code doc typo fixes

neo/core/analogsignal.py

@@ -2,7 +2,7 @@
 This module implements :class:`AnalogSignal`, an array of analog signals.
 
 :class:`AnalogSignal` inherits from :class:`basesignal.BaseSignal` which
-derives from :class:`BaseNeo`, and from :class:`quantites.Quantity`which
+derives from :class:`BaseNeo`, and from :class:`quantities.Quantity`which
 in turn inherits from :class:`numpy.array`.
 
 Inheritance from :class:`numpy.array` is explained here:

neo/core/basesignal.py

@@ -311,4 +311,4 @@ def concatenate(self, *signals):
             If `other` object has incompatible attributes.
         '''
 
-        NotImplementedError('Patching need to be implemented in sublcasses')
+        NotImplementedError('Patching need to be implemented in subclasses')

neo/core/block.py

@@ -1,6 +1,6 @@
 '''
 This module defines :class:`Block`, the main container gathering all the data,
-whether discrete or continous, for a given recording session. base class
+whether discrete or continuous, for a given recording session. base class
 used by all :module:`neo.core` classes.
 
 :class:`Block` derives from :class:`Container`,
@@ -14,7 +14,7 @@
 
 class Block(Container):
     '''
-    Main container gathering all the data, whether discrete or continous, for a
+    Main container gathering all the data, whether discrete or continuous, for a
     given recording session.
 
     A block is not necessarily temporally homogeneous, in contrast to :class:`Segment`.
@@ -78,7 +78,7 @@ def __init__(self, name=None, description=None, file_origin=None,
                  file_datetime=None, rec_datetime=None, index=None,
                  **annotations):
         '''
-        Initalize a new :class:`Block` instance.
+        Initialize a new :class:`Block` instance.
         '''
         super().__init__(name=name, description=description,
                                     file_origin=file_origin, **annotations)

neo/core/container.py

@@ -228,7 +228,7 @@ class Container(BaseNeo):
     def __init__(self, name=None, description=None, file_origin=None,
                  **annotations):
         """
-        Initalize a new :class:`Container` instance.
+        Initialize a new :class:`Container` instance.
         """
         super().__init__(name=name, description=description,
                          file_origin=file_origin, **annotations)
@@ -466,7 +466,7 @@ def create_many_to_one_relationship(self, force=False, recursive=True):
         that this method will link up.
 
         If force is True overwrite any existing relationships
-        If recursive is True desecend into child objects and create
+        If recursive is True descend into child objects and create
         relationships there
         """
         parent_name = _reference_name(self.__class__.__name__)
@@ -485,7 +485,7 @@ def create_many_to_many_relationship(self, append=True, recursive=True):
         of this type, put the current object in the parent list.
 
         If append is True add it to the list, otherwise overwrite the list.
-        If recursive is True desecend into child objects and create
+        If recursive is True descend into child objects and create
         relationships there
         """
         parent_name = _container_name(self.__class__.__name__)
@@ -517,7 +517,7 @@ def create_relationship(self, force=False, append=True, recursive=True):
 
         If force is True overwrite any existing relationships
         If append is True add it to the list, otherwise overwrite the list.
-        If recursive is True desecend into child objects and create
+        If recursive is True descend into child objects and create
         relationships there
         """
         self.create_many_to_one_relationship(force=force, recursive=False)

neo/core/dataobject.py

@@ -124,7 +124,7 @@ def _check_single_elem(element):
 
             # Check the first element for correctness
             # If its type is correct for annotations, all others are correct as well
-            # Note: Emtpy lists cannot reach this point
+            # Note: Empty lists cannot reach this point
             _check_single_elem(value[0])
 
     return value

neo/core/imagesequence.py

@@ -2,7 +2,7 @@
 This module implements :class:`ImageSequence`, a 3D array.
 
 :class:`ImageSequence` inherits from :class:`basesignal.BaseSignal` which
-derives from :class:`BaseNeo`, and from :class:`quantites.Quantity`which
+derives from :class:`BaseNeo`, and from :class:`quantities.Quantity`which
 in turn inherits from :class:`numpy.array`.
 
 Inheritance from :class:`numpy.array` is explained here:

neo/core/segment.py

@@ -20,7 +20,7 @@ class Segment(Container):
     '''
     A container for data sharing a common time basis.
 
-    A :class:`Segment` is a heterogeneous container for discrete or continous
+    A :class:`Segment` is a heterogeneous container for discrete or continuous
     data sharing a common clock (time basis) but not necessary the same
     sampling rate, start or end time.
 

neo/core/spiketrain.py

@@ -2,7 +2,7 @@
 This module implements :class:`SpikeTrain`, an array of spike times.
 
