Merge pull request #1487 from NeuralEnsemble/black-formatting

Black formatting
NeuralEnsemble · Jun 9, 2024 · d8639b4 · d8639b4
2 parents 5d66cce + 9c14ca4
commit d8639b4
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Showing 28 changed files with 30 additions and 21 deletions.
diff --git a/neo/core/imagesequence.py b/neo/core/imagesequence.py
@@ -17,7 +17,6 @@
 the old object.
 """
 
-
 import quantities as pq
 import numpy as np
 

diff --git a/neo/core/spiketrain.py b/neo/core/spiketrain.py
@@ -24,6 +24,7 @@
 import quantities as pq
 from neo.core.baseneo import BaseNeo, MergeError, merge_annotations
 from neo.core.dataobject import DataObject, ArrayDict
+
 # need this to avoid circular import issue
 import neo
 

diff --git a/neo/io/axonio.py b/neo/io/axonio.py
@@ -5,7 +5,6 @@
 from neo.core import Segment, AnalogSignal
 
 
-
 class AxonIO(AxonRawIO, BaseFromRaw):
     """
     Class for reading data from pCLAMP and AxoScope

diff --git a/neo/io/blkio.py b/neo/io/blkio.py
@@ -8,9 +8,6 @@
 from neo.core import ImageSequence, Segment, Block
 
 
-
-
-
 class BlkIO(BaseIO):
     """
     Neo IO module for optical imaging data stored as BLK file

diff --git a/neo/io/brainwaredamio.py b/neo/io/brainwaredamio.py
@@ -35,6 +35,7 @@
 
 # needed core neo modules
 from neo.core import AnalogSignal, Block, Group, Segment
+
 # need to subclass BaseIO
 from neo.io.baseio import BaseIO
 

diff --git a/neo/io/brainwaref32io.py b/neo/io/brainwaref32io.py
@@ -33,6 +33,7 @@
 
 # needed core neo modules
 from neo.core import Block, Group, Segment, SpikeTrain, NeoReadWriteError
+
 # need to subclass BaseIO
 from neo.io.baseio import BaseIO
 

diff --git a/neo/io/brainwaresrcio.py b/neo/io/brainwaresrcio.py
@@ -47,6 +47,7 @@
 
 # needed core neo modules
 from neo.core import Block, Event, Group, Segment, SpikeTrain
+
 # need to subclass BaseIO
 from neo.io.baseio import BaseIO
 

diff --git a/neo/io/elphyio.py b/neo/io/elphyio.py
@@ -85,6 +85,7 @@
 
 # I need to subclass BaseIO
 from neo.io.baseio import BaseIO
+
 # to import from core
 from neo.core import Block, Segment, AnalogSignal, Event, SpikeTrain, NeoReadWriteError
 

diff --git a/neo/io/tools.py b/neo/io/tools.py
@@ -4,7 +4,6 @@
     SPikeTrains
 """
 
-
 from collections.abc import MutableSequence
 
 from neo.core import (

diff --git a/neo/rawio/axonrawio.py b/neo/rawio/axonrawio.py
@@ -61,6 +61,7 @@
 )
 from neo.core import NeoReadWriteError
 
+
 class AxonRawIO(BaseRawIO):
     """
     Class for Class for reading data from pCLAMP and AxoScope files (.abf version 1 and 2)

diff --git a/neo/rawio/bci2000rawio.py b/neo/rawio/bci2000rawio.py
@@ -3,7 +3,6 @@
 https://www.bci2000.org/mediawiki/index.php/Technical_Reference:BCI2000_File_Format
 """
 
-
 import numpy as np
 import re
 
@@ -21,6 +20,7 @@
 )
 from neo.core import NeoReadWriteError
 
+
 class BCI2000RawIO(BaseRawIO):
     """
     Class for reading data from a BCI2000 .dat file, either version 1.0 or 1.1

diff --git a/neo/rawio/biocamrawio.py b/neo/rawio/biocamrawio.py
@@ -7,7 +7,6 @@
 Authors: Alessio Buccino, Robert Wolff
 """
 
