Merge pull request #1468 from NeuralEnsemble/black-formatting

alejoe91 · web-flow · commit 800525a3bdbf · 2024-05-05T14:33:14.000+02:00
Black formatting
diff --git a/neo/core/baseneo.py b/neo/core/baseneo.py
@@ -34,6 +34,7 @@
 class MergeError(Exception):
     pass
 
+
 class NeoReadWriteError(IOError):
     """
     This is the main neo-specific error that has to deal with
@@ -46,13 +47,14 @@ class NeoReadWriteError(IOError):
             * Different sampling rates among streams
             * Different expectations for a file format (could also be
             a NotImplementedError depending on circumstances)
-        
+
     It should NOT be used when other errors more accurately describe
     the problem:
         1) ValueError: for incorrect values (like t_start, t_stop)
         2) TypeError: use of an inappropriate type for an argument
         3) FileNotFoundError: for use when a file is not found
     """
+
     pass
 
 
diff --git a/neo/core/dataobject.py b/neo/core/dataobject.py
@@ -193,7 +193,7 @@ def array_annotate(self, **array_annotations):
         ----------
         **array_annotations: dict
             Series of keyword annotations to add to the object
-        
+
         Examples
         --------
         >>> obj.array_annotate(code=['a', 'b', 'a'], category=[2, 1, 1])
@@ -211,7 +211,7 @@ def array_annotations_at_index(self, index):
         ----------
         index: int | list | np.ndarray
             The index (indices) from which the annotations are extracted
-        
+
         Returns
         -------
         index_annotations: dict
@@ -252,12 +252,12 @@ def _merge_array_annotations(self, other):
         ----------
         other: any
             The annotation to attemp to merge
-        
+
         Returns
         -------
         merged_array_annotations: dict
             The merged annotations
-        
+
         Notes
         -----
         The merge happens in such a way that the result fits the merged data
@@ -312,12 +312,12 @@ def rescale(self, units, dtype=None):
             The units to convert the object to
         dtype: a numpy dtype
             Only exists for backward compatibility see [1]
-        
+
         Returns
         -------
         self.copy(): Any
             A copy of the object with the desired units
-        
+
         Notes
         -----
         [1] The `dtype` argument exists only for backward compatibility within quantities, see
@@ -358,7 +358,7 @@ def as_array(self, units=None):
         ----------
         units: quantities units | None, default: None
             The data return as a np.ndarray with units requested
-        
+
         Returns
         -------
         data_array: np.ndarray
@@ -430,7 +430,7 @@ def __deepcopy__(self, memo):
         return new_obj
 
 
-class ArrayDict(dict): 
+class ArrayDict(dict):
     """Dictionary subclass to handle array annotations
 
     When setting `obj.array_annotations[key]=value`, checks for consistency
diff --git a/neo/core/event.py b/neo/core/event.py
@@ -262,7 +262,7 @@ def merge(self, other):
         ---------
         other: neo.core.Event
             The `Event` to merge into this one
-        
+
         Notes
         -----
         * The :class:`Event` objects are concatenated horizontally
diff --git a/neo/core/filters.py b/neo/core/filters.py
@@ -41,7 +41,7 @@ def __init__(self, control: Any) -> None:
 
         Parameters
         ----------
-        control: Any 
+        control: Any
             The control value to be used for filtering.
 
         Notes
diff --git a/neo/core/irregularlysampledsignal.py b/neo/core/irregularlysampledsignal.py
@@ -110,7 +110,7 @@ class IrregularlySampledSignal(BaseSignal):
     array_annotations: dict | None, default: None
         Dict mapping strings to numpy arrays containing annotations for all data points
     **annotations: dict
-        Optional additional metadata supplied by the user as a dict. Will be stored in 
+        Optional additional metadata supplied by the user as a dict. Will be stored in
         the annotations attribute of the object
 
