[pre-commit.ci] pre-commit autoupdate (#4332)

pre-commit-ci[bot] · web-flow · commit d8f49ece6bc9 · 2026-01-20T15:51:05.000+01:00
Co-authored-by: pre-commit-ci[bot] &lt;66853113+pre-commit-ci[bot]@users.noreply.github.com&gt;
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.12.0
+    rev: 26.1.0
     hooks:
     -   id: black
         files: ^src/
diff --git a/src/spikeinterface/benchmark/benchmark_sorter.py b/src/spikeinterface/benchmark/benchmark_sorter.py
@@ -8,7 +8,6 @@
 from spikeinterface.sorters import run_sorter
 from spikeinterface.comparison import compare_sorter_to_ground_truth
 
-
 # TODO later integrate CollisionGTComparison optionally in this class.
 
 
diff --git a/src/spikeinterface/benchmark/benchmark_sorter_without_gt.py b/src/spikeinterface/benchmark/benchmark_sorter_without_gt.py
@@ -10,7 +10,6 @@
 
 from spikeinterface.benchmark import analyse_residual
 
-
 # TODO later integrate CollisionGTComparison optionally in this class.
 
 
diff --git a/src/spikeinterface/benchmark/tests/test_residual_analysis.py b/src/spikeinterface/benchmark/tests/test_residual_analysis.py
@@ -7,7 +7,6 @@
 
 from spikeinterface.benchmark import analyse_residual
 
-
 job_kwargs = dict(n_jobs=-1, progress_bar=True)
 
 
diff --git a/src/spikeinterface/comparison/tests/test_multisortingcomparison.py b/src/spikeinterface/comparison/tests/test_multisortingcomparison.py
@@ -9,7 +9,6 @@
 from spikeinterface.extractors import NumpySorting
 from spikeinterface.comparison import compare_multiple_sorters, MultiSortingComparison
 
-
 ON_GITHUB = bool(os.getenv("GITHUB_ACTIONS"))
 
 
diff --git a/src/spikeinterface/comparison/tests/test_templatecomparison.py b/src/spikeinterface/comparison/tests/test_templatecomparison.py
@@ -5,7 +5,6 @@
 from spikeinterface.core import create_sorting_analyzer, generate_ground_truth_recording
 from spikeinterface.comparison import compare_templates, compare_multiple_templates
 
-
 # def setup_module():
 #     if test_dir.is_dir():
 #         shutil.rmtree(test_dir)
diff --git a/src/spikeinterface/core/base.py b/src/spikeinterface/core/base.py
@@ -26,7 +26,6 @@
 )
 from .job_tools import _shared_job_kwargs_doc
 
-
 # base dtypes used throughout spikeinterface
 base_peak_dtype = [
     ("sample_index", "int64"),
diff --git a/src/spikeinterface/core/job_tools.py b/src/spikeinterface/core/job_tools.py
@@ -17,7 +17,6 @@
 import threading
 from threadpoolctl import threadpool_limits
 
-
 _shared_job_kwargs_doc = """**job_kwargs : keyword arguments for parallel processing:
     * chunk_duration or chunk_size or chunk_memory or total_memory
         - chunk_size : int
diff --git a/src/spikeinterface/core/loading.py b/src/spikeinterface/core/loading.py
@@ -6,7 +6,6 @@
 from .base import BaseExtractor
 from .core_tools import is_path_remote
 
-
 _error_msg = (
     "{file_path} is not a file or a folder. It should point to either a json, pickle file or a "
     "folder that is the result of extractor.save(...) or sortinganalyzer.save_as(...)"
diff --git a/src/spikeinterface/core/sparsity.py b/src/spikeinterface/core/sparsity.py
@@ -10,7 +10,6 @@
 from .job_tools import _shared_job_kwargs_doc
 from .waveform_tools import estimate_templates_with_accumulator
 
-
 _sparsity_doc = """
     method : str
         * "best_channels" : N best channels with the largest amplitude. Use the "num_channels" argument to specify the
diff --git a/src/spikeinterface/core/tests/test_node_pipeline.py b/src/spikeinterface/core/tests/test_node_pipeline.py
@@ -7,7 +7,6 @@
 from spikeinterface.core.base import spike_peak_dtype
 from spikeinterface.core.job_tools import divide_recording_into_chunks
 
