Merge pull request #55 from MetaCell/travis_fix

Travis fix

Author: adrianq

.travis.yml

@@ -9,7 +9,10 @@ env:
   global:
     secure: dn0FPQ5IG4M/3kdwnyI78ElQ308Vc3QnKAvkWfwMFb8QxDqxQdnTo7AV1qTMtbLrDNkeEWIgi4nc7jmXNtvGTwOfhAULVh6606Qs5B+ezTdwzajbbFMI8SKQx/pnTojOMu8dx7V4lMoR/YWcojR0VC1IWVC62TGbSB1k5BDGgH0=
 install:
-- git clone --quiet -b $TRAVIS_BRANCH https://github.com/MetaCell/geppetto-netpyne.git
+- git clone --quiet  https://github.com/MetaCell/geppetto-netpyne.git
+- cd geppetto-netpyne
+- if [ `git branch -a | egrep "remotes/origin/${TRAVIS_BRANCH}"` ]; then git checkout $TRAVIS_BRANCH ; else echo "Branch $TRAVIS_BRANCH does not exist for the dependent bundle, checking out development ..." && git checkout development; fi
+- cd ..
 - npm install --silent -g phantomjs 
 - npm install --silent -g casperjs 
 - npm install --silent -g slimerjs
@@ -38,7 +41,7 @@ before_script:
   - export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/
 
 script:
-  - travis_retry docker build -t="netpyne-ui" --build-arg netpyneuiBranch=$TRAVIS_BRANCH .
+  - travis_retry docker build -t="netpyne-ui" --build-arg netpyneuiBranch=$TRAVIS_BRANCH -f="./Dockerfile_dev" .
   - travis_retry docker run  -t -dit --name=netpyne-ui_container -h localhost -p 8888:8888 netpyne-ui:latest
   - cd $TRAVIS_BUILD_DIR/ && ls
   - cd geppetto-netpyne && ls

Dockerfile

@@ -47,7 +47,8 @@ RUN make --silent install -j4
 
 # Switch to non sudo, create a Python 2 virtual environment 
 USER $NB_USER
-RUN conda update conda
+# Commenting out the conda update things broke!
+# RUN conda update conda
 RUN conda create --name snakes python=2
 
 # Install NEURON python

Dockerfile_dev

@@ -51,7 +51,8 @@ RUN make --silent install -j4
 
 # Switch to non sudo, create a Python 2 virtual environment 
 USER $NB_USER
-RUN conda update conda
+# Commenting out the conda update things broke!
+# RUN conda update conda
 RUN conda create --name snakes python=2
 
 # Install NEURON python
@@ -67,7 +68,7 @@ RUN wget https://github.com/MetaCell/NetPyNE-UI/archive/$netpyneuiBranch.zip
 RUN unzip $netpyneuiBranch.zip
 WORKDIR NetPyNE-UI-$netpyneuiBranch/utilities
 RUN /bin/bash -c "source activate snakes && python --version"
-RUN /bin/bash -c "source activate snakes && exec python install.py"
+RUN /bin/bash -c "source activate snakes && exec python install.py branch $netpyneuiBranch"
 WORKDIR /home/jovyan
 RUN git clone https://github.com/Neurosim-lab/netpyne_workspace
 WORKDIR /home/jovyan/netpyne_workspace

netpyne_ui/netpyne_geppetto.py

@@ -452,8 +452,10 @@ def globalMessageHandler(identifier, command, parameters):
             response = eval(command + '(*parameters)')
         GeppettoJupyterModelSync.events_controller.triggerEvent(
             "receive_python_message", {'id': identifier, 'response': response})
-    except Exception as e:
-        return netpyne_geppetto.getJSONError("Unhandle exception in Global Message Handler",traceback.format_exc())
+    except:
+        response = netpyne_geppetto.getJSONError("Error while executing command "+command,traceback.format_exc())
+        GeppettoJupyterModelSync.events_controller.triggerEvent(
+            "receive_python_message", {'id': identifier, 'response': response})
 
 
 def configure_logging():

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="netpyne_ui",
-    version="0.3",
+    version="0.4",
     url="https://github.com/MetaCell/NetPyNE-UI",
     author="MetaCell",
     author_email="info@metacell.us",
@@ -28,6 +28,6 @@
     ],
     install_requires=[
         'jupyter_geppetto==0.4.1',
-        'netpyne==0.7.8.1'
+        'netpyne==0.7.8'
     ],
 )

utilities/install.py

@@ -2,47 +2,73 @@
 from setuptools.command.install import install
 import subprocess
 import json
-import os
+import os, sys
 from shutil import copyfile
 
