Literate programming is a concept promoted by Donald Knuth, the famous computer scientist (and the author of the Art of Computer Programming.) According to this concept, computer programs should be written in a combination of the programming language (the usual source code) and the natural language, which explains the logic of the program.
When it comes to scientific programming, using comments for natural-language explanations is not always convenient. Moreover, it is limited, because such explanations may require figures, equations, and other common elements of scientific texts. IPython/Jupyter notebooks provide a convenient tool for combining different text elements with code.
See the notebook at https://github.com/sfomel/ipython/blob/master/LiterateProgramming.ipynb for an example on how to implement literate programming using an IPython notebook with reproducible SConstruct data-analysis workflows in Madagascar.