Debugging GH actions for auto-conversion from Nipype #12
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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 ] | |
| tags: [ '*' ] | |
| pull_request: | |
| branches: [ main, develop ] | |
| repository_dispatch: | |
| types: [create-release] | |
| jobs: | |
| nipype-conv: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Revert version to most recent tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}') | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| - 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/afni/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@v3 | |
| - name: Revert version to most recent tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | 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/afni/auto | |
| - name: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| 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 "./related-packages/fileformats[dev]" "related-packages/fileformats-extras[dev]" | |
| pip install ${{ matrix.pip-flags }} ".[dev]" | |
| python -c "import pydra.tasks.afni 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_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import fileformats.extras.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| fileformats-test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Revert version to most recent tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}') | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install task package | |
| run: | | |
| pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]" | |
| python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| - name: Test fileformats with pytest | |
| run: | | |
| cd ./fileformats | |
| pytest -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml . | |
| test: | |
| needs: [nipype-conv, fileformats-test] | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| python-version: ['3.8'] # '3.11' | |
| steps: | |
| - name: Removed unnecessary tools to free space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Get Download cache Key | |
| id: cache-key | |
| run: echo "::set-output name=key::afni-linux-ubuntu22_amd64-7.4.1" | |
| - name: Cache FreeSurfer | |
| uses: actions/cache@v2 | |
| with: | |
| path: $HOME/downloads/afni | |
| key: ${{ steps.cache-key.outputs.key }} | |
| restore-keys: | | |
| afni-linux-ubuntu22_amd64-7.4.1 | |
| - name: Download FreeSurfer | |
| if: steps.cache-key.outputs.key != steps.cache-hit.outputs.key | |
| run: | | |
| mkdir -p $HOME/downloads/afni | |
| curl -s -o $HOME/downloads/afni/afni-linux-ubuntu22_amd64-7.4.1.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/afni/7.4.1/afni-linux-ubuntu22_amd64-7.4.1.tar.gz | |
| shell: bash | |
| - name: Install Freesurfer | |
| env: | |
| FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }} | |
| run: | | |
| pushd $HOME/downloads/afni | |
| tar -zxpf afni-linux-ubuntu22_amd64-7.4.1.tar.gz | |
| mv afni $HOME/ | |
| popd | |
| export FREESURFER_HOME=$HOME/afni | |
| source $FREESURFER_HOME/SetUpFreeSurfer.sh | |
| echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt | |
| export PATH=$FREESURFER_HOME/bin:$PATH | |
| - uses: actions/checkout@v3 | |
| - name: Revert version to most recent tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | 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/afni/auto | |
| - name: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/src\/pydra\/tasks\/afni\/auto/d' .gitignore | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| 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.afni 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 --doctest-modules ./pydra/tasks/afni \ | |
| --cov pydra.tasks.afni --cov-report xml | |
| - uses: codecov/codecov-action@v3 | |
| if: ${{ always() }} | |
| with: | |
| files: coverage.xml,./fileformats/coverage.xml | |
| name: pydra-afni | |
| deploy-fileformats: | |
| needs: [devcheck, test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }} | |
| packages-dir: ./related-packages/fileformats/dist | |
| deploy-fileformats-extras: | |
| needs: [deploy-fileformats] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats-extras | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats-extras/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }} | |
| packages-dir: ./related-packages/fileformats-extras/dist | |
| deploy: | |
| needs: [deploy-fileformats-extras] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Download tasks converted from Nipype | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: converted-nipype | |
| path: pydra/tasks/afni/auto | |
| - name: Tag release with a post-release based on Nipype and Nipype2Pydra versions | |
| if: github.event_name == 'repository_dispatch' | |
| run: | | |
| TAG=$(git tag -l | tail -n 1 | awk -F post '{print $1}') | |
| POST=$(python -c "from pydra.tasks.afni.auto._version import *; print(post_release)") | |
| git checkout $TAG | |
| git add -f pydra/tasks/afni/auto/_version.py | |
| git commit -am"added auto-generated version to make new tag for package version" | |
| git tag ${TAG}post${POST} | |
| - 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: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore | |
| - 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 == 'push' && startsWith(github.ref, 'refs/tags')) || 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 }} | |
| # 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 |