored
 # a NameError should be catched where these are used
 
-# PyGraph (used for generating dependency graphs)
-graph_errors = []
-try:
-    from pygraph.classes.digraph import digraph
-except ImportError, err:
-    graph_errors.append("Failed to import pygraph-core: try easy_install python-graph-core")
-
 try:
+    # PyGraph (used for generating dependency graphs)
+    # https://pypi.python.org/pypi/python-graph-core
+    import pygraph.classes.digraph as digraph
+    # https://pypi.python.org/pypi/python-graph-dot
     import pygraph.readwrite.dot as dot
-except ImportError, err:
-    graph_errors.append("Failed to import pygraph-dot: try easy_install python-graph-dot")
-
-# graphviz (used for creating dependency graph images)
-try:
+    # graphviz (used for creating dependency graph images)
     sys.path.append('..')
     sys.path.append('/usr/lib/graphviz/python/')
     sys.path.append('/usr/lib64/graphviz/python/')
+    # https://pypi.python.org/pypi/pygraphviz
+    # graphviz-python (yum) or python-pygraphviz (apt-get)
+    # or brew install graphviz --with-bindings (OS X)
     import gv
-except ImportError, err:
-    graph_errors.append("Failed to import graphviz: try yum install graphviz-python,"
-                        "or apt-get install python-pygraphviz,"
-                        "or brew install graphviz --with-bindings")
+except ImportError:
+    pass
 
 
 _log = fancylogger.getLogger('easyconfig.tools', fname=False)
@@ -147,7 +141,8 @@ def find_resolved_modules(unprocessed, avail_modules, retain_all_deps=False):
     return ordered_ecs, new_unprocessed, new_avail_modules
 
 
-def _dep_graph(fn, specs):
+@only_if_module_is_available('pygraph.classes.digraph', pkgname='python-graph-core')
+def dep_graph(filename, specs):
     """
     Create a dependency graph for the given easyconfigs.
     """
@@ -183,27 +178,31 @@ def mk_node_name(spec):
         for dep in spec['ec'].all_dependencies:
             dgr.add_edge((spec['module'], dep))
 
+    _dep_graph_dump(dgr, filename)
+
+    if not build_option('silent'):
+        print "Wrote dependency graph for %d easyconfigs to %s" % (len(specs), filename)
+
+
+@only_if_module_is_available('pygraph.readwrite.dot', pkgname='python-graph-dot')
+def _dep_graph_dump(dgr, filename):
+    """Dump dependency graph to file, in specified format."""
     # write to file
     dottxt = dot.write(dgr)
-    if fn.endswith(".dot"):
+    if os.path.splitext(filename)[-1] == '.dot':
         # create .dot file
-        write_file(fn, dottxt)
+        write_file(filename, dottxt)
     else:
-        # try and render graph in specified file format
-        gvv = gv.readstring(dottxt)
-        gv.layout(gvv, 'dot')
-        gv.render(gvv, fn.split('.')[-1], fn)
-
-    if not build_option('silent'):
-        print "Wrote dependency graph for %d easyconfigs to %s" % (len(specs), fn)
+        _dep_graph_gv(dottxt, filename)
 
 
-def dep_graph(*args, **kwargs):
-    try:
-        _dep_graph(*args, **kwargs)
-    except NameError, err:
-        raise EasyBuildError("An optional Python packages required to generate dependency graphs is missing: %s, %s",
-                             '\n'.join(graph_errors), err)
+@only_if_module_is_available('gv', pkgname='graphviz')
+def _dep_graph_gv(dottxt, filename):
+    """Render dependency graph to file using graphviz."""
+    # try and render graph in specified file format
+    gvv = gv.readstring(dottxt)
+    gv.layout(gvv, 'dot')
+    gv.render(gvv, os.path.splitext(filename)[-1], filename)
 
 
 def get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None):
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 21998b2512..2012ed2b94 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -36,6 +36,7 @@
 @author: Sotiris Fragkiskos (NTUA, CERN)
 """
 import glob
+import hashlib
 import os
 import re
 import shutil
@@ -93,23 +94,14 @@
     r'~': "_tilde_",
 }
 
-try:
-    # preferred over md5/sha modules, but only available in Python 2.5 and more recent
-    import hashlib
-    md5_class = hashlib.md5
-    sha1_class = hashlib.sha1
-except ImportError:
-    import md5, sha
-    md5_class = md5.md5
-    sha1_class = sha.sha
 
 # default checksum for source and patch files
 DEFAULT_CHECKSUM = 'md5'
 
 # map of checksum types to checksum functions
 CHECKSUM_FUNCTIONS = {
-    'md5': lambda p: calc_block_checksum(p, md5_class()),
-    'sha1': lambda p: calc_block_checksum(p, sha1_class()),
+    'md5': lambda p: calc_block_checksum(p, hashlib.md5()),
+    'sha1': lambda p: calc_block_checksum(p, hashlib.sha1()),
     'adler32': lambda p: calc_block_checksum(p, ZlibChecksum(zlib.adler32)),
     'crc32': lambda p: calc_block_checksum(p, ZlibChecksum(zlib.crc32)),
     'size': lambda p: os.path.getsize(p),
diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 60f05ac661..5e7437ab7f 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -39,6 +39,7 @@
 from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.config import build_option
 from easybuild.tools.job.backend import JobBackend
+from easybuild.tools.utilities import only_if_module_is_available
 
 
 _log = fancylogger.getLogger('gc3pie', fname=False)
@@ -60,25 +61,10 @@
     # instruct GC3Pie to not ignore errors, but raise exceptions instead
     gc3libs.UNIGNORE_ALL_ERRORS = True
 
-    # GC3Pie is available, no need guard against import errors
-    def gc3pie_imported(fn):
-        """No-op decorator."""
-        return fn
-
 except ImportError as err:
     _log.debug("Failed to import gc3libs from GC3Pie."
                " Silently ignoring, this is a real issue only when GC3Pie is used as backend for --job")
 
-    # GC3Pie not available, turn method in a raised EasyBuildError
-    def gc3pie_imported(_):
-        """Decorator which raises an EasyBuildError because GC3Pie is not available."""
-        def fail(*args, **kwargs):
-            """Raise EasyBuildError since GC3Pie is not available."""
-            errmsg = "Python modules 'gc3libs' is not available. Please make sure GC3Pie is installed and usable: %s"
-            raise EasyBuildError(errmsg, err)
-
-        return fail
-
 
 # eb --job --job-backend=GC3Pie
 class GC3Pie(JobBackend):
@@ -96,7 +82,7 @@ class GC3Pie(JobBackend):
     DEVELOPMENT_VERSION = 'development'  # 'magic' version string indicated non-released version
     REQ_SVN_REVISION = 4287  # use integer value, not a string!
 
-    @gc3pie_imported
+    @only_if_module_is_available('gc3libs.core', pkgname='gc3pie')
     def _check_version(self):
         """Check whether GC3Pie version complies with required version."""
         # location of __version__ to use may change, depending on the minimal required SVN revision for development versions
@@ -122,7 +108,7 @@ def _check_version(self):
             raise EasyBuildError("Failed to parse GC3Pie version string '%s' using pattern %s",
                                  version_str, version_regex.pattern)
 
-    @gc3pie_imported
+    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
     def init(self):
         """
         Initialise the GC3Pie job backend.
@@ -145,7 +131,7 @@ def init(self):
         # before polling again (in seconds)
         self.poll_interval = build_option('job_polling_interval')
 
-    @gc3pie_imported
+    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
     def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         """
         Create and return a job object with the given parameters.
@@ -209,7 +195,7 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
 
         return Application(['/bin/sh', '-c', script], **named_args)
 
-    @gc3pie_imported
+    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
     def queue(self, job, dependencies=frozenset()):
         """
         Add a job to the queue, optionally specifying dependencies.
@@ -220,7 +206,7 @@ def queue(self, job, dependencies=frozenset()):
         # since it's not trivial to determine the correct job count from self.jobs, we keep track of a count ourselves
         self.job_cnt += 1
 
-    @gc3pie_imported
+    @only_if_module_is_available('gc3libs.exceptions', pkgname='gc3pie')
     def complete(self):
         """
         Complete a bulk job submission.
@@ -267,7 +253,7 @@ def complete(self):
         print_msg("Done processing jobs", log=self.log, silent=build_option('silent'))
         self._print_status_report()
 
-    @gc3pie_imported
+    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
     def _print_status_report(self):
         """
         Print a job status report to STDOUT and the log file.
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index d511093583..d5f26e9792 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -38,6 +38,7 @@
 from easybuild.tools.build_log import EasyBuildError, print_msg
 from easybuild.tools.config import build_option
 from easybuild.tools.job.backend import JobBackend
+from easybuild.tools.utilities import only_if_module_is_available
 
 
 _log = fancylogger.getLogger('pbs_python', fname=False)
@@ -53,26 +54,10 @@
     from PBSQuery import PBSQuery
     KNOWN_HOLD_TYPES = [pbs.USER_HOLD, pbs.OTHER_HOLD, pbs.SYSTEM_HOLD]
 
-    # `pbs_python` is available, no need guard against import errors
-    def pbs_python_imported(fn):
-        """No-op decorator."""
-        return fn
-
 except ImportError as err:
-    _log.debug("Failed to import pbs from pbs_python."
+    _log.debug("Failed to import pbs/PBSQuery from pbs_python."
                " Silently ignoring, this is a real issue only when pbs_python is used as backend for --job")
 
-    # `pbs_python` not available, turn method in a raised EasyBuildError
-    def pbs_python_imported(_):
-        """Decorator which raises an EasyBuildError because pbs_python is not available."""
-        def fail(*args, **kwargs):
-            """Raise EasyBuildError since `pbs_python` is not available."""
-            errmsg = "Python modules 'PBSQuery' and 'pbs' are not available. "
-            errmsg += "Please make sure `pbs_python` is installed and usable: %s"
-            raise EasyBuildError(errmsg, err)
-
-        return fail
-
 
 class PbsPython(JobBackend):
     """
@@ -82,7 +67,7 @@ class PbsPython(JobBackend):
     # pbs_python 4.1.0 introduces the pbs.version variable we rely on
     REQ_VERSION = '4.1.0'
 
-    @pbs_python_imported
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def _check_version(self):
         """Check whether pbs_python version complies with required version."""
         version_regex = re.compile('pbs_python version (?P<version>.*)')
@@ -96,6 +81,7 @@ def _check_version(self):
             raise EasyBuildError("Failed to parse pbs_python version string '%s' using pattern %s",
                                  pbs.version, version_regex.pattern)
 
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def __init__(self, *args, **kwargs):
         """Constructor."""
         pbs_server = kwargs.pop('pbs_server', None)
@@ -115,7 +101,7 @@ def init(self):
         self.connect_to_server()
         self._submitted = []
 
-    @pbs_python_imported
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def connect_to_server(self):
         """Connect to PBS server, set and return connection."""
         if not self.conn:
@@ -162,13 +148,13 @@ def complete(self):
 
         self.log.info("Job ids of leaf nodes in dep. graph: %s" % ','.join(leaf_nodes))
 
-    @pbs_python_imported
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def disconnect_from_server(self):
         """Disconnect current connection."""
         pbs.pbs_disconnect(self.conn)
         self.conn = None
 
-    @pbs_python_imported
+    @only_if_module_is_available('PBSQuery', pkgname='pbs_python')
     def _get_ppn(self):
         """Guess PBS' `ppn` value for a full node."""
         # cache this value as it's not likely going to change over the
@@ -270,6 +256,7 @@ def add_dependencies(self, jobs):
         """
         self.deps.extend(jobs)
 
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def _submit(self):
         """Submit the jobscript txt, set self.jobid"""
         txt = self.script
@@ -354,6 +341,7 @@ def _submit(self):
             self.jobid = jobid
             os.remove(scriptfn)
 
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def set_hold(self, hold_type=None):
         """Set hold on job of specified type."""
         # we can't set this default for hold_type in function signature,
@@ -375,6 +363,7 @@ def set_hold(self, hold_type=None):
         else:
             self.log.warning("Hold type %s was already set for %s" % (hold_type, self.jobid))
 
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def release_hold(self, hold_type=None):
         """Release hold on job of specified type."""
         # we can't set this default for hold_type in function signature,
@@ -441,6 +430,7 @@ def get_uniq_hosts(txt, num=None):
         else:
             return 'running'
 
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def info(self, types=None):
         """
         Return jobinfo
@@ -483,6 +473,7 @@ def info(self, types=None):
         self.log.debug("Found jobinfo %s" % job_details)
         return job_details
 
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def remove(self):
         """Remove the job with id jobid"""
         result = pbs.pbs_deljob(self.pbsconn, self.jobid, '')  # use empty string, not NULL
diff --git a/easybuild/tools/repository/gitrepo.py b/easybuild/tools/repository/gitrepo.py
index 83a1dae18c..0964cf471a 100644
--- a/easybuild/tools/repository/gitrepo.py
+++ b/easybuild/tools/repository/gitrepo.py
@@ -46,6 +46,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import rmtree2
 from easybuild.tools.repository.filerepo import FileRepository
+from easybuild.tools.utilities import only_if_module_is_available
 from easybuild.tools.version import VERSION
 
 _log = fancylogger.getLogger('gitrepo', fname=False)
@@ -54,7 +55,7 @@
 # failing imports are just ignored
 # a NameError should be catched where these are used
 
-# GitPython
+# GitPython (http://gitorious.org/git-python)
 try:
     import git
     from git import GitCommandError
@@ -82,17 +83,14 @@ def __init__(self, *args):
         self.client = None
         FileRepository.__init__(self, *args)
 
+    @only_if_module_is_available('git', pkgname='GitPython')
     def setup_repo(self):
         """
         Set up git repository.
         """
-        try:
-            git.GitCommandError
-        except NameError, err:
-            raise EasyBuildError("It seems like GitPython is not available: %s", err)
-
         self.wc = tempfile.mkdtemp(prefix='git-wc-')
 
+    @only_if_module_is_available('git', pkgname='GitPython')
     def create_working_copy(self):
         """
         Create git working copy.
diff --git a/easybuild/tools/repository/svnrepo.py b/easybuild/tools/repository/svnrepo.py
index 7afc3dd74b..c3d2c5351a 100644
--- a/easybuild/tools/repository/svnrepo.py
+++ b/easybuild/tools/repository/svnrepo.py
@@ -46,12 +46,14 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import rmtree2
 from easybuild.tools.repository.filerepo import FileRepository
+from easybuild.tools.utilities import only_if_module_is_available
+
 
 _log = fancylogger.getLogger('svnrepo', fname=False)
 
+
 # optional Python packages, these might be missing
 # failing imports are just ignored
-# a NameError should be catched where these are used
 
 # PySVN
 try:
@@ -59,7 +61,7 @@
     from pysvn import ClientError  # IGNORE:E0611 pysvn fails to recognize ClientError is available
     HAVE_PYSVN = True
 except ImportError:
-    _log.debug('Failed to import pysvn module')
+    _log.debug("Failed to import pysvn module")
     HAVE_PYSVN = False
 
 
@@ -81,16 +83,12 @@ def __init__(self, *args):
         self.client = None
         FileRepository.__init__(self, *args)
 
+    @only_if_module_is_available('pysvn', url='http://pysvn.tigris.org/')
     def setup_repo(self):
         """
         Set up SVN repository.
         """
         self.repo = os.path.join(self.repo, self.subdir)
-        try:
-            pysvn.ClientError  # IGNORE:E0611 pysvn fails to recognize ClientError is available
-        except NameError, err:
-            raise EasyBuildError("pysvn not available (%s). Make sure it is installed properly. "
-                                 "Run 'python -c \"import pysvn\"' to test.", err)
 
         # try to connect to the repository
         self.log.debug("Try to connect to repository %s" % self.repo)
diff --git a/easybuild/tools/utilities.py b/easybuild/tools/utilities.py
index 555081d60e..b826839271 100644
--- a/easybuild/tools/utilities.py
+++ b/easybuild/tools/utilities.py
@@ -122,3 +122,27 @@ def import_available_modules(namespace):
                     raise EasyBuildError("import_available_modules: Failed to import %s: %s", modpath, err)
                 modules.append(mod)
     return modules
+
+
+def only_if_module_is_available(modname, pkgname=None, url=None):
+    """Decorator to guard functions/methods against missing required module with specified name."""
+    if pkgname and url is None:
+        url = 'https://pypi.python.org/pypi/%s' % pkgname
+
+    def wrap(orig):
+        """Decorated function, raises ImportError if specified module is not available."""
+        try:
+            __import__(modname)
+            return orig
+
+        except ImportError as err:
+            def error(*args):
+                msg = "%s; required module '%s' is not available" % (err, modname)
+                if pkgname:
+                    msg += " (provided by Python package %s, available from %s)" % (pkgname, url)
+                elif url:
+                    msg += " (available from %s)" % url
+                raise ImportError(msg)
+            return error
+
+    return wrap

From f9969a834b424f05d2f40d59f795bfdd393cf1e3 Mon Sep 17 00:00:00 2001
From: molden <martijn.oldenhof@kuleuven.be>
Date: Wed, 7 Oct 2015 16:46:13 +0200
Subject: [PATCH 1292/1356] give easyblocks the possibility to choose maxhits
 for run_cmd_qa

---
 easybuild/tools/run.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index 651042651e..85199370f4 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -130,7 +130,7 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
     return parse_cmd_output(cmd, stdouterr, ec, simple, log_all, log_ok, regexp)
 
 
-def run_cmd_qa(cmd, qa, no_qa=None, log_ok=True, log_all=False, simple=False, regexp=True, std_qa=None, path=None):
+def run_cmd_qa(cmd, qa, no_qa=None, log_ok=True, log_all=False, simple=False, regexp=True, std_qa=None, path=None, maxhits=50):
     """
     Executes a command cmd
     - looks for questions and tries to answer based on qa dictionary
@@ -227,7 +227,7 @@ def check_answers_list(answers):
     else:
         runLog = None
 
-    maxHitCount = 50
+    maxHitCount = maxhits 
 
     try:
         p = Popen(cmd, shell=True, stdout=PIPE, stderr=STDOUT, stdin=PIPE, close_fds=True, executable="/bin/bash")

From 72dc5e64d14cc2655edc24cd2628ddfaed846d75 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 7 Oct 2015 17:21:37 +0200
Subject: [PATCH 1293/1356] fix remarks

---
 easybuild/tools/job/gc3pie.py         | 11 +++++------
 easybuild/tools/job/pbs_python.py     | 13 ++++---------
 easybuild/tools/repository/gitrepo.py |  3 +--
 easybuild/tools/repository/svnrepo.py |  2 +-
 4 files changed, 11 insertions(+), 18 deletions(-)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 5e7437ab7f..376326c8c6 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -82,7 +82,11 @@ class GC3Pie(JobBackend):
     DEVELOPMENT_VERSION = 'development'  # 'magic' version string indicated non-released version
     REQ_SVN_REVISION = 4287  # use integer value, not a string!
 
-    @only_if_module_is_available('gc3libs.core', pkgname='gc3pie')
+    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
+    def __init__(self, *args, **kwargs):
+        """GC3Pie constructor."""
+        super(GC3Pie, self).__init__(*args, **kwargs)
+
     def _check_version(self):
         """Check whether GC3Pie version complies with required version."""
         # location of __version__ to use may change, depending on the minimal required SVN revision for development versions
@@ -108,7 +112,6 @@ def _check_version(self):
             raise EasyBuildError("Failed to parse GC3Pie version string '%s' using pattern %s",
                                  version_str, version_regex.pattern)
 
-    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
     def init(self):
         """
         Initialise the GC3Pie job backend.
@@ -131,7 +134,6 @@ def init(self):
         # before polling again (in seconds)
         self.poll_interval = build_option('job_polling_interval')
 
-    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
     def make_job(self, script, name, env_vars=None, hours=None, cores=None):
         """
         Create and return a job object with the given parameters.
@@ -195,7 +197,6 @@ def make_job(self, script, name, env_vars=None, hours=None, cores=None):
 
         return Application(['/bin/sh', '-c', script], **named_args)
 
-    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
     def queue(self, job, dependencies=frozenset()):
         """
         Add a job to the queue, optionally specifying dependencies.
@@ -206,7 +207,6 @@ def queue(self, job, dependencies=frozenset()):
         # since it's not trivial to determine the correct job count from self.jobs, we keep track of a count ourselves
         self.job_cnt += 1
 
-    @only_if_module_is_available('gc3libs.exceptions', pkgname='gc3pie')
     def complete(self):
         """
         Complete a bulk job submission.
@@ -253,7 +253,6 @@ def complete(self):
         print_msg("Done processing jobs", log=self.log, silent=build_option('silent'))
         self._print_status_report()
 
-    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
     def _print_status_report(self):
         """
         Print a job status report to STDOUT and the log file.
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index d5f26e9792..24925f0dc2 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -68,6 +68,10 @@ class PbsPython(JobBackend):
     REQ_VERSION = '4.1.0'
 
     @only_if_module_is_available('pbs', pkgname='pbs_python')
+    def __init__(self, *args, **kwargs):
+        """PbsPython constructor."""
+        super(GC3Pie, self).__init__(*args, **kwargs)
+
     def _check_version(self):
         """Check whether pbs_python version complies with required version."""
         version_regex = re.compile('pbs_python version (?P<version>.*)')
@@ -81,7 +85,6 @@ def _check_version(self):
             raise EasyBuildError("Failed to parse pbs_python version string '%s' using pattern %s",
                                  pbs.version, version_regex.pattern)
 
-    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def __init__(self, *args, **kwargs):
         """Constructor."""
         pbs_server = kwargs.pop('pbs_server', None)
@@ -101,7 +104,6 @@ def init(self):
         self.connect_to_server()
         self._submitted = []
 
-    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def connect_to_server(self):
         """Connect to PBS server, set and return connection."""
         if not self.conn:
@@ -148,13 +150,11 @@ def complete(self):
 
         self.log.info("Job ids of leaf nodes in dep. graph: %s" % ','.join(leaf_nodes))
 
-    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def disconnect_from_server(self):
         """Disconnect current connection."""
         pbs.pbs_disconnect(self.conn)
         self.conn = None
 
-    @only_if_module_is_available('PBSQuery', pkgname='pbs_python')
     def _get_ppn(self):
         """Guess PBS' `ppn` value for a full node."""
         # cache this value as it's not likely going to change over the
@@ -256,7 +256,6 @@ def add_dependencies(self, jobs):
         """
         self.deps.extend(jobs)
 
-    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def _submit(self):
         """Submit the jobscript txt, set self.jobid"""
         txt = self.script
@@ -341,7 +340,6 @@ def _submit(self):
             self.jobid = jobid
             os.remove(scriptfn)
 
-    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def set_hold(self, hold_type=None):
         """Set hold on job of specified type."""
         # we can't set this default for hold_type in function signature,
@@ -363,7 +361,6 @@ def set_hold(self, hold_type=None):
         else:
             self.log.warning("Hold type %s was already set for %s" % (hold_type, self.jobid))
 
-    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def release_hold(self, hold_type=None):
         """Release hold on job of specified type."""
         # we can't set this default for hold_type in function signature,
@@ -430,7 +427,6 @@ def get_uniq_hosts(txt, num=None):
         else:
             return 'running'
 
-    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def info(self, types=None):
         """
         Return jobinfo
@@ -473,7 +469,6 @@ def info(self, types=None):
         self.log.debug("Found jobinfo %s" % job_details)
         return job_details
 
-    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def remove(self):
         """Remove the job with id jobid"""
         result = pbs.pbs_deljob(self.pbsconn, self.jobid, '')  # use empty string, not NULL
diff --git a/easybuild/tools/repository/gitrepo.py b/easybuild/tools/repository/gitrepo.py
index 0964cf471a..0e7bf97007 100644
--- a/easybuild/tools/repository/gitrepo.py
+++ b/easybuild/tools/repository/gitrepo.py
@@ -75,6 +75,7 @@ class GitRepository(FileRepository):
 
     USABLE = HAVE_GIT
 
+    @only_if_module_is_available('git', pkgname='GitPython')
     def __init__(self, *args):
         """
         Initialize git client to None (will be set later)
@@ -83,14 +84,12 @@ def __init__(self, *args):
         self.client = None
         FileRepository.__init__(self, *args)
 
-    @only_if_module_is_available('git', pkgname='GitPython')
     def setup_repo(self):
         """
         Set up git repository.
         """
         self.wc = tempfile.mkdtemp(prefix='git-wc-')
 
-    @only_if_module_is_available('git', pkgname='GitPython')
     def create_working_copy(self):
         """
         Create git working copy.
diff --git a/easybuild/tools/repository/svnrepo.py b/easybuild/tools/repository/svnrepo.py
index c3d2c5351a..16dfa1ddc4 100644
--- a/easybuild/tools/repository/svnrepo.py
+++ b/easybuild/tools/repository/svnrepo.py
@@ -76,6 +76,7 @@ class SvnRepository(FileRepository):
 
     USABLE = HAVE_PYSVN
 
+    @only_if_module_is_available('pysvn', url='http://pysvn.tigris.org/')
     def __init__(self, *args):
         """
         Set self.client to None. Real logic is in setupRepo and createWorkingCopy
@@ -83,7 +84,6 @@ def __init__(self, *args):
         self.client = None
         FileRepository.__init__(self, *args)
 
-    @only_if_module_is_available('pysvn', url='http://pysvn.tigris.org/')
     def setup_repo(self):
         """
         Set up SVN repository.

