Installation of neuron, python compatibility

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cluff
Posts: 4
Joined: Fri May 14, 2021 11:47 am

Installation of neuron, python compatibility

Post by cluff »

Hi, I have a few questions

I have previously tried to install neuron (on ubuntu 20:04) following these instructions on the website:

https://www.neuron.yale.edu/neuron/down ... pile_linux

Everything (GUI etc.) seemed to work except I was never able to run the neurondemo programme, a problem I could never solve.

1. Does this version of neuron (7.7) work with new python versions e.g. 3.8?

Now, I am trying to install the newest version of neuron instead, as in:

https://www.neuron.yale.edu/neuron/download

It states:

"If NEURON is already installed, uninstall it before installing a different version."

I believe I have done this however I get an error:

Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: neuron in /usr/local/lib/python3.8/dist-packages (7.7)

2. Are there specific instructions to ensure a complete uninstall- can't find anything online?

3. Once I have uninstalled do I only have to run pip3 install neuron? i.e. the steps to compile as in the first link are no longer required?

4. Lastly, should neuron v8.2 work with python 3.8 or 3.9?

Many thanks,

Charlotte
ramcdougal
Posts: 243
Joined: Fri Nov 28, 2008 3:38 pm
Location: Yale School of Public Health

Re: Installation of neuron, python compatibility

Post by ramcdougal »

The binaries for NEURON 7.7 would not work with Python 3.8, which did not exist at the time 7.7 was released. I imagine it would work if it was compiled specifically for 3.8, but I would strongly suggest using a more recent version of NEURON.

My guess is that it's saying there's a folder called "neuron" in the path "/usr/local/lib/python3.8/dist-packages"... if so, try removing it?

By the way, if it's there, it was installed using sudo... so not as a user. (If you want to install globally, that's fine... in that case you can: sudo pip install --force neuron )

NEURON 8.2.1 supports: Python 3.7, 3.8, 3.9, and 3.10.
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