Re: [babel] org-babel for matlab?

From: Darlan Cavalcante Moreira <darcamo@gmail.com>
To: Dan Davison <davison@stats.ox.ac.uk>
Cc: emacs-orgmode@gnu.org, "stophl..."@yahoo.co.uk
Subject: Re: [babel] org-babel for matlab?
Date: Thu, 18 Feb 2010 15:41:11 +0100	[thread overview]
Message-ID: <4b7d5189.101abc0a.2dea.0a74@mx.google.com> (raw)
In-Reply-To: <871vgjolph.fsf_-_@stats.ox.ac.uk>

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I'm afraid I can't help much on this. I just used the org-babel-template.el file
provided by Eric and did a search and replace as told in the file comments in
order to make tangle work for octave and MATLAB. I didn't implement any function
(I only know enough lisp to understand my own .emacs file).

- Darlan

[-- Attachment #2: org-babel-matlab.el --]
[-- Type: application/octet-stream, Size: 5941 bytes --]

;;; org-babel-matlab.el --- org-babel functions for matlab evaluation

;; Copyright (C) your name here

;; Author: your name here
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
;; Version: 0.01

;;; License:

;; 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, 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 GNU Emacs; see the file COPYING.  If not, write to the
;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301, USA.

;;; Commentary:

;; This file is not intended to ever be loaded by org-babel, rather it
;; is a template for use in adding new language support to Org-babel.
;; Good first steps are to copy this file to a file named by the
;; language you are adding, and then use `query-replace' to replace
;; all strings of "template" in this file with the name of your new
;; language.
;;
;; If you have questions as to any of the portions of the file defined
;; below please look to existing language support for guidance.
;;
;; If you are planning on adding a language to org-babel we would ask
;; that if possible you fill out the FSF copyright assignment form
;; available at http://orgmode.org/request-assign-future.txt as this
;; will simplify the eventual inclusion of your addition into
;; org-babel and possibly at some point into org-mode and Emacs
;; proper.

;;; Requirements:

;; Use this section to list the requirements of this language.  Most
;; languages will require that at least the language be installed on
;; the user's system, and the Emacs major mode relevant to the
;; language be installed as well.

;;; Code:
(require 'org-babel)
;; possibly require modes required for your language

;; Add this language to the list of supported languages.  Org-babel
;; will match the string below against the declared language of the
;; source-code block.
(org-babel-add-interpreter "matlab")

;; specify the name, file extension, and shebang line for this language
(add-to-list 'org-babel-tangle-langs '("matlab" "m" "#!/usr/bin/env matlab"))

;; This is the main function which is called to evaluate a code
;; block.  It should setup the source code block according to all of
;; the header arguments packaged into params, including...
;; - defining variables
;; - optionally starting up a session (depending on the value of the
;;   :session) header argument
;;
;; This function will then evaluate the body of the source code and
;; return the results as emacs-lisp depending on the value of the
;; :results header argument
;; - output means that the output to STDOUT will be captured and
;;   returned
;; - value means that the value of the last statement in the
;;   source code block will be returned
;;
;; The most common first step in this function is the expansion of the
;; PARAMS argument using `org-babel-process-params'.
;;
;; Please feel free to not implement options which aren't appropriate
;; for your language (e.g. not all languages support interactive
;; "session" evaluation).  Also you are free to define any new header
;; arguments which you feel may be useful -- all header arguments
;; specified by the user will be available in the PARAMS variable.
(defun org-babel-execute:matlab (body params)
  "Execute a block of Matlab code with org-babel.  This function is
called by `org-babel-execute-src-block' via multiple-value-bind."
  (message "executing Matlab source code block")
  (let* ((processed-params (org-babel-process-params params))
         ;; set the session if the session variable is non-nil
         (session (org-babel-matlab-initiate-session (first processed-params)))
         ;; variables assigned for use in the block
         (vars (second processed-params))
         (result-params (third processed-params))
         ;; either OUTPUT or VALUE which should behave as described above
         (result-type (fourth processed-params))
         (full-body (concat
                     ;; prepend code to define all arguments passed to the code block
                     ;; (may not be appropriate for all languages)
                     (mapconcat
                      (lambda (pair)
                        (format "%s=%s"
                                (car pair)
                                (org-babel-matlab-var-to-matlab (cdr pair))))
                      vars "\n") "\n" body "\n")))
    ;; actually execute the source-code block either in a session or
    ;; possibly by dropping it to a temporary file and evaluating the
    ;; file.
    ;; 
    ;; for session based evaluation the helpers defined in
    ;; `org-babel-comint' will probably be helpful.
    ))

;; This function should be used to assign any variables in params in
;; the context of the session environment.
(defun org-babel-prep-session:matlab (session params)
  "Prepare SESSION according to the header arguments specified in PARAMS."
  )

