Testing & QA¶

Keep regressions away from your clinical workflows by leaning on the existing test suite and smoke runners. This page summarizes what already exists so you can extend it confidently.

Test taxonomy¶

Marker	Location	Purpose
`unit` (default)	`tests/unit/**`	Fast validation of model registry helpers, config utilities, CLI parser, etc.
`integration`	opt-in	Exercises multi-component flows (e.g., pipeline creation + formatter).
`slow`	opt-in	Runs heavier GLiNER or Hugging Face calls; disabled unless you pass `-m slow`.

Configure these markers via pytest.ini entries in pyproject.toml.

Running the suite¶

uv pip install ".[dev,hf]"
pytest                      # fast unit/integration mix
pytest -m "not slow"        # default behaviour
pytest -m slow              # only long-running cases

For zero-shot smoke checks:

uv pip install ".[gliner]"
python scripts/smoke_gliner.py --limit 2 --threshold 0.4 --adapter

tests/run-tests.sh stitches together typical workflows (lint, unit tests, smoke scripts). Use it as the baseline for CI.

Docs & CLI checks¶

Add uv run mkdocs build --strict to your CI to fail on missing nav entries, duplicate anchors, or broken markdown.
Combine CLI runs with fixtures to ensure packaging and extras stay in sync:

openmed analyze --model disease_detection_superclinical --text "QA ping" --output-format json >/tmp/result.json
jq .entities[0] /tmp/result.json

Coverage ideas¶

When adding new features, consider tests for:

Model registry entries (ensuring new keys appear in list_model_categories).
CLI options (e.g., new openmed analyze flag).
Formatter behaviours (HTML/CSS attributes, metadata propagation).
Zero-shot adapters (BIO/BILOU conversions).

Following this checklist keeps the docs accurate and the automation pipelines green.