Feat/calibration stage scoring#54

Merged

jspaezp merged 64 commits intomainfrom

feat/calibration_stage_scoring

Apr 13, 2026

Commits on Mar 28, 2026

feat: pyaccess
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Commits on Apr 10, 2026

refactor: remove dead uncalibrated scoring path from pipeline.rs
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refactor: rename ScoringPipeline to Scorer, inline tolerance fields
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feat: add ScoringFields, ScoredCandidate, CompetedCandidate, FinalResult types
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feat: add ScoredCandidateBuilder, update finalize_results
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refactor: migrate accumulator and calibrated scoring to ScoredCandidate
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refactor: typed pipeline stages (ScoredCandidate → CompetedCandidate → FinalResult)
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feat: manual Parquet writer with exhaustive destructure
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refactor: remove IonSearchResults, SearchResultBuilder, and parquet_derive
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refactor: apply all field and type renames (spec Section 4)
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refactor: plumb calibrated tolerances into execute_secondary_query, remove secondary_tolerance
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feat: PipelineReport with full timing (phases 4-6) and q-value counts
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feat: wire dp_lookback from CalibrationConfig into pathfinding
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chore: remove timsseek_rescore and timsseek_rts_receiver packages
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refactor: rename process_query_full to score_for_viewer, FullQueryResult to ViewerResult
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feat: structured logging -- file + stderr warn/error + stdout milestones
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fix: quiet index detection logging — use filesystem checks for local, debug-level for expected failures
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refactor: pipeline cleanup — speclib by ref, RunReport, early stopping, max-qvalue
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feat(calibrt): make Node pub, add Grid::reset() and grid_cells()
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refactor(calibrt): pathfinding accepts external DP buffers
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feat(calibrt): add CalibrationState with update/fit/reset cycle
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feat(timsseek): add library_rt_seconds to CalibrantCandidate, add CalibrantHeap::iter()
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refactor(timsseek): rename ApexFinder -> TraceScorer, add compute_traces + cached profiles
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feat(timsseek): add suggest_apex and score_at, rewrite find_apex/find_apex_location as wrappers
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refactor(timsseek): extract shared build_extraction() function
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refactor(viewer): migrate to TraceScorer (rename only, same behavior)
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refactor: remove ApexFinder alias, all code uses TraceScorer
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feat(viewer): add ViewerCalibrationState with background thread
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feat(viewer): wire calibration panel UI with grid+curve plot
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feat(viewer): add save/load calibration as JSON v1
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feat(cli): save calibration.json after Phase 2 (viewer-compatible v1 format)
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refactor: shared calibration JSON format — CalibrationSnapshot in calibrt, SavedCalibration in timsseek
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chore(viewer): remove unused arc_clone method and wrmse field from DerivedTolerances
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feat(viewer): render calibration grid as heatmap with per-cell colored rectangles
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feat(viewer): calibration panel polish — heatmap, projected RT, tolerance fixes
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feat(viewer): show separate Library RT (blue) and Calibrated RT (orange) reference lines
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feat(viewer): persist calibration across restarts via app state snapshot
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feat(viewer): parallelize calibration scoring via Rayon chunked par_iter
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feat(calibrt): ridge width measurement for tolerance estimation
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feat: position-dependent RT tolerance from ridge width measurement
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feat(viewer): display ridge tolerance envelope on calibration heatmap
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fix(viewer): ridge envelope as dashed boundary lines instead of filled polygon
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feat(cli): print calibration summary after Phase 2 (ridge width, tolerances)
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refactor: extract Array2D into standalone crate for shared use
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feat(calibrt): add LibraryRT<T> and ObservedRTSeconds<T> newtypes
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refactor(calibrt): rename Point fields x/y to library/observed
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feat(calibrt): type API boundary with LibraryRT/ObservedRTSeconds newtypes
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feat(calibrt): ping-pong weight buffers with 3x3 gaussian blur for ridge measurement
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feat(timsseek): use RT newtypes in CalibrationResult API
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Commits on Apr 11, 2026

Commits on Apr 12, 2026