From 2249f9cd3ef3bec30fe1fa7a509cfd9ec438c1c1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 7 Oct 2015 17:23:28 +0200
Subject: [PATCH 1294/1356] fix broken pygraph import

---
 easybuild/framework/easyconfig/tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/tools.py b/easybuild/framework/easyconfig/tools.py
index ed054b6c8a..abfd9c22d0 100644
--- a/easybuild/framework/easyconfig/tools.py
+++ b/easybuild/framework/easyconfig/tools.py
@@ -64,7 +64,7 @@
 try:
     # PyGraph (used for generating dependency graphs)
     # https://pypi.python.org/pypi/python-graph-core
-    import pygraph.classes.digraph as digraph
+    from pygraph.classes.digraph import digraph
     # https://pypi.python.org/pypi/python-graph-dot
     import pygraph.readwrite.dot as dot
     # graphviz (used for creating dependency graph images)

From d4e3ba561e9138ae95ff319c1b5f3bd28468c5be Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 7 Oct 2015 17:58:32 +0200
Subject: [PATCH 1295/1356] New test to check the guess_start_dir

---
 test/framework/easyblock.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 5561e46d7f..35af709e7a 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -695,6 +695,29 @@ def test_parallel(self):
         test_eb.check_readiness_step()
         self.assertEqual(test_eb.cfg['parallel'], 67)
 
+    def test_guess_start_dir(self):
+        """Test guessing the start dir."""
+        ec = process_easyconfig(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb'))[0]
+
+        fancylogger.logToScreen(enable=True)
+        fancylogger.setLogLevelDebug()
+
+        eb = EasyBlock(ec['ec'])
+        eb.silent = True
+        eb.cfg['stop'] = 'patch'
+        eb.run_all_steps(False)
+        eb.guess_start_dir()
+        self.assertEqual(os.getcwd(), os.path.join(eb.builddir, "toy-0.0"))
+
+        ec['ec']['start_dir'] = "%(name)s-%(version)s"
+
+        eb = EasyBlock(ec['ec'])
+        eb.silent = True
+        eb.cfg['stop'] = 'source'
+        eb.run_all_steps(False)
+        eb.guess_start_dir()
+        self.assertEqual(os.getcwd(), os.path.join(eb.builddir, "toy-0.0"))
+
 
 def suite():
     """ return all the tests in this file """

From 3e505449a21ed0ef23df630694bd99aed2cbde46 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 7 Oct 2015 18:00:24 +0200
Subject: [PATCH 1296/1356] Remove logger from test

---
 test/framework/easyblock.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 35af709e7a..fe2dde7354 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -699,9 +699,6 @@ def test_guess_start_dir(self):
         """Test guessing the start dir."""
         ec = process_easyconfig(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb'))[0]
 
-        fancylogger.logToScreen(enable=True)
-        fancylogger.setLogLevelDebug()
-
         eb = EasyBlock(ec['ec'])
         eb.silent = True
         eb.cfg['stop'] = 'patch'

From fcb5b6b803868dd1a49ae03042f22b422405b0e9 Mon Sep 17 00:00:00 2001
From: Ward Poelmans <wpoely86@gmail.com>
Date: Wed, 7 Oct 2015 18:01:06 +0200
Subject: [PATCH 1297/1356] Make both parts consistent

---
 test/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index fe2dde7354..30a79bbf8b 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -710,7 +710,7 @@ def test_guess_start_dir(self):
 
         eb = EasyBlock(ec['ec'])
         eb.silent = True
-        eb.cfg['stop'] = 'source'
+        eb.cfg['stop'] = 'patch'
         eb.run_all_steps(False)
         eb.guess_start_dir()
         self.assertEqual(os.getcwd(), os.path.join(eb.builddir, "toy-0.0"))

From 1f763162701a47747a8008a533bb90aba9aa9057 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 7 Oct 2015 19:03:03 +0200
Subject: [PATCH 1298/1356] enhance test for guess_start_dir, extra log
 statement

---
 easybuild/framework/easyblock.py |  2 ++
 test/framework/easyblock.py      | 44 ++++++++++++++++++++------------
 2 files changed, 29 insertions(+), 17 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 475454b77c..739411aa68 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1155,6 +1155,8 @@ def guess_start_dir(self):
                 else:
                     raise EasyBuildError("Specified start dir %s does not exist", abs_start_dir)
 
+        self.log.info("Using %s as start dir", self.cfg['start_dir'])
+
         try:
             os.chdir(self.cfg['start_dir'])
             self.log.debug("Changed to real build directory %s (start_dir)" % self.cfg['start_dir'])
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 30a79bbf8b..10c0509568 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -697,23 +697,33 @@ def test_parallel(self):
 
     def test_guess_start_dir(self):
         """Test guessing the start dir."""
-        ec = process_easyconfig(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb'))[0]
-
-        eb = EasyBlock(ec['ec'])
-        eb.silent = True
-        eb.cfg['stop'] = 'patch'
-        eb.run_all_steps(False)
-        eb.guess_start_dir()
-        self.assertEqual(os.getcwd(), os.path.join(eb.builddir, "toy-0.0"))
-
-        ec['ec']['start_dir'] = "%(name)s-%(version)s"
-
-        eb = EasyBlock(ec['ec'])
-        eb.silent = True
-        eb.cfg['stop'] = 'patch'
-        eb.run_all_steps(False)
-        eb.guess_start_dir()
-        self.assertEqual(os.getcwd(), os.path.join(eb.builddir, "toy-0.0"))
+        test_easyconfigs = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
+        ec = process_easyconfig(os.path.join(test_easyconfigs, 'toy-0.0.eb'))[0]
+
+        def check_start_dir(expected_start_dir):
+            """Check start dir."""
+            eb = EasyBlock(ec['ec'])
+            eb.silent = True
+            eb.cfg['stop'] = 'patch'
+            eb.run_all_steps(False)
+            eb.guess_start_dir()
+            abs_expected_start_dir = os.path.join(eb.builddir, expected_start_dir)
+            self.assertTrue(os.path.samefile(eb.cfg['start_dir'], abs_expected_start_dir))
+            self.assertTrue(os.path.samefile(os.getcwd(), abs_expected_start_dir))
+
+        # default (no start_dir specified): use unpacked dir as start dir
+        self.assertEqual(ec['ec']['start_dir'], None)
+        check_start_dir('toy-0.0')
+
+        # using start_dir equal to the one we're in is OK
+        ec['ec']['start_dir'] = '%(name)s-%(version)s'
+        self.assertEqual(ec['ec']['start_dir'], 'toy-0.0')
+        check_start_dir('toy-0.0')
+
+        # clean error when specified start dir does not exist
+        ec['ec']['start_dir'] = 'thisstartdirisnotthere'
+        err_pattern = "Specified start dir .*/toy-0.0/thisstartdirisnotthere does not exist"
+        self.assertErrorRegex(EasyBuildError, err_pattern, check_start_dir, 'whatever')
 
 
 def suite():

From 269ed5a467c5166022ec8c10fe192c80fdf12d4c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 09:00:44 +0200
Subject: [PATCH 1299/1356] use os.path.samefile

---
 test/framework/filetools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 7086add22c..abac787fa9 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -105,7 +105,7 @@ def test_find_base_dir(self):
         os.mkdir(os.path.join(tmpdir, 'easybuild'))
 
         os.chdir(tmpdir)
-        self.assertEqual(foodir, ft.find_base_dir())
+        self.assertTrue(os.path.samefile(foodir, ft.find_base_dir()))
 
     def test_encode_class_name(self):
         """Test encoding of class names."""

From a36fcec146928083c3548f366fe1abdb30b797df Mon Sep 17 00:00:00 2001
From: molden <martijn.oldenhof@kuleuven.be>
Date: Thu, 8 Oct 2015 09:15:27 +0200
Subject: [PATCH 1300/1356] remove maxHitCount -> maxhits

---
 easybuild/tools/run.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index 85199370f4..fe55d9d6a4 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -227,8 +227,6 @@ def check_answers_list(answers):
     else:
         runLog = None
 
-    maxHitCount = maxhits 
-
     try:
         p = Popen(cmd, shell=True, stdout=PIPE, stderr=STDOUT, stdin=PIPE, close_fds=True, executable="/bin/bash")
     except OSError, err:
@@ -296,7 +294,7 @@ def check_answers_list(answers):
         else:
             hitCount = 0
 
-        if hitCount > maxHitCount:
+        if hitCount > maxhits:
             # explicitly kill the child process before exiting
             try:
                 os.killpg(p.pid, signal.SIGKILL)
@@ -305,7 +303,7 @@ def check_answers_list(answers):
                 _log.debug("run_cmd_qa exception caught when killing child process: %s" % err)
             _log.debug("run_cmd_qa: full stdouterr: %s" % stdoutErr)
             raise EasyBuildError("run_cmd_qa: cmd %s : Max nohits %s reached: end of output %s",
-                                 cmd, maxHitCount, stdoutErr[-500:])
+                                 cmd, maxhits, stdoutErr[-500:])
 
         # the sleep below is required to avoid exiting on unknown 'questions' too early (see above)
         time.sleep(1)

From dbddb222e9bf5b97d38e5f13ebcbece906f6b322 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 09:29:14 +0200
Subject: [PATCH 1301/1356] add unit test for only_if_module_is_available
 decorator

---
 test/framework/general.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/test/framework/general.py b/test/framework/general.py
index 545e37c062..2f8cd84053 100644
--- a/test/framework/general.py
+++ b/test/framework/general.py
@@ -36,6 +36,7 @@
 
 import easybuild.framework
 from easybuild.tools.filetools import read_file
+from easybuild.tools.utilities import only_if_module_is_available
 
 
 class GeneralTest(EnhancedTestCase):
@@ -70,6 +71,30 @@ def test_error_reporting(self):
                 for regex in log_method_regexes:
                     self.assertFalse(regex.search(txt), "No match for '%s' in %s" % (regex.pattern, path))
 
+    def test_only_if_module_is_available(self):
+        """Test only_if_module_is_available decorator."""
+        @only_if_module_is_available('easybuild')
+        def foo():
+            pass
+
+        foo()
+
+        @only_if_module_is_available('nosuchmoduleoutthere', pkgname='nosuchpkg')
+        def bar():
+            pass
+
+        err_pat = "required module 'nosuchmoduleoutthere' is not available.*package nosuchpkg.*pypi/nosuchpkg"
+        self.assertErrorRegex(ImportError, err_pat, bar)
+
+        class Foo():
+            @only_if_module_is_available('thisdoesnotexist', url='http://example.com')
+            def foobar(self):
+                pass
+
+        err_pat = r"required module 'thisdoesnotexist' is not available \(available from http://example.com\)"
+        self.assertErrorRegex(ImportError, err_pat, Foo().foobar)
+
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(GeneralTest)

From 55ed7b04f3c321c05dfdc07a4eb1b809a3675f8a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 10:55:00 +0200
Subject: [PATCH 1302/1356] fix super call

---
 easybuild/tools/job/pbs_python.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 24925f0dc2..8add915874 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -70,7 +70,7 @@ class PbsPython(JobBackend):
     @only_if_module_is_available('pbs', pkgname='pbs_python')
     def __init__(self, *args, **kwargs):
         """PbsPython constructor."""
-        super(GC3Pie, self).__init__(*args, **kwargs)
+        super(PbsPython, self).__init__(*args, **kwargs)
 
     def _check_version(self):
         """Check whether pbs_python version complies with required version."""

From f9ce7cf51645f7fd4db8cae12e041de0faa85abb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 11:25:27 +0200
Subject: [PATCH 1303/1356] aslo add decorator to _check_version method in
 GC3Pie/PbsPython classes

---
 easybuild/tools/job/gc3pie.py     | 2 ++
 easybuild/tools/job/pbs_python.py | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/easybuild/tools/job/gc3pie.py b/easybuild/tools/job/gc3pie.py
index 376326c8c6..833fb9beb4 100644
--- a/easybuild/tools/job/gc3pie.py
+++ b/easybuild/tools/job/gc3pie.py
@@ -87,6 +87,8 @@ def __init__(self, *args, **kwargs):
         """GC3Pie constructor."""
         super(GC3Pie, self).__init__(*args, **kwargs)
 
+    # _check_version is called by __init__, so guard it (too) with the decorator
+    @only_if_module_is_available('gc3libs', pkgname='gc3pie')
     def _check_version(self):
         """Check whether GC3Pie version complies with required version."""
         # location of __version__ to use may change, depending on the minimal required SVN revision for development versions
diff --git a/easybuild/tools/job/pbs_python.py b/easybuild/tools/job/pbs_python.py
index 8add915874..2e581a9845 100644
--- a/easybuild/tools/job/pbs_python.py
+++ b/easybuild/tools/job/pbs_python.py
@@ -72,6 +72,8 @@ def __init__(self, *args, **kwargs):
         """PbsPython constructor."""
         super(PbsPython, self).__init__(*args, **kwargs)
 
+    # _check_version is called by __init__, so guard it (too) with the decorator
+    @only_if_module_is_available('pbs', pkgname='pbs_python')
     def _check_version(self):
         """Check whether pbs_python version complies with required version."""
         version_regex = re.compile('pbs_python version (?P<version>.*)')

From 0440376a382c5a180aaee0315134d844fefde9c3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 12:45:44 +0200
Subject: [PATCH 1304/1356] add log msg with test name

---
 test/framework/utilities.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 44e6905141..aba5a2a71c 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -88,6 +88,8 @@ def setUp(self):
         log = fancylogger.getLogger(fname=False)
         self.orig_log_handlers = log.handlers[:]
 
+        log.info("setting up test %s" % self._testMethodName)
+
         self.orig_tmpdir = tempfile.gettempdir()
         # use a subdirectory for this test (which we can clean up easily after the test completes)
         self.test_prefix = set_tmpdir()

From 5a6f2bc0cf93a3711f73eb7c8f395f8deaf050e0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 12:48:26 +0200
Subject: [PATCH 1305/1356] better log msg with test name

---
 test/framework/utilities.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index aba5a2a71c..a9a71dbe66 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -88,7 +88,7 @@ def setUp(self):
         log = fancylogger.getLogger(fname=False)
         self.orig_log_handlers = log.handlers[:]
 
-        log.info("setting up test %s" % self._testMethodName)
+        log.info("setting up test %s" % self.id())
 
         self.orig_tmpdir = tempfile.gettempdir()
         # use a subdirectory for this test (which we can clean up easily after the test completes)

From 8fcfac5b6c55dc78039a84fe8a4f8a15e80e3a72 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 12:50:30 +0200
Subject: [PATCH 1306/1356] add log msg in tearDown

---
 test/framework/utilities.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index a9a71dbe66..1210d08d0b 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -149,6 +149,8 @@ def tearDown(self):
         """Clean up after running testcase."""
         super(EnhancedTestCase, self).tearDown()
 
+        self.log.info("Cleaning up for test %s", self.id())
+
         # go back to where we were before
         os.chdir(self.cwd)
 

From 4bce8db99c93c98dd0e4b2b0d794030c849bde7e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 13:42:00 +0200
Subject: [PATCH 1307/1356] use sys.executable rather than 'python' when
 testing generate_software_list.py script

---
 test/framework/scripts.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 8c5e84e215..73df66f277 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -30,6 +30,7 @@
 import os
 import re
 import shutil
+import sys
 import tempfile
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
@@ -77,7 +78,7 @@ def test_generate_software_list(self):
             for ec_file in files:
                 shutil.copy2(os.path.join(root, ec_file), tmpdir)
 
-        cmd = "python %s --local --quiet --path %s" % (script, tmpdir)
+        cmd = "%s %s --local --quiet --path %s" % (sys.executable, script, tmpdir)
         out, ec = run_cmd(cmd, simple=False)
 
         # make sure output is kind of what we expect it to be

From ddb1034dd3fe555e8472277ce31bb7a9ec63c822 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 22:38:33 +0200
Subject: [PATCH 1308/1356] use strings rather than License instances as values
 that correspond with software license constants

---
 easybuild/framework/easyconfig/easyconfig.py  | 16 ++++++++-------
 .../easyconfig/format/pyheaderconfigobj.py    |  2 +-
 easybuild/framework/easyconfig/licenses.py    | 16 ++++++++++-----
 test/framework/easyconfig.py                  | 20 +++++++++++++++++++
 test/framework/easyconfigs/gzip-1.4.eb        |  3 +++
 test/framework/license.py                     |  7 +++++++
 6 files changed, 51 insertions(+), 13 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 0cd9c6ad0b..a479b959e5 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -214,6 +214,7 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         self.short_mod_name = mns.det_short_module_name(self)
         self.mod_subdir = mns.det_module_subdir(self)
 
+        self.software_license = None
 
     def copy(self):
         """
@@ -335,16 +336,17 @@ def validate(self, check_osdeps=True):
 
     def validate_license(self):
         """Validate the license"""
-        lic = self._config['software_license'][0]
+        lic = self['software_license']
         if lic is None:
             # when mandatory, remove this possibility
             if 'software_license' in self.mandatory:
-                raise EasyBuildError("License is mandatory, but 'software_license' is undefined")
-        elif not isinstance(lic, License):
-            raise EasyBuildError('License %s has to be a License subclass instance, found classname %s.',
-                                 lic, lic.__class__.__name__)
-        elif not lic.name in EASYCONFIG_LICENSES_DICT:
-            raise EasyBuildError('Invalid license %s (classname: %s).', lic.name, lic.__class__.__name__)
+                raise EasyBuildError("Software license is mandatory, but 'software_license' is undefined")
+        elif lic in EASYCONFIG_LICENSES_DICT:
+            # create License instance
+            self.software_license = EASYCONFIG_LICENSES_DICT[lic]()
+        else:
+            known_licenses = ', '.join(EASYCONFIG_LICENSES_DICT.keys())
+            raise EasyBuildError("Invalid license %s (known licenses: )", lic, known_licenses)
 
         # TODO, when GROUP_SOURCE and/or GROUP_BINARY is True
         #  check the owner of source / binary (must match 'group' parameter from easyconfig)
diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index 78d80be3e4..32983c4157 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -50,7 +50,7 @@ def build_easyconfig_constants_dict():
     all_consts = [
         ('TEMPLATE_CONSTANTS', dict([(x[0], x[1]) for x in TEMPLATE_CONSTANTS])),
         ('EASYCONFIG_CONSTANTS', dict([(key, val[0]) for key, val in EASYCONFIG_CONSTANTS.items()])),
-        ('EASYCONFIG_LICENSES', EASYCONFIG_LICENSES_DICT),
+        ('EASYCONFIG_LICENSES', dict([(x, x) for x in EASYCONFIG_LICENSES_DICT.keys()])),
     ]
     err = []
     const_dict = {}
diff --git a/easybuild/framework/easyconfig/licenses.py b/easybuild/framework/easyconfig/licenses.py
index 7485cfd549..110c0d7888 100644
--- a/easybuild/framework/easyconfig/licenses.py
+++ b/easybuild/framework/easyconfig/licenses.py
@@ -28,11 +28,13 @@
 be used within an Easyconfig file.
 
