It is simple. Code is one thing and data is another thing; you can mix arbitrary code with arbitrary data but the result might not make sense!

Neurotypicals have a hard time with this kind of contradiction and will try one simplistic answer that almost works and then try a different one and then go back to the old one and eventually they will get interested in something else then give up.

For instance, it makes sense to strip the data out of a jupyter notebook before checking in. You can version manage the code that way. However, people also really want to look at the notebook in github and see the analysis, the data, the results.