Merge pull request #11 from dilawar/master

Made script compatible with both python2 and python3.

Author: dilawar

.travis.yml

@@ -12,13 +12,12 @@ install:
     - sudo apt-key add - < Release.key  
     - sudo sh -c "echo 'deb http://download.opensuse.org/repositories/home:/moose/xUbuntu_12.04/ /' >> /etc/apt/sources.list.d/moose.list"
     - sudo apt-get -y update
-    - sudo apt-get install python-h5py
-    - sudo apt-get install python3
+    - sudo apt-get -y install python-qt4
     - sudo apt-get -y install moose
 
 script:
     - # Making sure no python3 incompatible file.
     - python3 -m compileall -q .
+    - python2 -m compileall -q .
     - python -c 'import moose'
-    - python -c 'import moogli'
     - cd _travis && ./find_scripts_to_run.sh && ./run_scripts.sh 

_travis/run_scripts.sh

@@ -10,7 +10,7 @@ TEMP=$PWD/__temp__
 rm -f $BLACKLISTED $SUCCEEDED $FAILED $TEMP TORUN
 $PWD/find_scripts_to_run.sh 
 
-PYC=`which python`
+PYC=`which python2`
 MATPLOTRC=$PWD/matplotlibrc
 if [ ! -f $MATPLOTRC ]; then
     echo "$MATPLOTRC not found"

hopfield/guiHopfield.py

@@ -53,7 +53,7 @@ def connectElements(self):
         self.connect(self.computeSynWeightsPushButton,QtCore.SIGNAL('clicked()'),self.computeAllWeights)
 
     def saveInput(self):
-        print 'saving current pattern as input'
+        print('saving current pattern as input')
         inpList = []
         for i in range(100):
             exec(('inpList.append(int(self.pushButton_%s.isChecked()))' %i))

hopfield/hopfield.py

@@ -58,9 +58,9 @@ def updateWeights(self, memory):
                         memory[j] = -1
                     self.synWeights[i*len(memory)+j] += memory[i]*memory[j]
 
-        print self.synWeights[0:100]
+        print((self.synWeights[0:100]))
         self.numMemories += 1
-        print self.numMemories, '#number Of saved memories'
+        print((self.numMemories, '#number Of saved memories'))
 
     def createNetwork(self):
         '''setting up of the cells and their connections'''

hopfield/test.py

@@ -37,20 +37,20 @@
 #else, goes back to 0 in tau time
 
 VmVal = moose.Table(cellPath+'/Vm_cell')
-print 'table>cellVm:', moose.connect(VmVal, 'requestOut', cell, 'getVm')
+print(('table>cellVm:', moose.connect(VmVal, 'requestOut', cell, 'getVm')))
 spikeTime = moose.Table(cellPath+'/spikeTimes')
-print 'table>cellSpike:', moose.connect(cell, 'spike', spikeTime, 'input')
+print(('table>cellSpike:', moose.connect(cell, 'spike', spikeTime, 'input')))
 
 inSpkGen = moose.SpikeGen(cellPath+'/inSpkGen')
 inSpkGen.setField('threshold', 2.0)
 inSpkGen.setField('edgeTriggered', True)
 
 if inputGiven == 1:
-    print 'pulse>spike:', moose.connect(pg, 'output', moose.element(cellPath+'/inSpkGen'), 'Vm')
+    print(('pulse>spike:', moose.connect(pg, 'output', moose.element(cellPath+'/inSpkGen'), 'Vm')))
     inTable = moose.Table(cellPath+'/inSpkGen/inTable')
-    print 'table>spike:',moose.connect(inTable, 'requestOut', inSpkGen, 'getHasFired')
+    print(('table>spike:',moose.connect(inTable, 'requestOut', inSpkGen, 'getHasFired')))
 
-print 'spike>cell:', moose.connect(inSpkGen, 'spikeOut', cell.synapse[0] ,'addSpike')
+print(('spike>cell:', moose.connect(inSpkGen, 'spikeOut', cell.synapse[0] ,'addSpike')))
 #print 'spike>cell:', moose.connect(pg, 'output', cell ,'injectDest')
 
 moose.setClock(0, 1e-4)

izhikevich/Izhikevich.py

@@ -197,7 +197,7 @@ def setup(self, key):
         neuron = self._get_neuron(key)
         pulsegen = self._make_pulse_input(key)
         if pulsegen is None:
-            print key, 'Not implemented.'
+            print((key, 'Not implemented.'))
 
