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matlab-org.el
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matlab-org.el
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;;; matlab-org.el --- enable use of MATLAB with org-mode -*- lexical-binding: t -*-
;; Copyright (C) 2024 Free Software Foundation, Inc.
;; Author: John Ciolfi <[email protected]>
;;
;; 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, 675 Mass Ave, Cambridge, MA 02139, USA.
;;
;;; Commentary:
;;
;; Enable use of org-mode with MATLAB for creation of scientific papers, thesis, etc.
;; leveraging org-mode babel literal programming capabilities. See
;;
;; https://github.com/mathworks/Emacs-MATLAB-Mode/tree/default/examples/matlab-and-org-mode
;;
;;; Code:
(require 'cl-seq)
(eval-when-compile
(require 'org)
(require 'ob-octave))
(defun matlab--org-evaluate-advice (orig-fun session body result-type &optional matlabp)
"Advise org evaluation for MATLAB to fix issues.
ORIG-FUN is `org-babel-octave-evaluate' with arguments SESSION
BODY RESULT-TYPE MATLABP."
;; ----
;; 1) For "#+begin_src matlab :results file graphics" blocks, fix the print command sent to
;; MATLAB.
;; `org-babel-execute:octave' (called from `org-babel-octave-evaluate'):
;; - Emacs 27.2 with org 9.4.4 and Emacs 28.2 with org 9.5.5 contains
;; (format "print -dpng %s" gfx-file)
;; resulting in the correct:
;; print -dpng FIGURE.PNG
;; - Emacs 29.2 with org 9.6.15 contains
;; (format "print -dpng %S\nans=%S" gfx-file gfx-file)
;; which results in the figure being quoted which is not correct for MATLAB (we need it
;; unquoted for command dual)
;; print -dpng "FIGURE.PNG" ==> should be: print -dpng FIGURE.PNG
;; This this advice fixes the incorrect quoting.
(setq body (replace-regexp-in-string "^\\(print -dpng \\)\"\\([^\"]+\\)\"" "\\1\\2" body t))
;; ----
;; 2) For "#+begin_src matlab :results verbatim" blocks, fix how we collect the results from the
;; MATLAB "ans" variable by locally correcting org-babel-octave-wrapper-method.
(let ((org-babel-octave-wrapper-method
(concat "\
cd('" default-directory "');
%s
if ~exist('ans', 'var') ans=''; end; \
orgTmpFile = '%s'; \
writematrix(ans, [orgTmpFile, '.txt'], 'Delimiter', 'tab'); \
movefile([orgTmpFile, '.txt'], orgTmpFile); \
clear orgTmpFile;
")))
;; ----
;; 3) For "#+begin_src matlab :exports both :results output" results, fix the results
;; - Add "%-<org-eval>-" comment to end of each line to the body code to be evaluated.
;; - Strip the "%-<org-eval>-" line from the results.
;;
(when (eq result-type 'output)
(setq body (replace-regexp-in-string "\n" " %-<org-eval>-\n" body))
(when (not (string-match "\n\\'" body))
(setq body (concat body " %-<org-eval>-"))))
(let ((results (funcall orig-fun session body result-type matlabp)))
(when (eq result-type 'output)
;; When we send multi-line input to `matlab-shell', we'll see the "body" code lines echoed in
;; the output. Therefore, leverage the "%-<org-eval>" to remove the unnecessary lines.
(setq results (replace-regexp-in-string "^[^\n]*%-<org-eval>-\n" "" results))
;; Remove unnecessary starting blank line
(setq results (replace-regexp-in-string "\\`[[:space:]\r\n]+" "" results))
;; matlab-shell wraps errors in <ERRORTXT> and </ERRORTXT> so remove those
(setq results (replace-regexp-in-string "</?ERRORTXT>[\r\n]?" "" results))
;; Org 9.5.5 shipped with Emacs 28 adds to the end of results the following, so remove it
;; 'org_babel_eoe'
;;
;; ans =
;;
;; 'org_babel_eoe'
(setq results (replace-regexp-in-string
"^\\(?:'org_babel_eoe'\n+\\)?ans =[ \t\n]+'org_babel_eoe'"
"" results)))
;; The `org-babel-octave-evaluate' results
results)))
(declare-function matlab-shell-busy-checker "ext:matlab-mode")
(defun matlab--org-initiate-session-advice (orig-fun &optional session params matlabp)
"After starting matlab-shell, wait for it to become ready.
ORIG-FUN is `org-babel-octave-initiate-session' with arguments SESSION
PARAMS MATLABP."
;; Consider
;; 1) start emacs
;; 2) open foo.org file containing "#+begin_src matlab :exports both :results output"
;; 3) C-c C-c in the code block
;; matlab-shell buffer *MATLAB* doesn't exist `org-babel-octave-initiate-session' will
;; run (matlab-shell) and without this advice, babel will insert the MATLAB code to
;; evaluate in the *MATLAB* buffer before it is ready. This will cause the "#+RESULTS:"
;; in foo.org to contain the MATLAB startup messages.
;; Therefore, we wait for the *MATLAB* buffer to become ready.
(when matlabp
(when (not (featurep 'matlab-shell))
;; make `matlab-shell-busy-checker' available
(require 'matlab-shell))
(matlab-shell-busy-checker 'error-if-busy))
(let ((session-buffer (funcall orig-fun session params matlabp)))
(when matlabp
;; When starting matlab-shell, wait for the prompt.
(matlab-shell-busy-checker 'wait-for-prompt))
session-buffer))
(defun matlab--org-setup ()
"Setup org mode to enable matlab code block evaluation."
;; See if we have newer org which works with MATLAB. We can tell if we have a
;; newer org version if ob-octave contains `org-babel-matlab-wrapper-method'. If we
;; have an older org version, then we advise org to make it work with MATLAB.
(require 'ob-octave)
(when (not (boundp 'org-babel-matlab-wrapper-method))
;; We have an older version of org mode and need to fix the MATLAB support
;; Tell org babel to use the "*MATLAB*" buffer created by `matlab-shell` for code evaluation.
(setq org-babel-default-header-args:matlab '((:session . "*MATLAB*")))
;; Setup for matlab code block export
(advice-add 'org-babel-octave-evaluate :around #'matlab--org-evaluate-advice)
(advice-add 'org-babel-octave-initiate-session :around #'matlab--org-initiate-session-advice)))
;;-------;;
;; Setup ;;
;;-------;;
(if (featurep 'org)
(matlab--org-setup) ;; org is already loaded
(eval-after-load "org"
'(matlab--org-setup)))
(provide 'matlab-org)
;;; matlab-org.el ends here
;; LocalWords: gmail defun setq isstring progn fixup matlabp dpng gfx funcall Tmp writematrix eoe
;; LocalWords: mapcar mapconcat featurep boundp