More linting fixes

c302/CompareMain.py

@@ -118,13 +118,13 @@ def getColumnsXls(fileIn):
         # print(indexName[c])
     while curr_row < num_rows:
         curr_row += 1
-        row = worksheet.row(curr_row)
+        #row = worksheet.row(curr_row)
         # print('Row:', curr_row)
         curr_cell = -1
         while curr_cell < num_cells:
             curr_cell += 1
             # Cell Types: 0=Empty, 1=Text, 2=Number, 3=Date, 4=Boolean, 5=Error, 6=Blank
-            cell_type = worksheet.cell_type(curr_row, curr_cell)
+            #cell_type = worksheet.cell_type(curr_row, curr_cell)
             cell_value = str(worksheet.cell_value(curr_row, curr_cell))
             # print('	', cell_type, ':', cell_value)
             cols[indexName[curr_cell]] += [cell_value]

c302/ConnectomeReader.py

@@ -507,7 +507,7 @@ def check_neurons(cells):
     not_in_preferred = []
     missing_preferred = [n for n in PREFERRED_NEURON_NAMES]
     for c in cells:
-        if not c in PREFERRED_NEURON_NAMES:
+        if c not in PREFERRED_NEURON_NAMES:
             not_in_preferred.append(c)
         else:
             preferred.append(c)
@@ -539,7 +539,7 @@ def analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_co
     nts_tot = {}
     for c in neuron_conns:
         nt = c.synclass
-        if not nt in nts:
+        if nt not in nts:
             nts[nt] = 0
             nts_tot[nt] = 0
         nts[nt] += 1
@@ -558,7 +558,7 @@ def analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_co
     print_("Found %s muscles: %s\n" % (len(muscles), sorted(muscles)))
     not_in_preferred = []
     for m in muscles:
-        if not m in PREFERRED_MUSCLE_NAMES:
+        if m not in PREFERRED_MUSCLE_NAMES:
             not_in_preferred.append(m)
 
     print_(
@@ -586,7 +586,7 @@ def analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_co
     nts_tot = {}
     for c in muscle_conns:
         nt = c.synclass
-        if not nt in nts:
+        if nt not in nts:
             nts[nt] = 0
             nts_tot[nt] = 0
         nts[nt] += 1

c302/Cook2019DataReader.py

@@ -9,12 +9,9 @@
 
 ############################################################
 
-import csv
 
 from c302.ConnectomeReader import ConnectionInfo
 from c302.ConnectomeReader import analyse_connections
-from c302.ConnectomeReader import convert_to_preferred_muscle_name
-from c302.ConnectomeReader import is_neuron
 from c302.ConnectomeReader import is_body_wall_muscle
 from c302.ConnectomeReader import remove_leading_index_zero
 

c302/NeuroMLUtilities.py

@@ -6,12 +6,8 @@
 
 ############################################################
 
-from c302 import print_
 
-from c302.ConnectomeReader import PREFERRED_NEURON_NAMES
-from c302.ConnectomeReader import PREFERRED_MUSCLE_NAMES
 
-from c302.ConnectomeReader import ConnectionInfo
 from c302.ConnectomeReader import analyse_connections
 
 
@@ -48,7 +44,7 @@ def fract(a, b, f):
 
 
 if __name__ == "__main__":
-    from SpreadsheetDataReader import read_data, read_muscle_data
+    #from SpreadsheetDataReader import read_data, read_muscle_data
     from WormNeuroAtlasReader import read_data, read_muscle_data
 
     cells, neuron_conns = read_data(include_nonconnected_cells=True)

c302/OpenWormReader.py

@@ -1,8 +1,8 @@
 import logging
 import re
 
-from c302.NeuroMLUtilities import ConnectionInfo
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import ConnectionInfo
+from c302.ConnectomeReader import analyse_connections
 from c302 import print_, MUSCLE_RE
 
 try:
@@ -11,7 +11,7 @@
     from owmeta.neuron import Neuron
     from owmeta.muscle import BodyWallMuscle
     from owmeta.worm import Worm
-except:
+except Exception:
     print("owmeta not installed! Cannot run OpenWormReader")
     exit()
 
@@ -158,7 +158,7 @@ def format_muscle_name(muscle_name):
     exit()
 
     conn_map_OWR = {}
-    for c in conns:
+    for c in muscle_conns:
         conn_map_OWR[c.short().lower()] = c
 
     from c302.UpdatedSpreadsheetDataReader import read_data as read_data_usr

c302/SpreadsheetDataReader.py

@@ -10,15 +10,15 @@
 ############################################################
 
