[dependabot]

Bumps linkml from 1.11.1 to 1.12.0.

Release notes

Sourced from linkml's releases.

v1.12.0

LinkML 1.12.0 brings 155 pull requests from 28 contributors since v1.11.1, after two release candidates. It ships linkml-model v1.12.0 (#4085).

Upgrade notes

These changes can alter generated output or affect code that uses LinkML:

• Metamodel 1.12.0. The status metaslot is now a plain string, and anonymous_class_expression.is_a only accepts class definitions. Generated artifacts report metamodel_version: 1.12.0, so projects that commit generated files will see that line change. See the model release notes.
• An explicit class_uri is recorded as skos:exactMatch (exact_mappings), not skos:mappingRelation (mappings), in JSON-LD, RDF and merged YAML, matching what OWL already did. class_uri itself is unchanged (#2693, #4073).
• JSON Schema handles extra_slots and closed classes. extra_slots is now implemented (#2940), and classes without it stay closed (additionalProperties: false), as the metamodel specifies (#3612, #4021). Optional enum-valued slots now accept null (#3737).
• Enum permissible values are real enum members. MyEnum.ALIVE returns a singleton member of the enum, not a loose PermissibleValue, so identity, equality and hashing behave like a normal Python enum (#3597, #3505, #3593, #3596, #3683).
• Generated Python renames slots that clash with Python keywords by appending an underscore (#3317).
• Generators warn about mixed SchemaLoader/SchemaView namespace access with a DeprecationWarning (#3796).

Known issue

• gen-owl no longer emits element-level status values (#4048). Schemas that set status (e.g. status: bibo:status/published) lose those annotations from OWL output. A fix is ready if this causes problems (linkml-model#282); please comment on #4048 if it affects you.

Since the release candidates

If you tested rc1 or rc2: gen-jsonld keeps class_uri and no longer adds class self-mappings (#4073), accepts relative schema paths like dist/schema.yaml (#4074), and --use-curies keeps identifier keys valid JSON-LD (#4072). The bundled model is now the final v1.12.0 (#4085).

New generators

• OpenAPI (gen-openapi), including OpenAPI 3.1 and configurable output (#3300, #3511, #3512, #3765, #3807, #3963, #3974)
• BigQuery schemas with ARRAY, STRUCT, PARTITION BY and CLUSTER BY support (#3585)

Reproducible output

• RDF output is canonicalised with RDFC-1.0 via pyoxigraph, so it's stable across runs and machines (#3407, #3524, #3703). That includes SHACL's sh:ignoredProperties (#3518).
• --no-generation-date leaves generation timestamps out, for byte-reproducible artifacts (#3696).

Generator improvements

JSON Schema

• Emits examples (#3378, #3500), readOnly for readonly slots (#3537), and LinkML arrays (#3622)
• --include-null / --no-include-null (#3715) and --use-curies for CURIE-based names and $refs (#2416, #3982). Identifiers keep their slot name, as the JSON-LD context requires (#4072)
• Fixes for duplicate subschemas (#3617), boolean-constraint defaults (#3619), the URI form of uriorcurie (#3843), missing required (#3398), and faster validation-context handling (#3430)

SHACL

• sh:sparql constraints generated from LinkML rules (#3451)
• --message-template for sh:message (#3450)
• Zero-cardinality constraints (#3473) and sh:node for native class names (#3821)

OWL, RDF and JSON-LD

• --default-language for language-tagged literals (#3449), and @type: @vocab coercion for eligible enums in contexts (#3447)
• Multiple JSON-LD contexts (#2602), unresolvable per-module contexts dropped before parsing (#3641), and uncompactable URI type designators preserved (#3839)
• OWL: imports resolved before URI expansion (#3753), correct predicate URIs for schemas with subschemas (#3750), enum-range slots with boolean expressions (#3468), declarations for metamodel grouping classes (#3681), and warnings for covering-axiom edge cases (#3309)

Python and Pydantic

... (truncated)

Commits

• 6ffd218 Vendor linkml-model 1.12.0 (#4085)
• 68e7e3d fix(javagen): report a missing --template-file as a usage error (#4076)
• dc38dec Keep identifier keys out of --use-curies
• 01ea592 Fix gen-jsonld with a relative schema path
• 79ad3ac Keep class_uri alongside its skos:exactMatch
• b2ebb17 feat(generator): shared config-file overlay for all generators (part 1) (#3973)
• 6f37745 Merge pull request #4053 from linkml/clean-up-issue-templates
• 3496e7c Merge branch 'main' into clean-up-issue-templates
• 5aa87ad build(deps-dev): bump gql from 4.0.0 to 4.4.0
• ddece8d build(deps): bump platformdirs from 4.11.13 to 4.12.1
• Additional commits viewable in compare view

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[dependabot]

Superseded by #1844.