(defun org-babel-matlab-var-to-matlab (var)
  "Convert an elisp var into a string of matlab source code
specifying a var of the same value."
  )

(defun org-babel-matlab-table-or-string (results)
  "If the results look like a table, then convert them into an
Emacs-lisp table, otherwise return the results as a string."
  )

(defun org-babel-matlab-initiate-session (&optional session)
  "If there is not a current inferior-process-buffer in SESSION
then create.  Return the initialized session."
  (unless (string= session "none")
    ))

(provide 'org-babel-matlab)
;;; org-babel-matlab.el ends here

[-- Attachment #3: org-babel-octave.el --]
[-- Type: application/octet-stream, Size: 5941 bytes --]

;;; org-babel-octave.el --- org-babel functions for octave evaluation

;; Copyright (C) your name here

;; Author: your name here
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
;; Version: 0.01

;;; License:

;; 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, 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 GNU Emacs; see the file COPYING.  If not, write to the
;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301, USA.

;;; Commentary:

;; This file is not intended to ever be loaded by org-babel, rather it
;; is a template for use in adding new language support to Org-babel.
;; Good first steps are to copy this file to a file named by the
;; language you are adding, and then use `query-replace' to replace
;; all strings of "template" in this file with the name of your new
;; language.
;;
;; If you have questions as to any of the portions of the file defined
;; below please look to existing language support for guidance.
;;
;; If you are planning on adding a language to org-babel we would ask
;; that if possible you fill out the FSF copyright assignment form
;; available at http://orgmode.org/request-assign-future.txt as this
;; will simplify the eventual inclusion of your addition into
;; org-babel and possibly at some point into org-mode and Emacs
;; proper.

;;; Requirements:

;; Use this section to list the requirements of this language.  Most
;; languages will require that at least the language be installed on
;; the user's system, and the Emacs major mode relevant to the
;; language be installed as well.

;;; Code:
(require 'org-babel)
;; possibly require modes required for your language

;; Add this language to the list of supported languages.  Org-babel
;; will match the string below against the declared language of the
;; source-code block.
(org-babel-add-interpreter "octave")

;; specify the name, file extension, and shebang line for this language
(add-to-list 'org-babel-tangle-langs '("octave" "m" "#!/usr/bin/env octave"))

;; This is the main function which is called to evaluate a code
;; block.  It should setup the source code block according to all of
;; the header arguments packaged into params, including...
;; - defining variables
;; - optionally starting up a session (depending on the value of the
;;   :session) header argument
;;
;; This function will then evaluate the body of the source code and
;; return the results as emacs-lisp depending on the value of the
;; :results header argument
;; - output means that the output to STDOUT will be captured and
;;   returned
;; - value means that the value of the last statement in the
;;   source code block will be returned
;;
;; The most common first step in this function is the expansion of the
;; PARAMS argument using `org-babel-process-params'.
;;
;; Please feel free to not implement options which aren't appropriate
;; for your language (e.g. not all languages support interactive
;; "session" evaluation).  Also you are free to define any new header
;; arguments which you feel may be useful -- all header arguments
;; specified by the user will be available in the PARAMS variable.
(defun org-babel-execute:octave (body params)
  "Execute a block of Octave code with org-babel.  This function is
called by `org-babel-execute-src-block' via multiple-value-bind."
  (message "executing Octave source code block")
  (let* ((processed-params (org-babel-process-params params))
         ;; set the session if the session variable is non-nil
         (session (org-babel-octave-initiate-session (first processed-params)))
         ;; variables assigned for use in the block
         (vars (second processed-params))
         (result-params (third processed-params))
         ;; either OUTPUT or VALUE which should behave as described above
         (result-type (fourth processed-params))
         (full-body (concat
                     ;; prepend code to define all arguments passed to the code block
                     ;; (may not be appropriate for all languages)
                     (mapconcat
                      (lambda (pair)
                        (format "%s=%s"
                                (car pair)
                                (org-babel-octave-var-to-octave (cdr pair))))
                      vars "\n") "\n" body "\n")))
    ;; actually execute the source-code block either in a session or
    ;; possibly by dropping it to a temporary file and evaluating the
    ;; file.
    ;; 
    ;; for session based evaluation the helpers defined in
    ;; `org-babel-comint' will probably be helpful.
    ))

;; This function should be used to assign any variables in params in
;; the context of the session environment.
(defun org-babel-prep-session:octave (session params)
  "Prepare SESSION according to the header arguments specified in PARAMS."
  )

(defun org-babel-octave-var-to-octave (var)
  "Convert an elisp var into a string of octave source code
specifying a var of the same value."
  )

(defun org-babel-octave-table-or-string (results)
  "If the results look like a table, then convert them into an
Emacs-lisp table, otherwise return the results as a string."
  )

(defun org-babel-octave-initiate-session (&optional session)
  "If there is not a current inferior-process-buffer in SESSION
then create.  Return the initialized session."
  (unless (string= session "none")
    ))

