Pip installation

Matteo Cantarelli edited this page Jul 15, 2018 · 16 revisions

Index

Install using Pip

Note: you need to have NEURON installed in your system before executing these steps. See instructions.

If you would like to setup a Python virtual environment (useful if you already have a different version of some of the libraries installed in your system and you want to avoid conflicts) jump here before installing NetPyNE UI.

To install NetPyNE-UI through pip run from your terminal:

pip install netpyne_ui
jupyter nbextension enable --py jupyter_geppetto
jupyter serverextension enable --py jupyter_geppetto
jupyter nbextension enable --py widgetsnbextension

The first line will download and install NetPyNE-UI while the next three lines will enable it. In the near future these additional three instructions will not be necessary. Once all the four instructions have executed without errors you can use NetPyNE-UI simply running NetPyNE-UI from your designated NetPyNE workspace folder. The workspace folder is any folder on your disk where you would like NetPyNE to create various files including the log and the python notebooks. If you would like to use a default workspace with some ready to import models you can clone https://github.com/Neurosim-lab/netpyne_workspace.

mkdir netpyne_workspace OR git clone https://github.com/Neurosim-lab/netpyne_workspace
cd netpyne_workspace
NetPyNE-UI

Any model you will export from NetPyNE-UI will end up in this folder. Similarly you will have to put in the workspace folder any model you would like to import into NetPyNE-UI. Running the NetPyNE-UI command will open your default browser at the URL http://localhost:8888/geppetto (on some Windows systems http://192.168.99.100:8888/geppetto) from where you will be able to use NetPyNE-UI.

Given NetPyNE-UI is still in development and this is just a preview alpha release you might encounter some problems, if that's the case please open an issue on this repo!

Setting up a Python virtual environment

Prepare the virtual environment

To make easier the installation you can use the python virtual environment to have a clean environment without issues related to different dependencies, etc.

First of all we need to install the virtualenv, we assume you have python 2.7 and pip already installed, so in order to install virtual we need to run from the terminal:

pip install virtualenv

Once the virtualenv utility has been installed we can proceed to created our virtual environment:

cd ~
mkdir netpyne-ui
cd netpyne-ui
virtualenv -p python2.7 ./
source bin/activate

Install NEURON in the virtual environment

In the next step we will download and compile NEURON from the source and once done this will be added to the virtual environment.

To download and compile NEURON we can follow these instructions.

Once the sources have been compiled we can copy the folder nrn, created during the instructions linked, inside our bin folder in the virtual environment and then run the python installation. Note, this procedure has to happen in the same terminal where you activated your virtual environment, to be sure you can run the command "which python" and check that the python interpreter is the one contained into your virtual environment.

cp -R nrn ~/netpyne-ui/bin/
cd ~/netpyne-ui/bin/nrn/src/nrnpython
python setup.py install

Once the python installation will be completed you should have NEURON installed in your virtual environment, at this point you can continue with the pip installation of NetPyNe-UI with the steps below.

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