test_bamread.yml

name: Install, lint, and test bamread

# Source: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#using-multiple-python-versions

on: [pull_request]

jobs:
  install_and_test:
    runs-on: ubuntu-latest
    strategy:
      # You can use PyPy versions in python-version.
      # For example, pypy2.7 and pypy3.9
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]

    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Test
        run: |
            pip install .
            cd tests && python -c "import bamread; print(bamread.read_bam_full('control.bam'))"

  isort:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python environment
        uses: actions/setup-python@v4
        with:
          python-version: "3.11"
      - run: pip install isort
      - run: isort --check --diff .

  black:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python environment
        uses: actions/setup-python@v4
        with:
          python-version: "3.11.0"
          max-line-length: "120"
      - run: pip install black
      - run: black --check --diff .

  flake8:
    runs-on: ubuntu-latest
    name: Lint
    steps:
      - name: Check out source repository
        uses: actions/checkout@v3
      - name: Set up Python environment
        uses: actions/setup-python@v4
      - name: flake8 Lint install
        run: pip install flake8
      - name: flake8 Lint
        run: flake8 --max-line-length=120 bamread

  mypy:
    runs-on: ubuntu-latest
    name: Mypy
    steps:
      - name: Check out source repository
        uses: actions/checkout@v3
      - name: Set up Python environment
        uses: actions/setup-python@v4
        with:
          python-version: "3.11"
      - name: Install mypy
        run: pip install mypy
      - name: mypy
        run: mypy --install-types --non-interactive bamread