Restore test collection and lint cleanliness after the Task B merge

[duckyquang]

Summary

Main stopped collecting tests for anyone without medspacy — tests/test_valvular_probes.py imports scripts/extract_valvular_labels.py at module scope, which imports medspacy and builds the full NER pipeline on import, and neither medspacy nor the extraction stack is a declared dependency. The import is now guarded, so only the one NER test (test_clinical_ner_extraction_negation_and_severity) skips when medspacy is missing; the other valvular tests keep running everywhere.

While in there I cleared the lint debt the Task B merge left on main: 55 ruff errors and 10 unformatted files, which means make lint / pre-commit was red for everyone. Mechanics: ruff check --fix + ruff format across the valvular files, # noqa: E402 on the deliberately-late imports (they sit after load_dotenv()/logging setup on purpose), and two unused local assignments removed (y_dict_va, confidence_dist — pure computations, no side effects).

Result

132 passed, 1 skipped (the NER test, on my machine without medspacy); ruff check and ruff format --check both fully clean. Real run on my Mac with the repo venv.

Notes

• @turkalpmd the reformat touches your Task B files — it's the repo's own ruff config doing the work, and the only behavioral edits are the two dead assignments. Can you confirm the NER test still runs green on your medspacy setup? I can't exercise that path locally.
• medspacy / the BigQuery client stack stay undeclared — maybe worth a task-b optional-dependencies group in pyproject.toml as a follow-up, so the skip behavior is documented rather than accidental.

[sebasmos]

Read the diff and verified both behavioral claims against the code: the import guard and skip are scoped to exactly one test, the two removed assignments are confirmed dead code. Real run: 132 passed, 1 skipped, ruff clean. APPROVE.