Don't follow symlinks when storing extractor paths

src/spikeinterface/core/zarrextractors.py

@@ -625,7 +625,7 @@ def resolve_zarr_path(folder_path: str | Path):
         return folder_path, folder_path
     else:
         folder_path = Path(folder_path)
-        folder_path_kwarg = str(Path(folder_path).resolve())
+        folder_path_kwarg = str(Path(folder_path).absolute())
         return folder_path, folder_path_kwarg
 
 

src/spikeinterface/extractors/alfsortingextractor.py

@@ -11,6 +11,7 @@ class ALFSortingExtractor(BaseSorting):
 
     Parameters
     ----------
+
     folder_path : str or Path
         Path to the ALF folder.
     sampling_frequency : int, default: 30000
@@ -40,7 +41,7 @@ def __init__(self, folder_path, sampling_frequency=30000):
         sorting_segment = ALFSortingSegment(spikes["clusters"], spikes["samples"])
         self.add_sorting_segment(sorting_segment)
         self.extra_requirements.append("ONE-api")
-        self._kwargs = {"folder_path": str(Path(folder_path).resolve()), "sampling_frequency": sampling_frequency}
+        self._kwargs = {"folder_path": str(Path(folder_path).absolute()), "sampling_frequency": sampling_frequency}
 
 
 class ALFSortingSegment(BaseSortingSegment):

src/spikeinterface/extractors/cbin_ibl.py

@@ -194,9 +194,9 @@ def __init__(self, folder_path=None, load_sync_channel=False, stream_name="ap",
             self.set_property("inter_sample_shift", sample_shifts)
 
         self._kwargs = {
-            "folder_path": str(Path(folder_path).resolve()),
+            "folder_path": str(Path(folder_path).absolute()),
             "load_sync_channel": load_sync_channel,
-            "cbin_file_path": str(Path(cbin_file_path).resolve()),
+            "cbin_file_path": str(Path(cbin_file_path).absolute()),
         }
 
 

src/spikeinterface/extractors/matlabhelpers.py

@@ -32,7 +32,7 @@ def __init__(self, file_path):
         if not isinstance(file_path, Path):
             raise TypeError(f"Expected a str or Path file_path but got '{type(file_path).__name__}'")
 
-        file_path = file_path.resolve()  # get absolute path to this file
+        file_path = file_path.absolute()  # get absolute path to this file
         if not file_path.is_file():
             raise ValueError(f"Specified file path '{file_path}' is not a file.")
 

src/spikeinterface/extractors/neoextractors/intan.py

@@ -70,7 +70,7 @@ def __init__(
             self._add_channel_groups()
 
         self._kwargs.update(
-            dict(file_path=str(Path(file_path).resolve()), ignore_integrity_checks=ignore_integrity_checks),
+            dict(file_path=str(Path(file_path).absolute()), ignore_integrity_checks=ignore_integrity_checks),
         )
 
     @classmethod
@@ -195,7 +195,7 @@ def __init__(
 
         # Update kwargs to include our specific parameters
         self._kwargs = dict(
-            folder_path=str(Path(folder_path).resolve()),
+            folder_path=str(Path(folder_path).absolute()),
             mode=mode,
             stream_id=stream_id,
             stream_name=stream_name,

src/spikeinterface/extractors/neoextractors/neuronexus.py

@@ -51,7 +51,7 @@ def __init__(
             **neo_kwargs,
         )
 
-        self._kwargs.update(dict(file_path=str(Path(file_path).resolve())))
+        self._kwargs.update(dict(file_path=str(Path(file_path).absolute())))
 
     @classmethod
     def map_to_neo_kwargs(cls, file_path):

src/spikeinterface/extractors/neoextractors/plexon.py

@@ -54,7 +54,7 @@ def __init__(
             use_names_as_ids=use_names_as_ids,
             **neo_kwargs,
         )
-        self._kwargs.update({"file_path": str(Path(file_path).resolve())})
+        self._kwargs.update({"file_path": str(Path(file_path).absolute())})
 
     @classmethod
     def map_to_neo_kwargs(cls, file_path):
@@ -82,7 +82,7 @@ def __init__(self, file_path):
         self.neo_reader = NeoBaseSortingExtractor.get_neo_io_reader(self.NeoRawIOClass, **neo_kwargs)
         sampling_frequency = self.neo_reader._global_ssampling_rate
         NeoBaseSortingExtractor.__init__(self, sampling_frequency=sampling_frequency, **neo_kwargs)
-        self._kwargs = {"file_path": str(Path(file_path).resolve())}
+        self._kwargs = {"file_path": str(Path(file_path).absolute())}
 
     @classmethod
     def map_to_neo_kwargs(cls, file_path):

src/spikeinterface/extractors/nwbextractors.py

@@ -1070,7 +1070,7 @@ def __init__(
                 self.set_property(property_name, values)
 
         if stream_mode is None and file_path is not None:
-            file_path = str(Path(file_path).resolve())
+            file_path = str(Path(file_path).absolute())
 
         if stream_mode == "fsspec" and stream_cache_path is not None:
             stream_cache_path = str(Path(self.stream_cache_path).absolute())
@@ -1404,7 +1404,7 @@ def __init__(
             self.extra_requirements.append(stream_mode)
 
         if stream_mode is None and file_path is not None:
-            file_path = str(Path(file_path).resolve())
+            file_path = str(Path(file_path).absolute())
 
         if storage_options is not None and stream_mode == "zarr":
             warnings.warn(