Feat feature customisation

[JemmaLDaniel]

Summary

• Add edit_distance to BeamFeatures: normalised token-level Levenshtein between top-1 and top-2 beam sequences, with I/L equivalence. Undefined cases (fewer than two candidates, null/empty beam rows, missing sequences) return 1.0.
• Add active_feature_columns to ProbabilityCalibrator: optional override of which metadata columns feed the sklearn MLP (excluding confidence). When unset, behaviour is unchanged: all registered feature columns are used.
• Harden beam computation for partial inputs: _beam_len, null-safe z-score, and _beam_edit_distance helper.

This replaces the revisions pattern of per-feature excluded_columns with calibrator-level selection only. The HF general model already expresses its trained subset via top-level feature_columns; this PR makes that pattern work on the sklearn calibrator path. I intend for this PR to be merged before #190 , which will then be rebased onto main.

---

Motivation

The HF general model config.json lists 10 feature columns (plus confidence -> 11 model inputs). Beam edit_distance, among others, are computed for diagnostics but excluded from the trained set. Calibrator-level column selection is required to match that layout without BeamFeatures(excluded_columns=…) on main.

Full HF checkpoint compatibility (safetensors load, feature_columns deserialisation from config.json) will land with #190; this PR is the sklearn-side prerequisite.

---

Changes

File	Change
winnow/calibration/features/beam.py	Levenshtein helpers, edit_distance column, null-safe beam handling
winnow/calibration/calibrator.py	active_feature_columns ctor arg; columns property override
tests/calibration/features/test_beam.py	Levenshtein unit tests, edit_distance integration tests, edge-case coverage
tests/calibration/test_calibrator.py	TestFeatureColumns for override vs default behaviour

Follow-ups

• Feat PyTorch calibrator and two-phase training pipeline #190 -- add in active_feature_columns deserialisation on load
• HF Hub -- Update config.json: remove dead excluded_columns, alter feature_columns to active_feature_columns and Koina server keys

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
__init__.py	0	0	100%
data_types.py	4	0	100%
calibration
__init__.py	0	0	100%
calibration_features.py	9	0	100%
calibrator.py	109	7	93%	77, 116, 143–144, 146, 172, 177
diagnostics.py	156	47	69%	74, 104, 108, 130, 192–207, 250–251, 255, 296, 298–313, 324–330
calibration/features
__init__.py	10	0	100%
base.py	8	0	100%
beam.py	91	0	100%
chimeric.py	82	1	98%	213
constants.py	9	0	100%
fragment_match.py	78	1	98%	203
mass_error.py	68	2	97%	17, 21
retention_time.py	160	14	91%	110, 113–114, 195, 202, 218, 269–271, 281, 284–285, 290–291
sequence.py	19	0	100%
token_score.py	37	1	97%	82
utils.py	261	3	98%	96, 368, 594
compat
__init__.py	0	0	100%
instanovo.py	10	6	40%	12, 14–15, 17, 24–25
datasets
__init__.py	0	0	100%
calibration_dataset.py	113	18	84%	155, 169, 171, 173, 180, 189, 202, 255, 257–258, 264–267, 269–272
interfaces.py	3	0	100%
psm_dataset.py	25	0	100%
datasets/data_loaders
__init__.py	5	0	100%
instanovo.py	106	16	84%	90, 93, 119, 142, 168–169, 172–174, 176–177, 179, 182–184, 191
mztab.py	179	32	82%	103, 106, 157, 161, 210–211, 223, 268, 271, 283–284, 296–298, 300–301, 303, 305, 311, 314–315, 322–324, 331, 333–336, 340, 472, 479
pointnovo.py	7	0	100%
utils.py	202	6	97%	14, 145–148, 216
winnow.py	44	4	90%	55–56, 101–102
fdr
__init__.py	0	0	100%
base.py	58	15	74%	81, 85–86, 91, 98–99, 105, 126, 129–130, 135, 137–138, 144, 186
database_grounded.py	25	0	100%
nonparametric.py	25	4	84%	62, 68–69, 72
scripts
__init__.py	0	0	100%
main.py	260	260	0%	8, 10–13, 16–20, 23–24, 26–28, 32, 39, 44, 47, 53, 55–56, 59, 68, 70–73, 75, 80, 87, 89–91, 93, 95–100, 103, 105–106, 111, 126, 129, 136–142, 145–146, 149, 162–164, 167, 170, 175, 177–179, 181, 183–184, 187–188, 191, 193–194, 196, 198, 200–201, 203, 206–207, 210–211, 214–215, 218–220, 222–225, 228–230, 232, 235, 249–251, 253, 255, 260, 262–264, 266–267, 269, 271–272, 274–276, 278, 280, 282–283, 287–290, 292–293, 295–296, 298–299, 301, 304, 318–320, 323, 326, 331, 333–335, 337–339, 341–342, 345–346, 349, 351–352, 354, 356, 358–359, 361, 364–365, 371–373, 375–378, 381–382, 385–386, 389–390, 393–394, 402–404, 408, 411, 415, 418, 424–426, 428–429, 436–437, 439, 441, 446, 448–450, 452–453, 456, 458–459, 461–464, 466–467, 469–470, 472–474, 480–481, 485–486, 489, 496, 501–502, 507–509, 512, 517, 527, 534, 536, 540, 542–543, 547–548, 551, 574, 587–588, 591, 613, 625–626, 629, 654, 667–668, 671, 686, 698–699, 702, 717, 729–730, 733, 745, 757–758, 761, 776, 788–789, 792, 801, 813–814
utils
__init__.py	4	0	100%
config_formatter.py	53	40	24%	29, 37–38, 40–42, 44, 55, 58–60, 62–63, 66–69, 72–74, 77–78, 80, 91, 102, 113, 127–128, 130–132, 145–147, 150, 153–154, 157–158, 160
config_path.py	76	5	93%	24–26, 117–118
peptide.py	25	1	96%	32
TOTAL	2321	483	79%

Tests	Skipped	Failures	Errors	Time
506	0 💤	0 ❌	0 🔥	38.203s ⏱️