;;; org-babel-octave.el --- org-babel functions for octave and matlab evaluation
;; Copyright (C) Dan Davison
;; Author: Dan Davison
;; 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:
;;; Requirements:
;; octave
;; octave-mode.el and octave-inf.el come with GNU emacs
;;; Code:
(require 'org-babel)
(require 'octave-inf)
(org-babel-add-interpreter "octave")
(add-to-list 'org-babel-tangle-langs '("octave" "m" "#!/usr/bin/env octave"))
(defvar org-babel-octave-shell-command "octave -q"
"Shell command to use to run octave as an external process.")
(defun org-babel-execute:octave (body params &optional matlabp)
"Execute a block of octave code with org-babel."
(message (format "executing %s source code block" (if matlabp "matlab" "octave")))
(let* ((processed-params (org-babel-process-params params))
;; set the session if the session variable is non-nil
(session (funcall (intern (format "org-babel-%s-initiate-session" lang))
(first processed-params) params))
(vars (second processed-params))
(result-params (third processed-params))
(result-type (fourth processed-params))
(out-file (cdr (assoc :file params)))
(augmented-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"))
(result (org-babel-octave-evaluate session augmented-body result-type matlabp)))
(or out-file result)))
(defun org-babel-octave-var-to-octave (var)
"Convert an emacs-lisp variable into an octave variable.
Converts an emacs-lisp variable into a string of octave code
specifying a variable of the same value."
(if (listp var)
(concat "[" (mapconcat #'org-babel-octave-var-to-octave var ", ") "]")
(format "%S" var)))
(defun org-babel-prep-session:octave (session params &optional matlabp)
"Prepare SESSION according to the header arguments specified in PARAMS."
(let* ((session (org-babel-octave-initiate-session session params matlabp))
(vars (org-babel-ref-variables params))
(var-lines (mapcar
(lambda (pair)
(format "%s=%s"
(car pair)
(org-babel-octave-var-to-octave (cdr pair))))
vars)))
(org-babel-comint-in-buffer session
(mapc (lambda (var)
(move-end-of-line 1) (insert var) (comint-send-input nil t)
(org-babel-comint-wait-for-output session)) var-lines))
session))
(defun org-babel-octave-initiate-session (&optional session params matlabp)
"Create octave inferior process buffer.
If there is not a current inferior-process-buffer in SESSION
then create. Return the initialized session."
(unless (string= session "none")
(let ((session (or session (if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
(if (org-babel-comint-buffer-livep session) session
(save-window-excursion
(if matlabp (matlab-shell) (run-octave))
(rename-buffer (if (bufferp session) (buffer-name session)
(if (stringp session) session (buffer-name)))) (current-buffer))))))
(defvar org-babel-octave-wrapper-method
"%s
if ischar(ans)
fid = fopen('%s', 'w')
fprintf(fid, ans)
fprintf(fid, '\\n')
fclose(fid)
else
save -ascii %s ans
end")
(defvar org-babel-octave-eoe-indicator "\'org_babel_eoe\'")
(defvar org-babel-octave-eoe-output "ans = org_babel_eoe")
(defun org-babel-octave-evaluate (session body result-type lang)
"Pass BODY to the octave process.
If RESULT-TYPE equals 'output then return the outputs of the
statements in BODY, if RESULT-TYPE equals 'value then return the
value of the last statement in BODY, as elisp."
(if session
(org-babel-octave-evaluate-session session body result-type matlabp)
(org-babel-octave-evaluate-external-process body result-type matlabp)))
(defun org-babel-octave-evaluate-external-process (body result-type matlabp)
(let ((cmd (if matlabp org-babel-matlab-shell-command org-babel-octave-shell-command)))
(save-excursion
(case result-type
(output
(with-temp-buffer
(insert body)
(org-babel-shell-command-on-region (point-min) (point-max) cmd 'current-buffer 'replace)
(buffer-string)))
(value
(let* ((tmp-file (make-temp-file "org-babel-results-")) exit-code
(stderr
(with-temp-buffer
(insert (format org-babel-octave-wrapper-method body tmp-file tmp-file))
(setq exit-code (org-babel-shell-command-on-region
(point-min) (point-max) cmd nil 'replace (current-buffer)))
(buffer-string))))
(if (> exit-code 0) (org-babel-error-notify exit-code stderr))
(org-babel-octave-import-elisp-from-file (org-babel-maybe-remote-file tmp-file))))))))
(defun org-babel-octave-evaluate-session (session body result-type &optional matlabp)
(let* ((tmp-file (make-temp-file "org-babel-results-"))
(full-body
(case result-type
(output
(mapconcat
#'org-babel-chomp
(list body org-babel-octave-eoe-indicator) "\n"))
(value
(mapconcat
#'org-babel-chomp
(list (format org-babel-octave-wrapper-method body tmp-file tmp-file) org-babel-octave-eoe-indicator) "\n"))))
(raw (org-babel-comint-with-output session
(if matlabp org-babel-octave-eoe-indicator org-babel-octave-eoe-output) t
(insert full-body) (comint-send-input nil t))) results)
(case result-type
(value
(org-babel-octave-import-elisp-from-file (org-babel-maybe-remote-file tmp-file)))
(output
(progn
(setq results
(if matlabp
(cdr (reverse (delq "" (mapcar #'org-babel-octave-read-string
(mapcar #'org-babel-trim raw)))))
(cdr (member org-babel-octave-eoe-output
(reverse (mapcar #'org-babel-octave-read-string
(mapcar #'org-babel-trim raw)))))))
(mapconcat #'identity (reverse results) "\n"))))))
(defun org-babel-octave-import-elisp-from-file (file-name)
"Import data written to file by octave.
This removes initial blank and comment lines and then calls
`org-babel-import-elisp-from-file'."
(let ((temp-file (make-temp-file "org-babel-results-")) beg end)
(with-temp-file temp-file
(insert-file-contents file-name)
(re-search-forward "^[ \t]*[^# \t]" nil t)
(if (< (setq beg (point-min))
(setq end (point-at-bol)))
(delete-region beg end)))
(org-babel-import-elisp-from-file temp-file)))
(defun org-babel-octave-read-string (string)
"Strip \\\"s from around octave string"
(if (string-match "^\"\\([^\000]+\\)\"$" string)
(match-string 1 string)
string))
(provide 'org-babel-octave)
;;; org-babel-octave.el ends here