Using PyPNS with up-to-date NEURON and Python

[WarrenDJ]

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 It would be great to not have to use out of date versions.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?

[chlubba]

Hi Warren,

thank you for the feedback!

NEURON 8.0 seems to have introduced quite deep changes to the Python interface. For example, the h.run function has been removed. According to the docs, this seems to have been replaced by h.continuerun. Also other functions such as h.Section have changed.

The amount of work required for making PyPNS NEURON-8.0-ready is therefore not easily predictable. We will update PyPNS, but cannot say when this update will be completed. Until then, users need to stick with NEURON 7.6.7.

If you happen to attempt to tweak PyPNS for NEURON 8.0, thank you for considering forking and submitting a pull request.

Best,
Carl

[WarrenDJ]

Thanks for getting back to me. With that advice, I might see if the last of the NEURON version 7.x builds works. If so, I will get back to you via GitHub. I would really like to help as part of a team to move PyPNS to be compatible with NEURON 8.0 but I am really a Python coder (but have coding experience going back to FORTRAN). Maybe when I retire. David J. Warren, Ph. D. Research Associate Professor Center for Neural Engineering Dept. of Biomedical Engineering 20 S 2030 E, Room 506E Salt Lake City, UT 84112-9458 Phone: 1-801-585-2697 Fax: 1-801-585-5151 ***@***.******@***.***> From: Carl H Lubba ***@***.***> Sent: Tuesday, March 1, 2022 02:09 To: chlubba/PyPNS ***@***.***> Cc: David James Warren ***@***.***>; Author ***@***.***> Subject: Re: [chlubba/PyPNS] Using PyPNS with up-to-date NEURON and Python (Issue #5) Hi Warren, thank you for the feedback! NEURON 8.0 seems to have introduced quite deep changes to the Python interface. <https://neuron.yale.edu/neuron/news/neuron-80-released> For example, the h.run function has been removed. According to the docs<https://nrn.readthedocs.io/en/latest/tutorials/scripting-neuron-basics.html>, this seems to have been replaced by h.continuerun. Also other functions such as h.Section have changed. The amount of work required for making PyPNS NEURON-8.0-ready is therefore not easily predictable. We will update PyPNS, but cannot say when this update will be completed. Until then, users need to stick with NEURON 7.6.7. If you happen to attempt to tweak PyPNS for NEURON 8.0, thank you for considering forking and submitting a pull request. Best, Carl — Reply to this email directly, view it on GitHub<#5 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIL3MEMYONNLA6JL6LWVWHDU5XNBJANCNFSM5PSFF5OQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[nrnhines]

For example, the h.run function has been removed.

h.run() is still present if neuron import gui or h.load_file("stdrun.hoc")
I believe the author of the mentioned docs page just prefers to explicitly use h.finitialize(...) instead of h.stdinit() with their global v_init and tstop variables. In stdrun.hoc it is still declared as

proc run() {
        running_ = 1
        stdinit()
        continuerun(tstop) 
}