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I'm writing my dissertation/thesis and it revolves around a program I have made. The program is a Rubik's cube solver that uses pre-existing solving methods, so nothing that exciting. I'm writing out my methodology section which I am assuming needs to contain explanations of the methods I used to produce the solving methods.

When referencing functions I have used in my program, would it be more conventional to write out a description of what that function does or would I make an internal hyperlink to the glossary with a description of what that function does.

Cheers!

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A glossary is

  1. a list of terms in a special subject, field, or area of usage, with accompanying definitions.
  2. such a list at the back of a book, explaining or defining difficult or unusual words and expressions used in the text.

so the wrong place for extended descriptions of what your functions do.

Whether those descriptions belong in the text where the function is used or in a separate section with links from the text depends on more context than you can provide here. Imagine the readers of your thesis, knowing what they know (but not what you know) and think about what would best help them follow your argument.

LaTeX can easily manage the cross referencing with a custom \newtheorem command.

Ask your advisor for advice.

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