PEP8 fixes for the 0.7.0 release (#608)

Author: mdenker

.pep8speaks.yml

@@ -1,5 +1,6 @@
 pycodestyle:
     max-line-length: 99  # Default is 79 in PEP8
     ignore:
+      - W503 # Change in PEP8, this warning is replaced by W504
       - E127
       - E128

doc/source/images/generate_diagram.py

@@ -32,20 +32,20 @@ def get_rect_height(name, obj):
     nlines += len(getattr(obj, '_single_child_objects', []))
     nlines += len(getattr(obj, '_multi_child_objects', []))
     nlines += len(getattr(obj, '_multi_parent_objects', []))
-    return nlines*line_heigth
+    return nlines * line_heigth
 
 
 def annotate(ax, coord1, coord2, connectionstyle, color, alpha):
     arrowprops = dict(arrowstyle='fancy',
-                      #~ patchB=p,
+                      # ~ patchB=p,
                       shrinkA=.3, shrinkB=.3,
                       fc=color, ec=color,
                       connectionstyle=connectionstyle,
                       alpha=alpha)
     bbox = dict(boxstyle="square", fc="w")
     a = ax.annotate('', coord1, coord2,
-                    #xycoords="figure fraction",
-                    #textcoords="figure fraction",
+                    # xycoords="figure fraction",
+                    # textcoords="figure fraction",
                     ha="right", va="center",
                     size=fontsize,
                     arrowprops=arrowprops,
@@ -55,7 +55,7 @@ def annotate(ax, coord1, coord2, connectionstyle, color, alpha):
 
 def calc_coordinates(pos, height):
     x = pos[0]
-    y = pos[1] + height - line_heigth*.5
+    y = pos[1] + height - line_heigth * .5
 
     return pos[0], y
 
@@ -102,45 +102,44 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
     for name, pos in rect_pos.items():
         htotal = all_h[name]
         obj = objs[name]
-        allrelationship = (list(getattr(obj, '_child_containers', [])) +
-                           list(getattr(obj, '_multi_parent_containers', [])))
+        allrelationship = (list(getattr(obj, '_child_containers', []))
+                           + list(getattr(obj, '_multi_parent_containers', [])))
 
         rect = Rectangle(pos, rect_width, htotal,
                          facecolor='w', edgecolor='k', linewidth=2.)
         ax.add_patch(rect)
 
         # title green
-        pos2 = pos[0], pos[1]+htotal - line_heigth*1.5
-        rect = Rectangle(pos2, rect_width, line_heigth*1.5,
+        pos2 = pos[0], pos[1] + htotal - line_heigth * 1.5
+        rect = Rectangle(pos2, rect_width, line_heigth * 1.5,
                          facecolor='g', edgecolor='k', alpha=.5, linewidth=2.)
         ax.add_patch(rect)
 
         # single relationship
         relationship = getattr(obj, '_single_child_objects', [])
-        pos2 = pos[1] + htotal - line_heigth*(1.5+len(relationship))
-        rect_height = len(relationship)*line_heigth
+        pos2 = pos[1] + htotal - line_heigth * (1.5 + len(relationship))
+        rect_height = len(relationship) * line_heigth
 
         rect = Rectangle((pos[0], pos2), rect_width, rect_height,
                          facecolor='c', edgecolor='k', alpha=.5)
         ax.add_patch(rect)
 
         # multi relationship
-        relationship = (list(getattr(obj, '_multi_child_objects', [])) +
-                        list(getattr(obj, '_multi_parent_containers', [])))
-        pos2 = (pos[1]+htotal - line_heigth*(1.5+len(relationship)) -
-                rect_height)
-        rect_height = len(relationship)*line_heigth
+        relationship = (list(getattr(obj, '_multi_child_objects', []))
+                        + list(getattr(obj, '_multi_parent_containers', [])))
+        pos2 = (pos[1] + htotal - line_heigth * (1.5 + len(relationship))
+                - rect_height)
+        rect_height = len(relationship) * line_heigth
 
         rect = Rectangle((pos[0], pos2), rect_width, rect_height,
                          facecolor='m', edgecolor='k', alpha=.5)
         ax.add_patch(rect)
 
