We don't want to affect your system in any way, so we will operate from a virtual environment and install all the necessary software there. In order to accomplish this, you can choose one of three options.
You can open a terminal and enter the following at the prompt:
mkdir netpyne_tuts && cd netpyne_tuts && export PATH=/bin:/usr/bin && python3 -m venv env && source env/bin/activate && python3 -m pip install --upgrade pip && python3 -m pip install --upgrade ipython && python3 -m pip install --upgrade ipykernel && python3 -m pip install --upgrade jupyter && ipython kernel install --user --name=env && python3 -m pip install --upgrade neuron && git clone --depth 1 https://github.com/suny-downstate-medical-center/netpyne.git && python3 -m pip install -e netpyne && cp -r netpyne/netpyne/tutorials . && cd tutorials && jupyter notebook
You can execute install_tuts.py by downloading it, opening a terminal and entering:
python3 install_tuts.py
You can execute install_tuts.sh by downloading it, opening a terminal and entering:
sh install_tuts.sh
Either of these options will do the same thing. They will:
- Create a directory netpyne_tuts and change into it
- Clear the PATH of all but essentials
- Create a virtual environment named env
- Activate (enter) the virtual environment
- Upgrade pip and install necessary packages
- Create a Jupyter kernel out of env
- Clone the NetPyNE GitHub repository (using shallow cloning)
- Install NetPyNE using pip
- Copy the NetPyNE tutorials directory into netpyne_tuts
- Change into the tutorials directory
- Start Jupyter Notebook
This installation step only needs to be performed once. To re-enter the virtual environment in the future, change to the netpyne_tuts directory and execute the following:
source env/bin/activate
jupyter notebook