Emacs + org-mode + python in reproducible research; SciPy 2013 Presentation
Why Hacker News recommends it
Repeatedly recommended as the canonical demo of org-mode for literate programming and reproducible research.
What it is
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.
Recommended by 5 HN commenters across 6 different months, 2014 to 2018.
What Hacker News said
Strong rec cube_yellow · 2014-05 · on “Let’s Make a Bubble Map”
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: [this video]
Recommends hsitz · 2014-03 · on “IPython: Beginners’ Guide”
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]
Recommends taeric · 2014-07 · on “Patoline: A modern digital typesetting system”
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]
Recommends taeric · 2014-08 · on “Show HN: Lit – a modern literate programming tool”
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]
Recommends taeric · 2014-08 · on “Typographic Programming Language”
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]
Recommends rndn · 2015-06 · on “Emacs for Data Science”
This SciPy presentation (Kitchin, John Carnegie Mellon University) on Emacs + org-mode + python in reproducible research is worth a watch: [this video]
Recommends dahart · 2018-04 · on “Jupyter, Mathematica, and the Future of the Research Paper”
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 po
Cites cube_yellow · 2014-05 · on “Anki – Powerful, intelligent flashcards”
If you use emacs org-mode, check out org-drill [LINK] . It uses the same algorithms, allows you to tweak everything, and you can keep your flashcards alongside the relevant notes/code/files/issues/ToDos/bookmarks/contacts/feeds/calendar-entry/emails/thesis/spreadsheets/journals/diagrams/pictures/evernotes/etc. [this video] , rather than in a totally separate program.