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
    strategy:
      matrix:
        hook:
          - name: "Check EOF format"
            args: "end-of-file-fixer"
          - name: "Check trailing whitespace"
            args: "trailing-whitespace"
          - name: "Check line ending format"
            args: "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 ${{ matrix.python-version }}
      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:  ${{ matrix.hook.name }}
      run: pre-commit run ${{ matrix.hook.args }} --all-files