Merge pull request #96 from openworm/development

 To v0.9.0

.gitignore

@@ -106,3 +106,6 @@ arm64
 /examples/test/images/c302_C1_Social.net.nml
 /examples/test/images/c302_C1_Syns.net.nml
 *ken.sh
+/examples/parametersweep/IClamp_GenericNeuronCellX__lems.xml
+/examples/parametersweep/LEMS_SimCanonical_X.png
+/examples/parametersweep/Canonical_X__lems.xml

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/NeuroML2/printNML2Info.py

@@ -1,4 +1,3 @@
-import neuroml
 
 import neuroml.loaders as loaders
 

c302/NeuroMLUtilities.py

@@ -6,12 +6,7 @@
 
 ############################################################
 
-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
 
 

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:

c302/SpreadsheetDataReader.py

@@ -10,8 +10,8 @@
 ############################################################
 
 
-from c302.NeuroMLUtilities import ConnectionInfo
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import ConnectionInfo
+from c302.ConnectomeReader import analyse_connections
 
 from xlrd import open_workbook
 import os

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/White_A.py

@@ -3,7 +3,7 @@
 
 from c302.WhiteDataReader import White_A
 
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 read_data = White_A.read_data
 read_muscle_data = White_A.read_muscle_data

c302/White_L4.py

@@ -3,7 +3,7 @@
 
 from c302.WhiteDataReader import White_L4
 
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 read_data = White_L4.read_data
 read_muscle_data = White_L4.read_muscle_data

c302/White_whole.py

@@ -3,7 +3,7 @@
 
 from c302.WhiteDataReader import White_whole
 
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 read_data = White_whole.read_data
 read_muscle_data = White_whole.read_muscle_data

c302/WitvlietDataReader1.py

@@ -2,7 +2,7 @@
 # Should be tidied up.
 
 from c302.W_SpreadsheetDataReader import WitvlietDataReader
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 wdr = WitvlietDataReader("witvliet_2020_7.xlsx")
 

c302/WitvlietDataReader2.py

@@ -2,7 +2,7 @@
 # Should be tidied up.
 
 from c302.W_SpreadsheetDataReader import WitvlietDataReader
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 wdr = WitvlietDataReader("witvliet_2020_8.xlsx")
 

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/__version__.py

@@ -1 +1 @@
-__version__ = "0.8.1"
+__version__ = "0.9.0"

c302/analyse.py

@@ -1,7 +1,6 @@
 import sys
 import matplotlib.pyplot as plt
 from pylab import *
-from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
 
 
 fig = plt.figure(facecolor="#FFFFFF", edgecolor="#FFFFFF")

c302/backers.py

@@ -1,7 +1,7 @@
 """
-    This method reads a generated list of cells vs. names as assigned by OpenWorm backers
+This method reads a generated list of cells vs. names as assigned by OpenWorm backers
 
-    This information will eventually be moved to owmeta/elsewhere...
+This information will eventually be moved to owmeta/elsewhere...
 """
 
 import os

c302/c302_IClampMuscle.py

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

c302/c302_TapWithdrawal.py

@@ -1,7 +1,7 @@
 """
 
-    Tap-Withdrawal circuit still under development - it does not produce the correct behavior!
-    
+Tap-Withdrawal circuit still under development - it does not produce the correct behavior!
+
 """
 
 import c302

c302/c302_TargetMuscle.py

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

c302/c302_info.py

@@ -1,9 +1,3 @@
-import sys
-import os
-from pyneuroml import pynml
-import matplotlib.pyplot as plt
-import numpy as np
-
 import c302
 
 
@@ -15,34 +9,34 @@ 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:
             if "inh" in c.post_component:
-                cc_inh_conns[cp.presynaptic_population][
-                    cp.postsynaptic_population
-                ] = float(c.weight)
+                cc_inh_conns[cp.presynaptic_population][cp.postsynaptic_population] = (
+                    float(c.weight)
+                )
             else:
-                cc_exc_conns[cp.presynaptic_population][
-                    cp.postsynaptic_population
-                ] = float(c.weight)
+                cc_exc_conns[cp.presynaptic_population][cp.postsynaptic_population] = (
+                    float(c.weight)
+                )
 
     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:
@@ -56,7 +50,6 @@ def generate_c302_info(nml_doc, verbose=False):
         from PyOpenWorm import (
             connect as pyow_connect,
             __version__ as pyow_version,
-            ConnectionFailError,
         )
 
         pow_conn = pyow_connect("./pyopenworm.conf")