Merge pull request #99 from openworm/development

 To v0.9.1

.github/workflows/non_omv.yml

@@ -65,6 +65,7 @@ jobs:
         
     - name: Run test script
       run: |
+        pip install ruff
         ./test.sh
         
     - name: Final version info

.gitignore

@@ -109,3 +109,4 @@ arm64
 /examples/parametersweep/IClamp_GenericNeuronCellX__lems.xml
 /examples/parametersweep/LEMS_SimCanonical_X.png
 /examples/parametersweep/Canonical_X__lems.xml
+/examples/parametersweep/average_last_1percent_GenericNeuronCellX.png

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]
@@ -256,10 +256,11 @@ def matchLists(cols1, cols2, indexName1, indexName2):
 # 'R', 'Rp', 'S', 'Sp' map to 'Send'.
 # 'NMJ' does not map.
 def typeMapping(cols1, cols2, indexName1, indexName2):
-    list1 = ["GapJunction", "Send"]
-    list2 = ["EJ", "NMJ", "R", "Rp", "S", "Sp"]
-    type1 = cols1[indexName1[2]]
-    type2 = cols2[indexName2[2]]
+    # list1 = ["GapJunction", "Send"]
+    # list2 = ["EJ", "NMJ", "R", "Rp", "S", "Sp"]
+    # type1 = cols1[indexName1[2]]
+    # type2 = cols2[indexName2[2]]
+    pass
 
 
 if __name__ == "__main__":

c302/NeuroMLUtilities.py

@@ -43,7 +43,7 @@ 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

@@ -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()
 
@@ -41,7 +41,7 @@ def read_data(self, include_nonconnected_cells=False):
 
         try:
             cell_names, pre, post, conns = self._read_connections("neuron")
-        except:
+        except Exception:
             print(
                 "\nProblem loading connections via owmeta! The package is installed however. You may need to try running:"
                 + "\n\n    owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'\n"
@@ -158,7 +158,7 @@ def format_muscle_name(muscle_name):
     exit()
 
     conn_map_OWR = {}
-    for c in conns:
+    for c in neuron_conns:
         conn_map_OWR[c.short().lower()] = c
 
     from c302.UpdatedSpreadsheetDataReader import read_data as read_data_usr

c302/SpreadsheetDataReader.py

@@ -12,13 +12,13 @@
 
 from c302.ConnectomeReader import ConnectionInfo
 from c302.ConnectomeReader import analyse_connections
+from c302 import print_
 
 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/__init__.py

@@ -23,7 +23,7 @@
 import neuroml.writers as writers
 import neuroml.loaders as loaders
 
-import c302.bioparameters
+# import c302.bioparameters
 
 import airspeed
 
@@ -39,6 +39,7 @@
 
 import json
 
+
 import collections
 
 try:
@@ -51,13 +52,14 @@
     from owmeta.muscle import Muscle
 
     owmeta_installed = True
-except:
+
+except Exception:
     print("owmeta not installed! Proceeding anyway...")
     owmeta_installed = False
 
 try:
     from urllib2 import URLError  # Python 2
-except:
+except Exception:
     from urllib.error import URLError  # Python 3
 
 logging.basicConfig()
@@ -519,7 +521,7 @@ def _get_cell_info(bnd, cells):
     all_muscle_info = collections.OrderedDict()
 
     if bnd is None:
-        if cached_owmeta_data == None:
+        if cached_owmeta_data is None:
             print_("Loading owmeta cached data from: %s" % OWMETA_CACHED_DATA_FILE)
             with open(OWMETA_CACHED_DATA_FILE) as f:
                 cached_owmeta_data = json.load(f)
@@ -1730,10 +1732,15 @@ def parse_dict_arg(dict_arg):
 
 
 def main():
+    import importlib
+
     print("Starting c302 v%s..." % __version__)
     args = process_args()
 
-    exec("from c302.%s import ParameterisedModel" % args.parameters, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.%s" % args.parameters),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
     generate(
         args.reference,

c302/__version__.py

@@ -1 +1 @@
-__version__ = "0.9.0"
+__version__ = "0.9.1"

c302/analyse.py

@@ -1,6 +1,5 @@
 import sys
 import matplotlib.pyplot as plt
-from pylab import *
 
 
 fig = plt.figure(facecolor="#FFFFFF", edgecolor="#FFFFFF")

c302/c302_FW.py

@@ -1,5 +1,6 @@
 import sys
 import os
+import importlib
 
 sys.path.insert(0, os.path.abspath("."))
 
