1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
|
;;; matlab-org.el --- enable use of MATLAB with org-mode -*- lexical-binding: t -*-
;; Copyright (C) 2024 Free Software Foundation, Inc.
;; Author: John Ciolfi <john.ciolfi.32@gmail.com>
;;
;; 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
|
