I program mainly in R and I always use RMarkdown. I write extensively about question definition, notes, reference, exploration, different directions in RMarkdow

I program mainly in R and I always use RMarkdown. I write extensively about question definition, notes, reference, exploration, different directions in RMarkdown. In the end if I ever need to have a script version I have some utility function to pick code chunks and output as script. This serve as a very good documentation and is much better than code comments.