Update lower bound python support to 3.10

pyproject.toml

@@ -7,7 +7,7 @@ authors = [
 ]
 description = "Python toolkit for analysis, visualization, and comparison of spike sorting output"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
     "Programming Language :: Python :: 3 :: Only",
     "License :: OSI Approved :: MIT License",

src/spikeinterface/benchmark/benchmark_base.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from pathlib import Path
 import shutil
 import json

src/spikeinterface/benchmark/benchmark_clustering.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from spikeinterface.sortingcomponents.clustering import find_clusters_from_peaks
 from spikeinterface.core import NumpySorting
 from spikeinterface.comparison import GroundTruthComparison

src/spikeinterface/benchmark/benchmark_matching.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import warnings
 
 from spikeinterface.sortingcomponents.matching import find_spikes_from_templates

src/spikeinterface/benchmark/benchmark_merging.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from spikeinterface.curation.auto_merge import auto_merge_units
 from spikeinterface.comparison import compare_sorter_to_ground_truth
 from spikeinterface.core.sortinganalyzer import create_sorting_analyzer

src/spikeinterface/benchmark/benchmark_motion_estimation.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import json
 from pathlib import Path
 import pickle

src/spikeinterface/benchmark/benchmark_motion_interpolation.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import numpy as np
 
 

src/spikeinterface/benchmark/benchmark_peak_detection.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from spikeinterface.sortingcomponents.peak_detection import detect_peaks
 from spikeinterface.core import NumpySorting
 from spikeinterface.comparison import GroundTruthComparison

src/spikeinterface/benchmark/benchmark_peak_localization.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from spikeinterface.postprocessing.localization_tools import (
     compute_center_of_mass,
     compute_monopolar_triangulation,

src/spikeinterface/benchmark/benchmark_peak_selection.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from spikeinterface.sortingcomponents.clustering import find_clusters_from_peaks
 from spikeinterface.core import NumpySorting
 from spikeinterface.comparison import GroundTruthComparison

src/spikeinterface/comparison/basecomparison.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from copy import deepcopy
 from typing import OrderedDict
 from concurrent.futures import ProcessPoolExecutor

src/spikeinterface/comparison/collision.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import importlib
 
 from .paircomparisons import GroundTruthComparison

src/spikeinterface/comparison/comparisontools.py

@@ -2,8 +2,6 @@
 Some functions internally use by SortingComparison.
 """
 
-from __future__ import annotations
-
 from spikeinterface.core.basesorting import BaseSorting
 
 import numpy as np

src/spikeinterface/comparison/correlogram.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from .paircomparisons import GroundTruthComparison
 
 # this import was previously used. Leave for now.

src/spikeinterface/comparison/hybrid.py

@@ -1,9 +1,6 @@
-from __future__ import annotations
-
 import warnings
 
 from pathlib import Path
-from typing import List, Union
 import numpy as np
 from spikeinterface.core import (
     BaseRecording,
@@ -65,13 +62,13 @@ def __init__(
         self,
         parent_recording: BaseRecording,
         templates: np.ndarray,
-        injected_sorting: Union[BaseSorting, None] = None,
-        nbefore: Union[List[int], int, None] = None,
+        injected_sorting: BaseSorting | None = None,
+        nbefore: list[int] | int | None = None,
         firing_rate: float = 10,
-        amplitude_factor: Union[np.ndarray, None] = None,
+        amplitude_factor: np.ndarray | None = None,
         amplitude_std: float = 0.0,
         refractory_period_ms: float = 2.0,
-        injected_sorting_folder: Union[str, Path, None] = None,
+        injected_sorting_folder: str | Path | None = None,
         seed=None,
     ):
 
@@ -172,12 +169,12 @@ class HybridSpikesRecording(InjectTemplatesRecording):
     def __init__(
         self,
         wvf_extractor,
-        injected_sorting: Union[BaseSorting, None] = None,
-        unit_ids: Union[List[int], None] = None,
+        injected_sorting: BaseSorting | None = None,
+        unit_ids: list[int] | None = None,
         max_injected_per_unit: int = 1000,
         injected_rate: float = 0.05,
         refractory_period_ms: float = 1.5,
-        injected_sorting_folder: Union[str, Path, None] = None,
+        injected_sorting_folder: str | Path | None = None,
     ) -> None:
 
         warnings.warn(

src/spikeinterface/comparison/multicomparisons.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 from pathlib import Path
 import json
 import pickle

src/spikeinterface/comparison/paircomparisons.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import numpy as np
 
 from spikeinterface.core import BaseSorting

src/spikeinterface/core/analyzer_extension_core.py

@@ -677,7 +677,7 @@ def get_templates(self, unit_ids=None, operator="average", percentile=None, save
 
