I suspect the answer is zero, but I’d like to be proven wrong. Of course it depends on the definition of “paper”, so let’s say anything indexed by Web of Science or Google Scholar.https://twitter.com/johnkitchin/status/982288371048366081 …
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written in? There's one with Rob Knight and Fernando Perez that was written in it. But publishers... *shrug* formats prevent.
Notebooks, dunno. But that's a weirdly constrained format. Things like http://neuralnetworksanddeeplearning.com (600 GS citations), http://distill.pub , http://worrydream.com , "The Nature of Code", SICM, etc all count as publication.
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for compatibility with publishers, one would have to use something like nbconvert to generate LaTeX for submission. That is what we do with orgmode. http://distill.pub AFAIK is handwritten html and javascript to produce high-end interactive publications.
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In the last two years, they have published 10 articles? They are beautiful, but serve a different role than your typical scientific article.
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