Merge pull request #1811 from NeuralEnsemble/black-formatting

zm711 · web-flow · commit d1f3719ce323 · 2026-01-24T14:06:55.000-05:00
Black formatting
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -247,9 +247,7 @@
 
 rst_epilog = """
 .. |neo_github_url| replace:: https://github.com/NeuralEnsemble/python-neo/archive/neo-{}.zip
-""".format(
-    neo_release
-)
+""".format(neo_release)
 
 sphinx_gallery_conf = {
     # 'only_warn_on_example_error': True, # helps with debugging broken examples
diff --git a/examples/convert_to_nwb.py b/examples/convert_to_nwb.py
@@ -8,7 +8,6 @@
 from urllib.parse import quote
 from neo.io import get_io
 
-
 dataset_url = "https://object.cscs.ch/v1/AUTH_63ea6845b1d34ad7a43c8158d9572867/hbp-d000017_PatchClamp-GranuleCells_pub"
 
 folder = "GrC_Subject15_180116"
diff --git a/examples/plot_imageseq.py b/examples/plot_imageseq.py
@@ -14,7 +14,6 @@
 
 import random
 
-
 ############################################################
 # Now we need to generate some data
 # We will just make a nice box and then we can attach this
diff --git a/examples/plot_read_proxy_with_lazy_load.py b/examples/plot_read_proxy_with_lazy_load.py
@@ -14,7 +14,6 @@
 import quantities as pq
 import numpy as np
 
-
 ###############################################
 # Let's get a file
 # NeuralEnsemble maintains a wide variety of small test
diff --git a/neo/core/analogsignal.py b/neo/core/analogsignal.py
@@ -523,10 +523,8 @@ def time_slice(self, t_start, t_stop):
             j = i + int(np.rint(delta.simplified.magnitude))
 
         if (i < 0) or (j > len(self)):
-            raise ValueError(
-                "t_start, t_stop have to be within the analog \
-                              signal duration"
-            )
+            raise ValueError("t_start, t_stop have to be within the analog \
+                              signal duration")
 
         # Time slicing should create a deep copy of the object
         obj = deepcopy(self[i:j])
diff --git a/neo/io/elphyio.py b/neo/io/elphyio.py
@@ -89,7 +89,6 @@
 # to import from core
 from neo.core import Block, Segment, AnalogSignal, Event, SpikeTrain, NeoReadWriteError
 
-
 # --------------------------------------------------------
 # OBJECTS
 
diff --git a/neo/io/nestio.py b/neo/io/nestio.py
@@ -111,7 +111,7 @@ def __read_analogsignals(
         t_start, t_stop = self._check_input_times(t_start, t_stop, mandatory=False)
 
         # checking value input parameters
-        (value_columns, value_types, value_units) = self._check_input_values_parameters(
+        value_columns, value_types, value_units = self._check_input_values_parameters(
             value_columns, value_types, value_units
         )
 
@@ -133,7 +133,7 @@ def __read_analogsignals(
             )
 
         # extracting condition and sorting parameters for raw data loading
-        (condition, condition_column, sorting_column) = self._get_conditions_and_sorting(
+        condition, condition_column, sorting_column = self._get_conditions_and_sorting(
             id_column, time_column, gid_list, t_start, t_stop
         )
         # loading raw data columns
@@ -210,7 +210,7 @@ def __read_spiketrains(self, gdf_id_list, time_unit, t_start, t_stop, id_column,
             if cid is None:
                 column_ids[i] = -1
 
-        (condition, condition_column, sorting_column) = self._get_conditions_and_sorting(
+        condition, condition_column, sorting_column = self._get_conditions_and_sorting(
             id_column, time_column, gdf_id_list, t_start, t_stop
         )
 
diff --git a/neo/io/nixio.py b/neo/io/nixio.py
@@ -19,7 +19,6 @@
 Neo: https://github.com/G-Node/python-neo/wiki
 """
 
-
 from datetime import date, time, datetime
 from collections.abc import Iterable
 from collections import OrderedDict
@@ -49,7 +48,6 @@
 from ..io.proxyobjects import BaseProxy
 from .. import __version__ as neover
 
-
 datetime_types = (date, time, datetime)
 
 EMPTYANNOTATION = "EMPTYLIST"
diff --git a/neo/io/nwbio.py b/neo/io/nwbio.py
@@ -34,7 +34,6 @@
     SpikeTrainProxy as BaseSpikeTrainProxy,
 )
 
-
 logger = logging.getLogger("Neo")
 
 GLOBAL_ANNOTATIONS = (
diff --git a/neo/io/proxyobjects.py b/neo/io/proxyobjects.py
@@ -19,7 +19,6 @@
 from neo.core import AnalogSignal, Epoch, Event, SpikeTrain
 from neo.core.dataobject import ArrayDict
 
-
 logger = logging.getLogger("Neo")
 
 
diff --git a/neo/rawio/baserawio.py b/neo/rawio/baserawio.py
@@ -79,7 +79,6 @@
 
 from .utils import get_memmap_chunk_from_opened_file
 
-
 possible_raw_modes = [
     "one-file",
     "multi-file",
@@ -262,8 +261,7 @@ def _repr_html_(self):
             html.append(f"<p><strong>nb_segment:</strong> {nb_seg}</p>")
 
             # CSS for tables - using only black, white, and gray colors
-            html.append(
-                """
+            html.append("""
             <style>
                 #{unique_id} table.neo-table {{
                     border-collapse: collapse;
@@ -308,8 +306,7 @@ def _repr_html_(self):
                     background-color: transparent;
                 }}
             </style>
-            """
-            )
+            """)
 