     Notes
@@ -354,7 +354,7 @@ def _check_consistency(self, other) -> None:
         ValueError
          * Dimensionality of objects don't match for signal
          * If times are different between the two objects
-        
+
         Returns
         -------
         None if check passes
@@ -488,8 +488,8 @@ def resample(self, sample_count, **kwargs):
     def time_slice(self, t_start, t_stop):
         """
         Creates a new :class:`IrregularlySampledSignal` corresponding to the time slice of
-        the original :class:`IrregularlySampledSignal` 
-        
+        the original :class:`IrregularlySampledSignal`
+
         Parameters
         ----------
         t_start: float | None
diff --git a/neo/core/spiketrain.py b/neo/core/spiketrain.py
@@ -74,7 +74,7 @@ def _check_time_in_range(value, t_start, t_stop, view=False) -> None:
         * If t_stop < t_start
         * value.min() < t_start
         * value.max() > t_start
-    
+
     Returns
     -------
     None: If check passes
@@ -106,7 +106,7 @@ def _check_waveform_dimensions(spiketrain) -> None:
     ----------
     spiketrain: neo.core.SpikeTrain
         The neo.core.SpikeTrain to check for waveforms
-    
+
     Raises
     ------
     ValueError
@@ -238,10 +238,10 @@ class SpikeTrain(DataObject):
     ----------
     times: quantity array 1D | numpy array 1D | list
         The times of each spike.
-    t_stop: quantity scalar | numpy scalar |float 
+    t_stop: quantity scalar | numpy scalar |float
         Time at which the SpikeTrain ended. This will be converted to thesame units as `times`.
         This argument is required because it specifies the period of time over which spikes could have occurred.
-        Note that :attr:`t_start` is highly recommended for the same reason.        
+        Note that :attr:`t_start` is highly recommended for the same reason.
     units: (quantity units) | None, default: None
         Required if `times` is a list or numpy.ndarray`
         Not required if times is a quantities.Quantity
@@ -266,7 +266,7 @@ class SpikeTrain(DataObject):
         A text description of this dataset
     file_origin: str | Filesystem path | URL | None, default: None
         The path or location of the original data file.
-    array_annotations: dict 
+    array_annotations: dict
         A dictonary mapping of strings to numpy arrays containing annotations for all data points
     **annotations: dict
         Other user defined metadata given as a dict
@@ -279,7 +279,7 @@ class SpikeTrain(DataObject):
             Interval between two samples (1/`sampling_rate`)
      * duration: quantity scalar
             Duration over which spikes can occur read-only (`t_stop` - `t_start`)
-     * spike_duration: quantity scalar 
+     * spike_duration: quantity scalar
             Duration of a waveform, read-only (`waveform`.shape[2] * `sampling_period`)
      * right_sweep: quantity scalar
             Time from the trigger times of the spikes to the end of the waveforms, read-only
@@ -293,7 +293,7 @@ class SpikeTrain(DataObject):
         metadata, except that :attr:`waveforms` is also sliced in the same way
         (along dimension 0). Note that t_start and t_stop are not changed
         automatically, although you can still manually change them.
-    
+
     Examples
     --------
 
@@ -311,7 +311,7 @@ class SpikeTrain(DataObject):
     <SpikeTrain(array([ 3.,  4.,  5.]) * s, [0.0 s, 10.0 s])>
     >>> train2
     <SpikeTrain(array([ 4.,  5.]) * s, [0.0 s, 10.0 s])>
-    
+
     """
 
     _parent_objects = ("Segment",)
diff --git a/neo/core/spiketrainlist.py b/neo/core/spiketrainlist.py
@@ -24,7 +24,7 @@ def unique(quantities):
     Parameters
     ----------
     quantities: array-like[pq.Quantity dtype]
-        An array-like object containing quantities 
+        An array-like object containing quantities
 
     Returns
     -------
@@ -257,7 +257,7 @@ def __radd__(self, other):
     def append(self, obj):
         """
         Appends to the SpikeTrainList with a new neo.core.SpikeTrain
-        
+
         Parameters
         ----------
         obj: neo.core.SpikeTrain
@@ -281,12 +281,12 @@ def append(self, obj):
 
     def extend(self, iterable):
         """Extends the SpikeTrainList with additional SpikeTrain's from an iterable
-        
+
         Parameters
         ----------
         iterable: iterable[neo.core.SpikeTrain]
             A list-like or array-like object containing neo.core.SpikeTrain to be added to the SpikeTrainList
-            
+
         Examples
         --------
         # with SpikeTrainList stl with two SpikeTrains and stl_other with three SpikeTrains
diff --git a/neo/core/view.py b/neo/core/view.py
@@ -30,7 +30,7 @@ class ChannelView(BaseNeo):
         Filesystem path or URL of the original data file.
     array_annotations: dict | None, default: None
         Dict mapping strings to numpy arrays containing annotations for all data points
-    **annotations: dict 
+    **annotations: dict
         Other use-specified metadata with keywords
     """
 
