Fixes to scripts

.ci/execute_travis_serial.py

@@ -70,7 +70,7 @@ def print_results():
     for k in result_:
         with open("%s.txt" % k, 'w') as f:
             for fl, r in result_[k]:
-                f.write('- %s\n' % fl)
+                f.write('- [ ] %s\n' % fl)
                 f.write('```')
                 try:
                     r = r.decode('utf8')

neuroml/lobster_pyloric/STG_net.py

@@ -78,12 +78,13 @@ def loadRunSTGNeuroML_L123(filename):
     for child in soma2.children:
         print((child.className, child.path))
     if graded_syn:
-        syn_path = soma2_path+'/DoubExpSyn_Ach__cells-0-_AB_PD_0-0-_Soma_0'
+        #  syn_path = soma2_path+'/DoubExpSyn_Ach__cells-0-_AB_PD_0-0-_Soma_0' #  # version < 3.2
+        syn_path = soma2_path+'/DoubExpSyn_Ach__cells_AB_PD_0_Soma_0' # version 3.2 +
         syn = moose.element(syn_path)
     else:
         syn_path = soma2_path+'/DoubExpSyn_Ach'
         syn = moose.element(syn_path)
-    syn_Ik = setupTable('DoubExpSyn_Ach_Ik',syn,'Ik')
+    syn_Ik = setupTable('DoubExpSyn_Ach_Ik', syn, 'Ik')
 
     print("Reinit MOOSE ... ")
     resetSim(['/elec',cells_path], simdt, plotdt, simmethod='hsolve')

neuroml2/run_hhcell.py

@@ -47,18 +47,6 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-
-# NOTE: This script does not work with python3 
-# See https://github.com/NeuroML/NeuroML2/issues/116 . If this bug is fixed then
-# remove this code block.
-import neuroml as nml
-a = nml.nml.nml.IonChannel()
-try:
-    b = {a : 1 }
-except TypeError as e:
-    print( 'Failed due to https://github.com/NeuroML/NeuroML2/issues/116' ) 
-    quit( 0 )
-
 def test_channel_gates():
     """Creates prototype channels under `/library` and plots the time
     constants (tau) and activation (minf, hinf, ninf) parameters for the

snippets/convert_Genesis2Sbml.py

@@ -57,7 +57,7 @@ def main():
     moose.loadModel('../genesis/Kholodenko.g','/Kholodenko')
 
     #Writes model to xml file
-    written = moose.mooseWriteSBML('/Kholodenko','../genesis/Kholodenko_tosbml.xml')
+    written = moose.writeSBML('/Kholodenko','../genesis/Kholodenko_tosbml.xml')
     print(written)
 
 if __name__ == '__main__':

snippets/crossComptSimpleReac.py.BROKEN

@@ -51,7 +51,7 @@ def makeModel():
     compt0.y0 += side
     compt2.x1 += side
     compt2.x0 += side
-    print(('Volumes = ', compt0.volume, compt1.volume, compt2.volume))
+    print('Volumes = ', compt0.volume, compt1.volume, compt2.volume)
 
     # create molecules and reactions
     a = moose.Pool( '/model/compt0/a' )
@@ -101,9 +101,9 @@ def makeModel():
     stoich0.ksolve = ksolve0
     stoich1.ksolve = ksolve1
     stoich2.ksolve = ksolve2
-    stoich0.path = '/model/compt0/#'
-    stoich1.path = '/model/compt1/#'
-    stoich2.path = '/model/compt2/#'
+    stoich0.reacSystemPath = '/model/compt0/#'
+    stoich1.reacSystemPath = '/model/compt1/#'
+    stoich2.reacSystemPath = '/model/compt2/#'
     stoich1.buildXreacs( stoich0 )
     stoich1.buildXreacs( stoich2 )
     stoich0.filterXreacs()

snippets/funcInputToPools.py

@@ -100,7 +100,7 @@ def main():
     """
 
     makeModel()
-    moose.seed()
+    moose.seed(10)
 
     moose.reinit()
     moose.start( 50.0 ) # Run the model for 100 seconds.

snippets/loadSbmlmodel.py

@@ -5,8 +5,8 @@
 # Maintainer:
 # Created: Fri Jan 29 11:43:15 2016 (+0530)
 # Version:
-# Last-Updated:
-#           By:
+# Last-Updated: Wed Sep 09 01:32:12 2020 (+0530)
+#           By: HarshaRani
 #     Update #: 0
 # URL:
 # Keywords:
@@ -21,6 +21,7 @@
 #
 
