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Org-mode for Literate Programming and Reproducible Research =========================================================== This presentation introduces the use of Org-mode [1] as a platform for Reproducible Research and Literate Programming. It closely follows the related JSS paper [2] in both content and form. Examples are included demonstrating the interactive use of code blocks from within Org-mode documents. Familiarity with Emacs is assumed. Footnotes: [1] http://orgmode.org [2] http://www.jstatsoft.org/v46/i03 Instructions ============ The intent is to first introduce the concepts and syntax of Code Blocks in Org-mode documents, and then to work through some illustrative examples. Follow these steps to work through this presentation: 1. Ensure that either a recent version of Emacs (24 or greater) or the latest version of Org-mode is installed. 2. Evaluate the following Emacs Lisp snippet to configure your Emacs to allow code block execution. #+begin_src emacs-lisp (org-babel-do-load-languages 'org-babel-load-languages '((sh . t) (emacs-lisp . t) (lisp . t) (gnuplot . t) (R . t) (dot . t) (python . t))) (setq org-confirm-babel-evaluate nil) #+end_src 3. Open the babel.org file in Emacs, and step through the top level headings. The follow headings require special instructions: "Export -- supporting reproducible research" This heading will be exported to pdf in order to demonstrate the automatic code evaluation RR features of Org-mode. First narrow to only this heading with "C-x n S", then export to pdf with "C-c C-e d". After viewing the resulting pdf, widen with "C-x n w". "Tangling -- supporting literate programming" This heading will be tangled to produce two shell scripts in this directory. Tangle with "C-c C-v t", then run the resulting "./run" shell script. Be careful on slower or older hardware as this script is *very* CPU intensive -- like many gnuplot "movies" it relies on processing time to control frame rate. "Example -- Pascal's Triangle with Lisp and Dot" To run the examples in this heading simply interactively execute the code blocks with "C-c C-c" in order and view the results. For more information and trouble shooting the "Working With Source Code" portion of the Org-mode manual, available with "M-x info" and online at http://orgmode.org/manual/Working-With-Source-Code.html.
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Presentation demonstrating the use of code blocks in Org-mode
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