     def simulate(self, key):
         self.setup(key)
@@ -207,7 +207,7 @@ def run(self, key):
         try:
             Vm = self.Vm_tables[key]
             u = self.u_tables[key]
-        except KeyError, e:
+        except KeyError as e:
             Vm = moose.Table(self.data_container.path + '/' + key + '_Vm')
             nrn = self.neurons[key]
             moose.connect(Vm, 'requestOut', nrn, 'getVm')
@@ -217,7 +217,7 @@ def run(self, key):
             self.u_tables[key] = utable
         try:
             Im = self.inject_tables[key]
-        except KeyError, e:
+        except KeyError as e:
             Im = moose.Table(self.data_container.path + '/' + key + '_inject') # May be different for non-pulsegen sources.
             Im.connect('requestOut', self._get_neuron(key), 'getIm')
             self.inject_tables[key] = Im
@@ -237,7 +237,7 @@ def run(self, key):
         time = linspace(0, IzhikevichDemo.parameters[key][7], len(Vm.vector))
         # DEBUG
         nrn = self._get_neuron(key)
-        print 'a = %g, b = %g, c = %g, d = %g, initVm = %g, initU = %g' % (nrn.a,nrn.b, nrn.c, nrn.d, nrn.initVm, nrn.initU)
+        print(('a = %g, b = %g, c = %g, d = %g, initVm = %g, initU = %g' % (nrn.a,nrn.b, nrn.c, nrn.d, nrn.initVm, nrn.initU)))
         #! DEBUG
         return (time, Vm, Im)
 
@@ -246,14 +246,14 @@ def _get_neuron(self, key):
         try:
             params = IzhikevichDemo.parameters[key]
         except KeyError as e:
-            print ' %s : Invalid neuron type. The valid types are:' % (key)
+            print((' %s : Invalid neuron type. The valid types are:' % (key)))
             for key in IzhikevichDemo.parameters:
-                print key
+                print(key)
             raise e
         try:
             neuron = self.neurons[key]
             return neuron
-        except KeyError, e:
+        except KeyError as e:
             neuron = moose.IzhikevichNrn(self.model_container.path + '/' + key)
 
         if key == 'integrator' or key == 'Class_1': # Integrator has different constants
@@ -354,7 +354,7 @@ def _make_pulse_input(self, key):
             self.inputs[key] = input_table
             return input_table                        
         else:
-            print key, ': Stimulus is not based on pulse generator.'
+            print((key, ': Stimulus is not based on pulse generator.'))
             raise
         pulsegen = self._make_pulsegen(key, 
                                       firstLevel,
@@ -529,9 +529,9 @@ def getEquation(self, key):
         plot(time, Im.vector)
         subplot(3,1,3)
         show()
-        print 'Finished simulation.'
+        print('Finished simulation.')
 except ImportError:
-    print 'Matplotlib not installed.'
+    print('Matplotlib not installed.')
 
 # 
 # Izhikevich.py ends here

izhikevich/demogui_qt.py

@@ -62,11 +62,11 @@ def __init__(self, *args):
         self.controlPanel = QtGui.QFrame(self.demoFrame)
         self.figureNo = {}
         self.buttons = {}
-        for key, value in IzhikevichDemo.parameters.items():
+        for key, value in list(IzhikevichDemo.parameters.items()):
             button = QtGui.QPushButton(key, self.controlPanel)
             self.figureNo[value[0]] = key
             self.buttons[key] = button
-        keys = self.figureNo.keys()
+        keys = list(self.figureNo.keys())
         keys.sort()
         length = len(keys)
         rows = int(numpy.rint(numpy.sqrt(length)))

kinetics/test_ksolve.py

@@ -306,7 +306,7 @@ def createChemModel( neuroCompt, spineCompt, psdCompt ):
 
 # Just for printf debugging
 def printMolVecs( title ):
-    print title
+    print(title)
     """    
     nCa = moose.vec( '/model/chem/neuroMesh/Ca' )
     sCa = moose.vec( '/model/chem/spineMesh/Ca' )
@@ -477,7 +477,7 @@ def testCubeMultiscale( useSolver ):
     moose.reinit()
     t = time.time()
     moose.start( 1.0 )
-    print("Total time taken: %s sec for 1.0 sec of simulation" % (time.time() - t))
+    print(("Total time taken: %s sec for 1.0 sec of simulation" % (time.time() - t)))
     dumpPlots( plotName )
 
 def main():

moogli/purkinje_simulation.py

@@ -26,8 +26,8 @@
 popdict, projdict = moose.neuroml.loadNeuroML_L123(filename)
 
 # setting up hsolve object for each neuron
-for popinfo in popdict.values():
-    for cell in popinfo[1].values():
+for popinfo in list(popdict.values()):
+    for cell in list(popinfo[1].values()):
         solver = moose.HSolve(cell.path + "/hsolve")
         solver.target = cell.path
 
