standardize docstrings using numpydoc format

neo/core/analogsignal.py

@@ -481,13 +481,13 @@ def time_shift(self, t_shift):
         """
         Shifts a :class:`AnalogSignal` to start at a new time.
 
-        Parameters:
-        -----------
+        Parameters
+        ----------
         t_shift: Quantity (time)
             Amount of time by which to shift the :class:`AnalogSignal`.
 
-        Returns:
-        --------
+        Returns
+        -------
         new_sig: :class:`AnalogSignal`
             New instance of a :class:`AnalogSignal` object starting at t_shift later than the
             original :class:`AnalogSignal` (the original :class:`AnalogSignal` is not modified).
@@ -538,19 +538,19 @@ def downsample(self, downsampling_factor, **kwargs):
         arguments, except for specifying the axis of resampling, which is fixed to the first axis
         here.
 
-        Parameters:
-        -----------
-        downsampling_factor: integer
+        Parameters
+        ----------
+        downsampling_factor: int
             Factor used for decimation of samples. Scipy recommends to call decimate multiple times
             for downsampling factors higher than 13 when using IIR downsampling (default).
 
-        Returns:
-        --------
+        Returns
+        -------
         downsampled_signal: :class:`AnalogSignal`
             New instance of a :class:`AnalogSignal` object containing the resampled data points.
             The original :class:`AnalogSignal` is not modified.
 
-        Note:
+        Notes
         -----
         For resampling the signal with a fixed number of samples, see `resample` method.
         """
@@ -581,19 +581,19 @@ def resample(self, sample_count, **kwargs):
         arguments, except for specifying the axis of resampling which is fixed to the first axis
         here, and the sample positions. .
 
-        Parameters:
-        -----------
-        sample_count: integer
+        Parameters
+        ----------
+        sample_count: int
             Number of desired samples. The resulting signal starts at the same sample as the
             original and is sampled regularly.
 
-        Returns:
-        --------
+        Returns
+        -------
         resampled_signal: :class:`AnalogSignal`
             New instance of a :class:`AnalogSignal` object containing the resampled data points.
             The original :class:`AnalogSignal` is not modified.
 
-        Note:
+        Notes
         -----
         For reducing the number of samples to a fraction of the original, see `downsample` method
         """
@@ -625,8 +625,8 @@ def rectify(self, **kwargs):
         This method is a wrapper of numpy.absolute() and accepts the same set of keyword
         arguments.
 
-        Returns:
-        --------
+        Returns
+        -------
         resampled_signal: :class:`AnalogSignal`
             New instance of a :class:`AnalogSignal` object containing the rectified data points.
             The original :class:`AnalogSignal` is not modified.

neo/core/dataobject.py

@@ -18,16 +18,22 @@ def _normalize_array_annotations(value, length):
     Recursively check that value is either an array or list containing only "simple" types
     (number, string, date/time) or is a dict of those.
 
-    Args:
-        :value: (np.ndarray, list or dict) value to be checked for consistency
-        :length: (int) required length of the array annotation
-
-    Returns:
-        np.ndarray The array_annotations from value in correct form
-
-    Raises:
-        ValueError: In case value is not accepted as array_annotation(s)
-
+    Parameters
+    ----------
+    value : np.ndarray or list or dict
+        Value to be checked for consistency.
+    length : int
+        Required length of the array annotation.
+
+    Returns
+    -------
+    np.ndarray
+        The array_annotations from value in correct form
+
+    Raises
+    ------
+    ValueError
+        In case value is not accepted as array_annotation(s)
     """
 
     # First stage, resolve dict of annotations into single annotations

neo/core/epoch.py

@@ -318,13 +318,13 @@ def time_shift(self, t_shift):
         """
         Shifts an :class:`Epoch` by an amount of time.
 
-        Parameters:
-        -----------
+        Parameters
+        ----------
         t_shift: Quantity (time)
             Amount of time by which to shift the :class:`Epoch`.
 
-        Returns:
-        --------
+        Returns
+        -------
         epoch: :class:`Epoch`
             New instance of an :class:`Epoch` object starting at t_shift later than the
             original :class:`Epoch` (the original :class:`Epoch` is not modified).

neo/core/event.py

@@ -287,13 +287,13 @@ def time_shift(self, t_shift):
         """
         Shifts an :class:`Event` by an amount of time.
 
