At the moment, I enjoy and work with both Pluto and Quarto. In general, Pluto works really well for data analysis and dashboard-like notebooks. It is possible to get footnotes and citations with Pluto but if you want more formatting control or cross-referencing capability, you have to implement it yourself in HTML within a notebook or use something like PlutoReports.jl. The main challenges I’ve found with Pluto notebooks is stitching them together to create a compendium. As mentioned in another post, Pluto now manages packages for you, so each notebook environment is stored as annotated comments in the .jl file, and therefore you need to run each notebook in isolation, which is good but also slow. The best solution I’ve found for combining Pluto notebooks is with PlutoStaticHTML.jl, but using this to turn a bunch of Pluto notebooks into a book-style website doesn’t seem so streamlined. This is where I think Quarto has the advantage. If you are trying to create a book or website that feels like a book, Quarto in VSCode will be the better option. Quarto would also be a good option to write a research paper with code, but I think the show your work project is a more elegant approach and supports Julia. You could also checkout the Books.jl package.
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