 # Change log:
+# updated function calls
 #
 #
 #
@@ -77,14 +78,14 @@ def main():
         runtime = float(sys.argv[2])
     sbmlId = moose.element('/')
     # Loading the sbml file into MOOSE, models are loaded in path/model
-    sbmlId = moose.mooseReadSBML(filepath,'/sbml')
+    sbmlId = moose.readSBML(filepath,'/sbml')[0]
     if isinstance(sbmlId, (list, tuple)):
         print(sbmlId)
 
     elif sbmlId.path != '/':
 
-        s1 = moose.element('/sbml/model/compartment/S1')
-        s2= moose.element('/sbml/model/compartment/S2')
+        s1 = moose.element('/sbml/compartment/S1')
+        s2 = moose.element('/sbml/compartment/S2')
 
         # Creating MOOSE Table, Table2 is for the chemical model
         graphs = moose.Neutral( '/sbml/graphs' )
@@ -96,7 +97,7 @@ def main():
         moose.connect( outputs2,'requestOut', s2, 'getConc' );
 
         # gsl solver is added, default is ee
-        moose.mooseAddChemSolver(sbmlId.path,"ee")
+        moose.addChemSolver(sbmlId.path,"ee")
 
         # Reset and Run
         moose.reinit()

snippets/rxdReacDiffusion.py

@@ -17,8 +17,8 @@ def main():
     # define the geometry
     compt = moose.CylMesh( '/cylinder' )
     compt.r0 = compt.r1 = 1
-    compt.x1 = 100
     compt.diffLength = 0.2
+    compt.x1 = 100
     assert( compt.numDiffCompts == compt.x1/compt.diffLength )
 
     #define the molecule. Its geometry is defined by its parent volume, cylinder

snippets/scriptKineticSolver.py

@@ -95,7 +95,7 @@ def main():
     stoich = moose.Stoich( '/model/compartment/stoich' )
     stoich.compartment = moose.element( '/model/compartment' )
     stoich.ksolve = ksolve
-    stoich.path = "/model/compartment/##"
+    stoich.reacSystemPath = "/model/compartment/##"
     #solver.method = "rk5"
     #mesh = moose.element( "/model/compartment/mesh" )
     #moose.connect( mesh, "remesh", solver, "remesh" )

snippets/showmsg.py

@@ -13,6 +13,9 @@ def main():
     synapse = syn.synapse.vec
     mid = moose.connect(net, 'spikeOut', synapse, 'addSpike', 'Sparse') # This creates a `Sparse` message from `spikeOut` source of net to `addSpike` destination on synapse.
     msg = moose.element(mid)
+    print(msg.setRandomConnectivity,'xx')
+    msg.setRandomConnectivity(connectionProbability, 5)
+    quit()
     msg.setRandomConnectivity(connectionProbability, 5)
     for n in net.vec:
         print(('Messages from %s.spikeOut' % (n.path)))

squid/electronics.py

@@ -1,38 +1,16 @@
-# electronics.py --- 
-# 
+# electronics.py ---
+#
 # Filename: electronics.py
-# Description: 
+# Description:
 # Author: Subhasis Ray
-# Maintainer: 
-# Created: Wed Feb 22 00:53:38 2012 (+0530)
-# Version: 
-# Last-Updated: Tue Jul 10 10:28:40 2012 (+0530)
-#           By: subha
-#     Update #: 221
-# URL: 
-# Keywords: 
-# Compatibility: 
-# 
-# 
+# Maintainer: Dilawar Singh
 
-# Commentary: 
-# 
-# 
-# 
-# 
-
-# Change log:
-# 
-# 2012-02-22 23:22:30 (+0530) Subha - the circuitry put in a class.
-# 
-
-# Code:
-
-import numpy
+import numpy as np
 import moose
 
