org-mode-mirror/doc/source-code-chapter.texi

@node Working With Source Code, Miscellaneous, Publishing, Top
@comment  node-name,  next,  previous,  up
@comment Working With Source Code, Miscellaneous, Publishing, Top
@chapter ``Working With Source Code'' or ``Embedded Source Code''

Source code can be included in Org-mode documents using a @samp{src} block:

@example
#+BEGIN_SRC emacs-lisp
(defun org-xor (a b)
   "Exclusive or."
   (if a (not b) b))
#+END_SRC
@end example

Org provides the following features for working with such code blocks:

@itemize @bullet
@item
Editing in the appropriate Emacs major-mode (@ref{Editing Source Code})
@item
Export with appropriate markup (@ref{Exporting Code Blocks})
@item
Extraction (``tangling'') into pure code files. (@ref{Extracting Source Code})
@item
Code execution, with results captured in the Org buffer (@ref{Evaluating Code Blocks})
@item
Using code blocks in table formulas
@end itemize

@menu
* Structure of Code Blocks::
* Editing Source Code::         
* Exporting Code Blocks::       
* Extracting Source Code::      
* Evaluating Code Blocks::      
@end menu


@node Structure of Code Blocks, Editing Source Code, Working With Source Code, Working With Source Code
@comment  node-name,  next,  previous,  up
@comment  Structure of Code Blocks, Editing Source Code, Working With Source Code, Working With Source Code
@section Structure of Code Blocks

The basic structure of code blocks is as follows:

@example
#+srcname: name
#+begin_src language header-arguments switches
body
#+end_src
@end example

@table @code
@item name
The initial name line is optional. If present it is used during code evaluation.
@item language
The language of the code in the block.
@item header-arguments
Header arguments control evaluation, export and tangling of source
code blocks. See the [[header-arguments][Header Arguments]] section.
@item switches
FIXME link/relocate switches discussion in ``Literal examples'' section
@item body
The code
@end table

@node Editing Source Code, Exporting Code Blocks, Structure of Code Blocks, Working With Source Code
@comment  node-name,  next,  previous,  up
@comment  Editing Source Code, Exporting Code Blocks, Structure of Code Blocks, Working With Source Code
@section Editing Source Code

Use @kbd{C-c '} to edit the code block at point. This brings up a
language major-mode buffer containing the body of the code
block. Saving this buffer will write the new contents back to the Org
buffer. Use @kbd{C-c '} again to exit.

The edit buffer has a minor mode active called
@code{org-src-mode}. The following variables can be used to configure
the behavior of the edit buffer. See also the customization group
@code{org-edit-structure} for futher configuration options.

@table @code
@item org-src-lang-modes
If an emacs major-mode named @code{<lang>-mode} exists, where
@code{<lang>} is the language named in header line of the code block,
then the edit buffer will be placed in that major-mode. This variable
can be used to map arbitrary language names to existing major modes.
@item org-src-window-setup
Controls the way Emacs windows are rearranged when the edit buffer is created.
@item org-src-preserve-indentation
This variable is expecially useful for tangling languages such as
python, where whitespace the indentation in the output is critical.
@item org-src-ask-before-returning-to-edit-buffer
By default, Org will ask before returning to an open edit buffer. Set
to a non-nil value to switch without asking.
@end table

@node Exporting Code Blocks, Extracting Source Code, Editing Source Code, Working With Source Code
@comment  node-name,  next,  previous,  up
@comment  Exporting Code Blocks, Extracting Source Code, Editing Source Code, Working With Source Code
@section Exporting Code Blocks

@node Extracting Source Code, Evaluating Code Blocks, Exporting Code Blocks, Working With Source Code
@comment  node-name,  next,  previous,  up
@comment  Extracting Source Code, Evaluating Code Blocks, Exporting Code Blocks, Working With Source Code
@section Extracting Source Code

@node Evaluating Code Blocks,  , Extracting Source Code, Working With Source Code
@comment  node-name,  next,  previous,  up
@comment  Evaluating Code Blocks,  , Extracting Source Code, Working With Source Code
@section Evaluating Code Blocks

This syntax can be expanded by naming the source code block.

@example
#+sourcename
#+begin_src language header-arguments switches
body
#+end_src
@end example

- name :: This name is associated with the source code block.  This is
     similar to the =#+tblname= lines that can be used to name tables
     in Org-mode files.  Referencing the name of a source code
     block makes it possible to evaluate the block from other places in
     the file, other files, or inside Org-mode tables.  It
     is also possible to pass arguments to a source code block through
     this =#+source:= line (see [[alternate-argument-syntax][Alternate argument syntax]]).

@subsection Library of Babel
[[file:library-of-babel.org][Library of Babel]] functions can be called using the following syntax.

