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This file in the documentation fails to get converted when running make docs, with the error:
Traceback (most recent call last):
File "/Users/jelic/software/nrn/env_arm64/bin/jupyter-nbconvert", line 8, in <module>
sys.exit(main())
^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/jupyter_core/application.py", line 283, in launch_instance
super().launch_instance(argv=argv, **kwargs)
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/traitlets/config/application.py", line 1075, in launch_instance
app.start()
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/nbconvertapp.py", line 420, in start
self.convert_notebooks()
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/nbconvertapp.py", line 597, in convert_notebooks
self.convert_single_notebook(notebook_filename)
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/nbconvertapp.py", line 563, in convert_single_notebook
output, resources = self.export_single_notebook(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/nbconvertapp.py", line 487, in export_single_notebook
output, resources = self.exporter.from_filename(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 201, in from_filename
return self.from_file(f, resources=resources, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 220, in from_file
return self.from_notebook_node(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/exporters/notebook.py", line 36, in from_notebook_node
nb_copy, resources = super().from_notebook_node(nb, resources, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 154, in from_notebook_node
nb_copy, resources = self._preprocess(nb_copy, resources)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 353, in _preprocess
nbc, resc = preprocessor(nbc, resc)
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/preprocessors/base.py", line 48, in __call__
return self.preprocess(nb, resources)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 102, in preprocess
self.preprocess_cell(cell, resources, index)
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 123, in preprocess_cell
cell = self.execute_cell(cell, index, store_history=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
return loop.run_until_complete(inner)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.11/3.11.6_1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/base_events.py", line 653, in run_until_compl
ete
return future.result()
^^^^^^^^^^^^^^^
File "/Users/jelic/software/nrn/env_arm64/lib/python3.11/site-packages/nbclient/client.py", line 1009, in async_execute_cell
raise DeadKernelError("Kernel died") from None
nbclient.exceptions.DeadKernelError: Kernel died
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:
I've also tried to convert the notebook to a script, and, curiously enough, I get a segfault (after commenting out the nrnivmodl line) when running python extracellular.py (converted using jupyter nbconvert --to script docs/rxd-tutorials/extracellular.ipynb).
Curiously, when I apply this diff:
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:nrn/docs/rxd-tutorials/extracellular.ipynb
Line 423 in 8e483a9
Going down the rabbit hole, it seems that the responsible line in that function call is:
nrn/docs/rxd-tutorials/extracellular.ipynb
Line 272 in 8e483a9
I'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.
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