Strict mode for expression evaluation (#213 runtime)

[amc-corey-cox]

Closes #213 (runtime side; the validate-spec side is closed by #231).

Summary

Adds a strict flag on the Transformer dataclass. With strict=False (default), an expression that references a name with no binding emits a warning and returns None — backward-compatible with today's silent-null behavior, but no longer entirely silent. With strict=True, the same condition raises TransformationError, surfacing typos, stale references, and wrong-table accesses that would otherwise produce silent nulls in transform output.

The trick is distinguishing two cases that today both produce None:

1. Field exists in source schema, value is absent on this row → None is correct (SQL NULL semantics).
2. Field does not exist in source schema at all → None masks a bug.

Bindings._collect_schema_slots() now pre-computes case 1 from SchemaView.class_induced_slots(source_type). Bindings.__getitem__ returns None for case 1 and raises KeyError (→ NameNotDefined → TransformationError in strict, warning + None in non-strict) for case 2.

Design choices

• Strict mode is a flag, not the default. Default-to-strict is a separate conversation deferred to follow-up. The flag is on the base Transformer dataclass alongside unrestricted_eval so all transformer subclasses inherit it.
• Warnings dedupe per unbound name across rows. The shared set lives on ObjectTransformer._warned_unbound_names and threads through eval_expr_with_mapping(..., warned_unbound=...). Without this, a typo in a spec used against a 10M-row dataset would log 10M lines for one underlying problem.
• Explicit-join target class slots are intentionally NOT added to the schema-slot set. Explicit joins are accessed via {Alias.column} (dotted), not bare. A bare {score} on a source class that doesn't declare score is almost certainly a typo for the dotted form. Documented in _collect_schema_slots's docstring.
• Implicit-join column resolution is out of scope. Belongs in the Sparse implicit-join semantics: nested object on no-match + data-dependent ambiguity enforcement #217 follow-up, where the auto-join runtime semantics live anyway. Strict mode with implicit-join specs may falsely reject slots that would be auto-resolved at runtime; this is a known gap that resolves cleanly when Sparse implicit-join semantics: nested object on no-match + data-dependent ambiguity enforcement #217 lands.
• unrestricted_eval fallback path is not covered by strict mode. When the restricted evaluator raises and asteval takes over, asteval has its own (also-permissive) handling. Marginal case — flagging here as a known limitation.

CLI

linkml-map map-data --strict/--no-strict (default off). Falls through map_data's **kwargs into ObjectTransformer(**kwargs) — same pattern as --unrestricted-eval.

Test plan

• uv run pytest tests/ — 819 passed, 4 skipped (was 804 passed before this PR; +15 new tests)
• uv run pytest --doctest-modules src/linkml_map/ — 18 passed
• uv run ruff check . + uv run ruff format --check . — clean
• New tests:
  • tests/test_utils/test_eval_utils.py — 4 direct evaluator tests (default returns None, default logs warning, strict raises, bound-None-in-strict still returns None)
  • tests/test_transformer/test_expr_strict_mode.py — 8 integration tests via ObjectTransformer.map_object covering typo / valid-slot / null-value / absent-from-row scenarios, parameterized over strict=True/False, plus a dedup-across-rows test
  • tests/test_cli/test_cli.py — 2 CLI tests (--strict makes a typo'd spec exit non-zero; default exits 0)

Coordination

This branch is off main at 5ff8b00. Independent of PR #231 (validate-spec side of the silent-null defense arc) — no shared files, no merge order requirement.

[Copilot]

Pull request overview

Adds an opt-in “strict mode” to LinkML expression evaluation so that typos / unbound variable references can be surfaced as errors (instead of silently propagating None), while preserving backward-compatible non-strict behavior (now with deduped warnings).

Changes:

• Introduce strict flag on Transformer / ObjectTransformer and thread it into expression evaluation.
• Make binding lookup schema-aware so “declared slot but missing on this row” returns None, while “not a schema slot” becomes unbound (→ warn/raise depending on strictness).
• Add CLI --strict/--no-strict and new unit/integration/CLI tests for strict-mode behavior and warning deduplication.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/linkml_map/utils/eval_utils.py	Adds strict-mode behavior and warning dedupe support to the evaluator when encountering unbound names.
src/linkml_map/transformer/transformer.py	Adds strict configuration flag to the base Transformer dataclass.
src/linkml_map/transformer/object_transformer.py	Adds schema-slot precomputation to Bindings, introduces per-transformer warning dedupe set, and passes strict/dedupe into expression evaluation.
src/linkml_map/cli/cli.py	Adds map-data --strict/--no-strict option to enable strict-mode at runtime via CLI.
tests/test_utils/test_eval_utils.py	Adds unit tests validating strict vs non-strict behavior for unbound vs bound-None names.
tests/test_transformer/test_expr_strict_mode.py	Adds integration tests for strict-mode behavior through ObjectTransformer.map_object, including deduped warnings across rows.
tests/test_cli/test_cli.py	Adds CLI tests verifying --strict fails on typos and default mode remains backward-compatible.