diff --git a/neo/io/basefromrawio.py b/neo/io/basefromrawio.py
@@ -244,7 +244,9 @@ def read_segment(
             if time_slice is not None:
                 raise ValueError("For lazy=True you must specify a time_slice when LazyObject.load(time_slice=...)")
             if load_waveforms:
-                raise ValueError("For lazy=True you must specify load_waveforms when SpikeTrain.load(load_waveforms=...)")
+                raise ValueError(
+                    "For lazy=True you must specify load_waveforms when SpikeTrain.load(load_waveforms=...)"
+                )
 
         if signal_group_mode is None:
             signal_group_mode = self._prefered_signal_group_mode
diff --git a/neo/io/baseio.py b/neo/io/baseio.py
@@ -35,7 +35,7 @@
     RectangularRegionOfInterest,
     CircularRegionOfInterest,
     PolygonRegionOfInterest,
-    NeoReadWriteError
+    NeoReadWriteError,
 )
 
 read_error = "This type is not supported by this file format for reading"
@@ -175,8 +175,10 @@ def write(self, bl, **kargs):
                 self.write_block(bl, **kargs)
         elif Segment in self.writeable_objects:
             if len(bl.segments) != 1:
-                raise NeoReadWriteError(f"{self.__class__.__name__} is based on segment so if you try to write a block it "
-                + "must contain only one Segment")
+                raise NeoReadWriteError(
+                    f"{self.__class__.__name__} is based on segment so if you try to write a block it "
+                    + "must contain only one Segment"
+                )
             self.write_segment(bl.segments[0], **kargs)
         else:
             raise NotImplementedError
diff --git a/neo/io/elphyio.py b/neo/io/elphyio.py
@@ -2685,7 +2685,7 @@ def get_tag(self, episode, tag_channel):
             if tag_mode == 1:
                 if tag_channel not in range(1, 3):
                     raise ValueError("Elphy format support only 2 tag channels for tag_mode == 1")
-            elif tag_mode == 2 or tag_mode ==3:
+            elif tag_mode == 2 or tag_mode == 3:
                 if tag_channel not in range(1, 17):
                     raise ValueError("Elphy format support only 16 tag channels for tag_mode == 2 or tag_mode == 3")
 
@@ -2812,7 +2812,9 @@ def get_spiketrain(self, episode, electrode_id):
         if episode not in range(1, self.n_episodes + 1):
             raise ValueError(f"`episode` must be in {range(1, self.n_episodes + 1)}, but is {episode}")
         if electrode_id not in range(1, self.n_spiketrains(episode) + 1):
-            raise ValueError(f"`eletrodee_id` must be in {range(1, self.n_spiketrains(episode)+1)}, but is {electrode_id}")
+            raise ValueError(
+                f"`eletrodee_id` must be in {range(1, self.n_spiketrains(episode)+1)}, but is {electrode_id}"
+            )
         # get some properties stored in the episode sub-block
         block = self.episode_block(episode)
         x_unit = block.ep_block.x_unit
diff --git a/neo/io/proxyobjects.py b/neo/io/proxyobjects.py
@@ -274,7 +274,9 @@ def load(self, time_slice=None, strict_slicing=True, channel_indexes=None, magni
 
         if magnitude_mode == "raw":
             if self._raw_units is None:
-                raise ValueError("raw magnitude is not supported if the gain are not the same for all channels or offset is not 0")
+                raise ValueError(
+                    "raw magnitude is not supported if the gain are not the same for all channels or offset is not 0"
+                )
             sig = raw_signal
             units = self._raw_units
         elif magnitude_mode == "rescaled":
diff --git a/neo/rawio/alphaomegarawio.py b/neo/rawio/alphaomegarawio.py
@@ -44,6 +44,7 @@
 )
 from neo.core import NeoReadWriteError
 
