feat(resolver): structure-guided re-resolution of conflated KG commits + lipid independent-structure source (port of fork #60) - #91
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trentleslie merged 1 commit intoSep 7, 2026
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…s + lipid independent-structure source (port of fork #60) Port of trentleslie/biomapper2 PR #60 (merged to fork dev 2026-09-01) to Phenome-Health. src/ + tests only — the studies/external_benchmarks benchmark harness (fork #61) stays off-org. Applied as a 3-way port onto org dev; verified green on the org base: pyright 0 errors, ruff clean, 776 passed / 227 skipped. Reviewer note: org dev has diverged resolver work (#75/#77/#82/#83 source-weighting / URL-resolver / InChIKey-blocks) — the port merged cleanly and the full suite passes, but confirm the re-resolution logic composes as intended with those. This promotion is the prerequisite for the D2 RefMet-bridge re-resolution work. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
trentleslie
marked this pull request as ready for review
September 7, 2026 22:57
trentleslie
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promote/kg-conflation-structure-guided-reresolution
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September 7, 2026 22:58
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Port of fork PR trentleslie/biomapper2#60 (merged to fork
dev2026-09-01) to Phenome-Health.Scope
src/+tests/only. Thestudies/external_benchmarksbenchmark harness (fork Dockerized + API Wrapper + Internal Pydantic Models #61) is fork-only and deliberately not promoted.src/files (structure-guided re-resolution + newlipid_structure_resolver.pyGoslin→LIPID MAPS→InChIKey source) + 8 test files.Verification (on this org base)
dev— no textual conflicts.pyright0 errors,ruffclean.Reviewer note
Org
devcarries diverged resolver work (#75 / #77 / #82 / #83 — source-weighting, URL resolver, InChIKey blocks) that the fork branch predates. The port merged cleanly and the suite is green, but please confirm the re-resolution logic composes as intended with those changes.Why now
This promotion is the prerequisite for the D2 RefMet-bridge re-resolution work (the next step to close the Monti cross-cohort gap).
Draft pending review of the port before marking ready.
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