Bump click and linkml floors for click 8.3 compat

[amc-corey-cox]

Closes #218.

Summary

• Bumps click>=8.2 (which removed CliRunner(mix_stderr=...) in favour of always-separate stdout/stderr).
• Bumps linkml>=1.11.0rc3 and linkml-runtime>=1.11.0rc3 (linkml 1.11 itself requires click>=8.2, so the floors move together).
• Drops the now-removed mix_stderr=False kwarg from the four CliRunner fixtures.

Why the data-model change is in scope

linkml 1.11rc3 tightens validate-spec's structural validation, which surfaced a latent inconsistency in linkml-map's data model:

• The runtime treats ClassDerivation.is_a / mixins as string name references (_class_derivation_ancestors in transformer/transformer.py calls _find_class_derivation_by_name(parent); schema_mapper.py assigns cd.is_a straight into ClassDefinition.is_a which is a string slot).
• But the generated JSON Schema for is_a was anyOf: [{$ref: ElementDerivation}, null] — no string variant — because ElementDerivation had no identifier: true slot. linkml 1.10 didn't run this structural check; 1.11rc3 does, and rejects any string is_a: value.

Switching ElementDerivation.name from key: true to identifier: true matches linkml's own meta.yaml convention for Element (where name: identifier: true is the canonical pattern for schema elements) and lets the JSON Schema generator emit the string-reference variant. This brings the validator in line with how the runtime actually uses these slots.

Regenerated transformer_model.py via make. The only diff in the regenerated pydantic file is the metamodel_version bump (1.7.0 → 1.11.0) — no class-shape changes.

Other changes

• tests/input/examples/personinfo_basic/transform/personinfo-to-agent.transform.yaml: added a description: to the previously empty Entity: derivation (cosmetic; not required after the data-model fix).
• AGENTS.md: removed stale just references — the repo doesn't use just, only uv run … and make targets.

Lock file

The lock is refreshed against the prereleases (uv lock --upgrade-package linkml --upgrade-package linkml-runtime --upgrade-package click --prerelease=allow) so CI passes now. Plan: sit on this PR until linkml 1.11.0 GA, then uv lock again to move from rc3 → 1.11.0 final before merging.

Test plan

• uv run pytest — 794 passed, 4 skipped locally
• uv run pytest --doctest-modules src/linkml_map/ — 18 passed locally
• uv run ruff check . and uv run ruff format --check . — clean locally
• After linkml 1.11.0 ships: refresh lock to final release, re-run CI before merging

[Copilot]

Pull request overview

Updates dependency minimums and related fixtures to stay compatible with newer click (8.3+) and linkml (1.11 validation behavior), and adjusts the LinkML-map transformer datamodel so validate-spec accepts the string-reference form the runtime already uses.

Changes:

• Bump dependency floors (click>=8.2, linkml>=1.11.0rc3, linkml-runtime>=1.11.0rc3) and refresh uv.lock accordingly.
• Remove the now-unsupported mix_stderr=False kwarg from CliRunner fixtures in CLI tests.
• Update the transformer LinkML schema (ElementDerivation.name) to be an identifier, and bump the generated model’s metamodel_version.

Reviewed changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pyproject.toml	Raises minimum dependency versions for click/linkml/linkml-runtime.
uv.lock	Refreshes the resolved dependency set to include the new minimums/RCs.
tests/test_cli/test_cli.py	Drops mix_stderr=False from CliRunner() fixture.
tests/test_cli/test_cli_validate.py	Drops mix_stderr=False from CliRunner() fixture.
tests/test_cli/test_cli_multi_spec.py	Drops mix_stderr=False from CliRunner() fixture.
tests/test_cli/test_cli_tabular.py	Drops mix_stderr=False from CliRunner() fixture.
src/linkml_map/datamodel/transformer_model.yaml	Changes ElementDerivation.name from key: true to identifier: true for LinkML 1.11 structural validation compatibility.
src/linkml_map/datamodel/transformer_model.py	Regenerated; bumps metamodel_version to 1.11.0.
tests/input/examples/personinfo_basic/transform/personinfo-to-agent.transform.yaml	Adds a description to the Entity derivation.
AGENTS.md	Updates repo workflow notes to uv run … / make (removes stale just references).

[Copilot]

Pull request overview

Copilot reviewed 9 out of 10 changed files in this pull request and generated 2 comments.

[amc-corey-cox]

Final state

• Floors: linkml>=1.11.0, linkml-runtime>=1.11.0 (GA, not rc3) and click>=8.2 — bumped in 7b4c0d5.
• Lock: refreshed to linkml 1.11.0 / linkml-runtime 1.11.0 final.
• Main caught up: merged main in 6d29212, picking up f2363c3, 4b449ad, c2584ec. PR diff against main is unchanged in scope.
• Test plan results:
  • uv run pytest — 821 passed, 4 skipped
  • uv run pytest --doctest-modules src/linkml_map/ — 18 passed
  • uv run ruff check . and uv run ruff format --check . — clean
  • CI passing across the 3.10–3.13 matrix

Description body intentionally preserved as written for history; this comment reflects the shipped state.