         # necessary attr
-        pos2 = (pos[1]+htotal -
-                line_heigth*(1.5+len(allrelationship) +
-                             len(obj._necessary_attrs)))
+        pos2 = (pos[1] + htotal
+                - line_heigth * (1.5 + len(allrelationship) + len(obj._necessary_attrs)))
         rect = Rectangle((pos[0], pos2), rect_width,
-                         line_heigth*len(obj._necessary_attrs),
+                         line_heigth * len(obj._necessary_attrs),
                          facecolor='r', edgecolor='k', alpha=.5)
         ax.add_patch(rect)
 
@@ -149,27 +148,27 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
             post = '* '
         else:
             post = ''
-        ax.text(pos[0]+rect_width/2., pos[1]+htotal - line_heigth*1.5/2.,
-                name+post,
+        ax.text(pos[0] + rect_width / 2., pos[1] + htotal - line_heigth * 1.5 / 2.,
+                name + post,
                 horizontalalignment='center', verticalalignment='center',
-                fontsize=fontsize+2,
+                fontsize=fontsize + 2,
                 fontproperties=FontProperties(weight='bold'),
                 )
 
-        #relationship
+        # relationship
         for i, relat in enumerate(allrelationship):
-            ax.text(pos[0]+left_text_shift, pos[1]+htotal - line_heigth*(i+2),
-                    relat+': list',
+            ax.text(pos[0] + left_text_shift, pos[1] + htotal - line_heigth * (i + 2),
+                    relat + ': list',
                     horizontalalignment='left', verticalalignment='center',
                     fontsize=fontsize,
                     )
         # attributes
         for i, attr in enumerate(obj._all_attrs):
             attrname, attrtype = attr[0], attr[1]
             t1 = attrname
-            if (hasattr(obj, '_quantity_attr') and
-                    obj._quantity_attr == attrname):
-                t1 = attrname+'(object itself)'
+            if (hasattr(obj, '_quantity_attr')
+                    and obj._quantity_attr == attrname):
+                t1 = attrname + '(object itself)'
             else:
                 t1 = attrname
 
@@ -185,9 +184,9 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
             else:
                 t2 = attrtype.__name__
 
-            t = t1+' :  '+t2
-            ax.text(pos[0]+left_text_shift,
-                    pos[1]+htotal - line_heigth*(i+len(allrelationship)+2),
+            t = t1 + ' :  ' + t2
+            ax.text(pos[0] + left_text_shift,
+                    pos[1] + htotal - line_heigth * (i + len(allrelationship) + 2),
                     t,
                     horizontalalignment='left', verticalalignment='center',
                     fontsize=fontsize,
@@ -206,15 +205,15 @@ def generate_diagram_simple():
     figsize = (18, 12)
     rw = rect_width = 3.
     bf = blank_fact = 1.2
-    rect_pos = {'Block': (.5+rw*bf*0, 4),
-                'Segment': (.5+rw*bf*1, .5),
-                'Event': (.5+rw*bf*4, 3.0),
-                'Epoch': (.5+rw*bf*4, 1.0),
-                'ChannelIndex': (.5+rw*bf*1, 7.5),
-                'Unit': (.5+rw*bf*2., 9.9),
-                'SpikeTrain': (.5+rw*bf*3, 7.5),
-                'IrregularlySampledSignal': (.5+rw*bf*3, 0.5),
-                'AnalogSignal': (.5+rw*bf*3, 4.9),
+    rect_pos = {'Block': (.5 + rw * bf * 0, 4),
+                'Segment': (.5 + rw * bf * 1, .5),
+                'Event': (.5 + rw * bf * 4, 3.0),
+                'Epoch': (.5 + rw * bf * 4, 1.0),
+                'ChannelIndex': (.5 + rw * bf * 1, 7.5),
+                'Unit': (.5 + rw * bf * 2., 9.9),
+                'SpikeTrain': (.5 + rw * bf * 3, 7.5),
+                'IrregularlySampledSignal': (.5 + rw * bf * 3, 0.5),
+                'AnalogSignal': (.5 + rw * bf * 3, 4.9),
                 }
     generate_diagram('simple_generated_diagram.svg',
                      rect_pos, rect_width, figsize)

