python-package.yaml

name: Python package

on:
  push:
  pull_request:

permissions:
  contents: read

jobs:
  test:
    name: test
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.11", "3.12", "3.13"]
    services:
      postgres:
        image: postgres:17
        env:
          POSTGRES_PASSWORD: postgres
        options: >-
          --health-cmd pg_isready
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          - 5432:5432
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: 'true'
      - name: Wait for Postgres
        run: |
          for i in {1..30}; do
            pg_isready -h localhost -p 5432 -U postgres && exit 0
            sleep 1
          done
          exit 1
      - name: Initialize GiST extension
        env:
          PGPASSWORD: postgres
        run: |
          psql -h localhost -p 5432 -U postgres -d postgres \
            -c "CREATE EXTENSION IF NOT EXISTS btree_gist;"
      - name: Set up Python
        uses: actions/setup-python@v5
        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

      - name: Run tests
        run: uv run pytest
        env:
          ANYVLM_TEST_STORAGE_URI: postgresql://postgres:postgres@localhost:5432/postgres
          ANYVLM_ANYVAR_TEST_STORAGE_URI: postgresql://postgres:postgres@localhost:5432/postgres
          HANDOVER_TYPE_ID: "CUSTOM:GREGoR-NCH"
          HANDOVER_TYPE_LABEL: "GREGoR AnyVLM Reference"
          BEACON_HANDOVER_URL: https://variants.gregorconsortium.org/
          BEACON_NODE_ID: org.anyvlm.gregor
  lint:
    name: lint
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Setup Python
        uses: actions/setup-python@v5
        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
  precommit_hooks:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        cmd:
          - "end-of-file-fixer"
          - "trailing-whitespace"
          - "mixed-line-ending"
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python 3.12
        uses: actions/setup-python@v5
        with:
          python-version: 3.12

      - uses: pre-commit/action@v3.0.1
        with:
          extra_args: ${{ matrix.cmd }} --all-files
  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@v7
        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