Merge commit 'origin/master'
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Dan Davison
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@ -98,7 +98,7 @@ then run `org-babel-pop-to-session'."
|
|||
(defun org-babel-set-interpreters (var value)
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(set-default var value)
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||||
(setq org-babel-src-block-regexp
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(concat "#\\+begin_src \\("
|
||||
(concat "^[ \t]*#\\+begin_src \\("
|
||||
(mapconcat 'regexp-quote value "\\|")
|
||||
"\\)[ \t]*"
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||||
"\\([ \t]+\\([^\n]+\\)\\)?\n" ;; match header arguments
|
||||
|
|
@ -331,9 +331,14 @@ may be specified in the properties of the current outline entry."
|
|||
|
||||
(defun org-babel-parse-src-block-match ()
|
||||
(let* ((lang (org-babel-clean-text-properties (match-string 1)))
|
||||
(lang-headers (intern (concat "org-babel-default-header-args:" lang))))
|
||||
(lang-headers (intern (concat "org-babel-default-header-args:" lang)))
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||||
(body (org-babel-clean-text-properties (match-string 4))))
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||||
(list lang
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(org-babel-strip-protective-commas (org-babel-clean-text-properties (match-string 4)))
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(with-temp-buffer ;; get src block body removing properties, protective commas, and indentation
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(save-match-data
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||||
(insert (org-babel-strip-protective-commas body))
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(org-do-remove-indentation)
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(buffer-string)))
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(org-babel-merge-params
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org-babel-default-header-args
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(org-babel-params-from-properties)
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|
|
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|||
|
|
@ -14,16 +14,20 @@
|
|||
</div>
|
||||
<div id="logo">
|
||||
<p>
|
||||
<img src="images/tower-of-babel.png" alt="images/tower-of-babel.png" />
|
||||
<img src="images/tower-of-babel.png" alt="images/tower-of-babel.png"
|
||||
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. Genesis 11:1-9"/>
|
||||
<div id="attr">
|
||||
from
|
||||
<a href="http://www.flickr.com/photos/23379658@N05/" title=""><b>Martijn Streefkerk</b></a>
|
||||
</div>
|
||||
</p>
|
||||
</p>
|
||||
</div>
|
||||
#+end_html
|
||||
|
||||
* Introduction
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:PROPERTIES:
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||||
:CUSTOM_ID: introduction
|
||||
:END:
|
||||
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. source code execution
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||||
|
|
@ -31,7 +35,15 @@
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|||
3. exportation of source code blocks to files (literate programming)
|
||||
|
||||
* Getting started
|
||||
Add the following lines to your .emacs, replacing the path as
|
||||
:PROPERTIES:
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||||
:CUSTOM_ID: getting-started
|
||||
:END:
|
||||
Grab the latest code from the git repo at [[http://github.com/eschulte/org-babel/tree/master][github/org-babel]]
|
||||
#+begin_src sh
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||||
git clone git://github.com/eschulte/org-babel.git
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||||
#+end_src
|
||||
|
||||
And 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]].
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||||
#+begin_src emacs-lisp
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||||
|
|
@ -40,36 +52,44 @@
|
|||
#+end_src
|
||||
|
||||
* Basic org-babel functionality
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: basic-functionality
|
||||
:END:
|
||||
*** Source code execution
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||||
: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
|
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results of excecution. E.g. place point anywhere in the following
|
||||
block and use C-c C-c to run the code:
|
||||
|
||||
#+begin_src python :results output
|
||||
import time
|
||||
x = 4
|
||||
print("hello\n")
|
||||
#print time.ctime()
|
||||
print [5, 10]
|
||||
[[http://www.ruby-lang.org/][Ruby]] source code
|
||||
#+begin_src ruby
|
||||
"This file was last evaluated on #{Date.today}"
|
||||
#+end_src
|
||||
|
||||
Results of Ruby evaluation
|
||||
#+resname:
|
||||
: hello
|
||||
: 510
|
||||
: This file was last evaluated on 2009-08-09
|
||||
|
||||
[[http://www.r-project.org/][R]] source code
|
||||
#+begin_src R :results value
|
||||
x = 4
|
||||
date()
|
||||
c(5, 10)
|
||||
#+end_src
|
||||
|
||||
Results of R evaluation
|
||||
#+resname:
|
||||
| 5 |
|
||||
| 10 |
|
||||
|
||||
*** 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:
|
||||
|
|
@ -91,13 +111,167 @@ c(5, 10)
|
|||
**** Additional :results settings
|
||||
|
||||
*** 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*.
|
||||
|
||||
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
|
||||
#+begin_src emacs-lisp :var fib-inputs=fibonacci-inputs
|
||||
(defun fibonacci (n)
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||||
(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
|
||||
: #+begin_src emacs-lisp :var fib-inputs=fibonacci-inputs
|
||||
: (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. Shell source code
|
||||
#+srcname: directories
|
||||
#+begin_src bash :results replace
|
||||
cd ~ && du -sc * |grep -v total
|
||||
#+end_src
|
||||
2. Results of the shell source code (on my system, grab this org-mode
|
||||
files and try running it on your own)
|
||||
#+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" |
|
||||
3. R source code (which calls the previous shell source code)
|
||||
#+srcname: directory-pie
|
||||
#+begin_src R :var dirs = directories :session R-pie-example
|
||||
pie(dirs[,1], labels = dirs[,2])
|
||||
#+end_src
|
||||
4. Results of R code [[file:images/dirs.png]]
|
||||
|
||||
* Spreadsheet plugins for org-mode in any language
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: spreadsheet
|
||||
:END:
|
||||
|
||||
*NOTE*: Maybe in-addition-to/in-stead-of this example we should do a
|
||||
more traditional "spreadsheet" example with R [Eric]
|
||||
|
||||
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]].
|
||||
|
||||
In fact the functional test suite for Org-babel is implemented as a
|
||||
large Org-mode table. To run the entire test suite you simple
|
||||
evaluate the table =C-u C-c C-c=, and all of the tests are run
|
||||
updating the table with 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) (progn (message (format "running %S" '(sbe $2 (n $3)))) (sbe $2 (n $3))) (sbe $2))::$6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5))
|
||||
#+TBLFM: $5=""::$6=""
|
||||
|
||||
*** code blocks for tests
|
||||
|
||||
#+srcname: basic-elisp
|
||||
#+begin_src emacs-lisp :var n=7
|
||||
(* 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
|
||||
|
||||
* Library of Babel
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: library-of-babel
|
||||
:END:
|
||||
What about those source code blocks which are so useful you want to
|
||||
have them available in every org-mode buffer?
|
||||
|
||||
|
|
@ -112,14 +286,48 @@ c(5, 10)
|
|||
(org-babel-lob-ingest "path/to/file.org")
|
||||
#+end_src
|
||||
|
||||
* Reproducible research
|
||||
- output vs. value mode
|
||||
- file & graphical output
|
||||
- controlling export
|
||||
* 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
|
||||
reproducing the research.
|
||||
|
||||
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.
|
||||
|
||||
Existing RR tools like [[http://en.wikipedia.org/wiki/Sweave][Sweave]] provide for the embedding of [[http://www.r-project.org/][R]] code into
|
||||
LaTeX documents. While this is very useful, such documents often
|
||||
still require a large degree of "glue code" in the form of external
|
||||
shell scripts, python scripts, and Makefiles. To my knowledge
|
||||
Org-babl is the only RR tool which allows multiple languages and data
|
||||
to coexist and cooperate inside of a single document.
|
||||
|
||||
* Literate programming
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: literate-programming
|
||||
:END:
|
||||
- org-babel-tangle
|
||||
- org-babel-load-file
|
||||
* Reference / Documentation
|
||||
:PROPERTIES:
|
||||
:CUSTOM_ID: reference-and-documentation
|
||||
:END:
|
||||
|
||||
*** Source Code block syntax
|
||||
|
||||
|
|
|
|||
|
|
@ -218,7 +218,13 @@ would then be [[#sandbox][the sandbox]].
|
|||
#+end_src
|
||||
|
||||
|
||||
* Tasks [41/62]
|
||||
* Tasks [41/64]
|
||||
** TODO org-bable-tangle: no default extension if one already exists
|
||||
** TODO source-name visible in LaTeX and html exports
|
||||
Maybe this should be done in backend specific manners.
|
||||
|
||||
The listings package may provide for naming a source-code block...
|
||||
|
||||
** PROPOSED new results types (org, html, latex)
|
||||
Thanks to Tom Short for this recommendation.
