Merge branch 'development' into appBar

Author: adrianq

.travis.yml

@@ -8,6 +8,8 @@ node_js:
 env:
   global:
     secure: dn0FPQ5IG4M/3kdwnyI78ElQ308Vc3QnKAvkWfwMFb8QxDqxQdnTo7AV1qTMtbLrDNkeEWIgi4nc7jmXNtvGTwOfhAULVh6606Qs5B+ezTdwzajbbFMI8SKQx/pnTojOMu8dx7V4lMoR/YWcojR0VC1IWVC62TGbSB1k5BDGgH0=
+before_install:
+- sudo apt-get install -y xserver-xorg-dev libxext-dev libxi-dev
 install:
 - git clone --quiet  https://github.com/MetaCell/geppetto-netpyne.git
 - cd geppetto-netpyne

netpyne_ui/netpyne_geppetto.py

@@ -12,7 +12,7 @@
 import threading
 import time
 import traceback
-
+import re
 
 from netpyne import specs, sim, analysis
 from netpyne.specs.utils import validateFunction
@@ -365,11 +365,11 @@ def rename(self, path, oldValue,newValue):
         command =  'sim.rename('+path+',"'+oldValue+'","'+newValue+'")'
         logging.debug('renaming '+command)
         eval(command)
-
         for model, synched_component in list(GeppettoJupyterGUISync.synched_models.items()):
-            if model != '' and oldValue in model:
+            if model != '' and oldValue in model and path in model: # 
                 GeppettoJupyterGUISync.synched_models.pop(model)
-                newModel = model.replace(oldValue,newValue)
+                newModel = re.sub("(['])(?:(?=(\\?))\2.)*?\1", lambda x:x.group(0).replace(oldValue,newValue, 1), model)
+                logging.debug("Rename funct - Model is "+model+" newModel is "+newModel)
                 GeppettoJupyterGUISync.synched_models[newModel]=synched_component
 
     def getPlotSettings(self, plot):

utilities/install.py

@@ -5,7 +5,7 @@
 import os, sys
 from shutil import copyfile
 
-branch = "development"
+branch = None
 
 #by default clones branch (which can be passed as a parameter python install.py branch test_branch)
 #if branch doesnt exist clones the default_branch
@@ -26,7 +26,7 @@ def checkout(folder, default_branch, cwdp):
     os.chdir(newPath)
     python_git=subprocess.Popen("git branch -a",shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
     outstd,errstd=python_git.communicate()
-    if branch in str(outstd):
+    if branch and branch in str(outstd):
         subprocess.call(['git', 'checkout', branch], cwd='./')
     else:
         subprocess.call(['git', 'checkout', default_branch], cwd='./')