updated auto-conv generate #45
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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 | |
| SCIGET_NAME: fsl | |
| SCIGET_VERSION: 6.0.7.18 | |
| 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: Revert version to most recent version tag on Nipype or Nipype2Pydra update | |
| if: github.event_name == 'repository_dispatch' | |
| run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}') | |
| - name: Install Apptainer and Lmod | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt-get update | |
| sudo apt-get install -y lmod apptainer | |
| - name: Install Neurocommand | |
| run: | | |
| git clone https://github.com/NeuroDesk/neurocommand.git | |
| pushd neurocommand | |
| pip3 install -r neurodesk/requirements.txt --user | |
| bash build.sh --cli | |
| echo "APPTAINER_BINDPATH=`pwd -P`" >> $GITHUB_ENV | |
| source /etc/profile.d/lmod.sh | |
| ./containers.sh "${{ env.SCIGET_NAME }}" | grep -E "^\s*\|\s*${{ env.SCIGET_NAME }}\s*\|\s*${{ env.SCIGET_VERSION }}\s*\|" | awk -F '|' '{gsub(/ /,"",$4); print $4}' | |
| SCIGET_BUILDVERSION=$(./containers.sh "${{ env.SCIGET_NAME }}" | grep -E "^\s*\|\s*${{ env.SCIGET_NAME }}\s*\|\s*${{ env.SCIGET_VERSION }}\s*\|" | awk -F '|' '{gsub(/ /,"",$4); print $4}') | |
| ./local/fetch_containers.sh ${{ env.SCIGET_NAME }} ${{ env.SCIGET_VERSION }} $SCIGET_BUILDVERSION | |
| echo "SCIGET_BUILDVERSION=$SCIGET_BUILDVERSION" >> $GITHUB_ENV | |
| popd | |
| - 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: ${{ matrix.python-version }} | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Install task package | |
| run: | | |
| pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]" | |
| python -c "import fileformats.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" | |
| - name: Test fileformats with pytest | |
| run: >- | |
| pytest ./related-packages -sv --cov fileformats.medimage_fsl | |
| --cov fileformats.extras.medimage_fsl --cov-report xml . | |
| deploy-fileformats: | |
| needs: [build, test, fileformats-test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }} | |
| packages-dir: ./related-packages/fileformats/dist | |
| deploy-fileformats-extras: | |
| needs: [deploy-fileformats] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Install build tools | |
| run: python -m pip install build twine | |
| - name: Build source and wheel distributions | |
| run: python -m build ./related-packages/fileformats-extras | |
| - name: Check distributions | |
| run: twine check ./related-packages/fileformats-extras/dist/* | |
| - name: Check for PyPI token on tag | |
| id: deployable | |
| if: github.event_name == 'release' | |
| env: | |
| PYPI_API_TOKEN: "${{ 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, deploy-fileformats, deploy-fileformats-extras] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| attestations: write | |
| id-token: write | |
| steps: | |
| - name: Download dist | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: Packages | |
| path: dist | |
| - name: Upload to PyPI | |
| if: github.event_name == 'release' | |
| 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 |