squidpy/.github/workflows/test.yml at 8bbef96ea87ee32c2265cefbd3de8fe6d8a85c5a · scverse/squidpy · GitHub

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name: Test

on:
  schedule:
    - cron: 00 00 * * 1 # every Monday at 00:00
  push:
    branches: [main]
  pull_request:
    branches: [main]
  workflow_dispatch:
    inputs:
      reason:
        description: Reason for the workflow dispatch. Only "release" is valid.
        required: true
        default: release

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        python: ["3.10", "3.11", "3.12"]
        os: [ubuntu-latest]
        include:
          - python: "3.12"
            os: macos-latest

    env:
      OS: ${{ matrix.os }}
      PYTHON: ${{ matrix.python }}

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Set up Python ${{ matrix.python }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python }}

      - name: Install uv
        uses: astral-sh/setup-uv@v3
        with:
          enable-cache: true

      - name: Install hatch
        run: uv tool install hatch

      - name: Install dependencies
        run: |
          ./.scripts/ci/install_dependencies.sh

      - name: Restore data cache
        id: data-cache
        uses: actions/cache@v4
        with:
          path: |
            ~/.cache/squidpy/*.h5ad
          key: data-${{ hashFiles('**/download_data.py') }}

      - name: Download datasets
        if: steps.data-cache.outputs.cache-hit != 'true'
        run: |
          hatch run data:download

      - name: Test
        timeout-minutes: 60
        env:
          MPLBACKEND: agg
          PLATFORM: ${{ matrix.os }}
          DISPLAY: :42
          PYTEST_ADDOPTS: "-n auto"
        run: |
          hatch test --python ${{ matrix.python }} --randomize --parallel --cover --all

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

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5
        with:
          name: coverage
          verbose: true
          token: ${{ secrets.CODECOV_TOKEN }}

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