jcvi/.github/workflows/pytest.yml at f5d49dbb634053d7ef68f3e2e4addb9a3a70f65c · tanghaibao/jcvi · GitHub

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name: Python Tests
on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      max-parallel: 4
      matrix:
        os: [ubuntu-latest, macos-latest]
        python-version: ["3.11", "3.13"]
    steps:
      - uses: actions/checkout@v6
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
      - name: Set up uv
        uses: astral-sh/setup-uv@v7
        with:
          cache-dependency-glob: |
            uv.lock
            pyproject.toml
      - name: Install BEDTools (Linux)
        run: |
          sudo apt-get update
          sudo apt-get install --fix-missing bedtools libmagickwand-dev
        if: matrix.os == 'ubuntu-latest'
      - name: Install BEDTools (macOS)
        run: brew install bedtools imagemagick
        if: matrix.os == 'macos-latest'
      - name: Install dependencies
        run: |
          if [ -f uv.lock ]; then
            uv sync --frozen --extra tests
          else
            uv sync --extra tests
          fi
      # Get pytest args from pyproject.toml
      - name: Test with pytest
        run: |
          uv run pytest

# Upload coverage report to Codecov
# Only upload coverage for the latest Python version on Ubuntu
#- name: Upload coverage reports to Codecov
#  uses: codecov/codecov-action@v5
#  if: matrix.python-version == '3.14' && matrix.os == 'ubuntu-latest'
#  with:
#    token: ${{ secrets.CODECOV_TOKEN }}
#    slug: tanghaibao/jcvi