Merge pull request #71 from dilawar/pybind11

Fixes to examples script for new python bindings.

Author: dilawar

.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')

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/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/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/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