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1d37d1a
feat: pyaccess
jspaezp Mar 28, 2026
aca217a
refactor: remove dead uncalibrated scoring path from pipeline.rs
jspaezp Apr 10, 2026
0c9d253
refactor: rename ScoringPipeline to Scorer, inline tolerance fields
jspaezp Apr 10, 2026
6eb710a
feat: add ScoringFields, ScoredCandidate, CompetedCandidate, FinalRes…
jspaezp Apr 10, 2026
30c4fa9
feat: add ScoredCandidateBuilder, update finalize_results
jspaezp Apr 10, 2026
5a5e10b
refactor: migrate accumulator and calibrated scoring to ScoredCandidate
jspaezp Apr 10, 2026
c4aaea7
refactor: typed pipeline stages (ScoredCandidate → CompetedCandidate …
jspaezp Apr 10, 2026
0ff4ca7
feat: manual Parquet writer with exhaustive destructure
jspaezp Apr 10, 2026
302c926
refactor: remove IonSearchResults, SearchResultBuilder, and parquet_d…
jspaezp Apr 10, 2026
38479d1
refactor: apply all field and type renames (spec Section 4)
jspaezp Apr 10, 2026
8a2d332
refactor: plumb calibrated tolerances into execute_secondary_query, r…
jspaezp Apr 10, 2026
6d06381
feat: PipelineReport with full timing (phases 4-6) and q-value counts
jspaezp Apr 10, 2026
373ff42
feat: wire dp_lookback from CalibrationConfig into pathfinding
jspaezp Apr 10, 2026
93550bb
chore: remove timsseek_rescore and timsseek_rts_receiver packages
jspaezp Apr 10, 2026
eb6605e
refactor: rename process_query_full to score_for_viewer, FullQueryRes…
jspaezp Apr 10, 2026
991c182
feat: structured logging -- file + stderr warn/error + stdout milestones
jspaezp Apr 10, 2026
ba3cae3
fix: quiet index detection logging — use filesystem checks for local,…
jspaezp Apr 10, 2026
0ef9665
refactor: pipeline cleanup — speclib by ref, RunReport, early stoppin…
jspaezp Apr 10, 2026
840d466
feat(calibrt): make Node pub, add Grid::reset() and grid_cells()
jspaezp Apr 10, 2026
de37d6a
refactor(calibrt): pathfinding accepts external DP buffers
jspaezp Apr 10, 2026
366b9c8
feat(calibrt): add CalibrationState with update/fit/reset cycle
jspaezp Apr 10, 2026
66d3aca
feat(timsseek): add library_rt_seconds to CalibrantCandidate, add Cal…
jspaezp Apr 10, 2026
ba8cf65
refactor(timsseek): rename ApexFinder -> TraceScorer, add compute_tra…
jspaezp Apr 10, 2026
739df17
feat(timsseek): add suggest_apex and score_at, rewrite find_apex/find…
jspaezp Apr 10, 2026
39cbcf3
refactor(timsseek): extract shared build_extraction() function
jspaezp Apr 10, 2026
f2ca852
refactor(viewer): migrate to TraceScorer (rename only, same behavior)
jspaezp Apr 10, 2026
3affdc2
refactor: remove ApexFinder alias, all code uses TraceScorer
jspaezp Apr 10, 2026
c342962
feat(viewer): add ViewerCalibrationState with background thread
jspaezp Apr 10, 2026
74a5d7b
feat(viewer): wire calibration panel UI with grid+curve plot
jspaezp Apr 10, 2026
b000f40
feat(viewer): add save/load calibration as JSON v1
jspaezp Apr 10, 2026
84177a4
feat(cli): save calibration.json after Phase 2 (viewer-compatible v1 …
jspaezp Apr 10, 2026
8544a6b
refactor: shared calibration JSON format — CalibrationSnapshot in cal…
jspaezp Apr 10, 2026
b6ab404
chore(viewer): remove unused arc_clone method and wrmse field from De…
jspaezp Apr 10, 2026
fc093e8
feat(viewer): render calibration grid as heatmap with per-cell colore…
jspaezp Apr 10, 2026
4469f20
feat(viewer): calibration panel polish — heatmap, projected RT, toler…
jspaezp Apr 10, 2026
fb22e3e
feat(viewer): show separate Library RT (blue) and Calibrated RT (oran…
jspaezp Apr 10, 2026
392c135
feat(viewer): persist calibration across restarts via app state snapshot
jspaezp Apr 10, 2026
cf5b456
feat(viewer): parallelize calibration scoring via Rayon chunked par_iter
jspaezp Apr 10, 2026
de0f41d
feat(calibrt): ridge width measurement for tolerance estimation
jspaezp Apr 10, 2026
0710cb2
feat: position-dependent RT tolerance from ridge width measurement
jspaezp Apr 10, 2026
4b0cf62
feat(viewer): display ridge tolerance envelope on calibration heatmap
jspaezp Apr 10, 2026
e4a5ce0
fix(viewer): ridge envelope as dashed boundary lines instead of fille…
jspaezp Apr 10, 2026
050559c
feat(cli): print calibration summary after Phase 2 (ridge width, tole…
jspaezp Apr 10, 2026
564acc9
refactor: extract Array2D into standalone crate for shared use
jspaezp Apr 10, 2026
f795c71
feat(calibrt): add LibraryRT<T> and ObservedRTSeconds<T> newtypes
jspaezp Apr 10, 2026
ac47f11
refactor(calibrt): rename Point fields x/y to library/observed
jspaezp Apr 10, 2026
971700e
feat(calibrt): type API boundary with LibraryRT/ObservedRTSeconds new…
jspaezp Apr 10, 2026
5079c23
feat(calibrt): ping-pong weight buffers with 3x3 gaussian blur for ri…
jspaezp Apr 10, 2026
fedcb60
feat(timsseek): use RT newtypes in CalibrationResult API
jspaezp Apr 10, 2026
c04a218
feat: propagate RT newtypes to CalibrantCandidate and all callers
jspaezp Apr 11, 2026
e87fdb0
feat(calibrt): greedy path extension, sqrt edge weights, and extrapol…
jspaezp Apr 11, 2026
49eff9b
feat(rescore): per-fold progress and remove redundant scoring pass
jspaezp Apr 11, 2026
ed75232
feat(calibrt): report in-ridge weight ratio as calibration quality me…
jspaezp Apr 11, 2026
446793a
chore: update deps
jspaezp Apr 11, 2026
8c7a1f9
chore: update uv lock
jspaezp Apr 11, 2026
a822c50
chore: update uv lock
jspaezp Apr 11, 2026
8954ee0
chore: bump versions
jspaezp Apr 11, 2026
844b242
fix: address 3 critical review findings
jspaezp Apr 11, 2026
f930b21
fix: address important review findings (I1-I3)
jspaezp Apr 11, 2026
bbdf646
fix: address remaining important review findings (I4-I10)
jspaezp Apr 11, 2026
1e908b9
chore: minor review suggestions
jspaezp Apr 11, 2026
a84462c
perf: prescore skips PeptideMetadata construction
jspaezp Apr 12, 2026
791c896
feat: optional rayon, Phase 1 timing breakdown, cleanup
jspaezp Apr 12, 2026
cdfabd0
refactor: add timed! macro and TimedStep for timing infrastructure
jspaezp Apr 12, 2026
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8 changes: 8 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -37,3 +37,11 @@ results.json
*search_results*/*

wandb/*
docs/superpowers/*
.plans/*
.claude/*
.prompts/*
sh*/
*plan*.md

docs/superpowers/
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