FIX: Copy interface before running to prevent task mutation on run #167
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 | |
| name: Python package | |
| # Set once | |
| env: | |
| SUBPACKAGE: nipype1 | |
| FSLCONDA: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ | |
| NO_ET: 1 # etelemetry causes order-of-magnitude slowdowns | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| release: | |
| types: | |
| - published | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| devcheck: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.12"] # Check oldest and newest versions | |
| pip-flags: ["", "--editable"] | |
| pydra: | |
| - "pydra" | |
| - "--editable git+https://github.com/nipype/pydra.git#egg=pydra" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - 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: | | |
| pip install ${{ matrix.pydra }} | |
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| - name: Install task package | |
| run: | | |
| pip install ${{ matrix.pip-flags }} ".[dev]" | |
| python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| channels: ${{ env.FSLCONDA }},conda-forge,defaults | |
| channel-priority: true | |
| - name: Install FSL | |
| run: | | |
| mamba install fsl-avwutils | |
| mamba env config vars set FSLDIR="$CONDA_PREFIX" FSLOUTPUTTYPE="NIFTI_GZ" | |
| # Hack because we're not doing a full FSL install | |
| echo "6.0.7.9" > $CONDA_PREFIX/etc/fslversion | |
| - name: Upgrade pip | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install task package | |
| run: | | |
| pip install ".[test]" | |
| python -c "import pydra.tasks.$SUBPACKAGE 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 --pyargs pydra.tasks.$SUBPACKAGE \ | |
| --cov pydra.tasks.$SUBPACKAGE --cov-report xml --cov-report term-missing | |
| - uses: codecov/codecov-action@v4 | |
| if: ${{ always() }} | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - uses: hynek/build-and-inspect-python-package@v2 | |
| deploy: | |
| needs: [build, devcheck, test] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| id-token: write | |
| if: github.repository_owner == 'nipype' && github.event.action == 'published' | |
| environment: Publish | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: Packages | |
| path: dist | |
| - uses: pypa/gh-action-pypi-publish@release/v1 |