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CI: Factor into three groups of tests
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‎.github/workflows/README

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These files implement NiBabel CI for GitHub actions.
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The testing logic is implemented in tools/ci/*.sh, and these files adapt
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the generic logic to the details of GH.
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Each file should differ only by strategy, and env and steps should be identical.

‎.github/workflows/misc.yml

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name: Miscellaneous checks
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# This file runs doctests on the documentation and style checks
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on: [push]
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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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misc:
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runs-on: 'ubuntu-latest'
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continue-on-error: true
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strategy:
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matrix:
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python-version: [3.8]
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install: ['setup']
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check: ['style', 'doc']
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pip-flags: ['']
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depends: ['DEFAULT_DEPENDS']
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env:
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# Options
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SETUP_REQUIRES: 'pip setuptools>=30.3.0 wheel'
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# Dependencies that should always be installable
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DEFAULT_DEPENDS: 'numpy scipy matplotlib pillow pydicom'
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REQUIREMENTS: '-r requirements.txt'
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# Full advertised range
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MIN_REQUIREMENTS: '-r min-requirements.txt'
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MIN_REQUIREMENTS_PLUS: '-r min-requirements.txt matplotlib==1.5.3 pydicom==0.9.9 pillow==2.6'
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PYDICOM_MASTER: 'numpy git+https://github.com/pydicom/pydicom.git@master'
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# Might not find wheels for these
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OPTIONAL_DEPENDS: 'h5py indexed_gzip'
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PRE_PIP_FLAGS: '--pre --extra-index-url https://pypi.anaconda.org/scipy-wheels-nightly/simple'
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# Selection
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DEPENDS: ${{ matrix.depends }}
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INSTALL_TYPE: ${{ matrix.install }}
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CHECK_TYPE: ${{ matrix.check }}
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EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
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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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architecture: ${{ matrix.architecture }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: tools/ci/create_env.sh
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- name: Build archive
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run: |
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source tools/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install dependencies
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run: tools/ci/install_dependencies.sh
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- name: Install NiBabel
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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: for_testing/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: for_testing/test-results.xml
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if: ${{ always() && matrix.check == 'test' }}

‎.github/workflows/pre-release.yml

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name: Pre-release checks
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# This file tests against pre-release wheels for dependencies
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on: [push]
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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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pre-release:
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# Check pre-releases of dependencies on stable Python
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runs-on: ${{ matrix.os }}
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continue-on-error: true
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strategy:
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matrix:
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os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
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python-version: [3.8, 3.9]
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architecture: ['x64', 'x86']
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install: ['setup']
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check: ['test']
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pip-flags: ['PRE_PIP_FLAGS']
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depends: ['DEFAULT_DEPENDS']
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include:
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# Pydicom master
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- os: ubuntu-latest
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python-version: 3.8
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install: setup
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check: test
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pip-flags: ''
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depends: PYDICOM_MASTER
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exclude:
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- os: ubuntu-latest
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architecture: x86
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- os: macos-latest
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architecture: x86
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- os: windows-latest
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python-version: 3.9
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- os: macos-latest
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python-version: 3.9
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env:
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# Options
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SETUP_REQUIRES: 'pip setuptools>=30.3.0 wheel'
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# Dependencies that should always be installable
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DEFAULT_DEPENDS: 'numpy scipy matplotlib pillow pydicom'
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REQUIREMENTS: '-r requirements.txt'
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# Full advertised range
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MIN_REQUIREMENTS: '-r min-requirements.txt'
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MIN_REQUIREMENTS_PLUS: '-r min-requirements.txt matplotlib==1.5.3 pydicom==0.9.9 pillow==2.6'
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PYDICOM_MASTER: 'numpy git+https://github.com/pydicom/pydicom.git@master'
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# Might not find wheels for these
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OPTIONAL_DEPENDS: 'h5py indexed_gzip'
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PRE_PIP_FLAGS: '--pre --extra-index-url https://pypi.anaconda.org/scipy-wheels-nightly/simple'
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# Selection
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DEPENDS: ${{ matrix.depends }}
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INSTALL_TYPE: ${{ matrix.install }}
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CHECK_TYPE: ${{ matrix.check }}
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EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
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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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architecture: ${{ matrix.architecture }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: tools/ci/create_env.sh
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- name: Build archive
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run: |
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source tools/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install dependencies
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run: tools/ci/install_dependencies.sh
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- name: Install NiBabel
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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: for_testing/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: for_testing/test-results.xml
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if: ${{ always() && matrix.check == 'test' }}