-
 # from spikeinterface.sortingcomponents.peak_detection import detect_peaks
 from spikeinterface.core.node_pipeline import (
     run_node_pipeline,
diff --git a/src/spikeinterface/core/tests/test_waveforms_extractor_backwards_compatibility.py b/src/spikeinterface/core/tests/test_waveforms_extractor_backwards_compatibility.py
@@ -11,7 +11,6 @@
 from spikeinterface.core.waveforms_extractor_backwards_compatibility import extract_waveforms as mock_extract_waveforms
 from spikeinterface.core.waveforms_extractor_backwards_compatibility import load_waveforms as load_waveforms_backwards
 
-
 # remove this when WaveformsExtractor will be removed
 from spikeinterface.core import extract_waveforms as old_extract_waveforms
 
diff --git a/src/spikeinterface/curation/__init__.py b/src/spikeinterface/curation/__init__.py
@@ -9,7 +9,6 @@
     get_potential_auto_merge,
 )
 
-
 # manual sorting,
 from .curationsorting import CurationSorting, curation_sorting
 from .mergeunitssorting import MergeUnitsSorting, merge_units_sorting
diff --git a/src/spikeinterface/curation/curation_tools.py b/src/spikeinterface/curation/curation_tools.py
@@ -3,7 +3,6 @@
 import numpy as np
 from spikeinterface import SortingAnalyzer
 
-
 try:
     import numba
 
diff --git a/src/spikeinterface/curation/remove_redundant.py b/src/spikeinterface/curation/remove_redundant.py
@@ -7,7 +7,6 @@
 from spikeinterface.core.template_tools import get_template_extremum_channel_peak_shift, get_template_amplitudes
 from spikeinterface.postprocessing import align_sorting
 
-
 _remove_strategies = ("minimum_shift", "highest_amplitude", "max_spikes")
 
 
diff --git a/src/spikeinterface/extractors/extractor_classes.py b/src/spikeinterface/extractors/extractor_classes.py
@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-
 # most important extractor are in spikeinterface.core
 from spikeinterface.core import (
     BinaryFolderRecording,
@@ -73,11 +72,9 @@
 # snippers
 from .waveclussnippetstextractors import WaveClusSnippetsExtractor, read_waveclus_snippets
 
-
 # misc
 from .alfsortingextractor import ALFSortingExtractor, read_alf_sorting
 
-
 ###############################################################################################
 # the following code is necessary for controlling what the end user imports from spikeinterface.
 # The strategy has three goals:
diff --git a/src/spikeinterface/extractors/iblextractors.py b/src/spikeinterface/extractors/iblextractors.py
@@ -13,7 +13,6 @@
 from spikeinterface.core.core_tools import define_function_from_class
 from spikeinterface.extractors.alfsortingextractor import ALFSortingSegment
 
-
 if importlib.util.find_spec("one") is not None and importlib.util.find_spec("one.api") is not None:
     HAVE_ONE = True
 else:
diff --git a/src/spikeinterface/extractors/neoextractors/neuroscope.py b/src/spikeinterface/extractors/neoextractors/neuroscope.py
@@ -12,7 +12,6 @@
 
 from .neobaseextractor import NeoBaseRecordingExtractor
 
-
 PathType = Union[str, Path]
 OptionalPathType = Optional[PathType]
 
diff --git a/src/spikeinterface/extractors/nwbextractors.py b/src/spikeinterface/extractors/nwbextractors.py
@@ -10,7 +10,6 @@
 from spikeinterface.core import BaseRecording, BaseRecordingSegment, BaseSorting, BaseSortingSegment
 from spikeinterface.core.core_tools import define_function_from_class
 
-
 if importlib.util.find_spec("pynwb") is not None:
     HAVE_PYNWB = True
 else:
diff --git a/src/spikeinterface/extractors/tests/test_cellexplorerextractor.py b/src/spikeinterface/extractors/tests/test_cellexplorerextractor.py
@@ -4,7 +4,6 @@
 from spikeinterface.extractors.cellexplorersortingextractor import CellExplorerSortingExtractor
 from spikeinterface.core.globals import get_global_dataset_folder
 
-
 local_folder = get_global_dataset_folder() / "ephy_testing_data"
 
 
diff --git a/src/spikeinterface/extractors/tests/test_combinatoextractors.py b/src/spikeinterface/extractors/tests/test_combinatoextractors.py
@@ -1,6 +1,5 @@
 import pytest
 
-
 # from spikeinterface.extractors import read_combinato
 
 
diff --git a/src/spikeinterface/extractors/tests/test_hdsortextractors.py b/src/spikeinterface/extractors/tests/test_hdsortextractors.py
@@ -1,6 +1,5 @@
 import pytest
 
