more fix after merge with main and the new pickle to file mechanism

src/spikeinterface/comparison/groundtruthstudy.py

@@ -194,10 +194,12 @@ def run_sorters(self, case_keys=None, engine='loop', engine_kwargs={}, keep=True
             sorter_name = params.pop("sorter_name")
             job = dict(sorter_name=sorter_name,
                        recording=recording,
-                       output_folder=sorter_folder)
+                       output_folder=sorter_folder,
+                       )
             job.update(params)
             # the verbose is overwritten and global to all run_sorters
             job["verbose"] = verbose
+            job["with_output"] = False
             job_list.append(job)
 
         run_sorter_jobs(job_list, engine=engine, engine_kwargs=engine_kwargs, return_output=False)
@@ -217,7 +219,8 @@ def copy_sortings(self, case_keys=None, force=True):
 
 
             if (sorter_folder / "spikeinterface_log.json").exists():
-                sorting = read_sorter_folder(sorter_folder, raise_error=False)
+                sorting = read_sorter_folder(sorter_folder, raise_error=False,
+                                             register_recording=False, sorting_info=False)
             else:
                 sorting = None
 
@@ -383,13 +386,12 @@ def get_count_units(
             index = pd.MultiIndex.from_tuples(case_keys, names=self.levels)
 
 
-        columns = ["num_gt", "num_sorter", "num_well_detected", "num_redundant", "num_overmerged"]
+        columns = ["num_gt", "num_sorter", "num_well_detected"]
         comp = self.comparisons[case_keys[0]]
         if comp.exhaustive_gt:
-            columns.extend(["num_false_positive", "num_bad"])
+            columns.extend(["num_false_positive", "num_redundant", "num_overmerged", "num_bad"])
         count_units = pd.DataFrame(index=index, columns=columns, dtype=int)
 
-
         for key in case_keys:
             comp = self.comparisons.get(key, None)
             assert comp is not None, "You need to do study.run_comparisons() first"
@@ -402,11 +404,12 @@ def get_count_units(
             count_units.loc[key, "num_well_detected"] = comp.count_well_detected_units(
                 well_detected_score
             )
-            count_units.loc[key, "num_overmerged"] = comp.count_overmerged_units(
-                overmerged_score
-            )
-            count_units.loc[key, "num_redundant"] = comp.count_redundant_units(redundant_score)
+
             if comp.exhaustive_gt:
+                count_units.loc[key, "num_redundant"] = comp.count_redundant_units(redundant_score)
+                count_units.loc[key, "num_overmerged"] = comp.count_overmerged_units(
+                    overmerged_score
+                )
                 count_units.loc[key, "num_false_positive"] = comp.count_false_positive_units(
                     redundant_score
                 )

src/spikeinterface/sorters/basesorter.py

@@ -202,7 +202,7 @@ def load_recording_from_folder(cls, output_folder, with_warnings=False):
                 recording = None
             else:
                 recording = load_extractor(json_file, base_folder=output_folder)
-        elif pickle_file.exits():
+        elif pickle_file.exists():
             recording = load_extractor(pickle_file)
 
         return recording
@@ -324,8 +324,12 @@ def get_result_from_folder(cls, output_folder, register_recording=True, sorting_
 
         if sorting_info:
             # set sorting info to Sorting object
-            with open(output_folder / "spikeinterface_recording.json", "r") as f:
-                rec_dict = json.load(f)
+            if (output_folder / "spikeinterface_recording.json").exists():
+                with open(output_folder / "spikeinterface_recording.json", "r") as f:
+                    rec_dict = json.load(f)
+            else:
+                rec_dict = None
+
             with open(output_folder / "spikeinterface_params.json", "r") as f:
                 params_dict = json.load(f)
             with open(output_folder / "spikeinterface_log.json", "r") as f:

src/spikeinterface/sorters/launcher.py

@@ -66,7 +66,8 @@ def run_sorter_jobs(job_list, engine="loop", engine_kwargs={}, return_output=Fal
     engine_kwargs: dict
 
     return_output: bool, dfault False
-        Return a sorting or None.
+        Return a sortings or None.
+        This also overwrite kwargs in  in run_sorter(with_sorting=True/False)
 
     Returns
     -------
@@ -88,8 +89,13 @@ def run_sorter_jobs(job_list, engine="loop", engine_kwargs={}, return_output=Fal
             "processpoolexecutor",
         ), "Only 'loop', 'joblib', and 'processpoolexecutor' support return_output=True."
         out = []
+        for kwargs in job_list:
+            kwargs['with_output'] = True
     else:
         out = None
+        for kwargs in job_list:
+            kwargs['with_output'] = False
+
 
     if engine == "loop":
         # simple loop in main process