vczstore/.github/workflows/ci.yml at 9b9532a70dee9e48cc172aeeb34647cc21e15c3b · sgkit-dev/vczstore · GitHub

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name: CI

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

jobs:
  lint:
    name: Lint
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@v6
        with:
          python-version: "3.12"

      - 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

  python_test:
    name: Python tests
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -el {0}
    strategy:
      matrix:
        os: [macos-14, ubuntu-latest]
        python-version: ["3.12", "3.13"]
        exclude:
          # Just run macos tests on one Python version
          - os: macos-14
            python-version: "3.13"
    steps:
      - uses: actions/checkout@v4.2.2
        with:
          fetch-depth: 0

      - 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 conda test tools
        run: conda install bcftools

      - name: Install uv
        uses: astral-sh/setup-uv@v6

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

      - name: Run tests
        run: |
          uv run pytest

  packaging:
    name: Packaging
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        with:
          fetch-depth: 0

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@v6
        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 vczstore CLI
        run: |
          ./cli-test/bin/vczstore --help
          cd tests
          ../cli-test/bin/python -m vczstore --help

  test-zarr-version:
    name: Test Zarr versions
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    strategy:
      matrix:
        zarr-format: [2, 3]
    steps:
      - uses: actions/checkout@v4.2.2
        with:
          fetch-depth: 0

      - name: Set up Miniconda
        uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          python-version: "3.12"
          channels: conda-forge,bioconda

      - name: Install conda test tools
        run: conda install bcftools

      - name: Install uv
        uses: astral-sh/setup-uv@v6

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

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