python-tests.yaml

name: Python Tests

on:
  merge_group:
  pull_request:
    types: [opened, reopened, synchronize]
    branches:
      - 'main'
  push:
    branches:
      - 'main'
  workflow_dispatch: {}

jobs:
  pytest:
    if: github.repository != 'milaboratory/platforma-sequence-properties'
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: software
    steps:
      - uses: actions/checkout@v4

      - uses: astral-sh/setup-uv@v5
        with:
          version: "0.11.16"
          enable-cache: true
          cache-dependency-glob: software/uv.lock

      - name: Install dependencies
        run: uv sync --locked

      - name: Ruff check
        run: uv run ruff check

      - name: Ruff format check
        run: uv run ruff format --check

      - name: Run pytest
        # Exclude @slow (the perf benchmark) from the gate — it asserts a
        # wall-clock budget that flakes on shared runners. Run it explicitly
        # with `uv run pytest -m slow`.
        run: uv run pytest -m "not slow"

  requirements-sync:
    # src/requirements.txt is generated from pyproject.toml (the single source of
    # truth) and is what pl-pkg builds from. This job fails if the committed file
    # has drifted from pyproject — e.g. someone changed a dependency but forgot to
    # regenerate. Fix locally with `pnpm deps:export` (see software/package.json).
    if: github.repository != 'milaboratory/platforma-sequence-properties'
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: software
    steps:
      - uses: actions/checkout@v4

      - uses: astral-sh/setup-uv@v5
        with:
          version: "0.11.16"
          enable-cache: true
          cache-dependency-glob: software/uv.lock

      - name: Regenerate requirements.txt from pyproject.toml
        # Same script `pnpm deps:export` runs locally — single source of truth.
        run: bash scripts/deps-export.sh

      - name: Verify requirements.txt is in sync with pyproject.toml
        run: |
          if ! git diff --exit-code -- src/requirements.txt; then
            echo ""
            echo "::error::src/requirements.txt is out of sync with pyproject.toml"
            echo "Dependencies are defined in software/pyproject.toml; src/requirements.txt is generated."
            echo "Resolve locally with:"
            echo "    cd software && pnpm deps:export"
            echo "then commit the updated src/requirements.txt."
            exit 1
          fi
          echo "src/requirements.txt is in sync with pyproject.toml."