feat: update to nnunetV2 #279
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| name: CI-CD | |
| # only run on pushes to main or pull requests | |
| on: | |
| push: | |
| branches: ["main"] | |
| pull_request: | |
| branches: ["*"] | |
| jobs: | |
| ################################################################################################ | |
| # Unit-Tests: Run unit tests using pytest | |
| ################################################################################################ | |
| Unit-Tests: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 15 # Consider increasing timeout | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, macos-14] # , windows-latest removed for now | |
| env: ["py310", "py311", "py312"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| environments: ${{ matrix.env }} | |
| pixi-version: v0.36.0 | |
| cache: true | |
| locked: false # wont be the same because of the tag | |
| - name: Run pytest | |
| run: | | |
| pixi run -e ${{ matrix.env }} test | |
| - name: Upload coverage report artifact to be used by Codecov | |
| # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12 | |
| if: matrix.os == 'ubuntu-latest' && matrix.env == 'py312' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-report | |
| path: coverage-report | |
| ################################################################################################ | |
| # Unit-Tests: Run unit tests using pytest | |
| ################################################################################################ | |
| Build-Docs: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 15 # Consider increasing timeout | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] # , windows-latest removed for now | |
| env: ["docs"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| environments: ${{ matrix.env }} | |
| pixi-version: v0.36.0 | |
| cache: true | |
| locked: false # wont be the same because of the tag | |
| - name: Run pytest | |
| run: | | |
| pixi run -e ${{ matrix.env }} doc-build | |
| ################################################################################################ | |
| # Codecov: Run codecov to check coverage | |
| ################################################################################################ | |
| Code-Coverage: | |
| needs: Unit-Tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Download coverage.xml artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: coverage-report | |
| path: coverage-report | |
| - name: Use Codecov to track coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage-report/coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| name: codecov-umbrella | |
| cd: | |
| concurrency: release | |
| permissions: | |
| id-token: write | |
| actions: read | |
| contents: write | |
| packages: write | |
| issues: write | |
| pull-requests: write | |
| needs: Unit-Tests | |
| if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/devel' | |
| # Set up operating system | |
| runs-on: ubuntu-latest | |
| outputs: | |
| released: ${{ steps.release.outputs.released }} | |
| version: ${{ steps.release.outputs.version }} | |
| tag: ${{ steps.release.outputs.tag }} | |
| # Define job steps | |
| steps: | |
| - uses: actions/create-github-app-token@v1 | |
| id: app-token | |
| with: | |
| app-id: ${{ vars.SEMVERPOLICE_ID }} | |
| private-key: ${{ secrets.SEMVER_APP_KEY }} | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| - name: Check-out repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Python Semantic Release | |
| uses: python-semantic-release/python-semantic-release@master | |
| id: release | |
| with: | |
| root_options: -v | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| git_committer_name: "gh-actions-semver" | |
| pip-squeak: | |
| needs: cd | |
| if: needs.cd.outputs.released == 'true' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout the code with tag ${{ needs.cd.outputs.tag }} | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ needs.cd.outputs.tag }} | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.12 | |
| - name: Install Package Builder | |
| run: python3 -m pip install build | |
| - name: Build package | |
| run: python3 -m build --sdist --wheel --outdir dist/ | |
| - name: Publish to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| verbose: true | |
| user: ${{ secrets.pypi_token }} | |
| password: ${{ secrets.pypi_api }} | |
| # does-the-pip-squeak: | |
| # needs: pip-squeak | |
| # runs-on: ${{ matrix.os }} | |
| # strategy: | |
| # matrix: | |
| # os: [ubuntu-latest, macos-latest, windows-latest] | |
| # python-version: ["3.12", "3.11", "3.10"] | |
| # steps: | |
| # - uses: actions/checkout@v3 | |
| # - name: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # - name: Install using PyPi | |
| # run: | | |
| # pip install med-imagetools | |
| # # autopipeline | |
| # # pip install med-imagetools ==${{ needs.cd.outputs.version }} |