Supporting python 3.13 #262
Workflow file for this run
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| name: ci | |
| on: | |
| push: | |
| tags: | |
| - v* | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v3 | |
| - uses: pre-commit/action@v3.0.1 | |
| tests: | |
| needs: [pre-commit] | |
| name: "pytest and snakemake" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12", "3.13"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up the environment | |
| uses: ./.github/actions/setup-python-env | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install extra dependencies | |
| run: uv sync --extra cellpose --extra wsi --dev && uv run pip install snakemake 'pulp<2.8' | |
| - name: Tests | |
| run: uv run pytest | |
| - name: Snakemake | |
| run: cd workflow && uv run snakemake --config sdata_path=tuto.zarr --configfile=config/toy/cellpose.yaml --workflow-profile profile/ci -c1 | |
| deploy-docs: | |
| needs: [tests] | |
| if: contains(github.ref, 'tags') | |
| name: "Deploy documentation" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up the environment | |
| uses: ./.github/actions/setup-python-env | |
| - name: Install extra dependencies | |
| run: uv sync --dev | |
| - name: Build documentation | |
| run: uv run mkdocs gh-deploy --force | |
| pypi-release: | |
| needs: [tests] | |
| if: contains(github.ref, 'tags') | |
| name: "PyPI release" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up the environment | |
| uses: ./.github/actions/setup-python-env | |
| - name: Build | |
| run: uv build | |
| - name: Publish | |
| run: uv publish -t ${{ secrets.PYPI_TOKEN }} | |
| docker-images-release: | |
| needs: [pypi-release] | |
| if: contains(github.ref, 'tags') | |
| name: "Docker images release" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| extra-name: | |
| [ | |
| "", | |
| "-baysor", | |
| "-cellpose", | |
| "-comseg", | |
| "-proseg", | |
| "-stardist", | |
| "-tangram", | |
| ] | |
| steps: | |
| - name: Export tag version | |
| run: | | |
| TAG="${GITHUB_REF#refs/tags/v}" | |
| echo "VERSION=$TAG" >> $GITHUB_ENV | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ vars.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build and push | |
| uses: docker/build-push-action@v6 | |
| with: | |
| push: true | |
| platforms: linux/amd64 | |
| tags: | | |
| ${{ vars.DOCKERHUB_USERNAME }}/sopa:${{ env.VERSION }}${{ matrix.extra-name }} | |
| ${{ vars.DOCKERHUB_USERNAME }}/sopa:latest${{ matrix.extra-name }} | |
| context: ./docker/sopa${{ matrix.extra-name }} | |
| build-args: | | |
| SOPA_VERSION=${{ env.VERSION }} |