Global pairing configuration is not effective in versions v0.7.*

[matthew-brett]

First - thanks very much for writing this - it's very very useful - it really changes the usability of Notebooks for writing anything more substantial than a quick demo.

Having said that, I'm running into almost constant trouble with pairing.

I have put this into ~/.jupyter/jupyter_notebook_config.py:

c.NotebookApp.contents_manager_class = "jupytext.TextFileContentsManager"
c.ContentsManager.default_jupytext_formats = "ipynb,Rmd"

With that setting, I am expecting that, whenever I save a Notebook from Jupyter, I will get a paired .Rmd file, and whenever I open and save an .Rmd file from Jupyter, I will get the matching .ipynb file. Is that expectation correct? Because, more often than not, I get neither effect, and I have to run jupytext --to manually to get the conversion.

Am I doing something wrong? What could I do, to debug?

[mwouts]

Hello @matthew-brett , thanks, I'm glad to know that the tool is helpful. Thanks also for reporting. Your expectation is completely correct: you should get the two forms of the notebook whenever you open a 'ipynb' or a 'Rmd' document in Jupyter, and save.

We will troubleshoot this. To start with, may I ask if you see any 'jupytext_formats' metadata in the notebook? (that one has a higher priority than the content's manager one)

[matthew-brett]

Aha - yes - in one of the notebooks I'm working on, this appeared, somehow:

 "jupytext_formats": "Rmd:rmarkdown",

[mwouts]

That's a good start! From the explicit format name I guess you are using a very recent version of jupytext. With the introduction of the multiple script formats (light and percent) I had to include them explicitly in that field, but I see now that this has the effect of creating a jupytext_formats entry in your notebook when there is none, and that causes the issue you experience.

I will add a new unit test to make sure this does not happen in the next release. Meanwhile, as the c.ContentsManager.default_jupytext_formats is not effective, I suggest that you change the "jupytext_formats": "Rmd:rmarkdown", entry to "jupytext_formats": "ipynb,Rmd" for every notebook.

[matthew-brett]

Thanks - that's a relief to know that I wasn't suffering from the effects of an unpredictable gap in space-time ...

[mwouts]

@matthew-brett , I expect that the new release (v0.8.0) will fix this. Please reopen if this is not the case! Also, I saw your nb2plots project, you must be familiar with the sphinx gallery format, aren't you? Please let me know if you want to recommend improvements on jupytext's implementation of that format.

[matthew-brett]

Actually, the nb2plots thing is a competitor to sphinx-gallery if anything. It does a one-way write of a notebook into ReST, putting code cells into sphinx directives, so the stuff is easier to edit, and then rebuilds the notebooks for download, at page build time.