fix: add safety checks for string peptides before computing number of matches in database-grounded FDR calculation

[JemmaLDaniel]

PR Type

Bug fix

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Description

• Clarify docstring column names and confidence description

• Add safety checks for string sequences and predictions

• Simplify num_matches computation lambda

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Changes walkthrough 📝

	Relevant files
Bug fix	database_grounded.py Add sequence/prediction safety checks and simplify matching winnow/fdr/database_grounded.py Renamed docstring field from 'peptide' to sequence Updated confidence description to "User-specified confidence column" Added type checks before splitting sequence and prediction Removed conditional in num_matches lambda for list type +9/-8

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[JemmaLDaniel]

/describe

[instadeep-pr-agent]

PR Description updated to latest commit (a1c0131)

[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	264	11	95%	148–149, 312–314, 549–551, 1024–1026
calibrator.py	91	15	83%	69–70, 72, 106–109, 134–135, 137, 162–163, 167, 194–195
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	87	12	86%	138, 191, 193–194, 200–203, 205–208
data_loaders.py	203	153	24%	62–64, 67, 69, 74, 79, 91, 93–96, 98, 102–103, 105, 107, 122, 128, 137–138, 142, 160–161, 163–165, 167–169, 171–172, 174, 188, 191–192, 194–195, 200, 206–207, 216, 219, 229, 247–249, 258, 272, 277–279, 281, 285–286, 288–289, 294, 297, 304, 310, 324–325, 328, 331–332, 341, 350, 407–408, 410–413, 415, 419–420, 422, 434–436, 439–440, 458–459, 461–462, 465–467, 472, 475–476, 479–480, 486–487, 489, 501, 504, 516–517, 524, 530, 534, 536, 539, 543, 565, 590–591, 593–594, 597–599, 609–610, 640, 653–654, 658, 662, 676, 696, 706–707, 718, 795, 815–816, 818–820, 826–830, 835–836, 839, 842, 847, 853–859, 865–866
interfaces.py	3	0	100%
psm_dataset.py	25	0	100%
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	28	1	96%	52
nonparametric.py	25	4	84%	62, 68–69, 72
scripts
__init__.py	0	0	100%
main.py	142	142	0%	8, 10–14, 17–21, 24–25, 27–29, 33, 40, 45, 48, 54, 56–57, 60, 69, 77, 80, 87, 89–91, 93, 95–100, 103, 105–106, 111, 126, 129, 135–136, 138–140, 143–144, 147, 160–162, 165, 168, 173, 175–177, 179, 181–182, 185–186, 189, 191–192, 194, 196, 198–199, 201, 204–205, 208–209, 212–213, 216–218, 220, 223, 237–239, 242, 245, 250, 252–254, 256–257, 259–260, 263–264, 267, 269–270, 272, 274, 276–277, 279, 282–283, 289–290, 293–294, 297–298, 301–302, 310–312, 315–318, 322, 325, 348, 361–362, 365, 390, 403–404, 407, 422, 434–435, 438, 453, 465–466
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	16	0	100%
TOTAL	1089	404	62%

Tests	Skipped	Failures	Errors	Time
174	0 💤	0 ❌	0 🔥	12.440s ⏱️