Merge pull request #2238 from alejoe91/fix-serializability-typo

Fix typo: `_serializablility` -> `_serializability`

src/spikeinterface/comparison/hybrid.py

@@ -84,7 +84,7 @@ def __init__(
             )
         # save injected sorting if necessary
         self.injected_sorting = injected_sorting
-        if not self.injected_sorting.check_serializablility("json"):
+        if not self.injected_sorting.check_serializability("json"):
             # TODO later : also use pickle
             assert injected_sorting_folder is not None, "Provide injected_sorting_folder to injected sorting object"
             self.injected_sorting = self.injected_sorting.save(folder=injected_sorting_folder)
@@ -181,7 +181,7 @@ def __init__(
             self.injected_sorting = injected_sorting
 
         # save injected sorting if necessary
-        if not self.injected_sorting.check_serializablility("json"):
+        if not self.injected_sorting.check_serializability("json"):
             # TODO later : also use pickle
             assert injected_sorting_folder is not None, "Provide injected_sorting_folder to injected sorting object"
             self.injected_sorting = self.injected_sorting.save(folder=injected_sorting_folder)

src/spikeinterface/comparison/multicomparisons.py

@@ -189,9 +189,9 @@ def save_to_folder(self, save_folder):
             stacklevel=2,
         )
         for sorting in self.object_list:
-            assert sorting.check_serializablility(
+            assert sorting.check_serializability(
                 "json"
-            ), "MultiSortingComparison.save_to_folder() need json serializable sortings"
+            ), "MultiSortingComparison.save_to_folder() needs json serializable sortings"
 
         save_folder = Path(save_folder)
         save_folder.mkdir(parents=True, exist_ok=True)
@@ -259,8 +259,8 @@ def __init__(
 
         BaseSorting.__init__(self, sampling_frequency=sampling_frequency, unit_ids=unit_ids)
 
-        self._serializablility["json"] = False
-        self._serializablility["pickle"] = True
+        self._serializability["json"] = False
+        self._serializability["pickle"] = True
 
         if len(unit_ids) > 0:
             for k in ("agreement_number", "avg_agreement", "unit_ids"):

src/spikeinterface/core/base.py

@@ -62,7 +62,7 @@ def __init__(self, main_ids: Sequence) -> None:
         #  * number of units for sorting
         self._properties = {}
 
-        self._serializablility = {"memory": True, "json": True, "pickle": True}
+        self._serializability = {"memory": True, "json": True, "pickle": True}
 
         # extractor specific list of pip extra requirements
         self.extra_requirements = []
@@ -507,22 +507,22 @@ def clone(self) -> "BaseExtractor":
         clone = BaseExtractor.from_dict(d)
         return clone
 
-    def check_serializablility(self, type):
+    def check_serializability(self, type):
         kwargs = self._kwargs
         for value in kwargs.values():
             # here we check if the value is a BaseExtractor, a list of BaseExtractors, or a dict of BaseExtractors
             if isinstance(value, BaseExtractor):
-                if not value.check_serializablility(type=type):
+                if not value.check_serializability(type=type):
                     return False
             elif isinstance(value, list):
                 for v in value:
-                    if isinstance(v, BaseExtractor) and not v.check_serializablility(type=type):
+                    if isinstance(v, BaseExtractor) and not v.check_serializability(type=type):
                         return False
             elif isinstance(value, dict):
                 for v in value.values():
-                    if isinstance(v, BaseExtractor) and not v.check_serializablility(type=type):
+                    if isinstance(v, BaseExtractor) and not v.check_serializability(type=type):
                         return False
-        return self._serializablility[type]
+        return self._serializability[type]
 
     def check_if_memory_serializable(self):
         """
@@ -533,7 +533,7 @@ def check_if_memory_serializable(self):
         bool
             True if the object is memory serializable, False otherwise.
         """
-        return self.check_serializablility("memory")
+        return self.check_serializability("memory")
 
     def check_if_json_serializable(self):
         """
@@ -546,11 +546,11 @@ def check_if_json_serializable(self):
         """
         # we keep this for backward compatilibity or not ????
         # is this needed ??? I think no.
-        return self.check_serializablility("json")
+        return self.check_serializability("json")
 
     def check_if_pickle_serializable(self):
         # is this needed ??? I think no.
-        return self.check_serializablility("pickle")
+        return self.check_serializability("pickle")
 
     @staticmethod
     def _get_file_path(file_path: Union[str, Path], extensions: Sequence) -> Path:
@@ -623,7 +623,7 @@ def dump_to_json(
         folder_metadata: str, Path, or None
             Folder with files containing additional information (e.g. probe in BaseRecording) and properties
         """
-        assert self.check_serializablility("json"), "The extractor is not json serializable"
+        assert self.check_serializability("json"), "The extractor is not json serializable"
 
         # Writing paths as relative_to requires recursively expanding the dict
         if relative_to:
@@ -882,7 +882,7 @@ def save_to_folder(self, name=None, folder=None, overwrite=False, verbose=True,
 
