Pin linkml-map to main and fix runtime 1.11 fallout

[amc-corey-cox]

Prerequisite for the EML importer (#208) and adjacent adapter work that needs unreleased linkml-map features: dot-path `populated_from`, safe-builtin functions, `dictionary_key`, strict expression mode.

Pinning surfaces fallout from the linkml-runtime 1.10 → 1.11 transition:

• `source_schema` / `target_schema` in trans-specs must be `SchemaReference` dicts (`{name: }`), not bare strings — three adapter specs updated.
• `ClassDefinition.attributes` no longer mutates via a local alias after `add_class` (pydantic v2 copy semantics); XSD importer swaps the order so attributes are populated before registration.
• `SlotDefinition.alias` returns `None` when not explicitly set (used to fall back to `slot.name`); `instance_extractor` now does the fallback inline.
• 1.11 `URIorCURIE` validation is stricter; `test_infer_prefix` had used a prefix without trailing separator that expanded to a malformed URI — test data fixed.

All 160 tests pass. Revert the pin (back to a version constraint) when linkml-map 0.5.3+ releases.

Test plan

• `pytest tests/` green (160 passed, 3 skipped)

[Copilot]

Pull request overview

This PR updates dependency resolution to use unreleased linkml-map behavior and adjusts affected schema/adapter/importer code for linkml-runtime 1.11 compatibility.

Changes:

• Pins linkml-map via uv source and refreshes locked LinkML-related dependencies.
• Updates adapter transform specs to use SchemaReference-style source_schema / target_schema.
• Fixes runtime fallout in XSD importing, instance extraction, and an RDFS prefix test fixture.

Reviewed changes

Copilot reviewed 7 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pyproject.toml	Adds uv source override for linkml-map and changes dependency declaration.
uv.lock	Refreshes locked dependency versions and records git-sourced linkml-map.
schema_automator/adapters/dbgap/dbgap_to_dd.transform.yaml	Converts schema references to mapping form.
schema_automator/adapters/frictionless/dd_to_frictionless.transform.yaml	Converts schema references to mapping form.
schema_automator/adapters/frictionless/frictionless_to_dd.transform.yaml	Converts schema references to mapping form.
schema_automator/importers/xsd_import_engine.py	Registers generated classes after attributes are populated.
schema_automator/utils/instance_extractor.py	Falls back from missing slot alias to slot name.
tests/test_importers/test_rdfs_importer.py	Updates prefix fixture and expected schema id with trailing slash.

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[amc-corey-cox]

Correct — [tool.uv.sources] is uv-only and the wheel's Requires-Dist is unconstrained. Not solving in this PR: we're deliberately holding this branch (and #212) until linkml-map 0.5.3 releases, at which point the pin reverts to a regular version constraint. Switching to a PEP 508 direct-URL form (linkml-map @ git+...) would propagate to pip but block any release from this state (PyPI rejects direct-URL deps), which is an even worse interim. Leaving open as a tracked concern; we expect this to be naturally resolved when 0.5.3 ships and we drop the pin.

[amc-corey-cox]

Acknowledged but by design — this PR is the temporary dev infrastructure noted in the PR body ("Revert the pin (back to a version constraint) when linkml-map 0.5.3+ releases"). The [tool.uv.sources] directive lets uv sync resolve to linkml-map main for local/CI work depending on unreleased features. Once linkml-map 0.5.3 hits PyPI, this becomes a normal >= 0.5.3 constraint in [project.dependencies] that the published wheel will carry. Leaving this thread open as a visible reminder to make that swap before merge.