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I think what's happening is that the --template option is equivalent to configuring TemplateExporter.template_file. LatexExporter subclasses TemplateExporter, so the more specific config field wins.
I don't see any general fix for that. We could probably hack a specific workaround for --template, but every such hack just makes configuration still more confusing.
To change the default template I added:
to my jupyter_nbconvert_config.py file.
So, running:
will use mytemplate.tplx as expected.
Occasionally, I still need to use a different template, so I run:
But that still compiles using mytemplate.tplx instead. If I remove the line from the config file, then the --template flag works as expected.
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