         # dump provenance
         provenance_file = folder / f"provenance.json"
-        if self.check_serializablility("json"):
+        if self.check_serializability("json"):
             self.dump(provenance_file)
         else:
             provenance_file.write_text(

src/spikeinterface/core/generate.py

@@ -1085,7 +1085,7 @@ def __init__(
         dtype = parent_recording.dtype if parent_recording is not None else templates.dtype
         BaseRecording.__init__(self, sorting.get_sampling_frequency(), channel_ids, dtype)
 
-        # Important : self._serializablility is not change here because it will depend on the sorting parents itself.
+        # Important : self._serializability is not change here because it will depend on the sorting parents itself.
 
         n_units = len(sorting.unit_ids)
         assert len(templates) == n_units

src/spikeinterface/core/numpyextractors.py

@@ -66,8 +66,8 @@ def __init__(self, traces_list, sampling_frequency, t_starts=None, channel_ids=N
             assert len(t_starts) == len(traces_list), "t_starts must be a list of same size than traces_list"
             t_starts = [float(t_start) for t_start in t_starts]
 
-        self._serializablility["json"] = False
-        self._serializablility["pickle"] = False
+        self._serializability["json"] = False
+        self._serializability["pickle"] = False
 
         for i, traces in enumerate(traces_list):
             if t_starts is None:
@@ -129,10 +129,10 @@ def __init__(self, spikes, sampling_frequency, unit_ids):
         """ """
         BaseSorting.__init__(self, sampling_frequency, unit_ids)
 
-        self._serializablility["memory"] = True
-        self._serializablility["json"] = False
+        self._serializability["memory"] = True
+        self._serializability["json"] = False
         # theorically this should be False but for simplicity make generators simples we still need this.
-        self._serializablility["pickle"] = True
+        self._serializability["pickle"] = True
 
         if spikes.size == 0:
             nseg = 1
@@ -367,9 +367,9 @@ def __init__(self, shm_name, shape, sampling_frequency, unit_ids, dtype=minimum_
 
         BaseSorting.__init__(self, sampling_frequency, unit_ids)
 
-        self._serializablility["memory"] = True
-        self._serializablility["json"] = False
-        self._serializablility["pickle"] = False
+        self._serializability["memory"] = True
+        self._serializability["json"] = False
+        self._serializability["pickle"] = False
 
         self.shm = SharedMemory(shm_name, create=False)
         self.shm_spikes = np.ndarray(shape=shape, dtype=dtype, buffer=self.shm.buf)
@@ -527,9 +527,9 @@ def __init__(self, snippets_list, spikesframes_list, sampling_frequency, nbefore
             dtype=dtype,
         )
 
-        self._serializablility["memory"] = False
-        self._serializablility["json"] = False
-        self._serializablility["pickle"] = False
+        self._serializability["memory"] = False
+        self._serializability["json"] = False
+        self._serializability["pickle"] = False
 
         for snippets, spikesframes in zip(snippets_list, spikesframes_list):
             snp_segment = NumpySnippetsSegment(snippets, spikesframes)

src/spikeinterface/core/old_api_utils.py

@@ -182,9 +182,9 @@ def __init__(self, oldapi_recording_extractor):
         )
 
         # set to False to use dumping mechanism of old extractor
-        self._serializablility["memory"] = False
-        self._serializablility["json"] = False
-        self._serializablility["pickle"] = False
+        self._serializability["memory"] = False
+        self._serializability["json"] = False
+        self._serializability["pickle"] = False
 
         self.annotate(is_filtered=oldapi_recording_extractor.is_filtered)
 
@@ -269,9 +269,9 @@ def __init__(self, oldapi_sorting_extractor):
         sorting_segment = OldToNewSortingSegment(oldapi_sorting_extractor)
         self.add_sorting_segment(sorting_segment)
 
-        self._serializablility["memory"] = False
-        self._serializablility["json"] = False
-        self._serializablility["pickle"] = False
+        self._serializability["memory"] = False
+        self._serializability["json"] = False
+        self._serializability["pickle"] = False
 
         # add old properties
         copy_properties(oldapi_extractor=oldapi_sorting_extractor, new_extractor=self)

src/spikeinterface/core/tests/test_base.py

@@ -40,7 +40,7 @@ def test_check_if_memory_serializable():
         assert extractor.check_if_memory_serializable()
 
     # make not not memory serilizable
-    test_extractor._serializablility["memory"] = False
+    test_extractor._serializability["memory"] = False
     extractors_not_mem_serializable = make_nested_extractors(test_extractor)
     for extractor in extractors_not_mem_serializable:
         assert not extractor.check_if_memory_serializable()
@@ -50,18 +50,18 @@ def test_check_if_serializable():
     test_extractor = generate_recording(seed=0, durations=[2])
 
