MNT: Update Python requirements, CI workflows, add Pydra 0.23 compatibility #132
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/ | ||
| on: | ||
| push: | ||
| branches: [main] | ||
| pull_request: | ||
| branches: [main] | ||
| 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" | ||
| mamba env config vars set FSLOUTPUTTYPE="NIFTI_GZ" | ||
| - name: Upgrade pip | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| - name: Install task package | ||
| run: | | ||
| pip install ".[test]" | ||
| python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | ||
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | ||
| - name: Test with pytest | ||
| run: | | ||
| pytest -sv --doctest-modules pydra/tasks/$SUBPACKAGE \ | ||
| --cov pydra.tasks.$SUBPACKAGE --cov-report xml | ||
| - uses: codecov/codecov-action@v4 | ||
| if: ${{ always() }} | ||
| 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 | ||
| steps: | ||
| - uses: actions/download-artifact@v4 | ||
| with: | ||
| name: Packages | ||
| path: dist | ||
| - uses: pypa/gh-action-pypi-publish@release/v1 | ||
