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Merge pull request #1889 from oesteban/circle/Codecov
[ENH] Move codecov to the end of each test
2 parents 22ca05c + 96a37eb commit addda24

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‎.circle/codecov.sh

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This file was deleted.

‎.circle/tests.sh

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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 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 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 && \
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docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /data/examples/ workflow4d
20+
docker run --rm=false -it -e CODECOV_TOKEN=${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
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;;
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1)
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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 fmri_spm_dartel Linear /data/examples/ level1 && \
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docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /data/examples/ l2pipeline
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docker run --rm=false -it -e CODECOV_TOKEN=${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
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;;
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2)
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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 && \
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docker run --rm=false -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ l2pipeline
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;;
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3)
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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 && \
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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 fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
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docker run --rm=false -it -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /data/examples/ level1 && \
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /data/examples/ l1pipeline && \
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docker run --rm=false -it -e CODECOV_TOKEN=${CODECOV_TOKEN} -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /data/examples/ level1_workflow
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;;
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esac

‎Dockerfile

Lines changed: 14 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -71,6 +71,20 @@ 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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# Install codecov inside container
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RUN curl -so /usr/bin/codecov.io https://codecov.io/bash && \
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chmod 755 /usr/bin/codecov.io
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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_*
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# Replace imglob with a Python3 compatible version
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COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
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RUN rm -rf ${FSLDIR}/bin/imglob && \
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chmod +x /usr/bin/fsl_imglob.py && \
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ln -s /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
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# Installing dev requirements (packages that are not in pypi)
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WORKDIR /src/
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COPY requirements.txt requirements.txt
@@ -83,16 +97,6 @@ RUN cd /src/nipype && \
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pip install -e .[all] && \
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rm -rf ~/.cache/pip
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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_*
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# Replace imglob with a Python3 compatible version
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COPY nipype/external/fsl_imglob.py /usr/bin/fsl_imglob.py
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RUN rm -rf ${FSLDIR}/bin/imglob && \
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chmod +x /usr/bin/fsl_imglob.py && \
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ln -s /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
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WORKDIR /work/
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ARG BUILD_DATE

‎circle.yml

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Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ dependencies:
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- 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
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- mkdir -p $HOME/docker $HOME/examples $WORKDIR/pytest $WORKDIR/logs
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- mkdir -p $HOME/docker $HOME/examples $WORKDIR/tests $WORKDIR/crashfiles $WORKDIR/logs ${CIRCLE_TEST_REPORTS}/tests/
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override:
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- if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; fi :
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timeout: 6000
@@ -50,9 +50,7 @@ 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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- mkdir -p ${CIRCLE_TEST_REPORTS}/tests/ && cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
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# Send coverage data to codecov.io
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- bash .circle/codecov.sh
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- cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
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general:
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artifacts:

‎docker/files/run_examples.sh

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Original file line numberDiff line numberDiff line change
@@ -25,8 +25,13 @@ fi
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coverage run /src/nipype/tools/run_examples.py $@
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exit_code=$?
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# Collect crashfiles and generate xml report
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# Generate coverage report and submit if token is defined
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coverage xml -o ${WORKDIR}/tests/smoketest_${example_id}.xml
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if [ "${CODECOV_TOKEN}" != "" ]; then
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codecov.io -f ${WORKDIR}/tests/smoketest_${example_id}.xml -t "${CODECOV_TOKEN}" -F smoketests
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fi
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# Collect crashfiles
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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

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Original file line numberDiff line numberDiff line change
@@ -28,17 +28,23 @@ 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 ${TESTPATH}
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exit_code=$?
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if [ "${CODECOV_TOKEN}" != "" ]; then
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codecov.io -f ${WORKDIR}/tests/coverage_py${PYTHON_VERSION}.xml -t "${CODECOV_TOKEN}" -F unittests
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fi
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# Workaround: run here the profiler tests in python 3
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if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
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echo '[execution]' >> ${HOME}/.nipype/nipype.cfg
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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 + $? ))
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if [ "${CODECOV_TOKEN}" != "" ]; then
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codecov.io -f ${WORKDIR}/tests/coverage_py${PYTHON_VERSION}_extra.xml -t "${CODECOV_TOKEN}" -F unittests
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fi
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fi
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# Collect crashfiles
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find /work -name "crash-*" -maxdepth 1 -exec mv {} ${WORKDIR}/crashfiles/ \;
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# Just in case output xml files are misplaced,
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# then circle would not tell the tests failed otherwise
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exit ${exit_code}

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