forked from mirrors/org-mode
58f1dbccf8
Also remove blank lines before the ";;; org*el ends here" declarations. Having a "Version" header forced us to update every file when releasing a new version of Org; it also forced us to update every file when merging Org with Emacs trunk, thus cluttering the diffs between the previously merged version and the new one with useless information. Glenn Morris suggested this in emacs-devel: http://lists.gnu.org/archive/html/emacs-devel/2011-08/msg00322.html
263 lines
9.5 KiB
EmacsLisp
263 lines
9.5 KiB
EmacsLisp
;;; ob-octave.el --- org-babel functions for octave and matlab evaluation
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;; Copyright (C) 2010-2011 Free Software Foundation, Inc.
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;; Author: Dan Davison
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;; Keywords: literate programming, reproducible research
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;; Homepage: http://orgmode.org
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;; This file is part of GNU Emacs.
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;; GNU Emacs is free software: you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; GNU Emacs is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
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;;; Commentary:
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;;; Requirements:
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;; octave
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;; octave-mode.el and octave-inf.el come with GNU emacs
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;;; Code:
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(require 'ob)
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(require 'ob-ref)
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(require 'ob-comint)
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(require 'ob-eval)
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(eval-when-compile (require 'cl))
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(declare-function matlab-shell "ext:matlab-mode")
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(declare-function matlab-shell-run-region "ext:matlab-mode")
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(defvar org-babel-default-header-args:matlab '())
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(defvar org-babel-default-header-args:octave '())
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(defvar org-babel-matlab-shell-command "matlab -nosplash"
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"Shell command to run matlab as an external process.")
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(defvar org-babel-octave-shell-command "octave -q"
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"Shell command to run octave as an external process.")
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(defvar org-babel-matlab-with-emacs-link nil
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"If non-nil use matlab-shell-run-region for session evaluation.
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This will use EmacsLink if (matlab-with-emacs-link) evaluates
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to a non-nil value.")
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(defvar org-babel-matlab-emacs-link-wrapper-method
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"%s
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if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
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else, save -ascii %s ans
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end
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delete('%s')
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")
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(defvar org-babel-octave-wrapper-method
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"%s
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if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
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else, dlmwrite('%s', ans, '\\t')
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end")
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(defvar org-babel-octave-eoe-indicator "\'org_babel_eoe\'")
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(defvar org-babel-octave-eoe-output "ans = org_babel_eoe")
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(defun org-babel-execute:matlab (body params)
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"Execute a block of matlab code with Babel."
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(org-babel-execute:octave body params 'matlab))
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(defun org-babel-execute:octave (body params &optional matlabp)
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"Execute a block of octave code with Babel."
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(let* ((session
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(funcall (intern (format "org-babel-%s-initiate-session"
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(if matlabp "matlab" "octave")))
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(cdr (assoc :session params)) params))
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(vars (mapcar #'cdr (org-babel-get-header params :var)))
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(result-params (cdr (assoc :result-params params)))
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(result-type (cdr (assoc :result-type params)))
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(out-file (cdr (assoc :file params)))
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(full-body
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(org-babel-expand-body:generic
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body params (org-babel-variable-assignments:octave params)))
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(result (org-babel-octave-evaluate
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session full-body result-type matlabp)))
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(org-babel-reassemble-table
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result
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(org-babel-pick-name
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(cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
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(org-babel-pick-name
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(cdr (assoc :rowname-names params)) (cdr (assoc :rownames params))))))
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(defun org-babel-prep-session:matlab (session params)
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"Prepare SESSION according to PARAMS."
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(org-babel-prep-session:octave session params 'matlab))
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(defun org-babel-variable-assignments:octave (params)
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"Return list of octave statements assigning the block's variables"
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(mapcar
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(lambda (pair)
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(format "%s=%s;"
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(car pair)
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(org-babel-octave-var-to-octave (cdr pair))))
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(mapcar #'cdr (org-babel-get-header params :var))))
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(defalias 'org-babel-variable-assignments:matlab
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'org-babel-variable-assignments:octave)
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(defun org-babel-octave-var-to-octave (var)
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"Convert an emacs-lisp value into an octave variable.
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Converts an emacs-lisp variable into a string of octave code
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specifying a variable of the same value."
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(if (listp var)
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(concat "[" (mapconcat #'org-babel-octave-var-to-octave var
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(if (listp (car var)) "; " ",")) "]")
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(format "%s" (or var "nil"))))
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(defun org-babel-prep-session:octave (session params &optional matlabp)
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"Prepare SESSION according to the header arguments specified in PARAMS."
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(let* ((session (org-babel-octave-initiate-session session params matlabp))
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(var-lines (org-babel-variable-assignments:octave params)))
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(org-babel-comint-in-buffer session
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(mapc (lambda (var)
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(end-of-line 1) (insert var) (comint-send-input nil t)
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(org-babel-comint-wait-for-output session)) var-lines))
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session))
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(defun org-babel-matlab-initiate-session (&optional session params)
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"Create a matlab inferior process buffer.