-
 # from spikeinterface.extractors import read_hdsort
 
 
diff --git a/src/spikeinterface/extractors/tests/test_klustaextractors.py b/src/spikeinterface/extractors/tests/test_klustaextractors.py
@@ -1,6 +1,5 @@
 import pytest
 
-
 # from spikeinterface.extractors import read_klusta
 
 
diff --git a/src/spikeinterface/extractors/tests/test_spykingcircusextractors.py b/src/spikeinterface/extractors/tests/test_spykingcircusextractors.py
@@ -1,6 +1,5 @@
 import pytest
 
-
 # from spikeinterface.extractors import read_spykingcircus
 
 
diff --git a/src/spikeinterface/extractors/tests/test_tridesclousextractors.py b/src/spikeinterface/extractors/tests/test_tridesclousextractors.py
@@ -1,6 +1,5 @@
 import pytest
 
-
 # from spikeinterface.extractors import read_tridesclous
 
 
diff --git a/src/spikeinterface/extractors/tests/test_waveclustextractors.py b/src/spikeinterface/extractors/tests/test_waveclustextractors.py
@@ -1,6 +1,5 @@
 import pytest
 
-
 # from spikeinterface.extractors import read_waveclus
 
 
diff --git a/src/spikeinterface/extractors/tests/test_yassextractors.py b/src/spikeinterface/extractors/tests/test_yassextractors.py
@@ -1,6 +1,5 @@
 import pytest
 
-
 # from spikeinterface.extractors import read_yass
 
 
diff --git a/src/spikeinterface/generation/drifting_generator.py b/src/spikeinterface/generation/drifting_generator.py
@@ -23,7 +23,6 @@
 from .drift_tools import DriftingTemplates, make_linear_displacement, InjectDriftingTemplatesRecording
 from .noise_tools import generate_noise
 
-
 # this should be moved in probeinterface but later
 _toy_probes = {
     "Neuropixels1-384": dict(
diff --git a/src/spikeinterface/metrics/quality/tests/test_metrics_functions.py b/src/spikeinterface/metrics/quality/tests/test_metrics_functions.py
@@ -55,7 +55,6 @@
 
 from spikeinterface.core.base import minimum_spike_dtype
 
-
 job_kwargs = dict(n_jobs=2, progress_bar=True, chunk_duration="1s")
 
 
diff --git a/src/spikeinterface/metrics/template/template_metrics.py b/src/spikeinterface/metrics/template/template_metrics.py
@@ -16,7 +16,6 @@
 
 from .metrics import get_trough_and_peak_idx, single_channel_metrics, multi_channel_metrics
 
-
 MIN_SPARSE_CHANNELS_FOR_MULTI_CHANNEL_WARNING = 10
 MIN_CHANNELS_FOR_MULTI_CHANNEL_METRICS = 64
 
diff --git a/src/spikeinterface/metrics/template/tests/test_template_metrics.py b/src/spikeinterface/metrics/template/tests/test_template_metrics.py
@@ -8,7 +8,6 @@
 )
 from spikeinterface.metrics.template.metrics import single_channel_metrics, multi_channel_metrics
 
-
 template_metrics = get_single_channel_template_metric_names()
 
 
diff --git a/src/spikeinterface/postprocessing/template_similarity.py b/src/spikeinterface/postprocessing/template_similarity.py
@@ -9,7 +9,6 @@
 from spikeinterface.core.template_tools import get_dense_templates_array
 from spikeinterface.core.sparsity import ChannelSparsity
 
-
 numba_spec = importlib.util.find_spec("numba")
 if numba_spec is not None:
     HAVE_NUMBA = True
diff --git a/src/spikeinterface/postprocessing/unit_locations.py b/src/spikeinterface/postprocessing/unit_locations.py
@@ -6,7 +6,6 @@
 from spikeinterface.core.sortinganalyzer import register_result_extension, AnalyzerExtension
 from .localization_tools import _unit_location_methods
 
-
 # this dict is for peak location
 dtype_localize_by_method = {
     "center_of_mass": [("x", "float64"), ("y", "float64")],
diff --git a/src/spikeinterface/preprocessing/deepinterpolation/tests/test_deepinterpolation.py b/src/spikeinterface/preprocessing/deepinterpolation/tests/test_deepinterpolation.py
@@ -11,7 +11,6 @@
 from spikeinterface.preprocessing.deepinterpolation import train_deepinterpolation, deepinterpolate
 from spikeinterface.preprocessing.deepinterpolation.train import train_deepinterpolation_process
 
