add graphviz to base, fix several problems #1538

Author: oesteban

Dockerfile

@@ -33,12 +33,6 @@ MAINTAINER Stanford Center for Reproducible Neuroscience <crn.poldracklab@gmail.
 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 && \
@@ -47,26 +41,32 @@ RUN mkdir -p .nipype && \
 
 # Install this branch's code
 WORKDIR /root/src
+
+# Install matplotlib, sphinx and coverage to build documentation
+# and run tests with coverage
+RUN source activate nipypetests-2.7 && \
+    pip install matplotlib sphinx coverage && \
+    source activate nipypetests-3.4 && \
+    pip install matplotlib sphinx coverage && \
+    source activate nipypetests-3.5 && \
+    pip install matplotlib sphinx coverage
+
 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 .
 
@@ -78,5 +78,4 @@ 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

@@ -27,11 +27,11 @@ 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 :
         timeout: 2600
   post:
     - mkdir -p ${CIRCLE_TEST_REPORTS}/nose
-    - mv ~/scratch/nose/${CIRCLE_PROJECT_REPONAME}.xml ${CIRCLE_TEST_REPORTS}/nose/
+    - mv ~/scratch/nosetests.xml ${CIRCLE_TEST_REPORTS}/nose/${CIRCLE_PROJECT_REPONAME}.xml
     - mkdir -p ~/docs
     - mv ~/scratch/docs/* ~/docs/
     - mv ~/scratch/builddocs.log ~/docs/log.txt

docker/circleci/run_nosetests.sh

@@ -5,4 +5,4 @@ done
 source activate nipypetests-2.7
 cd /root/src/nipype
 mkdir -p /scratch/nose
-nosetests --with-doctest -c /root/src/nipype/.noserc --logging-level=DEBUG --verbosity=3 $@
+nosetests --with-doctest -c /root/src/nipype/.noserc --logging-level=DEBUG --verbosity=3 --xunit-file="/scratch/nosetests.xml"

docker/test-image-base/Dockerfile

@@ -57,7 +57,8 @@ RUN apt-get update && \
                        libqhull-dev \
                        libxft-dev \
                        libjpeg-dev \
-                       libyaml-dev
+                       libyaml-dev \
+                       graphviz
 
 
 # Install ANTs