Merge branch 'fix/TestingCircle' into enh/WorkflowInterface

Author: oesteban

Dockerfile

@@ -31,6 +31,9 @@
 # Based on https://github.com/poldracklab/fmriprep/blob/9c92a3de9112f8ef1655b876de060a2ad336ffb0/Dockerfile
 #
 FROM ubuntu:xenial-20161213
+MAINTAINER The nipype developers https://github.com/nipy/nipype
+
+ARG DEBIAN_FRONTEND=noninteractive
 
 # Prepare environment
 RUN apt-get update && \
@@ -78,6 +81,7 @@ RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW
 # Installing Neurodebian packages (FSL, AFNI, git)
 RUN apt-get install -y --no-install-recommends \
                     fsl-core=5.0.9-1~nd+1+nd16.04+1 \
+                    fsl-mni152-templates=5.0.7-2 \
                     afni=16.2.07~dfsg.1-2~nd16.04+1
 
 ENV FSLDIR=/usr/share/fsl/5.0 \

docker/Dockerfile_base

@@ -14,24 +14,24 @@ fi
 # They may need to be rebalanced in the future.
 case ${CIRCLE_NODE_INDEX} in
   0)
-    time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1
     ;;
   1)
-    time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline
-    time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d
-    time docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_pytests.sh py35
-    time docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d
+    docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_pytests.sh py35
+    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
     ;;
   2)
-    time docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
-    time docker run --rm -it -v $SCRATCH:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
-    time docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_pytests.sh py27
-    time docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
+    docker run --rm -it -v $SCRATCH:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_pytests.sh py27
+    docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
     ;;
   3)
-    time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d
-    time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
-    time docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
     ;;
 esac
 
@@ -45,4 +45,3 @@ find "${CIRCLE_TEST_REPORTS}/pytest" -name 'coverage*.xml' -print0 | \
   xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F unittests
 find "${CIRCLE_TEST_REPORTS}/pytest" -name 'smoketests*.xml' -print0 | \
   xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests
-