 
-from c302.NeuroMLUtilities import ConnectionInfo
-from c302.NeuroMLUtilities import analyse_connections
+from c302 import print_
+from c302.ConnectomeReader import ConnectionInfo
+from c302.ConnectomeReader import analyse_connections
 
 from xlrd import open_workbook
 import os
 
 spreadsheet_location = os.path.dirname(os.path.abspath(__file__)) + "/data/"
 
-from c302 import print_
 
 READER_DESCRIPTION = (
     """Data extracted from CElegansNeuronTables.xls for neuronal connectivity"""

c302/UpdatedSpreadsheetDataReader.py

@@ -11,8 +11,8 @@
 
 import csv
 
-from c302.NeuroMLUtilities import ConnectionInfo
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import ConnectionInfo
+from c302.ConnectomeReader import analyse_connections
 import os
 
 from c302 import print_

c302/UpdatedSpreadsheetDataReader2.py

@@ -12,8 +12,8 @@
 import csv
 
 
-from c302.NeuroMLUtilities import ConnectionInfo
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import ConnectionInfo
+from c302.ConnectomeReader import analyse_connections
 import os
 
 from c302 import print_

c302/VarshneyDataReader.py

@@ -1,5 +1,5 @@
-from c302.NeuroMLUtilities import ConnectionInfo
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import ConnectionInfo
+from c302.ConnectomeReader import analyse_connections
 from openpyxl import load_workbook
 
 import os
@@ -70,7 +70,7 @@ def read_muscle_data():
             conns.append(ConnectionInfo(pre, post, num, syntype, synclass))
             if pre not in neurons:
                 neurons.append(pre)
-            if not post in muscles:
+            if post not in muscles:
                 muscles.append(post)
 
     return neurons, muscles, conns

c302/W_SpreadsheetDataReader.py

@@ -2,7 +2,6 @@
 from c302.ConnectomeReader import analyse_connections
 from c302.ConnectomeReader import convert_to_preferred_muscle_name
 from c302.ConnectomeReader import is_neuron
-from c302.ConnectomeReader import is_body_wall_muscle
 
 from openpyxl import load_workbook
 import os

c302/WhiteDataReader.py

@@ -9,7 +9,6 @@
 
 ############################################################
 
-import csv
 
 from c302.ConnectomeReader import ConnectionInfo
 from c302.ConnectomeReader import analyse_connections

c302/WormNeuroAtlasReader.py

@@ -1,8 +1,7 @@
 import logging
-import re
 
-from c302.NeuroMLUtilities import ConnectionInfo
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import ConnectionInfo
+from c302.ConnectomeReader import analyse_connections
 from c302 import print_
 
 import wormneuroatlas as wa
@@ -93,9 +92,9 @@ def read_data(self, include_nonconnected_cells=False):
                     connection = True
 
                 if connection:
-                    if not pre in connected_cells:
+                    if pre not in connected_cells:
                         connected_cells.append(pre)
-                    if not post in connected_cells:
+                    if post not in connected_cells:
                         connected_cells.append(post)
 
         if include_nonconnected_cells:

c302/__init__.py

@@ -44,7 +44,7 @@
 
 try:
     from urllib2 import URLError  # Python 2
-except:
+except Exception:
     from urllib.error import URLError  # Python 3
 
 logging.basicConfig()

c302/c302_IClampMuscle.py

@@ -1,6 +1,5 @@
 import c302
 import sys
-import neuroml.writers as writers
 
 
 def setup(

c302/c302_TargetMuscle.py

@@ -1,6 +1,5 @@
 import c302
 import sys
-import neuroml.writers as writers
 
 
 def setup(

c302/c302_info.py

@@ -1,8 +1,3 @@
-import sys
-import os
-from pyneuroml import pynml
-import matplotlib.pyplot as plt
-import numpy as np
 
 import c302
 
@@ -15,14 +10,14 @@ def generate_c302_info(nml_doc, verbose=False):
     all_cells = []
 
     for cp in net.continuous_projections:
-        if not cp.presynaptic_population in cc_exc_conns.keys():
+        if cp.presynaptic_population not in cc_exc_conns.keys():
             cc_exc_conns[cp.presynaptic_population] = {}
-        if not cp.presynaptic_population in cc_inh_conns.keys():
+        if cp.presynaptic_population not in cc_inh_conns.keys():
             cc_inh_conns[cp.presynaptic_population] = {}
 
-        if not cp.presynaptic_population in all_cells:
+        if cp.presynaptic_population not in all_cells:
             all_cells.append(cp.presynaptic_population)
-        if not cp.postsynaptic_population in all_cells:
+        if cp.postsynaptic_population not in all_cells:
             all_cells.append(cp.postsynaptic_population)
 
         for c in cp.continuous_connection_instance_ws:
@@ -37,12 +32,12 @@ def generate_c302_info(nml_doc, verbose=False):
 
     gj_conns = {}
     for ep in net.electrical_projections:
-        if not ep.presynaptic_population in gj_conns.keys():
+        if ep.presynaptic_population not in gj_conns.keys():
             gj_conns[ep.presynaptic_population] = {}
 
