Workflow for Jupyter Notebooks under version control


March 22, 2022

I’ll present here my strategy for keeping Jupyter Notebooks under version control.



  • Github handles ipynb pretty well, so I prefer not to use jupytext
  • I want small repositories, so only commit the input cells
  • I want to save the executed notebooks, not in the repo, but where I can easily reference them if needed


Notebooks and git

I work on Notebooks as I work with normal Python files, so I always run black on them to fix formatting, use git add -p to add snippet by snippet. I don’t mind the little extra escaping the Notebook introduces.

I have the nbstripout filters activated (nbstripout --install) so that even if the notebook is partially executed, when I run git add -p I only get the patches on the input cells.

Moreover, I configure nbstripout to remove metadata like the kernelspec or the Python version, which doesn’t do by default

Snapshot executed Notebooks

The Jupyter Notebook inside the repository has only the inputs, but I would like to save executed Notebooks for tracking purposes without increasing the size of the repository.

First I do a clean execution of the Notebook (with Restart & Run All), then I save the changes to the input cells to the repository. I don’t need to clear the outputs from the Notebook, nbstripout does it on th e fly before submitting changes to git.

Then I post the executed Notebook with all outputs to a Gist from the command line with the Github CLI:

gh gist create my_notebook.ipynb

Optionally with --public to make it show on my Gist profile.

The gh tool returns the link to the Gist, that I can add to the commit message or post in a Pull Request or an Issue.

Add executed Notebooks to the documentation

Once I have the final version of a Notebook, I often use nbsphinx to add it to the documentation.

So I disable nbstripout with:

nbstripout --uninstall

Then I add just the last executed state of the Notebook to the repository, so that Sphinx/Readthedocs can compile it into the documentation, including all plots.

See an example of a Notebook compiled into HTML by Sphinx

Automation script

I have created a bash script that automates the process:

  • call with snapshot_nb your_notebook.ipynb
  • creates a Gist with the Notebook
  • amends the last commit to add a link to it
  • it also creates a new Markdown cell with the tag snapshotlog and the title “Execution log” and appends a link to the gist with date and time of execution (Thanks @cosmic_mar for the suggestion), see how the Execution log looks like
  • it actually works with any text file, even multiple files, so it could be used for log outputs for example


Install it by symlinking the 2 scripts to an executable folder, for example ~/bin, also useful if you fork my Gist.


See this thread on Twitter