v11.19.0

What's Changed

• Guard against hand-written docs in build output directory by @turbomam in #2965
• Restore ontology-governance-current-state.md to src/docs/ by @turbomam in #2964
• Add ontology registry counts tooling (2/3: supporting data) by @turbomam in #2916
• Add OLS4 embeddings search for ontology term discovery (1/3: retrieval baseline) by @turbomam in #2909
• Add LinkML-ecosystem alignment comparison and review tooling (3/3: evaluation) by @turbomam in #2910
• Cap click<8.2 and drop linkml-store[llm] to unblock linkml 1.10.0 by @turbomam in #2986
• Raw data file mappings for missing 191 composite NEON soil samples by @sujaypatil96 in #2972
• Add exact_mapping IAO:0000030 to InformationObject by @turbomam in #2993
• Add exact_mapping BFO:0000040 to MaterialEntity by @turbomam in #2992
• Add descriptions to MaterialEntity and PlannedProcess by @turbomam in #2994
• Edit Biosample.name slot description to say it must be unique within a study by @eecavanna in #2988
• Bump lxml from 6.0.4 to 6.1.0 by @dependabot[bot] in #3006
• Add reporting-only test for slot constraint/range compatibility by @turbomam in #3011
• Bump pytest from 9.0.2 to 9.0.3 by @turbomam in #3012
• Fix bare except and reused loop variable (CodeQL findings) by @turbomam in #3013
• Add NcbiTaxon class (is_a OntologyClass) and classified_as slot by @turbomam in #2975
• Add new chemical entity permissible values for material processing metadata by @bmeluch in #3019
• deps: bump lxml 6.0.2 → 6.1.0 in poetry.lock (Dependabot #40) by @turbomam in #3039
• Fix broken ontology links in samp_collec_device slot description by @sujaypatil96 in #3005
• Ignore AI coding tool artifacts and ruff cache by @turbomam in #3045
• Fix grammar in calibration_object slot description by @turbomam in #3046
• Fix broken/inaccessible ontology URLs in 3 inherited MIxS slot descriptions by @turbomam in #3047
• Merge of 11.18.1 hotfix to main by @aclum in #3048
• Remove uv cruft and fix packaging issues by @pkalita-lbl in #3060

Full Changelog: v11.18.1...v11.19.0