 @author: Stijn De Weirdt (Ghent University)
+@author: Kenneth Hoste (Ghent University)
 """
 
 from vsc.utils import fancylogger
 from vsc.utils.missing import get_subclasses
 
+
 _log = fancylogger.getLogger('easyconfig.licenses', fname=False)
 
 
@@ -51,14 +53,20 @@ class License(object):
 
     CLASSNAME_PREFIX = 'License'
 
-    def __init__(self):
+    @property
+    def name(self):
+        """Return license name."""
         if self.NAME is None:
             name = self.__class__.__name__
             if name.startswith(self.CLASSNAME_PREFIX):
                 name = name[len(self.CLASSNAME_PREFIX):]
         else:
             name = self.NAME
-        self.name = name
+
+        return name
+
+    def __init__(self):
+        """License constructor."""
         self.version = self.VERSION
         self.description = self.DESCRIPTION
         self.distribute_source = self.DISTRIBUTE_SOURCE
@@ -153,14 +161,12 @@ def what_licenses():
     for lic in get_subclasses(License):
         if lic.HIDDEN:
             continue
-        lic_instance = lic()
-        res[lic_instance.name] = lic_instance
+        res[lic().name] = lic
 
     return res
 
 
 EASYCONFIG_LICENSES_DICT = what_licenses()
-EASYCONFIG_LICENSES = EASYCONFIG_LICENSES_DICT.keys()
 
 
 def license_documentation():
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 1a6e5f3885..98c0054bf9 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -46,6 +46,7 @@
 from easybuild.framework.easyconfig.easyconfig import ActiveMNS, EasyConfig
 from easybuild.framework.easyconfig.easyconfig import create_paths
 from easybuild.framework.easyconfig.easyconfig import get_easyblock_class
+from easybuild.framework.easyconfig.licenses import License, LicenseGPLv3
 from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig
 from easybuild.framework.easyconfig.templates import to_template_str
 from easybuild.framework.easyconfig.tools import dep_graph, find_related_easyconfigs, parse_easyconfigs
@@ -1491,6 +1492,25 @@ def test_find_related_easyconfigs(self):
         ec['name'] = 'nosuchsoftware'
         self.assertEqual(find_related_easyconfigs(test_easyconfigs, ec), [])
 
+    def test_software_license(self):
+        """Tests related to software_license easyconfig parameter."""
+        # default: None
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0.eb')
+        ec = EasyConfig(ec_file)
+        ec.validate_license()
+        self.assertEqual(ec['software_license'], None)
+        self.assertEqual(ec.software_license, None)
+
+        # specified software license gets handled correctly
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'gzip-1.4.eb')
+        ec = EasyConfig(ec_file)
+        ec.validate_license()
+        # constant GPLv3 is resolved as string
+        self.assertEqual(ec['software_license'], 'GPLv3')
+        # software_license is defined as License subclass
+        self.assertTrue(isinstance(ec.software_license, LicenseGPLv3))
+        self.assertTrue(issubclass(ec.software_license.__class__, License))
+
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/easyconfigs/gzip-1.4.eb b/test/framework/easyconfigs/gzip-1.4.eb
index c5a94274b3..f00f8d7197 100644
--- a/test/framework/easyconfigs/gzip-1.4.eb
+++ b/test/framework/easyconfigs/gzip-1.4.eb
@@ -35,3 +35,6 @@ sanity_check_paths = {
 # run 'gzip -h' and 'gzip --version' after installation
 sanity_check_commands = [True, ('gzip', '--version')]
 
+software_license = GPLv3
+
+moduleclass = 'tools'
diff --git a/test/framework/license.py b/test/framework/license.py
index 026b0a722a..6f705dbb77 100644
--- a/test/framework/license.py
+++ b/test/framework/license.py
@@ -55,6 +55,13 @@ def test_veryrestrictive_license(self):
         self.assertTrue(VeryRestrictive.GROUP_SOURCE)
         self.assertTrue(VeryRestrictive.GROUP_BINARY)
 
+    def test_licenses(self):
+        """Test format of available licenses."""
+        lics = what_licenses()
+        for lic in lics:
+            self.assertTrue(isinstance(lic, basestring))
+            self.assertTrue(issubclass(lics[lic], License))
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(LicenseTest)

From 9cb7e8b79b8d5f34858b4b5ae55f796a09af4f1e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 23:40:46 +0200
Subject: [PATCH 1309/1356] use License class name as key, but 'short' license
 name as constant name + fix license_documentation + add/enhance unit tests

---
 easybuild/framework/easyconfig/easyconfig.py   |  4 ++--
 .../easyconfig/format/pyheaderconfigobj.py     |  3 +--
 easybuild/framework/easyconfig/licenses.py     | 18 +++++++++++-------
 test/framework/docs.py                         | 12 +++++++++---
 test/framework/easyconfig.py                   |  4 ++--
 test/framework/easyconfigparser.py             | 17 +++++++++++++++++
 test/framework/license.py                      | 13 +++++++------
 7 files changed, 49 insertions(+), 22 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index a479b959e5..34d127af24 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -345,8 +345,8 @@ def validate_license(self):
             # create License instance
             self.software_license = EASYCONFIG_LICENSES_DICT[lic]()
         else:
-            known_licenses = ', '.join(EASYCONFIG_LICENSES_DICT.keys())
-            raise EasyBuildError("Invalid license %s (known licenses: )", lic, known_licenses)
+            known_licenses = ', '.join(sorted(EASYCONFIG_LICENSES_DICT.keys()))
+            raise EasyBuildError("Invalid license %s (known licenses: %s)", lic, known_licenses)
 
         # TODO, when GROUP_SOURCE and/or GROUP_BINARY is True
         #  check the owner of source / binary (must match 'group' parameter from easyconfig)
diff --git a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
index 32983c4157..0dc54d7da6 100644
--- a/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
+++ b/easybuild/framework/easyconfig/format/pyheaderconfigobj.py
@@ -46,11 +46,10 @@
 
 def build_easyconfig_constants_dict():
     """Make a dictionary with all constants that can be used"""
-    # sanity check
     all_consts = [
         ('TEMPLATE_CONSTANTS', dict([(x[0], x[1]) for x in TEMPLATE_CONSTANTS])),
         ('EASYCONFIG_CONSTANTS', dict([(key, val[0]) for key, val in EASYCONFIG_CONSTANTS.items()])),
-        ('EASYCONFIG_LICENSES', dict([(x, x) for x in EASYCONFIG_LICENSES_DICT.keys()])),
+        ('EASYCONFIG_LICENSES', dict([(klass().name, name) for name, klass in EASYCONFIG_LICENSES_DICT.items()])),
     ]
     err = []
     const_dict = {}
diff --git a/easybuild/framework/easyconfig/licenses.py b/easybuild/framework/easyconfig/licenses.py
index 110c0d7888..5ef1959b17 100644
--- a/easybuild/framework/easyconfig/licenses.py
+++ b/easybuild/framework/easyconfig/licenses.py
@@ -74,12 +74,12 @@ def __init__(self):
         self.group_binary = self.GROUP_BINARY
 
 
-class VeryRestrictive(License):
+class LicenseVeryRestrictive(License):
     """Default license should be very restrictive, so nothing to do here, just a placeholder"""
     pass
 
 
-class LicenseUnknown(VeryRestrictive):
+class LicenseUnknown(LicenseVeryRestrictive):
     """A (temporary) license, could be used as default in case nothing was specified"""
     pass
 
@@ -161,7 +161,7 @@ def what_licenses():
     for lic in get_subclasses(License):
         if lic.HIDDEN:
             continue
-        res[lic().name] = lic
+        res[lic.__name__] = lic
 
     return res
 
@@ -171,12 +171,16 @@ def what_licenses():
 
 def license_documentation():
     """Generate the easyconfig licenses documentation"""
-    indent_l0 = " " * 2
-    indent_l1 = indent_l0 + " " * 2
+    indent_l0 = ' ' * 2
+    indent_l1 = indent_l0 + ' ' * 2
     doc = []
 
     doc.append("Constants that can be used in easyconfigs")
     for lic_name, lic in EASYCONFIG_LICENSES_DICT.items():
-        doc.append('%s%s: %s (version %s)' % (indent_l1, lic_name, lic.description, lic.version))
+        lic_inst = lic()
+        strver = ''
+        if lic_inst.version:
+            strver = " (version: %s)" % '.'.join([str(d) for d in lic_inst.version])
+        doc.append("%s%s: %s%s" % (indent_l1, lic_inst.name, lic_inst.description, strver))
 
-    return "\n".join(doc)
+    return '\n'.join(doc)
diff --git a/test/framework/docs.py b/test/framework/docs.py
index dbb1d257cb..e68c5de5a9 100644
--- a/test/framework/docs.py
+++ b/test/framework/docs.py
@@ -25,16 +25,16 @@
 """
 Unit tests for docs.py.
 """
-
+import inspect
 import os
 import re
 import sys
-import inspect
+from unittest import TestLoader, main
 
+from easybuild.framework.easyconfig.licenses import license_documentation
 from easybuild.tools.docs import gen_easyblocks_overview_rst
 from easybuild.tools.utilities import import_available_modules
 from test.framework.utilities import EnhancedTestCase, init_config
-from unittest import TestLoader, main
 
 class DocsTest(EnhancedTestCase):
 
@@ -89,6 +89,12 @@ def test_gen_easyblocks(self):
         regex = re.compile(pattern)
         self.assertTrue(re.search(regex, ebdoc), "Pattern %s found in %s" % (regex.pattern, ebdoc))
 
+    def test_license_docs(self):
+        """Test license_documentation function."""
+        lic_docs = license_documentation()
+        gplv3 = "GPLv3: The GNU General Public License"
+        self.assertTrue(gplv3 in lic_docs, "%s found in: %s" % (gplv3, lic_docs))
+
 
 def suite():
     """ returns all test cases in this module """
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 98c0054bf9..b302fa7020 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -303,7 +303,7 @@ def test_exts_list(self):
             '       "source_urls": [("http://example.com", "suffix")],'
             '       "patches": ["toy-0.0.eb"],',  # dummy patch to avoid downloading fail
             '       "checksums": [',
-            '           "787393bfc465c85607a5b24486e861c5",',  # MD5 checksum for source (gzip-1.4.eb)
+            '           "a5464d79c2c8d4935e383ebd070b305e",',  # MD5 checksum for source (gzip-1.4.eb)
             '           "44893c3ed46a7c7ab2e72fea7d19925d",',  # MD5 checksum for patch (toy-0.0.eb)
             '       ],',
             '   }),',
@@ -1506,7 +1506,7 @@ def test_software_license(self):
         ec = EasyConfig(ec_file)
         ec.validate_license()
         # constant GPLv3 is resolved as string
-        self.assertEqual(ec['software_license'], 'GPLv3')
+        self.assertEqual(ec['software_license'], 'LicenseGPLv3')
         # software_license is defined as License subclass
         self.assertTrue(isinstance(ec.software_license, LicenseGPLv3))
         self.assertTrue(issubclass(ec.software_license.__class__, License))
diff --git a/test/framework/easyconfigparser.py b/test/framework/easyconfigparser.py
index e163c9f0e0..fce0b5e1cf 100644
--- a/test/framework/easyconfigparser.py
+++ b/test/framework/easyconfigparser.py
@@ -34,6 +34,7 @@
 
 import easybuild.tools.build_log
 from easybuild.framework.easyconfig.format.format import Dependency
+from easybuild.framework.easyconfig.format.pyheaderconfigobj import build_easyconfig_constants_dict
 from easybuild.framework.easyconfig.format.version import EasyVersion
 from easybuild.framework.easyconfig.parser import EasyConfigParser
 from easybuild.tools.build_log import EasyBuildError
@@ -170,6 +171,22 @@ def test_raw(self):
 
         self.assertErrorRegex(EasyBuildError, "Neither filename nor rawcontent provided", EasyConfigParser)
 
+    def test_easyconfig_constants(self):
+        """Test available easyconfig constants."""
+        constants = build_easyconfig_constants_dict()
+        # make sure both keys and values are only strings
+        for constant_name in constants:
+            self.assertTrue(isinstance(constant_name, basestring), "Constant name %s is a string" % constant_name)
+            val = constants[constant_name]
+            self.assertTrue(isinstance(val, basestring), "Constant value %s is a string" % val)
+
+        # check a couple of randomly picked constant values
+        self.assertEqual(constants['SOURCE_TAR_GZ'], '%(name)s-%(version)s.tar.gz')
+        self.assertEqual(constants['PYPI_SOURCE'], 'https://pypi.python.org/packages/source/%(nameletter)s/%(name)s')
+        self.assertEqual(constants['GPLv2'], 'LicenseGPLv2')
+        self.assertEqual(constants['EXTERNAL_MODULE'], 'EXTERNAL_MODULE')
+
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(EasyConfigParserTest)
diff --git a/test/framework/license.py b/test/framework/license.py
index 6f705dbb77..79b120514d 100644
--- a/test/framework/license.py
+++ b/test/framework/license.py
@@ -30,7 +30,7 @@
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
 
-from easybuild.framework.easyconfig.licenses import License, VeryRestrictive, what_licenses
+from easybuild.framework.easyconfig.licenses import License, LicenseVeryRestrictive, what_licenses
 
 
 class LicenseTest(EnhancedTestCase):
@@ -39,9 +39,9 @@ class LicenseTest(EnhancedTestCase):
     def test_common_ones(self):
         """Check if a number of common licenses can be found"""
         lics = what_licenses()
-        commonlicenses = ['VeryRestrictive', 'GPLv2', 'GPLv3']
+        commonlicenses = ['LicenseVeryRestrictive', 'LicenseGPLv2', 'LicenseGPLv3']
         for lic in commonlicenses:
-            self.assertTrue(lic in lics)
+            self.assertTrue(lic in lics, "%s found in %s" % (lic, lics.keys()))
 
     def test_default_license(self):
         """Verify that the default License class is very restrictive"""
@@ -51,9 +51,9 @@ def test_default_license(self):
 
     def test_veryrestrictive_license(self):
         """Verify that the very restrictive class is very restrictive"""
-        self.assertFalse(VeryRestrictive.DISTRIBUTE_SOURCE)
-        self.assertTrue(VeryRestrictive.GROUP_SOURCE)
-        self.assertTrue(VeryRestrictive.GROUP_BINARY)
+        self.assertFalse(LicenseVeryRestrictive.DISTRIBUTE_SOURCE)
+        self.assertTrue(LicenseVeryRestrictive.GROUP_SOURCE)
+        self.assertTrue(LicenseVeryRestrictive.GROUP_BINARY)
 
     def test_licenses(self):
         """Test format of available licenses."""
@@ -62,6 +62,7 @@ def test_licenses(self):
             self.assertTrue(isinstance(lic, basestring))
             self.assertTrue(issubclass(lics[lic], License))
 
+
 def suite():
     """ returns all the testcases in this module """
     return TestLoader().loadTestsFromTestCase(LicenseTest)

From 23d7e5f35128672013b1a0d0cdd0a76a7ce35304 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 23:49:20 +0200
Subject: [PATCH 1310/1356] also test handling of non-existing license

---
 test/framework/easyconfig.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index b302fa7020..abd10e398a 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1511,6 +1511,10 @@ def test_software_license(self):
         self.assertTrue(isinstance(ec.software_license, LicenseGPLv3))
         self.assertTrue(issubclass(ec.software_license.__class__, License))
 
+        ec['software_license'] = 'LicenseThatDoesNotExist'
+        err_pat = r"Invalid license LicenseThatDoesNotExist \(known licenses:"
+        self.assertErrorRegex(EasyBuildError, err_pat, ec.validate_license)
+
 
 def suite():
     """ returns all the testcases in this module """

From 54bbabf8285f5be46955f98e8136f9871bc8bdd9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Oct 2015 23:51:51 +0200
Subject: [PATCH 1311/1356] verify that key for licenses starts with 'License'

---
 test/framework/license.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/framework/license.py b/test/framework/license.py
index 79b120514d..445a1d1c5c 100644
--- a/test/framework/license.py
+++ b/test/framework/license.py
@@ -60,6 +60,7 @@ def test_licenses(self):
         lics = what_licenses()
         for lic in lics:
             self.assertTrue(isinstance(lic, basestring))
+            self.assertTrue(lic.startswith('License'))
             self.assertTrue(issubclass(lics[lic], License))
 
 

From bdb3a20f0b8f063060ec42be324c7d29a0b9898d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Oct 2015 01:02:19 +0200
Subject: [PATCH 1312/1356] fix broken test

---
 test/framework/easyconfigs/v1.0/gzip-1.4.eb | 3 +++
 test/framework/module_generator.py          | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/framework/easyconfigs/v1.0/gzip-1.4.eb b/test/framework/easyconfigs/v1.0/gzip-1.4.eb
index c5a94274b3..f00f8d7197 100644
--- a/test/framework/easyconfigs/v1.0/gzip-1.4.eb
+++ b/test/framework/easyconfigs/v1.0/gzip-1.4.eb
@@ -35,3 +35,6 @@ sanity_check_paths = {
 # run 'gzip -h' and 'gzip --version' after installation
 sanity_check_commands = [True, ('gzip', '--version')]
 
+software_license = GPLv3
+
+moduleclass = 'tools'
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 481d32a85a..5e92652200 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -369,7 +369,7 @@ def test_mns():
         # note: these checksums will change if another easyconfig parameter is added
         ec2mod_map = {
             'GCC-4.6.3.eb': 'GCC/9e9ab5a1e978f0843b5aedb63ac4f14c51efb859',
-            'gzip-1.4.eb': 'gzip/8805ec3152d2a4a08b6c06d740c23abe1a4d059f',
+            'gzip-1.4.eb': 'gzip/53d5c13e85cb6945bd43a58d1c8d4a4c02f3462d',
             'gzip-1.4-GCC-4.6.3.eb': 'gzip/863557cc81811f8c3f4426a4b45aa269fa54130b',
             'gzip-1.5-goolf-1.4.10.eb': 'gzip/b63c2b8cc518905473ccda023100b2d3cff52d55',
             'gzip-1.5-ictce-4.1.13.eb': 'gzip/3d49f0e112708a95f79ed38b91b506366c0299ab',

From 319237b1fbb0ba301ec81393dc33348841342199 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Oct 2015 09:43:26 +0200
Subject: [PATCH 1313/1356] sync up gzip test easyconfigs to fix tests

---
 test/framework/easyconfig.py                         | 12 +++++++-----
 test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb     |  3 +++
 test/framework/easyconfigs/gzip-1.5-goolf-1.4.10.eb  |  3 +++
 test/framework/easyconfigs/gzip-1.5-ictce-4.1.13.eb  |  3 +++
 .../framework/easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb |  3 +++
 .../easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb        |  3 +++
 .../easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb        |  3 +++
 test/framework/easyconfigs/v2.0/gzip.eb              |  2 +-
 test/framework/module_generator.py                   | 10 +++++-----
 9 files changed, 31 insertions(+), 11 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index abd10e398a..68a42e9f70 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -873,18 +873,20 @@ def test_format_equivalence_basic(self):
             ('gzip-1.4.eb', 'gzip.eb', {'version': '1.4'}),
             ('gzip-1.4.eb', 'gzip.eb', {'version': '1.4', 'toolchain': {'name': 'dummy', 'version': 'dummy'}}),
             ('gzip-1.4-GCC-4.6.3.eb', 'gzip.eb', {'version': '1.4', 'toolchain': {'name': 'GCC', 'version': '4.6.3'}}),
-            ('gzip-1.5-goolf-1.4.10.eb', 'gzip.eb', {'version': '1.5', 'toolchain': {'name': 'goolf', 'version': '1.4.10'}}),
-            ('gzip-1.5-ictce-4.1.13.eb', 'gzip.eb', {'version': '1.5', 'toolchain': {'name': 'ictce', 'version': '4.1.13'}}),
+            ('gzip-1.5-goolf-1.4.10.eb', 'gzip.eb',
+             {'version': '1.5', 'toolchain': {'name': 'goolf', 'version': '1.4.10'}}),
+            ('gzip-1.5-ictce-4.1.13.eb', 'gzip.eb',
+             {'version': '1.5', 'toolchain': {'name': 'ictce', 'version': '4.1.13'}}),
         ]:
             ec1 = EasyConfig(os.path.join(easyconfigs_path, 'v1.0', eb_file1), validate=False)
             ec2 = EasyConfig(os.path.join(easyconfigs_path, 'v2.0', eb_file2), validate=False, build_specs=specs)
 
             ec2_dict = ec2.asdict()
-            # reset mandatory attributes from format2 that are not in format 1
-            for attr in ['docurls', 'software_license', 'software_license_urls']:
+            # reset mandatory attributes from format2 that are not defined in format 1 easyconfigs
+            for attr in ['docurls', 'software_license_urls']:
                 ec2_dict[attr] = None
 
-            self.assertEqual(ec1.asdict(), ec2_dict)
+            self.assertEqual(ec1.asdict(), ec2_dict, "Parsed %s is equivalent with %s" % (eb_file1, eb_file2))
 
         # restore
         easybuild.tools.build_log.EXPERIMENTAL = orig_experimental
diff --git a/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb b/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
index c5f783e816..0775b46e33 100644
--- a/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/gzip-1.4-GCC-4.6.3.eb
@@ -38,3 +38,6 @@ sanity_check_paths = {
 # run 'gzip -h' and 'gzip --version' after installation
 sanity_check_commands = [True, ('gzip', '--version')]
 
+software_license = GPLv3
+
+moduleclass = 'tools'
diff --git a/test/framework/easyconfigs/gzip-1.5-goolf-1.4.10.eb b/test/framework/easyconfigs/gzip-1.5-goolf-1.4.10.eb
index d1636586c9..90465d7ce4 100644
--- a/test/framework/easyconfigs/gzip-1.5-goolf-1.4.10.eb
+++ b/test/framework/easyconfigs/gzip-1.5-goolf-1.4.10.eb
@@ -32,3 +32,6 @@ sanity_check_paths = {
 # run 'gzip -h' and 'gzip --version' after installation
 sanity_check_commands = [True, ('gzip', '--version')]
 
+software_license = GPLv3
+
+moduleclass = 'tools'
diff --git a/test/framework/easyconfigs/gzip-1.5-ictce-4.1.13.eb b/test/framework/easyconfigs/gzip-1.5-ictce-4.1.13.eb
index 9fb11ce6ca..d00ed713a4 100644
--- a/test/framework/easyconfigs/gzip-1.5-ictce-4.1.13.eb
+++ b/test/framework/easyconfigs/gzip-1.5-ictce-4.1.13.eb
@@ -32,3 +32,6 @@ sanity_check_paths = {
 # run 'gzip -h' and 'gzip --version' after installation
 sanity_check_commands = [True, ('gzip', '--version')]
 
+software_license = GPLv3
+
+moduleclass = 'tools'
diff --git a/test/framework/easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb b/test/framework/easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb
index 0f8d2efc28..4480e210df 100644
--- a/test/framework/easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb
+++ b/test/framework/easyconfigs/v1.0/gzip-1.4-GCC-4.6.3.eb
@@ -35,3 +35,6 @@ sanity_check_paths = {
 # run 'gzip -h' and 'gzip --version' after installation
 sanity_check_commands = [True, ('gzip', '--version')]
 
+software_license = GPLv3
+
+moduleclass = 'tools'
diff --git a/test/framework/easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb b/test/framework/easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb
index d1636586c9..90465d7ce4 100644
--- a/test/framework/easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb
+++ b/test/framework/easyconfigs/v1.0/gzip-1.5-goolf-1.4.10.eb
@@ -32,3 +32,6 @@ sanity_check_paths = {
 # run 'gzip -h' and 'gzip --version' after installation
 sanity_check_commands = [True, ('gzip', '--version')]
 
+software_license = GPLv3
+
+moduleclass = 'tools'
diff --git a/test/framework/easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb b/test/framework/easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb
index 9fb11ce6ca..d00ed713a4 100644
--- a/test/framework/easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb
+++ b/test/framework/easyconfigs/v1.0/gzip-1.5-ictce-4.1.13.eb
@@ -32,3 +32,6 @@ sanity_check_paths = {
 # run 'gzip -h' and 'gzip --version' after installation
 sanity_check_commands = [True, ('gzip', '--version')]
 
+software_license = GPLv3
+
+moduleclass = 'tools'
diff --git a/test/framework/easyconfigs/v2.0/gzip.eb b/test/framework/easyconfigs/v2.0/gzip.eb
index 602528e2af..ada19a7566 100644
--- a/test/framework/easyconfigs/v2.0/gzip.eb
+++ b/test/framework/easyconfigs/v2.0/gzip.eb
@@ -42,4 +42,4 @@ toolchains = dummy == dummy, goolf, GCC == 4.6.3, goolf == 1.4.10, ictce == 4.1.
 
