Feat: paper reproduction

[JemmaLDaniel]

Summary

Adds a reviewer-facing path to regenerate Winnow paper figures and tables from public pins.

• New paper_scripts/ analysis and plot helpers, documented in paper_scripts/README.md.
• New Makefile.paper with paper-plot-* (deposit replot) vs paper-recompute-* (predict / train / other benchmarks and analyses), plus laptop vs heavy umbrellas.
• paper dependency group (not a published extra) pins Glissade at a git SHA. The lockfile has also been updated.
• Root Makefile clean helpers and .gitignore entries for paper_data/, paper_results/, paper_plots/.
• Tiny package/docs touch: compute_features.yaml training_matrix_output_path: null, InstaNovo spelling in docs/cli.md.

The published winnow API is unchanged. Reproduction logic is not imported from paper_scripts/ into the package.

Test plan

• make -f Makefile.paper paper-sync-group-paper then make -f Makefile.paper help
• make -f Makefile.paper paper-setup (or selective downloads) then paper-check-artefacts
• make -f Makefile.paper paper-plot-light against deposited artefacts
• make -f Makefile.paper paper-recompute-laptop (needs Koina connection)
• Confirm uv sync without --group paper still installs the published package only

Note for reviewers

The logic in these scripts must be merged unchanged, but they should all be readable without too much work.

[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	496	32	93%	61, 64, 79, 84–85, 203, 302–303, 305, 308, 353–354, 495–496, 552, 616–617, 621, 626, 692–695, 1069–1070, 1221, 1225, 1251, 1255, 1264, 1281, 1286
diagnostics.py	138	44	68%	71, 156–171, 214–215, 219, 260, 262–277, 288–294
calibration/features
__init__.py	10	0	100%
base.py	26	1	96%	84
beam.py	90	0	100%
chimeric.py	82	1	98%	213
constants.py	9	0	100%
fragment_match.py	78	1	98%	203
mass_error.py	68	4	94%	17, 21, 37–38
retention_time.py	206	8	96%	111, 114–115, 226, 237, 351, 354, 435
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	144	15	89%	228, 238, 247, 260, 340, 342–343, 349–352, 354–357
feature_dataset.py	84	4	95%	21, 88, 183–184
interfaces.py	3	0	100%
psm_dataset.py	25	0	100%
datasets/data_loaders
__init__.py	6	0	100%
instanovo.py	105	16	84%	90, 93, 119, 142, 168–169, 172–174, 176–177, 179, 182–184, 191
mztab.py	179	30	83%	103, 106, 157, 161, 210–211, 223, 268, 271, 283–284, 317–318, 320–321, 323, 325, 331, 334–335, 342–344, 351, 353–356, 360, 501
pointnovo.py	9	0	100%
primenovo.py	121	10	91%	121, 124, 211, 242, 254, 261–262, 373, 384, 389
utils.py	186	3	98%	25, 170, 441
winnow.py	41	5	87%	55–56, 86, 100–101
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	37	1	97%	100
nonparametric.py	26	4	84%	64, 70–71, 74
scripts
__init__.py	0	0	100%
main.py	470	354	24%	23–26, 59, 61–62, 67–68, 78, 90, 95–97, 99–100, 102, 114, 119–120, 122–123, 125–126, 148, 152, 166–167, 182–183, 186, 195–196, 198, 215–216, 233, 252–253, 255–257, 259–260, 262–264, 266, 271, 296, 298–302, 323–324, 326–327, 330–331, 336, 341–342, 376–378, 380, 382, 387, 389, 393–395, 397, 399–401, 403, 405, 407–408, 411, 416, 418, 425–427, 432–435, 437–438, 440, 442, 457–458, 460–462, 464–469, 471, 485–486, 488–490, 492–493, 495–496, 498, 500–501, 508–511, 525, 527, 529–530, 532, 540–542, 544, 549, 555, 569, 571, 573–574, 576, 584–586, 588–589, 591–595, 597, 633–635, 637–640, 642, 646–649, 727, 748, 762, 780–784, 786–789, 815–817, 819, 821, 826, 828, 832–834, 836, 839, 841–844, 846, 854–856, 858, 860, 862, 865–867, 869–871, 878, 895–897, 900, 903, 908, 910, 913, 917–919, 921, 925–927, 929, 931–932, 937, 944, 952, 954, 956–957, 959, 961, 969–971, 973, 975–976, 978–979, 981–982, 984–985, 992–994, 1000, 1009–1010, 1012–1013, 1020–1022, 1024, 1026, 1031, 1033, 1036, 1040–1042, 1044–1045, 1048, 1051, 1053, 1059–1060, 1062–1063, 1067, 1074, 1082, 1084, 1086–1088, 1095–1097, 1099–1101, 1104, 1109, 1114, 1116–1117, 1119–1121, 1124, 1129, 1139, 1146, 1148, 1152, 1154–1155, 1159–1160, 1162, 1171–1174, 1176–1177, 1179, 1181, 1186, 1188–1190, 1192, 1195, 1197, 1203–1206, 1208–1209, 1211–1212, 1214–1215, 1217, 1223, 1230–1232, 1234, 1273–1274, 1315–1316, 1357–1358, 1388–1389, 1417–1418, 1448–1449, 1476–1477, 1507–1508, 1532–1533, 1557–1558
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
hydra_overrides.py	12	2	83%	12, 15
irt_calibration_config.py	89	57	35%	13–14, 21–24, 32–39, 43–44, 52–55, 57–60, 62, 64–65, 77–78, 96–103, 114–117, 124–125, 140–143, 146, 148–149, 153, 155–156, 163, 165–166, 197
koina_intensity_config.py	90	33	63%	42, 68, 76, 78, 108, 111, 131, 160–172, 177–178, 182–183, 189–192, 201–202, 204–205, 209
paths.py	21	0	100%
peptide.py	69	3	95%	37–38, 94
proteome.py	115	12	89%	41, 48, 68, 79, 84, 88, 119, 144–146, 174, 180
rich_console.py	7	0	100%
TOTAL	3573	710	80%

Tests	Skipped	Failures	Errors	Time
671	0 💤	0 ❌	0 🔥	50.384s ⏱️