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You can't embed graphs in a script, and plotting is an important part of systematic research. Also, it is easier to have an obvious sequential set of experiment

You can't embed graphs in a script, and plotting is an important part of systematic research. Also, it is easier to have an obvious sequential set of experiments over months in a notebook rather than a bunch of scripts. It's the same reason scientists use lab notebooks to keep track of things rather than just a bunch of loose papers.

alan-hn 2y ago
Yes, I have a lab notebook and I work in a lab. However I use folder structures to organize my scripts and as for graph outputs I save them as files. In my line of work I generate hundreds of graphs for data analysis verification and a notebook isn't set up to handle things like that as far as I can tell
- cqqxo4zV46cp 2y ago
  You are asking what the advantage of a notebook is. Can you truly not see a job / workflow in which inline plotting would be advantageous? I find that very hard to believe.
- williamcotton 2y ago
  My workflow normally starts in the shell (SQL, R/rush/ggplot csvtk, etc), moves to Jupyter (F# in .NET Interactive, with some SQL and R/ggplot inlined), and then to a Makefile when I’m ready to make some deliverables. I’ve got an ever growing tool set of F# data related functions that I’ve moved to a personal lib in my dotfiles and use in scripts, notebooks, etc.
- setopt 2y ago
  There’s also a hybrid version that I like: Write proper scripts (which are easier to e.g. push to HPC servers or deploy later), and explore them using something like Quarto (neé RMarkdown, renamed now that it supports Python). Then you still get a digital lab notebook that ties together scripts, plots, and documentation, but the scripts remain usable standalone.