Jupyter Notebook (IPython) VS nbstripout

Based on this conversation, this more or less means that your Python installation is kind of borked. By default it should use the built-in sqlite3, but apparently your installation is either ignoring it or it's missing for some reason.

this is just a summary of the jupyterhub docs: https://github.com/jupyterhub/jupyterhub/wiki/Using-sudo-to-run-JupyterHub-without-root-privileges

Something quite nifty I found about recently is that you can directly head over to the issues marked with these labels directly by going to the projects contributing page. For example, for JupyterHub, you would head over to https://github.com/jupyterhub/jupyterhub/contribute. Plus the Contribution guidelines are also made visible so you can access them directly!

If you'd like to automatically remove empty / tagged cells or retroactively apply this filter to your git history, you can read the nbstripout documentation on GitHub.

I used something as a precommit hook in the past that remove plots and other rendered content and only kept text and code in git index. I'm almost sure it was https://github.com/kynan/nbstripout but it's been a while and I could be wrong.

Once the hook was in place git diff worked well enough to not need any other diffing tool.

As far as versioning, I use nbstripout (notebook strip out) I think there are alternatives too.

You can use it with source control, I do it for about 18 notebooks I use on a daily basis:

https://github.com/kynan/nbstripout