-        Parameters:
-        -----------
+        Parameters
+        ----------
         t_shift: Quantity (time)
             Amount of time by which to shift the :class:`Event`.
 
-        Returns:
-        --------
+        Returns
+        -------
         epoch: Event
             New instance of an :class:`Event` object starting at t_shift later than the
             original :class:`Event` (the original :class:`Event` is not modified).

neo/core/irregularlysampledsignal.py

@@ -356,14 +356,14 @@ def resample(self, sample_count, **kwargs):
         arguments, except for specifying the axis of resampling which is fixed to the first axis
         here, and the sample positions. .
 
-        Parameters:
-        -----------
-        sample_count: integer
+        Parameters
+        ----------
+        sample_count: int
             Number of desired samples. The resulting signal starts at the same sample as the
             original and is sampled regularly.
 
-        Returns:
-        --------
+        Returns
+        -------
         resampled_signal: :class:`AnalogSignal`
             New instance of a :class:`AnalogSignal` object containing the resampled data points.
             The original :class:`AnalogSignal` is not modified.
@@ -431,13 +431,13 @@ def time_shift(self, t_shift):
         """
         Shifts a :class:`IrregularlySampledSignal` to start at a new time.
 
-        Parameters:
-        -----------
+        Parameters
+        ----------
         t_shift: Quantity (time)
             Amount of time by which to shift the :class:`IrregularlySampledSignal`.
 
-        Returns:
-        --------
+        Returns
+        -------
         new_sig: :class:`SpikeTrain`
             New instance of a :class:`IrregularlySampledSignal` object
             starting at t_shift later than the original :class:`IrregularlySampledSignal`

neo/core/segment.py

@@ -145,25 +145,22 @@ def time_slice(self, t_start=None, t_stop=None, reset_time=False, **kwargs):
         Creates a time slice of a Segment containing slices of all child
         objects.
 
-        Parameters:
-        -----------
+        Parameters
+        ----------
         t_start: Quantity
             Starting time of the sliced time window.
         t_stop: Quantity
             Stop time of the sliced time window.
-        reset_time: bool
+        reset_time: bool, optional, default: False
             If True the time stamps of all sliced objects are set to fall
             in the range from t_start to t_stop.
             If False, original time stamps are retained.
-            Default is False.
-
-        Keyword Arguments:
-        ------------------
+        **kwargs
             Additional keyword arguments used for initialization of the sliced
             Segment object.
 
-        Returns:
-        --------
+        Returns
+        -------
         subseg: Segment
             Temporal slice of the original Segment from t_start to t_stop.
         """

neo/core/spiketrain.py

@@ -640,13 +640,13 @@ def time_shift(self, t_shift):
         """
         Shifts a :class:`SpikeTrain` to start at a new time.
 
-        Parameters:
-        -----------
+        Parameters
+        ----------
         t_shift: Quantity (time)
             Amount of time by which to shift the :class:`SpikeTrain`.
 
-        Returns:
-        --------
+        Returns
+        -------
         spiketrain: :class:`SpikeTrain`
             New instance of a :class:`SpikeTrain` object starting at t_shift later than the
             original :class:`SpikeTrain` (the original :class:`SpikeTrain` is not modified).

neo/io/axonio.py

@@ -28,9 +28,9 @@ class AxonIO(AxonRawIO, BaseFromRaw):
      - `AxonIO._sampling_rate`
 
     The current AxonIO.read_protocol() method utilizes a subset of these.
-    In particular I know it doesn't consider `nDigitalEnable`, `EpochInfo`, or `nActiveDACChannel` and it doesn't account 
+    In particular I know it doesn't consider `nDigitalEnable`, `EpochInfo`, or `nActiveDACChannel` and it doesn't account
     for different types of Epochs offered by Clampex/pClamp other than discrete steps (such as ramp, pulse train, etc and
-    encoded by `nEpochType` in the EpochInfoPerDAC section). I'm currently parsing a superset of the properties used 
+    encoded by `nEpochType` in the EpochInfoPerDAC section). I'm currently parsing a superset of the properties used
     by read_protocol() in my analysis scripts, but that code still doesn't parse the full information and isn't in a state
     where it could be committed and I can't currently prioritize putting together all the code that would parse the full
     set of data. The `AxonIO._axon_info['EpochInfo']` section doesn't currently exist.
@@ -47,8 +47,11 @@ def read_protocol(self):
         Read the protocol waveform of the file, if present;
         function works with ABF2 only. Protocols can be reconstructed
         from the ABF1 header.
-        Returns: list of segments (one for every episode)
-                 with list of analog signls (one for every DAC).
+
+        Returns
+        -------
+        segments : list of segments
+            Segments, one for every episode, with list of analog signls (one for every DAC).
         """
         sigs_by_segments, sig_names, sig_units = self.read_raw_protocol()
         segments = []

