ci.yml

name: CI

on:
  merge_group:
  pull_request:
  push:
    branches:
      - main
  schedule:
    # At 04:44 on Monday, see https://crontab.guru/
    - cron: "44 4 * * 1"

permissions:
  contents: read

jobs:
  lint:
    name: Lint
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
        with:
          persist-credentials: false

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b  # v8.1.0
        with:
          python-version: "3.11"

      - name: Install lint group
        run: uv sync --locked --only-group lint

      - name: Run prek
        run: |
          uv run --locked --only-group lint \
          prek -c prek.toml run --all-files --show-diff-on-failure

  test:
    name: Test
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [macos-14, ubuntu-latest, windows-latest]
        python-version: ["3.11", "3.12", "3.13"]
        exclude:
          # Just run macos and windows tests on one Python version
          - os: macos-14
            python-version: "3.12"
          - os: macos-14
            python-version: "3.13"
          - os: windows-latest
            python-version: "3.12"
          - os: windows-latest
            python-version: "3.13"
    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
        with:
          fetch-depth: 0
          persist-credentials: false

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b  # v8.1.0
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install test dependencies
        run: uv sync --locked --group test --no-default-groups

      - name: Test console script entry point
        run: |
          uv run bio2zarr --help
      - name: Run basic vcf2zarr example
        if: runner.os != 'Windows'
        run: |
          uv run python -m bio2zarr vcf2zarr convert tests/data/vcf/sample.vcf.gz sample.vcz -f
      - name: Run two-pass vcf2zarr example
        if: runner.os != 'Windows'
        run: |
          uv run python -m bio2zarr vcf2zarr explode tests/data/vcf/sample.vcf.gz sample.icf -f
          uv run python -m bio2zarr vcf2zarr encode sample.icf sample.vcz -f
      - name: Run distributed explode example
        if: runner.os != 'Windows'
        run: |
          uv run python -m bio2zarr vcf2zarr dexplode-init tests/data/vcf/sample.vcf.gz sample.icf -fn 3
          uv run python -m bio2zarr vcf2zarr dexplode-partition sample.icf 0
          uv run python -m bio2zarr vcf2zarr dexplode-partition sample.icf 1
          uv run python -m bio2zarr vcf2zarr dexplode-partition sample.icf 2
          uv run python -m bio2zarr vcf2zarr dexplode-finalise sample.icf
      - name: Run distributed encode example
        if: runner.os != 'Windows'
        run: |
          uv run python -m bio2zarr vcf2zarr dencode-init sample.icf sample.vcz -fn 3 --variants-chunk-size=3
          uv run python -m bio2zarr vcf2zarr dencode-partition sample.vcz 0
          uv run python -m bio2zarr vcf2zarr dencode-partition sample.vcz 1
          uv run python -m bio2zarr vcf2zarr dencode-partition sample.vcz 2
          uv run python -m bio2zarr vcf2zarr dencode-finalise sample.vcz
      - name: Run tskit2zarr example
        run: |
          uv run python -m bio2zarr tskit2zarr convert tests/data/tskit/example.trees sample.vcz -f
      - name: Run plink2zarr example
        run: |
          uv run python -m bio2zarr plink2zarr convert tests/data/plink/example sample.vcz -f
      - name: Run tests
        run: |
          uv run pytest --cov=bio2zarr
      - name: Upload coverage to Coveralls
        uses: coverallsapp/github-action@648a8eb78e6d50909eff900e4ec85cab4524a45b  # v2.3.6
        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

  optional_dependencies:
    name: Optional dependencies
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
        with:
          fetch-depth: 0
          persist-credentials: false

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b  # v8.1.0
        with:
          python-version: "3.11"

      - name: Test optional dependencies
        run: |
          uv venv env-tskit
          uv pip install --python=env-tskit .
          source env-tskit/bin/activate
          python -m bio2zarr tskit2zarr convert tests/data/tskit/example.trees ts.vcz > ts.txt 2>&1 || echo $? > ts_exit.txt
          test "$(cat ts_exit.txt)" = "1"
            grep -q "This process requires the optional tskit module. Install it with: pip install bio2zarr\[tskit\]" ts.txt
          deactivate
          uv pip install --python=env-tskit '.[tskit]'
          source env-tskit/bin/activate
          python -m bio2zarr tskit2zarr convert tests/data/tskit/example.trees ts.vcz
          deactivate

          uv venv env-vcf
          uv pip install --python=env-vcf .
          source env-vcf/bin/activate
          python -m bio2zarr vcf2zarr convert tests/data/vcf/sample.vcf.gz sample.vcz > vcf.txt 2>&1 || echo $? > vcf_exit.txt
          test "$(cat vcf_exit.txt)" = "1"
          grep -q "This process requires the optional cyvcf2 module. Install it with: pip install bio2zarr\[vcf\]" vcf.txt
          deactivate
          uv pip install --python=env-vcf '.[vcf]'
          source env-vcf/bin/activate
          python -m bio2zarr vcf2zarr convert tests/data/vcf/sample.vcf.gz sample.vcz
          deactivate

  packaging:
    name: Packaging
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
        with:
          fetch-depth: 0
          persist-credentials: false

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b  # v8.1.0
        with:
          python-version: "3.12"

      - name: Install packaging deps
        run: uv sync --locked --group packaging --no-default-groups

      - name: Validate pyproject
        run: uv run --locked --group packaging --no-default-groups validate-pyproject pyproject.toml -v

      - name: Build artefacts
        run: uv build

      - name: Twine check
        run: uv run --locked --group packaging --no-default-groups twine check --strict dist/*

      - name: Install into venv
        run: |
          uv venv cli-test
          uv pip install --python=cli-test dist/*.whl

      - name: Check bio2zarr CLI
        run: |
          ./cli-test/bin/python -m bio2zarr --help
      - name: Check vcf2zarr CLI
        run: |
          ./cli-test/bin/vcf2zarr --help
          ./cli-test/bin/python -m bio2zarr vcf2zarr --help
      - name: Check vcfpartition CLI
        run: |
          ./cli-test/bin/vcfpartition --help
          ./cli-test/bin/python -m bio2zarr vcfpartition --help
      - name: Check tskit2zarr CLI
        run: |
          ./cli-test/bin/tskit2zarr --help
          ./cli-test/bin/python -m bio2zarr tskit2zarr --help
      - name: Check plink2zarr CLI
        run: |
          ./cli-test/bin/plink2zarr --help
          ./cli-test/bin/python -m bio2zarr plink2zarr --help

  test-zarr-version:
    name: Test Zarr versions
    runs-on: ubuntu-latest
    strategy:
      matrix:
        zarr-format: [2, 3]
    steps:
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd  # v6.0.2
        with:
          fetch-depth: 0
          persist-credentials: false

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b  # v8.1.0
        with:
          python-version: "3.11"

      - name: Install test dependencies
        run: uv sync --locked --group test --no-default-groups

      - name: Run tests
        run: |
          uv run python -m pytest
        env:
          BIO2ZARR_DEFAULT_ZARR_FORMAT: ${{ matrix.zarr-format }}