-class ClampCircuit(moose.Neutral):
+class ClampCircuit(object):
     """Container for a Voltage-Clamp/Current clamp circuit."""
+
     defaults = {
         'level1': 25.0,
         'width1': 50.0,
@@ -41,48 +19,59 @@ class ClampCircuit(moose.Neutral):
         'trigMode': 0,
         'delay3': 1e9
         }
-    def __init__(self, path, compartment):
-        moose.Neutral.__init__(self, path)        
+    def __init__(self, path, squid):
+        self.path = path
+        moose.Neutral(path)        
         self.pulsegen = moose.PulseGen(path+"/pulse") # holding voltage/current generator
         self.pulsegen.count = 2
         self.pulsegen.firstLevel = 25.0
         self.pulsegen.firstWidth = 50.0
         self.pulsegen.firstDelay = 2.0
         self.pulsegen.secondDelay = 0.0
         self.pulsegen.trigMode = 2
-        self.gate = moose.PulseGen(path+"/gate") # holding voltage/current generator
+        self.gate = moose.PulseGen(path + "/gate")  # holding voltage/current generator
         self.gate.level[0] = 1.0
         self.gate.delay[0] = 0.0
         self.gate.width[0] = 1e9
-        moose.connect(self.gate, 'output', self.pulsegen, 'input')
-        self.lowpass = moose.RC(path+"/lowpass") # lowpass filter
+        moose.connect(self.gate, "output", self.pulsegen, "input")
+        self.lowpass = moose.RC(path + "/lowpass")  # lowpass filter
         self.lowpass.R = 1.0
         self.lowpass.C = 0.03
-        self.vclamp = moose.DiffAmp(path+"/vclamp")
+        self.vclamp = moose.DiffAmp(path + "/vclamp")
         self.vclamp.gain = 0.0
         self.vclamp.saturation = 1e10
-        self.iclamp = moose.DiffAmp(path+"/iclamp")
+        self.iclamp = moose.DiffAmp(path + "/iclamp")
         self.iclamp.gain = 0.0
         self.iclamp.saturation = 1e10
-        self.pid = moose.PIDController(path+"/pid")
+        self.pid = moose.PIDController(path + "/pid")
         self.pid.gain = 0.5
         self.pid.tauI = 0.02
         self.pid.tauD = 0.005
         self.pid.saturation = 1e10
         # Connect current clamp circuitry
         moose.connect(self.pulsegen, "output", self.iclamp, "plusIn")
-        moose.connect(self.iclamp, "output", compartment, "injectMsg")
+        moose.connect(self.iclamp, "output", squid.C, "injectMsg")
         # Connect voltage clamp circuitry
         moose.connect(self.pulsegen, "output", self.lowpass, "injectIn")
         moose.connect(self.lowpass, "output", self.vclamp, "plusIn")
         moose.connect(self.vclamp, "output", self.pid, "commandIn")
-        moose.connect(compartment, "VmOut", self.pid, "sensedIn")
-        moose.connect(self.pid, "output", compartment, "injectMsg")
+        moose.connect(squid.C, "VmOut", self.pid, "sensedIn")
+        moose.connect(self.pid, "output", squid.C, "injectMsg")
         current_table = moose.Table("/data/Im")
-        moose.connect(current_table, "requestOut", compartment, "getIm")
+        moose.connect(current_table, "requestOut", squid.C, "getIm")
 
-    def configure_pulses(self, baseLevel=0.0, firstLevel=0.1, firstDelay=5.0, firstWidth=40.0, secondLevel=0.0, secondDelay=1e6, secondWidth=0.0, singlePulse=True):
-        """Set up the pulse generator."""        
+    def configure_pulses(
+        self,
+        baseLevel=0.0,
+        firstLevel=0.1,
+        firstDelay=5.0,
+        firstWidth=40.0,
+        secondLevel=0.0,
+        secondDelay=1e6,
+        secondWidth=0.0,
+        singlePulse=True,
+    ):
+        """Set up the pulse generator."""
         self.pulsegen.baseLevel = baseLevel
         self.pulsegen.firstLevel = firstLevel
         self.pulsegen.firstWidth = firstWidth
@@ -91,10 +80,10 @@ def configure_pulses(self, baseLevel=0.0, firstLevel=0.1, firstDelay=5.0, firstW
         self.pulsegen.secondDelay = secondDelay
         self.pulsegen.secondWidth = secondWidth
         if singlePulse:
-            self.pulsegen.trigMode = 1  
+            self.pulsegen.trigMode = 1
         else:
             self.pulsegen.trigMode = 0
-        
+
     def do_voltage_clamp(self):
         """Switch to voltage clamp circuitry. After this the simdt may
         need to be changed for correct performance."""
@@ -103,14 +92,10 @@ def do_voltage_clamp(self):
         self.pid.gain = 0.5
         self.pid.tauD = 0.005
         self.pid.tauI = 0.02
-            
+
     def do_current_clamp(self):
         """Switch to current clamp circuitry. After this the simdt may
         need to be changed for correct performance."""
         self.iclamp.gain = 1.0
         self.vclamp.gain = 0.0
         self.pid.gain = 0.0
-
-
-# 
-# electronics.py ends here