Feat use mgf for sample spectra

Makefile

@@ -137,7 +137,7 @@ sample-data:
 ## Run winnow train with sample data
 train-sample:
 	uv run winnow train \
-	dataset.spectrum_path_or_directory=examples/example_data/spectra.ipc \
+	dataset.spectrum_path_or_directory=examples/example_data/spectra.mgf \
 	dataset.predictions_path=examples/example_data/predictions.csv \
 	model_output_dir=models/new_model \
 	dataset_output_path=results/calibrated_dataset.csv \
@@ -148,7 +148,7 @@ predict-sample:
 	uv run winnow predict \
 	calibrator.pretrained_model_name_or_path=models/new_model \
 	fdr_control.fdr_threshold=1.0 \
-	dataset.spectrum_path_or_directory=examples/example_data/spectra.ipc \
+	dataset.spectrum_path_or_directory=examples/example_data/spectra.mgf \
 	dataset.predictions_path=examples/example_data/predictions.csv
 
 ## Clean output directories (does not delete sample data)

docs/configuration.md

@@ -108,7 +108,7 @@ defaults:
 
 dataset:
   # Path to the spectrum data file or to folder containing saved internal Winnow dataset
-  spectrum_path_or_directory: data/spectra.ipc
+  spectrum_path_or_directory: data/spectra.mgf
   # Path to the beam predictions file
   # Leave as null if data source is winnow, or loading will fail
   predictions_path: data/predictions.csv
@@ -326,7 +326,7 @@ defaults:
 
 dataset:
   # Path to the spectrum data file or to folder containing saved internal Winnow dataset
-  spectrum_path_or_directory: data/spectra.ipc
+  spectrum_path_or_directory: data/spectra.mgf
   # Path to the beam predictions file
   # Leave as null if data source is winnow, or loading will fail
   predictions_path: data/predictions.csv