-
 try:
     import tensorflow
     import deepinterpolation
diff --git a/src/spikeinterface/preprocessing/deepinterpolation/train.py b/src/spikeinterface/preprocessing/deepinterpolation/train.py
@@ -10,7 +10,6 @@
 from .tf_utils import import_tf
 from spikeinterface.core import BaseRecording
 
-
 global train_func
 
 
diff --git a/src/spikeinterface/preprocessing/filter.py b/src/spikeinterface/preprocessing/filter.py
@@ -8,7 +8,6 @@
 
 from spikeinterface.core import get_chunk_with_margin
 
-
 HIGHPASS_ERROR_THRESHOLD_HZ = 100
 MARGIN_TO_CHUNK_PERCENT_WARNING = 0.2  # 20%
 
diff --git a/src/spikeinterface/preprocessing/motion.py b/src/spikeinterface/preprocessing/motion.py
@@ -16,7 +16,6 @@
 from spikeinterface.core.job_tools import _shared_job_kwargs_doc
 from spikeinterface.core import BaseRecording
 
-
 motion_options_preset = {
     # dredge
     "dredge": {
diff --git a/src/spikeinterface/preprocessing/pipeline.py b/src/spikeinterface/preprocessing/pipeline.py
@@ -6,7 +6,6 @@
 from spikeinterface.core.zarrextractors import super_zarr_open
 from spikeinterface.preprocessing.preprocessing_classes import preprocessor_dict, _all_preprocesser_dict
 
-
 pp_names_to_functions = {preprocessor.__name__: preprocessor for preprocessor in preprocessor_dict.values()}
 pp_names_to_classes = {pp_function.__name__: pp_class for pp_class, pp_function in _all_preprocesser_dict.items()}
 
diff --git a/src/spikeinterface/sorters/basesorter.py b/src/spikeinterface/sorters/basesorter.py
@@ -21,7 +21,6 @@
 from spikeinterface.core.job_tools import fix_job_kwargs, split_job_kwargs
 from .utils import SpikeSortingError, ShellScript
 
-
 default_job_kwargs_description = {
     "n_jobs": "Number of jobs (when saving to binary) - default global",
     "chunk_size": "Number of samples per chunk (when saving to binary) - default global",
diff --git a/src/spikeinterface/sorters/external/combinato.py b/src/spikeinterface/sorters/external/combinato.py
@@ -11,7 +11,6 @@
 from spikeinterface.sorters.basesorter import BaseSorter
 from spikeinterface.extractors.extractor_classes import CombinatoSortingExtractor
 
-
 PathType = Union[str, Path]
 
 
diff --git a/src/spikeinterface/sorters/external/ironclust.py b/src/spikeinterface/sorters/external/ironclust.py
@@ -211,9 +211,7 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
             shell_cmd = """
                 #!/bin/bash
                 p_ironclust {tmpdir} {dataset_dir}/raw.mda {dataset_dir}/geom.csv '' '' {tmpdir}/firings.mda {dataset_dir}/argfile.txt
-            """.format(
-                tmpdir=str(tmpdir), dataset_dir=str(dataset_dir)
-            )
+            """.format(tmpdir=str(tmpdir), dataset_dir=str(dataset_dir))
         else:
             cmd = """
                 addpath('{source_dir}');
@@ -242,17 +240,13 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
                     {disk_move}
                     cd {tmpdir}
                     matlab -nosplash -wait -log -r run_ironclust
-                """.format(
-                    disk_move=str(tmpdir)[:2], tmpdir=tmpdir
-                )
+                """.format(disk_move=str(tmpdir)[:2], tmpdir=tmpdir)
             else:
                 shell_cmd = """
                     #!/bin/bash
                     cd "{tmpdir}"
                     matlab -nosplash -nodisplay -log -r run_ironclust
-                """.format(
-                    tmpdir=tmpdir
-                )
+                """.format(tmpdir=tmpdir)
 
         shell_script = ShellScript(
             shell_cmd,
diff --git a/src/spikeinterface/sorters/external/kilosort2_5.py b/src/spikeinterface/sorters/external/kilosort2_5.py
@@ -8,7 +8,6 @@
 from .kilosortbase import KilosortBase
 from spikeinterface.sorters.utils import get_git_commit
 
