forked from mirrors/org-mode
245d98786d
Currently, this uses the presence of a temporary file to signal that Matlab Emacs Link evaluation is not yet complete. Emacs Link support added in collaboration with Christopher Long.
224 lines
8.7 KiB
EmacsLisp
224 lines
8.7 KiB
EmacsLisp
;;; org-babel-octave.el --- org-babel functions for octave and matlab evaluation
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;; Copyright (C) Dan Davison
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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: 0.01
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;;; License:
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;; This program 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, or (at your option)
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;; any later version.
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;;
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;; This program 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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;;
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
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;; Boston, MA 02110-1301, USA.
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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 'org-babel)
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(require 'octave-inf)
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(org-babel-add-interpreter "octave")
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(add-to-list 'org-babel-tangle-langs '("octave" "m" "#!/usr/bin/env octave"))
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(defvar org-babel-octave-shell-command "octave -q"
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"Shell command to use to run octave as an external process.")
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(defun org-babel-expand-body:octave (body params &optional processed-params)
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(let ((vars (second (or processed-params (org-babel-process-params params)))))
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(concat
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;; prepend code to define all arguments passed to the code block
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;; (may not be appropriate for all languages)
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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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(defun org-babel-execute:octave (body params &optional matlabp)
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"Execute a block of octave code with org-babel."
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(message (format "executing %s source code block" (if matlabp "matlab" "octave")))
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(let* ((processed-params (org-babel-process-params params))
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;; set the session if the session variable is non-nil
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(session (funcall (intern (format "org-babel-%s-initiate-session" lang))
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(first processed-params) params))
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(vars (second processed-params))
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(result-params (third processed-params))
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(result-type (fourth processed-params))
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(out-file (cdr (assoc :file params)))
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(augmented-body (org-babel-expand-body:octave body params processed-params))
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(result (org-babel-octave-evaluate 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 (nth 4 processed-params) (cdr (assoc :colnames params)))
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(org-babel-pick-name (nth 5 processed-params) (cdr (assoc :rownames params)))))))
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(defun org-babel-octave-var-to-octave (var)
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"Convert an emacs-lisp variable 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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(move-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-octave-initiate-session (&optional session params matlabp)
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"Create octave inferior process buffer.
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If there is not a current inferior-process-buffer in SESSION
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then create. Return the initialized session."
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(unless (string= session "none")
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(let ((session (or session (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)))) (current-buffer))))))
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(defvar org-babel-octave-wrapper-method
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"%s
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if ischar(ans)
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fid = fopen('%s', 'w')
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fprintf(fid, '%%s', ans)
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fprintf(fid, '\\n')
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fclose(fid)
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else
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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-octave-evaluate (session body result-type lang)
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"Pass BODY to the octave process.
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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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(let ((cmd (if matlabp org-babel-matlab-shell-command org-babel-octave-shell-command)))
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(save-excursion
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(case result-type
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(output
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(with-temp-buffer
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(insert body)
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(org-babel-shell-command-on-region (point-min) (point-max) cmd 'current-buffer 'replace)
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(buffer-string)))
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(value
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(let* ((tmp-file (make-temp-file "org-babel-results-")) exit-code
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(stderr
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(with-temp-buffer
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(insert (format org-babel-octave-wrapper-method body tmp-file tmp-file))
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(setq exit-code (org-babel-shell-command-on-region
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(point-min) (point-max) cmd nil 'replace (current-buffer)))
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(buffer-string))))
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(if (> exit-code 0) (org-babel-error-notify exit-code stderr))
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(org-babel-octave-import-elisp-from-file (org-babel-maybe-remote-file tmp-file))))))))
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(defun org-babel-octave-evaluate-session (session body result-type &optional matlabp)
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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 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 session
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(if matlabp org-babel-octave-eoe-indicator org-babel-octave-eoe-output) t
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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 (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 #'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 #'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 written to file by octave.
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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 'org-babel-octave)
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;;; org-babel-octave.el ends here
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