Release hygiene: LICENSE file, odk.yaml license, fix stale obolibrary term-IRI references#466
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…x stale obolibrary refs - Add a LICENSE file (CC-BY-4.0 legalcode); the README linked the external CC URL but no local LICENSE existed (OBO/BioPortal/GitHub expect one). Matches the dcterms:license already in the ontology header and pyproject.toml. - Add `license: https://creativecommons.org/licenses/by/4.0/` to metpo-odk.yaml so the ODK config carries it (it was the only place the license was undeclared). - Fix sparql/metpo_phenotype_classes.rq: it filtered term IRIs on `http://purl.obolibrary.org/obo/METPO_`, which matches nothing now that METPO terms are `https://w3id.org/metpo/<id>` (the query returned empty). Update the filter + its sparql/README.md note. - Update metpo-proposal-lint docstring: the term-IRI scheme is settled (#458), no longer "an open question"; point remaining ODK-config/IRI cleanup at #465. No generated-Makefile or ontology-artifact changes; the IRI-scheme correction is tracked in #465 (must go through odk.yaml regeneration, not Makefile edits). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Pull request overview
Release-prep hygiene cleanup to make licensing metadata explicit and to align SPARQL/docs/lint messaging with METPO’s settled w3id-based term IRIs (avoiding stale obolibrary/METPO_ assumptions).
Changes:
- Add a local
LICENSEfile containing the CC-BY-4.0 legalcode and declare the license inmetpo-odk.yaml. - Fix
sparql/metpo_phenotype_classes.rqto matchhttps://w3id.org/metpo/term IRIs and update the associated SPARQL README note. - Update
metpo_proposal_lintmodule docstring to remove stale “open question” wording and reference the settled IRI scheme / follow-up tracking.
Reviewed changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
src/ontology/metpo-odk.yaml |
Declares the project license in the ODK config. |
sparql/README.md |
Updates documentation to reflect w3id-based METPO term IRIs. |
sparql/metpo_phenotype_classes.rq |
Fixes the namespace filter to return METPO classes under the current IRI scheme. |
metpo/scripts/metpo_proposal_lint.py |
Updates docstring guidance to match the settled term-IRI scheme and current tracking. |
LICENSE |
Adds CC-BY-4.0 license text locally for release/distribution expectations. |
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Small, low-risk hygiene cleanup found while prepping the release. No generated-Makefile or ontology-artifact changes.
dcterms:licensealready in the ontology header and thepyproject.tomllicense.metpo-odk.yamllicense:— the ODK config was the only place the license was undeclared.sparql/metpo_phenotype_classes.rq— its filterSTRSTARTS(?class, "http://purl.obolibrary.org/obo/METPO_")matches nothing now that terms arehttps://w3id.org/metpo/<id>, so the query returned empty. Fixed the filter + thesparql/README.mdnote.metpo-proposal-lintdocstring — the term-IRI scheme is settled (Consistent w3id IRI scheme; drop obolibrary claims (#434, #436) #458); dropped the stale "open question" wording and pointed the remaining ODK-config/IRI cleanup at Upgrade ODK 1.5.4 → 1.6.1 (make update_repo currently fails on version skew) #465.The IRI-scheme correction itself (resolvable main IRI, base-IRI vestiges) is deliberately not here — it must go through
odk.yamlregeneration, tracked in #465, not hand-edits to the generated Makefile.Leaving open for CI + Copilot review before merge.