 [DEFAULT]
 easyblock = ConfigureMake
-moduleclass = base
+moduleclass = tools
diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 5e92652200..64fd5a471f 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -370,9 +370,9 @@ def test_mns():
         ec2mod_map = {
             'GCC-4.6.3.eb': 'GCC/9e9ab5a1e978f0843b5aedb63ac4f14c51efb859',
             'gzip-1.4.eb': 'gzip/53d5c13e85cb6945bd43a58d1c8d4a4c02f3462d',
-            'gzip-1.4-GCC-4.6.3.eb': 'gzip/863557cc81811f8c3f4426a4b45aa269fa54130b',
-            'gzip-1.5-goolf-1.4.10.eb': 'gzip/b63c2b8cc518905473ccda023100b2d3cff52d55',
-            'gzip-1.5-ictce-4.1.13.eb': 'gzip/3d49f0e112708a95f79ed38b91b506366c0299ab',
+            'gzip-1.4-GCC-4.6.3.eb': 'gzip/585eba598f33c64ef01c6fa47af0fc37f3751311',
+            'gzip-1.5-goolf-1.4.10.eb': 'gzip/fceb41e04c26b540b7276c4246d1ecdd1e8251c9',
+            'gzip-1.5-ictce-4.1.13.eb': 'gzip/ae16b3a0a330d4323987b360c0d024f244ac4498',
             'toy-0.0.eb': 'toy/44a206d9e8c14130cc9f79e061468303c6e91b53',
             'toy-0.0-multiple.eb': 'toy/44a206d9e8c14130cc9f79e061468303c6e91b53',
         }
@@ -380,7 +380,7 @@ def test_mns():
 
         # test determining module name for dependencies (i.e. non-parsed easyconfigs)
         # using a module naming scheme that requires all easyconfig parameters
-        ec2mod_map['gzip-1.5-goolf-1.4.10.eb'] = 'gzip/.b63c2b8cc518905473ccda023100b2d3cff52d55'
+        ec2mod_map['gzip-1.5-goolf-1.4.10.eb'] = 'gzip/.fceb41e04c26b540b7276c4246d1ecdd1e8251c9'
         for dep_ec, dep_spec in [
             ('GCC-4.6.3.eb', {
                 'name': 'GCC',
@@ -517,7 +517,7 @@ def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
                              ['Compiler/GCC/4.7.2/%s' % c for c in moduleclasses]),
             'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2/mpi',
                              ['MPI/GCC/4.7.2/OpenMPI/1.6.4/%s' % c for c in moduleclasses]),
-            'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5', 'MPI/GCC/4.7.2/OpenMPI/1.6.4/base',
+            'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5', 'MPI/GCC/4.7.2/OpenMPI/1.6.4/tools',
                              []),
             'goolf-1.4.10.eb': ('goolf/1.4.10', 'Core/toolchain',
                              []),

From d32b8a27cdbb09877deeb67551264ddac8848cba Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Oct 2015 10:01:29 +0200
Subject: [PATCH 1314/1356] fix another broken test

---
 test/framework/options.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/options.py b/test/framework/options.py
index 64b8644d02..7f10003976 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -802,7 +802,7 @@ def test_dry_run_categorized(self):
             ("ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4/numlib",
              "ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2", 'x'),
             ("goolf-1.4.10.eb", "Core/toolchain", "goolf/1.4.10", 'x'),
-            ("gzip-1.5-goolf-1.4.10.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4/base", "gzip/1.5", ' '),  # listed but not there: ' '
+            ("gzip-1.5-goolf-1.4.10.eb", "MPI/GCC/4.7.2/OpenMPI/1.6.4/tools", "gzip/1.5", ' '),  # listed but not there: ' '
         ]
         for ec, mod_subdir, mod_name, mark in ecs_mods:
             regex = re.compile("^ \* \[%s\] \S+%s \(module: %s \| %s\)$" % (mark, ec, mod_subdir, mod_name), re.M)

From b3652990d8549daef31498beb883679d76d0da55 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Oct 2015 16:46:42 +0200
Subject: [PATCH 1315/1356] allow get_cpu_speed to return None if CPU freq
 could not be determined

---
 easybuild/tools/systemtools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/tools/systemtools.py b/easybuild/tools/systemtools.py
index b8c899b1c5..8f3c5891d0 100644
--- a/easybuild/tools/systemtools.py
+++ b/easybuild/tools/systemtools.py
@@ -229,7 +229,7 @@ def get_cpu_speed():
                 cpu_freq = float(res.group('cpu_freq'))
                 _log.debug("Found CPU frequency using regex '%s': %s" % (cpu_freq_regex.pattern, cpu_freq))
             else:
-                raise SystemToolsException("Failed to determine CPU frequency from %s" % PROC_CPUINFO_FP)
+                _log.debug("Failed to determine CPU frequency from %s", PROC_CPUINFO_FP)
         else:
             _log.debug("%s not found to determine max. CPU clock frequency without CPU scaling: %s" % PROC_CPUINFO_FP)
 

From 6a282d2edf303ba1ad09404217c53a861d5dfb22 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 9 Oct 2015 20:12:01 +0200
Subject: [PATCH 1316/1356] also accept None as return value in test for
 get_cpu_speed

---
 test/framework/systemtools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/systemtools.py b/test/framework/systemtools.py
index ee5cf4f2b5..5c03e4bd3c 100644
--- a/test/framework/systemtools.py
+++ b/test/framework/systemtools.py
@@ -240,8 +240,8 @@ def test_cpu_model_darwin(self):
     def test_cpu_speed_native(self):
         """Test getting CPU speed."""
         cpu_speed = get_cpu_speed()
-        self.assertTrue(isinstance(cpu_speed, float))
-        self.assertTrue(cpu_speed > 0.0)
+        self.assertTrue(isinstance(cpu_speed, float) or cpu_speed is None)
+        self.assertTrue(cpu_speed > 0.0 or cpu_speed is None)
 
     def test_cpu_speed_linux(self):
         """Test getting CPU speed (mocked for Linux)."""

From 490149cee58e22dbdc9870265efffa1294acc967 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Oct 2015 13:56:23 +0200
Subject: [PATCH 1317/1356] relax sanity_check_paths in EasyBuild bootstrap
 script to deal with possible zipped .egg

---
 easybuild/scripts/bootstrap_eb.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index c8a14b9ff0..0d73cc12b2 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -536,6 +536,14 @@ def main():
 allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
 
 preinstallopts = '%(preinstallopts)s'
+
+pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2])
+sanity_check_paths = {
+    'files': ['bin/eb'],
+    'dirs': ['lib/python%s/site-packages' % pyshortver],
+}
+
+moduleclass = 'tools'
 """
 
 # distribute_setup.py script (https://pypi.python.org/pypi/distribute)

From d66f75dbf1a557eaa0570dd8b6a18dbd775f1828 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Oct 2015 17:53:18 +0200
Subject: [PATCH 1318/1356] escape % where needed

---
 easybuild/scripts/bootstrap_eb.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 0d73cc12b2..fa7bec2385 100755
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -540,7 +540,7 @@ def main():
 pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2])
 sanity_check_paths = {
     'files': ['bin/eb'],
-    'dirs': ['lib/python%s/site-packages' % pyshortver],
+    'dirs': ['lib/python%%s/site-packages' %% pyshortver],
 }
 
 moduleclass = 'tools'

From 7f9ee97e0dcc52641a5c5a92114e7fc4b72421bf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 10 Oct 2015 20:20:10 +0200
Subject: [PATCH 1319/1356] also define

---
 easybuild/tools/toolchain/compiler.py  |  2 +-
 easybuild/tools/toolchain/constants.py |  4 ++--
 test/framework/toolchain.py            | 17 +++++++++--------
 3 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/easybuild/tools/toolchain/compiler.py b/easybuild/tools/toolchain/compiler.py
index 80df84ba51..12b5631e59 100644
--- a/easybuild/tools/toolchain/compiler.py
+++ b/easybuild/tools/toolchain/compiler.py
@@ -243,7 +243,7 @@ def _set_compiler_flags(self):
             self.variables.nappend(var, cflags)
             self.variables.join(var, 'OPTFLAGS', 'PRECFLAGS')
 
-        for var in ['FFLAGS', 'F90FLAGS']:  # FIXME F77FLAGS?
+        for var in ['FCFLAGS', 'FFLAGS', 'F90FLAGS']:
             self.variables.nappend(var, flags)
             self.variables.nappend(var, fflags)
             self.variables.join(var, 'OPTFLAGS', 'PRECFLAGS')
diff --git a/easybuild/tools/toolchain/constants.py b/easybuild/tools/toolchain/constants.py
index eea842d663..6c20f44dc0 100644
--- a/easybuild/tools/toolchain/constants.py
+++ b/easybuild/tools/toolchain/constants.py
@@ -45,9 +45,9 @@
 COMPILER_FLAGS = [
     ('CFLAGS', 'C compiler flags'),
     ('CXXFLAGS', 'C++ compiler flags'),
+    ('FCFLAGS', 'Fortran compiler flags'),
     ('FFLAGS', 'Fortran compiler flags'),
     ('F90FLAGS', 'Fortran 90 compiler flags'),
-    # FIXME F77FLAGS?
 ]
 
 COMPILER_MAP_CLASS = {
@@ -79,9 +79,9 @@
     FlagList: [
         ('CUDA_CFLAGS', 'CUDA C compiler flags'),
         ('CUDA_CXXFLAGS', 'CUDA C++ compiler flags'),
+        ('CUDA_FCFLAGS', 'CUDA Fortran compiler flags'),
         ('CUDA_FFLAGS', 'CUDA Fortran compiler flags'),
         ('CUDA_F90FLAGS', 'CUDA Fortran 90 compiler flags'),
-        # FIXME CUDA_F77FLAGS?
     ],
 }
 
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 4c196eafa7..743b102d74 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -167,7 +167,7 @@ def test_validate_pass_by_value(self):
     def test_optimization_flags(self):
         """Test whether optimization flags are being set correctly."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FCFLAGS', 'FFLAGS', 'F90FLAGS']
 
         # check default optimization flag (e.g. -O2)
         tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
@@ -194,7 +194,7 @@ def test_optimization_flags(self):
     def test_optimization_flags_combos(self):
         """Test whether combining optimization levels works as expected."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FCFLAGS', 'FFLAGS', 'F90FLAGS']
 
         # check combining of optimization flags (doesn't make much sense)
         # lowest optimization should always be picked
@@ -227,7 +227,7 @@ def test_optimization_flags_combos(self):
     def test_misc_flags_shared(self):
         """Test whether shared compiler flags are set correctly."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FCFLAGS', 'FFLAGS', 'F90FLAGS']
 
         # setting option should result in corresponding flag to be set (shared options)
         for opt in ['pic', 'verbose', 'debug', 'static', 'shared']:
@@ -248,7 +248,7 @@ def test_misc_flags_shared(self):
     def test_misc_flags_unique(self):
         """Test whether unique compiler flags are set correctly."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FCFLAGS', 'FFLAGS', 'F90FLAGS']
 
         # setting option should result in corresponding flag to be set (unique options)
         for opt in ['unroll', 'optarch', 'openmp']:
@@ -270,7 +270,7 @@ def test_misc_flags_unique(self):
 
     def test_override_optarch(self):
         """Test whether overriding the optarch flag works."""
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FCFLAGS', 'FFLAGS', 'F90FLAGS']
         for optarch_var in ['march=lovelylovelysandybridge', None]:
             build_options = {'optarch': optarch_var}
             init_config(build_options=build_options)
@@ -296,7 +296,7 @@ def test_override_optarch(self):
     def test_misc_flags_unique_fortran(self):
         """Test whether unique Fortran compiler flags are set correctly."""
 
-        flag_vars = ['FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
+        flag_vars = ['FCFLAGS', 'FFLAGS', 'F90FLAGS']
 
         # setting option should result in corresponding flag to be set (Fortran unique options)
         for opt in ['i8', 'r8']:
@@ -316,7 +316,7 @@ def test_misc_flags_unique_fortran(self):
     def test_precision_flags(self):
         """Test whether precision flags are being set correctly."""
 
-        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FFLAGS', 'F90FLAGS']  # FIXME F77FLAGS?
+        flag_vars = ['CFLAGS', 'CXXFLAGS', 'FCFLAGS', 'FFLAGS', 'F90FLAGS']
 
         # check default precision flag
         tc = self.get_toolchain("goalf", version="1.1.0-no-OFED")
@@ -470,8 +470,9 @@ def test_ictce_toolchain(self):
 
         self.assertTrue('-mt_mpi' in tc.get_variable('CFLAGS'))
         self.assertTrue('-mt_mpi' in tc.get_variable('CXXFLAGS'))
+        self.assertTrue('-mt_mpi' in tc.get_variable('FCFLAGS'))
         self.assertTrue('-mt_mpi' in tc.get_variable('FFLAGS'))
-        self.assertTrue('-mt_mpi' in tc.get_variable('F90FLAGS'))  # FIXME F77FLAGS?
+        self.assertTrue('-mt_mpi' in tc.get_variable('F90FLAGS'))
         self.assertEqual(tc.get_variable('CC'), 'mpicc')
         self.assertEqual(tc.get_variable('CXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('F77'), 'mpif77')

From febf4fee1eb8ff4fcb25b05d856d7c6dbb490197 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 11 Oct 2015 09:37:16 +0200
Subject: [PATCH 1320/1356] fix typo

---
 easybuild/toolchains/mpi/mpich.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/mpi/mpich.py b/easybuild/toolchains/mpi/mpich.py
index 43bf527667..8e2d2a6948 100644
--- a/easybuild/toolchains/mpi/mpich.py
+++ b/easybuild/toolchains/mpi/mpich.py
@@ -52,7 +52,7 @@ class Mpich(Mpi):
     #MPI_COMPILER_MPIFC = 'mpifort'
 
     # clear MPI wrapper command options
-    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var, '') for var in MPI_COMPILER_VARIABLES])
+    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var[0], '') for var in MPI_COMPILER_VARIABLES])
 
     def _set_mpi_compiler_variables(self):
         """Set the MPICH_{CC, CXX, F77, F90, FC} variables."""

From 2e8cba33215370dd3c51ffdeb628fc5b097e9630 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 11 Oct 2015 09:46:34 +0200
Subject: [PATCH 1321/1356] fix another typo

---
 easybuild/toolchains/mpi/openmpi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/mpi/openmpi.py b/easybuild/toolchains/mpi/openmpi.py
index 2f9f5a2ab9..51d187baac 100644
--- a/easybuild/toolchains/mpi/openmpi.py
+++ b/easybuild/toolchains/mpi/openmpi.py
@@ -53,7 +53,7 @@ class OpenMPI(Mpi):
     MPI_COMPILER_MPIFC = 'mpifc'
 
     # OpenMPI reads from CC etc env variables
-    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var, '') for var in MPI_COMPILER_VARIABLES])
+    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var[0], '') for var in MPI_COMPILER_VARIABLES])
 
     MPI_LINK_INFO_OPTION = '-showme:link'
 

From 3c1e83789109705ffb775c4154e17e204cb141b0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 11 Oct 2015 10:10:00 +0200
Subject: [PATCH 1322/1356] fix moar issues

---
 easybuild/toolchains/mpi/intelmpi.py |  4 ++--
 easybuild/toolchains/mpi/mpich.py    |  8 ++++----
 easybuild/toolchains/mpi/openmpi.py  | 23 ++++++++---------------
 3 files changed, 14 insertions(+), 21 deletions(-)

diff --git a/easybuild/toolchains/mpi/intelmpi.py b/easybuild/toolchains/mpi/intelmpi.py
index 06d842d784..1137a9ddec 100644
--- a/easybuild/toolchains/mpi/intelmpi.py
+++ b/easybuild/toolchains/mpi/intelmpi.py
@@ -54,7 +54,7 @@ def _set_mpi_compiler_variables(self):
         """Add I_MPI_XXX variables to set."""
 
         # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
-        for var in COMPILER_VARIABLES:
+        for var, _ in COMPILER_VARIABLES:
             self.variables.nappend('I_MPI_%s' % var, str(self.variables[var].get_first()), var_class=CommandFlagList)
 
         super(IntelMPI, self)._set_mpi_compiler_variables()
@@ -67,5 +67,5 @@ def set_variables(self):
         # add -mt_mpi flag to ensure linking against thread-safe MPI library when OpenMP is enabled
         if self.options.get('openmp', None) and self.options.get('usempi', None):
             mt_mpi_option = ['mt_mpi']
-            for flags_var in COMPILER_FLAGS:
+            for flags_var, _ in COMPILER_FLAGS:
                 self.variables.nappend(flags_var, mt_mpi_option)
diff --git a/easybuild/toolchains/mpi/mpich.py b/easybuild/toolchains/mpi/mpich.py
index 8e2d2a6948..4ddaed37ed 100644
--- a/easybuild/toolchains/mpi/mpich.py
+++ b/easybuild/toolchains/mpi/mpich.py
@@ -41,7 +41,7 @@
 
 class Mpich(Mpi):
     """MPICH MPI class"""
-    MPI_MODULE_NAME = ["MPICH"]
+    MPI_MODULE_NAME = ['MPICH']
     MPI_FAMILY = TC_CONSTANT_MPICH
     MPI_TYPE = TC_CONSTANT_MPI_TYPE_MPICH
 
@@ -52,13 +52,13 @@ class Mpich(Mpi):
     #MPI_COMPILER_MPIFC = 'mpifort'
 
     # clear MPI wrapper command options
-    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var[0], '') for var in MPI_COMPILER_VARIABLES])
+    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var, '') for var, _ in MPI_COMPILER_VARIABLES])
 
     def _set_mpi_compiler_variables(self):
         """Set the MPICH_{CC, CXX, F77, F90, FC} variables."""
 
         # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
-        for var in COMPILER_VARIABLES:
-            self.variables.nappend("MPICH_%s" % var, str(self.variables[var].get_first()), var_class=CommandFlagList)
+        for var, _ in COMPILER_VARIABLES:
+            self.variables.nappend('MPICH_%s' % var, str(self.variables[var].get_first()), var_class=CommandFlagList)
 
         super(Mpich, self)._set_mpi_compiler_variables()
diff --git a/easybuild/toolchains/mpi/openmpi.py b/easybuild/toolchains/mpi/openmpi.py
index 51d187baac..a8ac12e021 100644
--- a/easybuild/toolchains/mpi/openmpi.py
+++ b/easybuild/toolchains/mpi/openmpi.py
@@ -41,19 +41,19 @@
 
 class OpenMPI(Mpi):
     """OpenMPI MPI class"""
-    MPI_MODULE_NAME = ["OpenMPI"]
+    MPI_MODULE_NAME = ['OpenMPI']
     MPI_FAMILY = TC_CONSTANT_OPENMPI
     MPI_TYPE = TC_CONSTANT_MPI_TYPE_OPENMPI
 
     MPI_LIBRARY_NAME = 'mpi'
 
     # version-dependent, see http://www.open-mpi.org/faq/?category=mpi-apps#override-wrappers-after-v1.0
-    MPI_COMPILER_MPIF77 = 'mpif77'
-    MPI_COMPILER_MPIF90 = 'mpif90'
-    MPI_COMPILER_MPIFC = 'mpifc'
+    MPI_COMPILER_MPIF77 = None
+    MPI_COMPILER_MPIF90 = None
+    MPI_COMPILER_MPIFC = None
 
     # OpenMPI reads from CC etc env variables
-    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var[0], '') for var in MPI_COMPILER_VARIABLES])
+    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var, '') for var, _ in MPI_COMPILER_VARIABLES])
 
     MPI_LINK_INFO_OPTION = '-showme:link'
 
@@ -69,20 +69,13 @@ def __init__(self, *args, **kwargs):
         else:
             self.MPI_COMPILER_MPIF77 = 'mpif77'
             self.MPI_COMPILER_MPIF90 = 'mpif90'
-            self.MPI_COMPILER_MPIFC = 'mpif90'
+            self.MPI_COMPILER_MPIFC = 'mpifc'
 
     def _set_mpi_compiler_variables(self):
         """Add OMPI_* variables to set."""
 
         # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
-        for var in COMPILER_VARIABLES:
-            if isinstance(var, basestring):
-                source_var = var
-                target_var = var
-            else:
-                source_var = var[0]
-                target_var = var[1]
-            var = 'OMPI_%s' % target_var
-            self.variables.nappend(var, str(self.variables[source_var].get_first()), var_class=CommandFlagList)
+        for var, _ in COMPILER_VARIABLES:
+            self.variables.nappend('OMPI_%s' % var, str(self.variables[var].get_first()), var_class=CommandFlagList)
 
         super(OpenMPI, self)._set_mpi_compiler_variables()

From 94e09cd2b59e01546331d5a9f1601e633796bafc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 11 Oct 2015 11:18:41 +0200
Subject: [PATCH 1323/1356] set MPI wrapper comments via _set_compiler_vars in
 openmpi.py toolchain support for OpenMPI

---
 easybuild/toolchains/mpi/openmpi.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/toolchains/mpi/openmpi.py b/easybuild/toolchains/mpi/openmpi.py
index a8ac12e021..ce9a5dd8f0 100644
--- a/easybuild/toolchains/mpi/openmpi.py
+++ b/easybuild/toolchains/mpi/openmpi.py
@@ -57,10 +57,8 @@ class OpenMPI(Mpi):
 
     MPI_LINK_INFO_OPTION = '-showme:link'
 
-    def __init__(self, *args, **kwargs):
-        """Toolchain constructor."""
-        super(OpenMPI, self).__init__(*args, **kwargs)
-
+    def _set_compiler_vars(self):
+        """Set the compiler variables"""
         ompi_ver = self.get_software_version(self.MPI_MODULE_NAME)
         if LooseVersion(ompi_ver) >= LooseVersion('1.7'):
             self.MPI_COMPILER_MPIF77 = 'mpifort'
@@ -71,6 +69,8 @@ def __init__(self, *args, **kwargs):
             self.MPI_COMPILER_MPIF90 = 'mpif90'
             self.MPI_COMPILER_MPIFC = 'mpifc'
 
+        super(OpenMPI, self)._set_compiler_vars()
+
     def _set_mpi_compiler_variables(self):
         """Add OMPI_* variables to set."""
 

