updated config

alphadia/planning.py

@@ -165,7 +165,7 @@ def load_library(self, spec_lib_path):
         ])
 
         speclib = import_pipeline(spec_lib_path)
-        if self.config['library']['save_hdf']:
+        if self.config['library_loading']['save_hdf']:
             speclib.save_hdf(os.path.join(self.output_folder, 'speclib.hdf'))
 
         self.spectral_library = prepare_pipeline(speclib)
@@ -177,9 +177,10 @@ def get_run_data(self):
             raise ValueError('no spectral library loaded')
 
         # iterate over raw files and yield raw data and spectral library
-        for raw_location in self.raw_file_list:
-
+        for i, raw_location in enumerate(self.raw_file_list):
             raw_name = Path(raw_location).stem
+            logger.progress(f'Loading raw file {i+1}/{len(self.raw_file_list)}: {raw_name}')
+
             yield raw_name, raw_location, self.spectral_library
 
     def run(self, 

misc/config/default.yaml

@@ -14,6 +14,7 @@ library_loading:
   # rt_type: 'norm'
   channel_filter: '0'
   exclude_shared_ions: True
+  save_hdf: False
 
 calibration:
   min_epochs: 3
@@ -85,10 +86,6 @@ multiplexing:
   reference_channel: 0
   competetive_scoring: True
 
-library:
-  isotopes: 4
-  save_hdf: False
-
 # configuration for the optimization manager
 # initial parameters, will nbe optimized
 optimization_manager: