Getting email from MS outlook into emacs

[Doyley, Marvin M.]

Hi there,

I have been trying to configure mbsync to download email from MS Outlook.  
Unfortunately, the new oauth2 authentication makes things difficult, especially 
since my institution has disabled the Azure App permission.

Does anybody have a workaround?  I just want the email message to be linked to 
my todos, which is almost impossible.  I am working on a Mac and org-mac-link 
just hangs when I try to grab Outlook emails.


Thanks in advance for your help.

Cheers,
M

PS I have also tried Davmail, which almost worked, except my institution placed 
another roadblock.

Marvin M. Doyley, Ph.D.
Wilson Professor of Electronic Imaging
Professor and Chair of the Department of Electrical and Computer Engineering,
Professor of Biomedical Engineering
Professor Imaging Sciences,
University of Rochester
518 Computer Studies Building Rochester NY 14627
Tel: 585-275-3774 Fax: 585-273-4919
Website: http://www.ece.rochester.edu/projects/doyley_lab/

Re: Org-ref error

[Doyley, Marvin M.]

Still not working for me :(

On Jan 22, 2020, at 8:30 PM, John Kitchin 
mailto:jkitc...@andrew.cmu.edu>> wrote:

that is strange. I was able to reproduce it a few times, but now it works fine. 
all within a few minutes of trying to debug it.

This makes me think something was not right in the request or reply.

json-read-from-string("\n\015\n400 The plain HTTP request 
was sent to HTTPS port\015\n\015\n400 Bad 
Request\015\nThe plain HTTP request was sent to HTTPS 
port\015\ncloudflare\015\n\015\n\015\n")

John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=I1VldbLrMmiVdqzz6xm-zhhiNqpNimU3ZUNsYaZhsyg=Az4I3HmGnsMldRbgCoDskRbN_tDipsjAUXbH482gDA8=>



On Wed, Jan 22, 2020 at 8:08 PM Doyley, Marvin M. 
mailto:m.doy...@rochester.edu>> wrote:
-Hi Everybody,

For some reason, I keep getting an error (JSON readable error: 60) whenever I 
try to  add a BibTex entry to a BibTex file using 
doi-utils-add-bibtex-entry-from-doi. I would appreciate if someone could tell 
me how to resolve this problem.

Best Wishes,
M

Here is the backtrace that I got when I execute the command.

 Debugger entered--Lisp error: (json-readtable-error 60)
  signal(json-readtable-error (60))
  json-read()
  json-read-from-string("\n\015\n400 The plain HTTP request 
was sent to HTTPS port\015\n\015\n400 Bad 
Request\015\nThe plain HTTP request was sent to HTTPS 
port\015\ncloudflare\015\n\015\n\015\n")
  doi-utils-get-json-metadata("10.1109/TUFFC.2019.2961875")
  doi-utils-doi-to-bibtex-string("10.1109/TUFFC.2019.2961875")
  doi-utils-insert-bibtex-entry-from-doi("10.1109/TUFFC.2019.2961875")
  doi-utils-add-bibtex-entry-from-doi("10.1109/TUFFC.2019.2961875")
  funcall-interactively(doi-utils-add-bibtex-entry-from-doi 
"10.1109/TUFFC.2019.2961875")
  call-interactively(doi-utils-add-bibtex-entry-from-doi record nil)
  command-execute(doi-utils-add-bibtex-entry-from-doi record)
  helm-M-x-execute-command(doi-utils-add-bibtex-entry-from-doi)
  helm-execute-selection-action-1()
  helm-execute-selection-action()
  helm-internalname . "Emacs Commands history") (candidates . 
#f(compiled-function () #)) (keymap keymap (keymap (13 . 
helm-confirm-and-exit-minibuffer)) keymap (21 . helm-M-x-universal-argument) 
keymap (127 . delete-backward-char) (27 keymap (13 . helm-cr-empty-string)) 
(C-return . helm-cr-empty-string) keymap (tab . helm-execute-persistent-action) 
(26 . helm-select-action) (f13 lambda nil (interactive) (helm-select-nth-action 
12)) (f12 lambda nil (interactive) (helm-select-nth-action 11)) (f11 lambda nil 
(interactive) (helm-select-nth-action 10)) (f10 lambda nil (interactive) 
(helm-select-nth-action 9)) (f9 lambda nil (interactive) 
(helm-select-nth-action 8)) (f8 lambda nil (interactive) 
(helm-select-nth-action 7)) (f7 lambda nil (interactive) 
(helm-select-nth-action 6)) (f6 lambda nil (interactive) 
(helm-select-nth-action 5)) (f5 lambda nil (interactive) 
(helm-select-nth-action 4)) (f4 lambda nil (interactive) 
(helm-select-nth-action 3)) (f3 lambda nil (interactive) 
(helm-select-nth-action 2)) (f2 lambda nil (interactive) 
(helm-select-nth-action 1)) (menu-bar keymap (help-menu keymap (describe keymap 
(describe-mode . helm-help (help keymap (109 . helm-help)) (23 . 
evil-delete-backward-word) (f1 lambda nil (interactive) (helm-select-nth-action 
0)) (8 keymap (109 . helm-help) (104 . undefined) (8 . undefined) (99 . 
helm-customize-group) (4 . helm-enable-or-switch-to-debug)) (20 . 
helm-toggle-resplit-and-swap-windows) (C-tab . undefined) (67108897 . 
helm-toggle-suspend-update) (3 keymap (57 . 
helm-execute-selection-action-at-nth-+9) (56 . 
helm-execute-selection-action-at-nth-+8) (55 . 
helm-execute-selection-action-at-nth-+7) (54 . 
helm-execute-selection-action-at-nth-+6) (53 . 
helm-execute-selection-action-at-nth-+5) (52 . 
helm-execute-selection-action-at-nth-+4) (51 . 
helm-execute-selection-action-at-nth-+3) (50 . 
helm-execute-selection-action-at-nth-+2) (49 . 
helm-execute-selection-action-at-nth-+1) (63 . helm-help) (110 . 
#f(compiled-function () (interactive nil) #)) (108 . 
helm-display-line-numbers-mode) (62 . helm-toggle-truncate-line) (21 . 
helm-refresh) (6 . helm-follow-mode) (9 . helm-copy-to-buffer) (11 . 
helm-kill-selection-and-quit) (25 . helm-yank-selection) (37 . 
helm-exchange-minibuffer-and-header-line) (95 . helm-toggle-full-frame) (45 . 
helm-swap-windows)) (67108987 . helm-enlarge-window) (67108989 . 
helm-narrow-window) (19 . undefined) (24 keymap (57 . 
helm-execute-selection-action-at-nth-+9) (56 . 
helm-execute-selection-action-at-n

Re: Org-ref error

[Doyley, Marvin M.]

That is indeed very interesting.
Thanks for looking into this.
Cheers,
M

On Jan 22, 2020, at 8:30 PM, John Kitchin 
mailto:jkitc...@andrew.cmu.edu>> wrote:

that is strange. I was able to reproduce it a few times, but now it works fine. 
all within a few minutes of trying to debug it.

This makes me think something was not right in the request or reply.

json-read-from-string("\n\015\n400 The plain HTTP request 
was sent to HTTPS port\015\n\015\n400 Bad 
Request\015\nThe plain HTTP request was sent to HTTPS 
port\015\ncloudflare\015\n\015\n\015\n")

John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=I1VldbLrMmiVdqzz6xm-zhhiNqpNimU3ZUNsYaZhsyg=Az4I3HmGnsMldRbgCoDskRbN_tDipsjAUXbH482gDA8=>



On Wed, Jan 22, 2020 at 8:08 PM Doyley, Marvin M. 
mailto:m.doy...@rochester.edu>> wrote:
-Hi Everybody,

For some reason, I keep getting an error (JSON readable error: 60) whenever I 
try to  add a BibTex entry to a BibTex file using 
doi-utils-add-bibtex-entry-from-doi. I would appreciate if someone could tell 
me how to resolve this problem.

Best Wishes,
M

Here is the backtrace that I got when I execute the command.

 Debugger entered--Lisp error: (json-readtable-error 60)
  signal(json-readtable-error (60))
  json-read()
  json-read-from-string("\n\015\n400 The plain HTTP request 
was sent to HTTPS port\015\n\015\n400 Bad 
Request\015\nThe plain HTTP request was sent to HTTPS 
port\015\ncloudflare\015\n\015\n\015\n")
  doi-utils-get-json-metadata("10.1109/TUFFC.2019.2961875")
  doi-utils-doi-to-bibtex-string("10.1109/TUFFC.2019.2961875")
  doi-utils-insert-bibtex-entry-from-doi("10.1109/TUFFC.2019.2961875")
  doi-utils-add-bibtex-entry-from-doi("10.1109/TUFFC.2019.2961875")
  funcall-interactively(doi-utils-add-bibtex-entry-from-doi 
"10.1109/TUFFC.2019.2961875")
  call-interactively(doi-utils-add-bibtex-entry-from-doi record nil)
  command-execute(doi-utils-add-bibtex-entry-from-doi record)
  helm-M-x-execute-command(doi-utils-add-bibtex-entry-from-doi)
  helm-execute-selection-action-1()
  helm-execute-selection-action()
  helm-internalname . "Emacs Commands history") (candidates . 
#f(compiled-function () #)) (keymap keymap (keymap (13 . 
helm-confirm-and-exit-minibuffer)) keymap (21 . helm-M-x-universal-argument) 
keymap (127 . delete-backward-char) (27 keymap (13 . helm-cr-empty-string)) 
(C-return . helm-cr-empty-string) keymap (tab . helm-execute-persistent-action) 
(26 . helm-select-action) (f13 lambda nil (interactive) (helm-select-nth-action 
12)) (f12 lambda nil (interactive) (helm-select-nth-action 11)) (f11 lambda nil 
(interactive) (helm-select-nth-action 10)) (f10 lambda nil (interactive) 
(helm-select-nth-action 9)) (f9 lambda nil (interactive) 
(helm-select-nth-action 8)) (f8 lambda nil (interactive) 
(helm-select-nth-action 7)) (f7 lambda nil (interactive) 
(helm-select-nth-action 6)) (f6 lambda nil (interactive) 
(helm-select-nth-action 5)) (f5 lambda nil (interactive) 
(helm-select-nth-action 4)) (f4 lambda nil (interactive) 
(helm-select-nth-action 3)) (f3 lambda nil (interactive) 
(helm-select-nth-action 2)) (f2 lambda nil (interactive) 
(helm-select-nth-action 1)) (menu-bar keymap (help-menu keymap (describe keymap 
(describe-mode . helm-help (help keymap (109 . helm-help)) (23 . 
evil-delete-backward-word) (f1 lambda nil (interactive) (helm-select-nth-action 
0)) (8 keymap (109 . helm-help) (104 . undefined) (8 . undefined) (99 . 
helm-customize-group) (4 . helm-enable-or-switch-to-debug)) (20 . 
helm-toggle-resplit-and-swap-windows) (C-tab . undefined) (67108897 . 
helm-toggle-suspend-update) (3 keymap (57 . 
helm-execute-selection-action-at-nth-+9) (56 . 
helm-execute-selection-action-at-nth-+8) (55 . 
helm-execute-selection-action-at-nth-+7) (54 . 
helm-execute-selection-action-at-nth-+6) (53 . 
helm-execute-selection-action-at-nth-+5) (52 . 
helm-execute-selection-action-at-nth-+4) (51 . 
helm-execute-selection-action-at-nth-+3) (50 . 
helm-execute-selection-action-at-nth-+2) (49 . 
helm-execute-selection-action-at-nth-+1) (63 . helm-help) (110 . 
#f(compiled-function () (interactive nil) #)) (108 . 
helm-display-line-numbers-mode) (62 . helm-toggle-truncate-line) (21 . 
helm-refresh) (6 . helm-follow-mode) (9 . helm-copy-to-buffer) (11 . 
helm-kill-selection-and-quit) (25 . helm-yank-selection) (37 . 
helm-exchange-minibuffer-and-header-line) (95 . helm-toggle-full-frame) (45 . 
helm-swap-windows)) (67108987 . helm-enlarge-window) (67108989 . 
helm-narrow-window) (19 . undefined) (24 keymap (57 . 
helm-execute-selection-action-at-nth-

Org-ref error

[Doyley, Marvin M.]

-Hi Everybody,

For some reason, I keep getting an error (JSON readable error: 60) whenever I 
try to  add a BibTex entry to a BibTex file using 
doi-utils-add-bibtex-entry-from-doi. I would appreciate if someone could tell 
me how to resolve this problem.

Best Wishes,
M

Here is the backtrace that I got when I execute the command. 

 Debugger entered--Lisp error: (json-readtable-error 60)
  signal(json-readtable-error (60))
  json-read()
  json-read-from-string("\n\015\n400 The plain HTTP request 
was sent to HTTPS port\015\n\015\n400 Bad 
Request\015\nThe plain HTTP request was sent to HTTPS 
port\015\ncloudflare\015\n\015\n\015\n")
  doi-utils-get-json-metadata("10.1109/TUFFC.2019.2961875")
  doi-utils-doi-to-bibtex-string("10.1109/TUFFC.2019.2961875")
  doi-utils-insert-bibtex-entry-from-doi("10.1109/TUFFC.2019.2961875")
  doi-utils-add-bibtex-entry-from-doi("10.1109/TUFFC.2019.2961875")
  funcall-interactively(doi-utils-add-bibtex-entry-from-doi 
"10.1109/TUFFC.2019.2961875")
  call-interactively(doi-utils-add-bibtex-entry-from-doi record nil)
  command-execute(doi-utils-add-bibtex-entry-from-doi record)
  helm-M-x-execute-command(doi-utils-add-bibtex-entry-from-doi)
  helm-execute-selection-action-1()
  helm-execute-selection-action()
  helm-internalname . "Emacs Commands history") (candidates . 
#f(compiled-function () #)) (keymap keymap (keymap (13 . 
helm-confirm-and-exit-minibuffer)) keymap (21 . helm-M-x-universal-argument) 
keymap (127 . delete-backward-char) (27 keymap (13 . helm-cr-empty-string)) 
(C-return . helm-cr-empty-string) keymap (tab . helm-execute-persistent-action) 
(26 . helm-select-action) (f13 lambda nil (interactive) (helm-select-nth-action 
12)) (f12 lambda nil (interactive) (helm-select-nth-action 11)) (f11 lambda nil 
(interactive) (helm-select-nth-action 10)) (f10 lambda nil (interactive) 
(helm-select-nth-action 9)) (f9 lambda nil (interactive) 
(helm-select-nth-action 8)) (f8 lambda nil (interactive) 
(helm-select-nth-action 7)) (f7 lambda nil (interactive) 
(helm-select-nth-action 6)) (f6 lambda nil (interactive) 
(helm-select-nth-action 5)) (f5 lambda nil (interactive) 
(helm-select-nth-action 4)) (f4 lambda nil (interactive) 
(helm-select-nth-action 3)) (f3 lambda nil (interactive) 
(helm-select-nth-action 2)) (f2 lambda nil (interactive) 
(helm-select-nth-action 1)) (menu-bar keymap (help-menu keymap (describe keymap 
(describe-mode . helm-help (help keymap (109 . helm-help)) (23 . 
evil-delete-backward-word) (f1 lambda nil (interactive) (helm-select-nth-action 
0)) (8 keymap (109 . helm-help) (104 . undefined) (8 . undefined) (99 . 
helm-customize-group) (4 . helm-enable-or-switch-to-debug)) (20 . 
helm-toggle-resplit-and-swap-windows) (C-tab . undefined) (67108897 . 
helm-toggle-suspend-update) (3 keymap (57 . 
helm-execute-selection-action-at-nth-+9) (56 . 
helm-execute-selection-action-at-nth-+8) (55 . 
helm-execute-selection-action-at-nth-+7) (54 . 
helm-execute-selection-action-at-nth-+6) (53 . 
helm-execute-selection-action-at-nth-+5) (52 . 
helm-execute-selection-action-at-nth-+4) (51 . 
helm-execute-selection-action-at-nth-+3) (50 . 
helm-execute-selection-action-at-nth-+2) (49 . 
helm-execute-selection-action-at-nth-+1) (63 . helm-help) (110 . 
#f(compiled-function () (interactive nil) #)) (108 . 
helm-display-line-numbers-mode) (62 . helm-toggle-truncate-line) (21 . 
helm-refresh) (6 . helm-follow-mode) (9 . helm-copy-to-buffer) (11 . 
helm-kill-selection-and-quit) (25 . helm-yank-selection) (37 . 
helm-exchange-minibuffer-and-header-line) (95 . helm-toggle-full-frame) (45 . 
helm-swap-windows)) (67108987 . helm-enlarge-window) (67108989 . 
helm-narrow-window) (19 . undefined) (24 keymap (57 . 
helm-execute-selection-action-at-nth-+9) (56 . 
helm-execute-selection-action-at-nth-+8) (55 . 
helm-execute-selection-action-at-nth-+7) (54 . 
helm-execute-selection-action-at-nth-+6) (53 . 
helm-execute-selection-action-at-nth-+5) (52 . helm-select-4rd-action) (51 . 
helm-select-3rd-action) (50 . helm-select-2nd-action) (49 . 
helm-execute-selection-action-at-nth-+1) (2 . 
helm-resume-list-buffers-after-quit) (98 . 
helm-resume-previous-session-after-quit) (6 . helm-quit-and-find-file)) (11 . 
helm-delete-minibuffer-contents) (67108896 . helm-toggle-visible-mark-forward) 
(0 . helm-toggle-visible-mark) (C-M-up . helm-scroll-other-window-down) 
(C-M-down . helm-scroll-other-window) (M-prior . helm-scroll-other-window-down) 
(M-next . helm-scroll-other-window) (12 . 
helm-recenter-top-bottom-other-window) (15 . helm-next-source) (10 . 
helm-execute-persistent-action) (9 . helm-select-action) (13 . 
helm-maybe-exit-minibuffer) (7 . helm-keyboard-quit) ...) (action . 
helm-type-command-actions) (persistent-action . helm-M-x-persistent-action) 
(persistent-help . "Describe this command") (help-message . 
helm-M-x-help-message) (requires-pattern . 0) (filtered-candidate-transformer 
helm-M-x-transformer-no-sort helm-fuzzy-highlight-matches) (volatile) (match . 

Re: [O] Issue with internal links

[Doyley, Marvin M.]

Hi Nicolas,

(add-hook 'org-open-link-functions t)
Fixed the problem.

Thanks
M

> On Aug 8, 2019, at 4:53 PM, Nicolas Goaziou  wrote:
> 
> Hello,
> 
> "Doyley, Marvin M."  writes:
> 
>> Whenever I double click on an internal link I get the following error
>> “void-function org-pass-link-to-system”
> 
> The function above doesn't exist in Org base. You may want to
> investigate on whatever is adding it to `org-open-link-functions'.
> 
> Regards,
> 
> -- 
> Nicolas Goaziou

[O] Issue with internal links

[Doyley, Marvin M.]

Hi there,

Whenever I double click on an internal link I get the following error 
“void-function org-pass-link-to-system”

Does anybody know how to resolve this.

Thanks
M

PS.  Enclosed is the a back trace for a simple file

* Testing
* One
* Two
   [[*Testing]].   (I also tried [[Testing]] and I got the same error)

Debugger entered--Lisp error: (void-function org-pass-link-to-system)
  org-pass-link-to-system("*Testing")
  run-hook-with-args-until-success(org-pass-link-to-system "*Testing")
  (if (run-hook-with-args-until-success 'org-open-link-functions path) nil (if 
(not arg) (org-mark-ring-push) (switch-to-buffer-other-window 
(org-get-buffer-for-internal-link (current-buffer (let ((destination 
(save-excursion (save-restriction (widen) (if (equal type "radio") 
(org-search-radio-target (org-element-property :path context)) (org-link-search 
(cond ((equal type '"custom-id") (concat "#" path)) ((equal type '"coderef") 
(format "(%s)" path)) (t path)) (and (equal type "fuzzy") (+ 2 
(org-element-property :begin context) (point) (if (and (<= (point-min) 
destination) (>= (point-max) destination)) nil (widen)) (goto-char 
destination)))
  (cond ((equal type "file") (if (string-match "[*?{]" (file-name-nondirectory 
path)) (dired path) (let* ((option (org-element-property :search-option 
context)) (app (org-element-property :application context)) (dedicated-function 
(org-link-get-parameter (if app (concat type "+" app) type) :follow))) (if 
dedicated-function (funcall dedicated-function (concat path (and option (concat 
"::" option (apply (function org-open-file) path (cond (arg) ((equal app 
"emacs") 'emacs) ((equal app "sys") 'system)) (cond ((not option) nil) 
((string-match-p "\\`[0-9]+\\'" option) (list (string-to-number option))) (t 
(list nil option ((functionp (org-link-get-parameter type :follow)) 
(funcall (org-link-get-parameter type :follow) path)) ((member type '("coderef" 
"custom-id" "fuzzy" "radio")) (if (run-hook-with-args-until-success 
'org-open-link-functions path) nil (if (not arg) (org-mark-ring-push) 
(switch-to-buffer-other-window (org-get-buffer-for-internal-link 
(current-buffer (let ((destination (save-excursion (save-restriction 
(widen) (if (equal type "radio") (org-search-radio-target (org-element-property 
:path context)) (org-link-search (cond ((equal type '"custom-id") (concat "#" 
path)) ((equal type '"coderef") (format "(%s)" path)) (t path)) (and (equal 
type "fuzzy") (+ 2 (org-element-property :begin context) (point) (if 
(and (<= (point-min) destination) (>= (point-max) destination)) nil (widen)) 
(goto-char destination (t (browse-url-at-point)))
  (save-current-buffer (set-buffer (or reference-buffer (current-buffer))) 
(cond ((equal type "file") (if (string-match "[*?{]" (file-name-nondirectory 
path)) (dired path) (let* ((option (org-element-property :search-option 
context)) (app (org-element-property :application context)) (dedicated-function 
(org-link-get-parameter (if app (concat type "+" app) type) :follow))) (if 
dedicated-function (funcall dedicated-function (concat path (and option (concat 
"::" option (apply (function org-open-file) path (cond (arg) ((equal app 
"emacs") 'emacs) ((equal app "sys") 'system)) (cond ((not option) nil) 
((string-match-p "\\`[0-9]+\\'" option) (list (string-to-number option))) (t 
(list nil option ((functionp (org-link-get-parameter type :follow)) 
(funcall (org-link-get-parameter type :follow) path)) ((member type '("coderef" 
"custom-id" "fuzzy" "radio")) (if (run-hook-with-args-until-success 
'org-open-link-functions path) nil (if (not arg) (org-mark-ring-push) 
(switch-to-buffer-other-window (org-get-buffer-for-internal-link 
(current-buffer (let ((destination (save-excursion (save-restriction 
(widen) (if (equal type "radio") (org-search-radio-target (org-element-property 
:path context)) (org-link-search (cond ((equal type '"custom-id") (concat "#" 
path)) ((equal type '"coderef") (format "(%s)" path)) (t path)) (and (equal 
type "fuzzy") (+ 2 (org-element-property :begin context) (point) (if 
(and (<= (point-min) destination) (>= (point-max) destination)) nil (widen)) 
(goto-char destination (t (browse-url-at-point
  (let ((type (org-element-property :type context)) (path (org-element-property 
:path context))) (save-current-buffer (set-buffer (or reference-buffer 
(current-buffer))) (cond ((equal type "file") (if (string-match "[*?{]" 
(file-name-nondirectory path)) (dired path) (let* ((option 
(org-element-property :search-option context)) (app (org-element-property 
:application context)) (dedicated-function (org-link-get-parameter (if app 
(concat type "+" app) type) :follow))) (if dedicated-function (funcall 
dedicated-function (concat path (and option (concat "::" option (apply 
(function org-open-file) path (cond (arg) ((equal app "emacs") 'emacs) ((equal 
app "sys") 'system)) (cond ((not option) nil) ((string-match-p "\\`[0-9]+\\'" 

[O] Script for automatically linking to an external file

[Doyley, Marvin M.]

Hi there,

I trying to make a script that

(a) automatically creates a file e.g.  
notes-04-15-2019.org
(b) makes a link to notes-40-15-2019.org 
automatically in index.org under a specific heading
(c) open notes-04-2019.org in the buffer

Does anybody know how to do this.

Thanks
M

Re: [O] Json readable error

[Doyley, Marvin M.]

Thanks,

I will do the same, since I really use ipython in emacs.

Cheers,
M

> On Jul 21, 2018, at 2:31 PM, Xu Chunyang  wrote:
> 
> 
> Doyley, Marvin M. writes:
> 
>> Hi there,
>> 
>> For some strange reason whenever I switch to org-mode (M-x org-mode), I get 
>> json readtable error: 84, which I have been trying to resolve without much 
>> success.
>> 
>> Have anyone encountered this before or know how to resolve it?  This problem 
>> could be due to recent change that I have made to my default python (changed 
>> from anaconda 3.4 to intel’s python 3.4), but I am not sure why doing this 
>> would cause a problem.
>> 
>> Best Wishes,
>> M
>> 
>> Here is the backtrace.
>> 
>> Debugger entered--Lisp error: (json-readtable-error 84)
>>  signal(json-readtable-error (84))
>>  json-read()
>>  json-read-array()
>>  json-read()
>>  json-read-from-string("[TerminalIPythonApp] WARNING | Subcommand `ipython 
>> kernelspec` is deprecated and will be removed in future 
>> versions.\n[TerminalIPythonApp] WARNING | You likely want to use `jupyter 
>> kernelspec` in the future\n{\n  \"kernelspecs\": {\n\"python3\": {\n 
>>  \"resource_dir\": \"/anaconda/share/jupyter/kernels/python3\",\n  
>> \"spec\": {\n\"argv\": [\n  \"/anaconda/bin/python\",\n  
>> \"-m\",\n  \"ipykernel_launcher\",\n  \"-f\",\n  
>> \"{connection_file}\"\n],\n\"env\": {},\n
>> \"display_name\": \"Python 3\",\n\"language\": \"python\",\n
>> \"interrupt_mode\": \"signal\",\n\"metadata\": {}\n  }\n}\n  
>> }\n}\n")
>>  ob-ipython--get-kernels()
>>  ob-ipython-auto-configure-kernels()
>>  run-hooks(change-major-mode-after-body-hook text-mode-hook 
>> outline-mode-hook org-mode-hook)
>>  apply(run-hooks (change-major-mode-after-body-hook text-mode-hook 
>> outline-mode-hook org-mode-hook))
>>  run-mode-hooks(org-mode-hook)
>>  org-mode()
>>  funcall-interactively(org-mode)
>>  call-interactively(org-mode record nil)
>>  command-execute(org-mode record)
>>  helm-M-x(nil #("org-mode" 0 8 (match-part "org-mode")))
>>  funcall-interactively(helm-M-x nil #("org-mode" 0 8 (match-part 
>> "org-mode")))
>>  call-interactively(helm-M-x nil nil)
>>  command-execute(helm-M-x)
> 
> I encountered the same issue a few days ago, it is due to python version
> upgrade (jupyter no longer worked) and ob-ipython.el doesn't handle
> error very well, and ob-ipython.el also installs some code on
> org-mode-hook unconditionally. I simply delete ob-ipython.el and delete
> configuration of it in the init.el, then restart Emacs, since I've
> not used ob-ipython.el for a long time.

[O] Json readable error

[Doyley, Marvin M.]

Hi there,

For some strange reason whenever I switch to org-mode (M-x org-mode), I get 
json readtable error: 84, which I have been trying to resolve without much 
success. 

Have anyone encountered this before or know how to resolve it?  This problem 
could be due to recent change that I have made to my default python (changed 
from anaconda 3.4 to intel’s python 3.4), but I am not sure why doing this 
would cause a problem.  

Best Wishes,
M 

Here is the backtrace.

Debugger entered--Lisp error: (json-readtable-error 84)
  signal(json-readtable-error (84))
  json-read()
  json-read-array()
  json-read()
  json-read-from-string("[TerminalIPythonApp] WARNING | Subcommand `ipython 
kernelspec` is deprecated and will be removed in future 
versions.\n[TerminalIPythonApp] WARNING | You likely want to use `jupyter 
kernelspec` in the future\n{\n  \"kernelspecs\": {\n\"python3\": {\n  
\"resource_dir\": \"/anaconda/share/jupyter/kernels/python3\",\n  \"spec\": 
{\n\"argv\": [\n  \"/anaconda/bin/python\",\n  
\"-m\",\n  \"ipykernel_launcher\",\n  \"-f\",\n  
\"{connection_file}\"\n],\n\"env\": {},\n
\"display_name\": \"Python 3\",\n\"language\": \"python\",\n
\"interrupt_mode\": \"signal\",\n\"metadata\": {}\n  }\n}\n  
}\n}\n")
  ob-ipython--get-kernels()
  ob-ipython-auto-configure-kernels()
  run-hooks(change-major-mode-after-body-hook text-mode-hook outline-mode-hook 
org-mode-hook)
  apply(run-hooks (change-major-mode-after-body-hook text-mode-hook 
outline-mode-hook org-mode-hook))
  run-mode-hooks(org-mode-hook)
  org-mode()
  funcall-interactively(org-mode)
  call-interactively(org-mode record nil)
  command-execute(org-mode record)
  helm-M-x(nil #("org-mode" 0 8 (match-part "org-mode")))
  funcall-interactively(helm-M-x nil #("org-mode" 0 8 (match-part "org-mode")))
  call-interactively(helm-M-x nil nil)
  command-execute(helm-M-x)

Re: [O] Problem with python source block

[Doyley, Marvin M.]

Thanks John,

The problem is now fixed

cheers,
M
> On May 26, 2018, at 10:22 AM, Doyley, Marvin M. <m.doy...@rochester.edu> 
> wrote:
> 
> Hi there,
> 
> The problem seem to be cause by scimax-org-babel-python.el.
> When I disable this works fine, but doing this disables asynchronous  
> execution.
> 
> John do you have any suggestions  what is going on ?
> 
> Cheers,
> M
> 
>> On May 26, 2018, at 9:16 AM, Doyley, Marvin M. <m.doy...@rochester.edu 
>> <mailto:m.doy...@rochester.edu>> wrote:
>> 
>> 
>> Hi Thibault,
>> thanks for the info. I will dig around my config
>> cheers,
>> M
>> 
>> 
>> > Hi,
>> 
>> > For what it's worth, I cannot reproduce it on Org mode version 9.1.>13
>> >(release_9.1.13-763-g2621db) with -Q; the file is properly produced.
>> >
>> >I get the same error if I add the `session' header argument, maybe i>t is
>> >set elsewhere?
>> 
>> >Hope it helps.
>> 
>> >thibault
>> 
>> >Doyley, Marvin M. writes:
>> 
>> > Hi there,
>> >
>> > When I run the following code I get an error, does anybody know how to fix
>> > this
>> >
>> > I am using the latest version of org-mode.
>> >
>> > Thanks,
>> > M
>> >
>> >
>> > #+BEGIN_SRC python :results file
>> > import numpy as np
>> > import matplotlib.pyplot as plt
>> > import seaborn as sns
>> > x = np.random.rand(100)
>> > y= np.cos(x)
>> > plt.plot(x,y)
>> > plt.savefig('test.png')
>> > return 'test.png'
>> > #+END_SRC
>> >
>> > #+RESULTS:
>> > [[file:  File "Org SRC", line 8
>> > return 'test.png'
>> > ^
>> > SyntaxError: 'return' outside function
>> > ]]
>> 
>> 
>> I will do some digging around in my config file.
> 



signature.asc
Description: Message signed with OpenPGP

Re: [O] Problem with python source block

[Doyley, Marvin M.]

Hi there,

The problem seem to be cause by scimax-org-babel-python.el.
When I disable this works fine, but doing this disables asynchronous execution.

John do you have any suggestions what is going on ?

Cheers,
M

On May 26, 2018, at 9:16 AM, Doyley, Marvin M. 
<m.doy...@rochester.edu<mailto:m.doy...@rochester.edu>> wrote:



Hi Thibault,

thanks for the info. I will dig around my config

cheers,

M



> Hi,

> For what it's worth, I cannot reproduce it on Org mode version 9.1.>13
>(release_9.1.13-763-g2621db) with -Q; the file is properly produced.
>
>I get the same error if I add the `session' header argument, maybe i>t is
>set elsewhere?

>Hope it helps.

>thibault

>Doyley, Marvin M. writes:

> Hi there,
>
> When I run the following code I get an error, does anybody know how to fix
> this
>
> I am using the latest version of org-mode.
>
> Thanks,
> M
>
>
> #+BEGIN_SRC python :results file
> import numpy as np
> import matplotlib.pyplot as plt
> import seaborn as sns
> x = np.random.rand(100)
> y= np.cos(x)
> plt.plot(x,y)
> plt.savefig('test.png')
> return 'test.png'
> #+END_SRC
>
> #+RESULTS:
> [[file:  File "Org SRC", line 8
> return 'test.png'
> ^
> SyntaxError: 'return' outside function
> ]]



I will do some digging around in my config file.

Re: [O] Problem with python source block

[Doyley, Marvin M.]

Hi Thibault,
thanks for the info. I will dig around my config
cheers,
M


> Hi,

> For what it's worth, I cannot reproduce it on Org mode version 9.1.>13
>(release_9.1.13-763-g2621db) with -Q; the file is properly produced.
>
>I get the same error if I add the `session' header argument, maybe i>t is
>set elsewhere?

>Hope it helps.

>thibault

>Doyley, Marvin M. writes:

> Hi there,
>
> When I run the following code I get an error, does anybody know how to fix
> this
>
> I am using the latest version of org-mode.
>
> Thanks,
> M
>
>
> #+BEGIN_SRC python :results file
> import numpy as np
> import matplotlib.pyplot as plt
> import seaborn as sns
> x = np.random.rand(100)
> y= np.cos(x)
> plt.plot(x,y)
> plt.savefig('test.png')
> return 'test.png'
> #+END_SRC
>
> #+RESULTS:
> [[file:  File "Org SRC", line 8
> return 'test.png'
> ^
> SyntaxError: 'return' outside function
> ]]


I will do some digging around in my config file.


signature.asc
Description: Message signed with OpenPGP

[O] Problem with python source block

[Doyley, Marvin M.]

Hi there,

When I run the following code I get an error, does anybody know how to fix this

I am using the latest version of org-mode.

Thanks,
M


#+BEGIN_SRC python :results file
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
x = np.random.rand(100)
y= np.cos(x)
plt.plot(x,y)
plt.savefig('test.png')
return 'test.png'
#+END_SRC

#+RESULTS:
[[file:  File "Org SRC", line 8
return 'test.png'
^
SyntaxError: 'return' outside function
]]

Re: [O] Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[Doyley, Marvin M.]

Crossref-add-bibtex-entry is awesome. One quick question, how do you select 
multiple references ?

Cheers,
M

> On Jan 8, 2018, at 10:11 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> You might also consider the crossref search.
> 
> M-x crossref-add-bibtex-entry
> 
> It will download a bibtex and pdf (if it knows how to). I doubt you can
> do year range query, but certainly authors and keywords. It really
> excels at freeform citations as the query.
> 
> Doyley, Marvin M. writes:
> 
>> Hi there,
>> 
>> I am in the process of writing a broad literature review and was wondering 
>> if there is a way to get org-ref to search Pubmed and automatically pull 
>> (pdf, abstracts, etc) all the papers that satisfy a given  search terms 
>> (year range, keyword, authors) ?
>> 
>> Thanks,
>> 
>> M
> 
> 
> -- 
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=SvHYbzQWmnb9yyFa_ZsCzhc0a0UZZ2QycfE978DTDG8=_8S7VQ_YkQIojPf7ecqFGLP_cOZ0Fja9CqdHzFp9AQM=
>  

Re: [O] Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[Doyley, Marvin M.]

Thanks John,
I really appreciate this.

Cheers,
M
> On Jan 8, 2018, at 5:37 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> There is a command in org-ref-pubmed that will download a bibtex entry from a 
> pmid: pubmed-insert-bibtex-from-pmid. There is also the commands: 
> pubmed-simple-search which will prompt for a query and open the search in 
> pubmed, the command "pubmed" which just opens the pubmed site, and 
> "pubmed-advanced" which opens the advances search page.
> 
> There isn't however, anything as sophisticated as you want for pubmed. You 
> would have to use it to get the DOIs, and then use the doi-add-bibtex-entry 
> function to get the bibtex entry and (if it knows how) the pdf.
> 
> John
> 
> ---
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=H6YoFReSxOsGNCWFjFOb7BY7fkgnr_5tlTfCQEW7ck8=xak0y049_VKcjFA7_x91GoPfe7gxb85PFs6tKYiZrfI=>
> 
> 
> On Mon, Jan 8, 2018 at 3:32 PM, Doyley, Marvin M. <m.doy...@rochester.edu 
> <mailto:m.doy...@rochester.edu>> wrote:
> Hi there,
> 
> I am in the process of writing a broad literature review and was wondering if 
> there is a way to get org-ref to search Pubmed and automatically pull (pdf, 
> abstracts, etc) all the papers that satisfy a given  search terms (year 
> range, keyword, authors) ?
> 
> Thanks,
> 
> M
> 
> 
> 
> 
> 
> 



signature.asc
Description: Message signed with OpenPGP

[O] Using org-ref to automatically download articles from Pubmed that satisfies a given search term

[Doyley, Marvin M.]

Hi there,

I am in the process of writing a broad literature review and was wondering if 
there is a way to get org-ref to search Pubmed and automatically pull (pdf, 
abstracts, etc) all the papers that satisfy a given  search terms (year range, 
keyword, authors) ?

Thanks,

M

Re: [O] exporting org to docx

[Doyley, Marvin M.]

Hi John,

I really appreciate your help. I tried the latest version of ox-word.el that 
you place in scimax, but got the same error. I suspect that there is a bug in 
my set-up. 

I will investigate and keep you posted.

Cheers,
M 
> On Jun 27, 2017, at 7:21 PM, Doyley, Marvin M. <m.doy...@rochester.edu> wrote:
> 
> Here is a sample file that I have been using,
> 
> 
>> On Jun 27, 2017, at 10:53 AM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
>> 
>> can you post a small org file that has this problem?
>> 
>> Doyley, Marvin M. writes:
>> 
>>> Thanks for point this out, which I have now removed, but  I still get an 
>>> error. This time I get
>>> 
>>> pandoc: nil: openFile: does not exist (No such file or directory)
>>> helm-M-x: Wrong type argument: stringp, nil
>>> 
>>> Thanks,
>>> M
>>> PS here is the back trace
>>> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>>> delete-file(nil)
>>> (let* ((bibfiles (mapcar (quote expand-file-name) 
>>> (org-ref-find-bibliography))) (temp-bib) (bibtex-entries) biboption csl 
>>> (current-file (buffer-file-name)) (basename (file-name-sans-extension 
>>> current-file)) (tex-file (concat basename ".tex")) (docx-file (concat 
>>> basename ".docx"))) (save-buffer) (if bibfiles (progn (setq bibtex-entries 
>>> (let* ((bibtex-files bibfiles) (keys (reverse ...)) 
>>> (bibtex-entry-kill-ring-max (length keys)) (bibtex-entry-kill-ring (quote 
>>> nil))) (let ((wconfig ...)) (unwind-protect (progn ...) 
>>> (set-window-configuration wconfig))) (mapconcat (quote identity) 
>>> bibtex-entry-kill-ring "\n\n")) temp-bib (make-temp-file "ox-word-" nil 
>>> ".bib") biboption (format " --bibliography=%s " temp-bib)) (let ((temp-file 
>>> temp-bib) (temp-buffer (get-buffer-create (generate-new-buffer-name " *temp 
>>> file*" (unwind-protect (prog1 (save-current-buffer (set-buffer 
>>> temp-buffer) (insert bibtex-entries)) (save-current-buffer (set-buffer 
>>> temp-buffer) (write-region nil nil temp-file nil 0))) (and (buffer-name 
>>> temp-buffer) (kill-buffer temp-buffer)) (setq csl (cdr (assoc 
>>> "PANDOC-CSL" (org-element-map (org-element-parse-buffer) (quote keyword) 
>>> (function (lambda (key) (cons ... ...))) (if csl (setq csl (format " 
>>> --csl=%s " csl)) (setq csl " ")) (org-latex-export-to-latex async subtreep 
>>> visible-only body-only options) (if (file-exists-p docx-file) (progn 
>>> (delete-file docx-file))) (shell-command (format "pandoc -s -S %s%s\"%s\" 
>>> -o \"%s\"" biboption csl tex-file docx-file)) (delete-file temp-bib) 
>>> (org-open-file docx-file (quote (16
>>> ox-export-via-latex-pandoc-to-docx-and-open()
>>> funcall-interactively(ox-export-via-latex-pandoc-to-docx-and-open)
>>> call-interactively(ox-export-via-latex-pandoc-to-docx-and-open record nil)
>>> command-execute(ox-export-via-latex-pandoc-to-docx-and-open record)
>>> helm-M-x(nil #("ox-export-via-latex-pandoc-to-docx-and-open" 0 43 
>>> (match-part "ox-export-via-latex-pandoc-to-docx-and-open")))
>>> funcall-interactively(helm-M-x nil 
>>> #("ox-export-via-latex-pandoc-to-docx-and-open" 0 43 (match-part 
>>> "ox-export-via-latex-pandoc-to-docx-and-open")))
>>> call-interactively(helm-M-x nil nil)
>>> command-execute(helm-M-x)
>>> 
>>> 
>>> 
>>> 
>>>> On Jun 24, 2017, at 1:07 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
>>>> 
>>>> what is this function: my-other-delete-trailing-blank-lines
>>>> 
>>>> it appears it is not defined. but is getting called in a before-save-hook.
>>>> 
>>>> Doyley, Marvin M. writes:
>>>> 
>>>>> Hi there,
>>>>> 
>>>>> I am play with John’s ox-word.el function, which us pandoc to convert org 
>>>>> via latex to docx. However, when I try to use it, I get  the following 
>>>>> error
>>>>> 
>>>>> helm-M-x: Wrong type argument: stringp, nil
>>>>> 
>>>>> 
>>>>> Any suggestion on how to resolve this issue.
>>>>> 
>>>>> Cheers,
>>>>> M
>>>>> 
>>>>> Ps Here is the backtrace
>>>>> 
>>>>> Debugger entered--Lisp error: (void-fu

Re: [O] exporting org to docx

[Doyley, Marvin M.]

Here is a sample file that I have been using,



simple_test.org
Description: Binary data


simple_test.tex
Description: TeX document

> On Jun 27, 2017, at 10:53 AM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> can you post a small org file that has this problem?
> 
> Doyley, Marvin M. writes:
> 
>> Thanks for point this out, which I have now removed, but  I still get an 
>> error. This time I get
>> 
>> pandoc: nil: openFile: does not exist (No such file or directory)
>> helm-M-x: Wrong type argument: stringp, nil
>> 
>> Thanks,
>> M
>> PS here is the back trace
>> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>>  delete-file(nil)
>>  (let* ((bibfiles (mapcar (quote expand-file-name) 
>> (org-ref-find-bibliography))) (temp-bib) (bibtex-entries) biboption csl 
>> (current-file (buffer-file-name)) (basename (file-name-sans-extension 
>> current-file)) (tex-file (concat basename ".tex")) (docx-file (concat 
>> basename ".docx"))) (save-buffer) (if bibfiles (progn (setq bibtex-entries 
>> (let* ((bibtex-files bibfiles) (keys (reverse ...)) 
>> (bibtex-entry-kill-ring-max (length keys)) (bibtex-entry-kill-ring (quote 
>> nil))) (let ((wconfig ...)) (unwind-protect (progn ...) 
>> (set-window-configuration wconfig))) (mapconcat (quote identity) 
>> bibtex-entry-kill-ring "\n\n")) temp-bib (make-temp-file "ox-word-" nil 
>> ".bib") biboption (format " --bibliography=%s " temp-bib)) (let ((temp-file 
>> temp-bib) (temp-buffer (get-buffer-create (generate-new-buffer-name " *temp 
>> file*" (unwind-protect (prog1 (save-current-buffer (set-buffer 
>> temp-buffer) (insert bibtex-entries)) (save-current-buffer (set-buffer 
>> temp-buffer) (write-region nil nil temp-file nil 0))) (and (buffer-name 
>> temp-buffer) (kill-buffer temp-buffer)) (setq csl (cdr (assoc 
>> "PANDOC-CSL" (org-element-map (org-element-parse-buffer) (quote keyword) 
>> (function (lambda (key) (cons ... ...))) (if csl (setq csl (format " 
>> --csl=%s " csl)) (setq csl " ")) (org-latex-export-to-latex async subtreep 
>> visible-only body-only options) (if (file-exists-p docx-file) (progn 
>> (delete-file docx-file))) (shell-command (format "pandoc -s -S %s%s\"%s\" -o 
>> \"%s\"" biboption csl tex-file docx-file)) (delete-file temp-bib) 
>> (org-open-file docx-file (quote (16
>>  ox-export-via-latex-pandoc-to-docx-and-open()
>>  funcall-interactively(ox-export-via-latex-pandoc-to-docx-and-open)
>>  call-interactively(ox-export-via-latex-pandoc-to-docx-and-open record nil)
>>  command-execute(ox-export-via-latex-pandoc-to-docx-and-open record)
>>  helm-M-x(nil #("ox-export-via-latex-pandoc-to-docx-and-open" 0 43 
>> (match-part "ox-export-via-latex-pandoc-to-docx-and-open")))
>>  funcall-interactively(helm-M-x nil 
>> #("ox-export-via-latex-pandoc-to-docx-and-open" 0 43 (match-part 
>> "ox-export-via-latex-pandoc-to-docx-and-open")))
>>  call-interactively(helm-M-x nil nil)
>>  command-execute(helm-M-x)
>> 
>> 
>> 
>> 
>>> On Jun 24, 2017, at 1:07 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
>>> 
>>> what is this function: my-other-delete-trailing-blank-lines
>>> 
>>> it appears it is not defined. but is getting called in a before-save-hook.
>>> 
>>> Doyley, Marvin M. writes:
>>> 
>>>> Hi there,
>>>> 
>>>> I am play with John’s ox-word.el function, which us pandoc to convert org 
>>>> via latex to docx. However, when I try to use it, I get  the following 
>>>> error
>>>> 
>>>> helm-M-x: Wrong type argument: stringp, nil
>>>> 
>>>> 
>>>> Any suggestion on how to resolve this issue.
>>>> 
>>>> Cheers,
>>>> M
>>>> 
>>>> Ps Here is the backtrace
>>>> 
>>>> Debugger entered--Lisp error: (void-function 
>>>> my-other-delete-trailing-blank-lines)
>>>> my-other-delete-trailing-blank-lines()
>>>> run-hooks(before-save-hook)
>>>> basic-save-buffer(nil)
>>>> save-buffer()
>>>> write-file("./test.tex.tex")
>>>> (let ((coding-system-for-write encoding)) (write-file file))
>>>> (progn (insert output) (let ((coding-system-for-write encoding)) 
>>>> (write-file file)))
>>>> (unwind-protect (progn (insert output) (let ((coding-system-fo

Re: [O] exporting org to docx

[Doyley, Marvin M.]

Thanks for point this out, which I have now removed, but  I still get an error. 
This time I get

pandoc: nil: openFile: does not exist (No such file or directory)
helm-M-x: Wrong type argument: stringp, nil

Thanks,
M
PS here is the back trace
Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  delete-file(nil)
  (let* ((bibfiles (mapcar (quote expand-file-name) 
(org-ref-find-bibliography))) (temp-bib) (bibtex-entries) biboption csl 
(current-file (buffer-file-name)) (basename (file-name-sans-extension 
current-file)) (tex-file (concat basename ".tex")) (docx-file (concat basename 
".docx"))) (save-buffer) (if bibfiles (progn (setq bibtex-entries (let* 
((bibtex-files bibfiles) (keys (reverse ...)) (bibtex-entry-kill-ring-max 
(length keys)) (bibtex-entry-kill-ring (quote nil))) (let ((wconfig ...)) 
(unwind-protect (progn ...) (set-window-configuration wconfig))) (mapconcat 
(quote identity) bibtex-entry-kill-ring "\n\n")) temp-bib (make-temp-file 
"ox-word-" nil ".bib") biboption (format " --bibliography=%s " temp-bib)) (let 
((temp-file temp-bib) (temp-buffer (get-buffer-create (generate-new-buffer-name 
" *temp file*" (unwind-protect (prog1 (save-current-buffer (set-buffer 
temp-buffer) (insert bibtex-entries)) (save-current-buffer (set-buffer 
temp-buffer) (write-region nil nil temp-file nil 0))) (and (buffer-name 
temp-buffer) (kill-buffer temp-buffer)) (setq csl (cdr (assoc "PANDOC-CSL" 
(org-element-map (org-element-parse-buffer) (quote keyword) (function (lambda 
(key) (cons ... ...))) (if csl (setq csl (format " --csl=%s " csl)) (setq 
csl " ")) (org-latex-export-to-latex async subtreep visible-only body-only 
options) (if (file-exists-p docx-file) (progn (delete-file docx-file))) 
(shell-command (format "pandoc -s -S %s%s\"%s\" -o \"%s\"" biboption csl 
tex-file docx-file)) (delete-file temp-bib) (org-open-file docx-file (quote 
(16
  ox-export-via-latex-pandoc-to-docx-and-open()
  funcall-interactively(ox-export-via-latex-pandoc-to-docx-and-open)
  call-interactively(ox-export-via-latex-pandoc-to-docx-and-open record nil)
  command-execute(ox-export-via-latex-pandoc-to-docx-and-open record)
  helm-M-x(nil #("ox-export-via-latex-pandoc-to-docx-and-open" 0 43 (match-part 
"ox-export-via-latex-pandoc-to-docx-and-open")))
  funcall-interactively(helm-M-x nil 
#("ox-export-via-latex-pandoc-to-docx-and-open" 0 43 (match-part 
"ox-export-via-latex-pandoc-to-docx-and-open")))
  call-interactively(helm-M-x nil nil)
  command-execute(helm-M-x)




> On Jun 24, 2017, at 1:07 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> what is this function: my-other-delete-trailing-blank-lines
> 
> it appears it is not defined. but is getting called in a before-save-hook.
> 
> Doyley, Marvin M. writes:
> 
>> Hi there,
>> 
>> I am play with John’s ox-word.el function, which us pandoc to convert org 
>> via latex to docx. However, when I try to use it, I get  the following error
>> 
>> helm-M-x: Wrong type argument: stringp, nil
>> 
>> 
>> Any suggestion on how to resolve this issue.
>> 
>> Cheers,
>> M
>> 
>> Ps Here is the backtrace
>> 
>> Debugger entered--Lisp error: (void-function 
>> my-other-delete-trailing-blank-lines)
>>  my-other-delete-trailing-blank-lines()
>>  run-hooks(before-save-hook)
>>  basic-save-buffer(nil)
>>  save-buffer()
>>  write-file("./test.tex.tex")
>>  (let ((coding-system-for-write encoding)) (write-file file))
>>  (progn (insert output) (let ((coding-system-for-write encoding)) 
>> (write-file file)))
>>  (unwind-protect (progn (insert output) (let ((coding-system-for-write 
>> encoding)) (write-file file))) (and (buffer-name temp-buffer) (kill-buffer 
>> temp-buffer)))
>>  (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn 
>> (insert output) (let ((coding-system-for-write encoding)) (write-file 
>> file))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer
>>  (let ((temp-buffer (generate-new-buffer " *temp*"))) (save-current-buffer 
>> (set-buffer temp-buffer) (unwind-protect (progn (insert output) (let 
>> ((coding-system-for-write encoding)) (write-file file))) (and (buffer-name 
>> temp-buffer) (kill-buffer temp-buffer)
>>  (let ((output (org-export-as backend subtreep visible-only body-only 
>> ext-plist))) (let ((temp-buffer (generate-new-buffer " *temp*"))) 
>> (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (insert 
>> output) (let ((coding-system-for-write encoding)) (write-file file))) (and 
>> (buffer-name temp-buffer) (kill-

[O] exporting org to docx

[Doyley, Marvin M.]

Hi there,

I am play with John’s ox-word.el function, which us pandoc to convert org via 
latex to docx. However, when I try to use it, I get  the following error

helm-M-x: Wrong type argument: stringp, nil


Any suggestion on how to resolve this issue.

Cheers,
M

Ps Here is the backtrace

Debugger entered--Lisp error: (void-function 
my-other-delete-trailing-blank-lines)
  my-other-delete-trailing-blank-lines()
  run-hooks(before-save-hook)
  basic-save-buffer(nil)
  save-buffer()
  write-file("./test.tex.tex")
  (let ((coding-system-for-write encoding)) (write-file file))
  (progn (insert output) (let ((coding-system-for-write encoding)) (write-file 
file)))
  (unwind-protect (progn (insert output) (let ((coding-system-for-write 
encoding)) (write-file file))) (and (buffer-name temp-buffer) (kill-buffer 
temp-buffer)))
  (save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (insert 
output) (let ((coding-system-for-write encoding)) (write-file file))) (and 
(buffer-name temp-buffer) (kill-buffer temp-buffer
  (let ((temp-buffer (generate-new-buffer " *temp*"))) (save-current-buffer 
(set-buffer temp-buffer) (unwind-protect (progn (insert output) (let 
((coding-system-for-write encoding)) (write-file file))) (and (buffer-name 
temp-buffer) (kill-buffer temp-buffer)
  (let ((output (org-export-as backend subtreep visible-only body-only 
ext-plist))) (let ((temp-buffer (generate-new-buffer " *temp*"))) 
(save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn (insert 
output) (let ((coding-system-for-write encoding)) (write-file file))) (and 
(buffer-name temp-buffer) (kill-buffer temp-buffer) (if (and 
(org-export--copy-to-kill-ring-p) (org-string-nw-p output)) (progn 
(org-kill-new output))) (or (and (functionp post-process) (funcall post-process 
file)) file))
  (if async (let ((with-temp-message "Initializing asynchronous export 
process") (current-message)) (unwind-protect (progn (if with-temp-message 
(progn (setq current-message (current-message)) (message "%s" 
with-temp-message))) (let ((--copy-fun (org-export--generate-copy-script ...)) 
(--temp-file (make-temp-file "org-export-process")) (--coding 
buffer-file-coding-system)) (let ((temp-file --temp-file) (temp-buffer ...)) 
(unwind-protect (prog1 ... ...) (and ... ...))) (let* ((process-connection-type 
nil) (--proc-buffer ...) (--process ...)) (org-export-add-to-stack (get-buffer 
--proc-buffer) nil --process) (let (...) (set-process-sentinel --process 
...) (and with-temp-message (if current-message (message "%s" 
current-message) (message nil) (let ((output (org-export-as backend 
subtreep visible-only body-only ext-plist))) (let ((temp-buffer 
(generate-new-buffer " *temp*"))) (save-current-buffer (set-buffer temp-buffer) 
(unwind-protect (progn (insert output) (let (...) (write-file file))) (and 
(buffer-name temp-buffer) (kill-buffer temp-buffer) (if (and 
(org-export--copy-to-kill-ring-p) (org-string-nw-p output)) (progn 
(org-kill-new output))) (or (and (functionp post-process) (funcall post-process 
file)) file)))
  (let ((ext-plist (org-combine-plists (list (quote :output-file) file) 
ext-plist)) (encoding (or org-export-coding-system buffer-file-coding-system))) 
(if async (let ((with-temp-message "Initializing asynchronous export process") 
(current-message)) (unwind-protect (progn (if with-temp-message (progn (setq 
current-message ...) (message "%s" with-temp-message))) (let ((--copy-fun ...) 
(--temp-file ...) (--coding buffer-file-coding-system)) (let (... ...) 
(unwind-protect ... ...)) (let* (... ... ...) (org-export-add-to-stack ... nil 
--process) (let ... ... (and with-temp-message (if current-message (message 
"%s" current-message) (message nil) (let ((output (org-export-as backend 
subtreep visible-only body-only ext-plist))) (let ((temp-buffer 
(generate-new-buffer " *temp*"))) (save-current-buffer (set-buffer temp-buffer) 
(unwind-protect (progn (insert output) (let ... ...)) (and (buffer-name 
temp-buffer) (kill-buffer temp-buffer) (if (and 
(org-export--copy-to-kill-ring-p) (org-string-nw-p output)) (progn 
(org-kill-new output))) (or (and (functionp post-process) (funcall post-process 
file)) file
  (if (not (file-writable-p file)) (error "Output file not writable") (let 
((ext-plist (org-combine-plists (list (quote :output-file) file) ext-plist)) 
(encoding (or org-export-coding-system buffer-file-coding-system))) (if async 
(let ((with-temp-message "Initializing asynchronous export process") 
(current-message)) (unwind-protect (progn (if with-temp-message (progn ... 
...)) (let (... ... ...) (let ... ...) (let* ... ... ...))) (and 
with-temp-message (if current-message (message "%s" current-message) (message 
nil) (let ((output (org-export-as backend subtreep visible-only body-only 
ext-plist))) (let ((temp-buffer (generate-new-buffer " *temp*"))) 
(save-current-buffer (set-buffer temp-buffer) (unwind-protect (progn ... ...) 
(and ... ... 

Re: [O] Viewing pdf images

[Doyley, Marvin M.]

Hi Eduardo,
Thanks for the insight, I really appreciate this.
Cheers,
M
> On Apr 10, 2017, at 12:51 PM, Eduardo Mercovich  wrote:
> 
> Hi Marvin.
> 
>> I also agree that in terms of resolution (pix per inch ) pdf and jpg are the 
>> same. However, pdf (and SVG) allow the image to be scaled with little loss 
>> in image quality.
> 
> Sorry to disagree, but again, pdf images can be vector (like svg) and 
> infinitely scaled or raster (bitmap, as a jpg) and in this case the quality 
> is on the file. The pdf format only adds and envelope around the original jpg 
> image, or in the conversion it can be downscaled.
> 
> Just to test this you can extract the images from the pdf and check their 
> properties. The specific tools depend on your OS of choice, but at least in 
> Linux there are many options, some command line based and others GUI based.
> 
>> In my lab we typically save the images in pdf because the most biomedical 
>> journals don’t accept SVG file format (not yet).
> 
> Sure. But why not simply use a jpg or png?
> * Journals accept those formats perfectly well, * you will see them with 
> their best quality, and
> * you can see them in emacs buffers natively.
> 
> Just try it and you'll see that -if I understood you ok- you will gain in 
> every dimension. :)
> 
> Best...
> 
> 
> --
> eduardo mercovich
> 
> Donde se cruzan tus talentos con las necesidades del mundo, ahí está tu 
> vocación. (Anónimo)



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Re: [O] Viewing pdf images

[Doyley, Marvin M.]

Hi Eduardo,

I also agree that in terms of resolution (pix per inch ) pdf and jpg are the 
same. However, pdf (and SVG) allow the image to be scaled with little loss in 
image quality. In my lab we typically save the images in pdf because the most 
biomedical journals don’t accept SVG file format (not yet).

Thanks,
M
PS Since emacs can display SVG, we are planning to use this as our default file 
format during the manuscript generation stage, and then convert to pdf at the 
end (just before submitting)

> On Apr 9, 2017, at 6:06 PM, Eduardo Mercovich  wrote:
> 
> Hi Marvin.
> 
>> For manuscripts, my research group and I typically save images in pdf 
>> format, much better resolution. It would be nice to view pdf  images when 
>> working in org-mode.
>> Does anybody know how to view pdf images in org-mode.
> 
> Excuse my question but there is something I don't understand here... I'd like 
> to be sure we are not scratching where it doesn't itch.
> PDF files don't show images at a better resolution, they just "encapsulate" 
> and show them. So, if you have a 2000x2000 px jpg, putting it inside a pdf 
> will not add resolution (nor lower it, if it's not compressed), but just add 
> a wrapper around it. The resolution is a property of the image file.
> 
> OTOH, different image formats do change the quality: jpg and (some) png are 
> lossy formats while tiff is looseless.
> So what kind of images are you talking about? Are they produced by you and 
> your team (and using what tools/methods), scanned from physical artifacts, or 
> taken from other sources?
> 
> Maybe there is no need to do all this pdf magic.
>> PS We also work with svg images too, that would also love to view in org-mode
> 
> Again, this is quite similar. You can produce pdf from svg: both are vector 
> images and are resolution independent. But emacs con show svg files directly 
> (see 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.emacswiki.org_emacs_EmacsSvg=DwIDaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=ToUr47iyS79VqRe2JGHpKEuFdjOC7Ae_27eFPP0IW_w=7L3s6Qt1QD87OGVmmSwlgpqsI1HZOUvEVFP6izsIYmc=
>  ).
> 
> Best...
> --
> eduardo mercovich
> 
> Donde se cruzan tus talentos con las necesidades del mundo, ahí está tu 
> vocación. (Anónimo)



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Re: [O] Viewing pdf images

[Doyley, Marvin M.]

Thanks,

Much appreciated.

Cheers,
M
> On Mar 21, 2017, at 6:34 AM, Julian M. Burgos <julian.bur...@hafogvatn.is> 
> wrote:
> 
> I have the following in my .emacs file.  For this to work you need to
> have your emacs compiled with imagemagick support (and have imagemagick
> installed, of course).  It works well, although the images do not appear
> immediately the first time you toggle them because the conversion takes
> a little bit.
> 
> #+BEGIN_SRC emacs-lisp
> 
> (setq image-file-name-extensions
>   (quote
>("png" "jpeg" "jpg" "gif" "tiff" "tif" "xbm" "xpm" "pbm" "pgm" "ppm" "pnm" 
> "svg" "pdf" "bmp" "eps")))
> (add-to-list 'image-type-file-name-regexps '("\\.eps\\'" . imagemagick))
> (add-to-list 'image-file-name-extensions "eps")
> (add-to-list 'image-type-file-name-regexps '("\\.pdf\\'" . imagemagick))
> (add-to-list 'image-file-name-extensions "pdf")
> (setq imagemagick-types-inhibit (remove 'PDF imagemagick-types-inhibit))
> 
> #+END_SRC
> 
> 
> 
> 
> Doyley, Marvin M. writes:
> 
>> Doesn’t work. Emacs just Hangs :(
>>> On Mar 17, 2017, at 8:43 AM, Norwid Behrnd <nbeh...@yahoo.com> wrote:
>>> 
>>> 
>>> To include and display pdf files, perhaps the setup outlined here is
>>> still working (dates back 2014...)
>>> 
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__emacs.stackexchange.com_questions_390_display-2Dpdf-2Dimages-2Din-2Dorg-2Dmode=DwIC-g=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=cQ2XAFEKpHWcRH33Hvyanl-V2rE3v-7glys69pwm8CY=rmvwv-l1KvLkkUN0iG1d7bT6-MNbzQOFpz5U4-fLPt0=
>>> 
>>> Cheers.
>>> 
>>> 
>>> 
>>> On 03/17/2017 01:27 PM, Doyley, Marvin M. wrote:
>>>> Hi there,
>>>> 
>>>> For manuscripts, my research group and I typically save images in pdf
>>>> format, much better resolution. It would be nice to view pdf  images
>>>> when working in org-mode. Does anybody know how to view pdf images in
>>>> org-mode.
>>>> 
>>>> Thanks, M
>>>> 
>>>> PS We also work with svg images too, that would also love to view in
>>>> org-mode
>>>> 
> 
> 
> --
> Julian Mariano Burgos, PhD
> Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
> Marine and Freshwater Research Institute
> Skúlagata 4, 121 Reykjavík, Iceland
> Sími/Telephone : +354-5752037
> Bréfsími/Telefax:  +354-5752001
> Netfang/Email: julian.bur...@hafogvatn.is



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Re: [O] Viewing pdf images

[Doyley, Marvin M.]

Doesn’t work. Emacs just Hangs :(
> On Mar 17, 2017, at 8:43 AM, Norwid Behrnd <nbeh...@yahoo.com> wrote:
> 
> 
> To include and display pdf files, perhaps the setup outlined here is
> still working (dates back 2014...)
> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__emacs.stackexchange.com_questions_390_display-2Dpdf-2Dimages-2Din-2Dorg-2Dmode=DwIC-g=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=cQ2XAFEKpHWcRH33Hvyanl-V2rE3v-7glys69pwm8CY=rmvwv-l1KvLkkUN0iG1d7bT6-MNbzQOFpz5U4-fLPt0=
> 
> Cheers.
> 
> 
> 
> On 03/17/2017 01:27 PM, Doyley, Marvin M. wrote:
>> Hi there,
>> 
>> For manuscripts, my research group and I typically save images in pdf
>> format, much better resolution. It would be nice to view pdf  images
>> when working in org-mode. Does anybody know how to view pdf images in
>> org-mode.
>> 
>> Thanks, M
>> 
>> PS We also work with svg images too, that would also love to view in
>> org-mode
>> 



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[O] Viewing pdf images

[Doyley, Marvin M.]

Hi there,

For manuscripts, my research group and I typically save images in pdf format, 
much better resolution. It would be nice to view pdf  images when working in 
org-mode.
Does anybody know how to view pdf images in org-mode.

Thanks,
M

PS We also work with svg images too, that would also love to view in org-mode


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Re: [O] New markup for revising manuscripts

[Doyley, Marvin M.]

Hi John and Eric,

I decided to adopt your approaches, thanks for the suggestions.  So I can use 
either the response: or ++ to highlight changes in our manuscripts.

Cheers,
M

#+BEGIN_SRC emacs-lisp
(org-link-set-parameters
 "response"
 :export (lambda (keyword desc format)
   (cond
((eq 'latex format)
 (format "\\textcolor{red}{%s}" keyword
 :face '(:foreground "red"))
#+END_SRC


#+begin_src emacs-lisp
(setq org-emphasis-alist
  (cons '("+" '(:foreground "red"))
(delete* "+" org-emphasis-alist :key 'car :test 'equal)))

(custom-set-variables
  '(org-latex-text-markup-alist '((bold . "\\textbf{%s}")
 (code . verb)
 (italic . "\\emph{%s}")
 (strike-through . 
"\\textcolor{red}{%s}")
 (underline . "\\uline{%s}")
 (verbatim . protectedtexttt

#+end_src


> On Mar 10, 2017, at 4:47 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> You can  wait for it... make a colored link ;): 
> http://kitchingroup.cheme.cmu.edu/blog/2016/11/04/New-link-features-in-org-9/#org1bc1061
>  
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_04_New-2Dlink-2Dfeatures-2Din-2Dorg-2D9_-23org1bc1061=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=4DUIBEXq8WNk6qHHyXFoIwWG4FlD2NlDgz8AfT2VUS0=>
> 
> The example there has an html export defined, but you could as easily define 
> a latex exporter. It has some limitations, like it might not reliably work on 
> multiple lines, and you would not want to "highlight" across elements (or the 
> latex will get ugly and probably not work).
> 
> I have been working on some ways to get persistent highlighting using 
> overlays for a similar purpose: 
> http://kitchingroup.cheme.cmu.edu/blog/2016/11/10/Persistent-highlighting-in-Emacs/
>  
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_10_Persistent-2Dhighlighting-2Din-2DEmacs_=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=I0JDZ741rHEtzWzAF3lhW65rzNn4vdq4tiUyD10_7l0=>
> 
> so far I only can get reliable output to html. Latex seems possible, again if 
> you don't highlight across too many elements. It is a work in progress here: 
> https://github.com/jkitchin/scimax/blob/master/ov-highlighter.el 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_ov-2Dhighlighter.el=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=2LS5YZIgyAvGS3fmo8rEgaDS2Tbu3UL10uqdUgH-LXc=>
> 
> Towards the bottom of 
> https://github.com/jkitchin/scimax/blob/master/cm-mods.el 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_cm-2Dmods.el=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=hg-nJ1pgNjsD6TM3dFMEX7IADrW9iwU8e3nvulj1lFc=>
>  I was working on some ways to use the criticmarkup  in conjunction with git 
> diffs to automatically make these kinds of diffs.
> 
> I can't say I am fully satisified by any of these solutions (that is why 
> there are so many of them ;)
> 
> John
> 
> ---
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=9l9_vjFtxnWTTnFYN-Uy0mhhk-B5fKQeudqix5QWjqA=>
> 
> 
> On Fri, Mar 10, 2017 at 3:56 PM, Kaushal Modi <kaushal.m...@gmail.com 
> <mailto:kaushal.m...@gmail.com>> wrote:
> I use this macro to highlight text in html/latex(pdf):
> 
> #+MACRO: COLOR @@html:$2latex:\textcolor{$1}{$2}@@
> 
> This is from https://github.com/fniessen/org-macros/blob/master/README.org 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_fniessen_org-2Dmacros_blob_master_README.org=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=XDOhI8-iVimfEcDs18oR3i-Yyuic8

Re: [O] New markup for revising manuscripts

[Doyley, Marvin M.]

Hi Eric,

I really appreciate this. I will try it out too.

Cheers,
M
On Friday, 10 Mar 2017 at 20:33, Doyley, Marvin M. wrote:
> Hi there,
>
> When revising manuscripts, I usually highlight the changes (response
> to reviewer) in red. I use typically do this as follows:
> (1) #+latex_header: \newcommand{\response}[1]{\textcolor{red}{#1}}
> (2) \response{changes)
>
> Is there a more elegant way to do this ?

I don't know about elegant but my approach is to subvert the +...+
emphasis markers.  These usually indicate strike-through, something I
never use.  Instead, I have +some text+ be highlighted and exported to
LaTeX and HTML as such.

To achieve this, I customise a number org variables.  It took me some
time to find how I actually did this as it's been part of my org setup
for years, so much so that I almost thought it was default behaviour!
In any case, the following is an elided extract from my customised
variables:

#+begin_src emacs-lisp
  (custom-set-variables
   '(org-emphasis-alist
 (quote
  (("*" bold)
   ("/" italic)
   ("_" underline)
   ("=" org-verbatim verbatim)
   ("~" org-code verbatim)
   ("+" highlight
   '(org-html-text-markup-alist
 (quote
  ((bold . "%s")
   (code . "%s")
   (italic . "%s")
   (strike-through . "%s")
   (underline . "%s")
   (verbatim . "%s"
   '(org-latex-text-markup-alist
 (quote
  ((bold . "\\textbf{%s}")
   (code . protectedtexttt)
   (italic . "\\emph{%s}")
   (strike-through . "\\hl{%s}")
   (underline . "\\uline{%s}")
   (verbatim . protectedtexttt)
#+end_src

There are basically copies of the defaults with the strike-through
element changed.

Now I can write +highlighted text+ which appears as you wish in both
HTML and LaTeX exports as well as on the screen (customise the highlight
face to get what you want on screen).  For LaTeX, you also have to

  (add-to-list 'org-latex-packages-alist '("" "soul"))



signature.asc
Description: Message signed with OpenPGP using GPGMail

Re: [O] New markup for revising manuscripts

[Doyley, Marvin M.]

Hi John,

I like the idea of special block that definitely solve the multi-line problem. 
But I would need to write an latex exporter for the block, how challenging 
would that be ? I am still learning lisp :)

Cheers,
M
> On Mar 11, 2017, at 1:22 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> This is probably not feasible with links. that is also a challenge with
> Eric's markup approach. One way is to use visual wrapping so whole
> paragraphs are actually one line. Another is to use some kind of custom block.
> It has been a while since I tried this: 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2013_11_30_Custom-2Ddirectives_=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=HR848Kl27487mBHnj6hZWqJ4zVzwnz8yn_CYsmstLLc=CgaellrR4m7Y4Quba00w0ekyLA_np6lkrXxoWv4awZQ=
> 
> Multiline mostly works with criticmarks using multiline fontlock. The
> nice thing about this is that it is still plain text markup, but relies
> on font-lock which can be slow, and or unreliable in my experience.
> 
> This was one reason I started looking at the overlay approach in
> ov-highlighter. It nicely manages multiline comments, but is not part of
> org markup though. A downside is you have to store the overlays in the
> document to get persistence, and it is easily breakable if others edit
> the document without using the package.
> 
> Doyley, Marvin M. writes:
> 
>> Thanks John,
>> 
>> Works like a charm. Any idea how to write comments that spans multiple lines 
>> ?
>> 
>> cheers,
>> M
>>> On Mar 11, 2017, at 7:55 AM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
>>> 
>>> it looks like you forgot to include format in the (eq ..) sexp.
>>> 
>>> (org-link-set-parameters
>>> "response"
>>> :export (lambda (keyword desc format)
>>>  (cond
>>>   ((eq 'latex format)
>>>(format "\\textcolor{red}{%s}" keyword
>>> :face '(:foreground "red"))
>>> Doyley, Marvin M. writes:
>>> 
>>>> Hi John,
>>>> 
>>>> I make a colored link [[response: comments]], that makes the text 
>>>> following the response keyword red. The only snag is that when I export to 
>>>> latex I get [[response:comment]] rather than \textcolor{red}{comment}. Any 
>>>> thoughts on what I am doing wrong ?
>>>> 
>>>> Cheers,
>>>> M
>>>> 
>>>> PS.  Enclose is the code that I wrote based on your blog
>>>> 
>>>> 
>>>> (org-link-set-parameters
>>>> "response"
>>>> :export (lambda (keyword desc format)
>>>>  (cond
>>>>   ((eq 'latex)
>>>>(format "\\textcolor{red}{%s}" keyword
>>>> :face '(:foreground "red"))
>>>> 
>>>> 
>>>>> On Mar 10, 2017, at 4:47 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
>>>>> 
>>>>> You can  wait for it... make a colored link ;): 
>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_04_New-2Dlink-2Dfeatures-2Din-2Dorg-2D9_-23org1bc1061=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=K82CvGdcCIiUxLK-NulYuwGBzRdPZnZ9zByz2od0v9s=SVZmNbDCL0B9rvGIDHrFia_f1-mL_I_EmCUR_vcWkxg=
>>>>>   
>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_04_New-2Dlink-2Dfeatures-2Din-2Dorg-2D9_-23org1bc1061=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=4DUIBEXq8WNk6qHHyXFoIwWG4FlD2NlDgz8AfT2VUS0=>
>>>>> 
>>>>> The example there has an html export defined, but you could as easily 
>>>>> define a latex exporter. It has some limitations, like it might not 
>>>>> reliably work on multiple lines, and you would not want to "highlight" 
>>>>> across elements (or the latex will get ugly and probably not work).
>>>>> 
>>>>> I have been working on some ways to get persistent highlighting using 
>>>>> overlays for a similar purpose: 
>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_10_Persistent-2Dhighlighting-2Din-2DEmacs_=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=K82CvGdcCIiUxLK-NulYuwGBzRdPZnZ9zB

Re: [O] New markup for revising manuscripts

[Doyley, Marvin M.]

Thanks John,

Works like a charm. Any idea how to write comments that spans multiple lines ?

cheers,
M
> On Mar 11, 2017, at 7:55 AM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> it looks like you forgot to include format in the (eq ..) sexp.
> 
> (org-link-set-parameters
> "response"
> :export (lambda (keyword desc format)
>   (cond
>((eq 'latex format)
> (format "\\textcolor{red}{%s}" keyword
> :face '(:foreground "red"))
> Doyley, Marvin M. writes:
> 
>> Hi John,
>> 
>> I make a colored link [[response: comments]], that makes the text following 
>> the response keyword red. The only snag is that when I export to latex I get 
>> [[response:comment]] rather than \textcolor{red}{comment}. Any thoughts on 
>> what I am doing wrong ?
>> 
>> Cheers,
>> M
>> 
>> PS.  Enclose is the code that I wrote based on your blog
>> 
>> 
>> (org-link-set-parameters
>> "response"
>> :export (lambda (keyword desc format)
>>   (cond
>>((eq 'latex)
>> (format "\\textcolor{red}{%s}" keyword
>> :face '(:foreground "red"))
>> 
>> 
>>> On Mar 10, 2017, at 4:47 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
>>> 
>>> You can  wait for it... make a colored link ;): 
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_04_New-2Dlink-2Dfeatures-2Din-2Dorg-2D9_-23org1bc1061=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=K82CvGdcCIiUxLK-NulYuwGBzRdPZnZ9zByz2od0v9s=SVZmNbDCL0B9rvGIDHrFia_f1-mL_I_EmCUR_vcWkxg=
>>>   
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_04_New-2Dlink-2Dfeatures-2Din-2Dorg-2D9_-23org1bc1061=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=4DUIBEXq8WNk6qHHyXFoIwWG4FlD2NlDgz8AfT2VUS0=>
>>> 
>>> The example there has an html export defined, but you could as easily 
>>> define a latex exporter. It has some limitations, like it might not 
>>> reliably work on multiple lines, and you would not want to "highlight" 
>>> across elements (or the latex will get ugly and probably not work).
>>> 
>>> I have been working on some ways to get persistent highlighting using 
>>> overlays for a similar purpose: 
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_10_Persistent-2Dhighlighting-2Din-2DEmacs_=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=K82CvGdcCIiUxLK-NulYuwGBzRdPZnZ9zByz2od0v9s=11D132bMNfLVhS6-xXWo1p7tZ8EBpeZMgUvYmtcCD9I=
>>>   
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_10_Persistent-2Dhighlighting-2Din-2DEmacs_=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=I0JDZ741rHEtzWzAF3lhW65rzNn4vdq4tiUyD10_7l0=>
>>> 
>>> so far I only can get reliable output to html. Latex seems possible, again 
>>> if you don't highlight across too many elements. It is a work in progress 
>>> here: 
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_ov-2Dhighlighter.el=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=K82CvGdcCIiUxLK-NulYuwGBzRdPZnZ9zByz2od0v9s=Cz0LeGE0ds46QIsBHJLgKVddn1pKWKlxsO1WpKqk8g4=
>>>   
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_ov-2Dhighlighter.el=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=2LS5YZIgyAvGS3fmo8rEgaDS2Tbu3UL10uqdUgH-LXc=>
>>> 
>>> Towards the bottom of 
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_cm-2Dmods.el=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=K82CvGdcCIiUxLK-NulYuwGBzRdPZnZ9zByz2od0v9s=gIkKQ99iatYU867xq50LnefeG4ehMUlgunqp1tD_H08=
>>>   
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_cm-2Dmods.el=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=hg-nJ1pgNjsD6TM3dFMEX7IADrW9iwU8e3nvulj1lFc=>
>>>  I was working on some ways 

Re: [O] New markup for revising manuscripts

[Doyley, Marvin M.]

Hi John,

I make a colored link [[response: comments]], that makes the text following the 
response keyword red. The only snag is that when I export to latex I get 
[[response:comment]] rather than \textcolor{red}{comment}. Any thoughts on what 
I am doing wrong ?

Cheers,
M

PS.  Enclose is the code that I wrote based on your blog


(org-link-set-parameters
 "response"
 :export (lambda (keyword desc format)
   (cond
((eq 'latex)
 (format "\\textcolor{red}{%s}" keyword
 :face '(:foreground "red"))


> On Mar 10, 2017, at 4:47 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> You can  wait for it... make a colored link ;): 
> http://kitchingroup.cheme.cmu.edu/blog/2016/11/04/New-link-features-in-org-9/#org1bc1061
>  
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_04_New-2Dlink-2Dfeatures-2Din-2Dorg-2D9_-23org1bc1061=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=4DUIBEXq8WNk6qHHyXFoIwWG4FlD2NlDgz8AfT2VUS0=>
> 
> The example there has an html export defined, but you could as easily define 
> a latex exporter. It has some limitations, like it might not reliably work on 
> multiple lines, and you would not want to "highlight" across elements (or the 
> latex will get ugly and probably not work).
> 
> I have been working on some ways to get persistent highlighting using 
> overlays for a similar purpose: 
> http://kitchingroup.cheme.cmu.edu/blog/2016/11/10/Persistent-highlighting-in-Emacs/
>  
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_10_Persistent-2Dhighlighting-2Din-2DEmacs_=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=I0JDZ741rHEtzWzAF3lhW65rzNn4vdq4tiUyD10_7l0=>
> 
> so far I only can get reliable output to html. Latex seems possible, again if 
> you don't highlight across too many elements. It is a work in progress here: 
> https://github.com/jkitchin/scimax/blob/master/ov-highlighter.el 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_ov-2Dhighlighter.el=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=2LS5YZIgyAvGS3fmo8rEgaDS2Tbu3UL10uqdUgH-LXc=>
> 
> Towards the bottom of 
> https://github.com/jkitchin/scimax/blob/master/cm-mods.el 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_cm-2Dmods.el=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=hg-nJ1pgNjsD6TM3dFMEX7IADrW9iwU8e3nvulj1lFc=>
>  I was working on some ways to use the criticmarkup  in conjunction with git 
> diffs to automatically make these kinds of diffs.
> 
> I can't say I am fully satisified by any of these solutions (that is why 
> there are so many of them ;)
> 
> John
> 
> ---
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=9l9_vjFtxnWTTnFYN-Uy0mhhk-B5fKQeudqix5QWjqA=>
> 
> 
> On Fri, Mar 10, 2017 at 3:56 PM, Kaushal Modi <kaushal.m...@gmail.com 
> <mailto:kaushal.m...@gmail.com>> wrote:
> I use this macro to highlight text in html/latex(pdf):
> 
> #+MACRO: COLOR @@html:$2latex:\textcolor{$1}{$2}@@
> 
> This is from https://github.com/fniessen/org-macros/blob/master/README.org 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_fniessen_org-2Dmacros_blob_master_README.org=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=XDOhI8-iVimfEcDs18oR3i-Yyuic8xnEQRrHQ7lRlqI=>
> 
> Example use:
> {{{COLOR(red, This information is important.)}}}
> 
> It doesn't though highlight the text in red in org-mode.
> 
> On Fri, Mar 10, 2017 at 3:49 PM Doyley, Marvin M. <m.doy...@rochester.edu 
> <mailto:m.doy...@rochester.edu>> wrote:
> Hi there,
> 
> When revising manuscripts, I usually highlight the changes (response to 
> reviewer) in red. I use typically do this as follows:
> (1) #+latex_header: \newcommand{\response}[1]{\textcolor{red}{#1}}
> (2) \

Re: [O] New markup for revising manuscripts

[Doyley, Marvin M.]

Hi John,

Thanks for the info on making colored links, this will definitely help (i.e., 
show the changes in org). The only snag is how do I export the colored link 
automatically as \textcolor{red}{comments} during org export ?

Cheers,
M
> On Mar 10, 2017, at 4:47 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> You can  wait for it... make a colored link ;): 
> http://kitchingroup.cheme.cmu.edu/blog/2016/11/04/New-link-features-in-org-9/#org1bc1061
>  
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_04_New-2Dlink-2Dfeatures-2Din-2Dorg-2D9_-23org1bc1061=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=4DUIBEXq8WNk6qHHyXFoIwWG4FlD2NlDgz8AfT2VUS0=>
> 
> The example there has an html export defined, but you could as easily define 
> a latex exporter. It has some limitations, like it might not reliably work on 
> multiple lines, and you would not want to "highlight" across elements (or the 
> latex will get ugly and probably not work).
> 
> I have been working on some ways to get persistent highlighting using 
> overlays for a similar purpose: 
> http://kitchingroup.cheme.cmu.edu/blog/2016/11/10/Persistent-highlighting-in-Emacs/
>  
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2016_11_10_Persistent-2Dhighlighting-2Din-2DEmacs_=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=I0JDZ741rHEtzWzAF3lhW65rzNn4vdq4tiUyD10_7l0=>
> 
> so far I only can get reliable output to html. Latex seems possible, again if 
> you don't highlight across too many elements. It is a work in progress here: 
> https://github.com/jkitchin/scimax/blob/master/ov-highlighter.el 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_ov-2Dhighlighter.el=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=2LS5YZIgyAvGS3fmo8rEgaDS2Tbu3UL10uqdUgH-LXc=>
> 
> Towards the bottom of 
> https://github.com/jkitchin/scimax/blob/master/cm-mods.el 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_scimax_blob_master_cm-2Dmods.el=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=hg-nJ1pgNjsD6TM3dFMEX7IADrW9iwU8e3nvulj1lFc=>
>  I was working on some ways to use the criticmarkup  in conjunction with git 
> diffs to automatically make these kinds of diffs.
> 
> I can't say I am fully satisified by any of these solutions (that is why 
> there are so many of them ;)
> 
> John
> 
> ---
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=9l9_vjFtxnWTTnFYN-Uy0mhhk-B5fKQeudqix5QWjqA=>
> 
> 
> On Fri, Mar 10, 2017 at 3:56 PM, Kaushal Modi <kaushal.m...@gmail.com 
> <mailto:kaushal.m...@gmail.com>> wrote:
> I use this macro to highlight text in html/latex(pdf):
> 
> #+MACRO: COLOR @@html:$2latex:\textcolor{$1}{$2}@@
> 
> This is from https://github.com/fniessen/org-macros/blob/master/README.org 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_fniessen_org-2Dmacros_blob_master_README.org=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=9mMx6WEAeP-9u7CL3pjKmlORa7XXy-8WSBSwibTQWuo=XDOhI8-iVimfEcDs18oR3i-Yyuic8xnEQRrHQ7lRlqI=>
> 
> Example use:
> {{{COLOR(red, This information is important.)}}}
> 
> It doesn't though highlight the text in red in org-mode.
> 
> On Fri, Mar 10, 2017 at 3:49 PM Doyley, Marvin M. <m.doy...@rochester.edu 
> <mailto:m.doy...@rochester.edu>> wrote:
> Hi there,
> 
> When revising manuscripts, I usually highlight the changes (response to 
> reviewer) in red. I use typically do this as follows:
> (1) #+latex_header: \newcommand{\response}[1]{\textcolor{red}{#1}}
> (2) \response{changes)
> 
> Is there a more elegant way to do this ?  It would be nice if I could change 
> the color of the select text in both org and the exported latex file to red. 
> Seeing the highlighted text in org would be a huge plus.
> 
> Thanks
> M
> --
> Kaushal Modi
> 
> 



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[O] New markup for revising manuscripts

[Doyley, Marvin M.]

Hi there,

When revising manuscripts, I usually highlight the changes (response to 
reviewer) in red. I use typically do this as follows:
(1) #+latex_header: \newcommand{\response}[1]{\textcolor{red}{#1}}
(2) \response{changes)

Is there a more elegant way to do this ?  It would be nice if I could change 
the color of the select text in both org and the exported latex file to red. 
Seeing the highlighted text in org would be a huge plus.

Thanks
M


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Re: [O] Writing exams

[Doyley, Marvin M.]

Thanks I really appreciate this, I also use the exam style. Concerning the 
orgfile, if you have one for a multi part question that would be great.

Cheers,
M

---
Sent from my iPhone
I apologize in advance for any typos or spellings errors

On Mar 9, 2017, at 3:31 PM, Thomas Hunter 
<thunt...@swarthmore.edu<mailto:thunt...@swarthmore.edu>> wrote:

Funnilly enough, I am grading an exam written in org-mode right now.  I use the 
exam class from the ctan archives and set org-latex-classes to have an entry 
that looks like this:

  ("exam" "\\documentclass[12pt, addpoints, answers]{exam}"
  ("\\begin{questions}%%%s" "\\end{questions}" "\\begin{questions}%%%s" 
"\\end{questions}")
  ("\\begin{question}%%%s" "\\end{question}" "\\begin{question*}%%%s" 
"\\end{question*}")
  ("\\begin{parts}%%%s" "\\end{parts}" "\\begin{parts}%%%s" "\\end{parts}")
  ("\\begin{part}[%s]" "\\end{part}" "\\begin{part*}[%s]" "\\end{part*}")
  ("\\begin{solution}[%s]" "\\end{solution}" "\\begin{solution}[%s]" 
"\\end{solution}"))

After some latex header stuff, the structure looks like this where the first 
question has three parts worth 6, 7 and 7 points.
* Questions
** First question
text of first question
*** Rubric :noexport:
*** parts
 6
text of first part
 7
text of second part
 7
text of third part
** second question

[...]

I can send a copy of the orgfile or the produced pdf to any interested parties. 
 (It seems like maybe attaching files of any size to an email to this list is 
maybe not good etiquette, but I am a first time poster, so what do I know?)

If anyone else does something like this, but knows what they are doing and thus 
does it better, I'd love to hear about it.

Thomas Hunter

On Tue, Mar 7, 2017 at 8:14 PM, Doyley, Marvin M. 
<m.doy...@rochester.edu<mailto:m.doy...@rochester.edu>> wrote:
Thanks for the list.  I will try them out.

Cheers,
M
> On Mar 7, 2017, at 11:01 AM, Samuel Loury 
> <konubi...@gmail.com<mailto:konubi...@gmail.com>> wrote:
>
> Samuel Loury <konubi...@gmail.com<mailto:konubi...@gmail.com>> writes:
>
>> "Doyley, Marvin M." <m.doy...@rochester.edu<mailto:m.doy...@rochester.edu>> 
>> writes:
>>
>>> Does anybody have a good system for writing exam in Org-mode ?
>
>> - 
>> http://kitchingroup.cheme.cmu.edu/blog/2013/10/23/Writing-exams-in-org-mode/<https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu_blog_2013_10_23_Writing-2Dexams-2Din-2Dorg-2Dmode_=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=XC-kKZAdllQqK2ayk6oGRdv-0S88qgR0soAtKX_PHDw=cHamxKfbfvEhRDk7hWqt6VdbHZBm2wu-m7top--IcZY=>
>> - 
>> https://github.com/jkitchin/jmax/tree/master/techela<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_jmax_tree_master_techela=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=XC-kKZAdllQqK2ayk6oGRdv-0S88qgR0soAtKX_PHDw=YugVGW136pi2LfxJMU173yWTu1BXC01mB8Vc_riJB-o=>
>> - 
>> http://www-public.tem-tsp.eu/~berger_o/org-teaching/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www-2Dpublic.tem-2Dtsp.eu_-7Eberger-5Fo_org-2Dteaching_=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=XC-kKZAdllQqK2ayk6oGRdv-0S88qgR0soAtKX_PHDw=eIi5mX8PDPIl7873_WzKc3k1Ei2htH9qXLzUq0w2kUs=>
>> - 
>> https://github.com/gjkerns/samplequiz<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_gjkerns_samplequiz=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=XC-kKZAdllQqK2ayk6oGRdv-0S88qgR0soAtKX_PHDw=Cl-LlfFw-FMm0LRf7y1yvGOu7HVMemotIXJGmGZ-4Kw=>
>
> Forgot 
> https://github.com/mbork/org-edu-html<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_mbork_org-2Dedu-2Dhtml=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=XC-kKZAdllQqK2ayk6oGRdv-0S88qgR0soAtKX_PHDw=cnxh8oi5iDh9dl5x_w5NsvP_ZvlR_x6CR50Q0PnFFNE=>
>
> --
> Konubinix
> GPG Key: 7439106A
> Fingerprint: 5993 BE7A DA65 E2D9 06CE  5C36 75D2 3CED 7439 106A




--
Thomas Hunter
Department of Mathematics and Statistics
Swarthmore  College
Science Center, Rm 157
610-328-8244<tel:(610)%20328-8244>

Re: [O] Writing exams

[Doyley, Marvin M.]

Thanks for the list.  I will try them out.

Cheers,
M
> On Mar 7, 2017, at 11:01 AM, Samuel Loury <konubi...@gmail.com> wrote:
> 
> Samuel Loury <konubi...@gmail.com> writes:
> 
>> "Doyley, Marvin M." <m.doy...@rochester.edu> writes:
>> 
>>> Does anybody have a good system for writing exam in Org-mode ?
> 
>> - 
>> http://kitchingroup.cheme.cmu.edu/blog/2013/10/23/Writing-exams-in-org-mode/
>> - https://github.com/jkitchin/jmax/tree/master/techela
>> - http://www-public.tem-tsp.eu/~berger_o/org-teaching/
>> - https://github.com/gjkerns/samplequiz
> 
> Forgot https://github.com/mbork/org-edu-html
> 
> --
> Konubinix
> GPG Key: 7439106A
> Fingerprint: 5993 BE7A DA65 E2D9 06CE  5C36 75D2 3CED 7439 106A



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[O] Writing exams

[Doyley, Marvin M.]

Does anybody have a good system for writing exam in Org-mode ?

Thanks,
M


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[O] Exams

[Doyley, Marvin M.]

Does anybody have a good system for writing exams with Org mode ?

Thanks,
M


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Re: [O] Elpy in python code blocks

[Doyley, Marvin M.]

Works like a charm, I wasn’t aware of the special edit mode.
I guess I need to reread the manual, its been awhile :)
Cheers,
M
> On Mar 5, 2017, at 10:58 AM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> I am not sure what you mean. (elpy-enable) in an init file does it for me. It 
> is only active in the special edit mode, e.g. C-c ' in the code block.
> 
> John
> 
> ---
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=4JQl4kV3FYROSzCKpbcLS83hOwb13nIGKCmiw4LRFWU=zD78rXD-wUEOt6CcxfVqtoMXdwipACSFvCfX-WTCeSA=>
> 
> 
> On Sun, Mar 5, 2017 at 9:10 AM, Doyley, Marvin M. <m.doy...@rochester.edu 
> <mailto:m.doy...@rochester.edu>> wrote:
> Doesn't anybody know how to enable elpy mode when writing python or ipython 
> code blocks.
> 
> Thanks,
> M
> 
> Sent from my iPad
> 



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Re: [O] Elpy in python code blocks

[Doyley, Marvin M.]

Thanks for the quick response,
I'll try to special edit mode.
Cheers,
M

---
Sent from my iPhone
I apologize in advance for any typos or spellings errors

On Mar 5, 2017, at 10:58 AM, John Kitchin 
<jkitc...@andrew.cmu.edu<mailto:jkitc...@andrew.cmu.edu>> wrote:

I am not sure what you mean. (elpy-enable) in an init file does it for me. It 
is only active in the special edit mode, e.g. C-c ' in the code block.

John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=DwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=s3_3riAscdqtNAzgOuwYB9g0dZVGcp8BNCy_RylYdxU=4JQl4kV3FYROSzCKpbcLS83hOwb13nIGKCmiw4LRFWU=zD78rXD-wUEOt6CcxfVqtoMXdwipACSFvCfX-WTCeSA=>


On Sun, Mar 5, 2017 at 9:10 AM, Doyley, Marvin M. 
<m.doy...@rochester.edu<mailto:m.doy...@rochester.edu>> wrote:
Doesn't anybody know how to enable elpy mode when writing python or ipython 
code blocks.

Thanks,
M

Sent from my iPad

[O] Elpy in python code blocks

[Doyley, Marvin M.]

Doesn't anybody know how to enable elpy mode when writing python or ipython 
code blocks. 

Thanks,
M

Sent from my iPad

Re: [O] Problem with Org-capture mode

[Doyley, Marvin M.]

Thanks,
The problem is now solved
It turns out that the problem was yasnippet.
Cheers,
M
On Jan 4, 2017, at 2:30 PM, Kaushal Modi 
<kaushal.m...@gmail.com<mailto:kaushal.m...@gmail.com>> wrote:

You seem to have mixed installations.

org-set-local has been deprecated for a while now.

What are your org and emacs versions?

On Wed, Jan 4, 2017 at 2:23 PM Doyley, Marvin M. 
<m.doy...@rochester.edu<mailto:m.doy...@rochester.edu>> wrote:
Hi there,

Org capture template is not working.

I get the following message when I try to use it. Does anybody know how to fix 
this ?

Thanks
M


For information about GNU Emacs and the GNU system, type C-h C-a.
Problems while trying to load feature ‘org-mac-message’
File mode specification error: (void-function org-set-local)
Capture abort: (void-function org-set-local)







--

Kaushal Modi

Re: [O] Problem with Org-capture mode

[Doyley, Marvin M.]

Here is the backtrace
Debugger entered--Lisp error: (void-function org-set-local)
  (org-set-local (quote yas/trigger-key) [tab])
  (lambda nil (org-set-local (quote yas/trigger-key) [tab]) (define-key 
yas/keymap [tab] (quote yas/next-field-or-maybe-expand)))()
  run-hooks(change-major-mode-after-body-hook text-mode-hook outline-mode-hook 
org-mode-hook)
  apply(run-hooks (change-major-mode-after-body-hook text-mode-hook 
outline-mode-hook org-mode-hook))
  run-mode-hooks(org-mode-hook)
  org-mode()
  set-auto-mode-0(org-mode nil)
  set-auto-mode()
  normal-mode(t)
  after-find-file(nil t)
  find-file-noselect-1(# 
"~/Org-files/General/Master-todo.org" nil nil 
"~/Dropbox/Filing_Cabinet/O/Org-files/General/Master-todo.org" (31210154 
16777218))
  find-file-noselect("/Users/doyley/Org-files/General/Master-todo.org")
  org-capture-target-buffer("~/Org-files/General/Master-todo.org")
  org-capture-set-target-location()
  org-capture(nil "t")
  (lambda (template-shortcut) (org-capture nil template-shortcut))("t")
  helm-execute-selection-action-1()
  helm-execute-selection-action()
  #[0 "\311\211\211\211\305\206\n

[O] Problem with Org-capture mode

[Doyley, Marvin M.]

Hi there,

Org capture template is not working.

I get the following message when I try to use it. Does anybody know how to fix 
this ?

Thanks
M


For information about GNU Emacs and the GNU system, type C-h C-a.
Problems while trying to load feature ‘org-mac-message’
File mode specification error: (void-function org-set-local)
Capture abort: (void-function org-set-local)









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Re: [O] latex newcommand in org

[Doyley, Marvin M.]

Eric’s suggestion works like a charm with the following modification
#+latex_header:\newenvironment{response}{\color{red}}{\ignorespacesafterend}

Thanks I really appreciate the help.

Cheers,
M

On May 20, 2016, at 5:00 PM, Leslie Watter 
<les...@watter.net<mailto:les...@watter.net>> wrote:

You can use also macros in combination with latex \newcommand:

Following there's a sample with html:

#+MACRO: color @@html:$2@@
# macro sample: {{{color(red, aceitação)}}}


Note: untested with latex newcommand1


Cheers,

LEslie



On Fri, May 20, 2016 at 4:50 PM, Marcin Borkowski 
<mb...@mbork.pl<mailto:mb...@mbork.pl>> wrote:

On 2016-05-20, at 20:45, Eric S Fraga 
<e.fr...@ucl.ac.uk<mailto:e.fr...@ucl.ac.uk>> wrote:

> On Friday, 20 May 2016 at 18:10, Doyley, Marvin M. wrote:
>> Hi there,
>>
>> In my group, we typically response to reviewers comments (in latex) by first 
>> defining the  following command in the header
>>
>> \newcommand{\response}[1]{\textcolor{red}{#1}}
>> then marking up the text as follows
>>
>> \response{red text}
>>
>> I try to do the same in org,  i.e., putting
>>  #+latex_header:\newcommand{\response}[1]{\textcolor{red}{#1}}
>> then \response{BLAH BLAH} in the text. The only snag is that on export I get 
>> \response\{BLAH BLAH\}
>
> Easiest solution is @@latex:\response{blah blah}@@ but that will lose you
> all the org formatting.  Longer solution is to use environments, such as
>
> #+begin_response
> blah blah blah
> #+end_response
>
> and define a "response" LaTeX environment, along these lines:
>
> #+latex_header: 
> \makeatletter\newenvironment{response}{\textcolor{red}}{}\makeatother
>
> (untested)

Notice also that commands and environments in LaTeX are not
interchangeable; there are things only commands can do and things only
environments can do.  (Well, not really - technically, I guess,
environments are strictly more powerful than commands, though I'm not
100% sure - but some things are quite difficult to do with environments
and trivial with commands.)

See also
http://tex.stackexchange.com/questions/102141/what-are-the-consideration-when-choosing-either-newcommand-or-newenvironment<https://urldefense.proofpoint.com/v2/url?u=http-3A__tex.stackexchange.com_questions_102141_what-2Dare-2Dthe-2Dconsideration-2Dwhen-2Dchoosing-2Deither-2Dnewcommand-2Dor-2Dnewenvironment=CwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=VX_uCv1LGJK_oX4her-tCTorTtXocoyqvQv-bAOtWGI=E18ceWIZlt89thSTn5MiwO2G6Qdu3XH9Mjo0TR1B37o=>

Best,

--
Marcin Borkowski
http://octd.wmi.amu.edu.pl/en/Marcin_Borkowski<https://urldefense.proofpoint.com/v2/url?u=http-3A__octd.wmi.amu.edu.pl_en_Marcin-5FBorkowski=CwMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=VX_uCv1LGJK_oX4her-tCTorTtXocoyqvQv-bAOtWGI=3aRJKRHeKpjvY0YOvttPHrgWOpGqNNgIEP3SH_ZKcUU=>
Faculty of Mathematics and Computer Science
Adam Mickiewicz University




--
Leslie H. Watter

Re: [O] latex newcommand in org

[Doyley, Marvin M.]

Thanks,

I will give Eric’s suggestion a go.

Cheers,
M


On May 20, 2016, at 3:50 PM, Marcin Borkowski 
<mb...@mbork.pl<mailto:mb...@mbork.pl>> wrote:


On 2016-05-20, at 20:45, Eric S Fraga 
<e.fr...@ucl.ac.uk<mailto:e.fr...@ucl.ac.uk>> wrote:

On Friday, 20 May 2016 at 18:10, Doyley, Marvin M. wrote:
Hi there,

In my group, we typically response to reviewers comments (in latex) by first 
defining the  following command in the header

\newcommand{\response}[1]{\textcolor{red}{#1}}
then marking up the text as follows

\response{red text}

I try to do the same in org,  i.e., putting
#+latex_header:\newcommand{\response}[1]{\textcolor{red}{#1}}
then \response{BLAH BLAH} in the text. The only snag is that on export I get 
\response\{BLAH BLAH\}

Easiest solution is @@latex:\response{blah blah}@@ but that will lose you
all the org formatting.  Longer solution is to use environments, such as

#+begin_response
blah blah blah
#+end_response

and define a "response" LaTeX environment, along these lines:

#+latex_header: 
\makeatletter\newenvironment{response}{\textcolor{red}}{}\makeatother

(untested)

Notice also that commands and environments in LaTeX are not
interchangeable; there are things only commands can do and things only
environments can do.  (Well, not really - technically, I guess,
environments are strictly more powerful than commands, though I'm not
100% sure - but some things are quite difficult to do with environments
and trivial with commands.)

See also
https://urldefense.proofpoint.com/v2/url?u=http-3A__tex.stackexchange.com_questions_102141_what-2Dare-2Dthe-2Dconsideration-2Dwhen-2Dchoosing-2Deither-2Dnewcommand-2Dor-2Dnewenvironment=CwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=BXygbrudx0ZbLjXB7_QSNrR5Nwf_kj7fU2GbMseZG9Q=u6a29DcYPvJ-0G5l--k-db1OPj9GPF2DO89fbOOfje0=

Best,

--
Marcin Borkowski
https://urldefense.proofpoint.com/v2/url?u=http-3A__octd.wmi.amu.edu.pl_en_Marcin-5FBorkowski=CwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=BXygbrudx0ZbLjXB7_QSNrR5Nwf_kj7fU2GbMseZG9Q=msRYXf0n_C3V5ncax1tSsNPVzKQ8OOotiw7ibezCLxU=
Faculty of Mathematics and Computer Science
Adam Mickiewicz University

[O] latex newcommand in org

[Doyley, Marvin M.]

Hi there,

In my group, we typically response to reviewers comments (in latex) by first 
defining the  following command in the header

\newcommand{\response}[1]{\textcolor{red}{#1}}
then marking up the text as follows

\response{red text}

I try to do the same in org,  i.e., putting
 #+latex_header:\newcommand{\response}[1]{\textcolor{red}{#1}}
then \response{BLAH BLAH} in the text. The only snag is that on export I get 
\response\{BLAH BLAH\}

Any suggestion how to fix this

cheers,
M

Re: [O] org-ref

[Doyley, Marvin M.]

\ref{fig2,fig3} not legal unless you use crever-ref package
On Feb 16, 2016, at 10:48 AM, John Kitchin 
<jkitc...@andrew.cmu.edu<mailto:jkitc...@andrew.cmu.edu>> wrote:

Is \ref{fig2,fig3} legal LaTeX?

John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=BQMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=P4RAQ290xDFvKbWNvyGYOccZLnfZ5U3p_Pb8XtIN_Mc=Bt19oExXxO-LVeTcZiV0U8cwnTeGmv5Tbyy3GyICw8Q=>


On Tue, Feb 16, 2016 at 8:52 AM, Doyley, Marvin M. 
<mdoy...@ur.rochester.edu<mailto:mdoy...@ur.rochester.edu>> wrote:
John,

I have a quick question. Can I use org-ref to reference multiple figures 
similar to what can be done for citations.

For example, lets say I have three figure labels  fig1, fig2, and fig3.  I 
would like to reference fig2 and fig3 in my main text as follow ref: fig2,fig3. 
 This doesn’t seem to be possible, is there a work around ?

cheers,
M

Re: [O] org-ref

[Doyley, Marvin M.]

Thanks
On Feb 16, 2016, at 10:48 AM, John Kitchin 
<jkitc...@andrew.cmu.edu<mailto:jkitc...@andrew.cmu.edu>> wrote:

Is \ref{fig2,fig3} legal LaTeX?

John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=BQMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=P4RAQ290xDFvKbWNvyGYOccZLnfZ5U3p_Pb8XtIN_Mc=Bt19oExXxO-LVeTcZiV0U8cwnTeGmv5Tbyy3GyICw8Q=>


On Tue, Feb 16, 2016 at 8:52 AM, Doyley, Marvin M. 
<mdoy...@ur.rochester.edu<mailto:mdoy...@ur.rochester.edu>> wrote:
John,

I have a quick question. Can I use org-ref to reference multiple figures 
similar to what can be done for citations.

For example, lets say I have three figure labels  fig1, fig2, and fig3.  I 
would like to reference fig2 and fig3 in my main text as follow ref: fig2,fig3. 
 This doesn’t seem to be possible, is there a work around ?

cheers,
M

[O] CDlatex

[Doyley, Marvin M.]

Hi there,
I just upgrade my org-mode, and it seems that the function turn-on-org-cdlatex 
is no longer available, or maybe I am messing something.
M
---

[O] Fwd: Converting paragraph to plain lis

[Doyley, Marvin M.]

Hi John,
I really appreciate this.
Cheers,
M
---





Begin forwarded message:

From: John Kitchin <jkitc...@andrew.cmu.edu<mailto:jkitc...@andrew.cmu.edu>>
Date: December 16, 2015 at 6:38:51 AM EST
To: marvin doyley <marvin...@gmail.com<mailto:marvin...@gmail.com>>
Cc: emacs-orgmode@gnu.org<mailto:emacs-orgmode@gnu.org>
Subject: Re: [O] Converting paragraph to plain lis

Here is a solution that works on your paragraph.

#+BEGIN_SRC emacs-lisp
(defun explode-paragraph ()
 (interactive)
 (let (start end)
   ;; narrow to paragraph
   (backward-paragraph) (forward-line)
   (setq start (point))
   (forward-paragraph) (previous-line)
   (setq end (point))

   ;; now move by sentence, insert number and \n. at the end go to beginning
   ;; insert a number and use C-cC-c to renumber the list.
   (save-restriction
 (narrow-to-region start end)
 (goto-char (point-min))
 (while (< (point) (point-max))
   (forward-sentence)
   (insert "\n1. "))
 (goto-char (point-min))
 (insert "1. ")
 (org-ctrl-c-ctrl-c

(defun unfill-paragraph ()
 "Unfill paragraph at or after point."
 (interactive "*")
 (let ((fill-column most-positive-fixnum))
   (fill-paragraph nil (region-active-p

(defun list-to-paragraph ()
 "Convert list at point to a paragraph."
 (interactive)
 ;; make sure we are at the beginning of the list
 (beginning-of-line)
 (let ((element (org-element-context))
   contents)
   (when (eq 'item (car element))
 (setq element (org-element-property :parent (org-element-context)))
 (goto-char
  (org-element-property
   :begin
   element)))
   ;; collect each sentence, minus the numbers.
   (setq contents (loop for node in
(org-element-property :structure element)
collect
;; remove number and space
(replace-regexp-in-string
 (regexp-quote (nth 2 node)) ""
 (buffer-substring (nth 0 node)
   (nth 6 node)
   ;; replace the list, and then unfill the paragraph.
   (setf (buffer-substring (org-element-property :begin element)
   (- (org-element-property :end element) 1))
 (mapconcat 'identity contents ""))
   (goto-char (org-element-property :begin element))
   (unfill-paragraph)))
#+END_SRC

marvin doyley writes:

Hi there,

Does anybody know how to convert a paragraph to a plain list, and vice versa. 
For example, I would like to convert

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Suspendisse viverra 
consectetur euismod. Donec non tempor turpis.

to

1. Lorem ipsum dolor sit amet, consectetur adipiscing elit.
2.  Suspendisse viverra consectetur euismod.
3.  Donec non tempor turpis.

In one key stroke, this would speed up my brain storming process.

Thanks,
M

--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

Re: [O] Minning Org-files

[Doyley, Marvin M.]

Awesome,

I really appreciate this. I must teach myself how to code in lisp :)
cheers,
M
> On Oct 10, 2015, at 8:06 AM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> sure, if you make an interactive function that takes a search argument.
> Something like this
> 
> (defun some-name (search-arg)
> (interactive "sQuery: ")
> ; insert code below and change "TODO=\"DONE\"" to search-arg
> )
> 
> 
> Doyley, Marvin M. writes:
> 
>> Is there anyway of making the search term a variable ?
>> 
>>> On Oct 9, 2015, at 1:24 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
>>> 
>>> You can do something like this:
>>> 
>>> By TODO keyword to grab the DONE entries.
>>> 
>>> #+BEGIN_SRC emacs-lisp
>>> (let ((entries (org-map-entries
>>>   (lambda ()
>>> (save-restriction
>>>   (org-narrow-to-subtree)
>>>       (buffer-string)))
>>>   "TODO=\"DONE\"")))
>>> (switch-to-buffer (get-buffer-create "new"))
>>> (org-mode)
>>> (mapcar 'insert entries))
>>> #+END_SRC
>>> 
>>> 
>>> 
>>> Doyley, Marvin M. writes:
>>> 
>>>> Hi there,
>>>> 
>>>> I have a huge org-file with notes I have taken on various topics (my 
>>>> commonplace org file). Is there an easy way to grab all the entires with a 
>>>> given tag or keyword to a new org-file ?
>>>> 
>>>> Thanks,
>>>> M
>>>> 
>>>> ---
>>>> Marvin Doyley Ph.D.
>>>> University of Rochester
>>>> Associate Professor of Electrical and Computer Engineering
>>>> Associate Professor of Biomedical Engineering
>>>> 333 Hopeman Engineering Building
>>>> Rochester NY 14627
>>> 
>>> --
>>> Professor John Kitchin
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-7803
>>> @johnkitchin
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=BQIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=ZjP3xZzVOvLNMInBTkxBhV_-2rP9uP3owADCIadxXxk=ry0y4fD4NMUUCHUpPSK5djnyUZWt57fxbXHuhqUfSls=
> 
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=BQIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=hnMwDGuA_hdr-MPhQEOOEcDQ7Wd1eLgQFHotHKPOM2Y=KAVoqsDi0jWRU6Ilqh5eq16troIjU6lPlk-AQ99ZTv8=
>  

Re: [O] Minning Org-files

[Doyley, Marvin M.]

Hi John,

It works like a charm. 

Thank you so so so much
cheers,
M
> On Oct 10, 2015, at 8:06 AM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> sure, if you make an interactive function that takes a search argument.
> Something like this
> 
> (defun some-name (search-arg)
> (interactive "sQuery: ")
> ; insert code below and change "TODO=\"DONE\"" to search-arg
> )
> 
> 
> Doyley, Marvin M. writes:
> 
>> Is there anyway of making the search term a variable ?
>> 
>>> On Oct 9, 2015, at 1:24 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
>>> 
>>> You can do something like this:
>>> 
>>> By TODO keyword to grab the DONE entries.
>>> 
>>> #+BEGIN_SRC emacs-lisp
>>> (let ((entries (org-map-entries
>>>   (lambda ()
>>> (save-restriction
>>>   (org-narrow-to-subtree)
>>>       (buffer-string)))
>>>   "TODO=\"DONE\"")))
>>> (switch-to-buffer (get-buffer-create "new"))
>>> (org-mode)
>>> (mapcar 'insert entries))
>>> #+END_SRC
>>> 
>>> 
>>> 
>>> Doyley, Marvin M. writes:
>>> 
>>>> Hi there,
>>>> 
>>>> I have a huge org-file with notes I have taken on various topics (my 
>>>> commonplace org file). Is there an easy way to grab all the entires with a 
>>>> given tag or keyword to a new org-file ?
>>>> 
>>>> Thanks,
>>>> M
>>>> 
>>>> ---
>>>> Marvin Doyley Ph.D.
>>>> University of Rochester
>>>> Associate Professor of Electrical and Computer Engineering
>>>> Associate Professor of Biomedical Engineering
>>>> 333 Hopeman Engineering Building
>>>> Rochester NY 14627
>>> 
>>> --
>>> Professor John Kitchin
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-7803
>>> @johnkitchin
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=BQIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=ZjP3xZzVOvLNMInBTkxBhV_-2rP9uP3owADCIadxXxk=ry0y4fD4NMUUCHUpPSK5djnyUZWt57fxbXHuhqUfSls=
> 
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=BQIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=hnMwDGuA_hdr-MPhQEOOEcDQ7Wd1eLgQFHotHKPOM2Y=KAVoqsDi0jWRU6Ilqh5eq16troIjU6lPlk-AQ99ZTv8=
>  

Re: [O] Minning Org-files

[Doyley, Marvin M.]

Is there anyway of making the search term a variable ?

> On Oct 9, 2015, at 1:24 PM, John Kitchin <jkitc...@andrew.cmu.edu> wrote:
> 
> You can do something like this:
> 
> By TODO keyword to grab the DONE entries.
> 
> #+BEGIN_SRC emacs-lisp
> (let ((entries (org-map-entries
>(lambda ()
>  (save-restriction
>(org-narrow-to-subtree)
>(buffer-string)))
>"TODO=\"DONE\"")))
>  (switch-to-buffer (get-buffer-create "new"))
>  (org-mode)
>  (mapcar 'insert entries))
> #+END_SRC
> 
> 
> 
> Doyley, Marvin M. writes:
> 
>> Hi there,
>> 
>> I have a huge org-file with notes I have taken on various topics (my 
>> commonplace org file). Is there an easy way to grab all the entires with a 
>> given tag or keyword to a new org-file ?
>> 
>> Thanks,
>> M
>> 
>> ---
>> Marvin Doyley Ph.D.
>> University of Rochester
>> Associate Professor of Electrical and Computer Engineering
>> Associate Professor of Biomedical Engineering
>> 333 Hopeman Engineering Building
>> Rochester NY 14627
> 
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=BQIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=ZjP3xZzVOvLNMInBTkxBhV_-2rP9uP3owADCIadxXxk=ry0y4fD4NMUUCHUpPSK5djnyUZWt57fxbXHuhqUfSls=
>  

[O] Readcube

[Doyley, Marvin M.]

Hi there,

I have been using readcube to manage my pdfs, awesome software, for more than a 
year now. However, i would like to link it to my org-mode notes. Does anybody 
know how to grab readcube links on OS X.

Thanks,
M

---
Marvin Doyley Ph.D.
University of Rochester
Associate Professor of Electrical and Computer Engineering
Associate Professor of Biomedical Engineering
333 Hopeman Engineering Building
Rochester NY 14627

[O] Minning Org-files

[Doyley, Marvin M.]

Hi there,

I have a huge org-file with notes I have taken on various topics (my 
commonplace org file). Is there an easy way to grab all the entires with a 
given tag or keyword to a new org-file ?

Thanks,
M

---
Marvin Doyley Ph.D.
University of Rochester
Associate Professor of Electrical and Computer Engineering
Associate Professor of Biomedical Engineering
333 Hopeman Engineering Building
Rochester NY 14627

Re: [O] Readcube

[Doyley, Marvin M.]

Thanks John,
I really appreciate this.
Cheers,
M
---
Marvin Doyley Ph.D.
University of Rochester
Associate Professor of Electrical and Computer Engineering
343 Hopeman Engineering Building
Rochester NY 14627
Tel: 585-275-3774
Fax: 585-273-4919
Website: http://www.ece.rochester.edu/projects/doyley_lab/






On Oct 9, 2015, at 1:44 PM, John Kitchin 
<jkitc...@andrew.cmu.edu<mailto:jkitc...@andrew.cmu.edu>> wrote:

you would have to find an applescript api I think. Look at some examples in 
org-mac-link 
http://orgmode.org/worg/org-contrib/org-mac-link.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__orgmode.org_worg_org-2Dcontrib_org-2Dmac-2Dlink.html=BQMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=Bmxs608u3u9gou8iu8lQaHI6Frs3G0whL1fqtuWMobg=VBvnAhz53Cj-UkC19yly-1RJQCNoN5LUCQo8cKV8fQw=>
 or this project 
https://github.com/claviclaws/org-mac-protocol<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_claviclaws_org-2Dmac-2Dprotocol=BQMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=Bmxs608u3u9gou8iu8lQaHI6Frs3G0whL1fqtuWMobg=5S76FN9TQay7WhJYSFsrs9bzf6tN2G1i3sowB1Swgd8=>.

John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edu=BQMFaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=Bmxs608u3u9gou8iu8lQaHI6Frs3G0whL1fqtuWMobg=ZxToMNe5xuAc8Syy36ecJk5GpWhp8TT02uSSsS6euCw=>


On Fri, Oct 9, 2015 at 8:29 AM, Doyley, Marvin M. 
<mdoy...@ur.rochester.edu<mailto:mdoy...@ur.rochester.edu>> wrote:
Hi there,

I have been using readcube to manage my pdfs, awesome software, for more than a 
year now. However, i would like to link it to my org-mode notes. Does anybody 
know how to grab readcube links on OS X.

Thanks,
M

---
Marvin Doyley Ph.D.
University of Rochester
Associate Professor of Electrical and Computer Engineering
Associate Professor of Biomedical Engineering
333 Hopeman Engineering Building
Rochester NY 14627

Re: [O] org-link type

[Doyley, Marvin M.]

Thanks John,

I will try it out.
Cheers,
M
---

On May 13, 2015, at 11:39 AM, John Kitchin 
jkitc...@andrew.cmu.edumailto:jkitc...@andrew.cmu.edu wrote:

There is no built in way I know of. I have done this in org-ref though, and you 
can see how here: 
https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L311https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jkitchin_org-2Dref_blob_master_org-2Dref.el-23L311d=AwMFaQc=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOUr=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMUm=ABInZ3aazeW0zibrWLWQE1DBDpTbd1DkoRqwShNReyos=HZZQj4R15FveFP9wbXx9DQQgJK5ROMW_NFkZ6NcrbRce=



John

---
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.eduhttps://urldefense.proofpoint.com/v2/url?u=http-3A__kitchingroup.cheme.cmu.edud=AwMFaQc=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOUr=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMUm=ABInZ3aazeW0zibrWLWQE1DBDpTbd1DkoRqwShNReyos=L1Ygq2EOiXSQ_97_KYgP84pmZZpkCcLOtE6I4Wz81KUe=


On Wed, May 13, 2015 at 11:36 AM, Doyley, Marvin M. 
mdoy...@ur.rochester.edumailto:mdoy...@ur.rochester.edu wrote:
Dear all,

I would like to change the face (i.e., color and appearance) of a custom org 
link type and was wonder if there is a easy way to do this.

Thanks
M

[O] org-link type

[Doyley, Marvin M.]

Dear all,

I would like to change the face (i.e., color and appearance) of a custom org 
link type and was wonder if there is a easy way to do this.

Thanks
M

Re: [O] strange behavior with org-babel python

[Doyley, Marvin M.]

Thanks, this works when I use :session,
but I don’t get any results when I am not running a session. 
Doy you know why this is the case?

Cheers,
M
On May 11, 2015, at 11:20 PM, Puneeth Chaganti puncha...@gmail.com wrote:

 On Tue, May 12, 2015 at 6:37 AM, Doyley, Marvin M.
 mdoy...@ur.rochester.edu wrote:
 Hi there,
 
 If run the follow codes I get the following, could someone explain to me 
 what is going wrong
 [snip]
 PS in .emacs, I have (setq org-babel-python-command ipython --no-banner 
 --classic --no-confirm-exit)
 
 To reliably paste code blocks into IPython, you will have to use
 %cpaste magic command.  See any of these links[1][2][3] for code you
 can reuse.
 
 [1] - 
 https://github.com/punchagan/dot-emacs/blob/master/punchagan.org#python-customizations
 [2] - https://lists.gnu.org/archive/html/emacs-orgmode/2014-03/msg00405.html
 [3] - 
 http://emacs.stackexchange.com/questions/3859/working-setup-for-ipython-in-babel
 
 Hope that helps,
 Puneeth

[O] strange behavior with org-babel python

[Doyley, Marvin M.]

Hi there,

If run the follow codes I get the following, could someone explain to me what 
is going wrong

(1) The desired results
#+BEGIN_SRC python :results output :exports both :session
x=5
def foo(x):
if x0:
return x+1
else:
return x-1

print(foo(x))
#+END_SRC

#+RESULTS:
: 6

(2) No results
#+BEGIN_SRC python :results output raw :exports both 

x=5
if x0:
x= x+1
else:
x= x-1
print(x)
#+END_SRC

#+RESULTS:


(3) Not sure, why I get this error
#+BEGIN_SRC python :results output raw :exports both :session

x=5
if x0:
x= x+1
else:
x= x-1
print(x)
#+END_SRC

#+RESULTS:

... ...   File ipython-input-5-f6e13edbe7ef, line 3
else:
 ^
IndentationError: unindent does not match any outer indentation level

If you want to paste code into IPython, try the %paste and %cpaste magic 
functions.

Thanks,
M

PS in .emacs, I have (setq org-babel-python-command ipython --no-banner 
--classic --no-confirm-exit)

Re: [O] Trouble using julia with org-babel

[Doyley, Marvin M.]

Hi Ista,

It is now working for Winston, but I am having problems with PyPlot is the case 
for you ?

thanks
M

PS this is the error that I get when trying to load PyPlot

ERROR: could not load module python: dlopen(python.dylib, 9): image not found
 in pyinitialize at /Users/doyley/.julia/v0.3/PyCall/src/PyCall.jl:456
 in pyimport at /Users/doyley/.julia/v0.3/PyCall/src/PyCall.jl:105
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in reload_path at loading.jl:152
 in _require at loading.jl:67
 in require at loading.jl:51
 in _start at ./client.jl:394
 in _start at /julia/usr/lib/julia/sys.dylib
while loading /Users/doyley/.julia/v0.3/PyPlot/src/PyPlot.jl, in expression 
starting on line 32





On Oct 29, 2014, at 10:53 PM, Ista Zahn istaz...@gmail.com wrote:

 On Wed, Oct 29, 2014 at 10:09 PM, Doyley, Marvin M.
 mdoy...@ur.rochester.edu wrote:
 I am using release-0.3.0 what version are you using. I am also using 
 ob-julia.el
 
 I'm using julia version 0.3.1 with GNU Emacs 24.4.1 and Org-mode
 version 8.2.10. I'm using the ob-julia.el distributed with
 org-plus-contrib.
 
 Best,
 Ista
 
 Cheers,
 M
 
 Sent from my iPad
 
 On Oct 29, 2014, at 9:43 PM, Ista Zahn istaz...@gmail.com wrote:
 
 On Wed, Oct 29, 2014 at 12:35 PM, Doyley, Marvin M.
 mdoy...@ur.rochester.edu wrote:
 
 Hi there,
 
 I have been play  with julia the last couple of weeks and have been having
 some issues when I try to use it in org-babel
 
 More specifically, It get the following error
 
 ERROR: unsupported or misplaced expression using
 in _start at ./client.jl:394
 in _start at /julia/usr/lib/julia/sys.dylib
 
 
 When I execute the following code block
 
 #+begin_src julia
 using Winston
 #+end_src
 
 I get the same thing, though both of these variations work for me:
 
 #+begin_src julia
 using Winston
 1 + 1
 #+end_src
 
 #+RESULTS:
 : 2
 
 #+begin_src julia :results output
 using Winston
 #+end_src
 
 Hope this helps,
 Ista
 
 #+RESULTS:
 
 I should mention, that everything works perfectly in eshell or when I
 execute simple code blocks like
 
 
 #+begin_src julia
 linspace(0,10,5)
 #+end_src
 
 #+RESULTS:
 |   0 |
 | 2.5 |
 |   5 |
 | 7.5 |
 |  10 |
 
 
 Does Any body know how to resolve this issue.
 
 Cheers,
 M

[O] Trouble using julia with org-babel

[Doyley, Marvin M.]

Hi there,

I have been play  with julia the last couple of weeks and have been having some 
issues when I try to use it in org-babel

More specifically, It get the following error

ERROR: unsupported or misplaced expression using
 in _start at ./client.jl:394
 in _start at /julia/usr/lib/julia/sys.dylib


When I execute the following code block

#+begin_src julia
using Winston
#+end_src

#+RESULTS:

I should mention, that everything works perfectly in eshell or when I execute 
simple code blocks like


#+begin_src julia
linspace(0,10,5)
#+end_src

#+RESULTS:
|   0 |
| 2.5 |
|   5 |
| 7.5 |
|  10 |


Does Any body know how to resolve this issue.

Cheers,
M

Re: [O] Trouble using julia with org-babel

[Doyley, Marvin M.]

I am using release-0.3.0 what version are you using. I am also using ob-julia.el
Cheers,
M

Sent from my iPad

 On Oct 29, 2014, at 9:43 PM, Ista Zahn istaz...@gmail.com wrote:
 
 On Wed, Oct 29, 2014 at 12:35 PM, Doyley, Marvin M.
 mdoy...@ur.rochester.edu wrote:
 
 Hi there,
 
 I have been play  with julia the last couple of weeks and have been having
 some issues when I try to use it in org-babel
 
 More specifically, It get the following error
 
 ERROR: unsupported or misplaced expression using
 in _start at ./client.jl:394
 in _start at /julia/usr/lib/julia/sys.dylib
 
 
 When I execute the following code block
 
 #+begin_src julia
 using Winston
 #+end_src
 
 I get the same thing, though both of these variations work for me:
 
 #+begin_src julia
 using Winston
 1 + 1
 #+end_src
 
 #+RESULTS:
 : 2
 
 #+begin_src julia :results output
  using Winston
 #+end_src
 
 Hope this helps,
 Ista
 
 #+RESULTS:
 
 I should mention, that everything works perfectly in eshell or when I
 execute simple code blocks like
 
 
 #+begin_src julia
 linspace(0,10,5)
 #+end_src
 
 #+RESULTS:
 |   0 |
 | 2.5 |
 |   5 |
 | 7.5 |
 |  10 |
 
 
 Does Any body know how to resolve this issue.
 
 Cheers,
 M

[O] inline image size

[Doyley, Marvin M.]

Hi there,

Does anybody know how to change the size of inline images in org ?

I would like to do this using something like #+attr :with 200

thanks
M

Re: [O] inline image size

[Doyley, Marvin M.]

Hi there,

I found the solution 
http://lists.gnu.org/archive/html/emacs-orgmode/2014-10/msg00038.html

cheers,
M
On Oct 28, 2014, at 9:16 PM, Doyley, Marvin M. mdoy...@ur.rochester.edu wrote:

 Hi there,
 
 Does anybody know how to change the size of inline images in org ?
 
 I would like to do this using something like #+attr :with 200
 
 thanks
 M

Re: [O] real-time image rendering

[Doyley, Marvin M.]

I agree controlling the refresh rate make your approach better.
Thanks,
M
 Why better?  For which reason?

 Why not this:

 --8---cut here---start-8---
 (add-hook 'org-babel-after-execute-hook
 (lambda ()
 (org-display-inline-images nil t)))
 ; more efficient with refresh == t
--8---cut here---end---8---

?

Best regards,
  Seb

-- 
Sebastien Vauban

[O] real-time image rendering

[Doyley, Marvin M.]

Dear All,

I am currently using Org mode as a teaching tool for a course that I am 
teaching this semester. I would like to run some python simulations in class 
and save the results to a file. I would like to show the results in real time 
as I change various parameters.  I am using iimage-mode to display images. The 
only snag is that I have to toggle iimage-mode on and off to see the changes. 
Is there away to get iimage-mode to render in real time

thanks
M

Sent from my iPad

Re: [O] real-time image rendering

[Doyley, Marvin M.]

Thanks
Cheers,
M

Sent from my iPad

 On Oct 3, 2014, at 7:29 PM, Grant Rettke g...@wisdomandwonder.com wrote:
 
 Sorry for not discussing further:
 
 https://urldefense.proofpoint.com/v1/url?u=https://stackoverflow.com/questions/17621495/emacs-org-display-inline-imagesk=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=Z1cxylKq%2BcxQlQYWByza7usVlHiUrctSCJZH%2BrYsd2c%3D%0As=be48c9d91e056d8bd6c1d1087998c148178cd7448476c9cc4260be57508f602b
 
 On Fri, Oct 3, 2014 at 5:12 PM, Doyley, Marvin M.
 mdoy...@ur.rochester.edu wrote:
 Dear All,
 
 I am currently using Org mode as a teaching tool for a course that I am 
 teaching this semester. I would like to run some python simulations in class 
 and save the results to a file. I would like to show the results in real 
 time as I change various parameters.  I am using iimage-mode to display 
 images. The only snag is that I have to toggle iimage-mode on and off to see 
 the changes. Is there away to get iimage-mode to render in real time
 
 thanks
 M
 
 Sent from my iPad
 
 
 
 -- 
 Grant Rettke
 g...@wisdomandwonder.com | 
 https://urldefense.proofpoint.com/v1/url?u=http://www.wisdomandwonder.com/k=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=Z1cxylKq%2BcxQlQYWByza7usVlHiUrctSCJZH%2BrYsd2c%3D%0As=2ffec8f094fdc2745d8be47418e74b09f151f07ccb55412fafda2a0d19534ac5
 “Wisdom begins in wonder.” --Socrates
 ((λ (x) (x x)) (λ (x) (x x)))
 “Life has become immeasurably better since I have been forced to stop
 taking it seriously.” --Thompson

Re: [O] real-time image rendering

[Doyley, Marvin M.]

This works better
 (add-hook 'org-babel-after-execute-hook
  'org-display-inline-images)

https://www.mail-archive.com/emacs-orgmode@gnu.org/msg88358.html
thanks
m
On Oct 3, 2014, at 7:29 PM, Grant Rettke g...@wisdomandwonder.com wrote:

 Sorry for not discussing further:
 
 https://urldefense.proofpoint.com/v1/url?u=https://stackoverflow.com/questions/17621495/emacs-org-display-inline-imagesk=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=Z1cxylKq%2BcxQlQYWByza7usVlHiUrctSCJZH%2BrYsd2c%3D%0As=be48c9d91e056d8bd6c1d1087998c148178cd7448476c9cc4260be57508f602b
 
 On Fri, Oct 3, 2014 at 5:12 PM, Doyley, Marvin M.
 mdoy...@ur.rochester.edu wrote:
 Dear All,
 
 I am currently using Org mode as a teaching tool for a course that I am 
 teaching this semester. I would like to run some python simulations in class 
 and save the results to a file. I would like to show the results in real 
 time as I change various parameters.  I am using iimage-mode to display 
 images. The only snag is that I have to toggle iimage-mode on and off to see 
 the changes. Is there away to get iimage-mode to render in real time
 
 thanks
 M
 
 Sent from my iPad
 
 
 
 -- 
 Grant Rettke
 g...@wisdomandwonder.com | 
 https://urldefense.proofpoint.com/v1/url?u=http://www.wisdomandwonder.com/k=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=Z1cxylKq%2BcxQlQYWByza7usVlHiUrctSCJZH%2BrYsd2c%3D%0As=2ffec8f094fdc2745d8be47418e74b09f151f07ccb55412fafda2a0d19534ac5
 “Wisdom begins in wonder.” --Socrates
 ((λ (x) (x x)) (λ (x) (x x)))
 “Life has become immeasurably better since I have been forced to stop
 taking it seriously.” --Thompson

Re: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Doyley, Marvin]

jorge.a.alf...@gmail.com (Jorge A. Alfaro-Murillo) writes:

Thanks everybody for highlighting the benefits of python. I am exploring
python with a few undergraduates. I am impressed how well python plays
with Fortran, f2py is awesome. The syntax is very similar to MATLAB so
migration should be easy, if I decided to move in that direction.

Best Wishes,
M

 
 Grant Rettke g...@wisdomandwonder.com writes:

 Octave is an option, too: https://www.gnu.org/software/octave/

 Since people are championing python, and R and Octave have been
 mentioned, let me throw this one into the discussion:
 http://www.sagemath.org/

 Sage is a free open-source mathematics software system licensed under
 the GPL. It builds on top of many existing open-source packages: NumPy,
 SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more

 Many more includes Octave as well. If you know python, then you can
 use only python in Sage, no need for learning anything new.

 Actually you do not need to install anything to use it:
 https://cloud.sagemath.com/

 At Sage Math Cloud (SMC) besides Sage, you can access a terminal there
 and it has emacs already installed. Also you can ssh to their servers,
 and tramp with emacs locally works well connecting to it. That is what I
 use for research.

 Come to think about it, there is no ob-sage.el yet. I write my papers
 directly to LaTeX (and my collaborators write at SMC since they are not
 emacs users and it provides direct compilation and shows already the
 results) so I never thought about exporting to sage. Does someone have
 any plans for this?

 Jorge.




-- 

Re: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Doyley, Marvin M.]

Good point.
Thanks
On Jul 10, 2014, at 8:45 PM, Grant Rettke 
g...@wisdomandwonder.commailto:g...@wisdomandwonder.com wrote:

Doing all of your reproducible research with free software will
maximize the number of people who may reproduce your research. MATLAB
is a great, great tool, and not many people purchase it other than
universities or professional engineers, minimize the number of people
to reproduce your research.

Re: [O] An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Doyley, Marvin M.]

Thanks John,

The biggest challenge has been getting my team to use emacs, and appreciate its 
power. A few of the students are now comfortable with it, but most are still 
novices, even the computationally savvy  members of my team. For now I am 
forcing everybody to use org as a latex replacement no babel or beamer yet. 
However, In the fall I will mandate that all data analysis (matlab babel) 
should be included with all manuscripts. I notice that you prefer to use python 
rather than matlab. Is there a reason  for this ? Matlab is free at my 
institution so cost  is not an issue.

I welcome any advise or tips you may have 

Best Wishes,

M


On Jul 9, 2014, at 3:08 PM, John Kitchin jkitc...@andrew.cmu.edu wrote:

 That is great! Congratulations, and thanks for sharing. I have also
 converted my group into an org-centric group.  Did you find many
 challenges in implementing this in your group?
 
 Doyley, Marvin M. mdoy...@ur.rochester.edu writes:
 
 Dear All,
 
 Here is a link to a manuscript my research group produced completely with org
 https://urldefense.proofpoint.com/v1/url?u=http://medicalimaging.spiedigitallibrary.org/issue.aspxk=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0As=f6e37fd82613c5c7a791b1df10042b390be86728522e227f9316ec27d12c08c1.
  
 
 For the last 6 years, I have used org mainly for teaching (beamer),
 productivity, outlining ideas, and note taking. Inspired by John
 Kitchin's 2013 Scipy talk, I tried to encourage members of my research
 group to use Org. Since the gentle approach didn't work, I made it 
 mandatory requirement that all junior members must generate
 manuscripts in org, and now I am seeing the fruits of this decision--- we 
 are now a org-centric  research group :)
 
 I would like to thank  Carsten and all the other contributors for creating 
 such
 an awesome research tool. 
 
 Cheers,
 M
 
 
 -- 
 ---
 John Kitchin
 Professor
 Doherty Hall A207F
 Department of Chemical Engineering
 Carnegie Mellon University
 Pittsburgh, PA 15213
 412-268-7803
 https://urldefense.proofpoint.com/v1/url?u=http://kitchingroup.cheme.cmu.edu/k=p4Ly7qpEBiYPBVenR9G2iQ%3D%3D%0Ar=Fwb4ac3v7AhcQoTcqa9wemihF49yp0vUvrJ%2BiX5Re4w%3D%0Am=rV9Ve%2BKzfjY9BDOqxI1YYuowCcKG%2BP5hNOX3zMZtRDA%3D%0As=c42f68beb01d6c32f1ce25775cb9df73f29f6198e9a3dc71beb1514a293e1533

[O] An Org centric research lab: Goodbye MS word, excel, and powerpoint

[Doyley, Marvin M.]

Dear All,

Here is a link to a manuscript my research group produced completely with org
http://medicalimaging.spiedigitallibrary.org/issue.aspx. 

For the last 6 years, I have used org mainly for teaching (beamer),
productivity, outlining ideas, and note taking. Inspired by John
Kitchin's 2013 Scipy talk, I tried to encourage members of my research
group to use Org. Since the gentle approach didn't work, I made it 
mandatory requirement that all junior members must generate
manuscripts in org, and now I am seeing the fruits of this decision--- we are 
now a org-centric  research group :)

I would like to thank  Carsten and all the other contributors for creating such
an awesome research tool. 

Cheers,
M

Re: [O] Pushing and pulling to google calendar

[Doyley, Marvin]

Thanks,

I will try  MobileOrg.
Cheers,
M
-- 

[O] Pushing and pulling to google calendar

[Doyley, Marvin M.]

Hi Everybody,

Is there a way to sync org-agenda with google calendar so that I can exploit 
googles calendar reminder.

I wish there was a way to send calendar reminders (pop-up, emails, text message 
)  from org-mode rather than going through google.

Best Wishes,
M


Sent from my iPad

[O] org-ref in action

[Doyley, Marvin M.]

Hi John,

Thanks for sharing. My students and I love it.

Cheers,
M

Re: [O] babel python example not reproducible

[Doyley, Marvin]

Hi Shiyuan,

I think the problem is that Emacs or babel is using python located in
/usr/bin or /usr/local/sbin  rather than default python or ipython. The way I 
got
around this is rename python in these locations to python_old and then did
a soft link to ipython (i.e., ln -s /anaconda/bin/ipython python). 

I am sure there is a smarter way of telling babel to use ipython, but
this was my work around.

Hope this help
cheers,
M

Re: [O] org-weather for openweathermap.org

[Doyley, Marvin]

I love this app, but there is only one snag. Changing the temperature units
from Celsius to Fahrenheit doesn't work. I get the same results regards
of the units  in specified in the org-weather-unit variable

cheers,
M
--

Marvin Doyley
Associate Professor
343 Hopeman Engineering Building
University of Rochester
Department of Electrical and Computer Engineering
Rochester NY 14627
585-275-3774
http://www.ece.rochester.edu/projects/doyley_lab/

Re: [O] org-weather for openweathermap.org

[Doyley, Marvin]

Thanks,

I will change the api
cheers,
M
-- 

Re: [O] babel python example not reproducible

[Doyley, Marvin]

Hi Eric,

Thanks for showing me the smart way of doing this.

cheers,
M
-- 

Re: [O] babel python example not reproducible

[Doyley, Marvin]

Works for me, see example below
#+BEGIN_SRC python :results output :session foo

x=100
print hello
2
print bye
#+END_SRC

#+RESULTS:
: 
:  hello
: 2
: bye

#+BEGIN_SRC python :results output :session foo

print hello good bye
print Printing value from previous session, x
#+END_SRC

#+RESULTS:
: 
: hello good bye
: Printing value from previous session 100

The only difference is that I like to give my session a name and for
what it is worth I am using ipython (don't think this will make a difference). 
You can do this including the
following statement in your .emacs file

(setq python-shell-interpreter ipython)
(setq python-shell-interpreter-args --pylab)

Hope this help.
Cheers,
M

[O] Sauron and Org-mode

[Doyley, Marvin]

Hi there, 

Yesterday I discovered Sauron and now I am trying it out.
However, for some reason I can't get it to work. More specifically, it
runs, but appointments (due within the next 15 min) that I have included in my
org-agenda-file doesn't show up. Could someone tell me what I am doing
wrong. Also is it possible to change the priority time, I would like to
set it to days rather than mins. Enclosed are lines that I have included in my 
.emacs file

(require 'sauron)
(setq sauron-separate-frame nil
sauron-modules '(sauron-erc
 sauron-notifications
 sauron-org)
sauron-max-line-length nil
sauron-nick-insensitivity 15)
Thanks again for your help.
Best Wishes,
M

-- 

Marvin Doyley
Associate Professor
343 Hopeman Engineering Building
University of Rochester
Department of Electrical and Computer Engineering
Rochester NY 14627
585-275-3774
http://www.ece.rochester.edu/projects/doyley_lab/

[O] Sauron and Org-mode

[Doyley, Marvin M.]

I go this to work. It turns out that it works only for appointments not 
deadlines or schedule.

Cheers,
M

Re: [O] Fwd: Emphasizing multiple lines

[Doyley, Marvin M.]

 Yup, looks like that's how it works over here, too -- as far as I know
 it won't automatically display the face when you close emphasis past a
 newline. It's only cosmetic, though -- export and whatnot will parse it
 correctly. My guess is there's no easy way around it...

Hi Eric,
Since this is only cosmetic, I will work with the default values. 

Thanks,
M

[O] Fwd: Emphasizing multiple lines

[Doyley, Marvin M.]

 
 Check out the docstring for org-emphasis-regexp-components -- the fifth
 element determines how many newlines can be spanned by emphasis markers.
 For instance, I've got:
 
 (setf (nth 4 org-emphasis-regexp-components) 3)
 
 Hope that helps.
 
 E
 
 Hi Eric,
 
 This works like a charm. The only snag is that I have to refill the paragraph 
 to get it to work.
 Is there a way around this ?
 
 cheers,
 M
 

Re: [O] Counting number of children under heading

[Doyley, Marvin M.]

Hi Thorsten,

It is not working like a charm.

Thanks
M