[Beta Release / Development Invitation] Org-Babel --- code evaluation for reproducible-research and literate-programming in org-mode

[Beta Release / Development Invitation] Org-Babel --- code evaluation for reproducible-research and literate-programming in org-mode

[Eric Schulte]

For the past couple of months I have been working on Org-Babel, with Dan
Davison and (initially) Austin Frank.  Through Org-Babel Org-Mode can
communicate with programming languages.  Code contained in source-code
blocks can be evaluated and data can pass seamlessly between different
programming languages, Org-Mode constructs (tables, file links, example
text) and interactive comint buffers. One part of the project is the
"Library of Babel", which will be an extensible collection of ready-made
and easily-shortcut-callable source-code blocks for handling common
tasks.

Org-Babel provides a unified backend for source-code evaluation from
Org-Mode and with the "Library of Babel" does/will...
- allow seamless passing of data between source-code blocks and other
  org-mode constructs (tables, file links, example text)
- allow chaining of source-code blocks in different languages
- allow calling of source-code blocks from tables
- support literate programming (org-babel-tangle)
- enable reproducible research (multilingual Sweave-like functionality,
  i.e. plots and analysis results united with the code to generate them)
- replace org-exp-blocks enabling interactive evaluation of blocks
- replace org-plot
- replace org-R

We have been intending to share this with the list once development
stabilized, however this has proven to be a moving target as ideas for
new development have continually arisen faster than they have been
implemented.  Given the many recent related threads on list we've
decided now is a good time for an initial beta release and
development/feedback solicitation.

Please find the code at [1] or clone it from [2].  In the base directory
of the repo you will find org-babel.org, a monolithic file which
contains more information than you could ever want to know about the
functionality and development of Org-Babel.  If anyone wants to help
please send patches to Dan or myself, or contact me for commit access to
the repo.

Thanks and Enjoy,
Eric Schulte and Dan Davison

Footnotes: 
[1]  http://github.com/eschulte/org-babel/tree/master

[2]  git://github.com/eschulte/org-babel.git

Re: [Beta Release / Development Invitation] Org-Babel --- code evaluation for reproducible-research and literate-programming in org-mode

[Taru Karttunen]

Excerpts from Eric Schulte's message of Thu Jun 25 23:25:30 +0300 2009:
> For the past couple of months I have been working on Org-Babel, with Dan
> Davison and (initially) Austin Frank.  Through Org-Babel Org-Mode can
> communicate with programming languages.  Code contained in source-code
> blocks can be evaluated and data can pass seamlessly between different
> programming languages, Org-Mode constructs (tables, file links, example
> text) and interactive comint buffers. One part of the project is the
> "Library of Babel", which will be an extensible collection of ready-made
> and easily-shortcut-callable source-code blocks for handling common
> tasks.

How do I try it out?

I tried the following:
1) update org-mode to latest git
2) restart emacs and open org-babel.org
3) add the load path and (require 'org-babel)
4) press C-cC-c on a begin_src line
it only says "Local setup has been refreshed" and nothing happens.

ps. org-babel seems very nifty from reading things

- Taru Karttunen

Re: [Beta Release / Development Invitation] Org-Babel --- code evaluation for reproducible-research and literate-programming in org-mode

[Dan Davison]

Taru Karttunen <taruti@taruti.net> writes:

> Excerpts from Eric Schulte's message of Thu Jun 25 23:25:30 +0300 2009:
>> For the past couple of months I have been working on Org-Babel, with Dan
>> Davison and (initially) Austin Frank.  Through Org-Babel Org-Mode can
>> communicate with programming languages.  Code contained in source-code
>> blocks can be evaluated and data can pass seamlessly between different
>> programming languages, Org-Mode constructs (tables, file links, example
>> text) and interactive comint buffers. One part of the project is the
>> "Library of Babel", which will be an extensible collection of ready-made
>> and easily-shortcut-callable source-code blocks for handling common
>> tasks.
>
> How do I try it out?

Hi Taru and other potential org-babel collaborators,

org-babel-init.el is what you need, so:

(add-to-list 'load-path "/path/to/org-babel/lisp")
(require 'org-babel-init)

After that, good starting points to see in action some of the
functionality that Eric has implemented are the `Sandbox' section of
org-babel.org, and the large table in the `Tests' section. C-c C-c
anywhere in a source code block in the Sandbox should execute that
block. In the Tests section, C-u C-c C-c in the table runs a suite of
tests of org-babel functionality, updating the table with the results of
code evaluation in several languages, and flagging up failed tests (more
fun if you clear out the `results' and `pass' column first).

Dan

>
> I tried the following:
> 1) update org-mode to latest git
> 2) restart emacs and open org-babel.org
> 3) add the load path and (require 'org-babel)
> 4) press C-cC-c on a begin_src line
> it only says "Local setup has been refreshed" and nothing happens.
>
> ps. org-babel seems very nifty from reading things
>
> - Taru Karttunen
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Remember: use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode

Re: [Beta Release / Development Invitation] Org-Babel --- code evaluation for reproducible-research and literate-programming in org-mode

[Sebastian Rose]

Dan Davison <davison@stats.ox.ac.uk> writes:
> org-babel-init.el is what you need, so:
>
> (add-to-list 'load-path "/path/to/org-babel/lisp")
> (require 'org-babel-init)


and get:


Debugger entered--Lisp error: (file-error "Cannot open load file" "inf-ruby")
  require(inf-ruby)
  eval-buffer(#<buffer  *load*<2>> nil "/home/sebastian/emacs/lisp/ext/org-babel/lisp/langs/org-babel-ruby.el" nil t)  ; Reading at buffer position 1098
  load-with-code-conversion("/home/sebastian/emacs/lisp/ext/org-babel/lisp/langs/org-babel-ruby.el" "/home/sebastian/emacs/lisp/ext/org-babel/lisp/langs/org-babel-ruby.el" nil t)
  require(org-babel-ruby)
  eval-buffer(#<buffer  *load*> nil "/home/sebastian/emacs/lisp/ext/org-babel/lisp/org-babel-init.el" nil t)  ; Reading at buffer position 1393
  load-with-code-conversion("/home/sebastian/emacs/lisp/ext/org-babel/lisp/org-babel-init.el" "/home/sebastian/emacs/lisp/ext/org-babel/lisp/org-babel-init.el" nil t)
  require(org-babel-init)
  eval((require (quote org-babel-init)))
  eval-last-sexp-1(nil)
  eval-last-sexp(nil)
  call-interactively(eval-last-sexp nil nil)


file inf-ruby.el does not exist.

Where should it go, and what should it contain?


Looks sooo interesting, I need to know!! :)


   Sebastian

Re: [Beta Release / Development Invitation] Org-Babel --- code evaluation for reproducible-research and literate-programming in org-mode

[Eric Schulte]

Sebastian Rose <sebastian_rose@gmx.de> writes:

[...]

> file inf-ruby.el does not exist.
>
> Where should it go, and what should it contain?
>

inf-ruby.el is located in the util directory, however we were loading
files in the wrong order in the initialization file so it wasn't loaded
in time.  I just switched around the load order and committed, so please
pull the latest from git and git it another try.

Thanks -- Eric

>
> Looks sooo interesting, I need to know!! :)
>
>
>    Sebastian
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Remember: use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode

Re: [Beta Release / Development Invitation] Org-Babel --- code evaluation for reproducible-research and literate-programming in org-mode

[Sebastian Rose]

"Eric Schulte" <schulte.eric@gmail.com> writes:
> Sebastian Rose <sebastian_rose@gmx.de> writes:
>
> [...]
>
>> file inf-ruby.el does not exist.
>>
>> Where should it go, and what should it contain?
>>
>
> inf-ruby.el is located in the util directory, however we were loading
> files in the wrong order in the initialization file so it wasn't loaded
> in time.  I just switched around the load order and committed, so please
> pull the latest from git and git it another try.


Hey - that was it! Great, thanks Eric!


  Sebastian