@example
#+lob: R-plot(data=R-plot-example-data)
@end example

@subsection Aliases
   Keyword aliases are intended to make Org-babel feel natural to
   programmers fluent in a variety of languages.  For example,
   @example
     #+srcname: alias-example
     #+begin_src emacs-lisp
       '((call lob)
         (source function srcname)
         (results resname))
     #+end_src

     #+results: alias-example
     | call    | lob      |         |
     | source  | function | srcname |
     | results | resname  |         |
   @end example
     - =#+srcname:= can be replaced with either of two aliases,  =#+source:= or =#+function:=.
     - =#+results:= can be replaced with its alias, =#+resname:=.

   When calling Library of Babel functions, as in the following
   example, there are two acceptable keywords.  The =#+lob= call in
   the example could be replaced with its alias, =#+call=.
   @example
     #+lob: R-plot(data=R-plot-example-data)
   @end example

@subsection Languages
  :PROPERTIES:
  :CUSTOM_ID: languages
  :END:

  Org-babel has support for the following languages.

  | Language       | Documentation               | Identifier | Requirements                                |
  |----------------+-----------------------------+------------+---------------------------------------------|
  | Asymptote      | org-babel-doc-asymptote     | asymptote  | [[http://asymptote.sourceforge.net/][asymptote]], [[http://asymptote.sourceforge.net/doc/Editing-modes.html][asy-mode]]                         |
  | C              | [[file:languages/org-babel-doc-C.org][org-babel-doc-C]]             | C          | none                                        |
  | Clojure        | [[file:languages/org-babel-doc-clojure.org][org-babel-doc-clojure]]       | clojure    | [[http://clojure.org/][clojure]], [[http://www.emacswiki.org/emacs/clojure-mode.el][clojure-mode]], [[http://common-lisp.net/project/slime/][slime]], [[http://clojure.codestuffs.com/][swank-clojure]] |
  | css            | org-babel-doc-css           | css        | none                                        |
  | ditaa          | org-babel-doc-ditaa         | ditaa      | [[http://ditaa.org/ditaa/][ditaa]] (bundled with Org-mode)               |
  | Graphviz       | org-babel-doc-dot           | dot        | [[http://www.graphviz.org/][dot]]                                         |
  | Emacs Lisp     | org-babel-doc-emacs-lisp    | emacs-lisp | none                                        |
  | gnuplot        | org-babel-doc-gnuplot       | gnuplot    | [[http://www.gnuplot.info/][gnuplot]], [[http://cars9.uchicago.edu/~ravel/software/gnuplot-mode.html][gnuplot-mode]]                       |
  | Haskell        | org-babel-doc-haskell       | haskell    | [[http://www.haskell.org/][haskell]], [[http://projects.haskell.org/haskellmode-emacs/][haskell-mode]], [[http://www.haskell.org/haskellwiki/Haskell_mode_for_Emacs#inf-haskell.el:_the_best_thing_since_the_breadknife][inf-haskell]], [[http://people.cs.uu.nl/andres/lhs2tex/][lhs2tex]] |
  | Matlab         | [[file:languages/org-babel-doc-octave-matlab.org][org-babel-doc-octave-matlab]] | matlab     | matlab, [[http://sourceforge.net/projects/matlab-emacs/][matlab.el]]                           |
  | LaTeX          | [[file:languages/org-babel-doc-LaTeX.org][org-babel-doc-latex]]         | latex      | [[http://www.latex-project.org/][latex]], [[http://www.gnu.org/software/auctex/][auctex]], [[http://www.gnu.org/software/auctex/reftex.html][reftex]]                       |
  | Objective Caml | org-babel-doc-ocaml         | ocaml      | [[http://caml.inria.fr/][ocaml]], [[http://www-rocq.inria.fr/~acohen/tuareg/][tuareg-mode]]                          |
  | Octave         | [[file:languages/org-babel-doc-octave-matlab.org][org-babel-doc-octave-matlab]] | octave     | octave                                      |
  | OZ             | [[file:languages/org-babel-doc-oz.org][org-babel-doc-oz]]            | oz         | [[http://www.mozart-oz.org/][Mozart]] which includes a major mode          |
  | Perl           | org-babel-doc-perl          | perl       | [[http://www.perl.org/][perl]], [[http://www.emacswiki.org/emacs/CPerlMode][cperl-mode]] (optional)                 |
  | Python         | org-babel-doc-python        | python     | [[http://www.python.org/][python]], [[https://launchpad.net/python-mode][python-mode]] (optional)              |
  | R              | [[file:languages/org-babel-doc-R.org][org-babel-doc-R]]             | R          | [[http://www.r-project.org/][R]], [[http://ess.r-project.org/][ess-mode]]                                 |
  | Ruby           | org-babel-doc-ruby          | ruby       | [[http://www.ruby-lang.org/][ruby]], [[http://www.ruby-lang.org/][irb]], [[http://github.com/eschulte/rinari/raw/master/util/ruby-mode.el][ruby-mode]], [[http://github.com/eschulte/rinari/raw/master/util/inf-ruby.el][inf-ruby mode]]         |
  | Sass           | org-babel-doc-sass          | sass       | [[http://sass-lang.com/][sass]], [[http://github.com/nex3/haml/blob/master/extra/sass-mode.el][sass-mode]]                             |
  | GNU Screen     | [[file:languages/org-babel-doc-screen.org][org-babel-doc-screen]]        | screen     | [[http://www.gnu.org/software/screen/][screen]], a terminal                          |
  | shell          | org-babel-doc-sh            | sh[fn:1]   | a shell                                     |
  | SQL            | org-babel-doc-sql           | sql        | none                                        |

  To add support for a particular language to your Org-babel
  installation first make sure that the requirements of the language
  are met, then add a line like the following to your Emacs
  configuration, (replace "identifier" with one of the
  entries in the Identifier column of the table).
  @example
    (require 'org-babel-identifier)
  @end example

@section Header Arguments
    :PROPERTIES:
    :CUSTOM_ID: header-arguments
    :END:

Definitions of all Org-babel header arguments are given [[header-argument-specific-documentation][below]].  In
addition, some languages may add their own header arguments.  Please
see the language-specific documentation for information on
language-specific header arguments.

@subsection Using Header Arguments

The values of header arguments can be set in three different ways,
each more specific than the last.

@subsubsection System-wide
    :PROPERTIES:
    :CUSTOM_ID: system-wide-header-argument
    :END:

 System-wide values of header arguments can be specified by
 customizing the =org-babel-default-header-args= variable:
 @example
   org-babel-default-header-args is a variable defined in `org-babel.el'.
   Its value is
   ((:session . "none")
    (:results . "replace")
    (:exports . "code")
    (:cache . "no")
    (:noweb . "no"))


   Documentation:
   Default arguments to use when evaluating a source block.
 @end example
 [[#default-noweb]]
 For example, the following example could be used to set the default value
 of =:noweb= header arguments to =yes=.  This would have the effect of
 expanding =:noweb= references by default when evaluating source code blocks.
 @example
   (setq org-babel-default-header-args
         (cons '(:noweb . "yes")
               (assq-delete-all :noweb org-babel-default-header-args)))
 @end example

@subsubsection Org-mode Properties

 Header arguments are also read from [[http://orgmode.org/manual/Properties-and-Columns.html#Properties-and-Columns][Org-mode properties]], which
 means they can be set on the outline header level.  For example, the
 value of the =:cache= header argument will default to true in all
 source code blocks under the following example of an Org-mode outline header:
 @example
   * outline header
     :PROPERTIES:
     :cache:    yes
     :CUSTOM_ID: property-set-header-arguments
     :END:
 @end example
 Properties defined in this way override the properties set in
 =org-babel-default-header-args=.  It is convenient to use the
 =org-set-property= function bound to =C-c C-x p= to set properties
 in Org-mode documents.

@subsubsection Source Code Block
    :PROPERTIES:
    :CUSTOM_ID: single-block-header-arguments
    :END:
 The most common way to assign values to header arguments is at the
 source code block level.  This can be done by listing a sequence of
 header arguments and their values as part of the =#+begin_src=
 line.  Properties set in this way override both the values of
 =org-babel-default-header-args= and header argument specified as
 properties.  In the following example, the
 =:results= header argument is set to =silent=, meaning the results
 of execution will not be inserted in the buffer, and the =:exports=
 header argument is set to =code=, meaning only the body of the
 source code block
 will be preserved on export to HTML or LaTeX.
 @example
   #+source: factorial
   #+begin_src haskell :results silent :exports code
     fac 0 = 1
     fac n = n * fac (n-1)
   #+end_src
 @end example

@subsection Specific Header Arguments
    :PROPERTIES:
    :CUSTOM_ID: header-argument-specific-documentation
    :END:

@subsubsection =:var=
    :PROPERTIES:
    :CUSTOM_ID: header-argument-var
    :END:

    The =:var= header argument is used to pass arguments to
    source code blocks.  The specifics of how arguments are included
    in a source code block are language specific and are
    addressed in the language-specific documentation. However, the
    syntax used to specify arguments is the same across all
    languages.  The values passed to arguments can be or
    - literal values
    - values from org-mode tables
    - the results of other source code blocks

    These values can be indexed in a manner similar to arrays -- see
    [[var-argument-indexing][argument indexing]].

    The following syntax is used to pass arguments to source code
    blocks using the =:var= header argument.

    @example
      :var name=assign
    @end example

    where =assign= can take one of the following forms

    - literal value :: either a string ="string"= or a number =9=.
    - reference :: a table name:

         @example
           #+tblname: example-table
           | 1 |
           | 2 |
           | 3 |
           | 4 |

           #+source: table-length
           #+begin_src emacs-lisp :var table=example-table
             (length table)
           #+end_src

           #+results: table-length
           : 4
         @end example

         a source code block name, as assigned by =#+srcname:=,
         followed by parentheses:

         @example
           #+begin_src emacs-lisp :var length=table-length()
             (* 2 length)
           #+end_src

           #+results:
           : 8
         @end example

         In addition, an argument can be passed to the source code
         block referenced by =:var=.  The argument is passed within
         the parentheses following the source code block name:

         @example
           #+source: double
           #+begin_src emacs-lisp :var input=8
             (* 2 input)
           #+end_src

           #+results: double
           : 16

           #+source: squared
           #+begin_src emacs-lisp :var input=double(input=1)
             (* input input)
           #+end_src

           #+results: squared
           : 4
         @end example

@subsubheading alternate argument syntax
     :PROPERTIES:
     :CUSTOM_ID: alternate-argument-syntax
     :END:

     It is also possible to specify arguments in a potentially more
     natural way using the =#+source:= line of a source code block.
     As in the following example arguments can be packed inside of
     parenthesis following the source name.
     @example
       #+source: double(input=0)
       #+begin_src emacs-lisp
         (* 2 input)
       #+end_src
     @end example

**** indexable variable values
     :PROPERTIES:
     :CUSTOM_ID: var-argument-indexing
     :END:

     It is possible to assign a portion of a value to a
     variable in a source block.  The following example
     assigns the second and third rows of the table
     =example-table= to the variable =data=:

     @example
       :var data=example-table[1:2]
     @end example

     *Note:* ranges are indexed using the =:= operator.

     *Note:* indices are 0 based.

     The following example assigns the second column of the
     first row of =example-table= to =data=:

     @example
       :var data=example-table[0,1]
     @end example

     It is possible to index into the results of source code blocks
     as well as tables.  Any number of dimensions can be indexed.
     Dimensions are separated from one another by commas.

     For more information on indexing behavior see the documentation
     for the =org-babel-ref-index-list= function -- provided below.

     @example
       org-babel-ref-index-list is a Lisp function in `org-babel-ref.el'.

       (org-babel-ref-index-list INDEX LIS)

       Return the subset of LIS indexed by INDEX.  If INDEX is
       separated by ,s then each PORTION is assumed to index into the
       next deepest nesting or dimension.  A valid PORTION can consist
       of either an integer index, or two integers separated by a : in
       which case the entire range is returned.
     @end example

     *Note:* In Emacs, the documentation for any function or variable
     can be read using the =describe-function= (M-x describe
     function) and =describe-variable= (M-x describe variable)
     functions, respectively.

@subsubsection =:results=
    :PROPERTIES:
    :CUSTOM_ID: header-argument-results
    :END:

    There are three types of results header argument:
    - *collection* header arguments specify how the results should be collected from
       the source code block;
    - *type* header arguments specify what type of result the source code block
       will return -- which has implications for how they will be
       inserted into the Org-mode buffer; and
    - *handling* header arguments specify how the results of
       evaluating the source code block should be handled.

     *Note:* only one option from each type may be supplied per source code
       block.

@subsubheading collection
    :PROPERTIES:
    :CUSTOM_ID: header-argument-results-collection
    :END:
     The following options are mutually exclusive, and specify how the
     results should be collected from the source code block.

     - value :: This is the default.  The result is the value
                of the last statement in the source code block.
                This header argument places Org-babel in functional
                mode.  Note that in some languages, e.g., python,
                use of this result type requires that a =return=
                statement be included in the body of the source code
                block. E.g., =:results value=.
    - output :: The result is the collection of everything printed
                to stdout during the execution of the source code
                block.  This header argument places Org-babel in scripting
                mode.  E.g., =:results output=.

@subsubheading type
     The following options are mutually exclusive and specify what
     type of results the code block will return.  By default, results
     are inserted as either a *table* or *scalar* depending on their
     value.

     - table, vector :: The results should be interpreted as an Org-mode table.
                        If a single value is returned, Org-babel will convert it
                        into a table with one row and one column.  E.g., =:results
                        value table=.
     - scalar, verbatim :: The results should be interpreted
          literally -- meaning they will not be converted into a table.
          The results will be inserted into the Org-mode buffer as
          quoted text.  E.g., =:results value verbatim=.
     - file :: The results will be interpreted as the path to a file,
               and will be inserted into the Org-mode buffer as a file
               link.  E.g., =:results value file=.
     - raw, org :: The results are interpreted as raw Org-mode code and
                   are inserted directly into the buffer.  If the results look
                   like a table they will be aligned as such by Org-mode.
                   E.g., =:results value raw=.
     - html :: Results are assumed to be HTML and will be enclosed in
               a =begin_html= block.  E.g., =:results value html=.
     - latex :: Results assumed to be LaTeX and are enclosed in a
                =begin_latex= block.  E.g., =:results value latex=.
     - code :: Result are assumed to be parseable code and are
               enclosed in a code block.  E.g., =:results value code=.
     - pp :: The result is converted to pretty-printed code and is
             enclosed in a code block.  This option currently supports
             Emacs Lisp, python, and ruby.  E.g., =:results value pp=.

@subsubheading handling
     The following results options indicate what Org-babel should do
     with the results once they are collected.

     - silent :: The results will be echoed in the minibuffer but
                 will not be inserted into the Org-mode buffer.  E.g.,
                 =:results output silent=.
     - replace :: The default value.  The results will be inserted
                  into the Org-mode buffer.  E.g., =:results output
                  replace=.

@subsubsection =:file=
    :PROPERTIES:
    :CUSTOM_ID: header-argument-file
    :END:

    =:file= is used to specify a path for file output in which case an
    [[http://orgmode.org/manual/Link-format.html#Link-format][org style]] =file:= link is inserted into the buffer as the
    result. Common examples are graphical output from [[file:languages/org-babel-doc-R.org][R]], gnuplot,
    ditaa and [[file:languages/org-babel-doc-LaTeX.org][latex]] blocks.

    See the [[#header-argument-dir][=:dir= and remote execution]] section for examples.

    Note that for some languages, including [[file:languages/org-babel-doc-R.org][R]], gnuplot, [[file:languages/org-babel-doc-LaTeX.org][latex]] and
    ditaa, graphical output is sent to the specified file without the
    file being referenced explicitly in the code block. See the
    documentation for the individual languages for details. In
    contrast, general purpose languages such as python and ruby
    require that the code explicitly create output corresponding to
    the path indicated by =:file=.

    While the =:file= header argument can be used to specify the path
    to the output file,

@subsubsection =:dir= and remote execution
    :PROPERTIES:
    :CUSTOM_ID: header-argument-dir
    :END:
    =:dir= specifies the /default directory/ during code block
    execution. If it is absent, then the directory associated with the
    current buffer is used. In other words, supplying =:dir path=
    temporarily has the same effect as changing the current directory
    with =M-x cd path=, and then not supplying =:dir=. Under the
    surface, =:dir= simply sets the value of the emacs variable
    =default-directory=.

    When using =:dir=, you should supply a relative path for [[#header-argument-file][file
    output]] (e.g. =:file myfile.jpg= or =:file results/myfile.jpg=) in
    which case that path will be interpreted relative to the default
    directory.

    In other words, if you want your plot to go into a folder called
    Work in your home directory, you could use

@example 
  #+begin_src R :file myplot.png :dir ~/Work
  matplot(matrix(rnorm(100), 10), type="l")
  #+end_src
@end example

@subsubheading Remote execution
     A directory on a remote machine can be specified using [[http://www.gnu.org/software/tramp/#Filename-Syntax][tramp
     filename syntax]], in which case the code will be executed on the
     remote machine[fn:2]. An example is

@example 
#+begin_src R :file plot.png :dir /dand@@yakuba.princeton.edu:
  plot(1:10, main=system("hostname", intern=TRUE))
#+end_src
@end example

Text results will be returned to the local org buffer as normal, and
file output will be created on the remote machine with relative paths
interpreted relative to the remote directory. An org link to the
remote file will be created.

So in the above example a plot will be created on the remote machine,
and a link of the following form will be inserted in the org buffer:

@example 
[[file:/scp:dand@@yakuba.princeton.edu:/home/dand/plot.png][plot.png]]
@end example

Most of this functionality follows immediately from the fact that
=:dir= sets the value of the emacs variable =default-directory=,
thanks to [[http://www.gnu.org/software/tramp/][tramp]]. Those using XEmacs, or GNU Emacs prior to
version 23 may need to install tramp separately in order for the
above features to work correctly.

@subsubheading Further points
     - If =:dir= is used in conjunction with =:session=, although it
       will determine the starting directory for a new session as
       expected, no attempt is currently made to alter the directory
       associated with an existing session.
     - =:dir= should typically not be used to create files during
       export with =:exports results= or =:exports both=. The reason
       is that, in order to retain portability of exported material
       between machines, during export, links inserted into the buffer
       will *not* be expanded against default directory. Therefore, if
       default-directory is altered using =:dir=, it it probable that
       the file will be created in a location to which the link does
       not point.
@subsubsection =:exports=
    :PROPERTIES:
    :CUSTOM_ID: header-argument-exports
    :END:

    Specify what should be included in HTML or LaTeX exports of the
    Org-mode file.

    - code :: the default.  The body of code is included
              into the exported file.  E.g., =:exports code=.
    - results :: the result of evaluating the code is included in the
                  exported file. E.g., =:exports results=.
    - both :: both the code and results are included in the exported
               file. E.g., =:exports both=.
    - none :: nothing is included in the exported file.  E.g.,
               =:exports none=.

@subsubsection =:tangle=
    :PROPERTIES:
    :CUSTOM_ID: tangle-header-arguments
    :END:

    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.  E.g., =:tangle yes=.
    - no :: the default.  The source code block is not
          exported to a source code file.  E.g., =:tangle no=.
    - other :: Any other string passed to the =:tangle= header argument
                is interpreted as a file basename to which the block will
                be exported.  E.g., =:tangle basename=.

@subsubsection =:session=
    :PROPERTIES:
    :CUSTOM_ID: header-argument-session
    :END:

    Start a session for an interpreted language where state is
    preserved.  This applies particularly to the supported languages
    python, R and ruby.

    By default, a session is not started.

    A string passed to the =:session= header argument will give the
    session a name.  This makes it possible to run concurrent
    sessions for each interpreted language.

@subsubsection =:noweb=
    :PROPERTIES:
    :CUSTOM_ID: header-argument-noweb
    :END:

    Controls the expansion of [[noweb-reference-syntax][noweb syntax]] references in a
    source code block.  This header argument can have one of two
    values: =yes= or =no=.
    - =no= :: the default.  No [[noweb-reference-syntax][noweb syntax]] specific action is taken
         on evaluating source code blocks/  However, noweb references
         will still be expanded during tangling.
    - =yes= :: all [[noweb-reference-syntax][noweb syntax]] references in the body of the source
               code block will be expanded before the block is evaluated.

@subsubheading Noweb Prefix Lines

     Noweb insertions are now placed behind the line prefix of the
     =<<reference>>=.

     This behavior is illustrated in the following example.  Because
     the =<<example>>= noweb reference appears behind the SQL
     comment syntax, each line of the expanded noweb reference will
     be commented.

     This source code block:

     @example
       -- <<example>>
     @end example


     expands to:

     @example
       -- this is the
       -- multi-line body of example
     @end example

     Note that noweb replacement text that does *not* contain any
     newlines will not be affected by this change, so it is still
     possible to use inline noweb references.

     Thanks to Sébastien Vauban for this idea.

@subsubsection =:cache=
    :PROPERTIES:
    :CUSTOM_ID: header-argument-cache
    :END:

    Controls the use of in-buffer caching of source code block
    results to avoid re-running unchanged source code blocks.  This
    header argument can have one of two values: =yes= or =no=.
    - =no= :: The default.  No caching takes place and the source
         code block will be run every time it is executed.
    - =yes= :: every time the source code block is run a sha1 hash of
         the code and arguments passed to the block will be
         generated.  This hash is packed into the =#+results:= line
         of the results and will be checked on subsequent executions
         of the source code block.  If the source code block has not
         changed since the last time it was evaluated, it will not be
         re-evaluated.

@section Results
    :PROPERTIES:
    :CUSTOM_ID: results-specification
    :END:

    The way in which results are handled depends on whether a [[header-argument-session][session]]
    is invoked, as well as on whether
    [[header-argument-results-collection][=:results value=] or
    [[header-argument-results-collection][=:results output=]] is used. The following table shows the
    possibilities:

    |                   | non-session (default)    | =:session=                          |
    |-------------------+--------------------------+-------------------------------------|
    | =:results value=  | value of last expression | value of last expression            |
    | =:results output= | contents of stdout       | concatenation of interpreter output |

    *Note:*  With =:results value=, the result in both =:session= and
    non-session is returned to Org-mode as a table (a one- or
    two-dimensional vector of strings or numbers) when appropriate.

@subsection Non-session
@subsubsection =:results value=
      This is the default. Internally, the value is obtained by
      wrapping the code in a function definition in the external
      language, and evaluating that function. Therefore, code should be
      written as if it were the body of such a function. In particular,
      note that python does not automatically return a value from a
      function unless a =return= statement is present, and so a
      'return' statement will usually be required in python.

      This is the only one of the four evaluation contexts in which the
      code is automatically wrapped in a function definition.

@subsubsection =:results output=
      The code is passed to the interpreter as an external process, and
      the contents of the standard output stream are returned as
      text. (In certain languages this also contains the error output
      stream; this is an area for future work.)

@subsection =:session=
@subsubsection =:results value=
      The code is passed to the interpreter running as an interactive
      Emacs inferior process. The result returned is the result of the
      last evaluation performed by the interpreter. (This is obtained in
      a language-specific manner: the value of the variable =_= in
      python and ruby, and the value of =.Last.value= in R).

@subsubsection =:results output=
       The code is passed to the interpreter running as an interactive
       Emacs inferior process. The result returned is the concatenation
       of the sequence of (text) output from the interactive
       interpreter. Notice that this is not necessarily the same as what
       would be sent to stdout if the same code were passed to a
       non-interactive interpreter running as an external process. For
       example, compare the following two blocks:


@example
#+begin_src python :results output
       print "hello"
       2
       print "bye"
#+end_src

#+resname:
       : hello
       : bye
@end example

       In non-session mode, the '2' is not printed and does not appear.
@example
#+begin_src python :results output :session
       print "hello"
       2
       print "bye"
#+end_src

#+resname:
       : hello
       : 2
       : bye
@end example

       But in =:session= mode, the interactive interpreter receives input '2'
       and prints out its value, '2'. (Indeed, the other print statements are
       unnecessary here).

@section Noweb Reference Syntax
  :PROPERTIES:
  :CUSTOM_ID: noweb-reference-syntax
  :END:

  The [[http://www.cs.tufts.edu/~nr/noweb/][Noweb]] Literate Programming system allows named blocks of code to
  be referenced by using the familiar Noweb syntax:
  : <<code-block-name>>

  Noweb references are handled differently during evaluation and
  tangling.

  When a document is tangled, Noweb references are replaced with the
  named source code block.

  When a source code block is evaluated, the action depends upon the
  value of the =:noweb= header argument.  If =:noweb yes=, then a
  Noweb reference is expanded before evaluation.  If =:noweb no=,
  the default, then the reference is not expanded before
  evaluation.

  *Note:* the default value, =:noweb no=, was chosen to ensure that
  Org-babel does not break correct code in a language, such as Ruby,
  where =<<arg>>= is a syntactically valid construct.  If =<<arg>>= is
  not syntactically valid in languages that you use, then please
  consider [[*System%20wide][setting the default value]].

  An example that uses the Noweb reference syntax is provided in the
  [[literate programming example]].

@section Key Bindings & Useful Functions

  Org-babel re-binds many common Org-mode key sequences depending on
  the context.  Within a source-code block the following sequences
  are rebound:
  | =C-c C-c= | [[function-org-babel-execute][org-babel-execute-src-block]]     |
  | =C-c C-o= | [[function-org-babel-open-src-block-result][org-babel-open-src-block-result]] |
  | =C-up=    | [[function-org-babel-load-in-session][org-babel-load-in-session]]       |
  | =M-down=  | [[function-org-babel-pop-to-session][org-babel-pop-to-session]]        |

  Org-babel also exposes a number of functions behind the common
  =org-babel-key-prefix= of =C-c M-b=:
@example
  #+begin_src emacs-lisp :exports none
     (lambda (binding
       (list (format "\\C-c \\M-b %s"
                     (car binding))
             (format "[[function-%s][%s]]"
                     (cdr binding) (cdr binding))))
     org-babel-key-bindings)
  #+end_src
@end example

  | =C-c M-b t= | [[function-org-babel-tangle][org-babel-tangle]]                  |
  | =C-c M-b T= | [[function-org-babel-tangle-file][org-babel-tangle-file]]             |
  | =C-c M-b e= | [[function-org-babel-execute-src-block][org-babel-execute-src-block]]       |
  | =C-c M-b s= | [[function-org-babel-execute-subtree][org-babel-execute-subtree]]         |
  | =C-c M-b b= | [[function-org-babel-execute-buffer][org-babel-execute-buffer]]          |
  | =C-c M-b h= | [[function-org-babel-sha1-hash][org-babel-sha1-hash]]               |
  | =C-c M-b g= | [[function-org-babel-goto-named-source-block][org-babel-goto-named-source-block]] |
  | =C-c M-b l= | [[function-org-babel-lob-ingest][org-babel-lob-ingest]]              |

@subsection Functions
@subsubsection org-babel-execute-src-block
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-execute-src-block
    :END:

@example
  org-babel-execute-src-block is an interactive Lisp function in
  `org-babel.el'.

  (org-babel-execute-src-block &optional ARG INFO PARAMS)

  Execute the current source code block, and insert the results
  into the buffer.  Source code execution and the collection and
  formatting of results can be controlled through a variety of
  header arguments.

  Optionally supply a value for INFO in the form returned by
  `org-babel-get-src-block-info'.

  Optionally supply a value for PARAMS which will be merged with
  the header arguments specified at the front of the source code
  block.
@end example

@subsubsection org-babel-open-src-block-result
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-open-src-block-result
    :END:

@example
  org-babel-open-src-block-result is an interactive Lisp function in
  `org-babel.el'.

  (org-babel-open-src-block-result &optional RE-RUN)

  If `point' is on a src block then open the results of the
  source code block, otherwise return nil.  With optional prefix
  argument RE-RUN the source-code block is evaluated even if
  results already exist.
@end example

@subsubsection org-babel-load-in-session
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-load-in-session
    :END:

@example
  org-babel-load-in-session is an interactive Lisp function in
  `org-babel.el'.

  (org-babel-load-in-session &optional ARG INFO)

  Load the body of the current source-code block.  Evaluate the
  header arguments for the source block before entering the
  session.  After loading the body this pops open the session.

  [back]
@end example

@subsubsection org-babel-pop-to-session
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-pop-to-session
    :END:

@example
  org-babel-pop-to-session is an interactive Lisp function in
  `org-babel.el'.

  (org-babel-pop-to-session &optional ARG INFO)

  Pop to the session of the current source-code block.  If
  called with a prefix argument then evaluate the header arguments
  for the source block before entering the session.  Copy the body
  of the source block to the kill ring.

  [back]
@end example

@subsubsection org-babel-tangle
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-tangle
    :END:

@example
  org-babel-tangle is an interactive Lisp function in
  `org-babel-tangle.el'.

  It is bound to C-c M-b t.

  (org-babel-tangle &optional TARGET-FILE LANG)

  Extract the bodies of all source code blocks from the current
  file into their own source-specific files.  Optional argument
  TARGET-FILE can be used to specify a default export file for all
  source blocks.  Optional argument LANG can be used to limit the
  exported source code blocks by language.
@end example

@subsubsection org-babel-execute-subtree
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-execute-subtree
    :END:

@example
  org-babel-execute-subtree is an interactive Lisp function in
  `org-babel.el'.

  It is bound to C-c M-b s.

  (org-babel-execute-subtree &optional ARG)

  Replace EVAL snippets in the entire subtree.
@end example

@subsubsection org-babel-execute-buffer
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-execute-buffer
    :END:

@example
  org-babel-execute-buffer is an interactive Lisp function in
  `org-babel.el'.

  It is bound to C-c M-b b.

  (org-babel-execute-buffer &optional ARG)

  Replace EVAL snippets in the entire buffer.
@end example

@subsubsection org-babel-sha1-hash
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-sha1-hash
    :END:

@example
  org-babel-sha1-hash is an interactive Lisp function in `org-babel.el'.

  It is bound to C-c M-b h.

  (org-babel-sha1-hash &optional INFO)

  Not documented.
@end example

@subsubsection org-babel-goto-named-source-block
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-goto-named-source-block
    :END:

@example
  org-babel-goto-named-source-block is an interactive Lisp function in
  `org-babel.el'.

  It is bound to C-c M-b g.

  (org-babel-goto-named-source-block &optional NAME)

  Go to a named source-code block.
@end example

@subsubsection org-babel-lob-ingest
    :PROPERTIES:
    :CUSTOM_ID: function-org-babel-lob-ingest
    :END:

@example
  org-babel-lob-ingest is an interactive Lisp function in
  `org-babel-lob.el'.

  It is bound to C-c M-b l.

  (org-babel-lob-ingest &optional FILE)

  Add all source-blocks defined in FILE to `org-babel-library-of-babel'.
@end example

@section Batch Execution
It is possible to call Org-babel functions from the command line.
This shell script calls [[function-org-babel-tangle][org-babel-tangle]] on every one of its
arguments.

Be sure to adjust the paths to fit your system.
@example
  #!/bin/sh
  # -*- mode: shell-script -*-
  #
  # tangle a file with org-babel
  #
  DIR=`pwd`
  FILES=""

  # wrap each argument in the code required to call tangle on it
  for i in $@@; do
  FILES="$FILES \"$i\""
  done

  emacsclient \
  --eval "(progn
  (add-to-list 'load-path (expand-file-name \"~/src/org/lisp/\"))
  (add-to-list 'load-path (expand-file-name \"~/src/org/contrib/lisp/\"))
  (require 'org)(require 'org-exp)(require 'org-babel)
  (mapc (lambda (file)
         (find-file (expand-file-name file \"$DIR\"))
         (org-babel-tangle)
         (kill-buffer)) '($FILES)))"
@end example

@section Footnotes

[fn:1] The former use of the =shell= identifier is now deprecated.

[fn:2] As long as the interpreter executable is found on the remote
machine: see the variable =tramp-remote-path=