-        if not ep.presynaptic_population in all_cells:
+        if ep.presynaptic_population not in all_cells:
             all_cells.append(ep.presynaptic_population)
-        if not ep.postsynaptic_population in all_cells:
+        if ep.postsynaptic_population not in all_cells:
             all_cells.append(ep.postsynaptic_population)
 
         for e in ep.electrical_connection_instance_ws:

c302/c302_utils.py

@@ -1,12 +1,9 @@
 import sys
 import os
 import re
-import collections
-import traceback
 
 import matplotlib.pyplot as plt
 import numpy as np
-from pyneuroml import pynml
 from pyneuroml import plot as pyneuroml_plot
 
 import c302
@@ -414,7 +411,6 @@ def _show_conn_matrix(
     title = "%s: %s" % (type, t)
     plt.title(title)
     fig.canvas.manager.set_window_title(title)
-    import matplotlib
 
     # cm = matplotlib.cm.get_cmap('gist_stern_r')
     if colormap == None:
@@ -471,14 +467,14 @@ def generate_conn_matrix(
     all_cells = []
 
     for cp in net.continuous_projections:
-        if not cp.presynaptic_population in cc_exc_conns.keys():
+        if cp.presynaptic_population not in cc_exc_conns.keys():
             cc_exc_conns[cp.presynaptic_population] = {}
-        if not cp.presynaptic_population in cc_inh_conns.keys():
+        if cp.presynaptic_population not in cc_inh_conns.keys():
             cc_inh_conns[cp.presynaptic_population] = {}
 
-        if not cp.presynaptic_population in all_cells:
+        if cp.presynaptic_population not in all_cells:
             all_cells.append(cp.presynaptic_population)
-        if not cp.postsynaptic_population in all_cells:
+        if cp.postsynaptic_population not in all_cells:
             all_cells.append(cp.postsynaptic_population)
 
         for c in cp.continuous_connection_instance_ws:
@@ -493,12 +489,12 @@ def generate_conn_matrix(
 
     gj_conns = {}
     for ep in net.electrical_projections:
-        if not ep.presynaptic_population in gj_conns.keys():
+        if ep.presynaptic_population not in gj_conns.keys():
             gj_conns[ep.presynaptic_population] = {}
 
-        if not ep.presynaptic_population in all_cells:
+        if ep.presynaptic_population not in all_cells:
             all_cells.append(ep.presynaptic_population)
-        if not ep.postsynaptic_population in all_cells:
+        if ep.postsynaptic_population not in all_cells:
             all_cells.append(ep.postsynaptic_population)
 
         for e in ep.electrical_connection_instance_ws:
@@ -767,5 +763,5 @@ def generate_conn_matrix(
             colormap=colormap,
         )
 
-    if not "-nogui" in sys.argv:
+    if "-nogui" not in sys.argv:
         plt.show()

c302/parameters_C1.py

@@ -29,7 +29,7 @@ def set_default_bioparameters(self):
         param_C = ParameterisedModel_C()
         param_C.set_default_bioparameters()
         for b in param_C.bioparameters:
-            if not "syn" in b.name:
+            if "syn" not in b.name:
                 self.add_bioparameter_obj(b)
 
         self.add_bioparameter(

c302/parameters_D.py

@@ -20,9 +20,6 @@
 from neuroml import Morphology
 from neuroml import Point3DWithDiam
 from neuroml import Segment
-from neuroml import SegmentParent
-from neuroml import Member
-from neuroml import SegmentGroup
 from neuroml import BiophysicalProperties
 from neuroml import IntracellularProperties
 from neuroml import Resistivity

c302/parameters_D1.py

@@ -13,23 +13,8 @@
 
 """
 
-from neuroml import Cell
-from neuroml import Morphology
-from neuroml import Point3DWithDiam
-from neuroml import Segment
-from neuroml import BiophysicalProperties
-from neuroml import IntracellularProperties
-from neuroml import Resistivity
-from neuroml import Species
-from neuroml import MembraneProperties
-from neuroml import InitMembPotential
-from neuroml import SpecificCapacitance
-from neuroml import ChannelDensity
-from neuroml import SpikeThresh
-from neuroml import FixedFactorConcentrationModel
 
 from neuroml import GapJunction
-from neuroml import PulseGenerator
 
 from c302.parameters_D import ParameterisedModel as ParameterisedModel_D
 

c302/parameters_X.py

@@ -23,7 +23,6 @@
 from neuroml import ChannelDensity
 from neuroml import SpikeThresh
 
-from neuroml import GradedSynapse
 from neuroml import GapJunction
 from neuroml import PulseGenerator