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If there is not a current inferior-process-buffer in SESSION then
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create. Return the initialized session."
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(org-babel-octave-initiate-session session params 'matlab))
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(defun org-babel-octave-initiate-session (&optional session params matlabp)
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"Create an octave inferior process buffer.
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If there is not a current inferior-process-buffer in SESSION then
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create. Return the initialized session."
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(if matlabp (require 'matlab) (require 'octave-inf))
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(unless (string= session "none")
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(let ((session (or session
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(if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
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(if (org-babel-comint-buffer-livep session) session
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(save-window-excursion
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(if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
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(run-octave))
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(rename-buffer (if (bufferp session) (buffer-name session)
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(if (stringp session) session (buffer-name))))
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(current-buffer))))))
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(defun org-babel-octave-evaluate
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(session body result-type &optional matlabp)
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"Pass BODY to the octave process in SESSION.
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If RESULT-TYPE equals 'output then return the outputs of the
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statements in BODY, if RESULT-TYPE equals 'value then return the
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value of the last statement in BODY, as elisp."
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(if session
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(org-babel-octave-evaluate-session session body result-type matlabp)
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(org-babel-octave-evaluate-external-process body result-type matlabp)))
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(defun org-babel-octave-evaluate-external-process (body result-type matlabp)
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"Evaluate BODY in an external octave process."
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(let ((cmd (if matlabp
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org-babel-matlab-shell-command
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org-babel-octave-shell-command)))
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(case result-type
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(output (org-babel-eval cmd body))
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(value (let ((tmp-file (org-babel-temp-file "octave-")))
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(org-babel-eval
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cmd
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(format org-babel-octave-wrapper-method body
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(org-babel-process-file-name tmp-file 'noquote)
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(org-babel-process-file-name tmp-file 'noquote)))
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(org-babel-octave-import-elisp-from-file tmp-file))))))
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(defun org-babel-octave-evaluate-session
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(session body result-type &optional matlabp)
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"Evaluate BODY in SESSION."
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(let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
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(wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
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(full-body
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(case result-type
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(output
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(mapconcat
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#'org-babel-chomp
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(list body org-babel-octave-eoe-indicator) "\n"))
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(value
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(if (and matlabp org-babel-matlab-with-emacs-link)
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(concat
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(format org-babel-matlab-emacs-link-wrapper-method
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body
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(org-babel-process-file-name tmp-file 'noquote)
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(org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
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(mapconcat
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#'org-babel-chomp
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(list (format org-babel-octave-wrapper-method
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body
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(org-babel-process-file-name tmp-file 'noquote)
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(org-babel-process-file-name tmp-file 'noquote))
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org-babel-octave-eoe-indicator) "\n")))))
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(raw (if (and matlabp org-babel-matlab-with-emacs-link)
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(save-window-excursion
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(with-temp-buffer
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(insert full-body)
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(write-region "" 'ignored wait-file nil nil nil 'excl)
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(matlab-shell-run-region (point-min) (point-max))
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(message "Waiting for Matlab Emacs Link")
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(while (file-exists-p wait-file) (sit-for 0.01))
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"")) ;; matlab-shell-run-region doesn't seem to
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;; make *matlab* buffer contents easily
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;; available, so :results output currently
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;; won't work
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(org-babel-comint-with-output
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(session
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(if matlabp
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org-babel-octave-eoe-indicator
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org-babel-octave-eoe-output)
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t full-body)
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(insert full-body) (comint-send-input nil t)))) results)
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(case result-type
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(value
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(org-babel-octave-import-elisp-from-file tmp-file))
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(output
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(progn
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(setq results
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(if matlabp
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(cdr (reverse (delq "" (mapcar
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#'org-babel-octave-read-string
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(mapcar #'org-babel-trim raw)))))
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(cdr (member org-babel-octave-eoe-output
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(reverse (mapcar
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#'org-babel-octave-read-string
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(mapcar #'org-babel-trim raw)))))))
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(mapconcat #'identity (reverse results) "\n"))))))
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(defun org-babel-octave-import-elisp-from-file (file-name)
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"Import data from FILE-NAME.
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This removes initial blank and comment lines and then calls
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`org-babel-import-elisp-from-file'."
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(let ((temp-file (org-babel-temp-file "octave-matlab-")) beg end)
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(with-temp-file temp-file
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(insert-file-contents file-name)
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(re-search-forward "^[ \t]*[^# \t]" nil t)
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(if (< (setq beg (point-min))
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(setq end (point-at-bol)))
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(delete-region beg end)))
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(org-babel-import-elisp-from-file temp-file '(16))))
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(defun org-babel-octave-read-string (string)
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"Strip \\\"s from around octave string"
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(if (string-match "^\"\\([^\000]+\\)\"$" string)
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(match-string 1 string)
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string))
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(provide 'ob-octave)
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;;; ob-octave.el ends here
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