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oestebanoesteban
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normalizing paths
- Docker: install nipype in /src - Docker: work directory is now /work instead of /scratch - Circle: move from `$SCRATCH` to `$WORKDIR` since the former is more commonly set on HPC environments
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‎.circle/codecov.sh

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -13,13 +13,13 @@ set -x # Print command traces before executing command.
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curl -so codecov.io https://codecov.io/bash
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chmod 755 codecov.io
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find "${SCRATCH}/" -name 'coverage*.xml' -maxdepth 1 -print0 | \
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find "${WORKDIR}/" -name 'coverage*.xml' -maxdepth 1 -print0 | \
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xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F unittests
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find "${SCRATCH}/" -name 'smoketest*.xml' -maxdepth 1 -print0 | \
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find "${WORKDIR}/" -name 'smoketest*.xml' -maxdepth 1 -print0 | \
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xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests
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# Place test and coverage in the tests folder
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mkdir -p ${CIRCLE_TEST_REPORTS}/tests/
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cp ${SCRATCH}/pytest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
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cp ${SCRATCH}/coverage*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
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cp ${SCRATCH}/smoketest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
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cp ${WORKDIR}/pytest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
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cp ${WORKDIR}/coverage*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true
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cp ${WORKDIR}/smoketest*.xml ${CIRCLE_TEST_REPORTS}/tests/ || true

‎.circle/tests.sh

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -17,23 +17,23 @@ fi
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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="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /root/src/nipype nipype/nipype:py27 /usr/bin/run_pytests.sh py27 && \
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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:py35 /usr/bin/run_pytests.sh py35 && \
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docker run --rm -it -v $SCRATCH:/scratch -w /root/src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d
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docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /root/src/nipype nipype/nipype:py27 /usr/bin/run_pytests.sh py27 && \
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docker run --rm -it -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /root/src/nipype nipype/nipype:py35 /usr/bin/run_pytests.sh py35 && \
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docker run --rm -it -v $WORKDIR:/work -w /root/src/nipype/doc nipype/nipype:py35 /usr/bin/run_builddocs.sh && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d
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;;
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1)
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/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:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1 && \
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docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
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docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1 && \
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docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/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:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1 && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
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docker run --rm -it -e NIPYPE_NUMBER_OF_CPUS=4 -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1 && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline && \
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docker run --rm -it -v $HOME/examples:/root/examples:ro -v $WORKDIR:/work -w /work nipype/nipype:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
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;;
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esac

‎Dockerfile

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -78,14 +78,14 @@ RUN sed -i 's/\(backend *: \).*$/\1Agg/g' /usr/local/miniconda/lib/python${PYTHO
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python -c "from matplotlib import font_manager"
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# Installing dev requirements (packages that are not in pypi)
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WORKDIR /root/
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WORKDIR /src/
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COPY requirements.txt requirements.txt
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RUN pip install -r requirements.txt && \
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rm -rf ~/.cache/pip
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# Installing nipype
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COPY . /root/src/nipype
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RUN cd /root/src/nipype && \
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COPY . /src/nipype
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RUN cd /src/nipype && \
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pip install -e .[all] && \
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rm -rf ~/.cache/pip
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@@ -99,7 +99,7 @@ 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 ${FSLDIR}/bin/imglob
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WORKDIR /root/
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WORKDIR /work/
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LABEL org.label-schema.build-date=$BUILD_DATE \
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org.label-schema.name="NIPYPE" \

‎circle.yml

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ machine:
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DATA_NIPYPE_TUTORIAL_URL: "${OSF_NIPYPE_URL}/57f4739cb83f6901ed94bf21"
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DATA_NIPYPE_FSL_COURSE: "${OSF_NIPYPE_URL}/57f472cf9ad5a101f977ecfe"
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DATA_NIPYPE_FSL_FEEDS: "${OSF_NIPYPE_URL}/57f473066c613b01f113e7af"
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SCRATCH: "$HOME/scratch"
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WORKDIR: "$HOME/work"
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CODECOV_TOKEN: "ac172a50-8e66-42e5-8822-5373fcf54686"
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services:
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- docker
@@ -22,9 +22,9 @@ dependencies:
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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 scratch folder and force group permissions
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- mkdir -p $SCRATCH && sudo setfacl -d -m group:ubuntu:rwx $SCRATCH && sudo setfacl -m group:ubuntu:rwx $SCRATCH
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- mkdir -p $HOME/docker $HOME/examples $SCRATCH/pytest $SCRATCH/logs
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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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override:
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- if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; else echo 'No docker image found in cache'; fi :
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timeout: 6000
@@ -54,8 +54,8 @@ test:
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general:
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artifacts:
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- "~/scratch/docs"
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- "~/scratch/logs"
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- "~/work/docs"
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- "~/work/logs"
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deployment:
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production:

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