jupytext ignores lines starting with %

I am using jupytext --to ipynb *.Rmd or jupytext --to Rmd *.ipynb to keep the pairs of Rmd and ipynb files in sync. This works nicely if I add code in either document and use the jupytext calls to copy these to the other file type.

However, it does not work if that line of code starts with either % or # %, as in %autosave 0 or # %autosave 0. Such lines of code are simply not transferred between the formats. As a result, since we only edit the ipynb file and make code review of the .Rmd file, such code edits go unnoticed.

Could you please make jupytext stop ignoring such code changes?

[mwouts]

Hello @tordbb , thanks for asking.

It is expected that Jupytext comments out magic commands (by default, because they don’t make sense in a .Rmd document), but it should not remove any line when changing from one format to the other. If you have a reproducible example I would like very much to have a look.

Now, you can change that behavior with the comment_magics option (jupytext --opt comment_magics=False).

You can also change that for a single line with e.g.

%autosave 0 #noescape

[anineharto]

I found the source of the error, so I managed to fix it 😃 Thanks for your help!