fixing tests in circleCI w/docker #1538

Author: oesteban

Dockerfile

@@ -32,38 +32,50 @@ MAINTAINER Stanford Center for Reproducible Neuroscience <crn.poldracklab@gmail.
 # Preparations
 RUN ln -snf /bin/bash /bin/sh
 WORKDIR /root
+
+# Install graphviz to provide dot
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && \
+    apt-get install -y graphviz && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
 RUN mkdir -p .nipype && \
     echo '[logging]' > .nipype/nipype.cfg && \
     echo 'workflow_level = DEBUG' >> .nipype/nipype.cfg && \
     echo 'interface_level = DEBUG' >> .nipype/nipype.cfg && \
     echo 'filemanip_level = DEBUG' >> .nipype/nipype.cfg
 
-ADD docker/circleci/run_* /usr/bin/
-RUN chmod +x /usr/bin/run_*
-
 # Install this branch's code
-WORKDIR /scratch/src
+WORKDIR /root/src
 ADD . nipype/
 
 # Install the checked out version of nipype, check that requirements are
 # installed and install it for each of the three environments.
+# Additionally, install matplotlib and sphinx to build documentation
 RUN cd nipype/ && \
     source activate nipypetests-2.7 && \
+    pip install matplotlib sphinx coverage && \
     pip install -r requirements.txt && \
     pip install -e .
 
 RUN cd nipype/ && \
     source activate nipypetests-3.4 && \
+    pip install matplotlib sphinx coverage && \
     pip install -r requirements.txt && \
     pip install -e .
 
 RUN cd nipype/ && \
     source activate nipypetests-3.5 && \
+    pip install matplotlib sphinx coverage && \
     pip install -r requirements.txt && \
     pip install -e .
 
 WORKDIR /scratch
 
+# Install entrypoints
+ADD docker/circleci/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+
 # RUN echo 'source /etc/profile.d/nipype_tests.sh' >> /etc/bash.bashrc
 ENTRYPOINT ["/usr/bin/run_examples.sh"]
 CMD ["--help"]

circle.yml

@@ -27,13 +27,13 @@ test:
         timeout: 1600
     - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_fsl_reuse Linear level1_workflow
     - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_nested Linear level1 l2pipeline
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_nosetests.sh" nipype/testbench --xunit-file="/scratch/nose/${CIRCLE_PROJECT_REPONAME}.xml :
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_nosetests.sh" nipype/testbench --xunit-file="/scratch/nose/${CIRCLE_PROJECT_REPONAME}.xml" :
         timeout: 2600
   post:
     - mkdir -p ${CIRCLE_TEST_REPORTS}/nose
     - mv ~/scratch/nose/${CIRCLE_PROJECT_REPONAME}.xml ${CIRCLE_TEST_REPORTS}/nose/
     - mkdir -p ~/docs
-    - mv ~/scratch/nipype/doc/_build/html/* ~/docs/
+    - mv ~/scratch/docs/* ~/docs/
     - mv ~/scratch/builddocs.log ~/docs/log.txt
 
 general:

docker/circleci/run_builddocs.sh

@@ -4,6 +4,8 @@ for i in /etc/profile.d/*.sh; do
 done
 source activate nipypetests-2.7
 
-set -o pipefail && cd /scratch/src/nipype/doc && make html 2>&1 | tee /scratch/builddoc.log
+mkdir -p /scratch/docs
+set -o pipefail && cd /root/src/nipype/doc && make html 2>&1 | tee /scratch/builddoc.log
+cp -r /root/src/nipype/doc/_build/html/* /scratch/docs/
 cat /scratch/builddoc.log && if grep -q "ERROR" /scratch/builddoc.log; then false; else true; fi
 

docker/circleci/run_examples.sh

@@ -3,4 +3,4 @@ for i in /etc/profile.d/*.sh; do
     source $i
 done
 source activate nipypetests-2.7
-python /scratch/src/nipype/tools/run_examples.py $@
+python /root/src/nipype/tools/run_examples.py $@

docker/circleci/run_nosetests.sh

@@ -3,5 +3,6 @@ for i in /etc/profile.d/*.sh; do
     source $i
 done
 source activate nipypetests-2.7
-cd src/nipype
-nosetests --with-doctest -c ./.noserc --logging-level=DEBUG --verbosity=3 $@
+cd /root/src/nipype
+mkdir -p /scratch/nose
+nosetests --with-doctest -c /root/src/nipype/.noserc --logging-level=DEBUG --verbosity=3 $@