Release prep: generate v1.12.0-rc1 against linkml main

[amc-corey-cox]

Release prep for v1.12.0-rc1 so linkml can vendor and test against it. Does not cut the release.

The committed artifacts are stale against meta.yaml (#270/#271 changed it without a regeneration), and they don't reproduce under the next linkml either — regenerating with main rather than 1.11.1 changes rdf/*.ttl (linkml#3641), a meta.py type, and adds a java/ tree. So this generates against main.

• tool.uv.sources pins linkml + linkml-runtime to 063d4665f. Dev-side only; the wheel still carries project.dependencies.
• Exact pins became floors — a main checkout reports 1.11.0.post365.dev0+063d4665, which can't satisfy ==1.11.1.
• java excluded from gen-project: javagen joined its defaults, and nothing can address the output (Format has no JAVA member) — 44 files that would also land in the linkml-runtime wheel via make update_model.
• metamodel_version → 1.12.0, plus full regeneration.

Two notes for review:

metamodel_version lands unevenly — meta.py gets 1.12.0 from meta.yaml, the other modules get 1.11.0 from linkml-runtime's vendored metamodel (still model 1.11.1-rc1). Resolves once linkml vendors this rc.

The ~26k-line diff is almost entirely timestamps and RDF/SQL ordering. Checked by graph comparison: SHACL is semantically identical bar the is_a change (5,135 property shapes, zero differences); sorted SQL leaves only the real changes. The content is #271 propagating — AnonymousClassExpression.is_a narrowing to ClassDefinition across every artifact.

Before final release: swap the pin and floors for the released versions, regenerate, confirm no change.

Verified: make gen-project, make test (8 passed, 5 skipped), pre-commit run --all-files clean.

[Copilot]

🔵 Needs a closer look

The regeneration appears to introduce a semantic/field-mapping change in JSON-LD output (e.g., class_uri not being preserved) that should be validated and/or corrected before approving a release-prep RC artifact set.

Pull request overview

Prepares the linkml-model repository for the v1.12.0-rc1 cycle by regenerating committed model artifacts against linkml main (to match what downstream LinkML will vendor/test), bumping the metamodel version, and adjusting generation/tooling config to avoid unwanted outputs.

Changes:

• Bump metamodel_version to 1.12.0 and regenerate generated Python / JSON-LD / GraphQL / RDF / ShEx artifacts accordingly.
• Adjust dependency constraints (and add uv git sources) to allow generating against a specific linkml commit while keeping published-wheel deps as PEP 508 requirements.
• Exclude java/ from gen-project output to prevent introducing unshippable/unused Java artifacts.

File summaries

File	Description
pyproject.toml	Loosens linkml/linkml-runtime requirements and adds tool.uv.sources pins for dev-time generation.
gen_project_config.yaml	Excludes java from gen-project output.
linkml_model/model/schema/meta.yaml	Bumps metamodel_version to 1.12.0 in the source metamodel schema.
linkml_model/meta.py	Regenerated Python metamodel; reflects version bump and schema propagation (e.g., AnonymousClassExpression.is_a narrowing, updated coercions).
linkml_model/validation.py	Regenerated (removes embedded generation timestamp).
linkml_model/units.py	Regenerated (removes embedded generation timestamp).
linkml_model/types.py	Regenerated (removes embedded generation timestamp).
linkml_model/mappings.py	Regenerated (removes embedded generation timestamp).
linkml_model/extensions.py	Regenerated (removes embedded generation timestamp).
linkml_model/datasets.py	Regenerated (removes embedded generation timestamp).
linkml_model/array.py	Regenerated (removes embedded generation timestamp).
linkml_model/annotations.py	Regenerated (removes embedded generation timestamp).
linkml_model/shex/meta.shex	Updates embedded metamodel_version header to 1.12.0.
linkml_model/graphql/meta.graphql	Updates embedded metamodel_version header and narrows AnonymousClassExpression.isA type.
linkml_model/jsonld/meta.jsonld	Regenerated JSON-LD representation of the metamodel (includes new slots/usages and ordering/field changes).
linkml_model/rdf/types.ttl	Regenerated RDF TTL for types schema (ordering/formatting changes).
linkml_model/rdf/types.model.ttl	Regenerated RDF TTL model variant for types schema.
linkml_model/rdf/mappings.ttl	Regenerated RDF TTL for mappings schema (ordering/formatting changes).
linkml_model/rdf/extensions.ttl	Regenerated RDF TTL for extensions schema (ordering/formatting changes).
linkml_model/rdf/extensions.model.ttl	Regenerated RDF TTL model variant for extensions schema.
linkml_model/rdf/annotations.ttl	Regenerated RDF TTL for annotations schema (ordering/formatting changes).
linkml_model/rdf/annotations.model.ttl	Regenerated RDF TTL model variant for annotations schema.

Review details

Suppressed comments (2)

linkml_model/jsonld/meta.jsonld:7571

• structured_alias in meta.yaml sets class_uri: skosxl:Label, but this regenerated JSON-LD class definition omits class_uri and only keeps skosxl:Label under exact_mappings. That changes the meaning from an assigned RDF class URI to an equivalence mapping; if intentional, the source schema should be updated accordingly, otherwise the generator should emit class_uri here.

      "name": "StructuredAlias",
      "definition_uri": "https://w3id.org/linkml/StructuredAlias",
      "description": "object that contains meta data about a synonym or alias including where it came from (source) and its scope (narrow, broad, etc.)",
      "from_schema": "https://w3id.org/linkml/meta",
      "exact_mappings": [
        "skosxl:Label"
      ],
      "mixins": [

linkml_model/jsonld/meta.jsonld:8841

• extensions.yaml defines AnyValue.class_uri: linkml:Any, but in the regenerated JSON-LD this information is not represented as class_uri (it only appears under exact_mappings). If class_uri is still part of the model, this is a lossy serialization; if it is being deprecated, consider updating the source schema so the semantics remain unambiguous.

      "name": "AnyValue",
      "definition_uri": "https://w3id.org/linkml/AnyValue",
      "from_schema": "https://w3id.org/linkml/extensions",
      "imported_from": "linkml:extensions",
      "exact_mappings": [
        "linkml:Any"
      ],
      "slot_usage": {},
      "@type": "ClassDefinition"
    },

• Files reviewed: 30/39 changed files
• Comments generated: 1
• Review effort level: Lite

---

💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.

[kevinschaper]

no surprises found, looks good!