Updated syntax to match pydra refactor #17
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: Python package | |
| # Set once | |
| env: | |
| SUBPACKAGE: dcm2niix | |
| on: | |
| push: | |
| branches: [ main ] | |
| tags: [ '*' ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.11, 3.12, 3.13] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install task package | |
| run: | | |
| pip install ".[test]" | |
| - name: Install development Pydra and fileformats-medimage | |
| run: | | |
| pip uninstall pydra fileformats-medimage -y | |
| pip install --no-deps git+https://github.com/nipype/pydra.git@new-syntax | |
| pip install --no-deps git+https://github.com/arcanaframework/fileformats-medimage.git@pydra-syntax-changes | |
| - name: Test with pytest | |
| run: | | |
| pytest -sv --cov pydra.tasks.$SUBPACKAGE --cov-report xml | |
| - uses: codecov/codecov-action@v1 | |
| if: ${{ always() }} | |
| deploy: | |
| needs: [test] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.9] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Unset header | |
| # checkout@v2 adds a header that makes branch protection report errors | |
| # because the Github action bot is not a collaborator on the repo | |
| run: git config --local --unset http.https://github.com/.extraheader | |
| - name: Set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.12' | |
| - name: Install build tools | |
| run: python3 -m pip install --break-system-packages build twine | |
| - name: Build source and wheel distributions | |
| run: python3 -m build . | |
| - name: Check distributions | |
| run: twine check dist/* | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: built | |
| path: dist | |
| # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. | |
| # Secrets are not accessible in the if: condition [0], so set an output variable [1] | |
| # [0] https://github.community/t/16928 | |
| # [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| env: | |
| PYPI_API_TOKEN: "${{ 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@27b31702a0e7fc50959f5ad993c78deac1bdfc29 # v1.4.2 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |