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GNU GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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|
||||
occurring solely as a consequence of using peer-to-peer transmission
|
||||
to receive a copy likewise does not require acceptance. However,
|
||||
nothing other than this License grants you permission to propagate or
|
||||
modify any covered work. These actions infringe copyright if you do
|
||||
not accept this License. Therefore, by modifying or propagating a
|
||||
covered work, you indicate your acceptance of this License to do so.
|
||||
|
||||
10. Automatic Licensing of Downstream Recipients.
|
||||
|
||||
Each time you convey a covered work, the recipient automatically
|
||||
receives a license from the original licensors, to run, modify and
|
||||
propagate that work, subject to this License. You are not responsible
|
||||
for enforcing compliance by third parties with this License.
|
||||
|
||||
An "entity transaction" is a transaction transferring control of an
|
||||
organization, or substantially all assets of one, or subdividing an
|
||||
organization, or merging organizations. If propagation of a covered
|
||||
work results from an entity transaction, each party to that
|
||||
transaction who receives a copy of the work also receives whatever
|
||||
licenses to the work the party's predecessor in interest had or could
|
||||
give under the previous paragraph, plus a right to possession of the
|
||||
Corresponding Source of the work from the predecessor in interest, if
|
||||
the predecessor has it or can get it with reasonable efforts.
|
||||
|
||||
You may not impose any further restrictions on the exercise of the
|
||||
rights granted or affirmed under this License. For example, you may
|
||||
not impose a license fee, royalty, or other charge for exercise of
|
||||
rights granted under this License, and you may not initiate litigation
|
||||
(including a cross-claim or counterclaim in a lawsuit) alleging that
|
||||
any patent claim is infringed by making, using, selling, offering for
|
||||
sale, or importing the Program or any portion of it.
|
||||
|
||||
11. Patents.
|
||||
|
||||
A "contributor" is a copyright holder who authorizes use under this
|
||||
License of the Program or a work on which the Program is based. The
|
||||
work thus licensed is called the contributor's "contributor version".
|
||||
|
||||
A contributor's "essential patent claims" are all patent claims
|
||||
owned or controlled by the contributor, whether already acquired or
|
||||
hereafter acquired, that would be infringed by some manner, permitted
|
||||
by this License, of making, using, or selling its contributor version,
|
||||
but do not include claims that would be infringed only as a
|
||||
consequence of further modification of the contributor version. For
|
||||
purposes of this definition, "control" includes the right to grant
|
||||
patent sublicenses in a manner consistent with the requirements of
|
||||
this License.
|
||||
|
||||
Each contributor grants you a non-exclusive, worldwide, royalty-free
|
||||
patent license under the contributor's essential patent claims, to
|
||||
make, use, sell, offer for sale, import and otherwise run, modify and
|
||||
propagate the contents of its contributor version.
|
||||
|
||||
In the following three paragraphs, a "patent license" is any express
|
||||
agreement or commitment, however denominated, not to enforce a patent
|
||||
(such as an express permission to practice a patent or covenant not to
|
||||
sue for patent infringement). To "grant" such a patent license to a
|
||||
party means to make such an agreement or commitment not to enforce a
|
||||
patent against the party.
|
||||
|
||||
If you convey a covered work, knowingly relying on a patent license,
|
||||
and the Corresponding Source of the work is not available for anyone
|
||||
to copy, free of charge and under the terms of this License, through a
|
||||
publicly available network server or other readily accessible means,
|
||||
then you must either (1) cause the Corresponding Source to be so
|
||||
available, or (2) arrange to deprive yourself of the benefit of the
|
||||
patent license for this particular work, or (3) arrange, in a manner
|
||||
consistent with the requirements of this License, to extend the patent
|
||||
license to downstream recipients. "Knowingly relying" means you have
|
||||
actual knowledge that, but for the patent license, your conveying the
|
||||
covered work in a country, or your recipient's use of the covered work
|
||||
in a country, would infringe one or more identifiable patents in that
|
||||
country that you have reason to believe are valid.
|
||||
|
||||
If, pursuant to or in connection with a single transaction or
|
||||
arrangement, you convey, or propagate by procuring conveyance of, a
|
||||
covered work, and grant a patent license to some of the parties
|
||||
receiving the covered work authorizing them to use, propagate, modify
|
||||
or convey a specific copy of the covered work, then the patent license
|
||||
you grant is automatically extended to all recipients of the covered
|
||||
work and works based on it.
|
||||
|
||||
A patent license is "discriminatory" if it does not include within
|
||||
the scope of its coverage, prohibits the exercise of, or is
|
||||
conditioned on the non-exercise of one or more of the rights that are
|
||||
specifically granted under this License. You may not convey a covered
|
||||
work if you are a party to an arrangement with a third party that is
|
||||
in the business of distributing software, under which you make payment
|
||||
to the third party based on the extent of your activity of conveying
|
||||
the work, and under which the third party grants, to any of the
|
||||
parties who would receive the covered work from you, a discriminatory
|
||||
patent license (a) in connection with copies of the covered work
|
||||
conveyed by you (or copies made from those copies), or (b) primarily
|
||||
for and in connection with specific products or compilations that
|
||||
contain the covered work, unless you entered into that arrangement,
|
||||
or that patent license was granted, prior to 28 March 2007.
|
||||
|
||||
Nothing in this License shall be construed as excluding or limiting
|
||||
any implied license or other defenses to infringement that may
|
||||
otherwise be available to you under applicable patent law.
|
||||
|
||||
12. No Surrender of Others' Freedom.
|
||||
|
||||
If conditions are imposed on you (whether by court order, agreement or
|
||||
otherwise) that contradict the conditions of this License, they do not
|
||||
excuse you from the conditions of this License. If you cannot convey a
|
||||
covered work so as to satisfy simultaneously your obligations under this
|
||||
License and any other pertinent obligations, then as a consequence you may
|
||||
not convey it at all. For example, if you agree to terms that obligate you
|
||||
to collect a royalty for further conveying from those to whom you convey
|
||||
the Program, the only way you could satisfy both those terms and this
|
||||
License would be to refrain entirely from conveying the Program.
|
||||
|
||||
13. Use with the GNU Affero General Public License.
|
||||
|
||||
Notwithstanding any other provision of this License, you have
|
||||
permission to link or combine any covered work with a work licensed
|
||||
under version 3 of the GNU Affero General Public License into a single
|
||||
combined work, and to convey the resulting work. The terms of this
|
||||
License will continue to apply to the part which is the covered work,
|
||||
but the special requirements of the GNU Affero General Public License,
|
||||
section 13, concerning interaction through a network will apply to the
|
||||
combination as such.
|
||||
|
||||
14. Revised Versions of this License.
|
||||
|
||||
The Free Software Foundation may publish revised and/or new versions of
|
||||
the GNU General Public License from time to time. Such new versions will
|
||||
be similar in spirit to the present version, but may differ in detail to
|
||||
address new problems or concerns.
|
||||
|
||||
Each version is given a distinguishing version number. If the
|
||||
Program specifies that a certain numbered version of the GNU General
|
||||
Public License "or any later version" applies to it, you have the
|
||||
option of following the terms and conditions either of that numbered
|
||||
version or of any later version published by the Free Software
|
||||
Foundation. If the Program does not specify a version number of the
|
||||
GNU General Public License, you may choose any version ever published
|
||||
by the Free Software Foundation.
|
||||
|
||||
If the Program specifies that a proxy can decide which future
|
||||
versions of the GNU General Public License can be used, that proxy's
|
||||
public statement of acceptance of a version permanently authorizes you
|
||||
to choose that version for the Program.
|
||||
|
||||
Later license versions may give you additional or different
|
||||
permissions. However, no additional obligations are imposed on any
|
||||
author or copyright holder as a result of your choosing to follow a
|
||||
later version.
|
||||
|
||||
15. Disclaimer of Warranty.
|
||||
|
||||
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
|
||||
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
|
||||
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
|
||||
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
|
||||
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
|
||||
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
|
||||
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
|
||||
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
|
||||
|
||||
16. Limitation of Liability.
|
||||
|
||||
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
|
||||
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
|
||||
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
|
||||
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
|
||||
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
|
||||
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
|
||||
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
|
||||
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
|
||||
SUCH DAMAGES.
|
||||
|
||||
17. Interpretation of Sections 15 and 16.
|
||||
|
||||
If the disclaimer of warranty and limitation of liability provided
|
||||
above cannot be given local legal effect according to their terms,
|
||||
reviewing courts shall apply local law that most closely approximates
|
||||
an absolute waiver of all civil liability in connection with the
|
||||
Program, unless a warranty or assumption of liability accompanies a
|
||||
copy of the Program in return for a fee.
|
||||
|
||||
END OF TERMS AND CONDITIONS
|
||||
|
||||
How to Apply These Terms to Your New Programs
|
||||
|
||||
If you develop a new program, and you want it to be of the greatest
|
||||
possible use to the public, the best way to achieve this is to make it
|
||||
free software which everyone can redistribute and change under these terms.
|
||||
|
||||
To do so, attach the following notices to the program. It is safest
|
||||
to attach them to the start of each source file to most effectively
|
||||
state the exclusion of warranty; and each file should have at least
|
||||
the "copyright" line and a pointer to where the full notice is found.
|
||||
|
||||
<one line to give the program's name and a brief idea of what it does.>
|
||||
Copyright (C) <year> <name of author>
|
||||
|
||||
This program is free software: you can redistribute it and/or modify
|
||||
it under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
This program is distributed in the hope that it will be useful,
|
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
GNU General Public License for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with this program. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Also add information on how to contact you by electronic and paper mail.
|
||||
|
||||
If the program does terminal interaction, make it output a short
|
||||
notice like this when it starts in an interactive mode:
|
||||
|
||||
<program> Copyright (C) <year> <name of author>
|
||||
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
|
||||
This is free software, and you are welcome to redistribute it
|
||||
under certain conditions; type `show c' for details.
|
||||
|
||||
The hypothetical commands `show w' and `show c' should show the appropriate
|
||||
parts of the General Public License. Of course, your program's commands
|
||||
might be different; for a GUI interface, you would use an "about box".
|
||||
|
||||
You should also get your employer (if you work as a programmer) or school,
|
||||
if any, to sign a "copyright disclaimer" for the program, if necessary.
|
||||
For more information on this, and how to apply and follow the GNU GPL, see
|
||||
<http://www.gnu.org/licenses/>.
|
||||
|
||||
The GNU General Public License does not permit incorporating your program
|
||||
into proprietary programs. If your program is a subroutine library, you
|
||||
may consider it more useful to permit linking proprietary applications with
|
||||
the library. If this is what you want to do, use the GNU Lesser General
|
||||
Public License instead of this License. But first, please read
|
||||
<http://www.gnu.org/philosophy/why-not-lgpl.html>.
|
|
@ -1,4 +0,0 @@
|
|||
org-babel.el --- executable source code blocks in org-mode
|
||||
|
||||
- for information on org see the http://org-mode.org
|
||||
- for information on org-babel see the http://eschulte.github.com/org-babel/
|
Binary file not shown.
Before Width: | Height: | Size: 27 KiB |
Binary file not shown.
Before Width: | Height: | Size: 101 KiB |
Binary file not shown.
Before Width: | Height: | Size: 258 KiB |
Binary file not shown.
Before Width: | Height: | Size: 2.0 KiB |
|
@ -1,39 +0,0 @@
|
|||
|
||||
* Introduction
|
||||
[[http:orgmode.org][Emacs org-mode]] is an exceptionally rich emacs mode based around
|
||||
hierachically-structured text documents. The environment that has
|
||||
been designed around this central concept provides support for many
|
||||
different usage modes. At a high level, important areas include note
|
||||
taking, project planning and document publishing. Working with the
|
||||
text files is made efficient by document navigation and editing
|
||||
facilities which include creation, folding, restructuring and
|
||||
repositioning of subtrees and list items, and a plain-text
|
||||
spreadsheet for tabular data. Nevertheless, org is unobtrusive: an
|
||||
org-mode buffer may make use of only the most basic features, or
|
||||
even none at all. It is notoriously difficult to describe org
|
||||
briefly: good starting points include [...].
|
||||
|
||||
Org therefore provides an ideal environment for literate
|
||||
programming: chunks of source code in any language can be embedded
|
||||
within the org-mode text file. The hierarchical structure of the
|
||||
document may reflect, for example, the logic of the problem being
|
||||
addressed or the structure of the project within which the problem
|
||||
arises. Embedding source code within Org documents means that, for
|
||||
example, the project-planning features of org-mode are immediately
|
||||
available, and that the document may be published to HTML and LaTeX
|
||||
with appropriate formatting of the code.
|
||||
|
||||
In addition to the standard org functionality, org provides
|
||||
convenient switching between the org buffer with embedded code, and
|
||||
a separate buffer in the native language mode. Thus literate
|
||||
programming with org-mode does not impact upon language-specific
|
||||
modes for working with source code in emacs. For example, when
|
||||
working with [[http://www.r-project.org/][R]] code, you do not leave [[http://ess.r-project.org/][ess-mode]] until you flick back
|
||||
from the code buffer to view it embedded within an org buffer, which
|
||||
may also contain chunks of code in other languages.
|
||||
|
||||
* Org-Babel
|
||||
Org-Babel provides several extensions to the above-described method of
|
||||
working with source code in org mode:
|
||||
1. Code block execution for interpreted languages (python, ruby, shell, R, perl)
|
||||
2. [...]
|
|
@ -3,23 +3,6 @@
|
|||
#+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
|
||||
#+STARTUP: odd hideblocks
|
||||
|
||||
#+begin_html
|
||||
<div id="subtitle">
|
||||
<p>
|
||||
off-the-shelf functions for data analysis and plotting using <a href="org-babel-worg.html">org-babel</a><br/>
|
||||
<a href="http://downlode.org/Etext/library_of_babel.html">Full text of the Borges short story</a>
|
||||
</p>
|
||||
</div>
|
||||
<div id="logo">
|
||||
<p>
|
||||
<img src="images/library-of-babel.png" alt="images/tower-of-babel.png" />
|
||||
<div id="attr">
|
||||
from <a href="http://www.poetryfoundation.org/harriet/2008/01/random-poetry-02/">poetryfoundation.org</a>
|
||||
</div>
|
||||
</p>
|
||||
</div>
|
||||
#+end_html
|
||||
|
||||
* Introduction
|
||||
The Library of Babel is an extensible collection of ready-made and
|
||||
easily-shortcut-callable source-code blocks for handling common
|
||||
|
|
|
@ -1,863 +0,0 @@
|
|||
#+OPTIONS: H:3 num:nil toc:2 \n:nil @:t ::t |:t ^:{} -:t f:t *:t TeX:t LaTeX:t skip:nil d:(HIDE) tags:not-in-toc
|
||||
#+STARTUP: align fold nodlcheck hidestars oddeven lognotestate hideblocks
|
||||
#+SEQ_TODO: TODO(t) INPROGRESS(i) WAITING(w@) | DONE(d) CANCELED(c@)
|
||||
#+TAGS: Write(w) Update(u) Fix(f) Check(c)
|
||||
#+TITLE: Org-babel
|
||||
#+AUTHOR: Eric Schulte, Dan Davison
|
||||
#+EMAIL: schulte.eric at gmail dot com, davison at stats dot ox dot ac dot uk
|
||||
#+LANGUAGE: en
|
||||
#+CATEGORY: worg
|
||||
|
||||
# #+INFOJS_OPT: view:content
|
||||
|
||||
#+begin_html
|
||||
<div id="subtitle">
|
||||
<p>executable source code blocks in org-mode</p>
|
||||
</div>
|
||||
<div id="logo">
|
||||
<p>
|
||||
<img src="images/tower-of-babel.png" alt="images/tower-of-babel.png"/>
|
||||
<div id="attr">
|
||||
The Tower of Babel by
|
||||
<a href="http://commons.wikimedia.org/wiki/Pieter_Brueghel_the_Elder" title="">
|
||||
<b>Pieter Brueghel the Elder</b>
|
||||
</a>
|
||||
</div>
|
||||
<p>
|
||||
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. Genesis
|
||||
11:1-9
|
||||
</p>
|
||||
</p>
|
||||
</div>
|
||||
#+end_html
|
||||
|
||||
#+begin_html
|
||||
<p>
|
||||
</p>
|
||||
#+end_html
|
||||
|
||||
* Introduction
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: introduction
|
||||
:END:
|
||||
Org-babel is an extension to the very excellent [[http://orgmode.org/][Org-mode]], providing
|
||||
the ability to execute source code in many different languages
|
||||
within org-mode documents. The results of code execution --- text,
|
||||
tables and graphics --- can be integrated into the powerful
|
||||
publishing facilities of org-mode. Org-mode is an [[http://www.gnu.org/software/emacs/][Emacs]] major mode
|
||||
for doing almost anything with plain text. If you are not familiar
|
||||
with Org-mode please take a moment to read [[http://orgmode.org/][the Org-mode homepage]]
|
||||
before continuing.
|
||||
|
||||
Org-babel provides the following modifications to [[http://orgmode.org/manual/Literal-examples.html][the existing
|
||||
support]] for blocks of source code examples in the org-mode core.
|
||||
|
||||
1. Interactive source code execution
|
||||
2. Arguments to source code blocks
|
||||
3. Exportation of source code blocks to files (literate programming)
|
||||
|
||||
* Getting started
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: getting-started
|
||||
:END:
|
||||
|
||||
1) Grab the latest code from the git repo at [[http://github.com/eschulte/org-babel/tree/master][github/org-babel]]
|
||||
#+begin_src sh
|
||||
git clone git://github.com/eschulte/org-babel.git
|
||||
#+end_src
|
||||
|
||||
2) Add the following lines to your .emacs, replacing the path as
|
||||
appropriate. A good place to check that things are up and running
|
||||
would the examples in [[* Basic org-babel functionality][Basic org-babel functionality]].
|
||||
#+begin_src emacs-lisp
|
||||
(add-to-list 'load-path "/path/to/org-babel/lisp")
|
||||
(require 'org-babel-init)
|
||||
#+end_src
|
||||
|
||||
3) Finally, activate the subset of supported Org-babel languages
|
||||
which you want to be able to execute on your system. As an
|
||||
example, the following activates python, ruby and R. For a full
|
||||
list of languages, with notes on their dependencies see the
|
||||
[[#reference-and-documentation][Reference / Documentation]] section below.
|
||||
#+begin_src emacs-lisp
|
||||
(require 'org-babel-python)
|
||||
(require 'org-babel-ruby)
|
||||
(require 'org-babel-R)
|
||||
;;
|
||||
;; Once you've activated languages, load the library of babel to
|
||||
;; make pre-built helper functions available in the languages you will be using.
|
||||
(org-babel-load-library-of-babel)
|
||||
#+end_src
|
||||
|
||||
* Basic org-babel functionality
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: basic-functionality
|
||||
:END:
|
||||
*** Source code blocks
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: source-code-blocks
|
||||
:END:
|
||||
|
||||
Org-babel is all about *source code blocks* in org mode. These are
|
||||
blocks of code (in whatever language), that can occur anywhere in
|
||||
an org-mode file. For example, the following is a source block
|
||||
containing [[http://www.ruby-lang.org/][ruby]] code:
|
||||
|
||||
: #+begin_src ruby
|
||||
: "This file was last evaluated on #{Date.today}"
|
||||
: #+end_src
|
||||
|
||||
If you are unfamiliar with the notion of a source code block in
|
||||
org-mode, please have a look at the [[http://orgmode.org/manual/Literal-examples.html][relevant manual section]] before
|
||||
proceding.
|
||||
|
||||
Note that above is what the source block looks like in the org-mode
|
||||
file. We had to take [[http://orgmode.org/manual/Literal-examples.html#Literal-examples][special steps]] to make it look that way in the
|
||||
HTML output. Normally, when exported to HTML, source blocks are
|
||||
fontified according to their language, and the begin_src...end_src
|
||||
mark-up is omitted, like this:
|
||||
|
||||
#+begin_src ruby
|
||||
"This file was last evaluated on #{Date.today}"
|
||||
#+end_src
|
||||
|
||||
From now on, if you are viewing the HTML version, you will see the
|
||||
HTML output only. However, much of this document consists of
|
||||
interactive examples, and therefore in order to get a feeling for the
|
||||
mechanics of Org-babel it might make most sense to grab the plain text
|
||||
version of this file
|
||||
#+HTML: <a href="org-babel-worg.org">org-babel-worg.org</a>
|
||||
and work through it in Emacs. Alternatively the htmlized
|
||||
version of the plain text of this file at
|
||||
#+HTML: <a href="org-babel-worg.org.html">org-babel-worg.html</a>
|
||||
allows the plain text version to be viewed (non-interactively) in a web browser.
|
||||
*** Source code execution
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: source-code-execution
|
||||
:END:
|
||||
For interpreted languages such as shell, python, R, etc, org-babel
|
||||
allows source blocks to be executed: the code is passed to the
|
||||
interpreter and you have control over what is done with the results of
|
||||
execution. Here are three examples of code blocks in three different
|
||||
languages, followed by their output. If you are viewing the plain text
|
||||
version of this document in emacs, place point anywhere inside the
|
||||
blocks and use =C-c C-c= to run the code[fn:1] (and feel free to alter
|
||||
it!).
|
||||
|
||||
**** Ruby
|
||||
#+begin_src ruby
|
||||
"This file was last evaluated on #{Date.today}"
|
||||
#+end_src
|
||||
|
||||
#+resname:
|
||||
: This file was last evaluated on 2009-08-09
|
||||
|
||||
**** [[http://www.r-project.org/][R]]
|
||||
#+begin_src R :results value
|
||||
matrix(rnorm(6), nrow=2)
|
||||
#+end_src
|
||||
|
||||
#+resname:
|
||||
| -0.138279734486552 | -2.2476234005706 | -0.0839549402407832 |
|
||||
| 0.0730510956002737 | 0.0634015508602321 | 0.174013159381603 |
|
||||
|
||||
**** [[http://ditaa.sourceforge.net/][ditaa]]
|
||||
#+begin_src ditaa :file images/blue.png :cmdline -r
|
||||
+---------+
|
||||
| cBLU |
|
||||
| |
|
||||
| +----+
|
||||
| |cPNK|
|
||||
| | |
|
||||
+----+----+
|
||||
#+end_src
|
||||
|
||||
#+resname:
|
||||
[[file:images/blue.png]]
|
||||
|
||||
*** Source code block syntax
|
||||
|
||||
The basic syntax of source-code blocks in Org-babel is as follows:
|
||||
|
||||
: #+srcname: name(arguments)
|
||||
: #+begin_src language header-arguments
|
||||
: body
|
||||
: #+end_src
|
||||
|
||||
- name :: This name is associated with the source-code block. This is
|
||||
similar to the =#+tblname= lines which can be used to name tables
|
||||
in org-mode files. By referencing the srcname of a source-code
|
||||
block it is possible to evaluate the block from other places,
|
||||
files, or from inside tables.
|
||||
- arguments :: Code blocks can have arguments (see [[#arguments-to-source-code-blocks][below]]) which are
|
||||
provided using a familiar function-call syntax similar
|
||||
to (e.g.) python or R.
|
||||
- language :: The language of the code in the source-code block. Valid
|
||||
values must be members of `org-babel-interpreters'.
|
||||
- header-arguments :: Header arguments control many facets of the
|
||||
evaluation and output of source-code blocks. See the [[* Header Arguments][Header
|
||||
Arguments]] section for a complete review of available header
|
||||
arguments.
|
||||
- body :: The actual source code which will be evaluated. An
|
||||
important key-binding to become familiar with is =C-c
|
||||
'=. This calls `org-edit-special' which brings up an edit
|
||||
buffer containing the code using the emacs major mode
|
||||
appropriate to the language.
|
||||
|
||||
*** What happens to the results?
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: results
|
||||
:END:
|
||||
Org-babel provides two fundamentally different modes for capturing
|
||||
the results of code evaluation, specified by the =:results= header
|
||||
argument.
|
||||
**** =:results value= (functional mode)
|
||||
This means that the 'result' of code evaluation is defined to be
|
||||
the *value* of the last statement in the block. Thus with this
|
||||
setting, one can view the code block as a function with a return
|
||||
value. And not only can you view it that way, but you can
|
||||
actually use the return value of one source block as input for
|
||||
another (see [[meta-programming-language]]). This setting is the
|
||||
default.
|
||||
|
||||
As an example, consider the following block of python code and its
|
||||
output.
|
||||
|
||||
#+begin_src python :results value
|
||||
import time
|
||||
print("Hello, today's date is %s" % time.ctime())
|
||||
print('Two plus two is')
|
||||
2 + 2
|
||||
#+end_src
|
||||
|
||||
#+resname:
|
||||
: 4
|
||||
|
||||
Notice that in functional mode, the output consists of the value of
|
||||
the last statement, and nothing else.
|
||||
|
||||
**** =:results output= (scripting mode)
|
||||
With this setting, org-babel captures all the text output of the
|
||||
code block and places it in the org buffer. One can think of this
|
||||
as a 'scripting' mode: the code block contains a series of
|
||||
commands, and you get the output of all the commands. Unlike in
|
||||
the 'functional' mode, the code block has no return value. (This
|
||||
mode will be more familiar to Sweave users).
|
||||
|
||||
Now consider the result of evaluating the same source block as
|
||||
before, but under scripting mode.
|
||||
|
||||
#+srcname: name
|
||||
#+begin_src python :results output
|
||||
import time
|
||||
print("Hello, today's date is %s" % time.ctime())
|
||||
print('Two plus two is')
|
||||
2 + 2
|
||||
#+end_src
|
||||
|
||||
#+resname: name
|
||||
: Hello, today's date is Fri Sep 4 19:49:06 2009
|
||||
: Two plus two is
|
||||
|
||||
Again, we got what we asked for: all the text output (stdout) from
|
||||
python. Since we didn't print the last value (2 + 2), we didn't get it
|
||||
in our output.
|
||||
|
||||
*** Arguments to source code blocks
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: arguments-to-source-code-blocks
|
||||
:END:
|
||||
In addition to evaluation of code blocks, org-babel allows them to
|
||||
be parameterised (i.e. have arguments). Thus source code blocks
|
||||
now have the status of *functions*. Arguments to code blocks can
|
||||
be used in both functional and scripting mode.
|
||||
|
||||
**** Simple example of using a source block as a function
|
||||
|
||||
First let's look at a very simple example. The following source
|
||||
block defines an org-babel function that will square its input.
|
||||
|
||||
#+srcname: square(x)
|
||||
#+begin_src python
|
||||
x*x
|
||||
#+end_src
|
||||
|
||||
In the org-mode file that looks like this:
|
||||
: #+srcname: square(x)
|
||||
: #+begin_src python
|
||||
: x*x
|
||||
: #+end_src
|
||||
|
||||
|
||||
Now we use the source block:
|
||||
|
||||
: #+lob: square(x=6)
|
||||
(/for information on the/ =lob= /syntax see [[library-of-babel]]/)
|
||||
|
||||
#+lob: square(x=6)
|
||||
|
||||
#+resname: square(x=6)
|
||||
: 36
|
||||
|
||||
**** A more complex example: using an org-table as input
|
||||
|
||||
In this example we're going to define a function to compute a
|
||||
Fibonacci sequence, and we're going to make it take its input
|
||||
from a table in the org-mode buffer.
|
||||
|
||||
Here are the inputs for fibonacci-seq:
|
||||
|
||||
#+tblname: fibonacci-inputs
|
||||
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
|
||||
| 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
|
||||
|
||||
in the Org-mode buffer this looks like
|
||||
: #+tblname: fibonacci-inputs
|
||||
: | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
|
||||
: | 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
|
||||
|
||||
[[http://www.gnu.org/software/emacs/manual/elisp.html][Emacs Lisp]] source code
|
||||
#+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
|
||||
#+begin_src emacs-lisp
|
||||
(defun fibonacci (n)
|
||||
(if (or (= n 0) (= n 1))
|
||||
n
|
||||
(+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
|
||||
|
||||
(mapcar (lambda (row)
|
||||
(mapcar #'fibonacci row)) fib-inputs)
|
||||
#+end_src
|
||||
|
||||
in the Org-mode buffer this looks like
|
||||
: #+srcname: fibonacci-seq(fib-inputs=fibonacci-inputs)
|
||||
: #+begin_src emacs-lisp
|
||||
: (defun fibonacci (n)
|
||||
: (if (or (= n 0) (= n 1))
|
||||
: n
|
||||
: (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))
|
||||
:
|
||||
: (mapcar (lambda (row)
|
||||
: (mapcar #'fibonacci row)) fib-inputs)
|
||||
: #+end_src
|
||||
|
||||
Results of Emacs Lisp code evaluation
|
||||
#+resname:
|
||||
| 1 | 1 | 2 | 3 | 5 | 8 | 13 | 21 | 34 | 55 |
|
||||
| 1 | 3 | 8 | 21 | 55 | 144 | 377 | 987 | 2584 | 6765 |
|
||||
|
||||
* A meta-programming language for org-mode
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: meta-programming-language
|
||||
:END:
|
||||
|
||||
Since information can pass freely between source-code blocks and
|
||||
org-mode tables you can mix and match languages using each language
|
||||
for those tasks to which it is suited. This makes Org-mode files with
|
||||
Org-babel into a kind of meta-functional programming language in which
|
||||
functions from many languages can work together.
|
||||
|
||||
As an example, lets take some system diagnostics in the shell, and
|
||||
then graph them with R.
|
||||
|
||||
1. First we create a code block containing shell code creating a list
|
||||
of the directories in our home directory, together with their
|
||||
sizes. Org-babel automatically converts the output into an org
|
||||
table.
|
||||
|
||||
#+srcname: directories
|
||||
#+begin_src bash :results replace
|
||||
cd ~ && du -sc * |grep -v total
|
||||
#+end_src
|
||||
|
||||
#+resname: directories
|
||||
| 72 | "Desktop" |
|
||||
| 12156104 | "Documents" |
|
||||
| 3482440 | "Downloads" |
|
||||
| 2901720 | "Library" |
|
||||
| 57344 | "Movies" |
|
||||
| 16548024 | "Music" |
|
||||
| 120 | "News" |
|
||||
| 7649472 | "Pictures" |
|
||||
| 0 | "Public" |
|
||||
| 152224 | "Sites" |
|
||||
| 8 | "System" |
|
||||
| 56 | "bin" |
|
||||
| 3821872 | "mail" |
|
||||
| 10605392 | "src" |
|
||||
| 1264 | "tools" |
|
||||
2. Now we use a single line of R code to plot the data as a
|
||||
pie-chart. Note the way that this source block uses the =srcname=
|
||||
of the previous source block to obtain the data.
|
||||
#+srcname: directory-pie-chart(dirs = directories)
|
||||
#+begin_src R :session R-pie-example
|
||||
pie(dirs[,1], labels = dirs[,2])
|
||||
#+end_src
|
||||
[[file:images/dirs.png]]
|
||||
|
||||
* Multilingual spreadsheet plugins for org-mode
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: spreadsheet
|
||||
:END:
|
||||
Not only can Org-babel pass entire tables of data to source code
|
||||
blocks (see [[arguments-to-source-code-blocks]]), Org-babel can also be
|
||||
used to call source code blocks from *within* tables using the
|
||||
Org-mode's [[http://orgmode.org/manual/The-spreadsheet.html#The-spreadsheet][existing spreadsheet functionality]].
|
||||
|
||||
*** Example 1: data summaries using R
|
||||
As a simple example, we'll fill in a cell in an org-table with the
|
||||
average value of a few numbers. First, let's make some data. The
|
||||
following source block creates an org table filled with five random
|
||||
numbers between 0 and 1.
|
||||
|
||||
#+srcname: tbl-example-data()
|
||||
#+begin_src R
|
||||
runif(n=5, min=0, max=1)
|
||||
#+end_src
|
||||
|
||||
#+resname: tbl-example-data
|
||||
| 0.850250755203888 |
|
||||
| 0.745323235634714 |
|
||||
| 0.845673063071445 |
|
||||
| 0.761818468105048 |
|
||||
| 0.525476417969912 |
|
||||
|
||||
Now we define a source block to do the calculation we want.
|
||||
#+srcname: R-mean(x)
|
||||
#+begin_src R
|
||||
mean(x)
|
||||
#+end_src
|
||||
|
||||
Finally we create the table which is going to make use of the R
|
||||
code. This is done using the =sbe= ('source block evaluate') macro in
|
||||
the table formula line.
|
||||
#+tblname: summaries
|
||||
| mean |
|
||||
|-------------------|
|
||||
| 0.533130449522286 |
|
||||
#+TBLFM: @2$1='(sbe "R-mean" (x "generate-data()"))
|
||||
|
||||
To recalculate the table formula, use =C-u C-c C-c= in the
|
||||
table. Notice that as things stand the calculated value doesn't
|
||||
change, because the data (held in the table above named
|
||||
"tbl-example-data") are static. However, if you delete that data table
|
||||
then the reference will be interpreted as a reference to the source
|
||||
block responsible for generating the data; each time the table formula
|
||||
is recalculated the source block will be evaluated again, and
|
||||
therefore the calculated average value will change.
|
||||
|
||||
*** Example 2: Org-babel test suite
|
||||
While developing Org-babel, we have used a suite of tests implemented
|
||||
as a large Org-mode table. To run the entire test suite you simply
|
||||
evaluate the table with =C-u C-c C-c=, and all of the tests are run,
|
||||
the results are compared with expectations, and the table is updated
|
||||
with results and pass/fail statistics.
|
||||
|
||||
Here's a sample of our test suite.
|
||||
|
||||
#+TBLNAME: org-babel-tests
|
||||
| functionality | block | arg | expected | results | pass |
|
||||
|------------------+--------------+-----+-------------+-------------+------|
|
||||
| basic evaluation | | | | | pass |
|
||||
|------------------+--------------+-----+-------------+-------------+------|
|
||||
| emacs lisp | basic-elisp | 2 | 4 | 4 | pass |
|
||||
| shell | basic-shell | | 6 | 6 | pass |
|
||||
| ruby | basic-ruby | | org-babel | org-babel | pass |
|
||||
| python | basic-python | | hello world | hello world | pass |
|
||||
| R | basic-R | | 13 | 13 | pass |
|
||||
#+TBLFM: $5='(if (= (length $3) 1) (sbe $2 (n $3)) (sbe $2)) :: $6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5))
|
||||
|
||||
**** code blocks for tests
|
||||
|
||||
#+srcname: basic-elisp(n)
|
||||
#+begin_src emacs-lisp
|
||||
(* 2 n)
|
||||
#+end_src
|
||||
|
||||
#+srcname: basic-shell
|
||||
#+begin_src sh :results silent
|
||||
expr 1 + 5
|
||||
#+end_src
|
||||
|
||||
#+srcname: date-simple
|
||||
#+begin_src sh :results silent
|
||||
date
|
||||
#+end_src
|
||||
|
||||
#+srcname: basic-ruby
|
||||
#+begin_src ruby :results silent
|
||||
"org-babel"
|
||||
#+end_src
|
||||
|
||||
#+srcname: basic-python
|
||||
#+begin_src python :results silent
|
||||
'hello world'
|
||||
#+end_src
|
||||
|
||||
#+srcname: basic-R
|
||||
#+begin_src R :results silent
|
||||
b <- 9
|
||||
b + 4
|
||||
#+end_src
|
||||
|
||||
* The Library of Babel
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: library-of-babel
|
||||
:END:
|
||||
#+begin_html
|
||||
<div id="logo">
|
||||
<p>
|
||||
<img src="images/library-of-babel-clayette.png" />
|
||||
<div id="attr">
|
||||
The Library of Babel, by Pierre Clayette
|
||||
<p>
|
||||
<a href="http://downlode.org/Etext/library_of_babel.html">Full text of the Borges short story</a>
|
||||
</p>
|
||||
</div>
|
||||
</p>
|
||||
</div>
|
||||
#+end_html
|
||||
|
||||
As we saw above with the [[*Simple%20example%20of%20using%20a%20source%20block%20as%20a%20function][=square=]] example, once a source block
|
||||
function has been defined it can be called using the following short
|
||||
=lob= notation:
|
||||
|
||||
: #+lob: square(x=6)
|
||||
|
||||
But what about those source code blocks which are so useful you want
|
||||
to have them available in every org-mode buffer?
|
||||
|
||||
In addition to the current buffer, Org-babel searches for
|
||||
pre-defined source block functions in the Library of Babel. This is
|
||||
a user-extensible collection of ready-made source-code blocks for
|
||||
handling common tasks. One use for the LoB (not yet done!) will be
|
||||
to provide a choice of data graphing procedures for data held in
|
||||
org-mode tables, using languages such as R, gnuplot, asymptote,
|
||||
etc. If you implement something that might be of use to other org
|
||||
users, please consider adding it to the LoB; similarly, feel free to
|
||||
request help solving a problem using external code via org-babel --
|
||||
there's always a chance that other org users will be able to
|
||||
contribute some helpful code. Org-mode demonstrates that an enormous
|
||||
amount can be achieved using plain text and emacs lisp; the LoB is
|
||||
intended to fill in the gaps.
|
||||
|
||||
Org-babel comes pre-populated with the source-code blocks located in
|
||||
the [[file:library-of-babel.org][library-of-babel.org]] file. It is possible to add source-code
|
||||
blocks from any org-mode file to the library by calling
|
||||
|
||||
#+srcname: add-file-to-lob
|
||||
#+begin_src emacs-lisp
|
||||
(org-babel-lob-ingest "path/to/file.org")
|
||||
#+end_src
|
||||
|
||||
Note that it is also possible to pass table values or the output of
|
||||
a source-code block to lob functions, and it is possible to
|
||||
reference lob functions in source block arguments.
|
||||
|
||||
* Reproducible Research
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: reproducable-research
|
||||
:END:
|
||||
#+begin_quote
|
||||
An article about computational science in a scientific publication is
|
||||
not the scholarship itself, it is merely advertising of the
|
||||
scholarship. The actual scholarship is the complete software
|
||||
development environment and the complete set of instructions which
|
||||
generated the figures.
|
||||
|
||||
-- D. Donoho
|
||||
#+end_quote
|
||||
|
||||
[[http://reproducibleresearch.net/index.php/Main_Page][Reproducible Research]] (RR) is the practice of distributing along with
|
||||
an article of research all data, code, and tools required to reproduce
|
||||
the results discussed in the paper. As such the paper becomes not
|
||||
only a document describing the research but a complete laboratory in
|
||||
which the research can be reproduced and extended.
|
||||
|
||||
Org-mode already has exceptional support for [[http://orgmode.org/manual/Exporting.html#Exporting][exporting to html and
|
||||
LaTeX]]. Org-babel makes Org-mode a tool for RR by *activating* the
|
||||
data and source code embedded into Org-mode documents making the
|
||||
entire document executable. This makes it not only possible, but
|
||||
natural to distribute research in a format that encourages readers to
|
||||
recreate your results, and perform their own analysis.
|
||||
|
||||
One notable existing RR tool is [[http://en.wikipedia.org/wiki/Sweave][Sweave]] which provides for the
|
||||
embedding of [[http://www.r-project.org/][R]] code into LaTeX documents. While Sweave is a mature
|
||||
and very useful tool, we believe that Org-babel has several
|
||||
advantages:
|
||||
- It supports multiple languages (we're not aware of other RR tools that do this)
|
||||
- The [[http://orgmode.org/manual/Exporting.html#Exporting][export process]] is flexible and powerful, including HTML as a target in addition to LaTeX
|
||||
- The document can make native use of all the features of Org-mode,
|
||||
such as those for [[http://orgmode.org/manual/Agenda-Views.html#Agenda-Views][project planning]] and [[http://orgmode.org/manual/TODO-Items.html#TODO-Items][task management]]
|
||||
|
||||
* Literate programming
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: literate-programming
|
||||
:END:
|
||||
|
||||
#+begin_quote
|
||||
Let us change our traditional attitude to the construction of
|
||||
programs: Instead of imagining that our main task is to instruct a
|
||||
/computer/ what to do, let us concentrate rather on explaining to
|
||||
/human beings/ what we want a computer to do.
|
||||
|
||||
The practitioner of literate programming can be regarded as an
|
||||
essayist, whose main concern is with exposition and excellence of
|
||||
style. Such an author, with thesaurus in hand, chooses the names of
|
||||
variables carefully and explains what each variable means. He or she
|
||||
strives for a program that is comprehensible because its concepts have
|
||||
been introduced in an order that is best for human understanding,
|
||||
using a mixture of formal and informal methods that reinforce each
|
||||
other.
|
||||
|
||||
-- Donald Knuth
|
||||
#+end_quote
|
||||
|
||||
Org-babel supports [[http://en.wikipedia.org/wiki/Literate_programming][Literate Programming]] (LP) by allowing the act of
|
||||
programming to take place inside of Org-mode documents. The Org-mode
|
||||
file can then be exported (*woven* in LP speak) to html or LaTeX for
|
||||
consumption by a human, and the embedded source code can be extracted
|
||||
(*tangled* in LP speak) into structured source code files for
|
||||
consumption by a computer.
|
||||
|
||||
To support these operations Org-babel relies on Org-mode's [[http://orgmode.org/manual/Exporting.html#Exporting][existing
|
||||
exporting functionality]] for *weaving* of documentation, and on the
|
||||
=org-babel-tangle= function which makes use of [[http://www.cs.tufts.edu/~nr/noweb/][Noweb]] [[reference-expansion][reference syntax]]
|
||||
for *tangling* of code files.
|
||||
|
||||
The [[literate-programming-example][following example]] demonstrates the process of *tangling* in
|
||||
Org-babel.
|
||||
|
||||
*** Simple Literate Programming Example (Noweb syntax)
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: literate-programming-example
|
||||
:END:
|
||||
|
||||
Tangling functionality is controlled by the =tangle= family of
|
||||
[[header-arguments]]. These arguments can be used to turn tangling on or
|
||||
off (the default) on the source code block, or the outline heading
|
||||
level.
|
||||
|
||||
The following demonstrates the combination of three source code blocks
|
||||
into a single source code file using =org-babel-tangle=.
|
||||
|
||||
The following two blocks will not be tangled by default since they
|
||||
have no =tangle= header arguments.
|
||||
|
||||
#+srcname: hello-world-prefix
|
||||
#+begin_src sh :exports none
|
||||
echo "/-----------------------------------------------------------\\"
|
||||
#+end_src
|
||||
|
||||
: #+srcname: hello-world-prefix
|
||||
: #+begin_src sh :exports none
|
||||
: echo "/-----------------------------------------------------------\\"
|
||||
: #+end_src
|
||||
|
||||
#+srcname: hello-world-postfix
|
||||
#+begin_src sh :exports none
|
||||
echo "\-----------------------------------------------------------/"
|
||||
#+end_src
|
||||
|
||||
: #+srcname: hello-world-postfix
|
||||
: #+begin_src sh :exports none
|
||||
: echo "\-----------------------------------------------------------/"
|
||||
: #+end_src
|
||||
|
||||
|
||||
The third block does have a =tangle= header argument indicating the
|
||||
name of the file to which it should be written. It also has [[http://www.cs.tufts.edu/~nr/noweb/][Noweb]]
|
||||
style references to the two previous source code blocks which will be
|
||||
expanded during tangling to include them in the output file as well.
|
||||
|
||||
#+srcname: hello-world
|
||||
#+begin_src sh :tangle hello :exports none
|
||||
# <<hello-world-prefix>>
|
||||
echo "| hello world |"
|
||||
# <<hello-world-postfix>>
|
||||
#+end_src
|
||||
|
||||
: #+srcname: hello-world
|
||||
: #+begin_src sh :tangle hello :exports none
|
||||
: # <<hello-world-prefix>>
|
||||
: echo "| hello world |"
|
||||
: # <<hello-world-postfix>>
|
||||
: #+end_src
|
||||
|
||||
Calling =org-babel-tangle= will result in the following being written
|
||||
to the =hello.sh= file.
|
||||
|
||||
#+srcname: hello-world-output
|
||||
#+begin_src sh
|
||||
#!/usr/bin/env sh
|
||||
# generated by org-babel-tangle
|
||||
|
||||
# [[file:~/src/org-babel/org-babel-worg.org::#literate-programming-example][block-16]]
|
||||
# <<hello-world-prefix>>
|
||||
echo "/-----------------------------------------------------------\\"
|
||||
|
||||
echo "| hello world |"
|
||||
# <<hello-world-postfix>>
|
||||
echo "\-----------------------------------------------------------/"
|
||||
# block-16 ends here
|
||||
#+end_src
|
||||
|
||||
*** Emacs Initialization with Org-babel
|
||||
Org-babel has special support for embedding your emacs initialization
|
||||
into Org-mode files. The =org-babel-load-file= function can be used
|
||||
to load the emacs lisp embedded in a literate Org-mode file in the
|
||||
same way that you might load a regular elisp file.
|
||||
|
||||
This allows you to have all the niceness of Org-mode (folding, tags,
|
||||
notes, html export, etc...) available in your emacs initialization.
|
||||
|
||||
To try this out either see the simple [[literate-emacs-init][Literate Emacs Initialization]]
|
||||
example directly below, or check out the Org-babel Literate
|
||||
Programming version of Phil Hagelberg's excellent [[http://github.com/technomancy/emacs-starter-kit/tree/master][emacs-starter-kit]]
|
||||
available at [[http://github.com/eschulte/emacs-starter-kit/tree/master][Org-babel-emacs-starter-kit]].
|
||||
|
||||
***** Literate Emacs Initialization
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: literate-emacs-init
|
||||
:END:
|
||||
|
||||
For a simple example of usage follow these 4 steps.
|
||||
|
||||
1) create a directory named =.emacs.d= in the base of your home
|
||||
directory.
|
||||
#+begin_src sh
|
||||
mkdir ~/.emacs.d
|
||||
#+end_src
|
||||
2) checkout the latest versions of Org-mode and Org-babel into the src
|
||||
subdirectory of this new directory
|
||||
#+begin_src sh
|
||||
cd ~/.emacs.d
|
||||
mkdir src
|
||||
cd src
|
||||
git clone git://repo.or.cz/org-mode.git
|
||||
git clone git://github.com/eschulte/org-babel.git
|
||||
#+end_src
|
||||
3) place the following in a file called =init.el= in your emacs
|
||||
initialization directory (=~/.emacs.d=).
|
||||
#+srcname: emacs-init
|
||||
#+begin_src emacs-lisp
|
||||
;;; init.el --- Where all the magic begins
|
||||
;;
|
||||
;; This file loads both
|
||||
;; - Org-mode : http://orgmode.org/ and
|
||||
;; - Org-babel: http://eschulte.github.com/org-babel/
|
||||
;;
|
||||
;; It then loads the rest of our Emacs initialization from Emacs lisp
|
||||
;; embedded in literate Org-mode files.
|
||||
|
||||
;; Load up Org Mode and Org Babel for elisp embedded in Org Mode files
|
||||
(setq dotfiles-dir (file-name-directory (or (buffer-file-name) load-file-name)))
|
||||
(add-to-list 'load-path (expand-file-name
|
||||
"lisp" (expand-file-name
|
||||
"org" (expand-file-name
|
||||
"src" dotfiles-dir))))
|
||||
(add-to-list 'load-path (expand-file-name
|
||||
"lisp" (expand-file-name
|
||||
"org-babel" (expand-file-name
|
||||
"src" dotfiles-dir))))
|
||||
(require 'org-babel-init)
|
||||
|
||||
;; load up all literate org-mode files in this directory
|
||||
(mapc #'org-babel-load-file (directory-files dotfiles-dir t "\\.org$"))
|
||||
|
||||
;;; init.el ends here
|
||||
#+end_src
|
||||
4) Implement all of your emacs customizations inside of elisp
|
||||
source-code blocks located in Org-mode files in this directory.
|
||||
They will be loaded by emacs on startup.
|
||||
|
||||
* Reference / Documentation
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: reference-and-documentation
|
||||
:END:
|
||||
*** Languages
|
||||
The following can be added to your .emacs and used to activate
|
||||
languages. It includes a brief list of the requirements for each
|
||||
language. *Note*: this also serves as the list of languages
|
||||
currently supported by Org-babel.
|
||||
#+begin_src emacs-lisp
|
||||
;; Uncomment each of the following require lines if you want org-babel
|
||||
;; to support that language. Each language has a comment explaining
|
||||
;; it's dependencies. See the related files in lisp/langs for more
|
||||
;; detailed explanations of requirements.
|
||||
;; (require 'org-babel-R) ;; R and ess-mode
|
||||
;; (require 'org-babel-asymptote) ;; asymptote
|
||||
;; (require 'org-babel-css) ;; none
|
||||
;; (require 'org-babel-ditaa) ;; ditaa
|
||||
;; (require 'org-babel-dot) ;; dot
|
||||
;; (require 'org-babel-gnuplot) ;; gnuplot, and gnuplot-mode
|
||||
;; (require 'org-babel-haskell) ;; haskell, haskell-mode, inf-haskell
|
||||
;; (require 'org-babel-ocaml) ;; ocaml, and tuareg-mode
|
||||
;; (require 'org-babel-python) ;; python, and python-mode
|
||||
;; (require 'org-babel-ruby) ;; ruby, irb, ruby-mode, and inf-ruby
|
||||
;; (require 'org-babel-sass) ;; sass, sass-mode
|
||||
;; (require 'org-babel-sql) ;; none
|
||||
#+end_src
|
||||
|
||||
*** Header Arguments
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: header-arguments
|
||||
:END:
|
||||
|
||||
- results :: results arguments specify what should be done with the
|
||||
output of source-code blocks
|
||||
- The following options are mutually exclusive, and specify how the
|
||||
results should be collected from the source-code block
|
||||
- value ::
|
||||
- output ::
|
||||
- The following options are mutually exclusive and specify what type
|
||||
of results the code block will return
|
||||
- vector :: specifies that the results should be interpreted as a
|
||||
multidimensional vector (even if the vector is
|
||||
trivial), and will be inserted into the org-mode file
|
||||
as a table
|
||||
- scalar :: specifies that the results should be interpreted as a
|
||||
scalar value, and will be inserted into the org-mode
|
||||
file as quoted text
|
||||
- file :: specifies that the results should be interpreted as the
|
||||
path to a file, and will be inserted into the org-mode
|
||||
file as a link
|
||||
- The following options specify how the results should be inserted
|
||||
into the org-mode file
|
||||
- replace :: the current results replace any previously inserted
|
||||
results from the code block
|
||||
- silent :: rather than being inserted into the org-mode file the
|
||||
results are echoed into the message bar
|
||||
- exports :: exports arguments specify what should be included in html
|
||||
or latex exports of the org-mode file
|
||||
- code :: the body of code is included into the exported file
|
||||
- results :: the results of evaluating the code is included in the
|
||||
exported file
|
||||
- both :: both the code and results are included in the exported
|
||||
file
|
||||
- none :: nothing is included in the exported file
|
||||
- tangle :: tangle arguments specify whether or not the source-code
|
||||
block should be included in tangled extraction of
|
||||
source-code files
|
||||
- yes :: the source-code block is exported to a source-code file
|
||||
named after the basename (name w/o extension) of the
|
||||
org-mode file
|
||||
- no :: (default) the source-code block is not exported to a
|
||||
source-code file
|
||||
- other :: any other string passed to the =tangle= header argument
|
||||
is interpreted as a file basename to which the block will
|
||||
be exported
|
||||
|
||||
*** Noweb reference syntax
|
||||
The [[http://www.cs.tufts.edu/~nr/noweb/][Noweb]] Literate Programming system allows named blocks of code to
|
||||
be referenced by using a =<<code-block-name>>= syntax. When a
|
||||
document is tangled these references are replaced with the named code.
|
||||
An example is provided in the [[literate-programming-example]] in this
|
||||
document.
|
||||
|
||||
* Footnotes
|
||||
|
||||
[fn:1] Calling =C-c C-o= on a source-code block will open the
|
||||
block's results in a separate buffer.
|
||||
|
|
@ -1,77 +0,0 @@
|
|||
#+TITLE: Tools for publishing Org-babel documentation
|
||||
#+OPTIONS: toc:t h:3 num:nil ^:nil
|
||||
|
||||
This file contains the code required to export the documentation of Org-babel.
|
||||
|
||||
* org-babel-documentation Project
|
||||
|
||||
This defines the =org-babel-documentation= project, for ease of
|
||||
publishing. Publish a project with =C-c C-e X=.
|
||||
|
||||
#+begin_src emacs-lisp :results silent
|
||||
(setq org-babel-dir (file-name-directory (or load-file-name buffer-file-name)))
|
||||
(unless (boundp 'org-publish-project-alist)
|
||||
(setq org-publish-project-alist nil))
|
||||
(setq org-publish-project-alist
|
||||
(cons
|
||||
`("org-babel-documentation"
|
||||
:base-directory ,org-babel-dir
|
||||
:base-extension "org"
|
||||
:exclude ,(regexp-opt-group '("org-babel.org" "test-export.org" "test-tangle.org" "test-tangle-load.org"))
|
||||
:publishing-directory ,(expand-file-name "doc" org-babel-dir)
|
||||
:index-filename "org-babel-worg.org"
|
||||
:auto-postamble nil
|
||||
:style "<link rel=\"stylesheet\"href=\"stylesheet.css\"type=\"text/css\">"
|
||||
:publishing-function (org-publish-org-to-html org-publish-org-to-org)
|
||||
:plain-source t
|
||||
:htmlized-source t)
|
||||
org-publish-project-alist))
|
||||
#+end_src
|
||||
|
||||
* org-babel-documentation stylesheet
|
||||
|
||||
Calling =org-babel-tangle= in this file will export the css file for
|
||||
the Org-babel documentation.
|
||||
|
||||
#+begin_src sass :file doc/stylesheet.css :results silent
|
||||
#logo
|
||||
float: right
|
||||
text-align: center
|
||||
max-width: 240px
|
||||
font-size: 8pt
|
||||
margin-left: 1em
|
||||
#attr
|
||||
margin: -0.5em
|
||||
|
||||
#subtitle
|
||||
float: center
|
||||
text-align: center
|
||||
|
||||
#content
|
||||
color: #2e2e2e
|
||||
|
||||
.outline-text-2
|
||||
margin-left: 2em
|
||||
|
||||
.outline-text-3
|
||||
margin-left: 2em
|
||||
|
||||
.outline-text-4
|
||||
margin-left: 2em
|
||||
|
||||
.outline-text-5
|
||||
margin-left: 2em
|
||||
|
||||
.outline-text-6
|
||||
margin-left: 2em
|
||||
|
||||
h3
|
||||
margin-left: 1em
|
||||
color: #000
|
||||
|
||||
a
|
||||
text-decoration: none
|
||||
color: #4a708b
|
||||
a:hover
|
||||
text-decoration: underline
|
||||
#+end_src
|
|
@ -1,5 +0,0 @@
|
|||
#name : #+begin_...#+end_
|
||||
# --
|
||||
#+begin_$1 $2
|
||||
$0
|
||||
#+end_$1
|
|
@ -1,6 +0,0 @@
|
|||
#name : #+begin_src...#+end_src
|
||||
# --
|
||||
#+srcname: ${1:name}
|
||||
#+begin_src ${2:language} $3
|
||||
$0
|
||||
#+end_src
|
|
@ -1,60 +0,0 @@
|
|||
#+TITLE: Testing Org-Babel Export
|
||||
#+OPTIONS: toc:2 ^:nil
|
||||
|
||||
* all
|
||||
|
||||
** full source blocks
|
||||
|
||||
*** ruby
|
||||
|
||||
source block is here, but is shouldn't be exported...
