minor improvements

MannLabs · Dec 18, 2024 · 93d17c6 · 93d17c6
1 parent 8dd7d3c
commit 93d17c6
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Showing 2 changed files with 9 additions and 16 deletions.
diff --git a/alphadia/cli.py b/alphadia/cli.py
@@ -249,17 +249,11 @@ def run(*args, **kwargs):
         return
     reporting.init_logging(output_directory)
 
-    raw_path_list = parse_raw_path_list(args, config)
-
-    quant_dir = args.quant_dir
-    library_path = args.library
-    fasta_path_list = args.fasta
-
     cli_params_config = {
-        ConfigKeys.RAW_PATH_LIST: raw_path_list,
-        ConfigKeys.LIBRARY_PATH: library_path,
-        ConfigKeys.FASTA_PATH_LIST: fasta_path_list,
-        ConfigKeys.QUANT_DIR: quant_dir,
+        ConfigKeys.RAW_PATH_LIST: parse_raw_path_list(args, config),
+        ConfigKeys.LIBRARY_PATH: args.library,
+        ConfigKeys.FASTA_PATH_LIST: args.fasta,
+        ConfigKeys.QUANT_DIR: args.quant_dir,
     }
 
     # TODO rename all output_directory, output_folder => output_path, quant_dir->quant_path (except cli parameter)

diff --git a/alphadia/search_plan.py b/alphadia/search_plan.py
@@ -156,15 +156,14 @@ def run_plan(self):
                     self._library_step_output_dir
                 )
 
+            mbr_step_library_path = str(
+                self._library_step_output_dir / f"{SearchPlanOutput.LIBRARY_OUTPUT}.hdf"
+            )
+
             mbr_step_extra_config = (
                 self._multistep_config[MBR_STEP_NAME]
                 | optimized_values_config
-                | {
-                    ConfigKeys.LIBRARY_PATH: str(
-                        self._library_step_output_dir
-                        / f"{SearchPlanOutput.LIBRARY_OUTPUT}.hdf"
-                    )
-                }
+                | {ConfigKeys.LIBRARY_PATH: mbr_step_library_path}
             )
             self.run_step(
                 self._output_dir,