Going back to even some of the earliest literate programming exercises by Knuth, there's a lot of demonstrable usefulness in being able to write the code "out of order", or to at least demonstrate it in such form. It's not entirely out of the question that setup requirements aren't interesting to the main narrative flow, and maybe even distract from it, such that the "natural" place to put stuff in say a textbook is in the back as an Appendix.

A good notebook (again, similar to early literate programming tools) should help you piece the final execution flow back into the procedural flow needed for the given compiler/interpreter, but it probably should still let you rearrange it to best fit your narrative/thesis/arc.