From 5041846d93d9e41bf95b1333ad5ac12942ee2ea0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 11 Oct 2015 18:03:27 +0200
Subject: [PATCH 1324/1356] set MPI wrapper comments via _set_mpi_compiler_vars
 in openmpi.py toolchain support for OpenMPI

---
 easybuild/toolchains/mpi/openmpi.py | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/easybuild/toolchains/mpi/openmpi.py b/easybuild/toolchains/mpi/openmpi.py
index ce9a5dd8f0..1afd699cec 100644
--- a/easybuild/toolchains/mpi/openmpi.py
+++ b/easybuild/toolchains/mpi/openmpi.py
@@ -57,8 +57,8 @@ class OpenMPI(Mpi):
 
     MPI_LINK_INFO_OPTION = '-showme:link'
 
-    def _set_compiler_vars(self):
-        """Set the compiler variables"""
+    def _set_mpi_compiler_variables(self):
+        """Define MPI wrapper commands (depends on OpenMPI version) and add OMPI_* variables to set."""
         ompi_ver = self.get_software_version(self.MPI_MODULE_NAME)
         if LooseVersion(ompi_ver) >= LooseVersion('1.7'):
             self.MPI_COMPILER_MPIF77 = 'mpifort'
@@ -69,11 +69,6 @@ def _set_compiler_vars(self):
             self.MPI_COMPILER_MPIF90 = 'mpif90'
             self.MPI_COMPILER_MPIFC = 'mpifc'
 
-        super(OpenMPI, self)._set_compiler_vars()
-
-    def _set_mpi_compiler_variables(self):
-        """Add OMPI_* variables to set."""
-
         # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
         for var, _ in COMPILER_VARIABLES:
             self.variables.nappend('OMPI_%s' % var, str(self.variables[var].get_first()), var_class=CommandFlagList)

From 72d483527f110e9c877450aba6bd6450b46aacfb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 11 Oct 2015 18:13:13 +0200
Subject: [PATCH 1325/1356] fix typo

---
 easybuild/toolchains/mpi/openmpi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/toolchains/mpi/openmpi.py b/easybuild/toolchains/mpi/openmpi.py
index 1afd699cec..8308946c2a 100644
--- a/easybuild/toolchains/mpi/openmpi.py
+++ b/easybuild/toolchains/mpi/openmpi.py
@@ -59,7 +59,7 @@ class OpenMPI(Mpi):
 
     def _set_mpi_compiler_variables(self):
         """Define MPI wrapper commands (depends on OpenMPI version) and add OMPI_* variables to set."""
-        ompi_ver = self.get_software_version(self.MPI_MODULE_NAME)
+        ompi_ver = self.get_software_version(self.MPI_MODULE_NAME)[0]
         if LooseVersion(ompi_ver) >= LooseVersion('1.7'):
             self.MPI_COMPILER_MPIF77 = 'mpifort'
             self.MPI_COMPILER_MPIF90 = 'mpifort'

From 1ed1b2991b95d893341055278709dbd199232575 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 09:08:10 +0200
Subject: [PATCH 1326/1356] fix broken checks

---
 test/framework/toolchain.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 743b102d74..a9b148dd6f 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -89,7 +89,7 @@ def test_get_variable_compilers(self):
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
         self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
-        self.assertEqual(tc.get_variable('MPIFC'), 'mpif90')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpifc')
 
         self.assertEqual(tc.get_variable('OMPI_CC'), 'gcc')
         self.assertEqual(tc.get_variable('OMPI_CXX'), 'g++')
@@ -106,13 +106,13 @@ def test_get_variable_mpi_compilers(self):
         self.assertEqual(tc.get_variable('CXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('F77'), 'mpif77')
         self.assertEqual(tc.get_variable('F90'), 'mpif90')
-        self.assertEqual(tc.get_variable('FC'), 'mpif90')
+        self.assertEqual(tc.get_variable('FC'), 'mpifc')
 
         self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
         self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
-        self.assertEqual(tc.get_variable('MPIFC'), 'mpif90')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpifc')
 
         self.assertEqual(tc.get_variable('OMPI_CC'), 'gcc')
         self.assertEqual(tc.get_variable('OMPI_CXX'), 'g++')
@@ -455,11 +455,11 @@ def test_ictce_toolchain(self):
         self.assertEqual(tc.get_variable('CXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('F77'), 'mpif77')
         self.assertEqual(tc.get_variable('F90'), 'mpifc')
-        self.assertEqual(tc.get_variable('FC'), 'mpif90')
+        self.assertEqual(tc.get_variable('FC'), 'mpifc')
         self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
-        self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
+        self.assertEqual(tc.get_variable('MPIF90'), 'mpifc')
         self.assertEqual(tc.get_variable('MPIFC'), 'mpifc')
         modules.modules_tool().purge()
 

From 277a402348d89658b7f8ff3ff6983240ffc2c689 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 10:30:57 +0200
Subject: [PATCH 1327/1356] pick MPICH MPI compiler wrappers based on version,
 fix broken tests

---
 easybuild/toolchains/mpi/mpich.py       | 20 +++++++++++++++++---
 easybuild/toolchains/mpi/mpich2.py      | 10 ++++++++++
 easybuild/toolchains/mpi/openmpi.py     |  5 +++--
 test/framework/modules/imkl/10.3.12.361 |  2 +-
 test/framework/toolchain.py             | 20 +++++++++++---------
 5 files changed, 42 insertions(+), 15 deletions(-)

diff --git a/easybuild/toolchains/mpi/mpich.py b/easybuild/toolchains/mpi/mpich.py
index 4ddaed37ed..50e1a07229 100644
--- a/easybuild/toolchains/mpi/mpich.py
+++ b/easybuild/toolchains/mpi/mpich.py
@@ -30,6 +30,7 @@
 @author: Jens Timmerman (Ghent University)
 @author: Dmitri Gribenko (National Technical University of Ukraine "KPI")
 """
+from distutils.version import LooseVersion
 
 from easybuild.tools.toolchain.constants import COMPILER_VARIABLES, MPI_COMPILER_VARIABLES
 from easybuild.tools.toolchain.mpi import Mpi
@@ -47,15 +48,28 @@ class Mpich(Mpi):
 
     MPI_LIBRARY_NAME = 'mpich'
 
-    # FIXME version-dependent? see http://www.mpich.org/static/docs/v3.1.4/www1/mpifort.html
-    MPI_COMPILER_MPIFC = 'mpif90'
-    #MPI_COMPILER_MPIFC = 'mpifort'
+    # version-dependent, so defined at runtime
+    MPI_COMPILER_MPIF77 = None
+    MPI_COMPILER_MPIF90 = None
+    MPI_COMPILER_MPIFC = None
 
     # clear MPI wrapper command options
     MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var, '') for var, _ in MPI_COMPILER_VARIABLES])
 
     def _set_mpi_compiler_variables(self):
         """Set the MPICH_{CC, CXX, F77, F90, FC} variables."""
+        # determine MPI wrapper commands to use based on MPICH version
+        if self.MPI_COMPILER_MPIF77 is None and self.MPI_COMPILER_MPIF90 is None and self.MPI_COMPILER_MPIFC is None:
+            # mpif77/mpif90 for MPICH v3.1.0 and earlier, mpifort for MPICH v3.1.2 and newer
+            # see http://www.mpich.org/static/docs/v3.1/ vs http://www.mpich.org/static/docs/v3.1.2/
+            if LooseVersion(self.get_software_version(self.MPI_MODULE_NAME)[0]) >= LooseVersion('3.1.2'):
+                self.MPI_COMPILER_MPIF77 = 'mpif77'
+                self.MPI_COMPILER_MPIF90 = 'mpifort'
+                self.MPI_COMPILER_MPIFC = 'mpifort'
+            else:
+                self.MPI_COMPILER_MPIF77 = 'mpif77'
+                self.MPI_COMPILER_MPIF90 = 'mpif90'
+                self.MPI_COMPILER_MPIFC = 'mpif90'
 
         # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
         for var, _ in COMPILER_VARIABLES:
diff --git a/easybuild/toolchains/mpi/mpich2.py b/easybuild/toolchains/mpi/mpich2.py
index 8aacc85081..84157e9eb9 100644
--- a/easybuild/toolchains/mpi/mpich2.py
+++ b/easybuild/toolchains/mpi/mpich2.py
@@ -41,3 +41,13 @@ class Mpich2(Mpich):
     MPI_MODULE_NAME = ["MPICH2"]
     MPI_FAMILY = TC_CONSTANT_MPICH2
     MPI_TYPE = TC_CONSTANT_MPI_TYPE_MPICH
+
+    def _set_mpi_compiler_variables(self):
+        """Set the MPICH_{CC, CXX, F77, F90, FC} variables."""
+
+        # hardwire MPI wrapper commands (otherwise Mpich parent class sets them based on MPICH version)
+        self.MPI_COMPILER_MPIF77 = 'mpif77'
+        self.MPI_COMPILER_MPIF90 = 'mpif90'
+        self.MPI_COMPILER_MPIFC = 'mpif90'
+
+        super(Mpich2, self)._set_mpi_compiler_variables()
diff --git a/easybuild/toolchains/mpi/openmpi.py b/easybuild/toolchains/mpi/openmpi.py
index 8308946c2a..995e0b85e1 100644
--- a/easybuild/toolchains/mpi/openmpi.py
+++ b/easybuild/toolchains/mpi/openmpi.py
@@ -47,7 +47,7 @@ class OpenMPI(Mpi):
 
     MPI_LIBRARY_NAME = 'mpi'
 
-    # version-dependent, see http://www.open-mpi.org/faq/?category=mpi-apps#override-wrappers-after-v1.0
+    # version-dependent, so defined at runtime
     MPI_COMPILER_MPIF77 = None
     MPI_COMPILER_MPIF90 = None
     MPI_COMPILER_MPIFC = None
@@ -60,6 +60,7 @@ class OpenMPI(Mpi):
     def _set_mpi_compiler_variables(self):
         """Define MPI wrapper commands (depends on OpenMPI version) and add OMPI_* variables to set."""
         ompi_ver = self.get_software_version(self.MPI_MODULE_NAME)[0]
+        # version-dependent, see http://www.open-mpi.org/faq/?category=mpi-apps#override-wrappers-after-v1.0
         if LooseVersion(ompi_ver) >= LooseVersion('1.7'):
             self.MPI_COMPILER_MPIF77 = 'mpifort'
             self.MPI_COMPILER_MPIF90 = 'mpifort'
@@ -67,7 +68,7 @@ def _set_mpi_compiler_variables(self):
         else:
             self.MPI_COMPILER_MPIF77 = 'mpif77'
             self.MPI_COMPILER_MPIF90 = 'mpif90'
-            self.MPI_COMPILER_MPIFC = 'mpifc'
+            self.MPI_COMPILER_MPIFC = 'mpif90'
 
         # this needs to be done first, otherwise e.g., CC is set to MPICC if the usempi toolchain option is enabled
         for var, _ in COMPILER_VARIABLES:
diff --git a/test/framework/modules/imkl/10.3.12.361 b/test/framework/modules/imkl/10.3.12.361
index d63fb61362..edd8cc8328 100644
--- a/test/framework/modules/imkl/10.3.12.361
+++ b/test/framework/modules/imkl/10.3.12.361
@@ -13,7 +13,7 @@ module-whatis {Intel Math Kernel Library is a library of highly optimized,
  applications that require maximum performance. Core math functions include
  BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. - Homepage: http://software.intel.com/en-us/intel-mkl/}
 
-set root	/tmp/eb-bI0pBy/eb-DmuEpJ/eb-leoYDw/eb-UtJJqp/tmp8P3FOY
+set root	/var/folders/8s/_frgh9sj6m744mxt5w5lyztr0000gn/T/eb-WdZm_W/eb-y0XbqZ/eb-I_RMeR/tmp1USZhO
 
 conflict    imkl
 
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index a9b148dd6f..d952c57b66 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -87,9 +87,10 @@ def test_get_variable_compilers(self):
 
         self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
+        # OpenMPI 1.4.5, so old MPI compiler wrappers for Fortran
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
         self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
-        self.assertEqual(tc.get_variable('MPIFC'), 'mpifc')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpif90')
 
         self.assertEqual(tc.get_variable('OMPI_CC'), 'gcc')
         self.assertEqual(tc.get_variable('OMPI_CXX'), 'g++')
@@ -104,15 +105,16 @@ def test_get_variable_mpi_compilers(self):
 
         self.assertEqual(tc.get_variable('CC'), 'mpicc')
         self.assertEqual(tc.get_variable('CXX'), 'mpicxx')
+        # OpenMPI 1.4.5, so old MPI compiler wrappers for Fortran
         self.assertEqual(tc.get_variable('F77'), 'mpif77')
         self.assertEqual(tc.get_variable('F90'), 'mpif90')
-        self.assertEqual(tc.get_variable('FC'), 'mpifc')
+        self.assertEqual(tc.get_variable('FC'), 'mpif90')
 
         self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
         self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
-        self.assertEqual(tc.get_variable('MPIFC'), 'mpifc')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpif90')
 
         self.assertEqual(tc.get_variable('OMPI_CC'), 'gcc')
         self.assertEqual(tc.get_variable('OMPI_CXX'), 'g++')
@@ -454,13 +456,13 @@ def test_ictce_toolchain(self):
         self.assertEqual(tc.get_variable('CC'), 'mpicc')
         self.assertEqual(tc.get_variable('CXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('F77'), 'mpif77')
-        self.assertEqual(tc.get_variable('F90'), 'mpifc')
-        self.assertEqual(tc.get_variable('FC'), 'mpifc')
+        self.assertEqual(tc.get_variable('F90'), 'mpif90')
+        self.assertEqual(tc.get_variable('FC'), 'mpif90')
         self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
-        self.assertEqual(tc.get_variable('MPIF90'), 'mpifc')
-        self.assertEqual(tc.get_variable('MPIFC'), 'mpifc')
+        self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpif90')
         modules.modules_tool().purge()
 
         tc = self.get_toolchain("ictce", version="4.1.13")
@@ -477,12 +479,12 @@ def test_ictce_toolchain(self):
         self.assertEqual(tc.get_variable('CXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('F77'), 'mpif77')
         self.assertEqual(tc.get_variable('F90'), 'mpif90')
-        self.assertEqual(tc.get_variable('FC'), 'mpifc')
+        self.assertEqual(tc.get_variable('FC'), 'mpif90')
         self.assertEqual(tc.get_variable('MPICC'), 'mpicc')
         self.assertEqual(tc.get_variable('MPICXX'), 'mpicxx')
         self.assertEqual(tc.get_variable('MPIF77'), 'mpif77')
         self.assertEqual(tc.get_variable('MPIF90'), 'mpif90')
-        self.assertEqual(tc.get_variable('MPIFC'), 'mpifc')
+        self.assertEqual(tc.get_variable('MPIFC'), 'mpif90')
 
         # cleanup
         shutil.rmtree(tmpdir)

From 64a13a9e2eed5558bbf0a76a8146332096c45462 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 13:05:38 +0200
Subject: [PATCH 1328/1356] implement weld_paths function + use it to determine
 path to copy patch files to

---
 easybuild/framework/easyblock.py |  7 ++++---
 easybuild/tools/filetools.py     | 25 +++++++++++++++++++++++++
 test/framework/filetools.py      | 14 ++++++++++++++
 3 files changed, 43 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 739411aa68..32ad2453e4 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -64,7 +64,7 @@
 from easybuild.tools.filetools import DEFAULT_CHECKSUM
 from easybuild.tools.filetools import adjust_permissions, apply_patch, convert_name, download_file, encode_class_name
 from easybuild.tools.filetools import extract_file, mkdir, move_logs, read_file, rmtree2
-from easybuild.tools.filetools import write_file, compute_checksum, verify_checksum
+from easybuild.tools.filetools import write_file, compute_checksum, verify_checksum, weld_paths
 from easybuild.tools.run import run_cmd
 from easybuild.tools.jenkins import write_to_xml
 from easybuild.tools.module_generator import ModuleGeneratorLua, ModuleGeneratorTcl, module_generator
@@ -1358,8 +1358,9 @@ def patch_step(self, beginpath=None):
             else:
                 self.log.debug("Using specified begin path for patch %s: %s" % (patch['name'], beginpath))
 
-            src = os.path.abspath("%s/%s" % (beginpath, srcpathsuffix))
-            self.log.debug("Applying patch %s in path %s" % (patch, src))
+            # detect partial overlap between paths
+            src = weld_paths(beginpath, srcpathsuffix)
+            self.log.debug("Applying patch %s in path %s", patch, src)
 
             if not apply_patch(patch['path'], src, copy=copy_patch, level=level):
                 raise EasyBuildError("Applying patch %s failed", patch['name'])
diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 21998b2512..7d546726d3 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -848,6 +848,31 @@ def expand_glob_paths(glob_paths):
     return nub(paths)
 
 
+def weld_paths(path1, path2):
+    """Weld two paths together, taking into account overlap between tail of 1st path with head of 2nd path."""
+    # strip path1 for use in comparisons
+    path1s = path1.strip(os.path.sep)
+
+    # init part2 head/tail/parts
+    path2_head = path2.strip(os.path.sep)
+    path2_tail = ''
+    path2_parts = path2.split(os.path.sep)
+
+    while path2_parts and not path1s.endswith(path2_head):
+        path2_tail = os.path.join(path2_parts.pop(-1), path2_tail)
+        if path2_parts:
+            # os.path.join requires non-empty list
+            path2_head = os.path.join(*path2_parts).strip(os.path.sep)
+        else:
+            path2_head = None
+
+    # take into account that path2 is absolute path
+    if path2.startswith(os.path.sep):
+        path2_tail = os.path.sep + path2_tail
+
+    return os.path.join(path1, path2_tail)
+
+
 def symlink(source_path, symlink_path):
     """Create a symlink at the specified path to the given path."""
     try:
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 7086add22c..2ef98de5da 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -435,6 +435,20 @@ def test_multidiff(self):
 
         self.assertEqual(lines[-1], "=====")
 
+    def test_weld_paths(self):
+        """Test weld_paths."""
+        # works like os.path.join is there's no overlap
+        self.assertEqual(ft.weld_paths('/foo/bar', 'foobar/baz'), '/foo/bar/foobar/baz/')
+        self.assertEqual(ft.weld_paths('foo', 'bar/'), 'foo/bar/')
+        self.assertEqual(ft.weld_paths('foo/', '/bar'), '/bar/')
+
+        # overlap is taken into account
+        self.assertEqual(ft.weld_paths('foo/bar', 'bar/baz'), 'foo/bar/baz/')
+        self.assertEqual(ft.weld_paths('foo/bar/baz', 'bar/baz'), 'foo/bar/baz/')
+        self.assertEqual(ft.weld_paths('foo/bar', 'foo/bar/baz'), 'foo/bar/baz/')
+        self.assertEqual(ft.weld_paths('foo/bar', 'foo/bar'), 'foo/bar/')
+        self.assertEqual(ft.weld_paths('/foo/bar', 'foo/bar'), '/foo/bar/')
+
 
 def suite():
     """ returns all the testcases in this module """

From 7fab1fd9dfd1c77d6d1724be25ce8182fbed1da5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 13:23:13 +0200
Subject: [PATCH 1329/1356] extend test for patch_step to also check
 patch-by-copy

---
 test/framework/easyblock.py                      | 14 +++++++++++++-
 test/framework/easyconfigs/toy-0.0.eb            |  5 ++++-
 test/framework/sandbox/sources/toy/toy-extra.txt |  1 +
 3 files changed, 18 insertions(+), 2 deletions(-)
 create mode 100644 test/framework/sandbox/sources/toy/toy-extra.txt

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 10c0509568..4344e5be1a 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -618,9 +618,16 @@ def test_exclude_path_to_top_of_module_tree(self):
 
     def test_patch_step(self):
         """Test patch step."""
-        ec = process_easyconfig(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs', 'toy-0.0.eb'))[0]
+        test_easyconfigs = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'easyconfigs')
+        ec = process_easyconfig(os.path.join(test_easyconfigs, 'toy-0.0.eb'))[0]
         orig_sources = ec['ec']['sources'][:]
 
+        toy_patches = [
+            'toy-0.0_typo.patch',  # test for applying patch
+            ('toy-extra.txt', 'toy-0.0'), # test for patch-by-copy
+        ]
+        self.assertEqual(ec['ec']['patches'], toy_patches)
+
         # test applying patches without sources
         ec['ec']['sources'] = []
         eb = EasyBlock(ec['ec'])
@@ -634,6 +641,11 @@ def test_patch_step(self):
         eb.fetch_step()
         eb.extract_step()
         eb.patch_step()
+        # verify that patches were applied
+        toydir = os.path.join(eb.builddir, 'toy-0.0')
+        self.assertEqual(sorted(os.listdir(toydir)), ['toy-extra.txt', 'toy.source', 'toy.source.orig'])
+        self.assertTrue("and very proud of it" in read_file(os.path.join(toydir, 'toy.source')))
+        self.assertEqual(read_file(os.path.join(toydir, 'toy-extra.txt')), 'moar!\n')
 
     def test_extensions_sanity_check(self):
         """Test sanity check aspect of extensions."""
diff --git a/test/framework/easyconfigs/toy-0.0.eb b/test/framework/easyconfigs/toy-0.0.eb
index d3b5717f96..d4d9e4e108 100644
--- a/test/framework/easyconfigs/toy-0.0.eb
+++ b/test/framework/easyconfigs/toy-0.0.eb
@@ -15,7 +15,10 @@ checksums = [[
     ('sha1', 'f618096c52244539d0e89867405f573fdb0b55b0'),
     ('size', 273),
 ]]
-patches = ['toy-0.0_typo.patch']
+patches = [
+    'toy-0.0_typo.patch',
+    ('toy-extra.txt', 'toy-0.0'),
+]
 
 sanity_check_paths = {
     'files': [('bin/yot', 'bin/toy')],
diff --git a/test/framework/sandbox/sources/toy/toy-extra.txt b/test/framework/sandbox/sources/toy/toy-extra.txt
new file mode 100644
index 0000000000..1286a1af21
--- /dev/null
+++ b/test/framework/sandbox/sources/toy/toy-extra.txt
@@ -0,0 +1 @@
+moar!

