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https://git.savannah.gnu.org/git/emacs/org-mode.git
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238 lines
9.6 KiB
Org Mode
238 lines
9.6 KiB
Org Mode
#+OPTIONS: H:3 num:nil toc:2 \n:nil @:t ::t |:t ^:t -:t f:t *:t TeX:t LaTeX:t skip:nil d:(HIDE) tags:not-in-toc
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#+STARTUP: align fold nodlcheck hidestars oddeven lognotestate
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#+SEQ_TODO: TODO(t) INPROGRESS(i) WAITING(w@) | DONE(d) CANCELED(c@)
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#+TAGS: Write(w) Update(u) Fix(f) Check(c)
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#+TITLE: Org-babel
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#+AUTHOR: Dan Davison, Eric Schulte
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#+EMAIL: davison at stats dot ox dot ac dot uk
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#+LANGUAGE: en
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#+CATEGORY: worg
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#+begin_html
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<div id="subtitle">
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<p>executable source code blocks in org-mode</p>
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</div>
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<div id="logo">
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<p>
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<img src="images/tower-of-babel.png" alt="images/tower-of-babel.png"
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title="And the Lord said, Behold, the people is one, and they have all one language; and this they begin to do; and now nothing will be restrained from them, which they have imagined to do. Go to, let us go down, and there confound their language, that they may not understand one another's speech. So the Lord scattered them abroad from thence upon the face of all the earth: and they left off to build the city. Therefore is the name of it called Babel; because the Lord did there confound the language of all the earth: and from thence did the Lord scatter them abroad upon the face of all the earth. Genesis 11:1-9"/>
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<div id="attr">
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from
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<a href="http://www.flickr.com/photos/23379658@N05/" title=""><b>Martijn Streefkerk</b></a>
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</div>
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</p>
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</div>
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#+end_html
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* Introduction
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Org-babel provides the following modifications to [[http://orgmode.org/manual/Literal-examples.html][the existing
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support]] for blocks of source code examples in the org-mode core.
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1. source code execution
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2. arguments to source code blocks
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3. exportation of source code blocks to files (literate programming)
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* Getting started
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Grab the latest code from the git repo at [[http://github.com/eschulte/org-babel/tree/master][github/org-babel]]
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#+begin_src sh
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git clone git://github.com/eschulte/org-babel.git
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#+end_src
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And add the following lines to your .emacs, replacing the path as
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appropriate. A good place to check that things are up and running
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would the examples in [[* Basic org-babel functionality][Basic org-babel functionality]].
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#+begin_src emacs-lisp
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(add-to-list 'load-path "/path/to/org-babel/lisp")
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(require 'org-babel-init)
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#+end_src
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* Basic org-babel functionality
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*** Source code execution
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For interpreted languages such as shell, python, R, etc, org-babel
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allows source blocks to be executed: the code is passed to the
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interpreter and you have control over what is done with the
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results of excecution. E.g. place point anywhere in the following
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block and use C-c C-c to run the code:
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[[http://www.ruby-lang.org/][Ruby]] source code
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#+begin_src ruby
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"This file was last evaluated on #{Date.today}"
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#+end_src
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Results of Ruby evaluation
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#+resname:
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: This file was last evaluated on 2009-08-09
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[[http://www.r-project.org/][R]] source code
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#+begin_src R :results value
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x = 4
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date()
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c(5, 10)
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#+end_src
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Results of R evaluation
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#+resname:
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| 5 |
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| 10 |
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*** What happens to the results?
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Org-babel provides two fundamentally different modes for capturing
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the results of code evaluation, specified by the :results header
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argument:
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**** :results value
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This means that the 'result' of code evaluation is defined to be
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the *value* of the last statement in the block. Thus with this
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setting, one can view the code block as a function with a return
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value. And not only can one view it that way, but you can
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actually use the return value of one source block as input for
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another (see later). This setting is the default.
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**** :results output
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With this setting, org-babel captures all the text output of the
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code block and places it in the org buffer. One can think of this
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as a 'scripting' mode: the code block contains a series of
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commands, and you get the output of all the commands. Unlike in
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the 'functional' mode specified by =:results value=, the code
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block has no return value. (This mode will be familiar to Sweave
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users).
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**** Additional :results settings
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*** Arguments to source code blocks
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In addition to evaluation of code blocks, org-babel allows them to
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be parameterised (i.e. have arguments). Thus source code blocks
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now have the status of *functions*.
