chore(deps): bump biolink-model to 4.4.5 and drop absorbed class-field grants - #209
Merged
Merged
Conversation
…d grants The biolink-model 4.4.5 mixin consolidation attached the disease/phenotype qualifier stack to the pinned EntityToDiseaseAssociation / EntityToPhenotypicFeatureAssociation classes, renamed FDA_regulatory_approvals to the canonical regulatory_approvals on them, and added sex_qualifier to the phenotypic-feature side. The CLASS_FIELD_OVERRIDES tripwire fired exactly as designed: the grants for anatomical_context_qualifier, disease_context_qualifier, frequency_qualifier, and regulatory_approvals (both classes) plus sex_qualifier on EntityToPhenotypicFeatureAssociation are absorbed and removed. The remaining deliberate grants are population_context_qualifier and temporal_context_qualifier on both classes plus sex_qualifier on EntityToDiseaseAssociation. One behavioral consequence of absorption: prune_to_class now coerces natively declared multivalued slots (regulatory_approvals, anatomical_context_qualifier) on the pinned classes, so kept values wrap into lists where the grant used to pass them through verbatim. Known upstream quirk: the PyPI 4.4.5 wheel still carries a schema whose version string reads 4.4.4 (the v4.4.5 tag source says 4.4.5), so BIOLINK_VERSION keeps reporting 4.4.4 until the next upstream release. Note: the pin is bumped in pyproject.toml and uv.lock; versioned release cut left to the usual release flow.
|
Important
This repository does not receive automatic reviews because it has fewer than 10 stars. ⚙️ Run configurationConfiguration used: defaults Review profile: CHILL Plan: Advanced Run ID:
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
Rust 1.99.0 turned needless_borrows_for_generic_args on by default and CI denies warnings, so the five .map_err(&validation_ctx) calls in extract_validate_rename fail the rust job (main will hit the same on its next CI run). Passing validation_ctx by value is behavior-preserving; cargo fmt, clippy -D warnings, and the full cargo test suite pass under 1.99.0.
SkyeAv
added a commit
that referenced
this pull request
Oct 1, 2026
Cut 19.5.1 and bump the package version in pyproject.toml, CITATION.cff, and uv.lock. Patch: docs-only surface refresh plus a behavior-preserving dependency bump. biolink-model 4.4.5 absorbs the dropped CLASS_FIELD_OVERRIDES grants upstream (the effective field set on the pinned EntityToDiseaseAssociation / EntityToPhenotypicFeatureAssociation classes is unchanged) and the Rust layer passes validation_ctx by value to satisfy Rust 1.99's needless_borrows_for_generic_args lint (#209). Documentation gains a statement of need and audience, a Getting help pathway, experimental labels on the agent/optimize/distill surfaces, runnable fullmap prerequisites in the tutorial, a three-method installation guide, and plain-ASCII prose (#205); CODE_OF_CONDUCT.md ships Contributor Covenant 2.1 with CITATION.cff maintainer emails as enforcement contacts (#206); CITATION.cff gains verified ORCIDs for all three authors and a factual abstract (#207). Changelog: - Versioned the release as 19.5.1 dated 2026-10-01; added Changed entries for #205, #206, #207, and #209 with PR links. Docs: none needed here; the release changelog section is the docs update. Testing: - make check -> exit 0: ruff check/format clean, pyright clean, pytest 1674 passed / 52 skipped in 29.33s, cargo test 156 passed / 0 failed (127 + 11 + 17 + 1 across 5 suites), cargo clippy -D warnings clean
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Bumps the pinned
biolink-modeldependency from 4.4.4 to 4.4.5 and lets the model absorb theCLASS_FIELD_OVERRIDESgrants it now declares natively.Dependency bump
pyproject.tomlmovesbiolink-model>=4.4.4->>=4.4.5;uv.lockrelocked viauv lock --upgrade-package biolink-model(samelinkml-runtime==1.11.1pin, so no transitive churn).tests/test_biolink.pyare the designed instrument for this update.Absorbed grants
regulatory_approvalsrename (#1814), and the phenotypic-featuresex_qualifierattachment (#1817) made most of the original grant stack native toEntityToDiseaseAssociation/EntityToPhenotypicFeatureAssociation.anatomical_context_qualifier,disease_context_qualifier,frequency_qualifier, andregulatory_approvalson both pinned classes, plussex_qualifieronEntityToPhenotypicFeatureAssociation.population_context_qualifierandtemporal_context_qualifieron both classes, plussex_qualifieronEntityToDiseaseAssociationonly.tests/test_biolink.py::test_validate_record_tolerates_class_field_override_grantsnow probespopulation_context_qualifier; aregulatory_approvalsprobe would pass natively and exercise nothing.prune_to_classcoerces natively declared multivalued slots, so keptregulatory_approvals/anatomical_context_qualifiervalues now wrap into lists on the pinned classes where the grant used to pass them through verbatim.Docs
docs/configuration/table.md: the allow-list,category_override, andsplit_bysections now describe which qualifiers are native since 4.4.5 and which remain granted.Testing
make check:ruff check/ruff format --checkclean,pyright->0 errors, 0 warnings,pytest -q->1674 passed, 52 skipped,cargo test->127 + 11 + 17 passed,clippy -D warningsclean.needless_borrows_for_generic_argson by default and CI denies warnings, so the five.map_err(&validation_ctx)borrows inrust/src/fullmap.rsare dropped (behavior-preserving;cargo fmt --check,clippy -D warnings, and all 156cargo testcases pass under 1.99.0).Caveats
version:reads4.4.4(thev4.4.5tag source says4.4.5), soBIOLINK_VERSIONkeeps reporting4.4.4until the next upstream release;distill'sversions.biolink_modelreads distribution metadata and already reports4.4.5.chore(release)commit per repo convention.