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a5f0bb404f
2010-08-01 Dan Davison <davison@stats.ox.ac.uk> * ob-octave.el (org-babel-octave-evaluate): Fix formal argument list
267 lines
9.8 KiB
EmacsLisp
267 lines
9.8 KiB
EmacsLisp
;;; ob-octave.el --- org-babel functions for octave and matlab evaluation
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;; Copyright (C) 2010 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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;; Version: 7.01trans
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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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(defun org-babel-expand-body:matlab (body params &optional processed-params)
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"Expand BODY according to PARAMS, return the expanded body."
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(org-babel-expand-body:octave body params processed-params))
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(defun org-babel-expand-body:octave (body params &optional processed-params)
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"Expand BODY according to PARAMS, return the expanded body."
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(let ((vars (nth 1 (or processed-params (org-babel-process-params params)))))
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(concat
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(mapconcat
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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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vars "\n") "\n" body "\n")))
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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, save -ascii %s ans
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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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(require 'matlab)
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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* ((processed-params (org-babel-process-params params))
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(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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(nth 0 processed-params) params))
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(vars (nth 1 processed-params))
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(result-params (nth 2 processed-params))
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(result-type (nth 3 processed-params))
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(out-file (cdr (assoc :file params)))
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(augmented-body
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(org-babel-expand-body:octave body params processed-params))
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(result (org-babel-octave-evaluate
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session augmented-body result-type matlabp)))
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(or out-file
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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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(nth 4 processed-params) (cdr (assoc :colnames params)))
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(org-babel-pick-name
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(nth 5 processed-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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(require 'matlab)
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(org-babel-prep-session:octave session params 'matlab))
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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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(format "%S" var)))
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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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(vars (org-babel-ref-variables params))
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(var-lines (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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vars)))
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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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(require 'matlab)
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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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(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 (make-temp-file "org-babel-results-")))
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(org-babel-eval
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cmd
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(format org-babel-octave-wrapper-method body tmp-file tmp-file))
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(org-babel-eval-read-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 (make-temp-file "org-babel-results-"))
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(wait-file (make-temp-file "org-babel-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 tmp-file tmp-file 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 tmp-file tmp-file)
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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
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(org-babel-maybe-remote-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 (make-temp-file "org-babel-results-")) 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)))
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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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;; arch-tag: d8e5f68b-ba13-440a-a495-b653e989e704
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;;; ob-octave.el ends here
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