v0.2.0 #39
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: | |
| release: | |
| types: [published] | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| env: # Define environment variables | |
| # Force tox and pytest to use color | |
| FORCE_COLOR: true | |
| jobs: | |
| build: | |
| name: Build & verify package | |
| runs-on: ubuntu-latest | |
| permissions: | |
| attestations: write | |
| id-token: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: hynek/build-and-inspect-python-package@v2 | |
| with: | |
| attest-build-provenance-github: ${{ github.event_name != 'pull_request' }} | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11', '3.13'] | |
| fail-fast: false | |
| steps: | |
| - name: Removed unnecessary tools to free space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Install Minconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-activate-base: true | |
| activate-environment: "" | |
| - name: Install fsl Packages | |
| run: >- | |
| conda install -c conda-forge -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ | |
| ciftilib cli11 elc fsl-add_module fsl-armawrap fsl-asl_mfree fsl-avwutils fsl-base | |
| fsl-basil fsl-basisfield fsl-baycest fsl-bet2 fsl-bianca fsl-biancadata fsl-bint | |
| fsl-cluster fsl-copain fsl-cprob fsl-cudimot fsl-data_atlases | |
| fsl-data_atlases_xtract fsl-data_first_models_317_bin fsl-data_first_models_336_bin fsl-data_linearmni | |
| fsl-data_omm fsl-data_possum fsl-data_standard fsl-deface fsl-discreteopt fsl-dpm fsl-dwssfp | |
| fsl-easyfeat fsl-eddy fsl-eddy_qc fsl-fabber_core fsl-fabber_models_asl fsl-fabber_models_cest | |
| fsl-fabber_models_dce fsl-fabber_models_dsc fsl-fabber_models_dualecho fsl-fabber_models_dwi | |
| fsl-fabber_models_pet fsl-fabber_models_qbold fsl-fabber_models_t1 fsl-fast4 fsl-fastpdlib | |
| fsl-fdt fsl-feat5 fsl-film fsl-filmbabe fsl-first fsl-first_lib fsl-flameo | |
| fsl-flirt fsl-fnirt fsl-fugue fsl-get_standard fsl-giftiio fsl-gps | |
| fsl-gui-desktop fsl-installer fsl-lesions fsl-libgdc fsl-libmeshutils fsl-libvis fsl-load_dicom fsl-mcflirt | |
| fsl-melodic fsl-meshclass fsl-misc_c fsl-misc_scripts fsl-misc_tcl fsl-miscmaths fsl-miscvis | |
| fsl-mist fsl-mm fsl-msm fsl-msmreglib fsl-mvdisc fsl-nets fsl-newimage | |
| fsl-newmesh fsl-newnifti fsl-newran fsl-oxford_asl fsl-possum fsl-ptx2 fsl-pyfeeds | |
| fsl-pyfeeds-tests fsl-qboot fsl-randomise fsl-relax fsl-shapemodel fsl-siena fsl-slicetimer | |
| fsl-sub fsl-sub-plugin-sge fsl-sub-plugin-slurm fsl-surface fsl-susan fsl-swe fsl-tbss | |
| fsl-topup fsl-utils fsl-vbm fsl-verbena fsl-vtkio fsl-warpfns fsl-wire fsl-xtract fsl-xtract_data | |
| fsl-znzlib fsl_mrs fsl_sub fsl_sub_plugin_sge fsl_sub_plugin_slurm | |
| - name: Download tasks converted from Nipype | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: converted-nipype | |
| path: pydra/tasks/fsl/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\/fsl\/auto/d' .gitignore | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install the latest version of uv | |
| uses: astral-sh/setup-uv@v6 | |
| - name: Install tox | |
| run: | | |
| uv tool install tox --with=tox-uv --with=tox-gh-actions | |
| - name: Show tox config | |
| run: tox c | |
| - name: Run tox | |
| run: tox -v --exit-and-dump-after 1200 | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fileformats-test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11', '3.13'] | |
| 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: ${{ matrix.python-version }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install task package | |
| run: | | |
| pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]" | |
| python -c "import fileformats.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| - name: Test fileformats with pytest | |
| run: >- | |
| pytest ./related-packages -sv --cov fileformats.medimage_fsl | |
| --cov fileformats.extras.medimage_fsl --cov-report xml . | |
| deploy-fileformats: | |
| needs: [build, test, fileformats-test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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: [build, test] | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'release' | |
| permissions: | |
| attestations: write | |
| id-token: write | |
| steps: | |
| - name: Download dist | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: Packages | |
| path: dist | |
| - name: Upload to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| # 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 |