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Inputs for fibonacci-seq
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#+tblname: fibonacci-inputs
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| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
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| 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
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in the Org-mode buffer this looks like
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: #+tblname: fibonacci-inputs
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: | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
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: | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
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[[http://www.gnu.org/software/emacs/manual/elisp.html][Emacs Lisp]] source code
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#+srcname: fibonacci-seq
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#+begin_src emacs-lisp :var fib-inputs=fibonacci-inputs
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(defun fibonacci (n)
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(if (or (= n 0) (= n 1))
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n
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(+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
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(mapcar (lambda (row)
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(mapcar #'fibonacci row)) fib-inputs)
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#+end_src
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in the Org-mode buffer this looks like
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: #+srcname: fibonacci-seq
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: #+begin_src emacs-lisp :var fib-inputs=fibonacci-inputs
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: (defun fibonacci (n)
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: (if (or (= n 0) (= n 1))
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: n
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: (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
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:
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: (mapcar (lambda (row)
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: (mapcar #'fibonacci row)) fib-inputs)
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: #+end_src
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Results of Emacs Lisp code evaluation
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#+resname:
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| 1 | 1 | 2 | 3 | 5 | 8 | 13 | 21 | 34 | 55 |
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| 1 | 3 | 8 | 21 | 55 | 144 | 377 | 987 | 2584 | 6765 |
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* A meta-programming language for org-mode
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* Spreadsheet plugins for org-mode in any language
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* Library of Babel
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What about those source code blocks which are so useful you want to
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have them available in every org-mode buffer?
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The [[file:library-of-babel.org][Library of Babel]] is an extensible collection of ready-made and
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easily-shortcut-callable source-code blocks for handling common
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tasks. Org-babel comes pre-populated with the source-code blocks
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located in the [[file:library-of-babel.org][library-of-babel.org]] file. It is possible to add
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source-code blocks from any org-mode file to the library by calling
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#+srcname: add-file-to-lob
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#+begin_src emacs-lisp
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(org-babel-lob-ingest "path/to/file.org")
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#+end_src
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* Reproducible research
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- output vs. value mode
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- file & graphical output
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- controlling export
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* Literate programming
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- org-babel-tangle
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- org-babel-load-file
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* Reference / Documentation
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*** Source Code block syntax
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The basic syntax of source-code blocks is as follows:
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: #+srcname: name
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: #+begin_src language header-arguments
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: body
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: #+end_src
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- name :: This name is associated with the source-code block. This is
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similar to the =#+TBLNAME= lines which can be used to name tables
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in org-mode files. By referencing the srcname of a source-code
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block it is possible to evaluate the block for other places,
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files, or from inside tables.
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- language :: The language of the code in the source-code block, valid
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values must be members of `org-babel-interpreters'.
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- header-arguments :: Header arguments control many facets of the
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input to, evaluation of, and output of source-code blocks. See
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the [[* Header Arguments][Header Arguments]] section for a complete review of available
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header arguments.
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- body :: The actual source code which will be evaluated. This can be
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edited with `org-edit-special'.
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**** Header Arguments
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- results :: results arguments specify what should be done with the
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output of source-code blocks
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- The following options are mutually exclusive, and specify how the
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results should be collected from the source-code block
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- value ::
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- output ::
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- The following options are mutually exclusive and specify what type
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of results the code block will return
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- vector :: specifies that the results should be interpreted as a
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multidimensional vector (even if the vector is
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trivial), and will be inserted into the org-mode file
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as a table
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- scalar :: specifies that the results should be interpreted as a
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scalar value, and will be inserted into the org-mode
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file as quoted text
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- file :: specifies that the results should be interpreted as the
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path to a file, and will be inserted into the org-mode
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file as a link
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- The following options specify how the results should be inserted
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into the org-mode file
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- replace :: the current results replace any previously inserted
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results from the code block
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- silent :: rather than being inserted into the org-mode file the
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results are echoed into the message bar
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- exports :: exports arguments specify what should be included in html
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or latex exports of the org-mode file
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- code :: the body of code is included into the exported file
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- results :: the results of evaluating the code is included in the
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exported file
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- both :: both the code and results are included in the exported
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file
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- none :: nothing is included in the exported file
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- tangle :: tangle arguments specify whether or not the source-code
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block should be included in tangled extraction of
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source-code files
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- yes :: the source-code block is exported to a source-code file
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named after the basename (name w/o extension) of the
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org-mode file
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- no :: (default) the source-code block is not exported to a
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source-code file
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- other :: any other string passed to the =tangle= header argument
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is interpreted as a file basename to which the block will
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be exported
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