     # make a list of json serializable objects
-    test_extractor._serializablility["json"] = True
+    test_extractor._serializability["json"] = True
     extractors_json_serializable = make_nested_extractors(test_extractor)
     for extractor in extractors_json_serializable:
         print(extractor)
-        assert extractor.check_serializablility("json")
+        assert extractor.check_serializability("json")
 
     # make of not json serializable objects
-    test_extractor._serializablility["json"] = False
+    test_extractor._serializability["json"] = False
     extractors_not_json_serializable = make_nested_extractors(test_extractor)
     for extractor in extractors_not_json_serializable:
         print(extractor)
-        assert not extractor.check_serializablility("json")
+        assert not extractor.check_serializability("json")
 
 
 if __name__ == "__main__":

src/spikeinterface/core/tests/test_jsonification.py

@@ -144,9 +144,9 @@ def __init__(self, attribute, other_extractor=None, extractor_list=None, extract
 
         BaseExtractor.__init__(self, main_ids=["1", "2"])
         # this already the case by default
-        self._serializablility["memory"] = True
-        self._serializablility["json"] = True
-        self._serializablility["pickle"] = True
+        self._serializability["memory"] = True
+        self._serializability["json"] = True
+        self._serializability["pickle"] = True
 
         self._kwargs = {
             "attribute": attribute,

src/spikeinterface/core/waveform_extractor.py

@@ -284,14 +284,14 @@ def create(
             else:
                 relative_to = None
 
-            if recording.check_serializablility("json"):
+            if recording.check_serializability("json"):
                 recording.dump(folder / "recording.json", relative_to=relative_to)
-            elif recording.check_serializablility("pickle"):
+            elif recording.check_serializability("pickle"):
                 recording.dump(folder / "recording.pickle", relative_to=relative_to)
 
-            if sorting.check_serializablility("json"):
+            if sorting.check_serializability("json"):
                 sorting.dump(folder / "sorting.json", relative_to=relative_to)
-            elif sorting.check_serializablility("pickle"):
+            elif sorting.check_serializability("pickle"):
                 sorting.dump(folder / "sorting.pickle", relative_to=relative_to)
             else:
                 warn(
@@ -920,14 +920,14 @@ def save(
             (folder / "params.json").write_text(json.dumps(check_json(self._params), indent=4), encoding="utf8")
 
             if self.has_recording():
-                if self.recording.check_serializablility("json"):
+                if self.recording.check_serializability("json"):
                     self.recording.dump(folder / "recording.json", relative_to=relative_to)
-                elif self.recording.check_serializablility("pickle"):
+                elif self.recording.check_serializability("pickle"):
                     self.recording.dump(folder / "recording.pickle", relative_to=relative_to)
 
-            if self.sorting.check_serializablility("json"):
+            if self.sorting.check_serializability("json"):
                 self.sorting.dump(folder / "sorting.json", relative_to=relative_to)
-            elif self.sorting.check_serializablility("pickle"):
+            elif self.sorting.check_serializability("pickle"):
                 self.sorting.dump(folder / "sorting.pickle", relative_to=relative_to)
             else:
                 warn(
@@ -977,10 +977,10 @@ def save(
             # write metadata
             zarr_root.attrs["params"] = check_json(self._params)
             if self.has_recording():
-                if self.recording.check_serializablility("json"):
+                if self.recording.check_serializability("json"):
                     rec_dict = self.recording.to_dict(relative_to=relative_to, recursive=True)
                     zarr_root.attrs["recording"] = check_json(rec_dict)
-            if self.sorting.check_serializablility("json"):
+            if self.sorting.check_serializability("json"):
                 sort_dict = self.sorting.to_dict(relative_to=relative_to, recursive=True)
                 zarr_root.attrs["sorting"] = check_json(sort_dict)
             else:

src/spikeinterface/preprocessing/motion.py

@@ -333,7 +333,7 @@ def correct_motion(
         )
         (folder / "parameters.json").write_text(json.dumps(parameters, indent=4, cls=SIJsonEncoder), encoding="utf8")
         (folder / "run_times.json").write_text(json.dumps(run_times, indent=4), encoding="utf8")
-        if recording.check_serializablility("json"):
+        if recording.check_serializability("json"):
             recording.dump_to_json(folder / "recording.json")
 
         np.save(folder / "peaks.npy", peaks)

src/spikeinterface/sorters/basesorter.py

@@ -137,9 +137,9 @@ def initialize_folder(cls, recording, output_folder, verbose, remove_existing_fo
                 )
 
         rec_file = output_folder / "spikeinterface_recording.json"
-        if recording.check_serializablility("json"):
-            recording.dump(rec_file, relative_to=output_folder)
-        elif recording.check_serializablility("pickle"):
+        if recording.check_serializability("json"):
+            recording.dump(rec_file)
+        elif recording.check_serializability("pickle"):
             recording.dump(output_folder / "spikeinterface_recording.pickle", relative_to=output_folder)
         else:
             # TODO: deprecate and finally remove this after 0.100