+
 class AlphaOmegaRawIO(BaseRawIO):
     """
     AlphaOmega MPX file format 4 reader. Handles several segments.
diff --git a/neo/rawio/axographrawio.py b/neo/rawio/axographrawio.py
@@ -568,13 +568,13 @@ def _scan_axograph_file(self):
                 if format_ver != 1 and format_ver != 2:
                     raise ValueError(
                         f'Mismatch between header identifier "{header_id}" and format ' f'version "{format_ver}"!'
-                )
+                    )
             elif header_id == "axgx":
                 format_ver, n_cols = f.read_f("ll")
                 if format_ver < 3:
                     raise ValueError(
-                    f'Mismatch between header identifier "{header_id}" and format ' f'version "{format_ver}"!'
-                )
+                        f'Mismatch between header identifier "{header_id}" and format ' f'version "{format_ver}"!'
+                    )
             else:
                 raise NotImplementedError(f'unimplemented file header identifier "{header_id}"!')
             self.info["format_ver"] = format_ver
@@ -1061,11 +1061,11 @@ def _scan_axograph_file(self):
                     if font_settings_info["setting1"] not in [
                         FONT_BOLD,
                         FONT_NOT_BOLD,
-                    ]: 
+                    ]:
                         raise ValueError(
-                        f"expected setting1 ({ font_settings_info['setting1']}) to have value FONT_BOLD "
-                        f"({FONT_BOLD}) or FONT_NOT_BOLD ({FONT_NOT_BOLD})"
-                    )
+                            f"expected setting1 ({ font_settings_info['setting1']}) to have value FONT_BOLD "
+                            f"({FONT_BOLD}) or FONT_NOT_BOLD ({FONT_NOT_BOLD})"
+                        )
 
                     # size is stored 10 times bigger than real value
                     font_settings_info["size"] = font_settings_info["size"] / 10.0
diff --git a/neo/rawio/baserawio.py b/neo/rawio/baserawio.py
@@ -499,16 +499,17 @@ def _check_stream_signal_channel_characteristics(self):
         if signal_streams.size > 0:
             if signal_channels.size < 1:
                 raise ValueError("Signal stream exists but there are no signal channels")
-            
 
         for stream_index in range(signal_streams.size):
             stream_id = signal_streams[stream_index]["id"]
             mask = signal_channels["stream_id"] == stream_id
             characteristics = signal_channels[mask][_common_sig_characteristics]
             unique_characteristics = np.unique(characteristics)
             if unique_characteristics.size != 1:
-                raise ValueError(f"Some channels in stream_id {stream_id} "
-                                 f"do not have the same {_common_sig_characteristics} {unique_characteristics}")
+                raise ValueError(
+                    f"Some channels in stream_id {stream_id} "
+                    f"do not have the same {_common_sig_characteristics} {unique_characteristics}"
+                )
 
             # also check that channel_id is unique inside a stream
             channel_ids = signal_channels[mask]["id"]
@@ -788,8 +789,10 @@ def get_analogsignal_chunk(
         if isinstance(channel_indexes, np.ndarray):
             if channel_indexes.dtype == "bool":
                 if self.signal_channels_count(stream_index) != channel_indexes.size:
-                    raise ValueError("If channel_indexes is a boolean it must have be the same length as the "
-                                     f"number of channels {self.signal_channels_count(stream_index)}")
+                    raise ValueError(
+                        "If channel_indexes is a boolean it must have be the same length as the "
+                        f"number of channels {self.signal_channels_count(stream_index)}"
+                    )
                 (channel_indexes,) = np.nonzero(channel_indexes)
 
         if prefer_slice and isinstance(channel_indexes, np.ndarray):
diff --git a/neo/rawio/bci2000rawio.py b/neo/rawio/bci2000rawio.py
@@ -164,7 +164,7 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, strea
             raise ValueError("`i_start` is outside of data range")
         if (i_stop < 0) or (i_stop > self._read_info["n_samps"]):
             raise ValueError("`i_stop` is outside of data range")
-        
+
         if channel_indexes is None:
             channel_indexes = np.arange(self.header["signal_channels"].size)
         return self._memmap["raw_vector"][i_start:i_stop, channel_indexes]
diff --git a/neo/rawio/brainvisionrawio.py b/neo/rawio/brainvisionrawio.py
diff --git a/neo/rawio/openephysrawio.py b/neo/rawio/openephysrawio.py
diff --git a/neo/rawio/plexon2rawio/plexon2rawio.py b/neo/rawio/plexon2rawio/plexon2rawio.py
diff --git a/neo/rawio/tdtrawio.py b/neo/rawio/tdtrawio.py
diff --git a/neo/test/rawiotest/test_neuroscoperawio.py b/neo/test/rawiotest/test_neuroscoperawio.py
