anyvar/.github/workflows/python-package.yml at main · biocommons/anyvar · GitHub

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name: Python package

on:
  push:
  pull_request:

permissions:
  contents: read

jobs:
  lint:
    name: lint
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6

      - name: Setup Python
        uses: actions/setup-python@v6
        with:
          python-version: "3.11"

      - name: Install uv
        uses: astral-sh/setup-uv@v6
        with:
          enable-cache: true

      - name: Install dependencies
        run: uv sync --extra dev

      - name: Check style
        run: uv run ruff check && uv run ruff format --check
  test:
    name: test
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.11", "3.12", "3.13"]
        storage:
          - backend: postgres
            uri: postgresql://postgres:postgres@localhost:5432/postgres
            deps:

          - backend: duckdb
            uri: duckdb:///variants.duckdb
            deps: '--extra duckdb'
    services:
      redis:
        image: redis:alpine
        ports:
          - 6379:6379
    steps:
      - uses: actions/checkout@v6

      - name: Start Postgres
        if: matrix.storage.backend == 'postgres'
        run: |
          docker run -d \
            --name postgres \
            -e POSTGRES_PASSWORD=postgres \
            -p 5432:5432 \
            postgres:17

      - name: Wait for Postgres
        if: matrix.storage.backend == 'postgres'
        run: |
          for i in {1..30}; do
            pg_isready -h localhost -p 5432 -U postgres && exit 0
            sleep 1
          done
          docker logs postgres
          exit 1

      - name: Initialize GiST extension
        if: matrix.storage.backend == 'postgres'
        env:
          PGPASSWORD: postgres
        run: |
          psql -h localhost -p 5432 -U postgres -d postgres \
            -c "CREATE EXTENSION IF NOT EXISTS btree_gist;"

      - name: Cache chainfiles for liftover
        uses: actions/cache@v5
        with:
          path: ~/.local/share/wags_tails
          key: ${{ runner.os }}-test-${{ hashFiles('pyproject.toml') }}

      - name: Setup Python
        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install uv
        uses: astral-sh/setup-uv@v6
        with:
          enable-cache: true

      - name: Install dependencies
        run: uv sync --extra test --extra queueing ${{ matrix.storage.deps }}

      - name: Run tests
        run: uv run pytest -vv -m "ci_ok"
        env:
          ANYVAR_TEST_STORAGE_URI: ${{ matrix.storage.uri }}
          CELERY_BROKER_URL: redis://localhost:6379/0

  precommit_hooks:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6

      - uses: j178/prek-action@v2
        with:
          extra_args: '--all-files --skip "ruff-format" --skip "ruff-check"'

  docs:
    runs-on: ubuntu-latest
    env:
      SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v6

      - name: Set up Python
        uses: actions/setup-python@v6
        with:
          python-version: 3.11

      - name: Install uv
        uses: astral-sh/setup-uv@v6
        with:
          enable-cache: true

      - name: Install dependencies
        run: uv sync --extra docs

      - name: Attempt docs build
        working-directory: ./docs
        run: source ../.venv/bin/activate && make html