[pre-commit.ci] pre-commit autoupdate #21
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| #This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| # For deployment, it will be necessary to create a PyPI API token and store it as a secret | |
| # https://docs.github.com/en/actions/reference/encrypted-secrets | |
| name: CI/CD | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| release: | |
| types: [published] | |
| repository_dispatch: | |
| types: [create-release] | |
| env: | |
| MRTRIX_HOME: /opt/mrtrix3 | |
| MRTRIX_INSTALL: /opt/mrtrix3/install | |
| MRTRIX_VERSION: 3.0.4 | |
| SUBPKG_NAME: v3_1 | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.11, 3.13] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Set Git User | |
| # checkout@v2 adds a header that makes branch protection report errors | |
| # because the Github action bot is not a collaborator on the repo | |
| run: | | |
| git config --global user.email "auto@github-actions" | |
| git config --global user.name "GitHub Actions Runner" | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install clang qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build | |
| - name: Run sccache-cache | |
| uses: mozilla-actions/sccache-action@v0.0.3 | |
| - name: Get CMake | |
| uses: lukka/get-cmake@latest | |
| with: | |
| cmakeVersion: '3.16.3' | |
| - name: Print CMake version | |
| run: cmake --version | |
| - name: Create MRtrix install directory | |
| run: | | |
| sudo mkdir -p ${{ env.MRTRIX_INSTALL }} | |
| sudo chown $USER ${{ env.MRTRIX_INSTALL }} | |
| - name: Cache MRtrix Install | |
| id: cache-install | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.MRTRIX_INSTALL }} | |
| key: mrtrix-${{ env.MRTRIX_VERSION }}-${{ runner.os }} | |
| - name: Clone latest MRtrix and switch to latest tag | |
| run: | | |
| mkdir $MRTRIX_HOME | |
| sudo chown -R $USER $MRTRIX_HOME | |
| git clone https://github.com/tclose/mrtrix3.git $MRTRIX_HOME/src | |
| cd $MRTRIX_HOME/src | |
| git checkout print-pydra-dev | |
| git tag -a $MRTRIX_VERSION -m"Tag used to create a pydra-task-mrtrix3 release" | |
| git describe --abbrev=0 | |
| # echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV | |
| # git checkout $MRTRIX_VERSION | |
| - name: configure | |
| run: | | |
| cd $MRTRIX_HOME/src | |
| cmake \ | |
| -B build \ | |
| -G Ninja \ | |
| -D CMAKE_BUILD_TYPE=Release \ | |
| -D MRTRIX_BUILD_TESTS=ON \ | |
| -D MRTRIX_STL_DEBUGGING=ON \ | |
| -D MRTRIX_WARNINGS_AS_ERRORS=ON \ | |
| -D CMAKE_C_COMPILER=clang \ | |
| -D CMAKE_CXX_COMPILER=clang++ \ | |
| -D CMAKE_INSTALL_PREFIX=$MRTRIX_INSTALL | |
| - name: Build Mrtrix | |
| run: | | |
| cd $MRTRIX_HOME/src | |
| cmake --build build | |
| - name: Install Mrtrix | |
| run: | | |
| cd $MRTRIX_HOME/src | |
| cmake --install build | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| - name: Unset header | |
| # checkout@v2 adds a header that makes branch protection report errors | |
| # because the Github action bot is not a collaborator on the repo | |
| run: git config --local --unset http.https://github.com/.extraheader | |
| - name: Fetch tags | |
| run: git fetch --prune --unshallow | |
| - name: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore | |
| - name: Set PATH Variable | |
| run: echo "PATH=$PATH:$MRTRIX_INSTALL/bin" >> $GITHUB_ENV | |
| - name: Set LD_LIBRARY_PATH Variable | |
| run: echo "LD_LIBRARY_PATH=$MRTRIX_INSTALL/lib" >> $GITHUB_ENV | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install task package | |
| run: > | |
| pip install | |
| -e ./related-packages/fileformats | |
| -e ./related-packages/fileformats-extras | |
| -e '.[test]' | |
| - name: Test with pytest | |
| run: pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml | |
| - uses: codecov/codecov-action@v2 | |
| if: ${{ always() }} | |
| deploy-fileformats: | |
| needs: [test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Unset header | |
| # checkout@v2 adds a header that makes branch protection report errors | |
| # because the Github action bot is not a collaborator on the repo | |
| run: git config --local --unset http.https://github.com/.extraheader | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}" | |
| run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi | |
| - name: Upload to PyPI | |
| if: steps.deployable.outputs.DEPLOY | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }} | |
| packages-dir: ./related-packages/fileformats/dist | |
| deploy-fileformats-extras: | |
| needs: [deploy-fileformats] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Unset header | |
| # checkout@v2 adds a header that makes branch protection report errors | |
| # because the Github action bot is not a collaborator on the repo | |
| run: git config --local --unset http.https://github.com/.extraheader | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats-extras | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats-extras/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}" | |
| run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi | |
| - name: Upload to PyPI | |
| if: steps.deployable.outputs.DEPLOY | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }} | |
| packages-dir: ./related-packages/fileformats-extras/dist | |
| deploy: | |
| needs: [test, deploy-fileformats, deploy-fileformats-extras] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v2 | |
| - name: Set up Git user | |
| run: | | |
| git config --local user.email "action@github.com" | |
| git config --local user.name "GitHub Action" | |
| - name: Unset header | |
| # checkout@v2 adds a header that makes branch protection report errors | |
| # because the Github action bot is not a collaborator on the repo | |
| run: git config --local --unset http.https://github.com/.extraheader | |
| - name: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore | |
| - name: Set up Python 3 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.x | |
| - name: Install build tools | |
| run: python -m pip install --upgrade pip twine build | |
| - name: Build source and wheel distributions | |
| run: python -m build | |
| - name: Check distributions | |
| run: twine check dist/* | |
| - name: Upload sdist | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: SDist | |
| path: dist/*.tar.gz | |
| # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. | |
| # Secrets are not accessible in the if: condition [0], so set an output variable [1] | |
| # [0] https://github.community/t/16928 | |
| # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}" | |
| run: if [ -n "$PYPI_API_TOKEN" ]; then echo ::set-output name=DEPLOY::true; fi | |
| - name: Upload to PyPI | |
| if: steps.deployable.outputs.DEPLOY | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| packages-dir: dist/ |