Set up nipype2pydra converter templates #8
Workflow file for this run
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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, develop ] | |
| pull_request: | |
| branches: [ main, develop ] | |
| release: | |
| types: [published] | |
| repository_dispatch: | |
| types: [create-post-release] | |
| env: # Define environment variables | |
| ANTS_VERSION: v2.5.1 | |
| jobs: | |
| nipype-conv: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Revert version to most recent version tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}') | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| - name: Install build dependencies | |
| run: python -m pip install --upgrade pip | |
| - name: Install requirements | |
| run: python -m pip install ./related-packages/fileformats -r ./nipype-auto-conv/requirements.txt | |
| - name: Run automatic Nipype > Pydra conversion | |
| run: ./nipype-auto-conv/generate | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: converted-nipype | |
| path: pydra/tasks/ants/auto | |
| devcheck: | |
| needs: [nipype-conv] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.11'] # Check oldest and newest versions | |
| pip-flags: ['', '--editable'] | |
| pydra: | |
| - 'pydra' | |
| - '--editable git+https://github.com/nipype/pydra.git#egg=pydra' | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Revert version to most recent version tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}') | |
| - name: Download tasks converted from Nipype | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: converted-nipype | |
| path: pydra/tasks/ants/auto | |
| - name: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/pydra\/tasks\/ants\/auto/d' .gitignore | |
| sed -i '/^_version.py/d' .gitignore | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install Pydra | |
| run: | | |
| pushd $HOME | |
| pip install ${{ matrix.pydra }} | |
| popd | |
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| - name: Install task package | |
| run: | | |
| pip install ${{ matrix.pip-flags }} "./related-packages/fileformats[dev]" | |
| pip install ${{ matrix.pip-flags }} "related-packages/fileformats-extras[dev]" | |
| pip install ${{ matrix.pip-flags }} ".[dev]" | |
| python -c "import pydra.tasks.ants as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import fileformats.medimage_ants as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import fileformats.extras.medimage_ants as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| test: | |
| needs: [nipype-conv] | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.11'] | |
| steps: | |
| - name: Install prerequisite packages | |
| run: sudo apt install -y cmake | |
| - name: Removed unnecessary tools to free space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Cache ANTs Install | |
| id: cache-install | |
| uses: actions/cache@v4 | |
| with: | |
| path: install | |
| key: ants-${{ env.ANTS_VERSION }}-${{ runner.os }} | |
| - name: Install ANTs Package | |
| if: steps.cache-install.outputs.cache-hit != 'true' | |
| run: | | |
| workingDir=${PWD} | |
| git clone https://github.com/ANTsX/ANTs.git | |
| pushd ./ANTs | |
| git checkout ${{ env.ANTS_VERSION }} | |
| popd | |
| mkdir build install | |
| cd build | |
| cmake -DCMAKE_INSTALL_PREFIX=${workingDir}/install ../ANTs | |
| make -j 4 | |
| cd ANTS-build | |
| make install | |
| echo "Installation completed successfully" | |
| echo "PATH=${workingDir}/install/bin:$PATH" >> $GITHUB_ENV | |
| echo "LD_LIBRARY_PATH=${workingDir}/install/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Revert version to most recent version tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}') | |
| - name: Download tasks converted from Nipype | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: converted-nipype | |
| path: pydra/tasks/ants/auto | |
| - name: Show the contents of the auto-generated tasks | |
| run: tree pydra | |
| - name: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/pydra\/tasks\/ants\/auto/d' .gitignore | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install task package | |
| run: | | |
| pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]" | |
| python -c "import pydra.tasks.ants as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| - name: Test with pytest | |
| run: >- | |
| pytest -sv | |
| ./pydra/tasks/ants | |
| ./related-packages/fileformats | |
| ./related-packages/fileformats-extras | |
| --cov pydra.tasks.ants | |
| --cov fileformats.medimage_ants | |
| --cov fileformats.extras.medimage_ants | |
| --cov-report xml | |
| - name: Upload to CodeCov | |
| uses: codecov/codecov-action@v3 | |
| if: ${{ always() }} | |
| with: | |
| files: coverage.xml | |
| name: pydra-ants | |
| deploy-fileformats: | |
| needs: [devcheck, test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }} | |
| packages-dir: ./related-packages/fileformats/dist | |
| deploy-fileformats-extras: | |
| needs: [deploy-fileformats] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats-extras | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats-extras/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }} | |
| packages-dir: ./related-packages/fileformats-extras/dist | |
| deploy: | |
| needs: [nipype-conv, test, deploy-fileformats, deploy-fileformats-extras] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Git user | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Action" | |
| - name: Get latest version tag | |
| id: latest_tag | |
| run: | | |
| git fetch --tags | |
| echo "TAG=$(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')" >> $GITHUB_OUTPUT | |
| - name: Revert to latest tag | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout ${{ steps.latest_tag.outputs.TAG }} | |
| - name: Download tasks converted from Nipype | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: converted-nipype | |
| path: pydra/tasks/ants/auto | |
| - name: Show the contents of the auto-generated tasks | |
| run: tree pydra | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/pydra\/tasks\/ants\/auto/d' .gitignore | |
| cat .gitignore | |
| - name: Install task package to calculate post-release tag | |
| run: | | |
| pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]" | |
| - name: Generate post-release tag based on Nipype and Nipype2Pydra versions | |
| id: post_release_tag | |
| run: | | |
| POST=$(python -c "from pydra.tasks.ants.auto._version import *; print(post_release)") | |
| echo "TAG=${{ steps.latest_tag.outputs.TAG }}post${POST}" >> $GITHUB_OUTPUT | |
| - name: Add auto directory to git repo | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| run: | | |
| git add pydra/tasks/ants/auto | |
| git commit -am"added auto-generated version to make new tag for package version" | |
| git status | |
| - name: Overwrite the tag of release event with latest commit (i.e. including the auto directory) | |
| if: github.event_name == 'release' | |
| run: | | |
| git tag -d ${{ steps.latest_tag.outputs.TAG }}; | |
| git tag ${{ steps.latest_tag.outputs.TAG }}; | |
| - name: Tag repo with the post-release | |
| if: github.event_name == 'repository_dispatch' | |
| run: git tag ${{ steps.post_release_tag.outputs.TAG }} | |
| - name: Build source and wheel distributions | |
| run: python -m build . | |
| - name: Check distributions | |
| run: twine check dist/* | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: distributions | |
| path: dist/ | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ secrets.PYPI_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_API_TOKEN }} | |
| - name: Create post-release release for releases triggered by nipype2pydra dispatches | |
| if: steps.deployable.outputs.DEPLOY && github.event_name == 'repository_dispatch' | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token | |
| with: | |
| tag_name: ${{ steps.post_release_tag.outputs.TAG }} | |
| release_name: Release ${{ steps.post_release_tag.outputs.TAG }} | |
| draft: false | |
| prerelease: false | |
| # 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 |