From 9681295ad8dee260cc19bec76f7ddd18aad8e916 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 13:32:24 +0200
Subject: [PATCH 1330/1356] put abspath back

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 32ad2453e4..81099e3e25 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1359,7 +1359,7 @@ def patch_step(self, beginpath=None):
                 self.log.debug("Using specified begin path for patch %s: %s" % (patch['name'], beginpath))
 
             # detect partial overlap between paths
-            src = weld_paths(beginpath, srcpathsuffix)
+            src = os.path.abspath(weld_paths(beginpath, srcpathsuffix))
             self.log.debug("Applying patch %s in path %s", patch, src)
 
             if not apply_patch(patch['path'], src, copy=copy_patch, level=level):

From b018be78c73703e80d1787876968e43f38a4ab60 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 13:42:28 +0200
Subject: [PATCH 1331/1356] revert change in test imkl module

---
 test/framework/modules/imkl/10.3.12.361 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/framework/modules/imkl/10.3.12.361 b/test/framework/modules/imkl/10.3.12.361
index edd8cc8328..d63fb61362 100644
--- a/test/framework/modules/imkl/10.3.12.361
+++ b/test/framework/modules/imkl/10.3.12.361
@@ -13,7 +13,7 @@ module-whatis {Intel Math Kernel Library is a library of highly optimized,
  applications that require maximum performance. Core math functions include
  BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. - Homepage: http://software.intel.com/en-us/intel-mkl/}
 
-set root	/var/folders/8s/_frgh9sj6m744mxt5w5lyztr0000gn/T/eb-WdZm_W/eb-y0XbqZ/eb-I_RMeR/tmp1USZhO
+set root	/tmp/eb-bI0pBy/eb-DmuEpJ/eb-leoYDw/eb-UtJJqp/tmp8P3FOY
 
 conflict    imkl
 

From 466eaa242b88704be76e8a16c5f00982a20711c3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 13:57:02 +0200
Subject: [PATCH 1332/1356] fix broken tests

---
 test/framework/easyblock.py  | 2 +-
 test/framework/easyconfig.py | 4 ++--
 test/framework/filetools.py  | 8 ++++----
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 4344e5be1a..c8f19c3193 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -447,7 +447,7 @@ def test_fetch_patches(self):
         eb = get_easyblock_instance(ec)
 
         eb.fetch_patches()
-        self.assertEqual(len(eb.patches), 1)
+        self.assertEqual(len(eb.patches), 2)
         self.assertEqual(eb.patches[0]['name'], 'toy-0.0_typo.patch')
         self.assertFalse('level' in eb.patches[0])
 
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 1a6e5f3885..c0514ee223 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -303,7 +303,7 @@ def test_exts_list(self):
             '       "patches": ["toy-0.0.eb"],',  # dummy patch to avoid downloading fail
             '       "checksums": [',
             '           "787393bfc465c85607a5b24486e861c5",',  # MD5 checksum for source (gzip-1.4.eb)
-            '           "44893c3ed46a7c7ab2e72fea7d19925d",',  # MD5 checksum for patch (toy-0.0.eb)
+            '           "fad34da3432ee2fd4d6554b86c8df4bf",',  # MD5 checksum for patch (toy-0.0.eb)
             '       ],',
             '   }),',
             ']',
@@ -1122,7 +1122,7 @@ def test_update(self):
 
         # for list values: extend
         ec.update('patches', ['foo.patch', 'bar.patch'])
-        self.assertEqual(ec['patches'], ['toy-0.0_typo.patch', 'foo.patch', 'bar.patch'])
+        self.assertEqual(ec['patches'], ['toy-0.0_typo.patch', ('toy-extra.txt', 'toy-0.0'), 'foo.patch', 'bar.patch'])
 
     def test_hide_hidden_deps(self):
         """Test use of --hide-deps on hiddendependencies."""
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index 2ef98de5da..b88d88e4a5 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -404,9 +404,9 @@ def test_multidiff(self):
         self.assertTrue(lines[8].startswith(expected))
 
         # no postinstallcmds in toy-0.0-deps.eb
-        expected = "25 %s+ postinstallcmds = " % green
+        expected = "28 %s+ postinstallcmds = " % green
         self.assertTrue(any([line.startswith(expected) for line in lines]))
-        self.assertTrue("26 %s+%s (1/2) toy-0.0-deps.eb" % (green, endcol) in lines)
+        self.assertTrue("29 %s+%s (1/2) toy-0.0-deps.eb" % (green, endcol) in lines)
         self.assertEqual(lines[-1], "=====")
 
         lines = multidiff(os.path.join(test_easyconfigs, 'toy-0.0.eb'), other_toy_ecs, colored=False).split('\n')
@@ -429,9 +429,9 @@ def test_multidiff(self):
         self.assertEqual(lines[10], expected)
 
         # no postinstallcmds in toy-0.0-deps.eb
-        expected = "25 + postinstallcmds = "
+        expected = "28 + postinstallcmds = "
         self.assertTrue(any([line.startswith(expected) for line in lines]))
-        self.assertTrue("26 + (1/2) toy-0.0-deps.eb" in lines)
+        self.assertTrue("29 + (1/2) toy-0.0-deps.eb" in lines)
 
         self.assertEqual(lines[-1], "=====")
 

From f7b5b4b9ccc1492bd6b2b5ef057799fed6838d15 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 17:18:25 +0200
Subject: [PATCH 1333/1356] add test cases for weld_paths with absolute paths
 and fix the implementation to make them pass ^_^

---
 easybuild/tools/filetools.py | 15 +++++++--------
 test/framework/filetools.py  |  3 +++
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/easybuild/tools/filetools.py b/easybuild/tools/filetools.py
index 6bddad2571..287540acae 100644
--- a/easybuild/tools/filetools.py
+++ b/easybuild/tools/filetools.py
@@ -843,25 +843,24 @@ def expand_glob_paths(glob_paths):
 def weld_paths(path1, path2):
     """Weld two paths together, taking into account overlap between tail of 1st path with head of 2nd path."""
     # strip path1 for use in comparisons
-    path1s = path1.strip(os.path.sep)
+    path1s = path1.rstrip(os.path.sep)
 
     # init part2 head/tail/parts
-    path2_head = path2.strip(os.path.sep)
+    path2_head = path2.rstrip(os.path.sep)
     path2_tail = ''
     path2_parts = path2.split(os.path.sep)
+    # if path2 is an absolute path, make sure it stays that way
+    if path2_parts[0] == '':
+        path2_parts[0] = os.path.sep
 
     while path2_parts and not path1s.endswith(path2_head):
-        path2_tail = os.path.join(path2_parts.pop(-1), path2_tail)
+        path2_tail = os.path.join(path2_parts.pop(), path2_tail)
         if path2_parts:
             # os.path.join requires non-empty list
-            path2_head = os.path.join(*path2_parts).strip(os.path.sep)
+            path2_head = os.path.join(*path2_parts)
         else:
             path2_head = None
 
-    # take into account that path2 is absolute path
-    if path2.startswith(os.path.sep):
-        path2_tail = os.path.sep + path2_tail
-
     return os.path.join(path1, path2_tail)
 
 
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index a4aec8a2db..4e81c2b96e 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -441,6 +441,7 @@ def test_weld_paths(self):
         self.assertEqual(ft.weld_paths('/foo/bar', 'foobar/baz'), '/foo/bar/foobar/baz/')
         self.assertEqual(ft.weld_paths('foo', 'bar/'), 'foo/bar/')
         self.assertEqual(ft.weld_paths('foo/', '/bar'), '/bar/')
+        self.assertEqual(ft.weld_paths('/foo/', '/bar'), '/bar/')
 
         # overlap is taken into account
         self.assertEqual(ft.weld_paths('foo/bar', 'bar/baz'), 'foo/bar/baz/')
@@ -448,6 +449,8 @@ def test_weld_paths(self):
         self.assertEqual(ft.weld_paths('foo/bar', 'foo/bar/baz'), 'foo/bar/baz/')
         self.assertEqual(ft.weld_paths('foo/bar', 'foo/bar'), 'foo/bar/')
         self.assertEqual(ft.weld_paths('/foo/bar', 'foo/bar'), '/foo/bar/')
+        self.assertEqual(ft.weld_paths('/foo/bar', '/foo/bar'), '/foo/bar/')
+        self.assertEqual(ft.weld_paths('/foo', '/foo/bar/baz'), '/foo/bar/baz/')
 
 
 def suite():

From 44c7777118b18ad6c5a4ce247fdf1c2d4ec1b064 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 21:07:53 +0200
Subject: [PATCH 1334/1356] rename to modaltsoftname

---
 easybuild/framework/easyconfig/default.py    | 2 +-
 easybuild/framework/easyconfig/easyconfig.py | 6 +++---
 test/framework/easyconfig.py                 | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 858aa377b7..a9f7c932c0 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -160,7 +160,7 @@
     'modextravars': [{}, "Extra environment variables to be added to module file", MODULES],
     'modloadmsg': [{}, "Message that should be printed when generated module is loaded", MODULES],
     'modluafooter': ["", "Footer to include in generated module file (Lua syntax)", MODULES],
-    'modname': [None, "Module name to use (rather than using software name", MODULES],
+    'modaltsoftname': [None, "Module name to use (rather than using software name", MODULES],
     'modtclfooter': ["", "Footer to include in generated module file (Tcl syntax)", MODULES],
     'moduleclass': ['base', 'Module class to be used for this software', MODULES],
     'moduleforceunload': [False, 'Force unload of all modules when loading the extension', MODULES],
diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index e4772e91eb..bd32628ecd 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1097,9 +1097,9 @@ def _det_module_name_with(self, mns_method, ec, force_visible=False):
 
         # replace software name with desired replacement (if specified)
         orig_name = None
-        if ec.get('modname', None):
+        if ec.get('modaltsoftname', None):
             orig_name = ec['name']
-            ec['name'] = ec['modname']
+            ec['name'] = ec['modaltsoftname']
             self.log.info("Replaced software name '%s' with '%s' when determining module name", orig_name, ec['name'])
 
         mod_name = mns_method(self.check_ec_type(ec))
@@ -1149,7 +1149,7 @@ def det_short_module_name(self, ec, force_visible=False):
         self.log.debug("Obtained valid short module name %s" % mod_name)
 
         # sanity check: obtained module name should pass the 'is_short_modname_for' check
-        if not self.is_short_modname_for(mod_name, ec.get('modname', None) or ec['name']):
+        if not self.is_short_modname_for(mod_name, ec.get('modaltsoftname', None) or ec['name']):
             raise EasyBuildError("is_short_modname_for('%s', '%s') for active module naming scheme returns False",
                                  mod_name, ec['name'])
         return mod_name
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 38fb351990..e53900cd43 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1494,12 +1494,12 @@ def test_find_related_easyconfigs(self):
         ec['name'] = 'nosuchsoftware'
         self.assertEqual(find_related_easyconfigs(test_easyconfigs, ec), [])
 
-    def test_alt_name(self):
+    def test_modaltsoftname(self):
         """Test specifying an alternative name for the software name, to use when determining module name."""
         ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'toy-0.0-deps.eb')
         ectxt = read_file(ec_file)
         modified_ec_file = os.path.join(self.test_prefix, os.path.basename(ec_file))
-        write_file(modified_ec_file, ectxt + "\nmodname = 'notreallyatoy'")
+        write_file(modified_ec_file, ectxt + "\nmodaltsoftname = 'notreallyatoy'")
         ec = EasyConfig(modified_ec_file)
         self.assertEqual(ec.full_mod_name, 'notreallyatoy/0.0-deps')
         self.assertEqual(ec.short_mod_name, 'notreallyatoy/0.0-deps')

From 5cefe50600e98f7d1251b4aca4988cc4feabce9b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 12 Oct 2015 22:16:35 +0200
Subject: [PATCH 1335/1356] avoid duplicate check_ec_type call

---
 easybuild/framework/easyconfig/easyconfig.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index bd32628ecd..6478a188b1 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -1101,8 +1101,10 @@ def _det_module_name_with(self, mns_method, ec, force_visible=False):
             orig_name = ec['name']
             ec['name'] = ec['modaltsoftname']
             self.log.info("Replaced software name '%s' with '%s' when determining module name", orig_name, ec['name'])
+        else:
+            self.log.debug("No alternative software name specified to determine module name with")
 
-        mod_name = mns_method(self.check_ec_type(ec))
+        mod_name = mns_method(ec)
 
         # restore original software name if it was tampered with
         if orig_name is not None:

From 9362eb4a88b3f4d59fe44d309a90557663115cda Mon Sep 17 00:00:00 2001
From: Alan <a.ocais@fz-juelich.de>
Date: Tue, 13 Oct 2015 13:11:03 +0200
Subject: [PATCH 1336/1356] Add support for setting recursive unload in
 easyconfig file

---
 easybuild/framework/easyblock.py    | 2 +-
 easybuild/tools/module_generator.py | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 81099e3e25..a9da2d0ad4 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -844,7 +844,7 @@ def make_module_dep(self):
 
         deps = [d for d in deps if d not in excluded_deps]
         self.log.debug("List of retained dependencies: %s" % deps)
-        loads = [self.module_generator.load_module(d) for d in deps]
+        loads = [self.module_generator.load_module(d, self.cfg['recursive_mod_unload']) for d in deps]
         unloads = [self.module_generator.unload_module(d) for d in deps[::-1]]
 
         # Force unloading any other modules
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index be31a6b044..de0733293f 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -195,11 +195,11 @@ def get_description(self, conflict=True):
 
         return txt
 
-    def load_module(self, mod_name):
+    def load_module(self, mod_name, recursive_mod_unload):
         """
         Generate load statements for module.
         """
-        if build_option('recursive_mod_unload'):
+        if build_option('recursive_mod_unload' or recursive_mod_unload):
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the depedency "module load" is present,
             # it will get translated to "module unload"
@@ -359,11 +359,11 @@ def get_description(self, conflict=True):
 
         return txt
 
-    def load_module(self, mod_name):
+    def load_module(self, mod_name, recursive_mod_unload):
         """
         Generate load statements for module.
         """
-        if build_option('recursive_mod_unload'):
+        if build_option('recursive_mod_unload') or recursive_mod_unload:
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the depedency "module load" is present,
             # it will get translated to "module unload"

From 1a74affb7df65399f54f7a27d543b57e1c9a8a7f Mon Sep 17 00:00:00 2001
From: Alan <a.ocais@fz-juelich.de>
Date: Tue, 13 Oct 2015 18:07:55 +0200
Subject: [PATCH 1337/1356] Fix missing easconfig param and add default

---
 easybuild/framework/easyconfig/default.py | 1 +
 easybuild/tools/module_generator.py       | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index a9f7c932c0..9bbe3053f9 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -166,6 +166,7 @@
     'moduleforceunload': [False, 'Force unload of all modules when loading the extension', MODULES],
     'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", MODULES],
     'include_modpath_extensions': [True, "Include $MODULEPATH extensions specified by module naming scheme.", MODULES],
+    'recursive_mod_unload': [False, 'Recursive unload of all dependencies when unloading module', MODULES],
 
     # OTHER easyconfig parameters
     'buildstats': [None, "A list of dicts with build statistics", OTHER],
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index de0733293f..6c2e24326a 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -195,7 +195,7 @@ def get_description(self, conflict=True):
 
         return txt
 
-    def load_module(self, mod_name, recursive_mod_unload):
+    def load_module(self, mod_name, recursive_mod_unload=False):
         """
         Generate load statements for module.
         """
@@ -359,7 +359,7 @@ def get_description(self, conflict=True):
 
         return txt
 
-    def load_module(self, mod_name, recursive_mod_unload):
+    def load_module(self, mod_name, recursive_mod_unload=False):
         """
         Generate load statements for module.
         """

From 3ca44fde1bd4ed060711760f987b02566380b7c5 Mon Sep 17 00:00:00 2001
From: Alan <a.ocais@fz-juelich.de>
Date: Tue, 13 Oct 2015 18:30:58 +0200
Subject: [PATCH 1338/1356] Fixed typo, changed setting name

---
 easybuild/framework/easyblock.py          |  2 +-
 easybuild/framework/easyconfig/default.py |  2 +-
 easybuild/tools/module_generator.py       | 10 +++++-----
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index a9da2d0ad4..428f3b9f17 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -844,7 +844,7 @@ def make_module_dep(self):
 
         deps = [d for d in deps if d not in excluded_deps]
         self.log.debug("List of retained dependencies: %s" % deps)
-        loads = [self.module_generator.load_module(d, self.cfg['recursive_mod_unload']) for d in deps]
+        loads = [self.module_generator.load_module(d, recursive_module_unload=self.cfg['recursive_module_unload']) for d in deps]
         unloads = [self.module_generator.unload_module(d) for d in deps[::-1]]
 
         # Force unloading any other modules
diff --git a/easybuild/framework/easyconfig/default.py b/easybuild/framework/easyconfig/default.py
index 9bbe3053f9..e69e646b81 100644
--- a/easybuild/framework/easyconfig/default.py
+++ b/easybuild/framework/easyconfig/default.py
@@ -166,7 +166,7 @@
     'moduleforceunload': [False, 'Force unload of all modules when loading the extension', MODULES],
     'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", MODULES],
     'include_modpath_extensions': [True, "Include $MODULEPATH extensions specified by module naming scheme.", MODULES],
-    'recursive_mod_unload': [False, 'Recursive unload of all dependencies when unloading module', MODULES],
+    'recursive_module_unload': [False, 'Recursive unload of all dependencies when unloading module', MODULES],
 
     # OTHER easyconfig parameters
     'buildstats': [None, "A list of dicts with build statistics", OTHER],
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 6c2e24326a..49e64055ae 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -195,13 +195,13 @@ def get_description(self, conflict=True):
 
         return txt
 
-    def load_module(self, mod_name, recursive_mod_unload=False):
+    def load_module(self, mod_name, recursive_module_unload=False):
         """
         Generate load statements for module.
         """
-        if build_option('recursive_mod_unload' or recursive_mod_unload):
+        if build_option('recursive_mod_unload') or recursive_module_unload:
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
-            # when "module unload" is called on the module in which the depedency "module load" is present,
+            # when "module unload" is called on the module in which the dependency "module load" is present,
             # it will get translated to "module unload"
             load_statement = [self.LOAD_TEMPLATE, '']
         else:
@@ -359,11 +359,11 @@ def get_description(self, conflict=True):
 
         return txt
 
-    def load_module(self, mod_name, recursive_mod_unload=False):
+    def load_module(self, mod_name, recursive_module_unload=False):
         """
         Generate load statements for module.
         """
-        if build_option('recursive_mod_unload') or recursive_mod_unload:
+        if build_option('recursive_mod_unload') or recursive_module_unload:
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the depedency "module load" is present,
             # it will get translated to "module unload"

From b5cde030a58f2449e34726517a4e2b0525e348a4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 08:54:42 +0200
Subject: [PATCH 1339/1356] fix long lines, us recursive_unload for all
 module_generator.load_module statements

---
 easybuild/framework/easyblock.py    | 7 +++++--
 easybuild/tools/module_generator.py | 8 ++++----
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 428f3b9f17..293d2df533 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -771,6 +771,7 @@ def make_devel_module(self, create_in_builddir=False):
         load_lines = []
         # capture all the EBDEVEL vars
         # these should be all the dependencies and we should load them
+        recursive_unload = self.cfg['recursive_module_unload']
         for key in os.environ:
             # legacy support
             if key.startswith(DEVEL_ENV_VAR_NAME_PREFIX):
@@ -778,7 +779,8 @@ def make_devel_module(self, create_in_builddir=False):
                     path = os.environ[key]
                     if os.path.isfile(path):
                         mod_name = path.rsplit(os.path.sep, 1)[-1]
-                        load_lines.append(self.module_generator.load_module(mod_name))
+                        load_statement = self.module_generator.load_module(mod_name, recursive_unload=recursive_unload)
+                        load_lines.append(load_statement)
             elif key.startswith('SOFTDEVEL'):
                 self.log.nosupport("Environment variable SOFTDEVEL* being relied on", '2.0')
 
@@ -844,7 +846,8 @@ def make_module_dep(self):
 
         deps = [d for d in deps if d not in excluded_deps]
         self.log.debug("List of retained dependencies: %s" % deps)
-        loads = [self.module_generator.load_module(d, recursive_module_unload=self.cfg['recursive_module_unload']) for d in deps]
+        recursive_unload = self.cfg['recursive_module_unload']
+        loads = [self.module_generator.load_module(d, recursive_unload=recursive_unload) for d in deps]
         unloads = [self.module_generator.unload_module(d) for d in deps[::-1]]
 
         # Force unloading any other modules
diff --git a/easybuild/tools/module_generator.py b/easybuild/tools/module_generator.py
index 49e64055ae..5958508430 100644
--- a/easybuild/tools/module_generator.py
+++ b/easybuild/tools/module_generator.py
@@ -195,11 +195,11 @@ def get_description(self, conflict=True):
 
         return txt
 
-    def load_module(self, mod_name, recursive_module_unload=False):
+    def load_module(self, mod_name, recursive_unload=False):
         """
         Generate load statements for module.
         """
-        if build_option('recursive_mod_unload') or recursive_module_unload:
+        if build_option('recursive_mod_unload') or recursive_unload:
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the dependency "module load" is present,
             # it will get translated to "module unload"
@@ -359,11 +359,11 @@ def get_description(self, conflict=True):
 
         return txt
 
-    def load_module(self, mod_name, recursive_module_unload=False):
+    def load_module(self, mod_name, recursive_unload=False):
         """
         Generate load statements for module.
         """
-        if build_option('recursive_mod_unload') or recursive_module_unload:
+        if build_option('recursive_mod_unload') or recursive_unload:
             # not wrapping the 'module load' with an is-loaded guard ensures recursive unloading;
             # when "module unload" is called on the module in which the depedency "module load" is present,
             # it will get translated to "module unload"

From 3a62aa0d9db6a2419322cee07382779c498028c3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 09:02:42 +0200
Subject: [PATCH 1340/1356] enhance unit test for module_generator.load_module

---
 test/framework/module_generator.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 64fd5a471f..bf6c89d0f6 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -112,6 +112,7 @@ def test_load(self):
         """Test load part in generated module file."""
 
         if self.MODULE_GENERATOR_CLASS == ModuleGeneratorTcl:
+            # default: guarded module load (which implies no recursive unloading)
             expected = [
                 '',
                 "if { ![ is-loaded mod_name ] } {",
@@ -122,14 +123,17 @@ def test_load(self):
             self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
 