         Returns
         -------
-        templates : np.array | Templates
+        templates :np.ndarray | Templates
             The returned templates (num_units, num_samples, num_channels)
         """
         if operator != "percentile":

src/spikeinterface/core/base.py

@@ -1,7 +1,9 @@
 from __future__ import annotations
+
 from pathlib import Path
 import shutil
-from typing import Any, Iterable, List, Optional, Sequence, Union
+from typing import Any
+from collections.abc import Iterable, Sequence
 import importlib
 import warnings
 import weakref
@@ -144,11 +146,11 @@ def get_num_segments(self) -> int:
         # This is implemented in BaseRecording or BaseSorting
         raise NotImplementedError
 
-    def get_parent(self) -> Optional[BaseExtractor]:
+    def get_parent(self) -> BaseExtractor | None:
         """Returns parent object if it exists, otherwise None"""
         return getattr(self, "_parent", None)
 
-    def _check_segment_index(self, segment_index: Optional[int] = None) -> int:
+    def _check_segment_index(self, segment_index: int | None = None) -> int:
         if segment_index is None:
             if self.get_num_segments() == 1:
                 return 0
@@ -251,7 +253,7 @@ def get_annotation(self, key: str, copy: bool = True) -> Any:
             v = deepcopy(v)
         return v
 
-    def get_annotation_keys(self) -> List:
+    def get_annotation_keys(self) -> list:
         return list(self._annotations.keys())
 
     def set_property(
@@ -361,14 +363,14 @@ def set_property(
                 self._properties[key] = np.zeros_like(values, dtype=values.dtype)
                 self._properties[key][indices] = values
 
-    def get_property(self, key: str, ids: Optional[Iterable] = None) -> np.ndarray:
+    def get_property(self, key: str, ids: Iterable | None = None) -> np.ndarray:
         values = self._properties.get(key, None)
         if ids is not None and values is not None:
             inds = self.ids_to_indices(ids)
             values = values[inds]
         return values
 
-    def get_property_keys(self) -> List:
+    def get_property_keys(self) -> list:
         return list(self._properties.keys())
 
     def delete_property(self, key) -> None:
@@ -379,10 +381,10 @@ def delete_property(self, key) -> None:
 
     def copy_metadata(
         self,
-        other: "BaseExtractor",
+        other: BaseExtractor,
         only_main: bool = False,
-        ids: Union[Iterable, slice, None] = None,
-        skip_properties: Optional[Iterable[str]] = None,
+        ids: Iterable | slice | None = None,
+        skip_properties: Iterable[str] | None = None,
     ) -> None:
         """
         Copy metadata (annotations/properties) to another extractor (`other`).
@@ -436,7 +438,7 @@ def to_dict(
         self,
         include_annotations: bool = False,
         include_properties: bool = False,
-        relative_to: Union[str, Path, None] = None,
+        relative_to: str | Path | None = None,
         folder_metadata=None,
         recursive: bool = False,
     ) -> dict:
@@ -461,11 +463,11 @@ def to_dict(
             Whether to include all annotations in the dictionary
         include_properties : bool, default: False
             Whether to include all properties in the dictionary, by default False.
-        relative_to : Union[str, Path, None], default: None
+        relative_to : str | Path | None, default: None
             If provided, file and folder paths will be made relative to this path,
             enabling portability in folder formats such as the waveform extractor,
             by default None.
-        folder_metadata : Union[str, Path, None], default: None
+        folder_metadata : str | Path | None, default: None
             Path to a folder containing additional metadata files (e.g., probe information in BaseRecording)
             in numpy `npy` format, by default None.
         recursive : bool, default: False
@@ -568,7 +570,7 @@ def to_dict(
         return dump_dict
 
     @staticmethod
-    def from_dict(dictionary: dict, base_folder: Optional[Union[Path, str]] = None) -> "BaseExtractor":
+    def from_dict(dictionary: dict, base_folder: Path | str | None = None) -> BaseExtractor:
         """
         Instantiate extractor from dictionary
 
