squidpy/.github/workflows/test.yml at 78ce7215853b014e6e5f4bce273a398ec47e9775 · scverse/squidpy · GitHub

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name: CI

on:
  push:
    branches:
      - main
      - "[0-9]+.[0-9]+.x"
  pull_request:

env:
  PYTEST_ADDOPTS: "-v --color=yes -n auto"
  FORCE_COLOR: "1"
  MPLBACKEND: agg
  # It's impossible to ignore SyntaxWarnings for a single module,
  # so because leidenalg 0.10.0 has them, we pre-compile things: https://github.com/vtraag/leidenalg/issues/173
  UV_COMPILE_BYTECODE: "1"

defaults:
  run:
    shell: bash -e {0} # -e to fail on error

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        include:
          - name: hatch-test-py310
            os: ubuntu-latest
            python: "3.10"
          - name: hatch-test-py311
            os: ubuntu-latest
            python: "3.11"
          - name: hatch-test-py312
            os: ubuntu-latest
            python: "3.12"
          - name: hatch-test-py312-pre
            os: macos-latest
            python: "3.12"
            prerelease: "allow"
            test-type: coverage
    env: # environment variable for use in codecov's env_vars tagging
      ENV_NAME: ${{ matrix.name }}
      UV_PRERELEASE: ${{ matrix.prerelease || 'disallow' }}
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
          filter: blob:none

      - uses: astral-sh/setup-uv@v5
        with:
          enable-cache: true
          python-version: ${{ matrix.python }}
          cache-dependency-glob: pyproject.toml

      - name: Cache downloaded data
        uses: actions/cache@v4
        with:
          path: .pytest_cache/d/squidpy-data
          key: pytest

      - name: Install dependencies
        run: uvx hatch -v env create ${{ matrix.name }}

      - name: Run tests
        if: matrix.test-type == null
        run: uvx hatch run ${{ matrix.name }}:run

      - name: Run tests (coverage)
        if: matrix.test-type == 'coverage'
        run: uvx hatch run ${{ matrix.name }}:run-cov --cov --cov-report=xml

      - name: Archive figures generated during testing
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: visual_test_results_${{ matrix.name }}
          path: /home/runner/work/squidpy/squidpy/tests/figures/*

      - name: Upload coverage data
        if: matrix.test-type == 'coverage'
        uses: codecov/codecov-action@v5
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          env_vars: ENV_NAME
          fail_ci_if_error: true
          files: test-data/coverage.xml

  build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
          filter: blob:none
      - uses: actions/setup-python@v5
        with:
          python-version: "3.13"
      - uses: astral-sh/setup-uv@v5
        with:
          enable-cache: false
      - run: uvx --from build pyproject-build --sdist --wheel .
      - run: uvx twine check dist/*

  check:
    if: always()
    needs:
      - test
      - build
    runs-on: ubuntu-latest
    steps:
      - uses: re-actors/alls-green@release/v1
        with:
          jobs: ${{ toJSON(needs) }}