             # with recursive unloading: no if is-loaded guard
-            init_config(build_options={'recursive_mod_unload': True})
             expected = [
                 '',
                 "module load mod_name",
                 '',
             ]
+            self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name", recursive_unload=True))
+
+            init_config(build_options={'recursive_mod_unload': True})
             self.assertEqual('\n'.join(expected), self.modgen.load_module("mod_name"))
         else:
+            # default: guarded module load (which implies no recursive unloading)
             expected = '\n'.join([
                 '',
                 'if not isloaded("mod_name") then',
@@ -139,12 +143,15 @@ def test_load(self):
             ])
             self.assertEqual(expected,self.modgen.load_module("mod_name"))
 
-            init_config(build_options={'recursive_mod_unload': True})
+            # with recursive unloading: no if isloaded guard
             expected = '\n'.join([
                 '',
                 'load("mod_name")',
                 '',
             ])
+            self.assertEqual(expected, self.modgen.load_module("mod_name", recursive_unload=True))
+
+            init_config(build_options={'recursive_mod_unload': True})
             self.assertEqual(expected,self.modgen.load_module("mod_name"))
 
     def test_unload(self):

From b4ee3b52f4ebd4f9f99e380208857cfdcf292f5c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 11:00:37 +0200
Subject: [PATCH 1341/1356] implement basic support for type checking of
 easyconfig parameters

---
 easybuild/framework/easyconfig/parser.py | 16 +++++++
 easybuild/framework/easyconfig/types.py  | 61 ++++++++++++++++++++++++
 2 files changed, 77 insertions(+)
 create mode 100644 easybuild/framework/easyconfig/types.py

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 36173d35a1..bdc4505b68 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -35,6 +35,7 @@
 
 from easybuild.framework.easyconfig.format.format import FORMAT_DEFAULT_VERSION
 from easybuild.framework.easyconfig.format.format import get_format_version, get_format_version_classes
+from easybuild.framework.easyconfig.types import TYPES, check_type_of_param_value
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import read_file, write_file
 
@@ -99,6 +100,8 @@ def __init__(self, filename=None, format_version=None, rawcontent=None):
         else:
             raise EasyBuildError("Neither filename nor rawcontent provided to EasyConfigParser")
 
+        self.check_types()
+
         self._formatter.extract_comments(self.rawcontent)
 
     def process(self, filename=None):
@@ -106,6 +109,19 @@ def process(self, filename=None):
         self._read(filename=filename)
         self._set_formatter()
 
+    def check_types(self):
+        """Check types of easyconfig parameter values."""
+        params = self.get_config_dict()
+        wrong_type_msgs = []
+        for key in params:
+            if not check_type_of_param_value(key, params[key]):
+                wrong_type_msgs.append("value for '%s' should be of type '%s'" % (key, TYPES[key].__name__))
+
+        if wrong_type_msgs:
+            raise EasyBuildError("Type checking of easyconfig parameter values failed: %s", ' '.join(wrong_type_msgs))
+        else:
+            self.log.info("Type checking of easyconfig parameter values passed!")
+
     def _check_filename(self, fn):
         """Perform sanity check on the filename, and set mechanism to set the content of the file"""
         if os.path.isfile(fn):
diff --git a/easybuild/framework/easyconfig/types.py b/easybuild/framework/easyconfig/types.py
new file mode 100644
index 0000000000..9831ef9c38
--- /dev/null
+++ b/easybuild/framework/easyconfig/types.py
@@ -0,0 +1,61 @@
+# #
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+
+"""
+Support for checking types of easyconfig parameter values.
+
+@author: Kenneth Hoste (Ghent University)
+"""
+from vsc.utils import fancylogger
+
+EASY_TYPES = [basestring, int]
+# type checking is skipped for easyconfig parameters names not listed in TYPES
+TYPES = {
+    'name': basestring,
+    'version': basestring,
+}
+
+
+_log = fancylogger.getLogger('easyconfig.types', fname=False)
+
+
+def check_type_of_param_value(key, value):
+    """Check value type of specified easyconfig parameter."""
+    type_ok = True
+    if key in TYPES:
+        expected_type = TYPES[key]
+        if expected_type in EASY_TYPES:
+            if isinstance(value, expected_type):
+                _log.debug("Value type checking of easyconfig parameter '%s' passed: expected '%s', got '%s'",
+                           key, expected_type.__name__, type(value).__name__)
+            else:
+                type_ok = False
+                _log.warning("Value type checking of easyconfig parameter '%s' FAILED: expected '%s', got '%s'",
+                             key, expected_type.__name__, type(value).__name__)
+
+    else:
+        _log.debug("No type specified for easyconfig parameter '%s', so skipping type check.", key)
+
+    return type_ok

From e548f4d2484e04cf990c733a8f97ea1b5f46df87 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 11:15:14 +0200
Subject: [PATCH 1342/1356] add unit test for check_type_of_param_value, in new
 test module

---
 test/framework/suite.py         |  3 +-
 test/framework/type_checking.py | 61 +++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+), 1 deletion(-)
 create mode 100644 test/framework/type_checking.py

diff --git a/test/framework/suite.py b/test/framework/suite.py
index 34caa3ec8f..7207a56447 100755
--- a/test/framework/suite.py
+++ b/test/framework/suite.py
@@ -83,6 +83,7 @@
 import test.framework.toolchain as tc
 import test.framework.toolchainvariables as tcv
 import test.framework.toy_build as t
+import test.framework.type_checking as et
 import test.framework.tweak as tw
 import test.framework.variables as v
 
@@ -104,7 +105,7 @@
 # call suite() for each module and then run them all
 # note: make sure the options unit tests run first, to avoid running some of them with a readily initialized config
 tests = [gen, bl, o, r, ef, ev, ebco, ep, e, mg, m, mt, f, run, a, robot, b, v, g, tcv, tc, t, c, s, l, f_c, sc, tw,
-         p, i, pkg, d]
+         p, i, pkg, d, et]
 
 SUITE = unittest.TestSuite([x.suite() for x in tests])
 
diff --git a/test/framework/type_checking.py b/test/framework/type_checking.py
new file mode 100644
index 0000000000..b039b751b0
--- /dev/null
+++ b/test/framework/type_checking.py
@@ -0,0 +1,61 @@
+# #
+# Copyright 2015-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+# #
+"""
+Unit tests for easyconfig/types.py
+
+@author: Kenneth Hoste (Ghent University)
+"""
+from test.framework.utilities import EnhancedTestCase
+from unittest import TestLoader, main
+
+from easybuild.framework.easyconfig.types import check_type_of_param_value
+
+
+class TypeCheckingTest(EnhancedTestCase):
+    """Tests for value type checking of easyconfig parameters."""
+
+    def test_check_type_of_param_value(self):
+        """Test check_type_of_param_value function."""
+        # check selected values that should be strings
+        for key in ['name', 'version']:
+            self.assertTrue(check_type_of_param_value(key, 'foo'))
+            for not_a_string in [100, 1.5, ('bar',), ['baz'], None]:
+                self.assertFalse(check_type_of_param_value(key, not_a_string))
+            # value doesn't matter, only type does
+            self.assertTrue(check_type_of_param_value(key, ''))
+
+        # parameters with no type specification always pass the check
+        key = 'nosucheasyconfigparametereverhopefully'
+        for val in ['foo', 100, 1.5, ('bar',), ['baz'], '', None]:
+            self.assertTrue(check_type_of_param_value(key, val))
+
+
+def suite():
+    """ returns all the testcases in this module """
+    return TestLoader().loadTestsFromTestCase(TypeCheckingTest)
+
+
+if __name__ == '__main__':
+    main()

From 22226c096c0ea8cc584245124e46bf5594eed844 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 11:23:48 +0200
Subject: [PATCH 1343/1356] small style changes

---
 easybuild/framework/easyconfig/parser.py | 4 ++--
 easybuild/framework/easyconfig/types.py  | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index bdc4505b68..27251fc2e4 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -100,7 +100,7 @@ def __init__(self, filename=None, format_version=None, rawcontent=None):
         else:
             raise EasyBuildError("Neither filename nor rawcontent provided to EasyConfigParser")
 
-        self.check_types()
+        self.check_values_types()
 
         self._formatter.extract_comments(self.rawcontent)
 
@@ -109,7 +109,7 @@ def process(self, filename=None):
         self._read(filename=filename)
         self._set_formatter()
 
-    def check_types(self):
+    def check_values_types(self):
         """Check types of easyconfig parameter values."""
         params = self.get_config_dict()
         wrong_type_msgs = []
diff --git a/easybuild/framework/easyconfig/types.py b/easybuild/framework/easyconfig/types.py
index 9831ef9c38..e25dff4ccc 100644
--- a/easybuild/framework/easyconfig/types.py
+++ b/easybuild/framework/easyconfig/types.py
@@ -30,6 +30,7 @@
 """
 from vsc.utils import fancylogger
 
+# easy types, that can be verified with isinstance
 EASY_TYPES = [basestring, int]
 # type checking is skipped for easyconfig parameters names not listed in TYPES
 TYPES = {
@@ -44,6 +45,7 @@
 def check_type_of_param_value(key, value):
     """Check value type of specified easyconfig parameter."""
     type_ok = True
+
     if key in TYPES:
         expected_type = TYPES[key]
         if expected_type in EASY_TYPES:
@@ -54,7 +56,6 @@ def check_type_of_param_value(key, value):
                 type_ok = False
                 _log.warning("Value type checking of easyconfig parameter '%s' FAILED: expected '%s', got '%s'",
                              key, expected_type.__name__, type(value).__name__)
-
     else:
         _log.debug("No type specified for easyconfig parameter '%s', so skipping type check.", key)
 

From dcfd385bf14551fd5e0301d9c2a4633251f3c8eb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 11:38:38 +0200
Subject: [PATCH 1344/1356] move call to check_value_types in parser, add
 easyconfig with wrong value types as test case

---
 easybuild/framework/easyconfig/parser.py      | 15 +++----
 test/framework/easyconfig.py                  |  7 ++++
 test/framework/easyconfigparser.py            |  7 ++++
 test/framework/easyconfigs/gzip-1.4-broken.eb | 41 +++++++++++++++++++
 4 files changed, 63 insertions(+), 7 deletions(-)
 create mode 100644 test/framework/easyconfigs/gzip-1.4-broken.eb

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 27251fc2e4..46eb35e389 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -100,8 +100,6 @@ def __init__(self, filename=None, format_version=None, rawcontent=None):
         else:
             raise EasyBuildError("Neither filename nor rawcontent provided to EasyConfigParser")
 
-        self.check_values_types()
-
         self._formatter.extract_comments(self.rawcontent)
 
     def process(self, filename=None):
@@ -109,12 +107,11 @@ def process(self, filename=None):
         self._read(filename=filename)
         self._set_formatter()
 
-    def check_values_types(self):
+    def check_values_types(self, cfg):
         """Check types of easyconfig parameter values."""
-        params = self.get_config_dict()
         wrong_type_msgs = []
-        for key in params:
-            if not check_type_of_param_value(key, params[key]):
+        for key in cfg:
+            if not check_type_of_param_value(key, cfg[key]):
                 wrong_type_msgs.append("value for '%s' should be of type '%s'" % (key, TYPES[key].__name__))
 
         if wrong_type_msgs:
@@ -201,7 +198,11 @@ def get_config_dict(self, validate=True):
         # allows to bypass the validation step, typically for testing
         if validate:
             self._formatter.validate()
-        return self._formatter.get_config_dict()
+
+        cfg = self._formatter.get_config_dict()
+        self.check_values_types(cfg)
+
+        return cfg
 
     def dump(self, ecfg, default_values, templ_const, templ_val):
         """Dump easyconfig in format it was parsed from."""
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 8caa190229..35a8e99851 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1528,6 +1528,13 @@ def test_software_license(self):
         err_pat = r"Invalid license LicenseThatDoesNotExist \(known licenses:"
         self.assertErrorRegex(EasyBuildError, err_pat, ec.validate_license)
 
+    def test_param_value_type_checking(self):
+        """Test value tupe checking of easyconfig parameters."""
+        ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'gzip-1.4-broken.eb')
+        # name/version parameters have values of wrong type in this broken easyconfig
+        error_msg_pattern = "Type checking of easyconfig parameter values failed: .*'name'.*'version'.*"
+        self.assertErrorRegex(EasyBuildError, error_msg_pattern, EasyConfig, ec_file)
+
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/easyconfigparser.py b/test/framework/easyconfigparser.py
index fce0b5e1cf..ab1da7921e 100644
--- a/test/framework/easyconfigparser.py
+++ b/test/framework/easyconfigparser.py
@@ -186,6 +186,13 @@ def test_easyconfig_constants(self):
         self.assertEqual(constants['GPLv2'], 'LicenseGPLv2')
         self.assertEqual(constants['EXTERNAL_MODULE'], 'EXTERNAL_MODULE')
 
+    def test_check_value_types(self):
+        """Test checking of easyconfig parameter value types."""
+        test_ec = os.path.join(TESTDIRBASE, 'gzip-1.4-broken.eb')
+        error_msg_pattern = "Type checking of easyconfig parameter values failed: .*'name'.*'version'.*"
+        ecp = EasyConfigParser(test_ec)
+        self.assertErrorRegex(EasyBuildError, error_msg_pattern, ecp.get_config_dict)
+
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/easyconfigs/gzip-1.4-broken.eb b/test/framework/easyconfigs/gzip-1.4-broken.eb
new file mode 100644
index 0000000000..738d2765f0
--- /dev/null
+++ b/test/framework/easyconfigs/gzip-1.4-broken.eb
@@ -0,0 +1,41 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright (c) 2012-2013 Cyprus Institute / CaSToRC
+# Authors::   Thekla Loizou <t.loizou@cyi.ac.cy>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_06-19.html
+##
+easyblock = 'ConfigureMake'
+
+# wrong type of values, on purpose
+name = ['gzip']  # 'gzip'
+version = 1.4  # '1.4'
+
+homepage = "http://www.gzip.org/"
+description = "gzip (GNU zip) is a popular data compression program as a replacement for compress"
+
+# test toolchain specification
+toolchain = {'name':'dummy','version':'dummy'}
+
+# source tarball filename
+sources = [SOURCE_TAR_GZ]
+
+# download location for source files
+source_urls = ['http://ftpmirror.gnu.org/gzip']
+
+# make sure the gzip and gunzip binaries are available after installation
+sanity_check_paths = {
+    'files': ["bin/gunzip", "bin/gzip"],
+    'dirs': [],
+}
+
+# run 'gzip -h' and 'gzip --version' after installation
+sanity_check_commands = [True, ('gzip', '--version')]
+
+software_license = GPLv3
+
+moduleclass = 'tools'

From 7916783d78ac4fcb165e0d805b0525aa26137f01 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 12:05:43 +0200
Subject: [PATCH 1345/1356] exclude broken easyconfigs from tests that don't
 expect them

---
 test/framework/module_generator.py | 2 +-
 test/framework/scripts.py          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/framework/module_generator.py b/test/framework/module_generator.py
index 64fd5a471f..63424a447a 100644
--- a/test/framework/module_generator.py
+++ b/test/framework/module_generator.py
@@ -291,7 +291,7 @@ def test_module_naming_scheme(self):
         def test_mns():
             """Test default module naming scheme."""
             # test default naming scheme
-            for ec_file in ec_files:
+            for ec_file in [f for f in ec_files if not 'broken' in os.path.basename(f)]:
                 ec_path = os.path.abspath(ec_file)
                 ecs = process_easyconfig(ec_path, validate=False)
                 # derive module name directly from easyconfig file name
diff --git a/test/framework/scripts.py b/test/framework/scripts.py
index 73df66f277..1613e4128d 100644
--- a/test/framework/scripts.py
+++ b/test/framework/scripts.py
@@ -75,7 +75,7 @@ def test_generate_software_list(self):
         for root, subfolders, files in os.walk(easyconfigs_dir):
             if 'v2.0' in subfolders:
                 subfolders.remove('v2.0')
-            for ec_file in files:
+            for ec_file in [f for f in files if 'broken' not in os.path.basename(f)]:
                 shutil.copy2(os.path.join(root, ec_file), tmpdir)
 
         cmd = "%s %s --local --quiet --path %s" % (sys.executable, script, tmpdir)

From 58dad9fd3a1c53598c5765941a71e46bd4105cdf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 12:09:38 +0200
Subject: [PATCH 1346/1356] add a comma

---
 easybuild/framework/easyconfig/parser.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 46eb35e389..6717e16027 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -115,7 +115,7 @@ def check_values_types(self, cfg):
                 wrong_type_msgs.append("value for '%s' should be of type '%s'" % (key, TYPES[key].__name__))
 
         if wrong_type_msgs:
-            raise EasyBuildError("Type checking of easyconfig parameter values failed: %s", ' '.join(wrong_type_msgs))
+            raise EasyBuildError("Type checking of easyconfig parameter values failed: %s", ', '.join(wrong_type_msgs))
         else:
             self.log.info("Type checking of easyconfig parameter values passed!")
 

From 24534a96541be35010cb5a77ae78a7bb5b6bbb2b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 12:34:56 +0200
Subject: [PATCH 1347/1356] docstrings

---
 easybuild/framework/easyconfig/parser.py | 6 +++++-
 easybuild/framework/easyconfig/types.py  | 7 ++++++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 6717e16027..60bf0ae9be 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -108,7 +108,11 @@ def process(self, filename=None):
         self._set_formatter()
 
     def check_values_types(self, cfg):
-        """Check types of easyconfig parameter values."""
+        """
+        Check types of easyconfig parameter values.
+
+        @param cfg: dictionary with easyconfig parameter values (result of get_config_dict())
+        """
         wrong_type_msgs = []
         for key in cfg:
             if not check_type_of_param_value(key, cfg[key]):
diff --git a/easybuild/framework/easyconfig/types.py b/easybuild/framework/easyconfig/types.py
index e25dff4ccc..089039c152 100644
--- a/easybuild/framework/easyconfig/types.py
+++ b/easybuild/framework/easyconfig/types.py
@@ -43,7 +43,12 @@
 
 
 def check_type_of_param_value(key, value):
-    """Check value type of specified easyconfig parameter."""
+    """
+    Check value type of specified easyconfig parameter.
+
+    @param key: name of easyconfig parameter
+    @param value: easyconfig parameter value, of which type should be checked
+    """
     type_ok = True
 
     if key in TYPES:

From 604d05c5301763a50c5b7233e70786dd90b82c2e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 13:26:27 +0200
Subject: [PATCH 1348/1356] implement convert_value_type function

---
 easybuild/framework/easyconfig/types.py | 37 +++++++++++++++++++++++++
 test/framework/type_checking.py         | 29 ++++++++++++++++++-
 2 files changed, 65 insertions(+), 1 deletion(-)

diff --git a/easybuild/framework/easyconfig/types.py b/easybuild/framework/easyconfig/types.py
index 089039c152..ec32b6a814 100644
--- a/easybuild/framework/easyconfig/types.py
+++ b/easybuild/framework/easyconfig/types.py
@@ -30,6 +30,9 @@
 """
 from vsc.utils import fancylogger
 
+from easybuild.tools.build_log import EasyBuildError
+
+
 # easy types, that can be verified with isinstance
 EASY_TYPES = [basestring, int]
 # type checking is skipped for easyconfig parameters names not listed in TYPES
@@ -37,6 +40,12 @@
     'name': basestring,
     'version': basestring,
 }
+TYPE_CONVERSION_FUNCTIONS = {
+    basestring: str,
+    float: float,
+    int: int,
+    str: str,
+}
 
 
 _log = fancylogger.getLogger('easyconfig.types', fname=False)
@@ -65,3 +74,31 @@ def check_type_of_param_value(key, value):
         _log.debug("No type specified for easyconfig parameter '%s', so skipping type check.", key)
 
     return type_ok
+
+
+def convert_value_type(val, typ):
+    """
+    Try to convert type of provided value to specific type.
+
+    @param val: value to convert type of
+    @param typ: target type
+    """
+    res = None
+
+    if isinstance(val, typ):
+        _log.debug("Value %s is already of specified target type %s, no conversion needed", val, typ)
+        res = val
+
+    elif typ in TYPE_CONVERSION_FUNCTIONS:
+        func = TYPE_CONVERSION_FUNCTIONS[typ]
+        _log.debug("Trying to convert value %s (type: %s) to %s using %s", val, type(val), typ, func)
+        try:
+            res = func(val)
+            _log.debug("Type conversion seems to have worked, new type: %s", type(res))
+        except Exception as err:
+            raise EasyBuildError("Converting type of %s (%s) to %s using %s failed: %s", val, type(val), typ, func, err)
+
+    else:
+        raise EasyBuildError("No conversion function available (yet) for target type %s", typ)
+
+    return res
diff --git a/test/framework/type_checking.py b/test/framework/type_checking.py
index b039b751b0..b441e5ca2b 100644
--- a/test/framework/type_checking.py
+++ b/test/framework/type_checking.py
@@ -30,7 +30,8 @@
 from test.framework.utilities import EnhancedTestCase
 from unittest import TestLoader, main
 
-from easybuild.framework.easyconfig.types import check_type_of_param_value
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.framework.easyconfig.types import check_type_of_param_value, convert_value_type
 
 
 class TypeCheckingTest(EnhancedTestCase):
@@ -51,6 +52,32 @@ def test_check_type_of_param_value(self):
         for val in ['foo', 100, 1.5, ('bar',), ['baz'], '', None]:
             self.assertTrue(check_type_of_param_value(key, val))
 
+    def test_convert_value_type(self):
+        """Test convert_value_type function."""
+        # to string
+        self.assertEqual(convert_value_type(100, basestring), '100')
+        self.assertEqual(convert_value_type((100,), str), '(100,)')
+        self.assertEqual(convert_value_type([100], basestring), '[100]')
+        self.assertEqual(convert_value_type(None, str), 'None')
+
+        # to int/float
+        self.assertEqual(convert_value_type('100', int), 100)
+        self.assertEqual(convert_value_type('0', int), 0)
+        self.assertEqual(convert_value_type('-123', int), -123)
+        self.assertEqual(convert_value_type('1.6', float), 1.6)
+        self.assertErrorRegex(EasyBuildError, "Converting type of .* failed", convert_value_type, '', int)
+
+        # idempotency
+        self.assertEqual(convert_value_type('foo', basestring), 'foo')
+        self.assertEqual(convert_value_type('foo', str), 'foo')
+        self.assertEqual(convert_value_type(100, int), 100)
+        self.assertEqual(convert_value_type(1.6, float), 1.6)
+
+        # no conversion function available for specific type
+        class Foo():
+            pass
+        self.assertErrorRegex(EasyBuildError, "No conversion function available", convert_value_type, None, Foo)
+
 
 def suite():
     """ returns all the testcases in this module """

From 26a1924360d893f1e1ca864885cff138ea119532 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 14:03:34 +0200
Subject: [PATCH 1349/1356] add support for auto-converting to expected type in
 check_type_of_param_value

---
 easybuild/framework/easyconfig/parser.py |  3 +-
 easybuild/framework/easyconfig/types.py  | 46 +++++++++++++++---------
 test/framework/type_checking.py          | 12 ++++---
 3 files changed, 40 insertions(+), 21 deletions(-)

diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index 60bf0ae9be..ed3a7ba1a6 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -115,7 +115,8 @@ def check_values_types(self, cfg):
         """
         wrong_type_msgs = []
         for key in cfg:
-            if not check_type_of_param_value(key, cfg[key]):
+            type_ok, _ = check_type_of_param_value(key, cfg[key])
+            if not type_ok:
                 wrong_type_msgs.append("value for '%s' should be of type '%s'" % (key, TYPES[key].__name__))
 
         if wrong_type_msgs:
diff --git a/easybuild/framework/easyconfig/types.py b/easybuild/framework/easyconfig/types.py
index ec32b6a814..88ad008744 100644
--- a/easybuild/framework/easyconfig/types.py
+++ b/easybuild/framework/easyconfig/types.py
@@ -51,29 +51,40 @@
 _log = fancylogger.getLogger('easyconfig.types', fname=False)
 
 
-def check_type_of_param_value(key, value):
+def check_type_of_param_value(key, val, auto_convert=False):
     """
     Check value type of specified easyconfig parameter.
 