-
 PathType = Union[str, Path]
 
 
diff --git a/src/spikeinterface/sorters/external/klusta.py b/src/spikeinterface/sorters/external/klusta.py
@@ -142,16 +142,12 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
         if "win" in sys.platform and sys.platform != "darwin":
             shell_cmd = """
                         klusta --overwrite {klusta_config}
-                    """.format(
-                klusta_config=sorter_output_folder / "config.prm"
-            )
+                    """.format(klusta_config=sorter_output_folder / "config.prm")
         else:
             shell_cmd = """
                         #!/bin/bash
                         klusta {klusta_config} --overwrite
-                    """.format(
-                klusta_config=sorter_output_folder / "config.prm"
-            )
+                    """.format(klusta_config=sorter_output_folder / "config.prm")
 
         shell_script = ShellScript(
             shell_cmd,
diff --git a/src/spikeinterface/sorters/external/spyking_circus.py b/src/spikeinterface/sorters/external/spyking_circus.py
diff --git a/src/spikeinterface/sorters/external/tests/test_docker_containers.py b/src/spikeinterface/sorters/external/tests/test_docker_containers.py
diff --git a/src/spikeinterface/sorters/external/tests/test_singularity_containers.py b/src/spikeinterface/sorters/external/tests/test_singularity_containers.py
diff --git a/src/spikeinterface/sorters/runsorter.py b/src/spikeinterface/sorters/runsorter.py
diff --git a/src/spikeinterface/sorters/tests/test_launcher.py b/src/spikeinterface/sorters/tests/test_launcher.py
diff --git a/src/spikeinterface/sortingcomponents/clustering/merging_tools.py b/src/spikeinterface/sortingcomponents/clustering/merging_tools.py
diff --git a/src/spikeinterface/sortingcomponents/matching/circus.py b/src/spikeinterface/sortingcomponents/matching/circus.py
diff --git a/src/spikeinterface/sortingcomponents/matching/nearest.py b/src/spikeinterface/sortingcomponents/matching/nearest.py
diff --git a/src/spikeinterface/sortingcomponents/matching/tdc_peeler.py b/src/spikeinterface/sortingcomponents/matching/tdc_peeler.py
diff --git a/src/spikeinterface/sortingcomponents/matching/tests/test_template_matching.py b/src/spikeinterface/sortingcomponents/matching/tests/test_template_matching.py
diff --git a/src/spikeinterface/sortingcomponents/motion/tests/test_motion_estimation.py b/src/spikeinterface/sortingcomponents/motion/tests/test_motion_estimation.py
diff --git a/src/spikeinterface/sortingcomponents/peak_detection/locally_exclusive.py b/src/spikeinterface/sortingcomponents/peak_detection/locally_exclusive.py
diff --git a/src/spikeinterface/sortingcomponents/peak_detection/matched_filtering.py b/src/spikeinterface/sortingcomponents/peak_detection/matched_filtering.py
diff --git a/src/spikeinterface/sortingcomponents/peak_detection/tests/test_peak_detection.py b/src/spikeinterface/sortingcomponents/peak_detection/tests/test_peak_detection.py
diff --git a/src/spikeinterface/widgets/sorting_summary.py b/src/spikeinterface/widgets/sorting_summary.py
diff --git a/src/spikeinterface/widgets/tests/test_widgets.py b/src/spikeinterface/widgets/tests/test_widgets.py

Original file line number	Diff line number	Diff line change
`@@ -10,7 +10,6 @@`
`10`	`10`
`11`	`11`	`from spikeinterface.benchmark import analyse_residual`
`12`	`12`
`13`		`-`
`14`	`13`	`# TODO later integrate CollisionGTComparison optionally in this class.`
`15`	`14`
`16`	`15`
Original file line number	Diff line number	Diff line change
`@@ -7,7 +7,6 @@`
`7`	`7`
`8`	`8`	`from spikeinterface.benchmark import analyse_residual`
`9`	`9`
`10`		`-`
`11`	`10`	`job_kwargs = dict(n_jobs=-1, progress_bar=True)`
`12`	`11`
`13`	`12`
Original file line number	Diff line number	Diff line change
`@@ -26,7 +26,6 @@`
`26`	`26`	`)`
`27`	`27`	`from .job_tools import _shared_job_kwargs_doc`
`28`	`28`
`29`		`-`
`30`	`29`	`# base dtypes used throughout spikeinterface`
`31`	`30`	`base_peak_dtype = [`
`32`	`31`	`("sample_index", "int64"),`