Add Python libraries in neuron package

[rqcy]

Issue description

The NEURON simulation environment is often scripted with Python instead of its native hoc interpreter. Adding Python to the neuron package would be very useful.

[rqcy]

@adevress would it be difficult to implement?

Thanks for maintaining this (esoteric ;) ) package!

[adevress]

Hi rqcy,

No it should be doable and rather easy, I will add this in a future pull request.

[adevress]

@obadz Can you assign this ticket to me ? thank you in advance.

[obadz]

Hmmmm… apparently I can only assign to project members, sorry. I guess if anyone finds this issue they will know it's all yours.

[adevress]

@obadz That's fine but that's wierd, I was thinking I'm automatically attached for anything related to a package I maintain.

[rqcy]

No it should be doable and rather easy, I will add this in a future pull request.

Thanks, that's really great! Stefan

[FRidh]

when you mean you want to use Python with Neuron, is then the base interpreter enough or do you also want to use additional modules?

[rqcy]

when you mean you want to use Python with Neuron, is then the base interpreter enough or do you also want to use additional modules?

Hi, I'm not sure what do you mean by “base interpreter” and “additional modules”. I usually start Python or IPython, and import required modules, e.g.: import neuron from neuron import h import numpy as np import pandas as pd etc. Stefan

[FRidh]

I see, thanks for the example @rqcy .

Certain applications have a built-in interpreter that can be used to write plugins, e.g. FreeCAD, in which case you might want to use additional modules, like numpy.

But sometimes, you want to use the libraries offered by the program, like you seem to want to do with Neuron. If you want to use it like this, then it makes sense to make this package available as a Python library.

@adevress I recommend making the python parameter optional, that is, python ? null, and keep it as null for pkgs.neuron and pkgs.neuron-mpi. Then, in python-packages.nix you take pkgs.neuron and override it to add python. That way, pkgs.neuron is for those that want to use neuron without Python, andpkgs.pythonXXPackages.neuron` is build for the right interpreter version. We can discuss those details further in the PR.

[adevress]

Hi @FRidh

I updated the pull request following your recommendation.

You have now a standard neuron and neuron-mpi modules without python support.
and a pythonPackages.neuron and pythonPackages.neuron-mpi with the python support for every version of python.

[FRidh]

Great! Merged so closing this.

[FRidh]

Actually, the bindings don't work just yet.

[adevress]

@FRidh Ok I found the issue, the old prefix was not renamed properly, sorry for that.

Thank you for your testing @FRidh

I just fixed it and tested it in an isolated python environment. The fix is available in this pull request #18187