Remember to cover the basics, that is, what you expected to happen and
what in fact did happen. You don't know how to make a good report? See
https://orgmode.org/manual/Feedback.html#Feedback
Your bug report will be posted to the Org mailing list.
------------------------------------------------------------------------
Org-babel's handling of MATLAB block output with the =:results session=
argument is broken. Here is some sample code along with the expected result:
#+begin_src matlab :results output :session *MATLAB*
a = 3;
b = 4;
c = a + b
#+end_src
#+RESULTS:
: c =
:
: 7
However here is the actual result:
#+begin_src matlab :results output :session *MATLAB*
a = 3;
b = 4;
c = a + b
#+end_src
#+RESULTS:
#+begin_example
a = 3;
b = 4;
c = a + b
c =
7
'org_babel_eoe'
ans =
'org_babel_eoe'
#+end_example
There are two separate problems:
1. The =org-babel-octave-eoe-indicator= is not being stripped.
2. The comint input is being echoed in the output.
#1 is easy to fix. The problem is in the function
=org-babel-octave-evaluate-session=, in the line:
#+begin_src emacs-lisp
(cdr (reverse (delq "" (mapcar #'org-strip-quotes
(mapcar #'org-trim raw)))))
#+end_src
Where empty lines in the output are being removed with =delq=. =delq= compares
with =eq= instead of =equal=, which fails on blank lines. Replacing this with
=delete= works fine.
#2 is a much trickier problem to solve. Here is the body of the input as it
appears in the MATLAB session:
#+begin_example
>> a = 3;
b = 4;
c = a + b
'org_babel_eoe'
a = 3;
>> b = 4;
>> c = a + b
c =
7
>> 'org_babel_eoe'
ans =
'org_babel_eoe'
>>
#+end_example
Here `>>' is the shell prompt, which is absent from the raw comint output as
given to org by comint-mode. =matlab-shell= does not work like other comint
shells in that it doesn't echo bulk (/i.e./ multi-line) input all at once.
Instead, it echoes each line of input and follows it with its output. This
interspersal of input and output is causing =org-babel-comint-with-output=, the
function (actually macro) responsible for removing the comint input echo text
from the raw comint output, to fail. This macro assumes that the raw comint
output looks like
#+begin_example
<<contiguous comint input from org source block>>
<<contiguous comint output>>
#+end_example
as you can see from this code from =org-babel-comint-with-output=:
#+begin_src emacs-lisp
(when (and ,remove-echo ,full-body
(string-match
(replace-regexp-in-string
"\n" "[\r\n]+" (regexp-quote (or ,full-body "")))
string-buffer))
(setq string-buffer (substring string-buffer (match-end 0))))
#+end_src
To fix this, either =org-babel-octave-evaluate-session= or
=org-babel-comint-with-output= needs to be modified. This problem is local to
MATLAB, it does not happen with GNU Octave, which shares most of its org-babel
code with MATLAB's. So I wrote a patch to the former that does additional
line-by-line processing on the raw comint output to detect and remove the
echoed input. (Patch is attached.) However while this fixes the problem it's
not a robust solution.
-Karthik
--- ob-octave.el 2020-11-23 11:22:01.473682045 -0800
+++ ob-octave-new.el 2020-11-23 11:10:07.961900383 -0800
@@ -187,6 +187,7 @@
(org-babel-process-file-name tmp-file 'noquote)))
(org-babel-octave-import-elisp-from-file tmp-file))))))
+
(defun org-babel-octave-evaluate-session
(session body result-type &optional matlabp)
"Evaluate BODY in SESSION."