 :class:`SpikeTrain` derives from :class:`BaseNeo`, from
-:module:`neo.core.baseneo`, and from :class:`quantites.Quantity`, which
+:module:`neo.core.baseneo`, and from :class:`quantities.Quantity`, which
 inherits from :class:`numpy.array`.
 
 Inheritance from :class:`numpy.array` is explained here:
@@ -261,13 +261,13 @@ def __new__(cls, times, t_stop, units=None, dtype=None, copy=True, sampling_rate
                 t_start=0.0 * pq.s, waveforms=None, left_sweep=None, name=None, file_origin=None,
                 description=None, array_annotations=None, **annotations):
         '''
-        Constructs a new :clas:`Spiketrain` instance from data.
+        Constructs a new :class:`Spiketrain` instance from data.
 
         This is called whenever a new :class:`SpikeTrain` is created from the
         constructor, but not when slicing.
         '''
         if len(times) != 0 and waveforms is not None and len(times) != waveforms.shape[0]:
-            # len(times)!=0 has been used to workaround a bug occuring during neo import
+            # len(times)!=0 has been used to workaround a bug occurring during neo import
             raise ValueError("the number of waveforms should be equal to the number of spikes")
 
         if dtype is not None and hasattr(times, 'dtype') and times.dtype != dtype:
@@ -382,7 +382,7 @@ def __array_finalize__(self, obj):
         constructor, and these are set in __new__. Then they are just
         copied over here.
 
-        Note that the :attr:`waveforms` attibute is not sliced here. Nor is
+        Note that the :attr:`waveforms` attribute is not sliced here. Nor is
         :attr:`t_start` or :attr:`t_stop` modified.
         '''
         # This calls Quantity.__array_finalize__ which deals with

neo/rawio/alphaomegarawio.py

@@ -102,7 +102,7 @@ def __init__(self, dirname="", lsx_files=None, prune_channels=True):
 
     def _explore_folder(self):
         """
-        If class was instanciated with lsx_files (list of .lsx files), load only
+        If class was instantiated with lsx_files (list of .lsx files), load only
         the files referenced in these lsx files otherwise, load all *.mpx files
         in `dirname`.
         It does not explores the subfolders.
@@ -114,7 +114,7 @@ def _explore_folder(self):
                 with open(index_file, "r") as f:
                     for line in f:
                         # a line is a Microsoft Windows path. As we cannot
-                        # instanciate a WindowsPath on other OS than MS
+                        # instantiate a WindowsPath on other OS than MS
                         # Windows, we use the PureWindowsPath class
                         filename = PureWindowsPath(line.strip())
                         filename = self.dirname / filename.name
@@ -145,7 +145,7 @@ def _read_file_datablocks(self, filename, prune_channels=True):
         :param prune_channels: Remove references to channels and ports which
             doesn't contain any data recorded. Be careful when using this option
             with multiple-file data since it could theoretically leads to
-            expection raised when data recorded in further files are merged into
+            exception raised when data recorded in further files are merged into
             the first file pruned from these channels.
         :type prune_channels: bool
         """
@@ -1127,7 +1127,7 @@ def get_name(f, name_length):
     - mode_spike (2 bytes): read as hex data 0xMCCC:
         - M: 1=Master, 2=Slave
         - CCC: linked channel
-        Be carefull here, the first byte cover MC and the second byte the last
+        Be careful here, the first byte cover MC and the second byte the last
         part of the linked channel CC
 """
 SDefContinAnalog = struct.Struct("<fh")

neo/rawio/axographrawio.py

@@ -66,7 +66,7 @@
     data appears before the second column's. As an aside, because of this
     design choice AxoGraph cannot write data to disk as it is collected but
     must store it all in memory until data acquisition ends. This also affected
-    how file slicing was implmented for this RawIO: Instead of using a single
+    how file slicing was implemented for this RawIO: Instead of using a single
     memmap to address into a 2-dimensional block of data, AxographRawIO
     constructs multiple 1-dimensional memmaps, one for each column, each with
     its own offset.
@@ -127,7 +127,7 @@
     Segments in Neo. Certain criteria have to be met, such as all groups
     containing equal numbers of traces and each group having homogeneous signal
     parameters. If trace grouping was modified by the user after data
-    acquisition, this may result in the file being interpretted as
+    acquisition, this may result in the file being interpreted as
     non-episodic. Older versions of the AxoGraph file format lack group headers
     entirely, so these files are never deemed safe to interpret as episodic,
     even if the column names follow a repeating sequence as described above.
@@ -397,7 +397,7 @@ def _rescale_epoch_duration(self, raw_duration, dtype, event_channel_index):
 
     def _safe_to_treat_as_episodic(self):
         """
-        The purpose of this fuction is to determine if the file contains any
+        The purpose of this function is to determine if the file contains any
         irregularities in its grouping of traces such that it cannot be treated
         as episodic. Even "continuous" recordings can be treated as
         single-episode recordings and could be identified as safe by this
@@ -627,7 +627,7 @@ def _scan_axograph_file(self):
                 # COLUMN TYPE
 