@@ -37,9 +37,7 @@
 SIMULATION_DELTA = 0.001
 SIMULATION_TIME  = 0.03
 
-ALL_COMPARTMENTS = map( lambda x : x.path
-                      , moose.wildcardFind("/cells[0]/##[ISA=CompartmentBase]")
-                      )
+ALL_COMPARTMENTS = [x.path for x in moose.wildcardFind("/cells[0]/##[ISA=CompartmentBase]")]
 BASE_VM_VALUE = -0.065
 PEAK_VM_VALUE = -0.060
 BASE_VM_COLOR = [1.0, 0.0, 0.0, 0.1]
@@ -69,9 +67,7 @@
 
 # set initial color of all compartments in accordance with their vm
 morphology.set_color( "group-all"
-                    , map( lambda x : moose.element(x).Vm
-                         , ALL_COMPARTMENTS
-                         )
+                    , [moose.element(x).Vm for x in ALL_COMPARTMENTS]
                     )
 
 # instantiate the visualizer with the morphology object created earlier
@@ -90,9 +86,7 @@ def callback(morphology, viewer):
     # a value higher than peak value will be clamped to peak value
     # a value lower than base value will be clamped to base value.
     morphology.set_color( "group-all"
-                        , map( lambda x : x.Vm
-                            , moose.wildcardFind("/cells[0]/##[ISA=CompartmentBase]")
-                            )
+                        , [x.Vm for x in moose.wildcardFind("/cells[0]/##[ISA=CompartmentBase]")]
                         )
     # if the callback returns true, it will be called again.
     # if it returns false it will not be called ever again.

moogli/purkinje_simulation_with_rm.py

@@ -28,8 +28,8 @@
 popdict, projdict = moose.neuroml.loadNeuroML_L123(filename)
 
 # setting up hsolve object for each neuron
-for popinfo in popdict.values():
-    for cell in popinfo[1].values():
+for popinfo in list(popdict.values()):
+    for cell in list(popinfo[1].values()):
         solver = moose.HSolve(cell.path + "/hsolve")
         solver.target = cell.path
 
@@ -39,17 +39,11 @@
 SIMULATION_DELTA = 0.001
 SIMULATION_TIME  = 0.03
 
-ALL_COMPARTMENTS = map( lambda x : x.path
-                      , moose.wildcardFind("/cells[0]/##[ISA=CompartmentBase]")
-                      )
+ALL_COMPARTMENTS = [x.path for x in moose.wildcardFind("/cells[0]/##[ISA=CompartmentBase]")]
 
-BASE_RM_VALUE = min( map( lambda x : moose.element(x).Rm
-                        , ALL_COMPARTMENTS
-                        )
+BASE_RM_VALUE = min( [moose.element(x).Rm for x in ALL_COMPARTMENTS]
                    )
-PEAK_RM_VALUE = max( map( lambda x : moose.element(x).Rm
-                        , ALL_COMPARTMENTS
-                        )
+PEAK_RM_VALUE = max( [moose.element(x).Rm for x in ALL_COMPARTMENTS]
                    )
 BASE_RM_COLOR = [0.0, 1.0, 0.0, 0.1]
 PEAK_RM_COLOR = [1.0, 0.0, 0.0, 1.0]
@@ -86,9 +80,7 @@ def create_vm_visualizer():
 
     # set initial color of all compartments in accordance with their vm
     vm_morphology.set_color( "group-all"
-                           , map( lambda x : moose.element(x).Vm
-                                , ALL_COMPARTMENTS
-                                )
+                           , [moose.element(x).Vm for x in ALL_COMPARTMENTS]
                            )
 
     # instantiate the visualizer with the morphology object created earlier
@@ -105,9 +97,7 @@ def callback(morphology, viewer):
         # a value higher than peak value will be clamped to peak value
         # a value lower than base value will be clamped to base value.
         morphology.set_color( "group-all"
-                            , map( lambda x : moose.element(x).Vm
-                                 , ALL_COMPARTMENTS
-                                 )
+                            , [moose.element(x).Vm for x in ALL_COMPARTMENTS]
                             )
         # if the callback returns true, it will be called again.
         # if it returns false it will not be called again.
@@ -148,9 +138,7 @@ def create_rm_visualizer():
 
     # set initial color of all compartments in accordance with their rm
     morphology.set_color( "group-all"
-                        , map( lambda x : moose.element(x).Rm
-                             , ALL_COMPARTMENTS
-                             )
+                        , [moose.element(x).Rm for x in ALL_COMPARTMENTS]
                         )
 
     # instantiate the visualizer with the morphology object created earlier