neo/io/elphyio.py

@@ -3811,8 +3811,10 @@ def read_block(self, lazy=False, ):
         """
         Return :class:`Block`.
 
-        Parameters:
-             lazy : postpone actual reading of the file.
+        Parameters
+        ----------
+        lazy : bool
+            Postpone actual reading of the file.
         """
         assert not lazy, 'Do not support lazy'
 
@@ -4211,9 +4213,11 @@ def get_annotations_dict(self, annotations, prefix, items, name='', idx=0):
     def read_segment(self, episode):
         """
         Internal method used to return :class:`Segment` data to the main read method.
-        Parameters:
-            elphy_file : is the elphy object.
-            episode : number of elphy episode, roughly corresponding to a segment
+
+        Parameters
+        ----------
+        episode : int
+            Number of elphy episode, roughly corresponding to a segment
         """
         # print "name:",self.elphy_file.layout.get_episode_name(episode)
         episode_name = self.elphy_file.layout.get_episode_name(episode)
@@ -4254,10 +4258,12 @@ def read_event(self, episode, evt):
         Internal method used to return a list of elphy :class:`EventArray` acquired from event
         channels.
 
-        Parameters:
-            elphy_file : is the elphy object.
-            episode : number of elphy episode, roughly corresponding to a segment.
-            evt : index of the event.
+        Parameters
+        ----------
+        episode : int
+            Number of elphy episode, roughly corresponding to a segment.
+        evt : int
+            Index of the event.
         """
         event = self.elphy_file.get_event(episode, evt)
         neo_event = Event(
@@ -4270,10 +4276,12 @@ def read_spiketrain(self, episode, spk):
         """
         Internal method used to return an elphy object :class:`SpikeTrain`.
 
-        Parameters:
-            elphy_file : is the elphy object.
-            episode : number of elphy episode, roughly corresponding to a segment.
-            spk : index of the spike array.
+        Parameters
+        ----------
+        episode : int
+            Number of elphy episode, roughly corresponding to a segment.
+        spk : int
+            Index of the spike array.
         """
         block = self.elphy_file.layout.episode_block(episode)
         spike = self.elphy_file.get_spiketrain(episode, spk)

neo/io/igorproio.py

@@ -173,15 +173,21 @@ def key_value_string_parser(itemsep=";", kvsep=":"):
     """
     Parses a string into a dict.
 
-    Arguments:
-        itemsep - character which separates items
-        kvsep - character which separates the key and value within an item
-
-    Returns:
+    Parameters
+    ----------
+    itemsep : str
+        Character which separates items
+    kvsep : str
+        Character which separates the key and value within an item
+
+    Returns
+    -------
+    callable
         a function which takes the string to be parsed as the sole argument
         and returns a dict.
 
-    Example:
+    Examples
+    --------
 
         >>> parse = key_value_string_parser(itemsep=";", kvsep=":")
         >>> parse("a:2;b:3")

neo/io/kwikio.py

@@ -95,7 +95,8 @@ def read_block(self,
         """
         Reads a block with segments and groups
 
-        Parameters:
+        Parameters
+        ----------
         get_waveforms: bool, default = False
             Wether or not to get the waveforms
         get_raw_data: bool, default = False
@@ -152,7 +153,8 @@ def read_analogsignal(self, model, units='uV', lazy=False):
         """
         Reads analogsignals
 
-        Parameters:
+        Parameters
+        ----------
         units: str, default = "uV"
             SI units of the raw trace according to voltage_gain given to klusta
         """
@@ -172,7 +174,8 @@ def read_spiketrain(self, cluster_id, model,
         """
         Reads sorted spiketrains
 
-        Parameters:
+        Parameters
+        ----------
         get_waveforms: bool, default = False
             Wether or not to get the waveforms
         cluster_id: int,