biofuse/.github/workflows/ci.yml at main · sgkit-dev/biofuse · 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"

permissions:
  contents: read

jobs:
  lint:
    name: Lint
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
        with:
          persist-credentials: false

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39  # v8.2.0
        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 (Python ${{ matrix.python-version }})
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.11", "3.12", "3.13"]
    steps:
      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
        with:
          fetch-depth: 0
          persist-credentials: false

      - name: Install system packages
        run: |
          sudo apt-get update
          sudo apt-get install -y \
              fuse3 libfuse3-dev pkg-config \
              plink1.9 plink2

      - name: Install uv
        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39  # v8.2.0
        with:
          python-version: ${{ matrix.python-version }}

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

      - name: Test console script entry point
        run: |
          uv run biofuse --help

      - name: Run tests with coverage
        run: uv run pytest --cov=biofuse --cov-report=term-missing

      # FIXME dropping for now
      # - 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

  packaging:
    name: Packaging
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
        with:
          fetch-depth: 0
          persist-credentials: false

      # Needed to install pyfuse3, which builds from source.
      - name: Install system packages
        run: |
          sudo apt-get update
          sudo apt-get install -y fuse3 libfuse3-dev pkg-config

      - name: Install uv and set the python version
        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39  # v8.2.0
        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 biofuse CLI
        run: |
          ./cli-test/bin/biofuse --help