Emacs + org-mode + python in reproducible research; SciPy 2013 Presentation

The Orgmode extension to Emacs has quite an elegant, flexible, and powerful way of doing what you want. Can be hard to wrap your mind around at the beginning but has good payoff once you're up to speed. Here's a video showing how one guy uses it with Python (though it integrates with multitude of languages, including R): this video Here's paper (itself from LaTeX generated by Orgmode) describing use of Orgmode for this kind of "reproducible research": link

I know it gets said a lot, but have you considered emacs and org-mode. Because, it goes a very long way for this. See this great talk showing its use with python. this video

Do check out org-mode, then. It is surprising how far that tool has been extended. Many of these features are actually under the label "reproducible research" nowdays. There was a really good talk given on this at a pypy convention a couple of years ago.[1] [1] this video

Seriously, try emacs. You want to see what color you have put in a css field?[1] Want to see the image you are referencing in a repl?[2] More amazingly, want to combine TeX, lisp, a markdown like language, and python/whatever in a single document? Try org-mode.[3][4] [1] link [2] link [3] link [4] this video

This SciPy presentation (Kitchin, John Carnegie Mellon University) on Emacs + org-mode + python in reproducible research is worth a watch: this video

I Agree with all those points. I've used org mode for a few things, but not for python notebooks. I remember seeing a great video a few years back on using python in org mode to make a research notebook. It really made me want to try org mode for literate / notebook style programming. I think it was this one: this video It sounds like org mode does not store images inline, since you don't like the b64 images in Jupyter? I imagine that could go both ways depending on what you want. Even for diffing, you might like to see that the image changed (though I generally agree that diffing images is not ideal). If you have to package images separately when sharing, then wouldn't inline images score a point for easier sharing? > use other languages that python Agreed, and that is powerful, but this also goes to my point. Jupyter is made for python and org mode isn't. Jupyter comes with python and libraries, where with Emacs you're on your own to figure out how to install and use different languages, and setup your environment so Emacs can see them. You're on your own to bring in images and plots, where Jupyter already understands commands that output images. > Plus, you get to use a proper text editor instead of editing on a browser textarea. Yes, but the editor is Emacs. :) For a lot of people the browser textarea is a bonus because it's the same thing you use everywhere. It's uncomplicated and non-technical and utterly consistent, even if lacking any power.