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You can use LaTeX. Packages like listings or minted can be used to include code snippets and syntax highlighting. Both are supported by tex4ht, so conversion to html and then epub is possible. And as bonus, you can get perfect PDF file.

If you are interested, I have a sample document (in Czech language, but I hope the code is readable) where packages minted for syntax highlighting, biblatex for bibliographies, and glossaries for acronyms were used: TeX source and generated html. For conversion, make4ht was used. make4ht is frontend for tex4ht which allow you to use your own build scripts and it has some filters for generated html cleanup.

There is also another tool, tex4ebook, based on make4ht, which can be used to convert LaTeX to epub, epub3 and mobi formats. Note that I am the author of make4ht and tex4ebook.


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