@@ -622,7 +624,7 @@ def save_metadata_to_folder(self, folder_metadata):
             values = self.get_property(key)
             np.save(prop_folder / (key + ".npy"), values)
 
-    def clone(self) -> "BaseExtractor":
+    def clone(self) -> BaseExtractor:
         """
         Clones an existing extractor into a new instance.
         """
@@ -677,7 +679,7 @@ def check_if_pickle_serializable(self) -> bool:
         return self.check_serializability("pickle")
 
     @staticmethod
-    def _get_file_path(file_path: Union[str, Path], extensions: Sequence) -> Path:
+    def _get_file_path(file_path: str | Path, extensions: Sequence) -> Path:
         """
         Helper function to be used by various dump_to_file utilities.
 
@@ -708,7 +710,7 @@ def _get_file_path(file_path: Union[str, Path], extensions: Sequence) -> Path:
         )
         return file_path
 
-    def dump(self, file_path: Union[str, Path], relative_to=None, folder_metadata=None) -> None:
+    def dump(self, file_path: str | Path, relative_to=None, folder_metadata=None) -> None:
         """
         Dumps extractor to json or pickle
 
@@ -729,9 +731,9 @@ def dump(self, file_path: Union[str, Path], relative_to=None, folder_metadata=No
 
     def dump_to_json(
         self,
-        file_path: Union[str, Path, None] = None,
-        relative_to: Union[str, Path, bool, None] = None,
-        folder_metadata: Union[str, Path, None] = None,
+        file_path: str | Path | None = None,
+        relative_to: str | Path | bool | None = None,
+        folder_metadata: str | Path | None = None,
     ) -> None:
         """
         Dump recording extractor to json file.
@@ -770,10 +772,10 @@ def dump_to_json(
 
     def dump_to_pickle(
         self,
-        file_path: Union[str, Path, None] = None,
-        relative_to: Union[str, Path, bool, None] = None,
+        file_path: str | Path | None = None,
+        relative_to: str | Path | bool | None = None,
         include_properties: bool = True,
-        folder_metadata: Union[str, Path, None] = None,
+        folder_metadata: str | Path | None = None,
     ):
         """
         Dump recording extractor to a pickle file.
@@ -814,9 +816,7 @@ def dump_to_pickle(
         file_path.write_bytes(pickle.dumps(dump_dict))
 
     @staticmethod
-    def load(
-        file_or_folder_path: Union[str, Path], base_folder: Optional[Union[Path, str, bool]] = None
-    ) -> "BaseExtractor":
+    def load(file_or_folder_path: str | Path, base_folder: Path | str | bool | None = None) -> BaseExtractor:
         """
         Load extractor from file path (.json or .pkl)
 
@@ -839,7 +839,7 @@ def __reduce__(self):
         return (instance_constructor, intialization_args)
 
     @staticmethod
-    def load_from_folder(folder) -> "BaseExtractor":
+    def load_from_folder(folder) -> BaseExtractor:
         return BaseExtractor.load(folder)
 
     def _save(self, folder, **save_kwargs):
@@ -855,7 +855,7 @@ def _extra_metadata_to_folder(self, folder):
         # This implemented in BaseRecording for probe
         pass
 
-    def save(self, **kwargs) -> "BaseExtractor":
+    def save(self, **kwargs) -> BaseExtractor:
         """
         Save a SpikeInterface object.
 
@@ -891,7 +891,7 @@ def save(self, **kwargs) -> "BaseExtractor":
 
     save.__doc__ = save.__doc__.format(_shared_job_kwargs_doc)
 
-    def save_to_memory(self, sharedmem=True, **save_kwargs) -> "BaseExtractor":
+    def save_to_memory(self, sharedmem=True, **save_kwargs) -> BaseExtractor:
         save_kwargs.pop("format", None)
 
         cached = self._save(format="memory", sharedmem=sharedmem, **save_kwargs)
@@ -1188,7 +1188,7 @@ def __init__(self):
         self._parent_extractor = None
 
     @property
-    def parent_extractor(self) -> Union[BaseExtractor, None]:
+    def parent_extractor(self) -> BaseExtractor | None:
         return self._parent_extractor()
 
     def set_parent_extractor(self, parent_extractor: BaseExtractor) -> None:

src/spikeinterface/core/baseevent.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import numpy as np
 
 from .base import BaseExtractor, BaseSegment