Re: Citations merged!

2021-07-09 Thread Julian M. Burgos
Amazing!  Thank you to everyone that contributed.  I am looking forward to 
start playing with this. :)

Nicolas Goaziou writes:

> Hello,
>
> It took years, but citations are now full part of Org syntax.
>
> Thanks to everyone involved over the time!
>
> Now, it needs to be documented, but that will come a bit later.
>
> Regards,


-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
  Fornubúðir 5, IS-220 Hafnarfjörður, Iceland
www.hafogvatn.is
Sími/Telephone : +354-5752037
Netfang/Email: julian.bur...@hafogvatn.is



Re: wip-cite status question and feedback

2021-05-06 Thread M . ‘quintus’ Gülker
Am 05. Mai 2021 um 14:27 Uhr -0400 schrieb Bruce D'Arcus:
> Hope that explains.

Sure, thank you! I just wanted to provide some possibly useful input.
I am not to critise these exciting efforts.

  -quintus

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Re: wip-cite status question and feedback

2021-05-05 Thread M . ‘quintus’ Gülker
Am 05. Mai 2021 um 09:46 Uhr -0400 schrieb Bruce D'Arcus:
> We found three rules:
> 
> 1. what Chicago calls "American"
> 2. what it calls "British"
> 3. French (though Denis is still confirming how these work in actual books)
> 
> The output in each, when formatting as a note:
> 
> 1. A sentence ending in a "cited quote."[1]
> 2. A sentence ending in a "cited quote".[1]
> 3. A sentence ending in a "cited quote[1]."

While I have never seen it stated authoritatively somewhere, in German
it appears to be common to use 1) if the terminal period is in the
cited source, and 2) if it is not, that is, just being exact in
quoting. As a result, both variants can occur in the same document,
because it depends on the cited source.

3) is doubtful in German. It would mean that there is a footnote 1 in
the cited source, but there is not reference for the cited source.
Correct it would have to be

4) A sentence ending in a "cited quote¹"³.

or

5) A sentence ending in a "cited quote¹".³

If the cited quote referenced by footnote 3 indeed does have a
footnote 1 in that position. That being said, I never saw such a
construction.

At least, that are the rules I recall from my school time and which I
used ever since with nobody complaining.

I wonder, can the placement of the footnote not just be left to the
author...? I have the impression that something is being
over-engineered here with the attempt to automate this, but maybe this
is just me.

  -quintus

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Re: wip-cite status question and feedback

2021-04-24 Thread M . ‘quintus’ Gülker
Am 23. April 2021 um 09:24 Uhr -0400 schrieb Bruce D'Arcus:
> It can be that not only does the space get removed, but the note mark
> is moved outside the period.
> 
> So if you have ...
> 
> Some sentence with a concluding citation [cite:@key].
> 
> ... that should end up like this:
> 
> Some sentence with a concluding citation.[1]
> 
> Aside: looking through the CSL spec, it doesn't seem this is
> documented. It obviously should be.
> 
> And I don't remember if that convention is locale-specific; e.g. if
> while that's the standard in English, it could be different in
> France.

As for German, the semantics are different. In Law discipline, in some
journals (not all) both styles can be used within the very same
document and have different meanings. That is,

> This is an example sentence, with a half-sentence following.¹

means that the citation ¹ references the entire sentence, whereas

> This is an example sentence, with a half-sentence following¹.

means that it references only the part following the comma ("with a
half-sentence following"). Normalising this into one uniform style
would be a semantic error. Not all journals handle it like that,
though. Some do prefer uniform look and glance over the semantic
difference.

  -quintus

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Re: (Not so) Short note about citations in Org

2021-04-22 Thread M . ‘quintus’ Gülker
Hi,

Am 22. April 2021 um 01:34 Uhr +0200 schrieb Nicolas Goaziou:
> A noteworthy difference with the last merge is that I removed the
> opportunity to add some Org syntax (emphasis, sub/superscript…) in
> prefixes or suffixes. It makes the code a bit simpler. Of course, I'm
> open to discussion about this change.

I sometimes use emphasis around citations, but since my citation
styles all use footnotes, I think there should be no problem with
this. For example, I would write something like this (I hope I got the
syntax right):

This is a test sentence[fn:1].

* Footnotes

[fn:1] See e.g. [cite:@doe1993 pp. 32-35], who explicitely argues
/against/ the suggestion made by [cite:@someone1990 p. 50].

Since the emphasis markers on the word "against" are outside the two
citations, I would expect no problem here.

> WDYT?

Thank you so much for the hard work on this feature.

  -quintus

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Re: wip-cite status question and feedback

2021-04-17 Thread M . ‘quintus’ Gülker
Hi,

Am 12. April 2021 um 15:19 Uhr +0200 schrieb Nicolas Goaziou:
> The syntax is complete in "wip-cite-new" branch. For the record, in its
> full glory, it can look like this:
> 
>   [cite/style: global prefix; prefix -@key suffix ; ... ; global suffix]
> 
> [...]
>   - "exporting" action is trickier, because there are multiple ways to
> do the integration, and, since I'm not an implementor for citation
> processors, I don't have an accurate view about what is the best
> design. [...]
> The second mandatory function is obviously responsible for rendering
> citations. It is called with a citation object, the desired style,
> if any, and the export back-end, the full list of citations objets
> in the document, and the list of bibliography files. It should also
> return a string. Org provides a helper function to determine the
> footnote containing a citation (and its label, or number) from
> a citation object.
> 
> In the functions described above, I don't know if the arguments are
> sufficient.

The citation object will provide access to all elements of the new
cite syntax I assume, including things like key, prefix and suffix?

Several styles I am normally confronted with require crossreferencing
in citation footnotes (example: “Doe (see above Fn. 24), pp. 35-37”).
Formatting this requires access to the place where an @key first
occured in a footnote. The full list of citation objects probably
suffices for that information; on a first thought I would either use
the first citation object from that list with the @key at hand unequal
to the active citation object (if the list is in the order in which
the citations appear in the exported document, which might not match
the order in the org source) or use the citation object whose footnote
label has the lowest number and is unequal to the active citation
object (if the list is not guaranteed to be in said order). I would
prefer the former approach, because sometimes I deal with footnotes
with numbers like “4a” (a footnote inserted at a late stage in the
authoring process between footnotes 4 and 5), which defeats the
lowest-number approach.

For non-footnote-based citations, the “helper function to determine
the footnote containing a citation” should probably return nil.

  -quintus

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Re: Is it possible to #+include: src blocks and tangle them too?

2021-04-13 Thread Kevin M. Stout
On 2021-04-12 23:38, Nicolas Goaziou wrote:

> However, you may try calling `org-export-expand-include-keyword' from
> `org-babel-pre-tangle-hook'. Untested.

I've done this in the past and can verify that it works well.  That said, it by
definition creates cross-talk between org files, with all the potential for name
collisions and the like that that implies.  One could avoid such problems by
adding some kind of prefix to the block names in the included file (maybe
"common/" or "xyzzy-").  (Some kind of automatic prefixing on inclusion might be
cool.)

--Kevin M. Stout



Re: wip-cite status question and feedback

2021-03-24 Thread M . ‘quintus’ Gülker
Am 24. März 2021 um 09:22 Uhr -0400 schrieb Bruce D'Arcus:
> Anyone know anything else?

Not really. I would just like to say that I am eagerly watching this
thread and am earnestly curious about what will happen to wip-cite. A
proper cite system for org would be such a useful feature.

  -quintus

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Re: [EXT] Problem with org-ref

2021-03-10 Thread Marvin M. Doyley
HI Kyle,

This solved my problems

 Thanks, 

M




> On Mar 9, 2021, at 11:49 PM, Kyle Meyer  wrote:
> 
> Marvin M. Doyley writes:
> 
>> Hi there,
>> 
>> When I use crossref-add-bibtex-entry it download the BibTeX entry but cannot 
>> download the associated pdf.
>> I get the following error  (wrong-type-argument stringp 
>> ("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/“))
>> 
>> I configured org-ref as follows
>> 
>> (setq org-ref-bibliography-notes 
>> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref_notes.org") 
>>  org-ref-default-bibliography 
>> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref.bib") 
>>  org-ref-pdf-directory 
>> '("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")
>>org-ref-notes-citation-link '("cite")
>>  )
> 
> [ Caveat: I've never used org-ref ]
> 
> org-ref's 0383cc2 (support multiple pdf directories, 2016-06-10) updated
> org-ref-pdf-directory to accept a list value, so your value is valid,
> but...
> 
>> Debugger entered--Lisp error: (wrong-type-argument stringp 
>> ("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
>>  file-name-as-directory(("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
>>  doi-utils-get-bibtex-entry-pdf(nil)
> 
> ... doi-utils-get-bibtex-entry-pdf wasn't updated for that (+cc the
> author of that commit and John Kitchin).
> 
> It looks like org-ref-pdf-directory still supports a string, though, and
> you only have one item, so you should be able to work around the issue
> with
> 
>  (setq org-ref-pdf-directory 
> "/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")



Problem with org-ref

2021-03-08 Thread Marvin M. Doyley
Hi there,

When I use crossref-add-bibtex-entry it download the BibTeX entry but cannot 
download the associated pdf.
I get the following error  (wrong-type-argument stringp 
("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/“))

I configured org-ref as follows

(setq org-ref-bibliography-notes 
'("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref_notes.org") 
  org-ref-default-bibliography 
'("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref.bib") 
  org-ref-pdf-directory 
'("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/")
  org-ref-notes-citation-link '("cite")
  )

(setq bibtex-completion-bibliography  
'("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/ref.bib") 
  bibtex-completion-library-path '("~/Org-files/Notes/PDF"))

(setq bibtex-completion-notes-path "~/Org-files/Notes/ref_notes.org") 
(setq bibtex-completion-pdf-symbol "⌘")
(setq bibtex-completion-notes-symbol "✎")



Also enclosed is the backtrace
Thanks for your help in resolving this issue 
M

Debugger entered--Lisp error: (wrong-type-argument stringp 
("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
  file-name-as-directory(("/Users/doyley/Dropbox/Filing_Cabinet/B/refs/pdf/"))
  doi-utils-get-bibtex-entry-pdf(nil)
  funcall-interactively(doi-utils-get-bibtex-entry-pdf nil)
  call-interactively(doi-utils-get-bibtex-entry-pdf record nil)
  command-execute(doi-utils-get-bibtex-entry-pdf record)
  helm-M-x-execute-command(doi-utils-get-bibtex-entry-pdf)
  helm-execute-selection-action-1()
  helm-execute-selection-action()
  helm-internalname . "Emacs Commands history") (candidates . 
#f(compiled-function () #)) (keymap keymap (keymap 
...) keymap (21 . helm-M-x-universal-argument) keymap (127 . 
delete-backward-char) (27 keymap ...) (C-return . helm-cr-empty-string) keymap 
(tab . helm-execute-persistent-action) (normal-state keymap "Auxiliary keymap 
for Normal stat..." ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 
... ... ... ... ... ...) (insert-state keymap "Auxiliary keymap for Insert 
stat..." ... ... ... ... ... ... ... ...) (\(insert\ normal\)-state keymap 
"Auxiliary keymap for (insert nor...") (26 . helm-select-action) (f13 lambda 
nil ... ...) (f12 lambda nil ... ...) (f11 lambda nil ... ...) (f10 lambda nil 
... ...) (f9 lambda nil ... ...) (f8 lambda nil ... ...) (f7 lambda nil ... 
...) (f6 lambda nil ... ...) (f5 lambda nil ... ...) (f4 lambda nil ... ...) 
(f3 lambda nil ... ...) (f2 lambda nil ... ...) (menu-bar keymap ...) (help 
keymap ...) (23 . #f(compiled-function () ... #)) (f1 
lambda nil ... ...) (8 keymap ... ... ... ... ...) ...) (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 . t) 
(match . identity) (redisplay . identity) (nomark . t) (coerce . 
helm-symbolify) (header-line . "C-j: Describe this command (keep...") 
(must-match . t) (group . helm-command) (match-dynamic . t)) ((name . "Emacs 
Commands") (candidates . #f(compiled-function () #)) 
(keymap keymap (keymap ...) keymap (21 . helm-M-x-universal-argument) keymap 
(127 . delete-backward-char) (27 keymap ...) (C-return . helm-cr-empty-string) 
keymap (tab . helm-execute-persistent-action) (normal-state keymap "Auxiliary 
keymap for Normal stat..." ... ... ... ... ... ... ... ... ... ... ... ... ... 
... ... ... ... ... ... ... ...) (insert-state keymap "Auxiliary keymap for 
Insert stat..." ... ... ... ... ... ... ... ...) (\(insert\ normal\)-state 
keymap "Auxiliary keymap for (insert nor...") (26 . helm-select-action) (f13 
lambda nil ... ...) (f12 lambda nil ... ...) (f11 lambda nil ... ...) (f10 
lambda nil ... ...) (f9 lambda nil ... ...) (f8 lambda nil ... ...) (f7 lambda 
nil ... ...) (f6 lambda nil ... ...) (f5 lambda nil ... ...) (f4 lambda nil ... 
...) (f3 lambda nil ... ...) (f2 lambda nil ... ...) (menu-bar keymap ...) 
(help keymap ...) (23 . #f(compiled-function () ... #)) (f1 lambda nil ... ...) (8 keymap ... ... ... ... ...) ...) 
(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 . t) (match . identity) (redisplay . 
identity) (nomark . t) (coerce . helm-symbolify) (header-line . "C-j: Describe 
this command (keep...") (must-match . t) (group . helm-command) (match-dynamic 
. t))) nil "M-x " nil nil "*helm M-x*" nil nil helm-M-x-input-history)
  apply(helm-inte

Re: Org as a book publisher

2021-03-07 Thread M . ‘quintus’ Gülker
Am 06. März 2021 um 20:34 Uhr +0100 schrieb Juan Manuel Macías:
> I would like to share here two samples of one of the most intense
> uses that I give Org Mode: for typesetting, layout and editorial
> design. [...] The samples are from a book on classical philology,
> recently published here in Spain [...]. Naturally, what acts in the
> background here is TeX and LaTeX (specifically Lua(La)TeX), so what
> I really do is use Org and Org-Publish as a sort of high-level
> interface for LaTeX. But I don't mean to avoid LaTeX: in fact, I've
> been working with LaTeX for a long time. I like LaTeX and behind
> these jobs there is a lot of LaTeX code. But Org gives me a much
> more light and productive workflow, allowing me to work at two
> levels.

Thank you very much for sharing. This is an interesting insight. Many
people seem to use org rather than direct LaTeX because they dislike
LaTeX's syntax or find LaTeX too complex, which I never really
understood. But you make some great points for why this combination is
useful other than for that reason.

> 2. Control of the composition process at various points. One of the
>qualities of LuaTeX is the possibility to control TeX primitives
>through scripts in Lua, and to act at various points in the pre- or
>post-process. But I have realized that with the happy fusion of Elisp
>and Org we can be much more precise and "surgical" ;-). Here,
>Org/LaTeX is much more powerful than LuaLaTeX.

For those who still use pdfLaTeX rather than LuaLaTeX (probably due to
Microtype) there is not even an equivalent available.

> 4. An unique origin. The book can be produced on paper from a single
>source, but you can also export, from that source consistently, to
>other formats (HTML or Epub).

This is actually a strong argument. Even though I enjoy writing LaTeX
code, this one is a tough nut to crack with pure LaTeX, where I
achieved the best results with LaTeXML, but it was still lots of work.
May I ask what tooling you use to go from org to Epub?

  -quintus

-- 
Dipl.-Jur. M. Gülker | https://mg.guelker.eu |For security:
Passau, Germany  | kont...@guelker.eu| () Avoid HTML e-mail
European Union   | PGP: see homepage | /\ http://asciiribbon.org



Re: [tip for EXWM users] An alternative method for isolate trees

2021-03-02 Thread Julian M. Burgos
Hi Kyle,

You are right. When running emacs without my personal config things work as 
described in the manual.  I should have verified that first.

My best,

Julian

Kyle Meyer writes:

> Julian M. Burgos writes:
>
>> I have not noticed that org-tree-to-indirect-buffer
>> reuses the indirect buffer when you call it for a second time.
>> According to the manual, "with a C-u prefix, do not remove the
>> previously used indirect buffer", but that does not seem to work.
>> When you do Cu-Cc-Cx-b from a buffer that already has an indirect
>> buffer you get a "cannot modify an area being edited in a dedicated
>> buffer".  If you try it from a different buffer, the prefix is ignored
>> and the indirect buffer is assigned to the tree from the last buffer.
>
> Hmm, could you provide a reproducer for the problem?  Here's what I
> tried with the current master (afd75d05a), Emacs 27.1, and no custom
> configuration.
>
> --8<---cut here---start->8---
> * a
> a content
> * b
> b content
> --8<---cut here---end--->8---
>
>  - on "a", C-c C-x b  ;; org-tree-to-indirect-buffer
>Displays -a-1 buffer.
>
>  - move to "b", C-u C-c C-x b
>Displays -b-1 buffer, a-1 buffer still exists.


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
  Fornubúðir 5, IS-220 Hafnarfjörður, Iceland
www.hafogvatn.is
Sími/Telephone : +354-5752037
Netfang/Email: julian.bur...@hafogvatn.is



Re: [tip for EXWM users] An alternative method for isolate trees

2021-03-01 Thread Julian M. Burgos
Hi Juan,

You are right. :) I have not noticed that org-tree-to-indirect-buffer reuses 
the indirect buffer when you call it for a second time.  According to the 
manual, "with a C-u prefix, do not remove the previously used indirect buffer", 
but that does not seem to work.  When you do Cu-Cc-Cx-b from a buffer that 
already has an indirect buffer you get a "cannot modify an area being edited in 
a dedicated buffer".  If you try it from a different buffer, the prefix is 
ignored and the indirect buffer is assigned to the tree from the last buffer.

This does not seem to be a limitation from emacs, as it is possible to open 
multiple indirect buffers from a base buffer, using for example 
clone-indirect-buffer.  So it should be possible to make a function combining 
"clone-indirect-buffer" and "org-narrow-to-subtree" perhaps?  I am thinking so 
this option is available not only to EXWM users.

Ideally, there should be an option to allow org-tree-to-indirect-buffer to 
create more than one indirect buffer if desired.

My best,

Julian

Juan Manuel Macías writes:

> Hi Julian, thanks for your comment.
>
> "Julian M. Burgos"  writes:
>
>> Thank you, although I tested your functions and compared with the
>> original org-tree-to-indirect-buffer, the only difference I see is
>> that your function creates a new exwm workspace. The original function
>> already creates indirect buffers with their own names (using a slash
>> instead of the double colons). Or I am missing something?
>
> org-tree-to-indirect-buffer creates a new buffer, but (as far as I know)
> does not allow accumulating buffers. In other words, you cannot have
> several isolated trees at the time. In this method it just occurred to
> me to configure org-indirect-buffer-display as new-frame and take
> advantage of EXWM frame management.
>
> Best regards,
>
> Juan Manuel


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
  Fornubúðir 5, IS-220 Hafnarfjörður, Iceland
www.hafogvatn.is
Sími/Telephone : +354-5752037
Netfang/Email: julian.bur...@hafogvatn.is



Re: [tip for EXWM users] An alternative method for isolate trees

2021-03-01 Thread Julian M. Burgos
Hi Juan Manuel,

Thank you, although I tested your functions and compared with the original 
org-tree-to-indirect-buffer, the only difference I see is that your function 
creates a new exwm workspace.  The original function already creates indirect 
buffers with their own names (using a slash instead of the double colons).  Or 
I am missing something?

My best,

Julian

Juan Manuel Macías writes:

> Hi,
>
> Since EXWM uses Emacs frames as virtual desktops, I have written this
> alternative method of `org-tree-to-indirect-buffer', which I share here.
> With this method I can have several isolated trees, with their own name,
> and access them quickly (with helm-buffer-list, for example):
>
> #+begin_src emacs-lisp
>   (defun my-goto-buffer-regexp (regexp)
> (dolist (buffer (buffer-list))
>   (let ((name (buffer-name buffer)))
>   (when (and name (not (string-equal name ""))
>  (string-match regexp name))
> (switch-to-buffer buffer)
>
>   (defun my-org-tree-to-indirect-buffer ()
> (interactive)
> (let ((buf (buffer-name))
> (ind-buf (replace-regexp-in-string "\\[.+\\]" "" (nth 4 
> (org-heading-components
> (org-indirect-buffer-display 'new-frame))
>   (org-tree-to-indirect-buffer)
>   (my-goto-buffer-regexp ind-buf)
>   (rename-buffer (concat buf "::" ind-buf
> #+end_src
>
> Best regards,
>
> Juan Manuel


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
  Fornubúðir 5, IS-220 Hafnarfjörður, Iceland
www.hafogvatn.is
Sími/Telephone : +354-5752037
Netfang/Email: julian.bur...@hafogvatn.is



Re: [EXT] Org-ref-helm-insert-cite-link

2021-02-23 Thread Marvin M. Doyley
Installing bibtex-completion fixed the problem








> On Feb 23, 2021, at 5:53 PM, Kyle Meyer  wrote:
> 
> Marvin M. Doyley writes:
> 
>> Hi there,
>> 
>> For some reason org-ref-helm-insert-cite-link is not working anymore
>> for me. When I try to execute it, I get the following error
>> helm-bibtex-candidates-formatter: Symbol’s function definition is
>> void: bibtex-completion-candidates-formatter
> 
> I don't use org-ref or helm-bibtex, but, based on poking around in their
> repos, helm-bibtex removed bibtex-completion-candidates-formatter way
> back in 390e9c3 (move helm-specific code to helm-bibtex.el, 2016-09-27),
> which in turn led to 400c4f4 (use helm-bibtex-candidates-formatter,
> 2016-10-01) on org-ref's side.  So...
> 
>> Does anybody know how to fix this?
> 
> ... while it's not really a satisfying answer, I suspect your issue will
> be fixed by uninstalling both packages, including the *.elc files, and
> reinstalling.



Re: [EXT] Org-ref-helm-insert-cite-link

2021-02-23 Thread Marvin M. Doyley
Thanks Kyle,

I deleted both packages, but the problem still persists.

I am using the latest version of org and help-bibtex-2.0.0 that I just pulled 
from Melpa. I also pulled the latest version org-ref

Strange but I will keep digging 

Cheers,
M






> On Feb 23, 2021, at 5:53 PM, Kyle Meyer  wrote:
> 
> Marvin M. Doyley writes:
> 
>> Hi there,
>> 
>> For some reason org-ref-helm-insert-cite-link is not working anymore
>> for me. When I try to execute it, I get the following error
>> helm-bibtex-candidates-formatter: Symbol’s function definition is
>> void: bibtex-completion-candidates-formatter
> 
> I don't use org-ref or helm-bibtex, but, based on poking around in their
> repos, helm-bibtex removed bibtex-completion-candidates-formatter way
> back in 390e9c3 (move helm-specific code to helm-bibtex.el, 2016-09-27),
> which in turn led to 400c4f4 (use helm-bibtex-candidates-formatter,
> 2016-10-01) on org-ref's side.  So...
> 
>> Does anybody know how to fix this?
> 
> ... while it's not really a satisfying answer, I suspect your issue will
> be fixed by uninstalling both packages, including the *.elc files, and
> reinstalling.



Org-ref-helm-insert-cite-link

2021-02-23 Thread Marvin M. Doyley
Hi there,

For some reason org-ref-helm-insert-cite-link is not working anymore for me. 
When I try to execute it,  I get the following error 
helm-bibtex-candidates-formatter: Symbol’s function definition is void: 
bibtex-completion-candidates-formatter

Does anybody know how to fix this?

Enclosed is the backtrace,

thanks
M 


Debugger entered--Lisp error: (error "Command attempted to use minibuffer while 
in minib...")
  read-from-minibuffer(#("pattern: " 0 9 (face helm-minibuffer-prompt)) nil 
(keymap (tab . helm-execute-persistent-action) (normal-state keymap "Auxiliary 
keymap for Normal state" (32 . helm-toggle-visible-mark) (121 keymap (121 . 
helm-kill-selection-and-quit) (80 . helm-copy-to-buffer) (112 . 
helm-yank-selection)) (47 . helm-quit-and-find-file) (71 . helm-end-of-buffer) 
(107 . helm-previous-line) (106 . helm-next-line) (41 . helm-next-visible-mark) 
(40 . helm-prev-visible-mark) (103 keymap (114 . helm-refresh) (103 . 
helm-beginning-of-buffer) (106 . helm-next-source) (107 . 
helm-previous-source)) (93 keymap (93 . helm-next-source)) (91 keymap (91 . 
helm-previous-source)) (tab . helm-select-action) (4 . helm-next-page) (15 . 
helm-next-source) (14 . helm-next-line) (16 . helm-previous-line) (22 . 
helm-next-page) (13 . helm-maybe-exit-minibuffer) (2 . helm-previous-page) (6 . 
helm-next-page) (27 keymap (118 . helm-previous-page) (107 . 
helm-previous-line) (106 . helm-next-line) (108 . 
helm-execute-persistent-action) (93 . helm-next-source) (91 . 
helm-previous-source))) (insert-state keymap "Auxiliary keymap for Insert 
state" (15 . helm-next-source) (14 . helm-next-line) (16 . helm-previous-line) 
(22 . helm-next-page) (13 . helm-maybe-exit-minibuffer) (2 . 
helm-previous-page) (6 . helm-next-page) (27 keymap (118 . helm-previous-page) 
(107 . helm-previous-line) (106 . helm-next-line) (108 . 
helm-execute-persistent-action) (93 . helm-next-source) (91 . 
helm-previous-source))) (\(insert\ normal\)-state keymap "Auxiliary keymap for 
(insert normal) state") (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 . 
#f(compiled-function () (interactive nil) #)) (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-

Re: How do you name your code blocks?

2021-02-16 Thread Kevin M. Stout
On 2021-02-15 14:18, Rodrigo Morales wrote:
> 1. Do you use long names?

Usually.  Suppose you were doing a bit of genetic programming.  You might have a
function that computes the next generation from the current one.  You could
write the following snippet that looks suspiciously like pseudocode:

  #+HEADER::noweb-ref genetic/functions
  #+BEGIN_SRC python
  def next_generation(curr):
  <>
  <>
  <>
  <>
  return new
  #+END_SRC

You would then have a block dedicated to each major part of the evolutionary
step.

> 2. If not, how do you name your code blocks to avoid name conflicts?

I have been over the tangling and noweb expansion code quite a bit lately.  The
chief benefit of using #+NAME on a code block is ability to call it.  For
example, you might have

  #+NAME: generate keymap
  #+BEGIN_SRC elisp :var t=keymap
  ...
  #+END_SRC

whose sole purpose is to take a table from elsewhere in an Org file and generate
the code that sets up a keymap.  To use it, you might say

  #+BEGIN_SRC elisp
  <>
  #+END_SRC

For every other purpose, :noweb-ref works better.  In newer versions of org,
it's the sole means of accumulating code under a common name in the WEB/Noweb
tradition.  In older versions, duplicate #+NAMEs did result in accumulation, but
the behavior was undefined.

A word on syntax: I find 

  #+BEGIN_SRC language :noweb-ref "block name"
  ...
  #+END_SRC

less readable than

  #+HEADER::noweb-ref block name
  #+BEGIN_SRC language
  ...
  #+END_SRC

especially when there are further block-specific header args.  Either is more
cumbersome to type than the #+NAME syntax, but that can be dealt with using
something like

  (add-to-list 'org-structure-template-alist
   '("ss" "#+HEADER::noweb-ref ?\n#+BEGIN_SRC\n\n#+END_SRC"))

Then, to set up a safely-named block, 

Re: 2 Surprises and 2 Questions Regarding Org Tangle

2021-02-12 Thread Kevin M. Stout
On 2021-02-11 18:44, Diego Zamboni wrote:

> #2 is known (maybe documented? Not sure) behavior: using :noweb-ref
> accumulates multiple blocks with the same name, whereas #+NAME uses only
> the first one. I think #+NAME's are supposed to be unique within a document.

It seems that more recent versions of org-babel-expand-noweb-references (not
org-babel-tangle, as I said in an earlier message) no longer accumulate blocks
with common #+NAMEs. (Now, though, #+NAME has priority over :noweb-ref, which is
the opposite of how things were done before.) Looking through some older
discussions on the topic, I do see the downsides of accepting duplicate #+NAMEs,
which are rooted in the assumption of uniqueness made elsewhere. Even so, I
still hold that

#+NAME: this is a cool way to do something
#+BEGIN_SRC language
  stuff
#+END_SRC
 
is a much nicer syntax than

#+BEGIN_SRC language :noweb-ref "this is a cool way to do something"
  stuff
#+END_SRC

especially as a project grows.

Perhaps we could have a variation on #+NAME that doesn't need to be unique?
Maybe something like #+NOREF, to evoke :noweb-ref? Or #+NONAME?

Sincerely,
Kevin M. Stout



Re: 2 Surprises and 2 Questions Regarding Org Tangle

2021-02-12 Thread Kevin M. Stout
On 2021-02-11 18:44, Diego Zamboni wrote:

> #2 is known (maybe documented? Not sure) behavior: using :noweb-ref
> accumulates multiple blocks with the same name, whereas #+NAME uses only
> the first one.

Deep in org-babel-tangle,   





  (org-babel-map-src-blocks nil 


  (let ((i (let ((org-babel-current-src-block-location (point)))


   (org-babel-get-src-block-info 'light 


(when (equal (or (cdr (assq :noweb-ref (nth 2 i)))  


   (nth 4 i))   


 source-name)   


...)))

So, while :noweb-ref gets priority over #+NAME, we can still accumulate blocks
having the same #+NAME (provided there's no overriding :noweb-ref).

> I think #+NAME's are supposed to be unique within a document.

Even though I'm a huge fan of this behavior, which lines up well with the
traditional WEB and Noweb behavior, the Org manual's discussion of code blocks
does say, "For duplicate names, Org mode's behavior is undefined." [Section
14.1] So,

Dear Org Maintainers,

Please do not change org-babel-tangle's accumulation behavior for duplicate
#+NAME's. It's handy, and users of other literate programming tools will find it
familiar. Also, #+NAME is a nicer per-block syntax than :noweb-ref.

Sincerely,
Kevin M. Stout



Re: local variables and export processing in hooks

2021-02-11 Thread M . ‘quintus’ Gülker
Am 11. Februar 2021 um 21:12 Uhr +0100 schrieb Sébastien Miquel:
> The purpose of #+BIND is to set some variables in the copied buffer.
> 
> Also, these variables are set after macro expansion (and
> org-export-before-parsing-hook).

Thanks for the information. If they are set after macro expansion, it
will not help me (see below).

> 
> I'm curious, could you explain why/how you use macros to set variables in
> the original buffer ?

The how is easy enough. First I, define an automatically buffer-local
variable with

(defvar-local the-buffer-local-variable nil)

In the org-before-processing-hook and in the macro expansion function
then I effectively do this:

(with-current-buffer (car (buffer-list))
  (setq the-buffer-local-variable "thevalue"))

I agree that the heuristic on (buffer-list) may not be ideal, but for
the cases I had so far it works just fine and retrieves the original
.org buffer from which the system is currently exporting.

As for the why: I am working on a personal citation system for my
specific needs called zit.el (I am a German jurist, and we have quite
peculiar habits on citation, of which excessive use of footnotes and
not using LaTeX, instead having to submit in DOCX format are only
some). I use this functionality to implement a footnote crossreference
system. That is, the first time a citation appears it should appear in
the footnote as:

/Doe/, Some Awesome Work, 3rd edition 2014, pp. 44 ff.

Then the next time this source is cited it should appear as:

/Doe/ (Fn. 35), pp. 46.

If it was not clear from the above: my custom citation system relies
on org's macro system. In the org source I have something like this:

[fn:35] {{{zit(doe2014awesomework[44 ff.])}}}.
[fn:36] {{{zit(doe2014awesomework[46])}}}.

The `zit' macro is my custom macro which operates on a buffer-local
variable. If a citation is new, it adds an org target with a unique
name (<>) to the macro expansion value and records it in said
variable. If the citation is not new, it retrieves the target value
from the variable and expands to a link to the target instead; org is
smart enough to resolve links to targets in footnotes to the footnote
number, which I make use of here. All this only works because it is
possible to implement a macro in an elisp function by using #+MACRO
with an `eval' statement. This certainly is a cool functionality I am
quite grateful for.

Now that I think about it: actually a normal variable would suffice. I
used a buffer-local one a) because my custom citation system has some
per-document settings, like the "Fn." in the parantheses above being a
customisable string, which are naturally implemented as
file-local/buffer-local variables and b) because one might have
multiple org documents open at the same time. But because the citation
collection variable is transient anyway (in fact, it is reset to nil
in the org-before-processing hook so that on a subsequent run it
starts from a clean sheet) and one can only export one document
simultaneously at a time, a normal variable would be enough. I will
probably change that.

If #+BIND statements are not available in macros, they will not work
for my per-document settings as described before, so I will leave them
as file-local/buffer-local variables as they are currently. I needed
to read up on how to mark my own variables as "safe" for that purpose,
but I have now found out how to do that.

Thanks for your answer!

  -quintus

-- 
Dipl.-Jur. M. Gülker | https://mg.guelker.eu |For security:
Passau, Germany  | kont...@guelker.eu| () Avoid HTML e-mail
European Union   | PGP: see homepage | /\ http://asciiribbon.org



Re: local variables and export processing in hooks

2021-02-10 Thread M . ‘quintus’ Gülker
Am 09. Februar 2021 um 14:21 Uhr +0100 schrieb Sébastien Miquel:
> Eric S Fraga writes:
> > I tried but this doesn't seem to be propagated to the export as the
> > export works on a copy of the buffer, not the buffer itself.  That's
> > what #+BIND is for, supposedly...
> 
> I think this buffer copy preserves local variables. I know I use a such a
> local variable and its value can be read during macro expansion.
> 
> It seems the org-export-before-parsing-hook functions are run before the
> #+BIND values are collected (see org-export-as in ox.el).

Interesting. I did not know about #+BIND, but just today I came about
the issue where I needed file-local variables to be available both in
the org-export-before-parsing-hook and in macro expansion. I
circumvented the problem by picking the original buffer out of
`buffer-list' and temporaryly switching to that buffer with
`with-current-buffer'.

Now I wonder whether #+BIND is more elegant. But my macro expansion
function modifies a buffer-local variable. Does #+BIND allow for that,
so that the changed value is available in the original org buffer?

  -quintus

-- 
Dipl.-Jur. M. Gülker | https://mg.guelker.eu |For security:
Passau, Germany  | kont...@guelker.eu| () Avoid HTML e-mail
European Union   | PGP: see homepage | /\ http://asciiribbon.org



Re: Smart processing of http(s) links

2020-06-29 Thread Bonface M. K.
Ag Ibragimov  writes:

> Oh cool. This is exactly what I needed:
>
> I was able to build this:
>
> #+begin_src emacs-lisp
> (defun get-gh-item-title (uri  include-number?)
>   "Based on given github URI for (pull request or an issue),
>   returns its title"
>   (when (string-match "\\(github.com\\).*\\(issues\\|pull\\)" uri) ; either 
> PR or issue
> (pcase-let* ((`(_ _ ,owner ,repo ,type ,number) (remove "" (split-string 
> uri "/")))
>  (gh-resource (format "/repos/%s/%s/%s/%s"
>   owner
>   repo
>   (if (string= type "pull") "pulls" type)
>   number))
>  (resp (ghub-get gh-resource nil :auth 'forge)))
>   (when resp
> (format "%s%s" (alist-get 'title resp)
> (when include-number? (format " #%s" number)))
>
> (defun org-link-make-description-function* (link desc)
>   (cond ((string-match "\\(github.com\\).*\\(issues\\|pull\\)" link)
>  (get-gh-item-title link :with-number))
> (t desc)))
>
> (setq org-link-make-description-function 'org-link-make-description-function*)
> #+end_src
>

Thanks for this!

> https://gist.github.com/agzam/b2f2d441acb96e1d693a2c81e9c4518f
> On Sun 28 Jun 2020 at 14:02, Kyle Meyer  wrote:
>
>> Ag Ibragimov writes:
>>
>>> Whenever I I use org-insert-link and it turns out to be a URI that
>>> starts with "https://github.com; I would like it to be processed
>>> differently than any other link, one example - if it is a PR or a
>>> Github Issue, I'd like it to fetch summary(title) of it and create a
>>> link that looks like this:
>>>
>>> [[https://github.com/user/repo/issues/3899][This issue needs to be fixed 
>>> #3899]]
>>>
>>> Do we have any "built-in" mechanism for doing something like this? Can
>>> someone suggest how I can make it. Thank you!
>>
>> You can set org-link-make-description-function to a function that
>> detects links of interest and generates a custom description.
>
>

-- 
Bonface M. K. (https://www.bonfacemunyoki.com)
One Divine Emacs To Rule Them All
GPG key = D4F09EB110177E03C28E2FE1F5BBAE1E0392253F



Re: Splitting large org file into smaller ones

2020-05-30 Thread Marvin M. Doyley
Thanks Bill

> On May 30, 2020, at 11:36 AM, William Denton  wrote:
> 
> On 30 May 2020, Marvin M. Doyley wrote:
> 
>> How do I export the subtree to separate org files, say
>> 
>> - Candidate-a.org 
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__candidate-2Da.org_=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=bIZSMkqv64C1tMXjpulbll5ho0_g78uEvbSGB385-YQ=qfP2YDuIkAJM2S_aXOWV8p65RBNCtPMSSd8Y7h4nWPU=
>>  >
>> - Candidate-b.org 
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__candidate-2Db.org_=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=bIZSMkqv64C1tMXjpulbll5ho0_g78uEvbSGB385-YQ=m7juMWMKRPTM8hGOlYOQJy31TXiDJ52t2-Uu7t6i9EQ=
>>  >
> 
> I'll throw out an uninformed suggestion of a possible direction:  archiving 
> subtrees.  I guess you'd have to keep changing the name of the target archive 
> file, or rename it after you'd moved a tree to it, but at least it's getting 
> a whole tree out of the way at once.
> 
> Bill
> --
> William Denton :: Toronto, Canada   ---   Listening to Art: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__listeningtoart.org_=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=bIZSMkqv64C1tMXjpulbll5ho0_g78uEvbSGB385-YQ=3SYzbH-wXEZ1etjDC-J5keIPie3ll0ngiWihrTPputs=
>  
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.miskatonic.org_=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=bIZSMkqv64C1tMXjpulbll5ho0_g78uEvbSGB385-YQ=Eyy6EE7boaclNVgLZFy6YP4RM57VQQMr5pBFDOdY5Zo=
>   ---   GHG.EARTH: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__ghg.earth_=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=bIZSMkqv64C1tMXjpulbll5ho0_g78uEvbSGB385-YQ=WZpqujYA7GRmIP00WVRuyH4g-hRRFcrNhWV9O27p0F0=
>  Caveat lector.  ---   STAPLR: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__staplr.org_=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=bIZSMkqv64C1tMXjpulbll5ho0_g78uEvbSGB385-YQ=sKITlXUZ5Q6MQoPb4RFPynZVydyakhlNKabGQieVC7c=
>  




Re: Splitting large org file into smaller ones

2020-05-30 Thread Marvin M. Doyley
Cool! I will try this too

Thanks

Cheers,
M

> On May 30, 2020, at 6:23 PM, Diego Zamboni  wrote:
> 
> Hi Marvin,
> 
> I replied to a similar question some time ago, here's my answer (with
> updated links since the files have changed in the meantime):
> 
> I do something similar in my ox-leanpub-book module [1], which exports
> each top-level heading to a different file. The general idea is to use
> =org-map-entries= to loop over the entire buffer [2]. The function you
> call can then check whether the current entry is a header at the level
> you want [3] and then export it to the corresponding file. The title
> can be used to deduct the filename [4].
> 
> I found that I had to mark the entire subtree before calling the
> export function [5], otherwise the headline was not getting included
> in the export.
> 
> I based my code originally on this blog post, which might be a simpler
> starting point:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__medium.com_-40lakshminp_publishing-2Da-2Dbook-2Dusing-2Dorg-2Dmode-2D9e817a56d144=DwIBaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=249GZv4Zgx7zyEm64J3m2eEYuchXSdodRltw_gmrqlg=exfuDxb81D5anZ5KD-hCvUI4PRaQxsb812EaBW3b9p4=
>  
> - this code does not select the entire subtree before exporting, which
> means only the contents of the section is exported, but not the
> headline itself.
> 
> I wrote a simplified function which puts the above ideas together,
> feel free to use it:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__gist.github.com_zzamboni_2e6ac3c4f577249d98efb224d9d34488=DwIBaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=249GZv4Zgx7zyEm64J3m2eEYuchXSdodRltw_gmrqlg=ARDFenWJJT9XTsBKAReDC6bDx9VwbP3ADCw3o-_hQbY=
>  
> 
> Hope this helps!
> --Diego
> 
> [1] 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zzamboni_ox-2Dleanpub_tree_book-2Dand-2Dmarkua=DwIBaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=249GZv4Zgx7zyEm64J3m2eEYuchXSdodRltw_gmrqlg=peXBLnzs1ABFnCABzVUsley3-VMFDR0_2oLF3TgiBPM=
>  
> [2] 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zzamboni_ox-2Dleanpub_blob_f7ae0f86f517a321a5150e1c712554b12acf144b_ox-2Dleanpub-2Dbook.el-23L216-2DL217=DwIBaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=249GZv4Zgx7zyEm64J3m2eEYuchXSdodRltw_gmrqlg=3K2q6g7FxxjjxKJZtqdsE5bpMFT6RTf3S4mmyldNdLw=
>  
> [3] 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zzamboni_ox-2Dleanpub_blob_f7ae0f86f517a321a5150e1c712554b12acf144b_ox-2Dleanpub-2Dbook.el-23L145=DwIBaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=249GZv4Zgx7zyEm64J3m2eEYuchXSdodRltw_gmrqlg=QOtk1D413Gju7Agm6zgbAMlIwww6e-UV1SZsjomzuZA=
>  
> [4] 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zzamboni_ox-2Dleanpub_blob_f7ae0f86f517a321a5150e1c712554b12acf144b_ox-2Dleanpub-2Dbook.el-23L154-2DL158=DwIBaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=249GZv4Zgx7zyEm64J3m2eEYuchXSdodRltw_gmrqlg=ynLKEu4CLjIJqR3y3zl2UMEkS_onMBSSb2TDwOaixt4=
>  
> [5] 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zzamboni_ox-2Dleanpub_blob_f7ae0f86f517a321a5150e1c712554b12acf144b_ox-2Dleanpub-2Dbook.el-23L192=DwIBaQ=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=249GZv4Zgx7zyEm64J3m2eEYuchXSdodRltw_gmrqlg=quomDHaK1zPArr8wu5m8uwkgug6NZ6eDChE5VMZwrG4=
>  
> 
> On Sat, May 30, 2020 at 12:08 PM Marvin M. Doyley
>  wrote:
>> 
>> Hi there,
>> 
>> Is there an efficient way to split a large org file into smaller ones?
>> 
>> Lets say I have a master file with the following
>> 
>> 
>> * Notes
>> **  Candidate A
>> - Strong technical background
>> - High H-factor
>> - good funding
>> - More established investigator
>> - Huge startup need $$
>> 
>> **  Candidate B
>> - lower startup need
>> - signal processing
>> - young investigator
>> 
>> 
>> How do I export the subtree to separate org files, say
>> 
>> - Candidate-a.org
>> - Candidate-b.org
>> 
>> 
>> Thanks
>> 
>> M




Re: Splitting large org file into smaller ones

2020-05-30 Thread Marvin M. Doyley
Hi Marcin,

I appreciate this, I will give it a go.

Thanks,
M

> On May 30, 2020, at 9:13 AM, Marcin Borkowski  wrote:
> 
> 
> On 2020-05-30, at 11:51, Marvin M. Doyley  wrote:
> 
>> Hi there,
>> 
>> Is there an efficient way to split a large org file into smaller ones?
> 
> I do not know about "efficient", but you might find my org-one-to-many
> library useful: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_mbork_org-2Done-2Dto-2Dmany=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=iHWQZlKMtTtC96Iqx0ymA0VpA5m6A73UehcV_vuh1tM=6rsipfH8vh-XeWLb1NEWAcdpcTFAfyUOLHD5Pkmea2o=
>  
> (Note that I don't wven know if it works with newer versions of Org; if
> not, drop me a line, maybe I'll be able to fix it.)
> 
> Best,
> 
> -- 
> Marcin Borkowski
> https://urldefense.proofpoint.com/v2/url?u=http-3A__mbork.pl=DwIBAg=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU=T41F_5QsIVBGYhPPUkgYHUp9iPHgs2rOCjs7rfKaTMU=iHWQZlKMtTtC96Iqx0ymA0VpA5m6A73UehcV_vuh1tM=VLUzcQS7YObsdTrrwTldDMYEUZJlqE3mMIxxY8tN9JQ=
>  




Splitting large org file into smaller ones

2020-05-30 Thread Marvin M. Doyley
Hi there,

Is there an efficient way to split a large org file into smaller ones?

Lets say I have a master file with the following


* Notes
**  Candidate A
 - Strong technical background
 - High H-factor
 - good funding
- More established investigator
- Huge startup need $$

**  Candidate B
- lower startup need
- signal processing  
- young investigator


How do I export the subtree to separate org files, say

- Candidate-a.org <http://candidate-a.org/>
- Candidate-b.org <http://candidate-b.org/>


Thanks

M

Re: Email rendered equation

2020-05-19 Thread Marvin M. Doyley
Hi Eric,

This works like a charm.


Thanks,
M

> On May 19, 2020, at 10:14 AM, Eric S Fraga  wrote:
> 
> On Tuesday, 19 May 2020 at 09:19, Marvin M. Doyley wrote:
>> I have decided to take the plunge and switch to mu4e. I have also
>> installed the org-mu4e package. Most stuff works pretty well, except
>> latex equations are not rendered when I send them.
>> 
>> Does anybody know how to solve this problem?
> 
> I don't use mu4e so I don't know what org-mu4e actually brings to the
> table.  In gnus, if I want to send an email with LaTeX fragments
> (e.g. equations) shown as images, I invoke org-mime-htmlize on the
> message once written.  This creates an HTML message with org processing
> (links, tables, LaTeX, images).  Works well the infrequent times I do
> it.
> -- 
> : Eric S Fraga via Emacs 28.0.50, Org release_9.3.6-640-g9bc0cc




Re: Email rendered equation

2020-05-19 Thread Marvin M. Doyley
Thanks Eric,

I will give it a try

Cheers,
M


> On May 19, 2020, at 10:14 AM, Eric S Fraga  wrote:
> 
> On Tuesday, 19 May 2020 at 09:19, Marvin M. Doyley wrote:
>> I have decided to take the plunge and switch to mu4e. I have also
>> installed the org-mu4e package. Most stuff works pretty well, except
>> latex equations are not rendered when I send them.
>> 
>> Does anybody know how to solve this problem?
> 
> I don't use mu4e so I don't know what org-mu4e actually brings to the
> table.  In gnus, if I want to send an email with LaTeX fragments
> (e.g. equations) shown as images, I invoke org-mime-htmlize on the
> message once written.  This creates an HTML message with org processing
> (links, tables, LaTeX, images).  Works well the infrequent times I do
> it.
> -- 
> : Eric S Fraga via Emacs 28.0.50, Org release_9.3.6-640-g9bc0cc




Email rendered equation

2020-05-19 Thread Marvin M. Doyley
Hi there,

I have decided to take the plunge and switch to mu4e. I have also installed the 
org-mu4e package. Most stuff works pretty well, except latex equations are not 
rendered when I send them.


Does anybody know how to solve this problem?

Thanks,
M


Org-ref issues

2020-01-24 Thread Marvin M. Doyley
Hi there,

I just upload org-ref on my system via melpa and get the following error when I 
issue the command doi-utils-add-bibtex-entry-from-doi

Symbol’s function definition is void: org-ref-possible-bibfiles


Does anybody know how to resolve this

Thanks 

M

Here is the backtrace

Debugger entered--Lisp error: (void-function org-ref-possible-bibfiles)
  org-ref-possible-bibfiles()
  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 . 
#f(compiled-function () (interactive nil) #)) (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) (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 . identity) (redisplay . 
identity) (nomark) (coerce . helm-symbolify) (header-line . "C-j: Describe this 
command (keeping session)") (must-match) (group . helm-command) 
(match-dynamic)) ((name . "Emacs Commands") (candidates . #f(compiled-function 
() #)) (keymap keymap (keymap (13 . 
helm-confirm-and-exit-minibuffer)) keymap (21 . helm-M-x-universal-argument) 
keymap (127 .

Re: Org-ref error

2020-01-22 Thread 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

2020-01-22 Thread 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

2020-01-22 Thread 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-transform

Re: `org-next-link' skips links inside PROPERTIES drawer

2020-01-20 Thread Pedro R . M . Júnior
Hello Kyle,

> This behavior came up in a previous thread.  Quoting Nicolas:
>
> ,[ https://lists.gnu.org/archive/html/emacs-orgmode/2019-04/msg00075.html 
> ]
> | This is expected.
> |
> | The value in a properties drawer cannot be a link, even though
> | `org-open-at-point' would normally open it, as is done for comments.
> |
> | In addition to no being syntactically a valid link, I think it is
> | undesirable for an interactive command to display hidden internal data.
> |
> | If you want to reach it, just write a function calling
> |
> |(re-search-forward org-any-link-re nil t)
> `

In fact, this have passed unobserved to me.  Thanks for the
clarification and quoted suggestion.

Bests,
Pedro



`org-next-link' skips links inside PROPERTIES drawer

2020-01-20 Thread Pedro R . M . Júnior
Hello,

I am testing Emacs 28 (Org 9.3) from the Git repository and I have
noticed that, compared to version 26.3 (Org 9.1.9), `org-next-link'
function is skipping links located inside the PROPERTIES drawer.  (I
have not tested version 27.)  The same does not happen for the links
outsize drawers or links inside a drawer other than PROPERTIES one,
e.g., LOGBOOK drawer.

As an example, consider the Org file between "=" lines
below.  Set the cursor at the beginning of the file.  Then call
`org-next-link'.

=
* Heading
  :PROPERTIES:
  :MYLINK:   https://orgmode.org/
  :END:
  Another link: https://duckduckgo.com/
=

I would expect `org-next-link' to find the link inside the drawer (i.e.,
https://orgmode.org/) as in version 26.3.  Instead, it goes directly to
the second link (i.e., https://duckduckgo.com/).

The same happens with `org-previous-link'.

Let me know if this is an intentional behavior for newer versions of Org
mode.  If so, I think it could receive a customization option for this
behavior.

Bests,
Pedro R.M. Júnior



[O] [PATCH] ob-ocaml: Support for pretty-printed outputs

2019-10-04 Thread Robert M. Kovacsics

E.g. the following snippet produces multiple lines of output, due to
pretty-printing

 #+BEGIN_SRC ocaml :exports code :eval no-export :results verbatim
(* Note, no need to have parentheses around sqrt, as
application binds the tightest *)
let rec gamma n = if n = 0
  then (1.0 +. sqrt 5.0) /. 2.0
  else 1.0 /. (gamma (n-1) -. 1.0)

let nums = List.map gamma (List.init 5 (fun x -> x))
 #+END_SRC

 #+NAME: gamma-tbl
 #+RESULTS[1fd6a3e846afdef51350eb6d7ba15c6844ccc14e]:
: val gamma : int -> float = 
: val nums : float list =
:   [1.6180339887498949; 1.61803398874989468; 1.61803398874989535;
:1.61803398874989357; 1.61803398874989823]

(In reality this would have 50 or so outputs, point being mathematically
it shouldn't change, but due to floating point errors it does.)

The regexp has the following problems:

- The "." in group 5 (as-was) doesn't match new-lines, so it only
  matches the first line, e.g. as a list
  : - [1.6180339887498949, 1.61803398874989468, 1.61803398874989535,

- When using "\\(.\\|\n\\)", it includes the starting indentation of the
  list, which makes org-babel-script-escape choke (called from
  org-babel-ocaml-read-list, from org-babel-ocaml-parse-output, from
  org-babel-execute:ocaml, the code being modified.
From 281de8e248fdd70ecfc69237df83a155c9491f2e Mon Sep 17 00:00:00 2001
From: Kovacsics Robert 
Date: Fri, 4 Oct 2019 17:29:00 +0100
Subject: [PATCH] ob-ocaml: Support for pretty-printed outputs

E.g. the following snippet produces multiple lines of output, due to
pretty-printing

 #+BEGIN_SRC ocaml :exports code :eval no-export :results verbatim
(* Note, no need to have parentheses around sqrt, as
application binds the tightest *)
let rec gamma n = if n = 0
  then (1.0 +. sqrt 5.0) /. 2.0
  else 1.0 /. (gamma (n-1) -. 1.0)

let nums = List.map gamma (List.init 5 (fun x -> x))
 #+END_SRC

 #+NAME: gamma-tbl
 #+RESULTS[1fd6a3e846afdef51350eb6d7ba15c6844ccc14e]:
: val gamma : int -> float = 
: val nums : float list =
:   [1.6180339887498949; 1.61803398874989468; 1.61803398874989535;
:1.61803398874989357; 1.61803398874989823]

(In reality this would have 50 or so outputs, point being mathematically
it shouldn't change, but due to floating point errors it does.)

The regexp has the following problems:

- The "." in group 5 (as-was) doesn't match new-lines, so it only
  matches the first line, e.g. as a list
  : - [1.6180339887498949, 1.61803398874989468, 1.61803398874989535,

- When using "\\(.\\|\n\\)", it includes the starting indentation of the
  list, which makes org-babel-script-escape choke (called from
  org-babel-ocaml-read-list, from org-babel-ocaml-parse-output, from
  org-babel-execute:ocaml, the code being modified.
---
 lisp/ob-ocaml.el | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lisp/ob-ocaml.el b/lisp/ob-ocaml.el
index 0c0ffe442..54bc49a2f 100644
--- a/lisp/ob-ocaml.el
+++ b/lisp/ob-ocaml.el
@@ -83,11 +83,11 @@
 	 (raw (org-trim clean))
 	 (result-params (cdr (assq :result-params params
 (string-match
- "\\(\\(.*\n\\)*\\)[^:\n]+ : \\([^=\n]+\\) =\\(\n\\| \\)\\(.+\\)$"
+ "\\(\\(.*\n\\)*\\)[^:\n]+ : \\([^=\n]+\\) =[[:space:]]+\\(\\(.\\|\n\\)+\\)$"
  raw)
 (let ((output (match-string 1 raw))
 	  (type (match-string 3 raw))
-	  (value (match-string 5 raw)))
+	  (value (match-string 4 raw)))
   (org-babel-reassemble-table
(org-babel-result-cond result-params
 	 (cond
-- 
2.19.2



Re: [O] Issue with internal links

2019-08-09 Thread 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

2019-08-08 Thread 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* ((

[O] ox-html: proof-tree (bussproofs) latex fragment

2019-04-26 Thread Robert M. Kovacsics

Hi,

I have a latex-fragment like so

#+LATEX_HEADER: \usepackage{bussproofs}
#+OPTIONS: tex:dvipng
\begin{prooftree}
\AxiomC{}
\LeftLabel{(fn)}
\UnaryInfC{$\text{Env}\vdash C(\text{Env}', \text{fn } x \ \Rightarrow\ 
E_1)\ v \ \to\ \text{Env},\text{Env}',(x,v)\vdash E_1$}

\end{prooftree}


when I export this, it fails because it replaces the \begin{prooftree} 
with \begin{prooftree*}, and there is no such environment. I think the 
problem is with "org-html--unlabel-latex-environment" in ox-html.el, as 
it assumes any environment has a starred version. Perhaps that function 
should only be applied to a couple of environments, e.g. equation, 
according to a whitelist? Or have a blacklist for which it shouldn't 
apply.


Or perhaps I am including latex fragments wrong?

Thanks,
Robert



[O] Script for automatically linking to an external file

2019-04-15 Thread Doyley, Marvin M.
Hi there,

I trying to make a script that

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

Does anybody know how to do this.

Thanks
M



Re: [O] typo in org-track.el manual

2019-02-19 Thread Christopher M. Miles


binZMEXuhGks6.bin
Description: application/pgp-encrypted


binoD3igvt0Pw.bin
Description: Binary data


Re: [O] Rationale for org-directory (any?)

2019-02-19 Thread Christopher M. Miles


I use it for dynamic folder sync, I can use it different machine, just
change the ~org-directory~ variable. I use this variable in many place
to concatenate a whole path.

Carlos Pita  writes:

> Hi all,
>
> I often wonder if the way org-directory is currently used has any
> sense or is just a historical artifact.
>
> I mean, when I list my refile targets and agenda files I have to
> specify full paths, which isn't very convenient. But if instead of a
> list I provide a file listing the paths, then the items in this list
> are taken to be relative to org-directory. Also, capture targets are
> relative to this variable. The result is a mix of relative and
> absolute paths in my init.el that makes me turn everything absolute in
> order to keep it sane.
>
> Why does it work that way? Is it because some paths are resolved
> relative to the current directory (unless they are configured as
> absolute paths) while others don't?
>
> Thanks!


-- 
[ stardiviner ]
   I try to make every word tell the meaning what I want to express.

   Blog: https://stardiviner.github.io/
   IRC(freenode): stardiviner, Matrix: stardiviner
   GPG: F09F650D7D674819892591401B5DF1C95AE89AC3
  



[O] [Proposal] Make header argument :mkdirp yes work for other header arguments not just :tangle

2019-02-18 Thread Christopher M. Miles


I hope `:mkdirp` header argument can also work for other related header
arguments like `:dir`, `:file` etc not just `:tangle`. Like following
example.

#+begin_src sh :mkdirp yes :dir "data/code/mkdirp/dir" :file "test" :results 
file link
echo "hello"
#+end_src

Do you have any idea about this?

-- 
[ stardiviner ]
   I try to make every word tell the meaning what I want to express.

   Blog: https://stardiviner.github.io/
   IRC(freenode): stardiviner, Matrix: stardiviner
   GPG: F09F650D7D674819892591401B5DF1C95AE89AC3
  



[O] saving web resources with org

2018-10-12 Thread M. P.
How can I save a web page or a utube clip with org in some form of organized 
manner?


[O] Emacs mobile org

2018-09-09 Thread M. P.
Hello I am running emacs on a mac I have a galaxy s8 android phone. I am 
wanting to sync my phone with emacs on my computer.
I would prefer not to use a cloud service but instead use something 
like a usb or ther to sync with.


Re: [O] Json readable error

2018-07-21 Thread 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

2018-07-21 Thread 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)



[O] Replace default category displayed in org-agenda with directory name

2018-06-28 Thread Giacomo M

Dear helpful list,

I'm experimenting with an org-agenda setup where I have a directory for 
each project, and a README.org with the project TODOs in each directory. 
I'm using the elisp below:


#+BEGIN_SRC: emacs-lisp

  (setq org-agenda-file-regexp "\\`README\\.org\\'")
  (setq org-agenda-files projectile-known-projects)

#+END_SRC

where I feed the list of directories of projects to org-agenda from 
projectile.


My question is: how can I rename the category of the TODOs listed in the 
agenda from "README.org" to the directory name containing the file of 
the TODOs (which in my setup would also identify the parent project)?


Thanks,

Giacomo




Re: [O] running a source code by name

2018-05-30 Thread Julian M. Burgos
Thanks guys.  A combination of org-babel-goto-named-src-block and
org-babel-execute-src-block did the trick.

I am building an org template to create html presentations using the R
package xaringan.  In my case each slide is a markdown source block.
The elisp block tangles everything into a Rmd file, and the R block runs
rmarkdown::render and opens the resulting html file in a browser.

Thanks again. :)

Berry, Charles writes:

> OK, I have to note that this will also do the job that the OP requested:
>
> #+begin_src emacs-lisp :results silent :var result=myRcode
>
> #+end_src
>
> although it seems a little strange to write an empty src block for its side 
> effects.
>
> I suppose I should have suggested this in the first place:
>
> #+begin_src emacs-lisp :results silent :noweb yes
> <>
> #+end_src
>
> although the return value from the noweb reference could be troublesome 
> depending on what else is included in the latter src block.
>
> Chuck
>
>> On May 28, 2018, at 1:16 PM, John Kitchin  wrote:
>>
>> Here is yet another variation, that may be suitable for what you want:
>>
>>
>> #+name: myPyCode
>> #+BEGIN_SRC python
>> print('Hello')
>> #+END_SRC
>>
>>
>> #+BEGIN_SRC emacs-lisp :var results=myPyCode
>> results
>> #+END_SRC
>>
>> #+RESULTS:
>> : Hello
>>
>>
>> John
>>
>> ---
>> Professor John Kitchin
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkitchingroup.cheme.cmu.edu=02%7C01%7C%7Cfdaa27b411604ed32a0108d5c4d9fa01%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636631362846470731=4K%2B96NBf5KPaoz13laaAR0%2FaqY2FlefTLy%2BPXy6YtO8%3D=0
>>
>>
>> On Mon, May 28, 2018 at 9:25 AM, Berry, Charles  wrote:
>>
>>
>> > On May 28, 2018, at 7:35 AM, Eric S Fraga  wrote:
>> >
>> > On Monday, 28 May 2018 at 11:13, Julian M. Burgos wrote:
>> >> Dear list,
>> >>
>> >> I have an org file with an R source code block.  I want to have a second
>> >> code block with an elisp call to run that first code.  Something like this
>> >>
>> >>
>> >> #+begin_src emacs-lisp :results silent :tangle no
>> >>
>> >> ... Some elisp code to run the "myRcode" block.
>> >
>> > Something along the lines of:
>> >
>> >(org-babel-goto-named-src-block "myRcode")
>> >(org-babel-execute-src-block)
>> >
>> > should do the job?
>>
>> Maybe wrap it in
>>
>> (save-excursion ... )
>>
>> or use
>>
>> (org-sbe "myRcode")
>>
>> or
>>
>> (org-babel-ref-resolve "myRcode")
>>
>> which both can also pass :var args.
>>
>> HTH,
>>
>> Chuck
>>
>>
>>
>>
>>


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is



[O] running a source code by name

2018-05-28 Thread Julian M. Burgos
Dear list,

I have an org file with an R source code block.  I want to have a second
code block with an elisp call to run that first code.  Something like this



#+begin_src emacs-lisp :results silent :tangle no

... Some elisp code to run the "myRcode" block.

#+end_src


#+NAME: myRcode
#+beg in_src R :results silent :tangle no

... My R code here

#+end_src

What would be the best way to do it?

Many thanks,

Julian


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is



Re: [O] Problem with python source block

2018-05-26 Thread 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.
> 



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Re: [O] Problem with python source block

2018-05-26 Thread 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

2018-05-26 Thread 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.


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[O] Problem with python source block

2018-05-25 Thread 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
]]


[O] starting a line with #

2018-01-17 Thread Ali M.
What does starting a line or item with # mean to org-mode

for example

* list item one
* list item two
  # some stuff I wrote that

Notice that the line starting with # is indented under the second list item
I can notice that the line starting with # have a different color
but does it have a different meaning now to org-mode

I personally use this to add comments in my file and comment related to the
parent item list
its like am telling myself, this is a note a comment, it is not part of the
list

But what does starting lines with # mean for org-mode

Thanks
Ali


[O] Uninstall bbdb

2018-01-11 Thread M. P.
How do I uninstall bbdb?



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

2018-01-09 Thread 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

2018-01-08 Thread 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
> 
> 
> 
> 
> 
> 



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

2018-01-08 Thread 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







[O] Org agenda

2018-01-06 Thread M. P.
I create a TODO and save the file but I can’t see the todo when I select todo 
view in agenda? What am I doing wrong?


[O] Org Usenet

2018-01-03 Thread M. P.
Is their an org mode usenet group?



[O] TODO in org-mode

2017-12-30 Thread M. P.
I know this is basic but I am having difficulty getting TODO states to work. In 
ORG I select new heading than TODO from the menu but I don’t understand how to 
save this  so that it works with things like agenda view?


Re: [O] Can export the files with bibliography only to LaTeX

2017-12-14 Thread Julian M. Burgos
I do not think there is an out-of-the-box way to export a bibliography
directly from org-mode to formats other than LaTex.  What I usually do
is export to Tex and then use Pandoc (https://pandoc.org/) to convert that 
document to other
formats, usually Word so I can share my work with my colleagues.  Pandoc
can read the bibtex file and add the right citations, doing something
like this:

pandoc --bibliography /path/to/my_bib_file.bib my_document.docx my_document.tex

There is also the ox-pandoc package, that allows you to export directly
from org using pandoc.  I have not tried yet (it is in my to-do list).

https://github.com/kawabata/ox-pandoc

Julian

Melleus writes:

> I used to think that I can export from org to bunch of different
> formats. But all of a sudden when I need this feature I see that I can
> export only to LaTeX. But when I try exporting to other format I get
>
> Wrong type argument: stringp, nil   error message.
>
> When there's no bibtex references or exporting to LaTeX everything just
> works.
>
> How can I troubleshoot the situation and possibly find the clue? I
> couldn't find any documentation on the exporting references issues on
> Worg unfortunately.
>
> My environment: Gentoo with stable keyword, Emacs 25.3.1, Org 9.1.4.
>
> Thanks ahead of time.


--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is



Re: [O] bug report: + is not escaped in org-link-escape

2017-12-10 Thread D M German


Nicolas Goaziou twisted the bytes to say:

 Nicolas> Hello,
 Nicolas> dmg <d...@turingmachine.org> writes:

 >> org-link-escape only replaces space, [, ], and %
 >> 
 >> but search in google/gmail is replacing + also.
 >> 
 >> The simplest solution is to add 43 to org-link-escape-chars:
 >> 
 >> org-link-escape-chars is a variable defined in ‘org.el’.
 >> Its value is (32 91 93 37)
 >> 
 >> This variable may be risky if used as a file-local variable.

 Nicolas> `org-link-escape' is for internal links, not for general URL-encoding.
 Nicolas> You may want to use `url-encode-url' instead.

this indeed addresses the issue I was having.

thank you very much for your response.


