[FIX] CircleCI tests - error codes are not propagated

The former structure of the tests.sh file in which all the tests are called
did not exit with error if one of the test commands errored, since the
last exit code was from codecov, and no exit code tracking or propagation
was done.

This PR fixes that issue. Additionally, the scripts related to CircleCI
have been split up into a new .circle/ folder.

Author: oesteban

.circle/codecov.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+#
+# This script pull all coverage files into the $CIRCLE_TEST_REPORTS folder
+# and sends data to codecov.
+#
+#
+set -u
+set -e
+
+mkdir -p ${CIRCLE_TEST_REPORTS}/
+for report in $( ls ~/scratch/*.xml ); do
+    rname=$( basename $report )
+    cp ${report} ${CIRCLE_TEST_REPORTS}/${rname:: -4}_${CIRCLE_NODE_INDEX}.xml
+done
+
+# Send coverage data to codecov.io
+curl -so codecov.io https://codecov.io/bash
+chmod 755 codecov.io
+find "${CIRCLE_TEST_REPORTS}/" -name 'coverage*.xml' -print0 | \
+  xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F unittests
+find "${CIRCLE_TEST_REPORTS}/" -name 'smoketests*.xml' -print0 | \
+  xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests

docker/files/tests.sh renamed to .circle/tests.sh

@@ -14,15 +14,15 @@ fi
 # They may need to be rebalanced in the future.
 case ${CIRCLE_NODE_INDEX} in
   0)
-    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/ l2pipeline
-    ;;
-  1)
-    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 -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 -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 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 -v $SCRATCH:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
+    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 -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 -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
+    ;;
+  1)
+    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/ l2pipeline
     ;;
   2)
     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 && \
@@ -34,14 +34,3 @@ case ${CIRCLE_NODE_INDEX} in
     docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
     ;;
 esac
-
-# Put the artifacts in place
-bash docker/files/teardown.sh
-
-# Send coverage data to codecov.io
-curl -so codecov.io https://codecov.io/bash
-chmod 755 codecov.io
-find "${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

.dockerignore

@@ -23,11 +23,13 @@ src/
 # other
 docs/**/*
 docs/
+.circle/**/*
+.circle/
+circle.yml
 .coverage
 .coveragerc
 codecov.yml
 rtd_requirements.txt
-circle.yml
 Vagrantfile
 .travis.yml
 .noserc

circle.yml

@@ -43,23 +43,28 @@ dependencies:
 
 test:
   override:
-    - bash docker/files/tests.sh :
+    - bash .circle/tests.sh :
         timeout: 7200
         parallel: true
+  post:
+    # Send coverage data to codecov.io
+    - bash .circle/codecov.sh
 
 general:
   artifacts:
-    - "~/docs"
-    - "~/logs"
+    - "~/scratch/docs"
+    - "~/scratch/logs"
 
 deployment:
   production:
     tag: /.*/
     commands:
+      # Deploy to docker hub      
       - if [[ -n "$DOCKER_PASS" ]]; then docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS && docker push nipype/nipype:latest; fi :
           timeout: 21600
       - if [[ -n "$DOCKER_PASS" ]]; then docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS && docker tag nipype/nipype nipype/nipype:$CIRCLE_TAG && docker push nipype/nipype:$CIRCLE_TAG; fi :
           timeout: 21600
+
 # Automatic deployment to Pypi:
 #       - printf "[distutils]\nindex-servers =\n    pypi\n\n[pypi]\nusername:$PYPI_USER\npassword:$PYPI_PASS\n" > ~/.pypirc
 #       - python setup.py sdist upload -r pypi