(provide 'org-babel-octave)
;;; org-babel-octave.el ends here

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At Wed, 17 Feb 2010 11:45:14 -0500,
Dan Davison <davison@stats.ox.ac.uk> wrote:
> 
> Darlan Cavalcante Moreira <darcamo@gmail.com> writes:
> 
> > This is also important for me (in fact, for octave). For now I used the template
> > file and I can tangle the code correctly, but since I didn't implement any
> > function for code execution tangling is all I've got.
> >
> > - Darlan
> 
> I was also going to suggest that if someone did this, they might want to
> try to address octave at the same time. 
> 
> Darlan -- would you like to share your initial version of octave
> support? If we get it onto a git repository then we can all have a look
> and maybe make a bit of progress. Either post it, or contact me off-line
> for the admin details for http://repo.or.cz/w/org-mode/babel.git.
> 
> I don't use either language but here are some comments about the various
> tasks and guesses about how hard they would be.
> 
> If someone could comment on the extent to which differences between
> matlab and octave (running as command-line external processes) are going
> to make shared org-babel support problematic that would probably be
> useful.
> 
> - external process :results output
>   Running octave as an external process under linux/OS X and collecting
>   stdout shouldn't be too hard. Presumably same for matlab? Windows
>   support: unavailable for matlab, but probably feasible for octave.
> 
> - external process :results value
>   This basically involves (in matlab/octave) writing vectors and arrays
>   to a tabular file (and then using existing code to import the org
>   table, but this bit can be taken from the files for another language)
> 
> - :session
>   At first glance it looks like there's an inferior octave mode that
>   should be suitable for use
>   with :session. Darlan -- do you have experience with this?
> 
>   http://www.gnu.org/software/octave/doc/interpreter/Running-Octave-From-Within-Emacs.html#Running-Octave-From-Within-Emacs
> 
> - Matlab :session on Windows
>   Getting org-babel to work with the MatLab "EmacsLink" module may well be
>   possible, but I would only be able to help very superficially.
> 
> Dan
> 
> 
> >
> > At Tue, 16 Feb 2010 21:16:44 +0100,
> > Bob Jansen <bobjansen@gmail.com> wrote:
> >> 
> >> Hi list,
> >> 
> >> Has any progress been made on this? I'm fairly new to org-mode and
> >> org-babel but this sounds to me like a very useful feature.
> >> 
> >> > Hi Christopher,
> >> >
> >> > I do not know of anyone working on matlab support for org-babel.  I am
> >> > attaching a template file which contains instructions for adding support
> >> > for a new language.  Depending on your level of familiarity with elisp
> >> > it could take anywhere from a couple of hours to a couple of days.
> >> > We're still debugging some of the original language specific files :)
> >> >
> >> > Best of Luck! -- Eric
> >> >
> >> >
> >> > Attachment: org-babel-template.el
> >> > Description: application/emacs-lisp
> >> >
> >> > Christopher Long <stophl...@yahoo.co.uk> writes:
> >> >
> >> > Dear All,
> >> >
> >> >    Has anyone started on a babel mode for matlab?  Or is anyone else
> >> > interested
> >> > in making it happen?  Or have a suggestion for a good template to
> >> > start from (babel-python? babel-R?)  And anyone has an estimate of how
> >> > time consuming such a project would be?
> >> >
> >> >    I'd like it to work on Windows and there isn't a console mode of Matlab
> >> > on windows, but you can evaluate code with EmacsLink and likely direct
> >> > all output to temporary files.
> >> > (I know EmacsLink was dropped in R2009a, but some of us are avoiding
> >> > upgrading
> >> > and hoping that Matlab will return EmacsLink in the future.)
> >> >
> >> >
> >> > Thanks,
> >> >
> >> > Stoph
> >> >
> >> >
> >> > _______________________________________________
> >> > Emacs-orgmode mailing list
> >> > Please use `Reply All' to send replies to the list.
> >> > Emacs-orgmode@gnu.org
> >> > http://lists.gnu.org/mailman/listinfo/emacs-orgmode
> >> 
> >> _______________________________________________
> >> Emacs-orgmode mailing list
> >> Please use `Reply All' to send replies to the list.
> >> Emacs-orgmode@gnu.org
> >> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
> >> 
> >> 
> >> --
> >> Met vriendelijke groet,
> >> 
> >> Bob Jansen
> >> 
> >> 
> >> _______________________________________________
> >> Emacs-orgmode mailing list
> >> Please use `Reply All' to send replies to the list.
> >> Emacs-orgmode@gnu.org
> >> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
> >
> >
> > _______________________________________________
> > Emacs-orgmode mailing list
> > Please use `Reply All' to send replies to the list.
> > Emacs-orgmode@gnu.org
> > http://lists.gnu.org/mailman/listinfo/emacs-orgmode

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