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Merge branch 'master' of github.com:nipy/nipype into predicted_signal
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‎.circleci/config.yml

+4-34
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@@ -52,6 +52,7 @@ _build_main_image_py36: &build_main_image_py36
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--rm=false \
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--tag nipype/nipype:latest \
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--tag nipype/nipype:py36 \
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$(test -z "${CIRCLE_TAG}" || echo --tag nipype/nipype:"${CIRCLE_TAG}") \
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--build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
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--build-arg VCS_REF="$(git rev-parse --short HEAD)" \
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--build-arg VERSION="${CIRCLE_TAG}" /home/circleci/nipype
@@ -192,6 +193,7 @@ jobs:
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docker push nipype/nipype:base
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docker push nipype/nipype:latest
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docker push nipype/nipype:py36
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test -z "${CIRCLE_TAG}" || docker push nipype/nipype:"${CIRCLE_TAG}"
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- run:
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name: Move pruned Dockerfile to /tmp/docker/cache directory
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command: |
@@ -289,44 +291,10 @@ jobs:
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ssh-add ~/.ssh/id_ed25519
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/home/circleci/nipype/tools/feedstock.sh
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build_docs:
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docker:
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- image: python:3.7.4
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working_directory: /tmp/src/nipype
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environment:
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- FSLOUTPUTTYPE: 'NIFTI'
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steps:
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- checkout
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- run:
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name: Check Python version and upgrade pip
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command: |
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python --version
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python -m pip install -U pip
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- run:
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name: Install graphviz
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command: |
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apt-get update
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apt-get install -y graphviz
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- run:
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name: Install Requirements (may contain pinned versions)
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command: python -m pip install -r doc/requirements.txt
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- run:
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name: Install NiPype
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command: python -m pip install ".[doc]"
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- run:
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name: Build documentation
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command: make -C doc html
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- store_artifacts:
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path: /tmp/src/nipype/doc/_build/html
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workflows:
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version: 2
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build_test_deploy:
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jobs:
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- build_docs:
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filters:
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tags:
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only: /.*/
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- pypi_precheck:
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filters:
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branches:
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filters:
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branches:
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only: master
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tags:
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only: /.*/
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requires:
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- test_pytest
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- deploy_pypi:

‎.git-blame-ignore-revs

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# Commits with messages like "STY: black" or "run black"
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12deb959cccc431fb8222cc5854f1c92a0080021
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f64bf338f630a9ee5cbe7a3ec98c68292897e720
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83358d7f17aac07cb90d0330f11ea2322e2974d8
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faef7d0f93013a700c882f709e98fb3cd36ebb03
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d50c1858564c0b3073fb23c54886a0454cb66afa
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417b8897a116fcded5000e21e2b6ccbe29452a52
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aaf677a87f64c485f3e305799e4a5dc73b69e5fb
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f763008442d88d8ce00ec266698268389415f8d6
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b1eccafd4edc8503b02d715f5b5f6f783520fdf9
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70db90349598cc7f26a4a513779529fba7d0a797
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6c1d91d71f6f0db0e985bd2adc34206442b0653d
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97bdbd5f48ab242de5288ba4715192a27619a803
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78fa360f5b785224349b8b85b07e510d2233bb63
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7f85f43a34de8bff8e634232c939b17cee8e8fc5
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9c50b5daa797def5672dd057155b0e2c658853e2
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47194993ae14aceeec436cfb3769def667196668
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75653feadc6667d5313d83e9c62a5d5819771a9c
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497b44d680eee0892fa59c6aaaae22a17d70a536

‎.github/workflows/contrib.yml

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name: Contribution checks
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# This checks validate contributions meet baseline checks
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#
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# * specs - Ensure make
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on:
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push:
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branches:
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- master
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- maint/*
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pull_request:
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branches:
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- master
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- maint/*
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defaults:
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run:
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shell: bash
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jobs:
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stable:
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# Check each OS, all supported Python, minimum versions and latest releases
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ['ubuntu-18.04']
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python-version: [3.8]
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nipype-extras: ['dev']
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check: ['specs', 'style']
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env:
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DEPENDS: ""
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CHECK_TYPE: ${{ matrix.check }}
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NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
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EXTRA_PIP_FLAGS: ""
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INSTALL_DEB_DEPENDENCIES: false
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INSTALL_TYPE: pip
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CI_SKIP_TEST: 1
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: tools/ci/create_venv.sh
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- name: Build archive
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run: |
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source tools/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install Debian dependencies
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run: tools/ci/install_deb_dependencies.sh
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if: ${{ matrix.os == 'ubuntu-18.04' }}
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- name: Install dependencies
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run: tools/ci/install_dependencies.sh
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- name: Install Nipype
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run: tools/ci/install.sh
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- name: Run tests
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run: tools/ci/check.sh
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if: ${{ matrix.check != 'skiptests' }}
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- uses: codecov/codecov-action@v1
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with:
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file: coverage.xml
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if: ${{ always() }}
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- name: Upload pytest test results
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uses: actions/upload-artifact@v2
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with:
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name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
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path: test-results.xml
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if: ${{ always() && matrix.check == 'test' }}

‎.github/workflows/main.yml

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‎.github/workflows/tests.yml

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name: Stable tests
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# This file tests the claimed support range of nipype including
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#
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# * Operating systems: Linux, OSX
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# * Dependencies: minimum requirements, optional requirements
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# * Installation methods: setup.py, sdist, wheel, archive
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on:
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push:
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branches:
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- master
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- maint/*
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pull_request:
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branches:
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- master
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- maint/*
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defaults:
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run:
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shell: bash
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jobs:
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stable:
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# Check each OS, all supported Python, minimum versions and latest releases
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ['ubuntu-18.04']
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python-version: [3.6, 3.7, 3.8, 3.9]
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check: ['test']
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pip-flags: ['']
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depends: ['REQUIREMENTS']
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deb-depends: [false]
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nipype-extras: ['doc,tests,profiler']
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include:
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- os: ubuntu-18.04
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python-version: 3.8
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check: test
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pip-flags: ''
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depends: REQUIREMENTS
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deb-depends: true
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nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
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env:
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DEPENDS: ${{ matrix.depends }}
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CHECK_TYPE: ${{ matrix.check }}
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EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
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INSTALL_DEB_DEPENDENCIES: ${{ matrix.deb-depends }}
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NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
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INSTALL_TYPE: pip
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CI_SKIP_TEST: 1
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: tools/ci/create_venv.sh
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- name: Build archive
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run: |
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source tools/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install Debian dependencies
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run: tools/ci/install_deb_dependencies.sh
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if: ${{ matrix.os == 'ubuntu-18.04' }}
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- name: Install dependencies
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run: tools/ci/install_dependencies.sh
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- name: Install Nipype
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run: tools/ci/install.sh
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- name: Run tests
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run: tools/ci/check.sh
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if: ${{ matrix.check != 'skiptests' }}
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- uses: codecov/codecov-action@v1
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with:
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file: coverage.xml
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if: ${{ always() }}
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- name: Upload pytest test results
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uses: actions/upload-artifact@v2
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with:
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name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
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path: test-results.xml
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if: ${{ always() && matrix.check == 'test' }}

‎.pre-commit-config.yaml

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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v2.0.0
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rev: v3.4.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: https://github.com/psf/black
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rev: 19.3b0
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rev: 20.8b1
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hooks:
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- id: black

‎.travis.yml

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