-# Cloning Repos
-print("Cloning PyGeppetto...")
-subprocess.call(['git', 'clone', '-b', 'v0.4.1-M1', 'https://github.com/openworm/pygeppetto.git'], cwd='../')
-subprocess.call(['pip', 'install', '-e', '.'], cwd='../pygeppetto/')
+branch = "development"
+
+#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
+def clone(repository, folder, default_branch, cwdp='', recursive = False):
+    global branch
+    print("Cloning "+repository)
+    if recursive:
+        subprocess.call(['git', 'clone', '--recursive', repository], cwd='./'+cwdp)
+    else:
+        subprocess.call(['git', 'clone', repository], cwd='./'+cwdp)
+    checkout(folder, default_branch, cwdp)
 
-print("Cloning NetPyNE...")
-subprocess.call(['git', 'clone', '-b', 'v0.7.8_UI0.3Release', 'https://github.com/Neurosim-lab/netpyne.git'], cwd='../')
-subprocess.call(['pip', 'install', '-e', '.'], cwd='../netpyne/')
+def checkout(folder, default_branch, cwdp):
+    currentPath = os.getcwd()
+    print currentPath
+    newPath = currentPath+"/"+cwdp+folder
+    print newPath
+    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 outstd:
+        subprocess.call(['git', 'checkout', branch], cwd='./')
+    else:
+        subprocess.call(['git', 'checkout', default_branch], cwd='./')
+    os.chdir(currentPath)
 
-print("Cloning Geppetto Jupyter (Python package)...")
-subprocess.call(['git', 'clone', '--recursive', '-b', 'v0.4.1-M1', 'https://github.com/openworm/org.geppetto.frontend.jupyter.git'], cwd='../')
+def main(argv):
+    global branch
+    if(len(argv) > 0):
+        if(argv[0] == 'branch'):
+           branch = argv[1]
 
-print("Cloning Geppetto Frontend")
-subprocess.call(['git', 'checkout', 'v0.4.1-M1'], cwd='../org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/')
+if __name__ == "__main__":
+    main(sys.argv[1:])
 
-print("Cloning Geppetto NetPyNE Configuration ...")
-subprocess.call(['git', 'clone', 'https://github.com/MetaCell/geppetto-netpyne.git'],
-                cwd='../org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/extensions/')
+os.chdir(os.getcwd()+"/../")
+# Cloning Repos
+clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.1-M1')
+subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/')
 
-subprocess.call(['git', 'checkout', '0.3'], cwd='../org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/extensions/geppetto-netpyne/')
+clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','metadata')
+subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/')
+
+clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.1-M1','', True )
+checkout('geppetto', 'v0.4.1-M1','org.geppetto.frontend.jupyter/src/jupyter_geppetto/')
+clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','0.3','org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/extensions/')
 
 print("Enabling Geppetto NetPyNE Extension ...")
-geppetto_configuration = os.path.join(os.path.dirname(__file__), 'GeppettoConfiguration.json')
-copyfile(geppetto_configuration, '../org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/GeppettoConfiguration.json')
+geppetto_configuration = os.path.join(os.path.dirname(__file__), './utilities/GeppettoConfiguration.json')
+copyfile(geppetto_configuration, './org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/GeppettoConfiguration.json')
 
 # Installing and building
 print("NPM Install and build for Geppetto Frontend  ...")
-subprocess.call(['npm', 'install'], cwd='../org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/')
-subprocess.call(['npm', 'run', 'build-dev-noTest'], cwd='../org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/')
+subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/')
+subprocess.call(['npm', 'run', 'build-dev-noTest'], cwd='./org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/')
 
 print("Installing jupyter_geppetto python package ...")
-subprocess.call(['pip', 'install', '-e', '.'], cwd='../org.geppetto.frontend.jupyter')
+subprocess.call(['pip', 'install', '-e', '.'], cwd='./org.geppetto.frontend.jupyter')
 print("Installing jupyter_geppetto Jupyter Extension ...")
-subprocess.call(['jupyter', 'nbextension', 'install', '--py', '--symlink', '--user', 'jupyter_geppetto'], cwd='../org.geppetto.frontend.jupyter')
-subprocess.call(['jupyter', 'nbextension', 'enable', '--py', '--user', 'jupyter_geppetto'], cwd='../org.geppetto.frontend.jupyter')
-subprocess.call(['jupyter', 'nbextension', 'enable', '--py', 'widgetsnbextension'], cwd='../org.geppetto.frontend.jupyter')
-subprocess.call(['jupyter', 'serverextension', 'enable', '--py', 'jupyter_geppetto'], cwd='../org.geppetto.frontend.jupyter')
+subprocess.call(['jupyter', 'nbextension', 'install', '--py', '--symlink', '--user', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
+subprocess.call(['jupyter', 'nbextension', 'enable', '--py', '--user', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
+subprocess.call(['jupyter', 'nbextension', 'enable', '--py', 'widgetsnbextension'], cwd='./org.geppetto.frontend.jupyter')
+subprocess.call(['jupyter', 'serverextension', 'enable', '--py', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
 
 print("Installing NetPyNE UI python package ...")
-subprocess.call(['pip', 'install', '-e', '.'], cwd='..')
-
+subprocess.call(['pip', 'install', '-e', '.'], cwd='.')