|
||||
|
||||
#+begin_src ruby :results silent :exports none
|
||||
class Schulte
|
||||
def initialize
|
||||
puts :eric
|
||||
end
|
||||
end
|
||||
#+end_src
|
||||
|
||||
The source block is here, and lets see the code
|
||||
|
||||
#+begin_src ruby :results silent :exports code
|
||||
class Schulte
|
||||
def initialize
|
||||
puts :eric
|
||||
end
|
||||
end
|
||||
#+end_src
|
||||
|
||||
This is a source block, and lets see the results
|
||||
#+begin_src ruby :exports results :results replace
|
||||
:the_results
|
||||
#+end_src
|
||||
|
||||
lets see the source, and results for a ruby array
|
||||
#+begin_src ruby :results replace
|
||||
[1, 2, 3, 4].map{ |n| n * 2 }
|
||||
#+end_src
|
||||
|
||||
|
||||
*** emacs-lisp
|
||||
|
||||
a table
|
||||
|
||||
#+begin_src emacs-lisp
|
||||
'(1 2 3 4 5)
|
||||
#+end_src
|
||||
|
||||
hidden
|
||||
|
||||
#+begin_src emacs-lisp :exports none :results silent
|
||||
9
|
||||
#+end_src
|
||||
|
||||
|
||||
** in-line source blocks
|
||||
|
||||
This is an inline source code block src_ruby{1 + 6}. And another
|
||||
source block with text output src_emacs-lisp{"eric"}.
|
||||
|
|
@ -1,18 +0,0 @@
|
|||
#+TITLE: testing org-babel-load
|
||||
#+OPTIONS: toc:nil num:nil ^:nil
|
||||
|
||||
* elisp blocks
|
||||
|
||||
** lets look at the order
|
||||
|
||||
#+begin_src emacs-lisp
|
||||
(message "I'm the first")
|
||||
#+end_src
|
||||
|
||||
#+begin_src emacs-lisp
|
||||
(message "I'm the second")
|
||||
#+end_src
|
||||
|
||||
#+begin_src emacs-lisp
|
||||
(message "I'm the third")
|
||||
#+end_src
|
|
@ -1,108 +0,0 @@
|
|||
#+OPTIONS: toc:2 ^:nil
|
||||
#+TITLE: Testing Org-Babel Tangling
|
||||
|
||||
* Some file
|
||||
|
||||
Some text here
|
||||
|
||||
#+BEGIN_SRC sh
|
||||
echo "line 1"
|
||||
echo "line 2"
|
||||
#+END_SRC
|
||||
|
||||
more text
|
||||
|
||||
#+srcname: ruby-no-session
|
||||
#+begin_src ruby
|
||||
def hello
|
||||
puts "hello world"
|
||||
end
|
||||
#+end_src
|
||||
|
||||
#+srcname: first-ruby-block
|
||||
#+begin_src ruby :session special :tangle trivial-symbol
|
||||
:block_the_first
|
||||
#+end_src
|
||||
|
||||
#+srcname: ruby-with-noweb-references
|
||||
#+begin_src ruby :tangle yes
|
||||
# <<ruby-no-session>>
|
||||
hello()
|
||||
#+end_src
|
||||
|
||||
|
||||
|
||||
** Some subsection
|
||||
|
||||
#+BEGIN_SRC sh
|
||||
echo "line 3"
|
||||
echo "line 4"
|
||||
#+END_SRC
|
||||
|
||||
blah blah blah
|
||||
|
||||
#+BEGIN_EXAMPLE
|
||||
text line 1
|
||||
text line 2
|
||||
text line 3
|
||||
#+END_EXAMPLE
|
||||
|
||||
more stuff
|
||||
|
||||
#+srcname: i-have-a-name
|
||||
#+begin_src sh
|
||||
echo "I have a name"
|
||||
#+end_src
|
||||
|
||||
|
||||
foo foo bar baz
|
||||
|
||||
#+BEGIN_SRC sh
|
||||
echo "line 5"
|
||||
echo "line 6"
|
||||
#+END_SRC
|
||||
|
||||
|
||||
** Ruby blocks
|
||||
|
||||
#+srcname: another-ruby-block
|
||||
#+begin_src ruby :session special
|
||||
holder = 98
|
||||
#+end_src
|
||||
|
||||
|
||||
#+srcname: ruby-plus-2
|
||||
#+begin_src ruby :session special
|
||||
def plus_two(n)
|
||||
n + 2
|
||||
end
|
||||
#+end_src
|
||||
|
||||
#+srcname: final-ruby
|
||||
#+begin_src ruby :session special
|
||||
plus_two(holder)
|
||||
#+end_src
|
||||
|
||||
|
||||
** Emacs Lisp initialization stuff
|
||||
|
||||
#+srcname: lets-set-some-variables()
|
||||
#+begin_src emacs-lisp
|
||||
(setq test-tangle-loading "org-babel tangles")
|
||||
(setq test-tangle-advert "use org-babel-tangle for all your emacs initialization files!!")
|
||||
#+end_src
|
||||
|
||||
#+srcname: i-shouldnt-be-tangled
|
||||
#+begin_src emacs-lisp :tangle no
|
||||
(setq test-tangle-i-should-not-exist "hopefully I'm not included")
|
||||
#+end_src
|
||||
|
||||
*** Emacs Lisp (not to be tangled)
|
||||
:PROPERTIES:
|
||||
:tangle: no
|
||||
:END:
|
||||
|
||||
#+srcname: i-also-shouldnt-be-tangled
|
||||
#+begin_src emacs-lisp
|
||||
(setq test-tangle-me-either "i also shouldn't be tangled")
|
||||
#+end_src
|
|
@ -29,30 +29,40 @@
|
|||
;; for more information see the comments in org-babel.el
|
||||
|
||||
;;; Code:
|
||||
(require 'cl)
|
||||
(require 'org)
|
||||
(require 'org-exp-blocks)
|
||||
(require 'org-babel)
|
||||
(require 'org-babel-ref)
|
||||
(require 'org-babel-exp)
|
||||
(require 'org-babel-table)
|
||||
(require 'org-babel-comint)
|
||||
(require 'org-babel-lob)
|
||||
(require 'org-babel-tangle)
|
||||
(let* ((babel-dir (expand-file-name
|
||||
"lisp"
|
||||
(expand-file-name
|
||||
"babel"
|
||||
(expand-file-name
|
||||
".." (file-name-directory (or load-file-name buffer-file-name))))))
|
||||
|
||||
(langs-dir (expand-file-name "langs" babel-dir))
|
||||
(load-path (append
|
||||
(list babel-dir langs-dir)
|
||||
(or load-path nil))))
|
||||
|
||||
;; language specific files
|
||||
(add-to-list 'load-path (expand-file-name "langs" (file-name-directory (or load-file-name buffer-file-name))))
|
||||
(require 'org-babel-lisp)
|
||||
(require 'org-babel-sh)
|
||||
;; org-babel core
|
||||
(require 'cl)
|
||||
(require 'org)
|
||||
(require 'org-exp-blocks)
|
||||
(require 'org-babel)
|
||||
(require 'org-babel-ref)
|
||||
(require 'org-babel-exp)
|
||||
(require 'org-babel-table)
|
||||
(require 'org-babel-comint)
|
||||
(require 'org-babel-lob)
|
||||
(require 'org-babel-tangle)
|
||||
|
||||
;; Library of babel
|
||||
(defvar org-babel-lob-dir
|
||||
(expand-file-name ".."
|
||||
(file-name-directory
|
||||
(or load-file-name buffer-file-name)))
|
||||
"The directory holding the library-of-babel")
|
||||
(defun org-babel-load-library-of-babel ()
|
||||
(org-babel-lob-ingest (expand-file-name "library-of-babel.org" org-babel-lob-dir)))
|
||||
;; org-babel languages
|
||||
(require 'org-babel-lisp)
|
||||
(require 'org-babel-sh)
|
||||
|
||||
;; Library of babel
|
||||
(defvar org-babel-lob-dir
|
||||
(expand-file-name ".." babel-dir)
|
||||
"The directory holding the library-of-babel")
|
||||
(defun org-babel-load-library-of-babel ()
|
||||
(org-babel-lob-ingest (expand-file-name "library-of-babel.org" org-babel-lob-dir))))
|
||||
|
||||
(provide 'org-babel-init)
|
||||
;;; org-babel-init.el ends here
|
Loading…
Reference in New Issue