                 # depending on the format version, data columns may have a type
-                # - prior to verion 3, column types did not exist and data was
+                # - prior to version 3, column types did not exist and data was
                 #   stored in a fixed pattern
                 # - beginning with version 3, several data types are available
                 #   as documented in AxoGraph_ReadWrite.h

neo/rawio/axonarawio.py

@@ -288,7 +288,7 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop,
         and three samples of 2 bytes each for 64 channels (384 bytes), which
         are jumbled up in a strange order. Each channel is remapped to a
         certain position (see get_channel_offset), and a channel's samples are
-        allcoated as follows (example for channel 7):
+        allocated as follows (example for channel 7):
 
         sample 1: 32b (head) + 2*38b (remappedID) and 2*38b + 1b (2nd byte)
         sample 2: 32b (head) + 128 (all chan. 1st entry) + 2*38b and ...

neo/rawio/axonrawio.py

@@ -23,7 +23,7 @@
 All possible mode are possible :
     - event-driven variable-length mode 1 -> return several Segments per Block
     - event-driven fixed-length mode 2 or 5 -> return several Segments
-    - gap free mode -> return one (or sevral) Segment in the Block
+    - gap free mode -> return one (or several) Segment in the Block
 
 Supported : Read
 
@@ -277,8 +277,8 @@ def _event_count(self, block_index, seg_index, event_channel_index):
         return self._raw_ev_timestamps.size
 
     def _get_event_timestamps(self, block_index, seg_index, event_channel_index, t_start, t_stop):
-        # In ABF timstamps are not attached too any particular segment
-        # so each segmetn acees all event
+        # In ABF timestamps are not attached too any particular segment
+        # so each segment accesses all events
         timestamp = self._raw_ev_timestamps
         labels = self._ev_labels
         durations = None
@@ -306,7 +306,7 @@ def read_raw_protocol(self):
         from the ABF1 header.
 
         Returns: list of segments (one for every episode)
-                 with list of analog signls (one for every DAC).
+                 with list of analog signals (one for every DAC).
 
         Author:  JS Nowacki
         """
@@ -447,9 +447,9 @@ def parse_axon_soup(filename):
             # hack for reading channels names and units
             # this section is not very detailed and so the code
             # not very robust. The idea is to remove the first
-            # part by find ing one of th fowoling KEY
-            # unfortunatly the later part contains a the file
-            # taht can contain by accident also one of theses keys...
+            # part by finding one of th following KEY
+            # unfortunately the later part contains a the file
+            # that can contain by accident also one of theses keys...
             f.seek(sections['StringsSection']['uBlockIndex'] * BLOCKSIZE)
             big_string = f.read(sections['StringsSection']['uBytes'])
             goodstart = -1

neo/rawio/baserawio.py

@@ -47,7 +47,7 @@
 So this handles **only** one simplified but very frequent case of dataset:
     * Only one channel set  for AnalogSignal stable along Segment
     * Only one channel set  for SpikeTrain stable along Segment
-    * AnalogSignal have all the same sampling_rate acroos all Segment
+    * AnalogSignal have all the same sampling_rate across all Segment
     * t_start/t_stop are the same for many object (SpikeTrain, Event) inside a Segment
 
 Signal channels are handled by group of "stream".
@@ -448,7 +448,7 @@ def _check_stream_signal_channel_characteristics(self):
             # also check that channel_id is unique inside a stream
             channel_ids = signal_channels[mask]['id']
             assert np.unique(channel_ids).size == channel_ids.size, \
-                f'signal_channels dont have unique ids for stream {stream_index}'
+                f'signal_channels do not have unique ids for stream {stream_index}'
 
         self._several_channel_groups = signal_streams.size > 1
 
@@ -733,7 +733,7 @@ def setup_cache(self, cache_path, **init_kargs):
         d = dict(ressource_name=resource_name, mtime=os.path.getmtime(resource_name))
         hash = joblib.hash(d, hash_name='md5')
 
