Jupytext makes this all a lot less painful by keeping a Jupyter notebook up to date with a markdown counterpart (without output). It works a lot better to only

Jupytext makes this all a lot less painful by keeping a Jupyter notebook up to date with a markdown counterpart (without output). It works a lot better to only keep the markdown in source control. The downside is that anyone who starts from a clean repository scratch will need instructions on how to generate the .ipynb files.