neo/core/dataobject.py

@@ -174,7 +174,6 @@ def __init__(self, name=None, description=None, file_origin=None, array_annotati
                          **annotations)
 
     def array_annotate(self, **array_annotations):
-
         """
         Add array annotations (annotations for individual data points) as arrays to a Neo data
         object.
@@ -189,7 +188,6 @@ def array_annotate(self, **array_annotations):
         self.array_annotations.update(array_annotations)
 
     def array_annotations_at_index(self, index):
-
         """
         Return dictionary of array annotations at a given index or list of indices
         :param index: int, list, numpy array: The index (indices) from which the annotations

neo/io/axographio.py

@@ -149,4 +149,4 @@ def read_block(self, **kargs):
 
         blk.create_many_to_one_relationship()
 
-        return blk
+        return blk

neo/io/basefromrawio.py

@@ -134,7 +134,7 @@ def read_block(self, block_index=0, lazy=False, signal_group_mode=None,
                     for j in ind_abs:
                         for key in list(self.raw_annotations['signal_channels'][i].keys()):
                             chidx_annotations[key].append(self.raw_annotations[
-                                                              'signal_channels'][j][key])
+                                'signal_channels'][j][key])
                 if 'name' in list(chidx_annotations.keys()):
                     chidx_annotations.pop('name')
                 chidx_annotations = check_annotations(chidx_annotations)

neo/io/blackrockio_v4.py

@@ -278,7 +278,7 @@ def __init__(self, filename, nsx_override=None, nev_override=None,
         exts = ['nsx', 'nev', 'sif', 'ccf']
         ext_overrides = [nsx_override, nev_override, sif_override, ccf_override]
         for ext, ext_override in zip(exts, ext_overrides):
-            if ext_override is not None and self._avail_files[ext] == False:
+            if ext_override is not None and self._avail_files[ext] is False:
                 raise ValueError('Specified {} file {} could not be '
                                  'found.'.format(ext, ext_override))
 
@@ -1108,8 +1108,8 @@ def __get_nsx_rec_times_variant_a(self, nsx_nb):
         bytes_in_headers = self.__nsx_params[self.__nsx_spec[nsx_nb]](
             'bytes_in_headers', nsx_nb)
         nb_data_points = int(
-            (self.__get_file_size(filename) - bytes_in_headers) /
-            (2 * self.__nsx_basic_header[nsx_nb]['channel_count']) - 1)
+            (self.__get_file_size(filename) - bytes_in_headers)
+            / (2 * self.__nsx_basic_header[nsx_nb]['channel_count']) - 1)
 
         # add n_start
         n_starts = [(0 * t_unit).rescale(highest_res)]
@@ -1267,8 +1267,8 @@ def __get_nsx_param_variant_a(self, param_name, nsx_nb):
         nsx_parameters = {
             'labels': labels,
             'units': np.array(
-                [b'uV'] *
-                self.__nsx_basic_header[nsx_nb]['channel_count']),
+                [b'uV']
+                * self.__nsx_basic_header[nsx_nb]['channel_count']),
             'min_analog_val': -1 * np.array(dig_factor),
             'max_analog_val': np.array(dig_factor),
             'min_digital_val': np.array(
@@ -1277,9 +1277,9 @@ def __get_nsx_param_variant_a(self, param_name, nsx_nb):
                 [1000] * self.__nsx_basic_header[nsx_nb]['channel_count']),
             'timestamp_resolution': 30000,
             'bytes_in_headers':
-                self.__nsx_basic_header[nsx_nb].dtype.itemsize +
-                self.__nsx_ext_header[nsx_nb].dtype.itemsize *
-                self.__nsx_basic_header[nsx_nb]['channel_count'],
+                self.__nsx_basic_header[nsx_nb].dtype.itemsize
+                + self.__nsx_ext_header[nsx_nb].dtype.itemsize
+                * self.__nsx_basic_header[nsx_nb]['channel_count'],
             'sampling_rate':
                 30000 / self.__nsx_basic_header[nsx_nb]['period'] * pq.Hz,
             'time_unit': pq.CompoundUnit("1.0/{0}*s".format(
@@ -1310,11 +1310,11 @@ def __get_nsx_param_variant_b(self, param_name, nsx_nb):
             'bytes_in_headers':
                 self.__nsx_basic_header[nsx_nb]['bytes_in_headers'],
             'sampling_rate':
-                self.__nsx_basic_header[nsx_nb]['timestamp_resolution'] /
-                self.__nsx_basic_header[nsx_nb]['period'] * pq.Hz,
+                self.__nsx_basic_header[nsx_nb]['timestamp_resolution']
+                / self.__nsx_basic_header[nsx_nb]['period'] * pq.Hz,
             'time_unit': pq.CompoundUnit("1.0/{0}*s".format(
-                self.__nsx_basic_header[nsx_nb]['timestamp_resolution'] /
-                self.__nsx_basic_header[nsx_nb]['period']))}
+                self.__nsx_basic_header[nsx_nb]['timestamp_resolution']
+                / self.__nsx_basic_header[nsx_nb]['period']))}
 
