Re-arrange Dockerfiles, move fsl_imglob.py to external

Author: oesteban

circle.yml

@@ -19,7 +19,7 @@ dependencies:
     - if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/nipype-fsl_course_data.tar.gz && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
     - if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q https://3552243d5be815c1b09152da6525cb8fe7b900a6.googledrive.com/host/0BxI12kyv2olZVUswazA3NkFvOXM/fsl-5.0.9-feeds.tar.gz && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
-    - docker build -f docker/nipype_test_py35/Dockerfile -t nipype/nipype_test:py35 . :
+    - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600
     - mkdir -p ~/docker; docker save nipype/nipype_test:py35 > ~/docker/image.tar :
         timeout: 1600

docker/nipype_test_base/Dockerfile renamed to docker/nipype_test/Dockerfile_base

@@ -30,7 +30,6 @@ FROM neurodebian:latest
 MAINTAINER Nipype developers
 
 # Preparations
-
 ARG DEBIAN_FRONTEND=noninteractive
 RUN sed -i -e 's,main$,main contrib non-free,g' /etc/apt/sources.list.d/neurodebian.sources.list && \
     apt-get -y update && \
@@ -92,9 +91,9 @@ RUN curl -sSL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/sp
     unzip spm12.zip && \
     rm -rf spm12.zip
 
-ENV MATLABCMD "/opt/mcr/v85/toolbox/matlab"
-ENV SPMMCRCMD "/opt/spm12/run_spm12.sh /opt/mcr/v85/ script"
-ENV FORCE_SPMMCR 1
+ENV MATLABCMD "/opt/mcr/v85/toolbox/matlab" \
+    SPMMCRCMD "/opt/spm12/run_spm12.sh /opt/mcr/v85/ script" \
+    FORCE_SPMMCR 1
 
 
 CMD ["/bin/bash"]

docker/nipype_test_py27/Dockerfile renamed to docker/nipype_test/Dockerfile_py27

@@ -48,19 +48,23 @@ ENV LC_ALL C.UTF-8
 RUN conda config --add channels conda-forge && \
     conda update -y conda && \
     conda update --all -y python=3.4 && \
-    conda install -y lockfile nipype
+    conda install -y lockfile nipype matplotlib sphinx boto boto3 coverage mock pbr nitime dipy && \
+    pip install nose-cov doctest-ignore-unicode configparser
+   
+COPY docker/circleci/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
 
 RUN mkdir -p /root/src/nipype
 COPY . /root/src/nipype
 
-RUN cd /root/src/nipype && \
-    pip install nose-cov doctest-ignore-unicode && \
+RUN rm -r /usr/local/miniconda/lib/python3.5/site-packages/nipype* && \
+    cd /root/src/nipype && \
     pip install -r requirements.txt && \
-    pip install -e .
-
+    pip install -e . && \
+    make specs
 
-COPY docker/circleci/run_* /usr/bin/
-RUN chmod +x /usr/bin/run_*
-ENV SHELL /bin/bash
+# Replace imglob with Python3 compatible version
+RUN rm -r ${FSLDIR}/bin/imglob && \
+    ln -s $(which fsl_imglob.py) ${FSLDIR}/bin/imglob
 
 CMD ["/bin/bash"]

docker/nipype_test_py34/Dockerfile renamed to docker/nipype_test/Dockerfile_py34

@@ -434,7 +434,7 @@ def main(**extra_args):
           # python -- duplicating things into MANIFEST.in but this is admittedly
           # only a workaround to get things started -- not a solution
           package_data={'nipype': testdatafiles},
-          scripts=glob('bin/*'),
+          scripts=glob('bin/*') + ['nipype/external/fsl_imglob.py'],
           cmdclass=cmdclass,
           **extra_args
           )