Notebooks are good for exploring a problem, especially questions about data. I also don't think they are great for "software engineering", but as the name sugge

Notebooks are good for exploring a problem, especially questions about data. I also don't think they are great for "software engineering", but as the name suggest, they are for notes, not applications. When developing something closer to a program, I usually write code line by line in a text editor, but basically every line has been developed in the IPython REPL. Sometimes I write a few cells in Jupyter Notebook to learn an API. It is really nice that you can have the output of a call in cell 1 while working on refining that call in cell 2. Once I feel I've learned what is needed, I move the code into a .py file and turn it into a script or a module. Despite of this workflow, I haven't found a great pairing between editor and IPython REPL and I am manually copy-pasting code between the two. RStudio works really well in this regard, but I think that the editor runs on the same R kernel instance as the program you are developing, which makes restarting R a pain.