@@ -21,7 +22,10 @@ def setup(
     verbose=True,
     config_param_overrides={},
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     params.set_bioparameter(
@@ -34,13 +38,14 @@ def setup(
         "unphysiological_offset_current_dur", "2000 ms", "Testing TapWithdrawal", "0"
     )
 
+    """
     VA_motors = ["VA%s" % c for c in range_incl(1, 12)]
-    VB_motors = ["VB%s" % c for c in range_incl(1, 11)]
     DA_motors = ["DA%s" % c for c in range_incl(1, 9)]
+    AS_motors = ["AS%s" % c for c in range_incl(1, 11)]"""
+    VB_motors = ["VB%s" % c for c in range_incl(1, 11)]
     DB_motors = ["DB%s" % c for c in range_incl(1, 7)]
     DD_motors = ["DD%s" % c for c in range_incl(1, 6)]
     VD_motors = ["VD%s" % c for c in range_incl(1, 13)]
-    AS_motors = ["AS%s" % c for c in range_incl(1, 11)]
 
     cells = list(["AVBL", "AVBR"] + DB_motors + VD_motors + VB_motors + DD_motors)
 

c302/c302_Full.py

@@ -1,6 +1,8 @@
 import c302
 import sys
 
+import importlib
+
 
 def setup(
     parameter_set,
@@ -14,7 +16,10 @@ def setup(
     config_param_overrides={},
     verbose=True,
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     # Some random set of neurons

c302/c302_IClamp.py

@@ -2,6 +2,8 @@
 import sys
 import neuroml.writers as writers
 
+import importlib
+
 
 def setup(
     parameter_set,
@@ -17,11 +19,14 @@ def setup(
     reference = "c302_%s_IClamp" % parameter_set
     c302.print_("Setting up %s" % reference)
 
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     stim_amplitudes = ["1pA", "2pA", "3pA", "4pA", "5pA", "6pA"]
-    if duration == None:
+    if duration is None:
         duration = (len(stim_amplitudes)) * 1000
 
     my_cells = ["ADAL", "PVCL"]

c302/c302_IClampMuscle.py

@@ -1,6 +1,8 @@
 import c302
 import sys
 
+import importlib
+
 
 def setup(
     parameter_set,
@@ -12,7 +14,10 @@ def setup(
     param_overrides={},
     verbose=True,
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     my_cells = []

c302/c302_MultiSyns.py

@@ -1,14 +1,18 @@
-from c302 import generate, add_new_input
+from c302 import generate, add_new_input, print_
 
 import neuroml.writers as writers
 
+import importlib
 import sys
 
 
 if __name__ == "__main__":
     parameter_set = sys.argv[1] if len(sys.argv) == 2 else "A"
 
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     cells = ["URYDL", "SMDDR", "ADAL", "RIML", "IL2VL", "RIPL"]
@@ -26,7 +30,7 @@
         duration=1000,
         dt=0.1,
         target_directory=target_directory,
-        verbose=verbose,
+        verbose=True,
     )
 
     stim_amplitude = "0.35nA"
@@ -39,4 +43,4 @@
         nml_doc, nml_file
     )  # Write over network file written above...
 
-    c302.print_("(Re)written network file to: " + nml_file)
+    print_("(Re)written network file to: " + nml_file)

c302/c302_MuscleTest.py

@@ -1,5 +1,6 @@
 import sys
 import os
+import importlib
 
 sys.path.insert(0, os.path.abspath("."))
 
@@ -21,7 +22,10 @@ def setup(
     verbose=True,
     config_param_overrides={},
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     params.set_bioparameter(
@@ -34,13 +38,14 @@ def setup(
         "unphysiological_offset_current_dur", "2000 ms", "Testing TapWithdrawal", "0"
     )
 
+    """
     VA_motors = ["VA%s" % c for c in range_incl(1, 12)]
     VB_motors = ["VB%s" % c for c in range_incl(1, 11)]
     DA_motors = ["DA%s" % c for c in range_incl(1, 9)]
     DB_motors = ["DB%s" % c for c in range_incl(1, 7)]
     DD_motors = ["DD%s" % c for c in range_incl(1, 6)]
     VD_motors = ["VD%s" % c for c in range_incl(1, 13)]
-    AS_motors = ["AS%s" % c for c in range_incl(1, 11)]
+    AS_motors = ["AS%s" % c for c in range_incl(1, 11)]"""
 
     cells = []
 
@@ -75,7 +80,7 @@ def setup(
         "ca_conc_rho_muscle": "0.002138919 mol_per_m_per_A_per_s",
     }
 
-    end = "%sms" % (int(duration) - 100)
+    # end = "%sms" % (int(duration) - 100)
 
     input_list = []
 
@@ -174,4 +179,4 @@ def setup(
     if len(sys.argv) == 3:
         setup_kwargs["data_reader"] = sys.argv[2]
 
-    setup(parameter_set, generate=True, data_reader=data_reader)
+    # setup(parameter_set, generate=True, data_reader=data_reader)

c302/c302_Muscles.py

@@ -1,6 +1,8 @@
 import c302
 import sys
 
+import importlib
+
 
 def setup(
     parameter_set,
@@ -13,7 +15,10 @@ def setup(
     config_param_overrides={},
     verbose=True,
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     params.set_bioparameter(

c302/c302_MusclesSine.py

@@ -1,5 +1,6 @@
 import c302
 import sys
+import importlib
 
 
 def setup(
@@ -13,7 +14,10 @@ def setup(
     config_param_overrides={},
     verbose=True,
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     params.set_bioparameter(