v2.0.1 Unit Test issues #43
Description
@jj-umn, I'm having issues with the pandas dependency. Any ideas on how to fix this?
> python -m unittest discover tests
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_go_data_dwnld/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_go_data_dwnld/go-basic.obo: fmt(1.2) rel(2021-02-01) 47,291 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_go_data_dwnld/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_go_data_dwnld/goslim_metagenomics.obo: fmt(1.2) rel(None) 201 GO Terms
.NCBI database format is outdated. Upgrading
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...
Loading node names...
2311792 names loaded.
241707 synonyms loaded.
Loading nodes...
2311792 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_test_tax_dwnld/taxa.sqlite ...
2311000 generating entries...
Uploading to /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/tmp_test_tax_dwnld/taxa.sqlite
Inserting synonyms: 240000
Inserting taxid merges: 60000
Inserting taxids: 2310000
.....300
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
......Traceback (most recent call last):
File "metaquantome/cli.py", line 10, in <module>
from metaquantome.modules.expand import expand
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
import metaquantome.util.expand_io as expand_io
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
File "metaquantome/cli.py", line 10, in <module>
from metaquantome.modules.expand import expand
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
import metaquantome.util.expand_io as expand_io
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
File "metaquantome/cli.py", line 10, in <module>
from metaquantome.modules.expand import expand
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
import metaquantome.util.expand_io as expand_io
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
File "metaquantome/cli.py", line 10, in <module>
from metaquantome.modules.expand import expand
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
import metaquantome.util.expand_io as expand_io
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
File "metaquantome/cli.py", line 10, in <module>
from metaquantome.modules.expand import expand
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
import metaquantome.util.expand_io as expand_io
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
File "metaquantome/cli.py", line 10, in <module>
from metaquantome.modules.expand import expand
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
import metaquantome.util.expand_io as expand_io
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
FTraceback (most recent call last):
File "metaquantome/cli.py", line 10, in <module>
from metaquantome.modules.expand import expand
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/modules/expand.py", line 3, in <module>
import metaquantome.util.expand_io as expand_io
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/util/expand_io.py", line 1, in <module>
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
F........load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
...load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
..load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
.load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
..................................................load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/goslim_metagenomics.obo: fmt(1.2) rel(None) 185 GO Terms
..load obo file /Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo
/Users/rsajulga/Projects/umn/galaxyp/metaquantome/metaquantome/data/test/go-basic.obo: fmt(1.2) rel(2018-10-30) 47,358 GO Terms
............
======================================================================
FAIL: testFuncBar (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 93, in testFuncBar
self.assertEqual(test_status, 0)
AssertionError: 1 != 0
======================================================================
FAIL: testHeatmapViz (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 108, in testHeatmapViz
self.assertEqual(test_status, 0)
AssertionError: 1 != 0
======================================================================
FAIL: testMultipleInt (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 34, in testMultipleInt
self.assertEqual(exp_status, 0)
AssertionError: 1 != 0
======================================================================
FAIL: testPCABig (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 130, in testPCABig
self.assertEqual(test_status, 0)
AssertionError: 1 != 0
======================================================================
FAIL: testSingleInt (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 20, in testSingleInt
self.assertEqual(status, 0)
AssertionError: 1 != 0
======================================================================
FAIL: testViz (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 59, in testViz
self.assertEqual(test_status, 0)
AssertionError: 1 != 0
======================================================================
FAIL: testVizTabfile (travis.testCLI.TestCLI)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/rsajulga/Projects/umn/galaxyp/metaquantome/tests/travis/testCLI.py", line 74, in testVizTabfile
self.assertEqual(test_status, 0)
AssertionError: 1 != 0
----------------------------------------------------------------------
Ran 101 tests in 243.798s
FAILED (failures=7)