Using include directive, conf.py configuration is not picked up
Describe the bug
context When I include a notebook into sphinx from a different location as described here, the conf.py parameter is not picked up:
.. include:: ../../some/nexted/path/include.ipynb
:parser: myst_nb.docutils_
My notebook is executed correctly in the local context and included.
expectation
I expected it to pick up the configuration from my conf.py.
bug
But instead I ran into a "Executing notebook failed: CellTimeoutError [mystnb.exec]" error, which I tried to fix using the following configuration in conf.py
# https://myst-nb.readthedocs.io/en/latest/configuration.html#global-configuration
nb_execution_timeout = 240 # otherwise it's a 30 seconds maximum per cell,
# https://myst-nb.readthedocs.io/en/latest/configuration.html
# Execution
nb_execution_raise_on_error = True
problem
So it might be only a documentation question, but: How do I set the configuration if I want to include a notebook which is not present in the docs folder with the sphinx conf.py file?
If I try to set the docutils.conf file as
[general]
nb_execution_mode = auto
nb_execution_raise_on_error = true
nb_merge_streams = true
nb_execution_timeout = 120
I get the warning: (ERROR/3) myst-nb configuration invalid: 'execution_timeout' must be of type <class 'int'> (got '120' that is a <class 'str'>). [mystnb]
Is there any way to set the NbParserConfig in the include directive?
Reproduce the bug
- Use the
includedirective and add it to theextra/test.rstfile:
.. include:: ../../project/test.ipynb
:parser: myst_nb.docutils_
and then include that into index.rst:
.. toctree::
:maxdepth: 2
:caption: test
extra/test
List your environment
myst-nb 0.17.2
myst-parser 0.18.1
I don't have jupyter book installed.
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Adding the desired configuration to the notebook metadata works, see documentation here.