‎.github/workflows/test.yml renamed to ‎.github/workflows/stable.yml

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name: NiBabel tests
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name: Stable tests
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# This file tests the claimed support range of NiBabel including
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#
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# * Operating systems: Linux, Windows (x64 & x86), 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: [push]
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shell: bash
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jobs:
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test:
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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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continue-on-error: ${{ matrix.experimental }}
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strategy:
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matrix:
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os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
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pip-flags: ['']
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depends: ['DEFAULT_DEPENDS']
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include:
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# Mark Windows experimental but not Linux or OSX
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- os: ubuntu-latest
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experimental: false
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- os: macos-latest
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experimental: false
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- os: windows-latest
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experimental: true
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# Basic dependencies only
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- os: ubuntu-latest
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python-version: 3.6
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install: setup
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check: test
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pip-flags: ''
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depends: REQUIREMENTS
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experimental: false
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# Absolute minimum dependencies
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- os: ubuntu-latest
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python-version: 3.6
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install: setup
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check: test
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pip-flags: ''
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depends: MIN_REQUIREMENTS
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experimental: false
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# Absolute minimum dependencies plus old MPL, Pydicom, Pillow
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- os: ubuntu-latest
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python-version: 3.6
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install: setup
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check: test
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pip-flags: ''
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depends: MIN_REQUIREMENTS_PLUS
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experimental: false
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# Clean install imports only with package-declared dependencies
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- os: ubuntu-latest
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python-version: 3.6
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install: setup
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check: skiptests
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pip-flags: ''
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depends: ''
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experimental: false
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# Check all installation methods
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- os: ubuntu-latest
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python-version: 3.8
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install: wheel
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check: test
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pip-flags: ''
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depends: DEFAULT_DEPENDS
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experimental: false
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- os: ubuntu-latest
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python-version: 3.8
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install: sdist
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check: test
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pip-flags: ''
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depends: DEFAULT_DEPENDS
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experimental: false
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- os: ubuntu-latest
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python-version: 3.8
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install: archive
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check: test
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pip-flags: ''
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depends: DEFAULT_DEPENDS
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experimental: false
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# Check pre-releases if available
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- os: ubuntu-latest
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python-version: 3.8
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install: setup
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check: test
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pip-flags: PRE_PIP_FLAGS
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depends: DEFAULT_DEPENDS
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experimental: true
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- os: ubuntu-latest
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python-version: 3.9
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install: setup
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check: test
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pip-flags: PRE_PIP_FLAGS
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depends: DEFAULT_DEPENDS
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experimental: true
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- os: macos-latest
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python-version: 3.8
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install: setup
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check: test
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pip-flags: PRE_PIP_FLAGS
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depends: DEFAULT_DEPENDS
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experimental: true
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- os: windows-latest
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python-version: 3.8
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install: setup
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check: test
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pip-flags: PRE_PIP_FLAGS
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depends: DEFAULT_DEPENDS
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experimental: true
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# Style check
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- os: ubuntu-latest
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python-version: 3.8
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install: setup
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check: style
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experimental: false
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# Documentation doctests
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- os: ubuntu-latest
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python-version: 3.8
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install: setup
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check: doc
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experimental: false
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exclude:
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- os: ubuntu-latest
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architecture: x86

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