promote to main (3/4): resolution-determinism stack (fork #64/#67/#68/#69/#70) - #96
Merged
Merged
Conversation
…cture-guided-reresolution
…70 Brings org dev src to fork dev src for the resolution-determinism stack (org was current through fork #60 / org #91). Ports the 14 differing src files (making org src == fork src) plus the 17 src-coupled test files + refmet freeze fixtures. Studies-coupled tests and the entire studies/ tree stay fork-only, as does the fork-specific prose-figure/off-category-audit guard (both assert the studies tree exists). Bundled (per the batching policy) since the changes are entangled in shared files (certificate.py/mapper.py/kestrel annotators) and cannot be cleanly separated: - fork #64: Kestrel search sends schema field names category/prefix (server-side filtering) - fork #67: resolver deterministic majority tie-break (_stable_majority) - fork #68: RefMet availability surfacing + bounded batch resilience - fork #69: deterministic Kestrel candidate order (stable_result_order) - fork #70: pinned /match freeze as authoritative RefMet source + refmet_source provenance All Greptile 5/5 on the fork. Offline gate green in this worktree (817 passed, 0 failed); ruff/black/pyright clean on src. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Stacked promotion dev→main, 3 of 4. #94 (#59) + #95 (#60) merged; this is the determinism stack (matches org #92).
This PR
All live-proven in the dev-vs-prod scoreboard (dev halved false cross-cohort links, matched Monti ~99%). The freeze consumer (#70) is inert in prod unless
REFMET_SNAPSHOT_PATHis set — prod will not set it, so RefMet stays on the live path.Series
Handle accidental double colons in input curies #59✅ (promote to main (1/4): text/vector search window scan (fork #59) #94) 2.Dockerize Biomapper2 #60✅ (promote to main (2/4): structure-guided re-resolution of conflated commits (fork #60) #95) 3. Implement retry loop for API startup wait #64/PR: Return equivalent IDs from KG nodes - Feat/equivalent ids #67/PR: feat: Dynamic entity types and vocabulary presets from Kestrel #68/feat: HGNC human-preference re-ranking for gene/protein resolution #69/feat: gene/protein resolution — HGNC human-preference + curated gene-symbol fallback (dev → main) #70 ← this PR 4. feat: curated gene-symbol fallback resolver for drug-conflated human genes #71/feat: canonical-namespace preference + gene gold-set fix (unblocks release CI) #72 (fallback + candidate_limit)dev→main; no
studies/; org CIgateruns.🤖 Generated with Claude Code