sopa/.github/workflows/ci.yml at 9b19079932f033a2ecb956ab5445884a8d660566 · prism-oncology/sopa · GitHub

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name: ci

on:
  push:
    tags:
      - v*
  pull_request:
    branches: [main]
    types: [opened, synchronize, reopened]
  schedule:
    - cron: "0 0 * * 1,3,5"

permissions:
  contents: write

env:
  GITHUB_TOKEN: ${{ github.token }}

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:
        os: [ubuntu-latest, macOS-latest, windows-latest]
        python-version: ["3.11", "3.12", "3.13"]
        exclude:
          - os: macos-latest
            python-version: "3.13"

    steps:
      - uses: actions/checkout@v5

      - name: Set up Miniconda
        uses: conda-incubator/setup-miniconda@v3

      - 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 --dev && uv pip install 'snakemake>=7.32.4,<9.0' 'pulp<2.8' 'cellpose==3.1.1'

      - name: Tests
        run: uv run poe test

      - name: Snakemake
        run: cd workflow && uv run snakemake --config sdata_path=tuto.zarr --configfile=config/toy/cellpose.yaml --workflow-profile profile/ci -c1

  test_wsi:
    needs: [pre-commit]
    name: "${{ matrix.os }} | pytest wsi"
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macOS-latest, windows-latest]

    steps:
      - uses: actions/checkout@v5

      - name: Set up the environment
        uses: ./.github/actions/setup-python-env

      - name: Install extra dependencies
        run: uv sync --extra wsi --dev && uv pip install 'openslide-bin==4.0.0.8' 'openslide-python==1.4.2' 'slideio==2.7.1' 'timm==1.0.21'

      - name: Tests
        run: uv run poe test_wsi

  test_cellpose_v4:
    needs: [pre-commit]
    name: "${{ matrix.os }} | pytest cellpose v4"
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macOS-latest, windows-latest]

    steps:
      - uses: actions/checkout@v5

      - name: Set up the environment
        uses: ./.github/actions/setup-python-env

      - name: Install extra dependencies
        run: uv sync --extra cellpose --dev

      - name: Tests
        run: uv run poe test_long

  test_pip_install:
    needs: [pre-commit]
    name: "${{ matrix.os }} | pytest with pip install"
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macOS-latest, windows-latest]
    steps:
      - uses: actions/checkout@v5

      - name: Set up Python
        uses: actions/setup-python@v6
        with:
          python-version: "3.12"

      - name: Install sopa with pip
        run: pip install -e . && pip install pytest-cov poethepoet

      - name: Run short tests
        run: poe test_short

  deploy-docs:
    needs: [tests, test_wsi, test_cellpose_v4, test_pip_install]
    if: contains(github.ref, 'tags')
    name: "Deploy documentation"
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v5

      - 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, test_wsi, test_cellpose_v4, test_pip_install]
    if: contains(github.ref, 'tags')
    name: "PyPI release"
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v5

      - 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 }}