python-cqa.yml

name: Python CQA

on: [push, pull_request]


# TODO: separate lint and test jobs; lint first, test "needs" lint
# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobs

jobs:
  test:

    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12"]
    env:
      SEQREPO_ROOT_DIR: ./tests/data/seqrepo/latest

    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive
    - uses: actions/cache@v4
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-test-${{ hashFiles('pyproject.toml') }}
        restore-keys: |
          ${{ runner.os }}-pip-
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Update pip and setuptools
      run: |
        python -m pip install --upgrade pip setuptools
    - name: Install dependencies
      run: |
        pip install -e .[dev,extras]
    - name: Test with pytest
      run: |
        python -m pytest

  precommit_hooks:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - uses: actions/setup-python@v5
    - uses: pre-commit/action@v3.0.1
    # strategy:
    #   matrix:
    #     hook:
    #       - cmd: "end-of-file-fixer"
    #       - cmd: "trailing-whitespace"
    #       - cmd: "mixed-line-ending"
    # steps:
    # - uses: actions/checkout@v4
    # - uses: actions/cache@v4
    #   with:
    #     path: ~/.cache/pip
    #     key: ${{ runner.os }}-pip-precommit-${{ hashFiles('pyproject.toml') }}
    #     restore-keys: |
    #       ${{ runner.os }}-pip-
    # - name: Set up Python 3.12
    #   uses: actions/setup-python@v5
    #   with:
    #     python-version: 3.12
    # - name: Update pip and setuptools
    #   run: |
    #     python -m pip install --upgrade pip setuptools
    # - name: Install dependencies
    #   run: |
    #     pip install -e .[dev]
    # - name: Run pre-commit ${{ matrix.hook.cmd }} hook
    #   run: pre-commit run ${{ matrix.hook.cmd }} --all-files