Deprecate object_derivations in favor of slot-level class_derivations

[amc-corey-cox]

Summary

• Add class_derivations to SlotDerivation as the direct replacement for object_derivations
• Normalization flattens object_derivations → class_derivations with deprecation warning; errors if both present
• Nested class_derivations inherit populated_from from their parent when unspecified, eliminating redundant source declarations in deeply nested specs (e.g., MeasurementObservationSet → MeasurementObservation → Quantity)
• Remove object_derivations from the transformer execution path — only class_derivations is checked at runtime

Before / After

# Before (object_derivations):
slot_derivations:
  conditions:
    object_derivations:
      - class_derivations:
          Condition:
            populated_from: Person
            slot_derivations: ...

# After (class_derivations with inherited populated_from):
slot_derivations:
  conditions:
    class_derivations:
      - Condition:
          slot_derivations: ...  # inherits populated_from from parent

Test plan

• New: test_nested_class_derivations — verifies slot-level class_derivations
• New: test_nested_class_derivations_inherit_populated_from — verifies populated_from inheritance
• New: test_object_derivations_backward_compat — old specs still work via normalization
• New: test_object_derivations_and_class_derivations_conflict — errors when both present
• Updated: test_object_derivations_emits_deprecation_warning — warning now fires during normalization
• All 589 tests pass (534 unit + 55 compliance)
• Ruff clean

Closes #112

[Copilot]

Pull request overview

This PR deprecates object_derivations in favor of slot-level, list-based class_derivations, shifting both normalization and runtime execution to the new construct while preserving backward compatibility via normalization.

Changes:

• Add SlotDerivation.class_derivations (list-based) as the runtime-supported mechanism for nested object construction.
• Normalize legacy object_derivations into class_derivations with a deprecation warning, and add populated_from inheritance for nested entries.
• Update tests, inference behavior, datamodel schema, and CLI help text to match the new approach.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/test_transformer/test_object_transformer.py	Adds coverage for slot-level list-based class_derivations, inheritance of populated_from, and backward-compat normalization from object_derivations.
tests/test_deprecations.py	Moves the object_derivations warning expectation to normalization time and adds a conflict test for both fields on the same slot.
src/linkml_map/transformer/transformer.py	Implements recursive normalization: flattens object_derivations → class_derivations, expands compact YAML keys, and supports populated_from inheritance.
src/linkml_map/transformer/object_transformer.py	Removes runtime handling of object_derivations and derives nested objects solely from slot_derivation.class_derivations.
src/linkml_map/inference/inference.py	Stops emitting runtime deprecation warnings for object_derivations and updates inference skip logic to key off class_derivations.
src/linkml_map/datamodel/transformer_model.yaml	Adds class_derivations to SlotDerivation and keeps object_derivations marked deprecated.
src/linkml_map/datamodel/transformer_model.py	Regenerates/updates the Python datamodel to include SlotDerivation.class_derivations.
src/linkml_map/cli/cli.py	Updates CLI help text to remove the object_derivations-specific requirement wording for --target-schema.