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
  test:
    name: Test
    runs-on: ${{ matrix.os }}
    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", "3.12"]
        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-13
            python-version: "3.12"
          - os: macos-14
            python-version: "3.9"
          - os: macos-14
            python-version: "3.10"
          - os: macos-14
            python-version: "3.12"
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install '.[dev]'
      - name: Run basic vcf2zarr example
        run: |
          python -m bio2zarr vcf2zarr convert tests/data/vcf/sample.vcf.gz sample.vcz -f
      - name: Run two-pass vcf2zarr example
        run: |
          python -m bio2zarr vcf2zarr explode tests/data/vcf/sample.vcf.gz sample.icf -f
          python -m bio2zarr vcf2zarr encode sample.icf sample.vcz -f
      - name: Run distributed explode example
        run: |
          python -m bio2zarr vcf2zarr dexplode-init tests/data/vcf/sample.vcf.gz sample.icf -fn 3
          python -m bio2zarr vcf2zarr dexplode-partition sample.icf 0
          python -m bio2zarr vcf2zarr dexplode-partition sample.icf 1
          python -m bio2zarr vcf2zarr dexplode-partition sample.icf 2
          python -m bio2zarr vcf2zarr dexplode-finalise sample.icf
      - name: Run distributed encode example
        run: |
          python -m bio2zarr vcf2zarr dencode-init sample.icf sample.vcz -fn 3 --variants-chunk-size=3
          python -m bio2zarr vcf2zarr dencode-partition sample.vcz 0
          python -m bio2zarr vcf2zarr dencode-partition sample.vcz 1
          python -m bio2zarr vcf2zarr dencode-partition sample.vcz 2
          python -m bio2zarr vcf2zarr dencode-finalise sample.vcz
      - name: Run tests
        run: |
          pytest --cov=bio2zarr
      - name: Upload coverage to Coveralls
        uses: coverallsapp/github-action@v2.3.0
        with:
          github-token: ${{ secrets.GITHUB_TOKEN }}
          # The first coveralls upload will succeed and others seem to fail now.
          # This is a quick workaround for doing a proper "parallel" setup:
          # https://github.com/coverallsapp/github-action
          fail-on-error: false

  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 vcf2zarr CLI
        run: |
          vcf2zarr --help
          python -m bio2zarr vcf2zarr --help
      - name: Check vcfpartition CLI
        run: |
          vcfpartition --help
          python -m bio2zarr vcfpartition --help

  test-numpy-version:
    name: Test numpy versions
    runs-on: ubuntu-latest
    strategy:
      matrix:
        numpy: ["==1.26", ">=2"]
    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 '.[dev]'
      - name: Install numpy${{ matrix.numpy }}
        run: |
          python -m pip install 'numpy${{ matrix.numpy }}'
      - name: Run tests
        run: |
          # We just run the CLI tests here because it doesn't require other upstream
          # packages like sgkit (which are tangled up with the numpy 2 dependency)
          python -m pytest tests/test_cli.py

  test-zarr-version:
    name: Test Zarr versions
    runs-on: ubuntu-latest
    strategy:
      matrix:
        zarr: ["==2.18.3", ">=3"]
    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 '.[dev]'
      - name: Install zarr${{ matrix.zarr }}
        run: |
          python -m pip install 'zarr${{ matrix.zarr }}'
      - name: Run tests
        run: |
          python -m pytest -k "not test_double_encode_partition"