Merge branch 'main' into better_error_in_load

Author: h-mayorquin

src/spikeinterface/core/base.py

@@ -7,7 +7,6 @@
 import weakref
 import json
 import pickle
-import os
 import random
 import string
 from packaging.version import parse
@@ -956,13 +955,14 @@ def save_to_folder(
         folder.mkdir(parents=True, exist_ok=False)
 
         # dump provenance
-        provenance_file = folder / f"provenance.json"
         if self.check_serializability("json"):
+            provenance_file = folder / f"provenance.json"
+            self.dump(provenance_file)
+        elif self.check_serializability("pickle"):
+            provenance_file = folder / f"provenance.pkl"
             self.dump(provenance_file)
         else:
-            provenance_file.write_text(
-                json.dumps({"warning": "the provenace is not json serializable!!!"}), encoding="utf8"
-            )
+            warnings.warn("The extractor is not serializable to file. The provenance will not be saved.")
 
         self.save_metadata_to_folder(folder)
 
@@ -1029,7 +1029,6 @@ def save_to_zarr(
         cached: ZarrExtractor
             Saved copy of the extractor.
         """
-        import zarr
         from .zarrextractors import read_zarr
 
         save_kwargs.pop("format", None)

src/spikeinterface/core/generate.py

@@ -1803,6 +1803,8 @@ def __init__(
             )
             self.add_recording_segment(recording_segment)
 
+        # to discuss: maybe we could set json serializability to False always
+        # because templates could be large!
         if not sorting.check_serializability("json"):
             self._serializability["json"] = False
         if parent_recording is not None:

src/spikeinterface/extractors/extractorlist.py

@@ -116,3 +116,21 @@
 event_extractor_full_list += neo_event_extractors_list
 
 snippets_extractor_full_list = [NpySnippetsExtractor, WaveClusSnippetsExtractor]
+
+recording_extractor_full_dict = {}
+for rec_class in recording_extractor_full_list:
+    # here we get the class name, remove "Recording" and "Extractor" and make it lower case
+    rec_class_name = rec_class.__name__.replace("Recording", "").replace("Extractor", "").lower()
+    recording_extractor_full_dict[rec_class_name] = rec_class
+
+sorting_extractor_full_dict = {}
+for sort_class in sorting_extractor_full_list:
+    # here we get the class name, remove "Extractor" and make it lower case
+    sort_class_name = sort_class.__name__.replace("Sorting", "").replace("Extractor", "").lower()
+    sorting_extractor_full_dict[sort_class_name] = sort_class
+
+event_extractor_full_dict = {}
+for event_class in event_extractor_full_list:
+    # here we get the class name, remove "Extractor" and make it lower case
+    event_class_name = event_class.__name__.replace("Event", "").replace("Extractor", "").lower()
+    event_extractor_full_dict[event_class_name] = event_class

src/spikeinterface/extractors/neoextractors/__init__.py

@@ -36,7 +36,7 @@
 )
 from .spike2 import Spike2RecordingExtractor, read_spike2
 from .spikegadgets import SpikeGadgetsRecordingExtractor, read_spikegadgets
-from .spikeglx import SpikeGLXRecordingExtractor, read_spikeglx
+from .spikeglx import SpikeGLXRecordingExtractor, SpikeGLXEventExtractor, read_spikeglx, read_spikeglx_event
 from .tdt import TdtRecordingExtractor, read_tdt
 
 from .neo_utils import get_neo_streams, get_neo_num_blocks
@@ -73,4 +73,9 @@
     Plexon2SortingExtractor,
 ]
 
-neo_event_extractors_list = [AlphaOmegaEventExtractor, OpenEphysBinaryEventExtractor, Plexon2EventExtractor]
+neo_event_extractors_list = [
+    AlphaOmegaEventExtractor,
+    OpenEphysBinaryEventExtractor,
+    Plexon2EventExtractor,
+    SpikeGLXEventExtractor,
+]

src/spikeinterface/generation/drift_tools.py

@@ -458,6 +458,9 @@ def __init__(
 
         self.set_probe(drifting_templates.probe, in_place=True)
 
+        # templates are too large, we don't serialize them to JSON
+        self._serializability["json"] = False
+
         self._kwargs = {
             "sorting": sorting,
             "drifting_templates": drifting_templates,