Open JCGoran opened 8 months ago
Sorry I've not yet managed to reproduce the issue with runsim, but it looks like the problem with the RTD build was fixed in this commit; https://github.com/neuronsimulator/nrn/commit/8a23590b84a1e76b6182311568718029f70f9c7e
Context
This file in the documentation fails to get converted when running
make docs
, with the error:The same issue happens when running the notebook in an interactive session.
After some debugging by using
jupyter nbconvert --to notebook --inplace --Application.log_level=DEBUG --execute
, the issue seems to be this line here: https://github.com/neuronsimulator/nrn/blob/8e483a912e35f0e919746b71ac251acc0676671a/docs/rxd-tutorials/extracellular.ipynb#L423 Going down the rabbit hole, it seems that the responsible line in that function call is: https://github.com/neuronsimulator/nrn/blob/8e483a912e35f0e919746b71ac251acc0676671a/docs/rxd-tutorials/extracellular.ipynb#L272I've also tried to convert the notebook to a script, and, curiously enough, I get a segfault (after commenting out the
nrnivmodl
line) when runningpython extracellular.py
(converted usingjupyter nbconvert --to script docs/rxd-tutorials/extracellular.ipynb
). Curiously, when I apply this diff:it runs fine.
Note that the issue is also present on the current stable release, 8.2.3.
Also note that the automated build on RTD fails with a different error (see here).
Python packages and versions
This is on Python 3.11, but I am able to reproduce also with Python 3.9.