Per-tool YAML licenses (#4) + review-grounded meta-skills (#7)#20
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Propagate license_tier/license/license_detection from tools_index.json into
the 909 tools/<slug>.yaml LinkML records, schema-correctly.
- scripts/enrich_tool_yaml.py: tier_map(tools_index) -> per-slug license rows;
enrich(collection_dir) joins by slug and writes the three fields right after
schema_version (idempotent, _yaml_dump style-preserving, no git/network).
- asb_skill_bundle.yaml: vendor the LinkML schema at repo root (where
validate.yml gate 1 expects it) and add optional license_tier/license/
license_detection slots to the ASBTool class + a LicenseTierEnum
{open,noncommercial,restricted}. Verified: ASBTool instances with the new
fields validate clean and an invalid tier is rejected; the gate's result on
collection.yaml is unchanged.
- check_tools_index.check_collection: cross-check each tools/<slug>.yaml
license_tier == its tools_index license_tier (tools without a yaml skipped).
- Ran on collections/metabolomics/v2: 909 enriched, 0 mismatches
(511 open / 389 restricted / 9 noncommercial); re-run is a byte-stable no-op.
Tests: 19 new (enrich + cross-check), full suite 397 passed.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
A super-skill can now be grounded in a review article instead of being
purely composed from the skills it orchestrates.
- synthesize_meta_skill.meta_frontmatter: optional review_doi=None. When
given -> provenance_tier="literature", metadata.dois=[review_doi],
derived_from=[{doi:review_doi}], keeping skill_kind="super"+orchestrates.
Default path stays synthetic (no dois/derived_from).
- check_proposals.check_collection: accept staged literature super-skills,
reusing scripts.provenance_tier.validate_entry semantics
(literature => >=1 doi; synthetic => synthesized_from; community =>
related_skills key). Super/skill_kind/orchestrates checks intact.
- governance/META_SKILLS.md: document the three meta-skill origins
(synthetic / community / literature = review-grounded) + review-DOI flow.
- commands/synthesize-meta-skill.md: document the --review-doi option.
- Tests: literature super-skill with a review DOI passes; without a doi
fails; synthetic path unchanged. Full suite 404 passed.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…asb-schema package The LinkML Tool-class slots (license_tier/license/license_detection) should be added in the unpublished asb-schema sibling package, not vendored as a 639-line copy here (divergence risk; the gate is warn-only + asb-schema not on PyPI, so this preserves dev's behavior). The real deliverable — 909 enriched tools/*.yaml + the check_tools_index cross-check + enrich_tool_yaml — is retained. FOLLOW-UP (asb-schema repo): add the 3 license slots to the Tool class so the enriched tools/*.yaml validate once asb-schema is published. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…iew-meta # Conflicts: # scripts/check_proposals.py
lfnothias
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Auto-review — VERDICT: MERGEABLE ✅
Workflow final review returned MERGEABLE; its one Important finding (a vendored 639-line asb_skill_bundle.yaml that won't load under local linkml) is resolved by removing that file — the schema is owned by the unpublished asb-schema package, the gate is warn-only, and the data deliverable is independent of it. Independently verified in the worktree:
pytest→ 434 passed (includes #19's tests after mergingdevin).check_proposals/check_tools_index/check_provenance_tiers/check_license_tiers→ exit 0.- #4: all 909
tools/*.yamlcarrylicense_tier/license/license_detectionmatchingtools_index(0 mismatch);enrich_tool_yamlidempotent. - #7: a review-grounded super-skill validates as
literature(≥1 doi); the synthetic path is unchanged. - Merge with #19: clean — no conflict markers;
validate_provenance(provenance) +contributor_violations(contributors) both wired incheck_proposals. - No git/gh/network in new scripts.
Follow-up flagged (separate asb-schema repo): add the 3 license slots to the Tool class so enriched YAMLs validate once asb-schema is published.
Gate 15: Paper Access Tier Validation FAILEDOne or more papers in this PR have missing or non-open-access tiers. Please:
See OPEN_ACCESS_POLICY.md for the full policy and allowed access tiers. |
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Propagates two post-#19 merges into the 8 packs (which weren't rebuilt after): - synthesize-meta-skill.md: the #7 --review-doi addition (PR #20) - kb_bundle.json: related_skills from the #1 embedding precompute (PR #21) claim-skill.md was already shipped to all packs in 2be335f (PR #19) and is unchanged here. Idempotent: re-running build_all_grounding.sh now yields no diff. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Two features (#4 per-tool YAML licenses, #7 review-grounded meta-skills). Merged
devin to resolve thecheck_proposals.pyoverlap with #19. 434 tests; all gates green.#4 — per-tool YAML license enrichment
scripts/enrich_tool_yaml.pywriteslicense_tier/license/license_detectioninto all 909tools/<slug>.yaml(joined by slug fromtools_index.json), idempotent + byte-identical torender_tool_yamlstyle.check_tools_indexextended to cross-check eachtools/<slug>.yamllicense_tier== itstools_indextier (0 mismatch on real data).asb_skill_bundle.yamlthe workflow had added: that schema is owned by the unpublishedasb-schemasibling package (the LinkML gate is warn-only +asb-schemanot on PyPI). Vendoring a 639-line copy here = divergence risk with no CI benefit. Follow-up (asb-schema repo): add the 3 license slots to the Tool class so the enriched YAMLs validate once published.#7 — review-grounded (literature-tier) meta-skills
synthesize_meta_skill.meta_frontmattergainsreview_doi=→ a super-skill grounded in a review article becomesprovenance_tier: literature(dois/derived_fromset), vs the defaultsyntheticpath.check_proposalsnow delegates the provenance invariant toprovenance_tier.validate_entry(community/synthetic/literature ⇒ ≥1 doi), a DRY refactor;META_SKILLS.md+synthesize-meta-skill.mddocument--review-doi.Verification
pytest→ 434 passed;check_proposals/check_tools_index/check_provenance_tiers/check_license_tiersexit 0.validate_provenance+contributor_violationscoexist incheck_proposals.