[TST] Docker use tags #1558. Close #1552

Author: oesteban

circle.yml

@@ -5,33 +5,42 @@ machine:
 dependencies:
   cache_directories:
     - "~/docker"
+    - "~/examples"
 
   pre:
     - mkdir -p "~/scratch/nose"
 
   override:
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
-    - docker build -t nipype/testbench:latest . :
+    - docker build -f docker/nipype_test_py27/Dockerfile -t nipype/nipype_test:py27 . :
         timeout: 1600
-    - mkdir -p ~/docker; docker save nipype/testbench:latest > ~/docker/image.tar :
+    - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
         timeout: 1600
+    - if [[ ! -d ~/examples/data ]]; then \
+      wget -O nipype-tutorial.tar.bz2 https://googledrive.com/host/0BxI12kyv2olZR05SU1lPampNcVE && \
+      tar jxvf nipype-tutorial.tar.bz2 && \
+      mv nipype-tutorial/* ~/examples/; fi
+    - if [[ ! -d ~/examples/feeds ]]; then \
+      wget -O fsl-feeds.tar.gz https://googledrive.com/host/0BxI12kyv2olZNXBONlJKV0Y1Tm8 && \
+      tar xzf fsl-feeds.tar.gz && \
+      mv feeds ~/examples/; fi
 
 test:
   override:
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_builddocs.sh" nipype/testbench
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench test_spm Linear /root/examples/ workflow3d :
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_builddocs.sh
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
         timeout: 1600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench test_spm Linear /root/examples/ workflow4d :
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
         timeout: 1600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_fsl_feeds Linear /root/examples/ l1pipeline
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_dartel Linear /root/examples/ level1 :
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
         timeout: 1600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_dartel Linear /root/examples/ l2pipeline :
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
         timeout: 1600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_fsl_reuse Linear /root/examples/ level1_workflow
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_nested Linear /root/examples/ level1
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch nipype/testbench fmri_spm_nested Linear /root/examples/ l2pipeline
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_nosetests.sh" nipype/testbench :
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested Linear /root/examples/ level1
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested Linear /root/examples/ l2pipeline
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v $(pwd)/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_nosetests.sh :
         timeout: 2600
   post:
     - bash docker/circleci/teardown.sh

docker/circleci/run_builddocs.sh

@@ -1,8 +1,4 @@
 #!/bin/bash
-for i in /etc/profile.d/*.sh; do
-    source $i
-done
-source activate nipypetests-2.7
 
 mkdir -p /scratch/docs
 set -o pipefail && cd /root/src/nipype/doc && make html 2>&1 | tee /scratch/builddocs.log

docker/circleci/run_examples.sh

@@ -1,13 +1,9 @@
 #!/bin/bash
-for i in /etc/profile.d/*.sh; do
-    source $i
-done
 
 mkdir -p /root/.nipype
 echo '[logging]' > /root/.nipype/nipype.cfg
 echo 'workflow_level = DEBUG' >> /root/.nipype/nipype.cfg
 echo 'interface_level = DEBUG' >> /root/.nipype/nipype.cfg
 echo 'filemanip_level = DEBUG' >> /root/.nipype/nipype.cfg
 
-source activate nipypetests-2.7
 python /root/src/nipype/tools/run_examples.py $@

docker/circleci/run_nosetests.sh

@@ -1,8 +1,5 @@
 #!/bin/bash
-for i in /etc/profile.d/*.sh; do
-    source $i
-done
-source activate nipypetests-2.7
+
 cd /root/src/nipype
 mkdir -p /scratch/nose
 nosetests -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests.xml" --cover-xml-file="/scratch/coverage.xml"

docker/nipype_test_py27/Dockerfile

@@ -27,8 +27,7 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 FROM nipype/nipype_test:base
-MAINTAINER Stanford Center for Reproducible Neuroscience <[email protected]>
-
+MAINTAINER The nipype developers https://github.com/nipy/nipype
 # Preparations
 RUN ln -snf /bin/bash /bin/sh
 WORKDIR /root
@@ -45,9 +44,19 @@ ENV PATH /usr/local/miniconda/bin:$PATH
 ENV LANG C.UTF-8
 
 # Add conda-forge channel in conda
-RUN conda config --add channels conda-forge
+RUN conda config --add channels conda-forge && \
+    conda install -y lockfile nipype
+
+RUN mkdir -p /root/src/nipype
+COPY . /root/src/nipype
+
+RUN cd /root/src/nipype && \
+    pip install -r requirements.txt && \
+    pip install -e .
+
 
-# Create conda environment
-RUN conda install -y lockfile nipype
+COPY docker/circleci/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
+ENV SHELL /bin/bash
 
 CMD ["/bin/bash"]