chore(typing): add return-type annotations + enable disallow_incomplete_defs

[haoyu-haoyu]

Summary

Adds return-type annotations to 29 functions across 11 files in scispacy/, and tightens mypy to catch this class of bug going forward.

Changes

• 29 return-type annotations — all inferred from reading each function body (details in the diff).
• pyproject.toml — added [tool.mypy] disallow_incomplete_defs = true. Rationale: the existing mypy invocation (mypy scispacy --ignore-missing-imports) did not flag partially-annotated functions (typed params + missing return type), which is how the 29 cases slipped through. disallow_incomplete_defs catches this without the broader fallout of disallow_untyped_defs (which would require annotating every function at once, including fully-unannotated legacy code).

Bug caught by the tighter config

scispacy/train_utils.py:evaluate_ner declared -> PerClassScorer but actually returns scorer.get_metric(), i.e. Dict[str, float]. Fixed the return type to match reality and added Collection[Tuple[str, Dict[str, Any]]] for the previously-untyped eval_data param. The only in-repo caller (scripts/evaluate_ner.py:38) ignores the return value, so no behavioral break.

Deliberately out of scope

• disallow_untyped_defs — would surface dozens of unrelated unannotated functions; not this PR.

Test plan

• bash scripts/mypy.sh → Success: no issues found in 20 source files
• black scispacy --check --line-length 88 → no changes
• flake8 scispacy → 0 errors
• pytest tests/ (excluding tests needing en_core_sci_sm / nmslib locally): 26 passed