         return nsx_parameters[param_name]
 
@@ -1336,8 +1336,8 @@ def __get_nsx_databl_param_variant_a(
         # extract parameters from nsx basic extended and data header
         data_parameters = {
             'nb_data_points': int(
-                (self.__get_file_size(filename) - bytes_in_headers) /
-                (2 * self.__nsx_basic_header[nsx_nb]['channel_count']) - 1),
+                (self.__get_file_size(filename) - bytes_in_headers)
+                / (2 * self.__nsx_basic_header[nsx_nb]['channel_count']) - 1),
             'databl_idx': 1,
             'databl_t_start': t_starts[0],
             'databl_t_stop': t_stops[0]}
@@ -1410,8 +1410,8 @@ def __get_nonneural_evtypes_variant_a(self, data):
                 'name': 'serial_input_port',
                 'field': 'digital_input',
                 'mask':
-                    self.__is_set(data['packet_insertion_reason'], 0) &
-                    self.__is_set(data['packet_insertion_reason'], 7),
+                    self.__is_set(data['packet_insertion_reason'], 0)
+                    & self.__is_set(data['packet_insertion_reason'], 7),
                 'desc': "Events of the serial input port"}}
 
         # analog input events via threshold crossings
@@ -1451,8 +1451,8 @@ def __get_nonneural_evtypes_variant_b(self, data):
                 'name': 'serial_input_port',
                 'field': 'digital_input',
                 'mask':
-                    self.__is_set(data['packet_insertion_reason'], 0) &
-                    self.__is_set(data['packet_insertion_reason'], 7),
+                    self.__is_set(data['packet_insertion_reason'], 0)
+                    & self.__is_set(data['packet_insertion_reason'], 7),
                 'desc': "Events of the serial input port"}}
 
         return event_types
@@ -1658,7 +1658,7 @@ def __merge_time_ranges(
                     "".format(user_n_stops[start_stop_id]))
 
             if (user_n_stops[start_stop_id] < min_time
-                or user_n_starts[start_stop_id] > max_time):
+                    or user_n_starts[start_stop_id] > max_time):
                 user_n_stops.pop(start_stop_id)
                 user_n_starts.pop(start_stop_id)
                 self._print_verbose(
@@ -1721,7 +1721,7 @@ def __merge_time_ranges(
                 mask = (n_stops_files > start) & (n_stops_files < stop)
                 red_n_stops_files = np.array(n_stops_files)[mask]
                 merged_n_stops = [
-                                     tp * highest_res for tp in red_n_stops_files] + [stop]
+                    tp * highest_res for tp in red_n_stops_files] + [stop]
             else:
                 merged_n_stops = [stop]
             # Define combined user and file n_starts and n_stops
@@ -1747,7 +1747,7 @@ def __merge_time_ranges(
                 n_stops.extend(merged_n_stops)
 
         if len(n_starts) > len(user_n_starts) and \
-                        len(n_stops) > len(user_n_stops):
+                len(n_stops) > len(user_n_stops):
             self._print_verbose(
                 "Additional recording pauses were detected. There will be "
                 "more segments than the user expects.")
@@ -1826,9 +1826,9 @@ def __read_spiketrain(
 
