tests.yml

# Run lint, format-check, and tests on every push to main and on every PR.
#
# The workflow `name` is "tests" because that's what the README badge
# displays — readers (especially the biology audience) parse "tests
# passing" more readily than "CI passing". Behaviorally, this workflow
# also runs ruff and black (i.e. it's the project's full CI gate, not
# only tests); the slight label overload is intentional.
#
# Local equivalent: `scripts/check.sh` (which expects a local .venv;
# this workflow uses the runner's python directly so it doesn't depend
# on that layout).

name: tests

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  workflow_dispatch:

permissions:
  contents: read

# Cancel in-flight runs on the same ref when a new commit lands; PRs
# rebased many times in quick succession don't queue up wasted minutes.
concurrency:
  group: ci-${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

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

      - uses: actions/setup-python@v6
        with:
          python-version: "3.13"

      - name: Install package + dev extras
        run: |
          python -m pip install --upgrade pip
          pip install -e ".[dev]"

      - name: Fetch upstream Kikawa Auspice JSONs
        # Real-data tests in tests/test_real_data.py and tests/test_cli.py
        # skip cleanly when these files are absent. We want them to
        # actually run in CI, so fetch the upstream JSONs first.
        run: python examples/fetch_auspice_data.py

      - name: Build Kikawa titer chart specs
        # tests/test_real_data.py also reads the saved Vega-Lite specs
        # produced by this script. Ditto for tests/test_cli.py end-to-end.
        run: python examples/flu-seqneut-2025to2026_titer_charts.py

      - name: Lint (ruff)
        run: ruff check .

      - name: Format check (black)
        run: black --check .

      - name: Tests (pytest)
        run: pytest tests/