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tsalotsalo
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Merge remote-tracking branch 'nipy/master'
2 parents 1f99dea + cf2b1f8 commit 6df4b26

39 files changed

+765
-357
lines changed

‎.circle/codecov.sh

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‎.circle/tests.sh

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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 -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /src/nipype nipype/nipype:py27 /usr/bin/run_pytests.sh py27 && \
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docker run --rm -it -e FSL_COURSE_DATA="/data/examples/nipype-fsl_course_data" -v $HOME/examples:/data/examples:ro -v $WORKDIR:/work -w /src/nipype nipype/nipype:py35 /usr/bin/run_pytests.sh py35 && \
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docker run --rm -it -v $WORKDIR:/work -w /src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
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docker run --rm -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 -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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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
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;;
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1)
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docker run --rm -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 -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 -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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;;
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2)
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docker run --rm -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 -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 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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;;
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3)
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docker run --rm -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 -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 -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 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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;;
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esac
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cp ${WORKDIR}/tests/*.xml ${CIRCLE_TEST_REPORTS}/tests/
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codecov -f "coverage*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F unittests -e CIRCLE_NODE_INDEX
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codecov -f "smoketest*.xml" -s "${WORKDIR}/tests/" -R "${HOME}/nipype/" -F smoketests -e CIRCLE_NODE_INDEX

‎.coveragerc

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[run]
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branch = True
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include = */nipype/*
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omit =
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*/nipype/external/*
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*/nipype/fixes/*
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*/setup.py

‎.dockerignore

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# python cache
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__pycache__/**/*
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__pycache__
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**/__pycache__
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**/*.pyc
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*.pyc
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# python distribution
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# other
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docs/**/*
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docs/
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.cache/
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.circle/**/*
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.circle/
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circle.yml
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.coverage
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.coveragerc
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codecov.yml
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rtd_requirements.txt
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Vagrantfile
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.travis.yml
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.noserc
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.mailmap
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# Previous coverage results
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.coverage

‎.gitignore

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htmlcov/
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__pycache__/
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*~
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.*.swp
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.ipynb_checkpoints/
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.ruby-version

‎.noserc

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‎.travis.yml

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install:
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- travis_retry pip install -e .[$NIPYPE_EXTRAS]
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script:
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- py.test --doctest-modules nipype
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- py.test -v --doctest-modules nipype
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deploy:
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provider: pypi
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user: satra

‎Dockerfile

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@@ -71,6 +71,16 @@ 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 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
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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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- "~/docker"
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- "~/examples"
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- "~/.apt-cache"
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- "~/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
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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/logs $WORKDIR/crashfiles ${CIRCLE_TEST_REPORTS}/tests/
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- if [[ ! -e "$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:
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- if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; fi :
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- if [[ -e "$HOME/docker/cache.tar" ]]; then docker load --input $HOME/docker/cache.tar; fi :
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timeout: 6000
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- docker images
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- docker pull nipype/base:latest
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- bash .circle/tests.sh :
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timeout: 7200
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parallel: true
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post:
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# Send coverage data to codecov.io
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- bash .circle/codecov.sh
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general:
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artifacts:
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- "~/work/docs"
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- "~/work/logs"
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- "~/work/tests"
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- "~/work/crashfiles"
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deployment:
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production:

‎codecov.yml

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threshold: 100
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flags:
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- "smoketests"
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ignore: # files and folders that will be removed during processing
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- "nipype/external/*"
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- "tools/*"
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- "doc/*"

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