#299: review comments

alphadia/constants/default.yaml

@@ -11,9 +11,9 @@ general:
   wsl: false
   mmap_detector_events: false
   use_gpu: true
-  # whether to save the (MBR) library to the output directory
-  save_library: True
-  save_mbr_library: True
+  # whether to save the libraries to the output directory
+  save_library: True       # input library
+  save_mbr_library: True   # output library
 
 library_loading:
   rt_heuristic: 180

alphadia/outputtransform.py

@@ -368,7 +368,6 @@ def build(
         _ = self.build_library(
             base_spec_lib,
             psm_df=psm_df,
-            save=self.config["general"]["save_mbr_library"],
         )
 
         if self.config["transfer_library"]["enabled"]:
@@ -775,7 +774,6 @@ def build_library(
         self,
         base_spec_lib: base.SpecLibBase,
         psm_df: pd.DataFrame | None = None,
-        save: bool = True,
     ):
         """Build spectral library
 
@@ -788,9 +786,6 @@ def build_library(
         psm_df: Union[pd.DataFrame, None]
             Combined precursor table. If None, the precursor table is loaded from disk.
 
-        save: bool
-            Save the generated spectral library to disk
-
         """
         logger.progress("Building spectral library")
 
@@ -812,7 +807,7 @@ def build_library(
             f"MBR spectral library contains {precursor_number:,} precursors, {protein_number:,} proteins"
         )
 
-        if save:
+        if self.config["general"]["save_mbr_library"]:
             logger.info("Writing MBR spectral library to disk")
             mbr_spec_lib.save_hdf(os.path.join(self.output_folder, "speclib.mbr.hdf"))