Py3 + MyPy

.gitignore

@@ -1 +1,23 @@
-.*
+.nfs*
+*.swp
+*.swo
+*~
+*.so
+*.egg
+*.bak
+*.pyc
+*Log.out
+*.log
+*.DS_Store
+
+.mypy_cache
+install/PriceSource*
+install/cdhit
+*.egg-info
+*__pycache__*
+
+
+databases/test/
+databases/human-bowtie
+databases/star-index-dir/
+docs/_build

.mypy.ini

@@ -0,0 +1,22 @@
+
+# Global options:
+
+[mypy]
+warn_return_any = True
+warn_unused_configs = True
+strict_equality = True
+no_implicit_optional = True
+disallow_untyped_calls = True
+disallow_untyped_defs = True
+disallow_any_expr = True
+mypy_path = ./stubs/
+# Per-module options:
+
+# [mypy-mycode.foo.*]
+# disallow_untyped_defs = True
+# 
+# [mypy-mycode.bar]
+# warn_return_any = False
+# 
+# [mypy-somelibrary]
+# ignore_missing_imports = True

Dockerfile

@@ -1,26 +1,29 @@
 FROM centos:centos7
 MAINTAINER Michael Panciera
 
-ARG GIT_USER
-ARG GIT_TOKEN
+ENV PYTHON_VERSION 3.6
 
 RUN yum -y update \
     && yum -y install curl bzip2 git wget make gcc-c++ \
-    && curl -sSL https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -o /tmp/miniconda.sh \
+    && curl -sSL https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/miniconda.sh \ 
     && bash /tmp/miniconda.sh -bfp /usr/local/ \
     && rm -rf /tmp/miniconda.sh \
-    && conda install -y python=2 \
+    && conda install -y python=$PYTHON_VERSION \
     && conda update conda \
     && conda clean --all --yes \
     && rpm -e --nodeps curl bzip2 \
     && yum clean all
 
 ENV PATH "/usr/local/bin/:$PATH"
 
-RUN mkdir /HERE && cd /HERE && git clone https://${GIT_USER}:${GIT_TOKEN}@github.com/averagehat/pathos.git \
-    && cd pathos/install \
-    && sh assume-conda-install.sh /usr/local/bin/ \ 
+ENV RUNTYPE "TEST"
+ADD . /app
+WORKDIR /app
+
+RUN    cd install \
+    && bash assume-conda-install.sh /usr/local/bin/ \ 
     && cd .. \
     && sh mk_yaml.sh > test.yaml \
     && cd databases \
-    && make krona 
+    && sh test-setup.sh \
+    && pip install -r ../install/test-requirements.txt 

Dockerfile.local

@@ -0,0 +1,35 @@
+FROM centos:centos7
+MAINTAINER Michael Panciera
+
+ARG GIT_USER
+ARG GIT_TOKEN
+ENV PYTHON_VERSION 3.7.1
+
+RUN yum -y update \
+    && yum -y install curl bzip2 git wget make gcc-c++ \
+    && curl -sSL https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/miniconda.sh \ 
+    && bash /tmp/miniconda.sh -bfp /usr/local/ \
+    && rm -rf /tmp/miniconda.sh \
+    && conda install -y python=$PYTHON_VERSION \
+    && conda update conda \
+    && conda clean --all --yes \
+    && rpm -e --nodeps curl bzip2 \
+    && yum clean all
+
+ENV PATH "/usr/local/bin/:$PATH"
+
+ENV RUNTYPE "TEST"
+
+ADD . /pathos/
+
+WORKDIR /pathos/
+
+RUN    cd install \
+    && sh assume-conda-install.sh /usr/local/bin/ \ 
+    && cd .. \
+    && sh mk_yaml.sh > test.yaml \
+    && sh test-setup.sh \
+    && pip install -r ../install/test-requirements.txt 
+#    && cd databases \
+#    && make krona 
+