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Is PyPNS working with new versions of NEURON. #1831
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Using
Generates the stdout/stderr
and the figure |
Using
And a figure similar to 8.1.0 above (though different in detail). |
It seems likely that a major part (or all) of the issue stems from #596 change due to issue #509 . Building the version just prior to this change, Note that to speed things up, I modified test.py so that
Also note that there are many places in the code that make use of randomness and I could not immediately figure out how to make the simulation deterministic. |
The versions that contain that commit are:
|
Hello, I tried to replicate some of the figures (https://github.com/chlubba/PyPNS-PaperFigures) of the PyPNS paper using The I was also able to reproduce figure 7 (a, b, c) from the paper. However, I'm not able to replicate the content of figures 8 and 9. Is it possible that there is still some incompatibility between Figures generatedFigures in the paper |
@AnaMachadoLuis Thanks, I was hoping someone would check on those figures. I suspect the issue is the same. Can you tell me how to run those |
Yes, of course. First I also considered that the influence of randomness could be an explanation, but then after looking more carefully at the differences between the figures I obtained and the ones in the paper, I realized they are quite significant. This repository https://github.com/chlubba/PyPNS-PaperFigures contains the scripts to generate the figures in the PyPNS paper. There is a python script (sometimes two in the case when some previous calculations are necessary) for every figure. In the same directory should be the following elements: -python script to generate the desired figure (I ran it as a jupyter notebook) |
@AnaMachadoLuis
The former is my working directory.
and to make sure I have the mod files
Then I tried for fig8 and got:
Any suggestions? |
By using
and see similar results for and |
@nrnhines Ok, I can see the results are the same, even though they don't match the contents of the original figures. But based on this, it should not be a NEURON version problem. Thank you. |
@AnaMachadoLuis
NEURON -- VERSION 7.6.7 HEAD (603da17) 2019-04-19 'NEURON -- VERSION 8.2.dev-54-gfe112466a master (fe11246) 2022-05-25' |
When I use NEURON-8.1.0 with python3.9 on my linux desktop and install PyPNS from github and run
I get
Note: https://www.neuron.yale.edu/phpBB/viewtopic.php?p=19436#p19436
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