-
 import json
 import numpy as np
 

diff --git a/neo/rawio/brainvisionrawio.py b/neo/rawio/brainvisionrawio.py
@@ -22,6 +22,7 @@
 
 from neo.core import NeoReadWriteError
 
+
 class BrainVisionRawIO(BaseRawIO):
     """Class for reading BrainVision files
 

diff --git a/neo/rawio/cedrawio.py b/neo/rawio/cedrawio.py
@@ -20,8 +20,6 @@
 Author : Samuel Garcia
 """
 
-
-
 import numpy as np
 
 from .baserawio import (
@@ -32,6 +30,7 @@
     _event_channel_dtype,
 )
 
+
 class CedRawIO(BaseRawIO):
     """
     Class for reading data from CED (Cambridge Electronic Design) spike2.

diff --git a/neo/rawio/edfrawio.py b/neo/rawio/edfrawio.py
@@ -27,6 +27,7 @@
     _event_channel_dtype,
 )
 
+
 class EDFRawIO(BaseRawIO):
     """
     Class for reading European Data Format files (EDF and EDF+).

diff --git a/neo/rawio/elanrawio.py b/neo/rawio/elanrawio.py
@@ -32,6 +32,7 @@
 
 from neo.core import NeoReadWriteError
 
+
 class ElanRawIO(BaseRawIO):
     """
     Class for reading time-frequency EEG data maps from the Elan software

diff --git a/neo/rawio/intanrawio.py b/neo/rawio/intanrawio.py
@@ -198,7 +198,7 @@ def _parse_header(self):
 
         # Data Integrity checks
         self._assert_timestamp_continuity()
-        
+
         # signals
         signal_channels = []
         for c, chan_info in enumerate(self._ordered_channel_info):
@@ -445,13 +445,13 @@ def _get_analogsignal_chunk_one_file_per_signal(self, i_start, i_stop, stream_in
         signal_data_memmap = self._raw_data[stream_index]
 
         return signal_data_memmap[i_start:i_stop, channel_indexes]
-    
+
     def _assert_timestamp_continuity(self):
         """
         Asserts the continuity of timestamps in the data.
 
-        This method verifies that the timestamps in the raw data are sequential, 
-        indicating a continuous recording. If discontinuities are found, a flag 
+        This method verifies that the timestamps in the raw data are sequential,
+        indicating a continuous recording. If discontinuities are found, a flag
         is set to indicate potential data integrity issues, and an error is raised
         unless `ignore_integrity_checks` is True.
 
@@ -491,7 +491,7 @@ def _assert_timestamp_continuity(self):
                     "\nTimestamps are not continuous, likely due to a corrupted file or inappropriate file merge.\n"
                     "To open the file anyway, initialize the reader with `ignore_integrity_checks=True`.\n\n"
                     "Discontinuities Found:\n"
-                    "+-----------------+-----------------+-----------------+-----------------------+\n"  
+                    "+-----------------+-----------------+-----------------+-----------------------+\n"
                     "| Discontinuity   | Previous        | Next            | Time Difference       |\n"
                     "| Index           | (Frames)        | (Frames)        | (Seconds)             |\n"
                     "+-----------------+-----------------+-----------------+-----------------------+\n"
@@ -503,12 +503,14 @@ def _assert_timestamp_continuity(self):
                     next_ts = timestamp[discontinuity_index + 1]
                     time_diff = (next_ts - prev_ts) / amplifier_sampling_rate
 
