Merge pull request #82 from MetaCell/refactor-sync

Jupyter extension refactor

Author: tarelli

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "netpyne_ui/geppetto"]
+	path = netpyne_ui/geppetto
+	url = https://github.com/openworm/org.geppetto.frontend.git

Dockerfile_dev

@@ -60,4 +60,4 @@ RUN /bin/bash -c "source activate snakes && exec python install.py branch $netpy
 WORKDIR /home/jovyan
 RUN git clone https://github.com/Neurosim-lab/netpyne_workspace
 WORKDIR /home/jovyan/netpyne_workspace
-CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token=''"
+CMD /bin/bash -c "source activate snakes && exec jupyter notebook --debug --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui"

NetPyNE-UI

@@ -1,2 +1,2 @@
 #!/bin/sh
-exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token=''
+exec jupyter notebook --NotebookApp.default_url=/geppetto --NotebookApp.token='' --library=netpyne_ui

netpyne_ui/geppetto

@@ -1,6 +1,19 @@
-from setuptools import setup, find_packages
+import setuptools
+import fnmatch
+import os
+from glob import glob
 
-setup(
+#This block copies resources to the server so we avoid jupyter nbextension install --py --sys-prefix jupyter_geppetto
+data_files = []
+data_files.append(('geppetto/src/main/webapp/build/', glob('src/jupyter_geppetto/geppetto/src/main/webapp/build/*.js')))
+data_files.append(('geppetto/src/main/webapp/build/', glob('src/jupyter_geppetto/geppetto/src/main/webapp/build/*.vm')))
+data_files.append(('geppetto/geppetto/src/main/webapp/build/', glob('src/jupyter_geppetto/geppetto/src/main/webapp/build/fonts/*')))
+for root, dirnames, filenames in os.walk('src/jupyter_geppetto/geppetto/src/main/webapp/js/'):
+    for filename in fnmatch.filter(filenames, '*'):
+        data_files.append((root[3:], [os.path.join(root, filename)]))
+
+
+setuptools.setup(
     name="netpyne_ui",
     version="0.4",
     url="https://github.com/MetaCell/NetPyNE-UI",
@@ -9,7 +22,8 @@
     description="NetPyNE User interface",
     license="MIT",
     long_description=open('README.rst').read(),
-    packages=find_packages(),
+    data_files=data_files,
+    packages=setuptools.find_packages(),
     package_data={
         '': ['*.hoc']
     },

netpyne_ui/netpyne_geppetto.py

@@ -35,12 +35,12 @@
         },
         {
             "name": "org.geppetto.frontend",
-            "path": "../org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/",
+            "path": "../netpyne_ui/geppetto/",
             "url": "https://github.com/openworm/org.geppetto.frontend"
         },
         {
             "name": "Geppetto Netpyne extension",
-            "path": "../org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/extensions/geppetto-netpyne/",
+            "path": "../netpyne_ui/geppetto/src/main/webapp/extensions/geppetto-netpyne/",
             "url": "https://github.com/MetaCell/geppetto-netpyne"
         }
     ]

setup.py

@@ -9,13 +9,16 @@
 
 #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):
+def clone(repository, folder, default_branch, cwdp='', recursive = False, destination_folder = None):
     global branch
     print("Cloning "+repository)
     if recursive:
         subprocess.call(['git', 'clone', '--recursive', repository], cwd='./'+cwdp)
     else:
-        subprocess.call(['git', 'clone', repository], cwd='./'+cwdp)
+        if destination_folder:
+                subprocess.call(['git', 'clone', repository, destination_folder], cwd='./'+cwdp)
+        else:
+                subprocess.call(['git', 'clone', repository], cwd='./'+cwdp)
     checkout(folder, default_branch, cwdp)
 
 def checkout(folder, default_branch, cwdp):
@@ -49,18 +52,23 @@ def main(argv):
 clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','ui')
 subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/')
 
-clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','development','', True )
-checkout('geppetto', 'development','org.geppetto.frontend.jupyter/src/jupyter_geppetto/')
-clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','development','org.geppetto.frontend.jupyter/src/jupyter_geppetto/geppetto/src/main/webapp/extensions/')
+clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','development')
+subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js')
+subprocess.call(['npm', 'run', 'build-dev'], cwd='./org.geppetto.frontend.jupyter/js')
+
+#subprocess.call(['git', 'submodule', 'update', '--init'], cwd='./')
+clone('https://github.com/openworm/org.geppetto.frontend.git','geppetto','development','netpyne_ui/', False, 'geppetto')
+# checkout('geppetto', 'development','org.geppetto.frontend.jupyter/src/jupyter_geppetto/')
+clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','development','netpyne_ui/geppetto/src/main/webapp/extensions/')
 
 print("Enabling Geppetto NetPyNE Extension ...")
 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')
+copyfile(geppetto_configuration, './netpyne_ui/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='./netpyne_ui/geppetto/src/main/webapp/')
+subprocess.call(['npm', 'run', 'build-dev-noTest'], cwd='./netpyne_ui/geppetto/src/main/webapp/')
 
 print("Installing jupyter_geppetto python package ...")
 subprocess.call(['pip', 'install', '-e', '.'], cwd='./org.geppetto.frontend.jupyter')