[dependabot]

Bumps linkml from 1.11.1 to 1.12.1.

Release notes

Sourced from linkml's releases.

v1.12.1

A small point release that fixes install problems in 1.12.0 and one JSON Schema bug.

Install fixes

1.12.0 could be installed alongside dependency versions it doesn't work with. Both problems show up as import errors.

• linkml-runtime must now be ≥ 1.12.0. linkml 1.12 uses linkml_runtime.utils.rdf_canonicalize, which first shipped in linkml-runtime 1.12.0. With an older runtime, from linkml.validator import validate failed with ModuleNotFoundError. (#4119, fixes #4120)
• click must now be ≥ 8.3.3. With click 8.2.0–8.3.2, importing any generator failed with an ImportError on ParameterSource. (#4117)

Generator fixes

• gen-json-schema: a slot whose range is a type with no base now gets "type": "string". Before, the property was emitted as {} (1.12.0) or crashed the generator (1.11.1). (#4079, fixes #4078)
• gen-openapi:
  • Templates can now override the annotations on generated schemas. (#3961)
  • Schemas referenced under items, oneOf and allOf are now included. (#4098)

Documentation

• --use-curies is now documented for gen-json-schema and gen-jsonld-context. It explains that identifier slots keep their slot-name key, which maps to @id. (#4080)

Full Changelog: linkml/linkml@v1.12.0...v1.12.1

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)

... (truncated)

Commits

• bd10206 fix(jsonschema): type without a base gets a type
• c558879 Fix add use curies documentation
• 14b2871 fix(deps): require click >= 8.3.3
• d54d355 fix(deps): require linkml-runtime >= 1.12.0
• b64c36c Update office-hours.md
• 73530c1 Update metamodel test fixtures from linkml-model
• 8ded63c build(deps): bump platformdirs from 4.12.1 to 4.12.2 in the patch-updates gro...
• dcaf6a0 fix(openapigen): seed schemas referenced under items, oneOf and allOf
• 615ac58 feat(openapigen): let templates override generated schema annotations (#3961)
• 6ffd218 Vendor linkml-model 1.12.0 (#4085)
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)