-                    error_msg += f"| {discontinuity_index + 1:>15,} | {prev_ts:>15,} | {next_ts:>15,} | {time_diff:>21.6f} |\n" 
+                    error_msg += (
+                        f"| {discontinuity_index + 1:>15,} | {prev_ts:>15,} | {next_ts:>15,} | {time_diff:>21.6f} |\n"
+                    )
 
                 error_msg += "+-----------------+-----------------+-----------------+-----------------------+\n"
 
                 raise NeoReadWriteError(error_msg)
-        
+
 
 def read_qstring(f):
     length = np.fromfile(f, dtype="uint32", count=1)[0]

diff --git a/neo/rawio/mearecrawio.py b/neo/rawio/mearecrawio.py
@@ -21,6 +21,7 @@
     _event_channel_dtype,
 )
 
+
 class MEArecRawIO(BaseRawIO):
     """
     Class for "reading" simulated data from a MEArec file.

diff --git a/neo/rawio/medrawio.py b/neo/rawio/medrawio.py
@@ -6,8 +6,6 @@
 Authors: Dan Crepeau, Matt Stead
 """
 
-
-
 import numpy as np
 
 from .baserawio import (
@@ -18,6 +16,7 @@
     _event_channel_dtype,
 )
 
+
 class MedRawIO(BaseRawIO):
     """
     Class for reading MED (Multiscale Electrophysiology Data) Format.

diff --git a/neo/rawio/micromedrawio.py b/neo/rawio/micromedrawio.py
@@ -23,6 +23,7 @@
 
 from neo.core import NeoReadWriteError
 
+
 class StructFile(io.BufferedReader):
     def read_f(self, fmt, offset=None):
         if offset is not None:

diff --git a/neo/rawio/neuroexplorerrawio.py b/neo/rawio/neuroexplorerrawio.py
@@ -22,6 +22,7 @@
 Author: Samuel Garcia, luc estebanez, mark hollenbeck
 
 """
+
 from collections import OrderedDict
 
 import numpy as np

diff --git a/neo/rawio/nixrawio.py b/neo/rawio/nixrawio.py
@@ -7,7 +7,6 @@
 Author: Chek Yin Choi, Julia Sprenger
 """
 
-
 import numpy as np
 
 from .baserawio import (

diff --git a/neo/rawio/rawmcsrawio.py b/neo/rawio/rawmcsrawio.py
@@ -24,6 +24,7 @@
     _event_channel_dtype,
 )
 
+
 class RawMCSRawIO(BaseRawIO):
     """
     Class for reading an mcs file converted by the MC_DataToo binary converter

diff --git a/neo/rawio/spike2rawio.py b/neo/rawio/spike2rawio.py
@@ -17,6 +17,7 @@
 Author: Samuel Garcia
 
 """
+
 from collections import OrderedDict
 
 import numpy as np
@@ -30,6 +31,7 @@
 )
 from neo.core import NeoReadWriteError
 
+
 class Spike2RawIO(BaseRawIO):
     """
     This implementation in neo reads only old smr files.

diff --git a/neo/rawio/spikeglxrawio.py b/neo/rawio/spikeglxrawio.py
@@ -64,6 +64,7 @@
     _event_channel_dtype,
 )
 
+
 class SpikeGLXRawIO(BaseRawIO):
     """
     Class for reading data from a SpikeGLX system

diff --git a/neo/rawio/tdtrawio.py b/neo/rawio/tdtrawio.py
@@ -42,6 +42,7 @@
 
 from neo.core import NeoReadWriteError
 
+
 class TdtRawIO(BaseRawIO):
     extensions = ["tbk", "tdx", "tev", "tin", "tnt", "tsq", "sev", "txt"]
     rawmode = "one-dir"

diff --git a/neo/rawio/winedrrawio.py b/neo/rawio/winedrrawio.py
@@ -9,7 +9,6 @@
 
 """
 
-
 import numpy as np
 
 from .baserawio import (

diff --git a/neo/rawio/winwcprawio.py b/neo/rawio/winwcprawio.py
@@ -21,6 +21,7 @@
     _common_sig_characteristics,
 )
 
+
 class WinWcpRawIO(BaseRawIO):
     """
     Class for reading WinWCP data