trellixvulnteam/netpyne-ui_9wfw

NetPyNE User interface

This repository hosts the User Interface for NetPyNE. NetPyNE is a python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator.

Install NetPyNE User Interface

Select one option to install the NetPyNE User Interface.

If you are familiar with NEURON and have already NEURON installed in your machine you can proceed using Pip. If you want a container which comes with everything preinstalled including NEURON you can use the Docker image. Using docker you will still be able to mount a local folder which will be your NetPyNE workspace. If you don't have docker installed in your system and you have had troubles installing it you can opt for the Virtual Machine installation.

Install NetPyNE User Interface from sources (for developers)

Python Dependencies

We recommend the use of a new python 3 virtual environment:

python3 -m venv npenv
source npenv/bin/activate

Or, with conda

conda create -n netpyne python=3.7
conda activate netpyne

Run install script

python utilities/install.py

Start application

./NetPyNE-UI

For debugging you can use run.py instead

python run.py

Run NetPyNE User Interface in Docker

Ensure that you have Docker installed on your system.

Build the image

docker build -t netpyne-ui .

Run the image

docker run -p 8888:8888 netpyne-ui 

End-to-end tests

End-to-end tests are located in tests/deployment/frontend/e2e. Ensure that the application is running in a blank state, since end-to-end tests interact with the running application.

Install packages

cd tests/frontend/e2e
npm install

Start tests

npm run test

Containerized tests

You can also use docker-compose to run the tests. Ensure that you have Docker installed on your system.

Build the images

cd tests/deployment
sh build.sh

Run the tests

docker-compose up --abort-on-container-exit --exit-code-from netpyne-ui-e2e

Additional Notes

NetPyNE-UI is being developed in collaboration with the Neurosim Lab. See the Wiki for more info!