             # Signal Streams
             signal_streams = self.header["signal_streams"]
diff --git a/neo/rawio/nixrawio.py b/neo/rawio/nixrawio.py
@@ -19,7 +19,6 @@
 )
 from ..io.nixio import check_nix_version
 
-
 # When reading metadata properties, the following keys are ignored since they
 # are used to store Neo object properties.
 # This dictionary is used in the _filter_properties() method.
diff --git a/neo/rawio/openephysrawio.py b/neo/rawio/openephysrawio.py
@@ -23,7 +23,6 @@
 )
 from neo.core import NeoReadWriteError
 
-
 RECORD_SIZE = 1024
 HEADER_SIZE = 1024
 
diff --git a/neo/test/coretest/test_block.py b/neo/test/coretest/test_block.py
@@ -24,7 +24,6 @@
 from neo.test.tools import assert_neo_object_is_compliant, assert_same_sub_schema
 from neo.test.generate_datasets import random_block, simple_block, random_signal
 
-
 N_EXAMPLES = 5
 
 
diff --git a/neo/test/coretest/test_segment.py b/neo/test/coretest/test_segment.py
@@ -27,7 +27,6 @@
 from neo.rawio.examplerawio import ExampleRawIO
 from neo.io.proxyobjects import AnalogSignalProxy, SpikeTrainProxy, EventProxy, EpochProxy
 
-
 N_EXAMPLES = 5
 
 
diff --git a/neo/test/iotest/common_io_test.py b/neo/test/iotest/common_io_test.py
@@ -471,9 +471,7 @@ def test_create_group_across_segment(self):
         Test read_block method of BaseFromRaw with different test cases
         for create_group_across_segment.
 
-        """.format(
-            io_name=self.ioclass.__name__
-        )
+        """.format(io_name=self.ioclass.__name__)
 
         test_cases = [
             {"SpikeTrain": True},
diff --git a/neo/test/iotest/test_mearecio.py b/neo/test/iotest/test_mearecio.py
@@ -7,7 +7,6 @@
 from neo.io import MEArecIO
 from neo.test.iotest.common_io_test import BaseTestIO
 
-
 try:
     import MEArec as mr
 
diff --git a/neo/test/iotest/test_plexon2io.py b/neo/test/iotest/test_plexon2io.py
@@ -10,7 +10,6 @@
 
 from neo.test.rawiotest.test_plexon2rawio import TestPlexon2RawIO
 
-
 try:
     from neo.rawio.plexon2rawio.pypl2 import pypl2lib
 
diff --git a/neo/test/rawiotest/test_alphaomegarawio.py b/neo/test/rawiotest/test_alphaomegarawio.py
@@ -32,7 +32,6 @@ class and a full test will be done to test if the new coded IO
 
 from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
 
-
 logging.getLogger().setLevel(logging.INFO)
 
 
diff --git a/neo/test/rawiotest/test_mearecrawio.py b/neo/test/rawiotest/test_mearecrawio.py
@@ -9,7 +9,6 @@
 
 from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
 
-
 try:
     import MEArec as mr
 
diff --git a/neo/test/rawiotest/test_nixrawio.py b/neo/test/rawiotest/test_nixrawio.py
@@ -2,7 +2,6 @@
 from neo.rawio.nixrawio import NIXRawIO
 from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
 
-
 testfname = ""
 
 
diff --git a/neo/test/rawiotest/tools.py b/neo/test/rawiotest/tools.py
@@ -6,7 +6,6 @@
 import os
 import importlib.util
 
-
 logger = logging.getLogger("neo.test")
 
 

Original file line number	Diff line number	Diff line change
`@@ -111,7 +111,7 @@ def __read_analogsignals(`
`111`	`111`	`t_start, t_stop = self._check_input_times(t_start, t_stop, mandatory=False)`
`112`	`112`
`113`	`113`	`# checking value input parameters`
`114`		`- (value_columns, value_types, value_units) = self._check_input_values_parameters(`
	`114`	`+ value_columns, value_types, value_units = self._check_input_values_parameters(`
`115`	`115`	`value_columns, value_types, value_units`
`116`	`116`	`)`
`117`	`117`
`@@ -133,7 +133,7 @@ def __read_analogsignals(`
`133`	`133`	`)`
`134`	`134`
`135`	`135`	`# extracting condition and sorting parameters for raw data loading`
`136`		`- (condition, condition_column, sorting_column) = self._get_conditions_and_sorting(`
	`136`	`+ condition, condition_column, sorting_column = self._get_conditions_and_sorting(`
`137`	`137`	`id_column, time_column, gid_list, t_start, t_stop`
`138`	`138`	`)`
`139`	`139`	`# loading raw data columns`
`@@ -210,7 +210,7 @@ def __read_spiketrains(self, gdf_id_list, time_unit, t_start, t_stop, id_column,`
`210`	`210`	`if cid is None:`
`211`	`211`	`column_ids[i] = -1`
`212`	`212`
`213`		`- (condition, condition_column, sorting_column) = self._get_conditions_and_sorting(`
	`213`	`+ condition, condition_column, sorting_column = self._get_conditions_and_sorting(`
`214`	`214`	`id_column, time_column, gdf_id_list, t_start, t_stop`
`215`	`215`	`)`
`216`	`216`
Original file line number	Diff line number	Diff line change
`@@ -34,7 +34,6 @@`
`34`	`34`	`SpikeTrainProxy as BaseSpikeTrainProxy,`
`35`	`35`	`)`
`36`	`36`
`37`		`-`
`38`	`37`	`logger = logging.getLogger("Neo")`
`39`	`38`
`40`	`39`	`GLOBAL_ANNOTATIONS = (`