chlubba / pypns Goto Github PK

I recently assigned to graduates students to model the compound action potential using PyPNS, where I was somewhat directing students as they did the work. I soon found out that using NEURON 8.0 and Python 3.9 was mostly a bust. We all found out that we were able run simulations with myelinated axons, but the results were reliably zero (under Windows, WSL, Ubuntu, and MacOS). Since that experience, I have played around with the code a lot to see if it works with the version of NEURON mentioned in the paper (7.6.7). Using that version, I was able to replicate the contents of Figure 9A to 9D from the paper. It would be great to not have to use out of date versions. Anyone have any ideas what broke between NEURON 7.6.7 and 8.0, and how to fix it?

File "setup.py", line 9
raise ie, 'please install setuptools'
^
SyntaxError: invalid syntax

Hello, I have trouble with the installation on my Mac (10.14.5) as it says that setuptools is not installed, even though it is. Any ideas about what might be causing the issue?

Requirement already satisfied: setuptools in /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages (40.8.0)

Collecting pypns
Downloading https://files.pythonhosted.org/packages/f8/e1/29e2d66ada5bb765455fcab783b57a4a977de35e7a45db638ec54f521220/PyPNS-0.0.4.tar.gz (44kB)
100% |████████████████████████████████| 51kB 1.4MB/s
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "", line 1, in
File "/private/tmp/pip-install-hpdrgh6u/pypns/setup.py", line 9
raise ie, 'please install setuptools'
^
SyntaxError: invalid syntax
Command "python setup.py egg_info" failed with error code 1 in /private/tmp/pip-install-hpdrgh6u/pypns/

Hello Dr. Lubba,

I Installed the package but does not work correctly when I am executing text.py
I will get these errors:

File "test.py", line 1, in <module> import PyPNS File "/home/jovyan/PyPNS/PyPNS/__init__.py", line 1, in <module> from PyPNS.bundleClass import Bundle File "/home/jovyan/PyPNS/PyPNS/bundleClass.py", line 10, in <module> mpl.use('TkAgg') File "/opt/conda/lib/python3.7/site-packages/matplotlib/cbook/deprecation.py", line 296, in wrapper return func(*args, **kwargs) File "/opt/conda/lib/python3.7/site-packages/matplotlib/cbook/deprecation.py", line 358, in wrapper return func(*args, **kwargs) File "/opt/conda/lib/python3.7/site-packages/matplotlib/__init__.py", line 1281, in use plt.switch_backend(name) File "/opt/conda/lib/python3.7/site-packages/matplotlib/pyplot.py", line 237, in switch_backend newbackend, required_framework, current_framework)) ImportError: Cannot load backend 'TkAgg' which requires the 'tk' interactive framework, as 'headless' is currently running
I tried that on my Macbook, I intalled on a linux mechine and on a docker container but so far none of them are working.
What do you suggest?

Thanks,
Morteza.