From 114dc47413cac48e51fdceb1c773e514c3f9f0df Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Fri, 23 Nov 2018 16:33:57 +0000 Subject: [PATCH 1/7] Update install.py Point to fixed tags for the master branch --- utilities/install.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/utilities/install.py b/utilities/install.py index 794d6ccc..23e9a0ad 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -29,7 +29,7 @@ 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 and branch in str(outstd) and branch != 'development': # don't ckeckout development for netpyne + if branch and branch in str(outstd) and branch != 'master' and branch != 'development': # don't ckeckout development for netpyne subprocess.call(['git', 'checkout', branch], cwd='./') else: subprocess.call(['git', 'checkout', default_branch], cwd='./') @@ -46,21 +46,21 @@ def main(argv): os.chdir(os.getcwd()+"/../") # Cloning Repos -clone('https://github.com/openworm/pygeppetto.git','pygeppetto','development') +clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.2-alpha') subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/') -clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','ui') +clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.0') subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/') -clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','development') +clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.2-alpha') with open('npm_frontend_jupyter_log', 'a') as stdout: subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js', stdout=stdout) subprocess.call(['npm', 'run', 'build-dev'], cwd='./org.geppetto.frontend.jupyter/js') # We can't clone org.geppetto.frontend as a regular submodule because Travis doesn't have .gitmodules in the zip # subprocess.call(['git', 'submodule', 'update', '--init'], cwd='./') -clone('https://github.com/openworm/org.geppetto.frontend.git','geppetto','development','netpyne_ui/', False, 'geppetto') -clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','development','netpyne_ui/geppetto/src/main/webapp/extensions/') +clone('https://github.com/openworm/org.geppetto.frontend.git','geppetto','v0.4.1-syncRefactor','netpyne_ui/', False, 'geppetto') +clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','master','netpyne_ui/geppetto/src/main/webapp/extensions/') print("Enabling Geppetto NetPyNE Extension ...") geppetto_configuration = os.path.join(os.path.dirname(__file__), './utilities/GeppettoConfiguration.json') @@ -81,4 +81,4 @@ def main(argv): 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='.') \ No newline at end of file +subprocess.call(['pip', 'install', '-e', '.'], cwd='.') From 45a254dbf1846ab9cca0d08cd0d87a0b4f7f1cd4 Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Sat, 24 Nov 2018 15:06:47 +0000 Subject: [PATCH 2/7] Update install.py --- utilities/install.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/utilities/install.py b/utilities/install.py index 23e9a0ad..2306ca49 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -49,7 +49,7 @@ def main(argv): clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.2-alpha') subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/') -clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.0') +clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.0_UI0.5Release') subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/') clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.2-alpha') @@ -60,7 +60,7 @@ def main(argv): # We can't clone org.geppetto.frontend as a regular submodule because Travis doesn't have .gitmodules in the zip # subprocess.call(['git', 'submodule', 'update', '--init'], cwd='./') clone('https://github.com/openworm/org.geppetto.frontend.git','geppetto','v0.4.1-syncRefactor','netpyne_ui/', False, 'geppetto') -clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','master','netpyne_ui/geppetto/src/main/webapp/extensions/') +clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','0.5','netpyne_ui/geppetto/src/main/webapp/extensions/') print("Enabling Geppetto NetPyNE Extension ...") geppetto_configuration = os.path.join(os.path.dirname(__file__), './utilities/GeppettoConfiguration.json') From 4002b12f21051ab21c453493b35b23ad8f32ead6 Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Thu, 29 Nov 2018 01:40:33 +0100 Subject: [PATCH 3/7] Update install.py --- utilities/install.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/utilities/install.py b/utilities/install.py index 2306ca49..c490aadb 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -49,7 +49,7 @@ def main(argv): clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.2-alpha') subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/') -clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.0_UI0.5Release') +clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.1') subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/') clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.2-alpha') @@ -60,7 +60,7 @@ def main(argv): # We can't clone org.geppetto.frontend as a regular submodule because Travis doesn't have .gitmodules in the zip # subprocess.call(['git', 'submodule', 'update', '--init'], cwd='./') clone('https://github.com/openworm/org.geppetto.frontend.git','geppetto','v0.4.1-syncRefactor','netpyne_ui/', False, 'geppetto') -clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','0.5','netpyne_ui/geppetto/src/main/webapp/extensions/') +clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','0.5.1','netpyne_ui/geppetto/src/main/webapp/extensions/') print("Enabling Geppetto NetPyNE Extension ...") geppetto_configuration = os.path.join(os.path.dirname(__file__), './utilities/GeppettoConfiguration.json') From 972700ee315f3facf454fb0232add603c445a48a Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Thu, 13 Dec 2018 11:51:43 +0100 Subject: [PATCH 4/7] Update install.py --- utilities/install.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/utilities/install.py b/utilities/install.py index c490aadb..ed8b947f 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -49,7 +49,7 @@ def main(argv): clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.2-alpha') subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/') -clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.1') +clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.1.1') subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/') clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.2-alpha') @@ -60,7 +60,7 @@ def main(argv): # We can't clone org.geppetto.frontend as a regular submodule because Travis doesn't have .gitmodules in the zip # subprocess.call(['git', 'submodule', 'update', '--init'], cwd='./') clone('https://github.com/openworm/org.geppetto.frontend.git','geppetto','v0.4.1-syncRefactor','netpyne_ui/', False, 'geppetto') -clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','0.5.1','netpyne_ui/geppetto/src/main/webapp/extensions/') +clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','0.5.2','netpyne_ui/geppetto/src/main/webapp/extensions/') print("Enabling Geppetto NetPyNE Extension ...") geppetto_configuration = os.path.join(os.path.dirname(__file__), './utilities/GeppettoConfiguration.json') From 8350e938194ac4c9bc76bd56856fa63932a4907a Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Wed, 30 Jan 2019 18:02:35 +0000 Subject: [PATCH 5/7] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 2ef70ded..d561cd1a 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ [![Docker Automated buil](https://img.shields.io/docker/automated/jrottenberg/ffmpeg.svg)](https://hub.docker.com/r/metacell/netpyne-ui/)

- +

-![Screenshot](https://github.com/metacell/netpyne-ui/raw/updated_documentation/docs/netpyneui.png) +![Screenshot](https://github.com/metacell/netpyne-ui/raw/master/docs/netpyneui.png) This repository hosts the User Interface for [NetPyNE](http://www.neurosimlab.org/netpyne/). NetPyNE is a python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator. From 1c70accbf440bfbf784e17657f7cef4b8c121d7f Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Thu, 31 Jan 2019 11:22:07 +0000 Subject: [PATCH 6/7] Update to patched version of NetPyNE v0.9.1.2 --- utilities/install.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utilities/install.py b/utilities/install.py index ed8b947f..c4dab594 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -49,7 +49,7 @@ def main(argv): clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.2-alpha') subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/') -clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.1.1') +clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.1.2') subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/') clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.2-alpha') From e9a6a9b98980c467b10fa8a0927a6d44336d40ca Mon Sep 17 00:00:00 2001 From: Matteo Cantarelli Date: Sat, 2 Feb 2019 13:00:05 +0000 Subject: [PATCH 7/7] Update to patched version of NetPyNE v0.9.1.3 --- utilities/install.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utilities/install.py b/utilities/install.py index c4dab594..0e8f93f8 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -49,7 +49,7 @@ def main(argv): clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.2-alpha') subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/') -clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.1.2') +clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.9.1.3') subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/') clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.2-alpha')