|
||||
|
||||
|
|
@ -2776,8 +2782,45 @@ dot("$(2a,0)$",(2,0),N+E);
|
|||
*** DONE sh
|
||||
|
||||
|
||||
* Bugs [31/40]
|
||||
** TODO export problems when support for a language is missing
|
||||
* Bugs [32/40]
|
||||
** PROPOSED require users to explicitly turn on each language
|
||||
As we continue to add more languages to org-babel, many of which will
|
||||
require new major-modes we need to re-think how languages are added to
|
||||
org-babel.
|
||||
|
||||
Currently we are requiring all available languages in the
|
||||
[[file:lisp/org-babel-init.el][org-babel-init.el]] file. I think we need to change this to a user
|
||||
setting so that only the language which have their requirements met
|
||||
(in terms of system executables and emacs major modes) are loaded. It
|
||||
is one more step for install, but it seems to me to be the only
|
||||
solution. Thoughts?
|
||||
|
||||
*** proposed
|
||||
|
||||
we add something like the following to the instillation instructions
|
||||
|
||||
#+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-ruby) ;; inf-ruby mode, ruby and irb must be installed on your system
|
||||
;; (require 'org-babel-python) ;; python-mode
|
||||
;; (require 'org-babel-R) ;; ess-mode
|
||||
;; (require 'org-babel-gnuplot) ;; gnuplot-mode
|
||||
;; (require 'org-babel-dot) ;; dot be installed on your system
|
||||
;; (require 'org-babel-asymptote) ;; asymptote be installed on your system
|
||||
;; (require 'org-babel-ditaa) ;; ditaa be installed on your system
|
||||
;; (require 'org-babel-sql) ;; none
|
||||
;; (require 'org-babel-css) ;; none
|
||||
#+end_src
|
||||
|
||||
note that =org-babel-sh=, =org-babel-emacs-lisp=, and
|
||||
are not included in the list as they can safely be
|
||||
assumed to work on any system.
|
||||
|
||||
*** impetus
|
||||
we should come up with a way to gracefully degrade when support for a
|
||||
specific language is missing
|
||||
|
||||
|
|
@ -2901,12 +2944,6 @@ even a third"
|
|||
#+begin_src sh
|
||||
size=5
|
||||
#+end_src
|
||||
|
||||
** TODO Allow source blocks to be recognised when #+ are not first characters on the line
|
||||
I think Carsten has recently altered the core so that #+ can have
|
||||
preceding whitespace, at least for literal/code examples. org-babel
|
||||
should support this.
|
||||
|
||||
** TODO non-orgtbl formatted lists
|
||||
for example
|
||||
|
||||
|
|
@ -2962,6 +2999,26 @@ the same for the other languages. [Dan]
|
|||
find . \( -path \*/SCCS -o -path \*/RCS -o -path \*/CVS -o -path \*/MCVS -o -path \*/.svn -o -path \*/.git -o -path \*/.hg -o -path \*/.bzr -o -path \*/_MTN -o -path \*/_darcs -o -path \*/\{arch\} \) -prune -o -type f \( -iname \*.el \) -exec grep -i -nH -e org-babel-trim {} \;
|
||||
#+end_src
|
||||
|
||||
** DONE Allow source blocks to be recognised when #+ are not first characters on the line
|
||||
I think Carsten has recently altered the core so that #+ can have
|
||||
preceding whitespace, at least for literal/code examples. org-babel
|
||||
should support this.
|
||||
|
||||
#+srcname: testing-indentation
|
||||
#+begin_src emacs-lisp :results silent
|
||||
(message "i'm indented")
|
||||
#+end_src
|
||||
|
||||
#+srcname: testing-non-indentation
|
||||
#+begin_src emacs-lisp :results silent
|
||||
(message "I'm not indented")
|
||||
#+end_src
|
||||
|
||||
#+srcname: i-resolve-references-to-the-indented
|
||||
#+begin_src emacs-lisp :var speech=testing-indentation :results silent
|
||||
(message "I said %s" speech)
|
||||
#+end_src
|
||||
|
||||
** DONE are the org-babel-trim s necessary?
|
||||
at the end of e.g. org-babel-R-evaluate, org-babel-python-evaluate, but
|
||||
not org-babel-ruby-evaluate
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@ publishing. Publish a project with =C-c C-e X=.
|
|||
`("org-babel-documentation"
|
||||
:base-directory ,org-babel-dir
|
||||
:base-extension "org"
|
||||
:exclude "org-babel.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
|
||||
|
|
|
|||
Loading…
Reference in New Issue