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

Enthought · 49.7K views · 2013-07-02 · 21:16

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Overview

John Kitchin shows how Emacs org-mode with Python lets researchers combine narrative, math, figures and executable code in one document. It exports to LaTeX, HTML and PDF, and he used it for papers and e-books.

On Hacker News

Repeatedly recommended as the canonical demo of org-mode for literate programming and reproducible research.

Recommended by 5 HN people across 6 months · HN mentions 2014–2018

Topics

Testing, debugging & developer toolsData science & statisticsPython, Ruby & scripting languages
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org-modeemacspythonliterate programmingscipy

What people said

cube_yellow · 2014-05 · Strong recommendation

A lot of people are starting to use org-mode for that kind of thing. Fully reproducible research in a single file. To check the work, just export the file to pdf/html/etc., or "C-c C-c" the code blocks as you read through in org-mode. It's fantastic. For python specifically, this video is a must watch: [VIDEO]

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dahart · 2018-04 · Recommendation

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: [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.

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rndn · 2015-06 · Recommendation

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

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Sources

Video by Enthought, played through YouTube.

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