merge with development

Author: facu.r

netpyne_ui/netpyne_geppetto.py

@@ -438,7 +438,57 @@ def deleteParam(self, paramToDel):
 
     def validateFunction(self, functionString):
         return utils.ValidateFunction(functionString, netParams.__dict__)
-    
+         
+    def generateScript(self, metadata):
+        def convert2bool(string):
+            return string.replace('true', 'True').replace('false', 'False')
+            
+        def header(title, spacer='-'):
+            return '\n# ' + title.upper() + ' ' + spacer*(77-len(title)) + '\n'
+        
+        try :
+            params =  ['popParams' , 'cellParams', 'synMechParams']
+            params += ['connParams', 'stimSourceParams', 'stimTargetParams']
+            
+            fname = metadata['scriptName'] if metadata['scriptName'][-3:]=='.py' else metadata['scriptName']+'.py'
+            
+            with open(fname, 'w') as script:
+                script.write('from netpyne import specs, sim\n')
+                script.write(header('documentation'))
+                script.write("''' Script generated with NetPyNE-UI. Please visit:\n")
+                script.write("    - https://www.netpyne.org\n    - https://github.com/MetaCell/NetPyNE-UI\n'''\n")
+                script.write(header('script', spacer='='))
+                script.write('netParams = specs.NetParams()\n')
+                script.write('simConfig = specs.SimConfig()\n')
+                script.write(header('single value attributes'))
+                for attr, value in netParams.__dict__.items():
+                    if attr not in params:
+                        if value!=getattr(specs.NetParams(), attr):
+                            script.write('netParams.' + attr + ' = ')
+                            script.write(convert2bool(json.dumps(value, indent=4))+'\n')
+                        
+                script.write(header('network attributes'))
+                for param in params:
+                    for key, value in getattr(netParams, param).items():
+                        script.write("netParams." + param + "['" + key + "'] = ")
+                        script.write(convert2bool(json.dumps(value, indent=4))+'\n')
+                
+                script.write(header('network configuration'))
+                for attr, value in simConfig.__dict__.items():
+                    if value!=getattr(specs.SimConfig(), attr):
+                        script.write('netParams.' + attr + ' = ')
+                        script.write(convert2bool(json.dumps(value, indent=4))+'\n')
+                
+                script.write(header('create simulate analyze  network'))
+                script.write('sim.createSimulateAnalyze(netParams=netParams, simConfig=simConfig)\n')
+                
+                script.write(header('end script', spacer='='))
+            
+            return self.getJSONReply()
+        
+        except:
+            return self.getJSONError("Error while importing the NetPyNE model", traceback.format_exc())
+            
 class LoopTimer(threading.Thread):
     """
     a Timer that calls f every interval

utilities/install.py

@@ -46,7 +46,7 @@ def main(argv):
 clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.1-M1')
 subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/')
 
-clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','0.7.9')
+clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.7.9')
 subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/')
 
 clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.1-M2','', True )