Nipype auto conv #1
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: | |
| push: | |
| branches: [ master, develop ] | |
| pull_request: | |
| branches: [ master, develop ] | |
| release: | |
| types: [published] | |
| repository_dispatch: | |
| types: [create-post-release] | |
| env: | |
| FSL_VERSION: 6.0.7.9 | |
| FSL_HOME: ${{ github.workspace }}/fsl-install | |
| jobs: | |
| nipype-conv: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Revert version to most recent version tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}') | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| - 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/fsl/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@v4 | |
| - name: Revert version to most recent version tag on upstream update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | grep 'v.*' | 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/fsl/auto | |
| - name: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/pydra\/tasks\/fsl\/auto/d' .gitignore | |
| sed -i '/^_version.py/d' .gitignore | |
| - 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: | | |
| 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 ${{ matrix.pip-flags }} "./related-packages/fileformats[dev]" | |
| pip install ${{ matrix.pip-flags }} "related-packages/fileformats-extras[dev]" | |
| pip install ${{ matrix.pip-flags }} ".[dev]" | |
| python -c "import pydra.tasks.fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import fileformats.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| python -c "import fileformats.extras.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| test: | |
| needs: [nipype-conv] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.11'] | |
| steps: | |
| - name: Removed unnecessary tools to free space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Install Minconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| 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-cudabasisfield-cuda-10 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-cuda-10 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-fdt-cuda-10 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-gradunwarp fsl-gui-bet | |
| 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-mmorf-cuda-10 fsl-msm fsl-msmreglib fsl-mvdisc fsl-nets fsl-newimage | |
| fsl-newmesh fsl-newnifti fsl-newran fsl-oxford_asl fsl-possum fsl-ptx2 fsl-ptx2-cuda-10 fsl-pyfeeds | |
| fsl-pyfeeds-tests fsl-pyfix 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-tirl | |
| 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@v3 | |
| 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 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.fsl 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 | |
| ./pydra/tasks/fsl | |
| ./related-packages/fileformats | |
| ./related-packages/fileformats-extras | |
| --cov pydra.tasks.fsl | |
| --cov fileformats.medimage_fsl | |
| --cov fileformats.extras.medimage_fsl | |
| --cov-report xml | |
| - name: Upload to CodeCov | |
| uses: codecov/codecov-action@v3 | |
| if: ${{ always() }} | |
| with: | |
| files: coverage.xml | |
| name: pydra-fsl | |
| deploy-fileformats: | |
| needs: [devcheck, test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }} | |
| packages-dir: ./related-packages/fileformats-extras/dist | |
| deploy: | |
| needs: [nipype-conv, test, deploy-fileformats, deploy-fileformats-extras] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Git user | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Action" | |
| - name: Get latest version tag | |
| id: latest_tag | |
| run: | | |
| git fetch --tags | |
| echo "TAG=$(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')" >> $GITHUB_OUTPUT | |
| - name: Revert to latest tag | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout ${{ steps.latest_tag.outputs.TAG }} | |
| - name: Download tasks converted from Nipype | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: converted-nipype | |
| path: pydra/tasks/fsl/auto | |
| - name: Show the contents of the auto-generated tasks | |
| run: tree pydra | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Strip auto package from gitignore so it is included in package | |
| run: | | |
| sed -i '/\/pydra\/tasks\/fsl\/auto/d' .gitignore | |
| cat .gitignore | |
| - name: Install task package to calculate post-release tag | |
| run: | | |
| pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]" | |
| - name: Generate post-release tag based on Nipype and Nipype2Pydra versions | |
| id: post_release_tag | |
| run: | | |
| POST=$(python -c "from pydra.tasks.fsl.auto._version import *; print(post_release)") | |
| echo "TAG=${{ steps.latest_tag.outputs.TAG }}post${POST}" >> $GITHUB_OUTPUT | |
| - name: Add auto directory to git repo | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| run: | | |
| git add pydra/tasks/fsl/auto | |
| git commit -am"added auto-generated version to make new tag for package version" | |
| git status | |
| - name: Overwrite the tag of release event with latest commit (i.e. including the auto directory) | |
| if: github.event_name == 'release' | |
| run: | | |
| git tag -d ${{ steps.latest_tag.outputs.TAG }}; | |
| git tag ${{ steps.latest_tag.outputs.TAG }}; | |
| - name: Tag repo with the post-release | |
| if: github.event_name == 'repository_dispatch' | |
| run: git tag ${{ steps.post_release_tag.outputs.TAG }} | |
| - name: Build source and wheel distributions | |
| run: python -m build . | |
| - name: Check distributions | |
| run: twine check dist/* | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: distributions | |
| path: dist/ | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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 }} | |
| - name: Create post-release release for releases triggered by nipype2pydra dispatches | |
| if: steps.deployable.outputs.DEPLOY && github.event_name == 'repository_dispatch' | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token | |
| with: | |
| tag_name: ${{ steps.post_release_tag.outputs.TAG }} | |
| release_name: Release ${{ steps.post_release_tag.outputs.TAG }} | |
| draft: false | |
| prerelease: false | |
| report_progress: | |
| needs: [deploy] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Generate progress report | |
| id: generate-report | |
| run: | | |
| tools/report_progress.py outputs/progress-report.json | |
| echo "progress_report=$(cat outputs/progress-report.json)" >> $GITHUB_OUTPUT | |
| - name: Report progress to Nipype2Pydra repo | |
| if: github.event_name == 'release' || github.event_name == 'repository_dispatch' | |
| run: >- | |
| curl -XPOST -u "${{ env.POST_RELEASE_PAT }}" -H "Accept: application/vnd.github.everest-preview+json" | |
| "https://api.github.com/repos/nipype/pydra-fsl/dispatches" | |
| -d '{ | |
| "event_type": "progress-report", | |
| "client_payload": ${{ steps.generate-report.output.progress_report }} | |
| }' | |
| env: | |
| PAT: ${{ env.PROGRESS_REPORT_PAT }} | |
| # 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 |