test.yml

name: Run Tests

on:
  push:
    branches: [ "main", "dev" ]
  pull_request:
    branches: [ "main", "dev" ]

jobs:
  test:
    name: Test on Python ${{ matrix.python-version }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.9", "3.10", "3.11", "3.12"]

    steps:
    # 1. Check out your code (including tests/data)
    - uses: actions/checkout@v4

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

    # 3. CRITICAL: Install zlib (Required for building mappy/minimap2 from source)
    - name: Install System Dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y zlib1g-dev

    # 4. Install your package and pytest
    - name: Install Dependencies
      run: |
        python -m pip install --upgrade pip
        pip install pytest build
        # Installs your package and dependencies defined in pyproject.toml
        pip install . 

    # 5. Run the tests
    - name: Run Pytest
      run: |
        pytest -v