ci.yml

name: CI

on:
  pull_request:
  push:
    branches:
      - main

jobs:
  pre-commit:
    name: Lint
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.11'
      - uses: pre-commit/action@v3.0.1
  python_test:
    name: Python tests
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -el {0}
    strategy:
      matrix:
        # Use macos-13 because pip binary packages for ARM aren't
        # available for many dependencies
        os: [macos-13, macos-14, ubuntu-latest]
        python-version: ["3.9", "3.10", "3.11"]
        exclude:
          # Just run macos tests on one Python version
          - os: macos-13
            python-version: "3.10"
          - os: macos-13
            python-version: "3.11"
          - os: macos-14
            python-version: "3.9"
          - os: macos-14
            python-version: "3.10"
    steps:
      - uses: actions/checkout@v4
      - name: Set up Miniconda with Python ${{ matrix.python-version }}
        uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          channels: conda-forge,bioconda
      - name: Install dependencies
        run: |
          conda install bcftools
          python -m pip install --upgrade pip
          python -m pip install '.[dev]'
          # Build the extension module in-place so pytest can find it
          python3 setup.py build_ext --inplace
      - name: Run tests
        run: |
          pytest

  c_python_test:
    name: CPython interface tests
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.11'
      - name: Install system dependencies
        run: |
          sudo apt install -y gcovr
      - name: Install python dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install numpy pytest pytest_cov
      - name: Build module with coverage
        run: |
          # Build the extension module in-place so pytest can find it
          CFLAGS="--coverage" python3 setup.py build_ext --inplace
      - name: Run tests
        run: |
          pytest -vs tests/test_cpython_interface.py
      - name: Show coverage
        run: |
          gcovr --filter vcztools

  c_test:
    name: C tests
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Install dependencies
        run: |
          sudo apt install -y ninja-build libcunit1-dev valgrind meson gcovr
      - name: Build
        working-directory: ./lib
        run: |
          meson setup -Db_coverage=true build
      - name: Tests
        working-directory: ./lib
        run: |
          ninja -C build test
      - name: Show coverage
        working-directory: ./lib
        run: |
          ninja -C build coverage-text
          cat build/meson-logs/coverage.txt
      - name: Valgrind
        working-directory: ./lib
        run: |
          valgrind --leak-check=full --error-exitcode=1 ./build/tests

  packaging:
    name: Packaging
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.11'
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install build twine validate-pyproject[all]
      - name: Check and install package
        run: |
          validate-pyproject pyproject.toml
          python -m build
          python -m twine check --strict dist/*
          python -m pip install dist/*.whl
      - name: Check vcztools CLI
        run: |
          vcztools --help
          # Make sure we don't have ``vcztools`` in the CWD
          cd tests
          python -m vcztools --help