osprey: Surfaced single-peak multiple-ID co-assignment in --model-diagnostics - #4558

Merged

brendanx67 merged 33 commits into

Skyline/work/20260808_peak_coassignment_diagnostics

Aug 13, 2026

Commits on Aug 11, 2026

Added opt-in peak co-assignment panel to --model-diagnostics

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d9c3c00
Removed the --model-diagnostics opt-in tokens and fixed panel defects

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078baac
Added the co-assignment HTML panel and reworked decoy inclusion

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9498c83
Persisted the experiment aggregate score in the FDR sidecar (v3 to v4)

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4ab0732
Fixed the co-assignment decoy class and collapsed two panel implementations

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c7cdabe
Seeded ExperimentAggregateScore and taught the sidecar gate the v4 record

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14d66b4
Fixed eight code-review findings in the co-assignment panel

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aab9f63
Rebaselined the diagnostics golden for the co-assignment metrics

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8cdc09d
Wrote the experiment aggregate score on the default pass-2 path

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7a0c9d0
Corrected the pass1 to pass2 direction claim with a second dataset

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0df2627
Removed the O(files x entries) map from the co-assignment builder

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5efdb05
Addressed the Copilot review of #4558

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ebcee57

Commits on Aug 12, 2026

Reported the spectra cache write instead of writing it silently

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1268809
Made a deleted --model-diagnostics report regenerate on its own

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113fe13
Stopped a target inheriting its paired decoy's experiment q-value

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2704cc2
Reported the co-assignment apex-RT join instead of running it silent

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7211398
Reported the pass-2 survivor scan instead of running it silent

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891bd58
Counted only decoys that won their own target-decoy competition

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37af75b
Re-keyed the last two experiment-q lookups onto the winner entry_id

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ccd628e
Rebaselined the goldens for the experiment q-value fixes

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54796e5
Re-indented the pass-2 survivor merge under its progress block

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86adfaa
Fixed four verified findings from the code review of #4558

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67975e6

Commits on Aug 13, 2026

Merge branch 'master' into Skyline/work/20260808_peak_coassignment_diagnostics
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5605b98
Fixed the co-assignment and sidecar findings from the review

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0d4dd42
Reported the composite acceptance score and the score each pass needs

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02a2db0
Stopped declaring an unwritable diagnostics report, dropped dead state

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57858bb
Took the deepest score within the FDR as the crossing, not the first over

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8d0d7ed
Rebaselined the goldens for the acceptance-score metrics

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1ac5b33
Refused the co-assignment panel on a partially read sidecar

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6b7a98f
Reported the co-assignment sidecar scan instead of running it silent

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bb367e2
Fixed defects the second review found in this branch's own new code

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b53c35b
Completed the version-fence and partial-read fixes at their last sites

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42f9d12
Left RunSimpleFdr's Score unassigned, as it was

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e740ddf