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Merge branch 'master' of git://github.com/nipy/nipype into fix/mrtrix
2 parents c5d5f06 + a17af6b commit bb2b08a

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‎.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="/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 && \
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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_test: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_test: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_test: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_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/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:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test: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_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/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:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test: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_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/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:/root/examples:ro -v $SCRATCH:/scratch -w /scratch nipype/nipype_test: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_test: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_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/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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source = nipype
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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

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