@@ -237,12 +238,31 @@
(`output
(setq results
(if matlabp
- (cdr (reverse (delq "" (mapcar #'org-strip-quotes
+ (cdr (reverse (delete "" (mapcar #'org-strip-quotes
(mapcar #'org-trim raw)))))
(cdr (member org-babel-octave-eoe-output
(reverse (mapcar #'org-strip-quotes
(mapcar #'org-trim raw)))))))
- (mapconcat #'identity (reverse results) "\n")))))
+ ;; This kludge is to remove the input lines from the output. Because of
+ ;; the special way that MATLAB processes bulk comint output (the output
+ ;; of each line follows that line) the macro
+ ;; `org-babel-comint-with-output' cannot remove the echoed commands. The
+ ;; following handles this manually, by splitting both the original input
+ ;; (`BODY') and full output (`RESULTS') on newlines, comparing them line
+ ;; by line and removing all lines in BODY from RESULTS. Note that RESULTS
+ ;; is already a list of strings so additional care is needed.
+ (let* ((body-lines (split-string body "\n+"))
+ (result-lines (flatten-list
+ (mapcar
+ (lambda (entry) (reverse (split-string entry "\n")))
+ results))))
+ (mapconcat
+ #'identity
+ (reverse (cl-remove-if
+ (lambda (line) (member line body-lines))
+ result-lines)) "\n")
+ )))))
+
(defun org-babel-octave-import-elisp-from-file (file-name)
"Import data from FILE-NAME.
Emacs : GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.22,
cairo version 1.17.3)
of 2020-08-28
Package: Org mode version 9.3 (release_9.3 @ /usr/share/emacs/27.1/lisp/org/)
current state:
==============
(setq
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-link-shell-confirm-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
org-mode-hook '(#[0 "\300\301\302\303\304$\207" [add-hook
change-major-mode-hook org-show-all append local] 5]
#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-babel-show-result-all
append local] 5]
org-babel-result-hide-spec org-babel-hide-all-hashes)
org-archive-hook '(org-attach-archive-delete-maybe)
org-confirm-elisp-link-function 'yes-or-no-p
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-metaup-hook '(org-babel-load-in-session-maybe)
org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3 "\n\n(fn
ENTRY)"]
org-babel-pre-tangle-hook '(save-buffer)
org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-occur-hook '(org-first-headline-recenter)
org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lines
org-optimize-window-after-visibility-change)
org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
org-confirm-shell-link-function 'yes-or-no-p
org-link-parameters '(("attachment" :follow org-attach-open-link :export
org-attach-export-link :complete
org-attach-complete-link)
("id" :follow org-id-open) ("eww" :follow eww :store
org-eww-store-link)
("rmail" :follow org-rmail-open :store
org-rmail-store-link)
("mhe" :follow org-mhe-open :store org-mhe-store-link)
("irc" :follow org-irc-visit :store org-irc-store-link
:export org-irc-export)
("info" :follow org-info-open :export org-info-export
:store org-info-store-link)
("gnus" :follow org-gnus-open :store org-gnus-store-link)
("docview" :follow org-docview-open :export
org-docview-export :store
org-docview-store-link)
("bibtex" :follow org-bibtex-open :store
org-bibtex-store-link)
("bbdb" :follow org-bbdb-open :export org-bbdb-export
:complete org-bbdb-complete-link
:store org-bbdb-store-link)
("w3m" :store org-w3m-store-link) ("file+sys")
("file+emacs")
("shell" :follow org-link--open-shell)
("news" :follow #[257 "\301\300\302Q!\207" ["news"
browse-url ":"] 5 "\n\n(fn URL)"])
("mailto" :follow #[257 "\301\300\302Q!\207" ["mailto"
browse-url ":"] 5 "\n\n(fn URL)"])
("https" :follow #[257 "\301\300\302Q!\207" ["https"
browse-url ":"] 5 "\n\n(fn URL)"])
("http" :follow #[257 "\301\300\302Q!\207" ["http"
browse-url ":"] 5 "\n\n(fn URL)"])
("ftp" :follow #[257 "\301\300\302Q!\207" ["ftp"
browse-url ":"] 5 "\n\n(fn URL)"])
("help" :follow org-link--open-help) ("file" :complete
org-link-complete-file)
("elisp" :follow org-link--open-elisp) ("doi" :follow
org-link--open-doi))
org-link-elisp-confirm-function 'yes-or-no-p
)
