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No matter how much you comment your code, you are not going to bring people up to speed on an algorithm that requires background knowledge on dozens of scientific papers, hundreds of pages, with a few code comments. This code is aimed at researchers who are familiar with the techniques and have the necessary background knowledge. For such people, the code is very readable.

Think about it like this: If you write a game engine, are you going to document each function with proofs that explain how the underlying Physics works for people who don't have such knowledge? No, you assume that people who read game engine code have read some basic physics books.