test.yml

name: Test

on:
  - pull_request

jobs:
  test:
    runs-on: ${{ matrix.platform }}
    strategy:
      fail-fast: false
      matrix:
        platform:
        - ubuntu-latest
        - windows-latest
        - macos-latest
        python-version:
        - "3.10"
        - "3.11"
        - "3.12"
        numpy-version:
        - "<2"
        - ">=2"

    steps:

    - uses: actions/checkout@v4

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

    - name: Prerequisites (Linux)
      if: matrix.platform == 'ubuntu-latest'
      run: |
        sudo apt-get -y install tabix

    - name: Install
      run: |
        python -m pip install --upgrade pip
        python -m pip install "numpy${{ matrix.numpy-version }}"
        python -m pip install -r requirements_dev_base.txt -r requirements_test.txt -r requirements_dev_optional.txt -r requirements_rtfd.txt
        python -m pip install -e .

    - name: Lint
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 allel --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 allel --count --exit-zero --max-line-length=127 --statistics

    - name: Test
      run: |
        pytest -v allel

    # - name: Test with doctest
    #   if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' && matrix.numpy-version == '>=2'
    #   run: |
    #     pytest -v --cov=allel --doctest-modules allel
    #     coverage report -m

    # - name: Build docs
    #   if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12' && matrix.numpy-version == '>=2'
    #   run: |
    #     cd docs && make html