-        # name is constructed from the real_n,ame and the hash
+        # name is constructed from the resource_name and the hash
         name = '{}_{}'.format(os.path.basename(resource_name), hash)
         self.cache_filename = os.path.join(dirname, name)
 

neo/rawio/biocamrawio.py

@@ -29,7 +29,7 @@ class BiocamRawIO(BaseRawIO):
         >>> r.parse_header()
         >>> print(r)
         >>> raw_chunk = r.get_analogsignal_chunk(block_index=0, seg_index=0,
-                                                 i_start=0, i_stop=1024,  
+                                                 i_start=0, i_stop=1024,
                                                  channel_names=channel_names)
         >>> float_chunk = r.rescale_signal_raw_to_float(raw_chunk, dtype='float64',
                                                         channel_indexes=[0, 3, 6])
@@ -119,7 +119,7 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop,
 
 
 def open_biocam_file_header(filename):
-    """Open a Biocam hdf5 file, read and return the recording info, pick te correct method to access raw data,
+    """Open a Biocam hdf5 file, read and return the recording info, pick the correct method to access raw data,
     and return this to the caller."""
     assert HAVE_H5PY, 'h5py is not installed'
 

neo/rawio/blackrockrawio.py

@@ -106,7 +106,7 @@ class BlackrockRawIO(BaseRawIO):
             IDs of nsX file from which to load data, e.g., if set to
             5 only data from the ns5 file are loaded.
             If 'all', then all nsX will be loaded.
-            Contrary to previsous version of the IO  (<0.7), nsx_to_load
+            Contrary to previous version of the IO  (<0.7), nsx_to_load
             must be set at the init before parse_header().
 
     Examples:
@@ -371,7 +371,7 @@ def _parse_header(self):
                         units = chan['units']
                     sig_dtype = 'int16'
                     # max_analog_val/min_analog_val/max_digital_val/min_analog_val are int16!!!!!
-                    # dangarous situation so cast to float everyone
+                    # dangerous situation so cast to float everyone
                     if np.isnan(float(chan['min_analog_val'])):
                         gain = 1
                         offset = 0
@@ -387,7 +387,7 @@ def _parse_header(self):
             # check nb segment per nsx
             nb_segments_for_nsx = [len(self.nsx_datas[nsx_nb]) for nsx_nb in self.nsx_to_load]
             assert all(nb == nb_segments_for_nsx[0] for nb in nb_segments_for_nsx),\
-                   'Segment nb not consistanent across nsX files'
+                   'Segment nb not consistent across nsX files'
             self._nb_segment = nb_segments_for_nsx[0]
 
             self.__delete_empty_segments()
@@ -494,7 +494,7 @@ def _parse_header(self):
             seg_ann['description'] = "Segment containing data from t_start to t_stop"
             if seg_index == 0:
                 # if more than 1 segment means pause
-                # so datetime is valide only for seg_index=0
+                # so datetime is valid only for seg_index=0
                 seg_ann['rec_datetime'] = rec_datetime
 
             for c in range(signal_streams.size):
@@ -768,7 +768,7 @@ def __read_nsx_header_variant_a(self, nsx_nb):
         # basic header (file_id: NEURALCD)
         dt0 = [
             ('file_id', 'S8'),
-            # label of sampling groun (e.g. "1kS/s" or "LFP Low")
+            # label of sampling group (e.g. "1kS/s" or "LFP Low")
             ('label', 'S16'),
             # number of 1/30000 seconds between data points
             # (e.g., if sampling rate "1 kS/s", period equals "30")
@@ -1119,7 +1119,7 @@ def __get_event_segment_ids(self, raw_event_data, masks, nev_data_masks):
             reset_ev_ids = np.where(reset_ev_mask)[0]
 
             # consistency check for monotone increasing time stamps
-            # explicitely converting to int to allow for negative diff values
+            # explicitly converting to int to allow for negative diff values
             jump_ids = \
                 np.where(np.diff(np.asarray(raw_event_data['timestamp'], dtype=int)) < 0)[0] + 1
             overlap = np.in1d(jump_ids, reset_ev_ids)
@@ -1594,7 +1594,7 @@ def __get_waveforms_dtype(self):
         """
         Extracts the actual waveform dtype set for each channel.
         """
-        # Blackrock code giving the approiate dtype
+        # Blackrock code giving the appropriate dtype
         conv = {0: 'int8', 1: 'int8', 2: 'int16', 4: 'int32'}
 
         # get all electrode ids from nev ext header
@@ -1639,7 +1639,7 @@ def __get_channel_labels_variant_b(self):
 
     def __get_waveform_size_variant_a(self):
         """
-        Returns wavform sizes for all channels for file spec 2.1 and 2.2
+        Returns waveform sizes for all channels for file spec 2.1 and 2.2
         """
         wf_dtypes = self.__get_waveforms_dtype()
         nb_bytes_wf = self.__nev_basic_header['bytes_in_data_packets'] - 8
@@ -1652,7 +1652,7 @@ def __get_waveform_size_variant_a(self):
 
     def __get_waveform_size_variant_b(self):
         """
-        Returns wavform sizes for all channels for file spec 2.3
+        Returns waveform sizes for all channels for file spec 2.3
         """
         elids = self.__nev_ext_header[b'NEUEVWAV']['electrode_id']
         spike_widths = self.__nev_ext_header[b'NEUEVWAV']['spike_width']