Feat: compute-features command

[JemmaLDaniel]

Summary

This branch introduces a feature-only pipeline: load a dataset the same way as training, run the calibrator’s configured feature stack via ProbabilityCalibrator.compute_features, and write enriched metadata to a single CSV. It does not fit the MLP or save a calibrator checkpoint.

Description

• winnow compute-features - Hydra entry point using compute_features.yaml (defaults mirror training settings: residues, calibrator, data_loader).
• winnow config compute-features - print the resolved config without running the pipeline.
• Config - dataset_output_path, optional filter_empty_predictions, and labelled mode (with validation: e.g. RetentionTimeFeature is rejected for unlabelled runs; labelled runs require a sequence column).
• Docs - updates in docs/configuration.md and docs/cli.md for the new command and config layout.

Motivation

Lets users export calibration features for inspection or downstream use without paying the cost of full model training.

[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	316	7	97%	247–248, 443, 728, 916, 920, 1215
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	109	17	84%	155, 169, 171, 173, 183, 196, 249, 251–252, 258–261, 263–266
data_loaders.py	226	13	94%	130, 161–162, 318, 359, 751, 755, 804, 815, 927–928, 956–957
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	185	185	0%	8, 10–13, 16–20, 23–24, 26–28, 32, 39, 44, 47, 53, 55–56, 59, 68, 76, 79, 86, 88–90, 92, 94–99, 102, 104–105, 110, 125, 128, 135–141, 144–145, 148, 161–163, 166, 169, 174, 176–178, 180, 182–183, 186–187, 190, 192–193, 195, 197, 199–200, 202, 205–206, 209–210, 213–214, 217–219, 221, 224, 238–240, 242, 244, 249, 251–253, 255–256, 258–260, 265–266, 268–270, 272, 274, 276–277, 281–284, 286–287, 289–290, 292–293, 295, 298, 312–314, 317, 320, 325, 327–329, 331–333, 335–336, 339–340, 343, 345–346, 348, 350, 352–353, 355, 358–359, 365–366, 369–370, 373–374, 377–378, 386–388, 392, 395, 399, 402, 425, 438–439, 442, 464, 476–477, 480, 505, 518–519, 522, 537, 549–550, 553, 565, 577–578, 581, 596, 608–609
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	1229	308	74%

Tests	Skipped	Failures	Errors	Time
287	0 💤	0 ❌	0 🔥	13.302s ⏱️

[BioGeek]

Shouldn't this command use the example data?

[BioGeek]

Don't forget to change this to spectra.mgf later if you also merge #173