             if scaling == 'voltage':
                 st.waveforms = (
-                    waveforms[mask] * self.__nev_params('waveform_unit') *
-                    self.__nev_params('digitization_factor')[channel_id] /
-                    1000.)
+                    waveforms[mask] * self.__nev_params('waveform_unit')
+                    * self.__nev_params('digitization_factor')[channel_id]
+                    / 1000.)
             elif scaling == 'raw':
                 st.waveforms = waveforms[mask] * pq.dimensionless
             else:
@@ -2008,11 +2008,11 @@ def __read_channelindex(
                     nev_dig_factor=self.__nev_ext_header[
                         b'NEUEVWAV']['digitization_factor'][get_idx],
                     nev_energy_threshold=self.__nev_ext_header[
-                                             b'NEUEVWAV']['energy_threshold'][get_idx] * pq.uV,
+                        b'NEUEVWAV']['energy_threshold'][get_idx] * pq.uV,
                     nev_hi_threshold=self.__nev_ext_header[
-                                         b'NEUEVWAV']['hi_threshold'][get_idx] * pq.uV,
+                        b'NEUEVWAV']['hi_threshold'][get_idx] * pq.uV,
                     nev_lo_threshold=self.__nev_ext_header[
-                                         b'NEUEVWAV']['lo_threshold'][get_idx] * pq.uV,
+                        b'NEUEVWAV']['lo_threshold'][get_idx] * pq.uV,
                     nb_sorted_units=self.__nev_ext_header[
                         b'NEUEVWAV']['nb_sorted_units'][get_idx],
                     waveform_size=self.__waveform_size[self.__nev_spec](
@@ -2027,15 +2027,15 @@ def __read_channelindex(
                     # filter type codes (extracted from blackrock manual)
                     chidx.annotate(
                         nev_hi_freq_corner=self.__nev_ext_header[b'NEUEVFLT'][
-                                               'hi_freq_corner'][get_idx] /
-                                           1000. * pq.Hz,
+                            'hi_freq_corner'][get_idx]
+                        / 1000. * pq.Hz,
                         nev_hi_freq_order=self.__nev_ext_header[b'NEUEVFLT'][
                             'hi_freq_order'][get_idx],
                         nev_hi_freq_type=flt_type[self.__nev_ext_header[
                             b'NEUEVFLT']['hi_freq_type'][get_idx]],
                         nev_lo_freq_corner=self.__nev_ext_header[
-                                               b'NEUEVFLT']['lo_freq_corner'][get_idx] /
-                                           1000. * pq.Hz,
+                            b'NEUEVFLT']['lo_freq_corner'][get_idx]
+                        / 1000. * pq.Hz,
                         nev_lo_freq_order=self.__nev_ext_header[
                             b'NEUEVFLT']['lo_freq_order'][get_idx],
                         nev_lo_freq_type=flt_type[self.__nev_ext_header[
@@ -2051,9 +2051,9 @@ def __read_channelindex(
                     channel_id)
                 chidx.annotate(
                     nsx_hi_freq_corner=self.__nsx_ext_header[k][
-                                           'hi_freq_corner'][get_idx] / 1000. * pq.Hz,
+                        'hi_freq_corner'][get_idx] / 1000. * pq.Hz,
                     nsx_lo_freq_corner=self.__nsx_ext_header[k][
-                                           'lo_freq_corner'][get_idx] / 1000. * pq.Hz,
+                        'lo_freq_corner'][get_idx] / 1000. * pq.Hz,
                     nsx_hi_freq_order=self.__nsx_ext_header[k][
                         'hi_freq_order'][get_idx],
                     nsx_lo_freq_order=self.__nsx_ext_header[k][
@@ -2558,8 +2558,8 @@ def __str__(self):
                 'sampling_rate', nsx_nb)
             avail_el = [
                 el for el in self.__nsx_ext_header[nsx_nb]['electrode_id']]
-            output += "\nAnalog Parameters (NS" + str(nsx_nb) + ")" \
-                                                                "\n===================================="
+            output += "\nAnalog Parameters (NS" \
+                + str(nsx_nb) + ")\n===================================="
             output += "\nResolution (Hz): %i" % analog_res
             output += "\nAvailable channel IDs: " + \
                       ", ".join(["%i" % a for a in avail_el]) + "\n"