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One disadvantage is that github is a bit of an outlier in providing readable diffs for notebooks; in other systems (critique, git diff, etc.) diffs are harder to read, and even with github's nice diffs, notebook merge conflicts are still near impossible to do without corrupting the file.
But having to run jupytext on modified files does create some friction, so I could see the desire to be rid of it.
github has now a nice way to diff notebooks (https://github.blog/changelog/2023-03-01-feature-preview-rich-jupyter-notebook-diffs/)
I think we could drop the markdown part of the notebooks (https://jaxopt.github.io/stable/developer.html#update-notebooks), which I think adds an unnecessary overhead for contributors. What do you think @mblondel ?
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