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chrisgorgochrisgorgo
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Merge pull request #1895 from oesteban/revert/Codecov
Revert "[ENH] Move codecov to the end of each test #1889"
2 parents dfde970 + 037254a commit f85dd1f

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+24
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‎.circle/tests.sh

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -13,27 +13,27 @@ if [ "${CIRCLE_NODE_TOTAL:-}" != "4" ]; then
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exit 1
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fi
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# These tests are manually balanced based on previous build timings.
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# These tests are manually balanced based on previous build timings.
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# They may need to be rebalanced in the future.
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case ${CIRCLE_NODE_INDEX} in
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0)
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_pytests.sh && \
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -v $WORKDIR:/work -w /src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
20+
docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_pytests.sh && \
21+
docker run --rm=false -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_pytests.sh && \
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docker run --rm=false -it -v $WORKDIR:/work -w /src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
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docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow3d && \
24+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
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;;
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1)
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ level1 && \
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
27+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ level1 && \
28+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
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;;
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2)
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
32-
docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
31+
docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
32+
docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
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;;
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3)
35-
docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
36-
docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
37-
docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
35+
docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
36+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
37+
docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
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;;
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esac

‎Dockerfile

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -71,10 +71,6 @@ RUN conda config --add channels conda-forge; sync && \
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RUN sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages/matplotlib/mpl-data/matplotlibrc && \
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python -c "from matplotlib import font_manager"
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74-
# Install codecov inside container
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RUN curl -so /usr/bin/codecov.io https://codecov.io/bash && \
76-
chmod 755 /usr/bin/codecov.io
77-
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# Install CI scripts
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COPY docker/files/run_* /usr/bin/
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RUN chmod +x /usr/bin/run_*

‎circle.yml

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -17,16 +17,18 @@ dependencies:
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- "~/docker"
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- "~/examples"
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- "~/.apt-cache"
20+
- "~/bin"
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pre:
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# Let CircleCI cache the apt archive
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- mkdir -p ~/.apt-cache/partial && sudo rm -rf /var/cache/apt/archives && sudo ln -s ~/.apt-cache /var/cache/apt/archives
2425
- sudo apt-get -y update && sudo apt-get install -y wget bzip2
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# Create work folder and force group permissions
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- mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR
27-
- mkdir -p $HOME/docker $HOME/examples $WORKDIR/tests $WORKDIR/crashfiles $WORKDIR/logs ${CIRCLE_TEST_REPORTS}/tests/
28+
- mkdir -p $HOME/docker $HOME/examples $WORKDIR/tests $WORKDIR/logs $WORKDIR/crashfiles ${CIRCLE_TEST_REPORTS}/tests/
29+
- if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi
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override:
29-
- if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; fi :
31+
- if [[ -e "$HOME/docker/cache.tar" ]]; then docker load --input $HOME/docker/cache.tar; fi :
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timeout: 6000
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- docker images
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- docker pull nipype/base:latest
@@ -50,7 +52,10 @@ test:
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parallel: true
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post:
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# Place reports in the appropriate folder
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- cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
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- cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
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# Send coverage data to codecov.io
57+
- codecov -f "coverage*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F unittests -v -K
58+
- codecov -f "smoketest*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F smoketests -v -K
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general:
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artifacts:

‎docker/files/run_examples.sh

Lines changed: 1 addition & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -25,13 +25,8 @@ fi
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coverage run /src/nipype/tools/run_examples.py $@
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exit_code=$?
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# Generate coverage report and submit if token is defined
28+
# Collect crashfiles and generate xml report
2929
coverage xml -o ${WORKDIR}/tests/smoketest_${example_id}.xml
30-
if [ "${CODECOV_TOKEN}" != "" ]; then
31-
codecov.io -f ${WORKDIR}/tests/smoketest_${example_id}.xml -t "${CODECOV_TOKEN}" -F smoketests
32-
fi
33-
34-
# Collect crashfiles
3530
find /work -name "crash-*" -maxdepth 1 -exec mv {} ${WORKDIR}/crashfiles/ \;
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exit $exit_code
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‎docker/files/run_pytests.sh

Lines changed: 2 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -28,23 +28,16 @@ export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}
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py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}.xml --cov nipype --cov-config /src/nipype/.coveragerc --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}.xml ${TESTPATH}
2929
exit_code=$?
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31-
if [ "${CODECOV_TOKEN}" != "" ]; then
32-
codecov.io -f ${WORKDIR}/tests/coverage_py${PYTHON_VERSION}.xml -t "${CODECOV_TOKEN}" -F unittests
33-
fi
34-
3531
# Workaround: run here the profiler tests in python 3
3632
if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
3733
echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
3834
echo 'profile_runtime = true' >> ${HOME}/.nipype/nipype.cfg
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export COVERAGE_FILE=${WORKDIR}/tests/.coverage.py${PYTHON_VERSION}_extra
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py.test -v --junitxml=${WORKDIR}/tests/pytests_py${PYTHON_VERSION}_extra.xml --cov nipype --cov-report xml:${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml /src/nipype/nipype/interfaces/tests/test_runtime_profiler.py /src/nipype/nipype/pipeline/plugins/tests/test_multiproc*.py
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exit_code=$(( $exit_code + $? ))
42-
43-
if [ "${CODECOV_TOKEN}" != "" ]; then
44-
codecov.io -f ${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml -t "${CODECOV_TOKEN}" -F unittests
45-
fi
4638
fi
4739

4840
# Collect crashfiles
49-
find /work -name "crash-*" -maxdepth 1 -exec mv {} ${WORKDIR}/crashfiles/ \;
41+
find ${WORKDIR} -name "crash-*" -maxdepth 1 -exec mv {} ${WORKDIR}/crashfiles/ \;
42+
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exit ${exit_code}

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