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I have a makefile that turns the whole thing into one PDF and if I want, reruns the whole thing. R has more mature stuff in this area, but the gap between mine is small. But the graphs are so much prettier. (And tables too. I gotta write a package for that. Low hanging fruit.)
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are you using nbdime (https://nbdime.readthedocs.io/en/ ) so that your version control software can understand your jupyter notebooks? The one thing I like about R Markdown over jupyter is that this minor extra step isn't necessary -- R Markdown/R notebooks are just text.
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