     @param key: name of easyconfig parameter
-    @param value: easyconfig parameter value, of which type should be checked
+    @param val: easyconfig parameter value, of which type should be checked
+    @param auto_convert: try to automatically convert to expected value type if required
     """
-    type_ok = True
-
-    if key in TYPES:
-        expected_type = TYPES[key]
-        if expected_type in EASY_TYPES:
-            if isinstance(value, expected_type):
-                _log.debug("Value type checking of easyconfig parameter '%s' passed: expected '%s', got '%s'",
-                           key, expected_type.__name__, type(value).__name__)
-            else:
-                type_ok = False
-                _log.warning("Value type checking of easyconfig parameter '%s' FAILED: expected '%s', got '%s'",
-                             key, expected_type.__name__, type(value).__name__)
-    else:
+    type_ok, newval = False, None
+    expected_type = TYPES.get(key)
+
+    if expected_type is None:
         _log.debug("No type specified for easyconfig parameter '%s', so skipping type check.", key)
+        type_ok, newval = True, val
+
+    elif expected_type in EASY_TYPES:
+        # easy types can be checked using isinstance
+        if isinstance(val, expected_type):
+            type_ok, newval = True, val
+            _log.debug("Value type checking of easyconfig parameter '%s' passed: expected '%s', got '%s'",
+                       key, expected_type.__name__, type(val).__name__)
+
+        else:
+            _log.warning("Value type checking of easyconfig parameter '%s' FAILED: expected '%s', got '%s'",
+                         key, expected_type.__name__, type(val).__name__)
+    else:
+        raise EasyBuildError("Don't know how to check whether specified value is of type %s", expected_type)
 
-    return type_ok
+    if not type_ok and auto_convert:
+        _log.debug("Value type check failed, going to try to automatically convert to %s", expected_type)
+        newval = convert_value_type(val, expected_type)
+        type_ok = True
+
+    return type_ok, newval
 
 
 def convert_value_type(val, typ):
@@ -98,6 +109,9 @@ def convert_value_type(val, typ):
         except Exception as err:
             raise EasyBuildError("Converting type of %s (%s) to %s using %s failed: %s", val, type(val), typ, func, err)
 
+        if not isinstance(res, typ):
+            raise EasyBuildError("Converting value %s to type %s didn't work as expected: got %s", val, typ, type(res))
+
     else:
         raise EasyBuildError("No conversion function available (yet) for target type %s", typ)
 
diff --git a/test/framework/type_checking.py b/test/framework/type_checking.py
index b441e5ca2b..fe8e7872c8 100644
--- a/test/framework/type_checking.py
+++ b/test/framework/type_checking.py
@@ -41,16 +41,20 @@ def test_check_type_of_param_value(self):
         """Test check_type_of_param_value function."""
         # check selected values that should be strings
         for key in ['name', 'version']:
-            self.assertTrue(check_type_of_param_value(key, 'foo'))
+            self.assertEqual(check_type_of_param_value(key, 'foo'), (True, 'foo'))
             for not_a_string in [100, 1.5, ('bar',), ['baz'], None]:
-                self.assertFalse(check_type_of_param_value(key, not_a_string))
+                self.assertEqual(check_type_of_param_value(key, not_a_string), (False, None))
             # value doesn't matter, only type does
-            self.assertTrue(check_type_of_param_value(key, ''))
+            self.assertEqual(check_type_of_param_value(key, ''), (True, ''))
 
         # parameters with no type specification always pass the check
         key = 'nosucheasyconfigparametereverhopefully'
         for val in ['foo', 100, 1.5, ('bar',), ['baz'], '', None]:
-            self.assertTrue(check_type_of_param_value(key, val))
+            self.assertEqual(check_type_of_param_value(key, val), (True, val))
+
+        # check use of auto_convert
+        self.assertEqual(check_type_of_param_value('version', 1.5), (False, None))
+        self.assertEqual(check_type_of_param_value('version', 1.5, auto_convert=True), (True, '1.5'))
 
     def test_convert_value_type(self):
         """Test convert_value_type function."""

From 404668c4a65fb071f6e2242cca0b1049aafab867 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 14 Oct 2015 15:42:38 +0200
Subject: [PATCH 1350/1356] add extra test cases suggested by @wpoely86

---
 test/framework/type_checking.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test/framework/type_checking.py b/test/framework/type_checking.py
index fe8e7872c8..d5283b1269 100644
--- a/test/framework/type_checking.py
+++ b/test/framework/type_checking.py
@@ -69,7 +69,10 @@ def test_convert_value_type(self):
         self.assertEqual(convert_value_type('0', int), 0)
         self.assertEqual(convert_value_type('-123', int), -123)
         self.assertEqual(convert_value_type('1.6', float), 1.6)
+        self.assertEqual(convert_value_type('5', float), 5.0)
         self.assertErrorRegex(EasyBuildError, "Converting type of .* failed", convert_value_type, '', int)
+        # 1.6 can't be parsed as an int (yields "invalid literal for int() with base 10" error)
+        self.assertErrorRegex(EasyBuildError, "Converting type of .* failed", convert_value_type, '1.6', int)
 
         # idempotency
         self.assertEqual(convert_value_type('foo', basestring), 'foo')

From eb78f7c858867bf7517bf24e65b4dc6a4c3c249a Mon Sep 17 00:00:00 2001
From: Stephane Thiell <sthiell@stanford.edu>
Date: Fri, 16 Oct 2015 14:23:28 -0700
Subject: [PATCH 1351/1356] extension: use empty list as default value for
 src/patches

The dictionary fallback value None of Extension src/patches variables
did not correspond with the default values of EasyBlock patches/src.
Replaced by an empty list that won't break for-loops.

Closes #1433.
---
 easybuild/framework/extension.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/framework/extension.py b/easybuild/framework/extension.py
index d8c6f371de..1713130057 100644
--- a/easybuild/framework/extension.py
+++ b/easybuild/framework/extension.py
@@ -57,8 +57,9 @@ def __init__(self, mself, ext):
         if not 'name' in self.ext:
             raise EasyBuildError("'name' is missing in supplied class instance 'ext'.")
 
-        self.src = self.ext.get('src', None)
-        self.patches = self.ext.get('patches', None)
+        # list of source/patch files: we use an empty list as default value like in EasyBlock
+        self.src = self.ext.get('src', [])
+        self.patches = self.ext.get('patches', [])
         self.options = copy.deepcopy(self.ext.get('options', {}))
 
         self.toolchain.prepare(self.cfg['onlytcmod'])

From 8c3eab670c65c3f05655bc8a1774c8d1e9eacdc5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Oct 2015 10:30:05 +0200
Subject: [PATCH 1352/1356] fix check for existing files/dirs in sanity check

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 293d2df533..b8809def46 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1600,7 +1600,7 @@ def sanity_check_step(self, custom_paths=None, custom_commands=None, extension=F
                 found = False
                 for name in xs:
                     path = os.path.join(self.installdir, name)
-                    if os.path.exists(path):
+                    if check_fn(path):
                         self.log.debug("Sanity check: found %s %s in %s" % (key[:-1], name, self.installdir))
                         found = True
                         break

From 0595a2ca96d9181f0133655ee81ed641a2c12a89 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Oct 2015 10:34:53 +0200
Subject: [PATCH 1353/1356] make sure that files are not directories

---
 easybuild/framework/easyblock.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index b8809def46..ba52da9052 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -1563,7 +1563,7 @@ def sanity_check_step(self, custom_paths=None, custom_commands=None, extension=F
         """
         # supported/required keys in for sanity check paths, along with function used to check the paths
         path_keys_and_check = {
-            'files': lambda fp: os.path.exists(fp),  # files must exist
+            'files': lambda fp: os.path.exists(fp) and not os.path.isdir(fp),  # files must exist and not be a directory
             'dirs': lambda dp: os.path.isdir(dp) and os.listdir(dp),  # directories must exist and be non-empty
         }
         # prepare sanity check paths

From aa7414a21cecbb463e7f21ea43fa0b0102110b1d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Oct 2015 16:09:49 +0200
Subject: [PATCH 1354/1356] enable auto-converting type of easyconfig parameter
 values

---
 easybuild/framework/easyconfig/easyconfig.py |  8 ++++++--
 easybuild/framework/easyconfig/parser.py     | 21 ++++++++++++++++----
 test/framework/easyconfig.py                 |  2 +-
 test/framework/easyconfigparser.py           |  2 +-
 4 files changed, 25 insertions(+), 8 deletions(-)

diff --git a/easybuild/framework/easyconfig/easyconfig.py b/easybuild/framework/easyconfig/easyconfig.py
index 6478a188b1..227b0b1f6e 100644
--- a/easybuild/framework/easyconfig/easyconfig.py
+++ b/easybuild/framework/easyconfig/easyconfig.py
@@ -109,7 +109,8 @@ class EasyConfig(object):
     Class which handles loading, reading, validation of easyconfigs
     """
 
-    def __init__(self, path, extra_options=None, build_specs=None, validate=True, hidden=None, rawtxt=None):
+    def __init__(self, path, extra_options=None, build_specs=None, validate=True, hidden=None, rawtxt=None,
+                 auto_convert_value_types=True):
         """
         initialize an easyconfig.
         @param path: path to easyconfig file to be parsed (ignored if rawtxt is specified)
@@ -118,6 +119,8 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
         @param validate: indicates whether validation should be performed (note: combined with 'validate' build option)
         @param hidden: indicate whether corresponding module file should be installed hidden ('.'-prefixed)
         @param rawtxt: raw contents of easyconfig file
+        @param auto_convert_value_types: indicates wether types of easyconfig values should be automatically converted
+                                         in case they are wrong
         """
         self.template_values = None
         self.enable_templating = True  # a boolean to control templating
@@ -184,7 +187,8 @@ def __init__(self, path, extra_options=None, build_specs=None, validate=True, hi
 
         # parse easyconfig file
         self.build_specs = build_specs
-        self.parser = EasyConfigParser(filename=self.path, rawcontent=self.rawtxt)
+        self.parser = EasyConfigParser(filename=self.path, rawcontent=self.rawtxt,
+                                       auto_convert_value_types=auto_convert_value_types)
         self.parse()
 
         # handle allowed system dependencies
diff --git a/easybuild/framework/easyconfig/parser.py b/easybuild/framework/easyconfig/parser.py
index ed3a7ba1a6..e5a6d1a341 100644
--- a/easybuild/framework/easyconfig/parser.py
+++ b/easybuild/framework/easyconfig/parser.py
@@ -79,18 +79,27 @@ class EasyConfigParser(object):
         Can contain references to multiple version and toolchain/toolchain versions
     """
 
-    def __init__(self, filename=None, format_version=None, rawcontent=None):
-        """Initialise the EasyConfigParser class"""
+    def __init__(self, filename=None, format_version=None, rawcontent=None,
+                 auto_convert_value_types=True):
+        """
+        Initialise the EasyConfigParser class
+        @param filename: path to easyconfig file to parse (superseded by rawcontent, if specified)
+        @param format_version: version of easyconfig file format, used to determine how to parse supplied easyconfig
+        @param rawcontent: raw content of easyconfig file to parse (preferred over easyconfig file supplied via filename)
+        @param auto_convert_value_types: indicates whether types of easyconfig values should be automatically converted
+                                         in case they are wrong
+        """
         self.log = fancylogger.getLogger(self.__class__.__name__, fname=False)
 
         self.rawcontent = None  # the actual unparsed content
 
+        self.auto_convert = auto_convert_value_types
+
         self.get_fn = None  # read method and args
         self.set_fn = None  # write method and args
 
         self.format_version = format_version
         self._formatter = None
-
         if rawcontent is not None:
             self.rawcontent = rawcontent
             self._set_formatter()
@@ -115,9 +124,13 @@ def check_values_types(self, cfg):
         """
         wrong_type_msgs = []
         for key in cfg:
-            type_ok, _ = check_type_of_param_value(key, cfg[key])
+            type_ok, newval = check_type_of_param_value(key, cfg[key], self.auto_convert)
             if not type_ok:
                 wrong_type_msgs.append("value for '%s' should be of type '%s'" % (key, TYPES[key].__name__))
+            elif newval != cfg[key]:
+                self.log.warning("Value for '%s' easyconfig parameter was converted from %s (type: %s) to %s (type: %s)",
+                                 key, cfg[key], type(cfg[key]), newval, type(newval))
+                cfg[key] = newval
 
         if wrong_type_msgs:
             raise EasyBuildError("Type checking of easyconfig parameter values failed: %s", ', '.join(wrong_type_msgs))
diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index 35a8e99851..d0d3db0d56 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1533,7 +1533,7 @@ def test_param_value_type_checking(self):
         ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'gzip-1.4-broken.eb')
         # name/version parameters have values of wrong type in this broken easyconfig
         error_msg_pattern = "Type checking of easyconfig parameter values failed: .*'name'.*'version'.*"
-        self.assertErrorRegex(EasyBuildError, error_msg_pattern, EasyConfig, ec_file)
+        self.assertErrorRegex(EasyBuildError, error_msg_pattern, EasyConfig, ec_file, auto_convert_value_types=False)
 
 
 def suite():
diff --git a/test/framework/easyconfigparser.py b/test/framework/easyconfigparser.py
index ab1da7921e..b2b1e5e457 100644
--- a/test/framework/easyconfigparser.py
+++ b/test/framework/easyconfigparser.py
@@ -190,7 +190,7 @@ def test_check_value_types(self):
         """Test checking of easyconfig parameter value types."""
         test_ec = os.path.join(TESTDIRBASE, 'gzip-1.4-broken.eb')
         error_msg_pattern = "Type checking of easyconfig parameter values failed: .*'name'.*'version'.*"
-        ecp = EasyConfigParser(test_ec)
+        ecp = EasyConfigParser(test_ec, auto_convert_value_types=False)
         self.assertErrorRegex(EasyBuildError, error_msg_pattern, ecp.get_config_dict)
 
 

From 9b1194846f23e3c3018a662469c31bc5c76e17d4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 21 Oct 2015 17:12:17 +0200
Subject: [PATCH 1355/1356] check default behaviour w.r.t. converting
 mismatching type for easyconfig parameter values

---
 test/framework/easyconfig.py                  | 6 +++++-
 test/framework/easyconfigparser.py            | 7 ++++++-
 test/framework/easyconfigs/gzip-1.4-broken.eb | 4 ++--
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/test/framework/easyconfig.py b/test/framework/easyconfig.py
index d0d3db0d56..225f848ba4 100644
--- a/test/framework/easyconfig.py
+++ b/test/framework/easyconfig.py
@@ -1532,9 +1532,13 @@ def test_param_value_type_checking(self):
         """Test value tupe checking of easyconfig parameters."""
         ec_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'gzip-1.4-broken.eb')
         # name/version parameters have values of wrong type in this broken easyconfig
-        error_msg_pattern = "Type checking of easyconfig parameter values failed: .*'name'.*'version'.*"
+        error_msg_pattern = "Type checking of easyconfig parameter values failed: .*'version'.*"
         self.assertErrorRegex(EasyBuildError, error_msg_pattern, EasyConfig, ec_file, auto_convert_value_types=False)
 
+        # test default behaviour: auto-converting of mismatching value types
+        ec = EasyConfig(ec_file)
+        self.assertEqual(ec['version'], '1.4')
+
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/easyconfigparser.py b/test/framework/easyconfigparser.py
index b2b1e5e457..c73cb01c04 100644
--- a/test/framework/easyconfigparser.py
+++ b/test/framework/easyconfigparser.py
@@ -189,10 +189,15 @@ def test_easyconfig_constants(self):
     def test_check_value_types(self):
         """Test checking of easyconfig parameter value types."""
         test_ec = os.path.join(TESTDIRBASE, 'gzip-1.4-broken.eb')
-        error_msg_pattern = "Type checking of easyconfig parameter values failed: .*'name'.*'version'.*"
+        error_msg_pattern = "Type checking of easyconfig parameter values failed: .*'version'.*"
         ecp = EasyConfigParser(test_ec, auto_convert_value_types=False)
         self.assertErrorRegex(EasyBuildError, error_msg_pattern, ecp.get_config_dict)
 
+        # test default behaviour: auto-converting of mismatched value types
+        ecp = EasyConfigParser(test_ec)
+        ecdict = ecp.get_config_dict()
+        self.assertEqual(ecdict['version'], '1.4')
+
 
 def suite():
     """ returns all the testcases in this module """
diff --git a/test/framework/easyconfigs/gzip-1.4-broken.eb b/test/framework/easyconfigs/gzip-1.4-broken.eb
index 738d2765f0..716c1804b6 100644
--- a/test/framework/easyconfigs/gzip-1.4-broken.eb
+++ b/test/framework/easyconfigs/gzip-1.4-broken.eb
@@ -11,8 +11,8 @@
 ##
 easyblock = 'ConfigureMake'
 
-# wrong type of values, on purpose
-name = ['gzip']  # 'gzip'
+name = 'gzip'
+# wrong type of value (on purpose, for testing), should be a string
 version = 1.4  # '1.4'
 
 homepage = "http://www.gzip.org/"

From 3c89573eaa4ce3ae2bbe712ebc61197c9308d068 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 27 Oct 2015 08:48:33 +0100
Subject: [PATCH 1356/1356] fix @geimer's remarks

---
 easybuild/toolchains/mpi/craympich.py  | 11 +++--------
 easybuild/tools/toolchain/constants.py | 14 +++++++-------
 2 files changed, 10 insertions(+), 15 deletions(-)

diff --git a/easybuild/toolchains/mpi/craympich.py b/easybuild/toolchains/mpi/craympich.py
index b940bfbd9f..284281fdf7 100644
--- a/easybuild/toolchains/mpi/craympich.py
+++ b/easybuild/toolchains/mpi/craympich.py
@@ -31,7 +31,8 @@
 from easybuild.toolchains.compiler.craype import CrayPECompiler
 from easybuild.toolchains.mpi.mpich import TC_CONSTANT_MPICH, TC_CONSTANT_MPI_TYPE_MPICH
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.toolchain.constants import COMPILER_VARIABLES, MPI_COMPILER_TEMPLATE, SEQ_COMPILER_TEMPLATE
+from easybuild.tools.toolchain.constants import COMPILER_VARIABLES, MPI_COMPILER_TEMPLATE, MPI_COMPILER_VARIABLES
+from easybuild.tools.toolchain.constants import SEQ_COMPILER_TEMPLATE
 from easybuild.tools.toolchain.mpi import Mpi
 
 
@@ -50,13 +51,7 @@ class CrayMPICH(Mpi):
     MPI_COMPILER_MPIFC = CrayPECompiler.COMPILER_FC
 
     # no MPI wrappers, so no need to specify serial compiler
-    MPI_SHARED_OPTION_MAP = {
-        '_opt_MPICC': '',
-        '_opt_MPICXX': '',
-        '_opt_MPIF77': '',
-        '_opt_MPIF90': '',
-        '_opt_MPIFC': '',
-    }
+    MPI_SHARED_OPTION_MAP = dict([('_opt_%s' % var, '') for var, _ in MPI_COMPILER_VARIABLES])
 
     def _set_mpi_compiler_variables(self):
         """Set the MPI compiler variables"""
diff --git a/easybuild/tools/toolchain/constants.py b/easybuild/tools/toolchain/constants.py
index 6c20f44dc0..2cdc52a6a0 100644
--- a/easybuild/tools/toolchain/constants.py
+++ b/easybuild/tools/toolchain/constants.py
@@ -45,8 +45,8 @@
 COMPILER_FLAGS = [
     ('CFLAGS', 'C compiler flags'),
     ('CXXFLAGS', 'C++ compiler flags'),
-    ('FCFLAGS', 'Fortran compiler flags'),
-    ('FFLAGS', 'Fortran compiler flags'),
+    ('FCFLAGS', 'Fortran 77/90 compiler flags'),
+    ('FFLAGS', 'Fortran 77 compiler flags'),
     ('F90FLAGS', 'Fortran 90 compiler flags'),
 ]
 
@@ -72,15 +72,15 @@
     CommandFlagList: [
         ('CUDA_CC', 'CUDA C compiler command'),
         ('CUDA_CXX', 'CUDA C++ compiler command'),
-        ('CUDA_F77', 'CUDA Fortran77 compiler command'),
-        ('CUDA_F90', 'CUDA Fortran90 compiler command'),
-        ('CUDA_FC', 'CUDA Fortran compiler command'),
+        ('CUDA_F77', 'CUDA Fortran 77 compiler command'),
+        ('CUDA_F90', 'CUDA Fortran 90 compiler command'),
+        ('CUDA_FC', 'CUDA Fortran 77/90 compiler command'),
     ],
     FlagList: [
         ('CUDA_CFLAGS', 'CUDA C compiler flags'),
         ('CUDA_CXXFLAGS', 'CUDA C++ compiler flags'),
-        ('CUDA_FCFLAGS', 'CUDA Fortran compiler flags'),
-        ('CUDA_FFLAGS', 'CUDA Fortran compiler flags'),
+        ('CUDA_FCFLAGS', 'CUDA Fortran 77/90 compiler flags'),
+        ('CUDA_FFLAGS', 'CUDA Fortran 77 compiler flags'),
         ('CUDA_F90FLAGS', 'CUDA Fortran 90 compiler flags'),
     ],
 }