--daniel



--
Daniel M. German  "It is useless to punish a man
   unless he knows why he is punished...
   Punishment must be unusual
   R. Heinlein ->  or it serves no purpose."
http://turingmachine.org/
http://silvernegative.com/
dmg (at) uvic (dot) ca
replace (at) with @ and (dot) with .




[O] Confused about org-duration-format

2017-12-04 Thread Julian M. Burgos
Dear list,

I do not quite follow how to set up org-duration-format.  In particular,
I would like to have my clock tables represented as decimal hours (e.g.
3.50 h, rather than 3:30 h).

Any help would be welcomed.

Julian

--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is



[O] org-clock-in only in current buffer

2017-10-09 Thread Julian M. Burgos
Dear org-moders,

Until a recent update (or an unintended change in my configuration), I
was able to clock in a task (org-clock-in) *without* org mode trying to
find open clocks.  I cannot figure out what changed, but now
org-clock-in opens all my agenda buffers searching for open clocks, which is 
not very convenient as I have dozens of agenda files.
What would be the best way to a) restrict the search of open clocks to
the current buffer, or b) turn off the search of open clocks?

Many thanks

Julian

--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian.bur...@hafogvatn.is



[O] Donating money to mobile org.

2017-07-02 Thread M. P.
Hello If I want to donate specifically to mobile org what would I do?



Re: [O] exporting org to docx

2017-06-28 Thread 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

2017-06-27 Thread 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] After Gmane shutdown: how can I read/write to the org-mode mailing list online

2017-06-27 Thread M

@ Uwe Brauer: 
I was using the gmane web page to read and reply to this mailing list and if
I try to open the link from the org-mode website
http://news.gmane.org/gmane.emacs.orgmode , I get "Page not found".

@Eric:
does MUA mean mail software (mail user agent)?!
At home, I'm using my mail sofware (currently Entourage on MacOS X) to
read/reply to the group.

If I'm away from home, I can only use the web page of my mail provider to
read/reply to the list, but as my mail account is limited in the number of
emails which can be stored, I'm deleting mails on the mail server regularly
and don't have access to all the mail history, if I'm not at home.

That's, why it was nice to be able to read and post online on a web page
without having to log in to a private mail account.

Kind regards

Martin 


> Von: Eric S Fraga 
> Organisation: On the Interweb somewhere
> Antworten an: Eric S Fraga 
> Datum: Tue, 27 Jun 2017 15:15:56 +0100
> An: 
> Betreff: Re: [O] After Gmane shutdown: how can I read/write to the org-mode
> mailing list online
> 
> On Tuesday, 27 Jun 2017 at 12:56, Uwe Brauer wrote:
>> Ooh, what makes you say gmane was shut down? right now I am using gmane
>> to read this message and to reply.
> 
> I think the OP means a web interface to gmane which I think no longer
> exists?  I assume you are using an MUA to access gmane lists?
> -- 
> : Eric S Fraga via Emacs 26.0.50, Org release_9.0.9-551-g92e8c8





Re: [O] Replace macros on tangle

2017-06-27 Thread Giacomo M

Dear Nicolas and Chuck,

thanks for pointing me in the right direction. I never thought that 
macros were actually just an export feature, and that noweb replacements 
could be used as macros!


I am experiencing a little quirk though. Since I often edit this org 
file under Windows, the tangled files have Windows new lines, and 
(cygwin or any) bash doesn't like it. So I added a 
org-babel-post-tangle-hook that set-buffer-file-coding-system to unix. 
But the scripts that I tangle with a noweb ref end up with a weird ^M 
after each end of line. It seems this happens after the post-tangle 
hook. How could I take care of those ^M?


Thanks a lot,

Giacomo


Il 6/26/2017 7:06 PM, Charles C. Berry ha scritto:

On Mon, 26 Jun 2017, Nicolas Goaziou wrote:


Hello,

Giacomo M <jackja...@gmail.com> writes:


Dear all,
how can I add macro replacement support when a source block is being
tangled?


I don't think so. Macro replacement is an export feature.


If Giacomo's macros operate outside of src blocks, he could export 
using `org-org-export-to-org', then tangle the resulting file.


Giacomo, if you want something to operate inside of src blocks you can 
use noweb replacements that execute code as outlined in


(info "(org) Noweb reference syntax")

In a way these are like macros.

HTH,

Chuck





[O] Replace macros on tangle

2017-06-26 Thread Giacomo M

Dear all,
how can I add macro replacement support when a source block is being 
tangled?

Thanks,
Giacomo



Re: [O] exporting org to docx

2017-06-24 Thread 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

2017-06-24 Thread 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-o

Re: [O] Controlling new line characters during tangle

2017-06-22 Thread Giacomo M

  
  
Ok, rudimentary elisp knowledge seems to help here:
#+BEGIN_SRC emacs-lisp
  (defun jack/dos2unix-post-tangle-hook ()
    (set-buffer-file-coding-system 'unix 't)
    (save-buffer)
    )
  (add-hook 'org-babel-post-tangle-hook
  'jack/dos2unix-post-tangle-hook)
  #+END_SRC

Thanks,

Giacomo

Il 6/21/2017 1:02 PM, Kaushal Modi ha
  scritto:


  
On Wed, Jun 21, 2017, 5:21 AM Giacomo M <jackja...@gmail.com>
  wrote:

Hi all,
  
  I'm using emacs also under Windows, and would need to tangle
  scripts/config files to be used under Unix.
  
  
  
  
 Is there
  any header argument
  to enforce the desired new line characters in the tangled
  files?

  
  
  
  At which point would you like to enforce the new line
characters?
  
  
  Can you post a MWE and explain what that it tangles to vs
what you'd actually like to see in the tangled file?
  


  
  -- 
  
  
Kaushal Modi
  


  




Re: [O] Controlling new line characters during tangle

2017-06-21 Thread Giacomo M
Dear Kashual,

1. I visit a (Unix EOL[1]) org file on Windows.
2. I write a shell script in a shell source block to be tangled.
3. I tangle it.
4. As a result, I get a (Windows EOL) shell script, while I would like a
Unix EOL shell script.

Thanks,

Giacomo

[1] End Of Line convention

On Jun 21, 2017 13:02, "Kaushal Modi" <kaushal.m...@gmail.com> wrote:

> On Wed, Jun 21, 2017, 5:21 AM Giacomo M <jackja...@gmail.com> wrote:
>
>> Hi all,
>>
>> I'm using emacs also under Windows, and would need to tangle
>> scripts/config files to be used under Unix.
>
>
> Is there any header argument
>> to enforce the desired new line characters in the tangled files?
>>
>
> At which point would you like to enforce the new line characters?
>
> Can you post a MWE and explain what that it tangles to vs what you'd
> actually like to see in the tangled file?
>
>> --
>
> Kaushal Modi
>


[O] Controlling new line characters during tangle

2017-06-21 Thread Giacomo M

Hi all,

I'm using emacs also under Windows, and would need to tangle 
scripts/config files to be used under Unix. Is there any header argument 
to enforce the desired new line characters in the tangled files?


Thanks,

Giacomo




Re: [O] How do you organize a project and its related sub-tasks

2017-06-20 Thread Giacomo M
Does anybody have thoughts on using a PROJECT todo keyword (in a different
sequence set from the TODO NEXT one)?

On Jun 20, 2017 4:35 AM, "Samuel Wales"  wrote:

> i have long thought it would be useful to dim entries in the agenda
> that are ancestors of entries in the same agenda view.  regardless of
> sort order.  similar to dim blocked.
>
> --
> The Kafka Pandemic: 
>
> The disease DOES progress. MANY people have died from it. And ANYBODY
> can get it at any time.
>
> "You’ve really gotta quit this and get moving, because this is murder
> by neglect." ---
>  being-murdered-by-neglect>.
>
>


Re: [O] org to static site?

2017-06-01 Thread Julian M. Burgos
Hi Matt,

Recently I started to use Hugo to maintain our project's website:

http://novasarc.hafogvatn.is/

I am liking it very much. I keep the entire site in a single file, with
each page in a single subtree. Modifications to the template are also
kept in subtrees.  I edit this page directly, rather than using the hugo
tools to create content.  Then to update the site I tangle the org file
to create all the htlm files of the site, and run hugo to create the
site files that are then copied to the server.  Pretty easy.

Julian


Matt Price writes:

> I'm trying to wean myself off of Wordpress for next year's teaching
> websites, and am wondering what solutions other people are using for
> turning a collection of org pages and/or subtrees into a static html site.
> I am leaning towards Hugo but honestly not for any sensible reason; I've
> seen other people use Jekyll, though the fact that Github doesn't support
> direct conversion from org-mode removes some of Jekyll's appeal; and I know
> there are a number of other solutions too.
>
> So, I would love to hear what you all recommend.
>
> Thanks,
> Matt


--
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



Re: [O] Viewing pdf images

2017-04-12 Thread 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 <edua...@mercovich.net> 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

2017-04-09 Thread 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 <edua...@mercovich.net> 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

2017-04-06 Thread Julian M. Burgos
So if I have an org file with links to pdfs, your function will convert
those pdfs to images and also will replace the link to the pdf for the
link to the newly created png?

Kaushal Modi writes:

> On Wed, Apr 5, 2017, 5:21 AM Julian M. Burgos <julian.bur...@hafogvatn.is>
> wrote:
>
>> Can you clarify the purpose of this function?  I understand that
>> produces an image of each pdf linked to the file.
>
>
> That's correct, but the user can control when that happens by adding that
> function to the appropriate hook.
>
>  But
>
> the question in
>> emacs.stackexchange was about displaying pdf's as inline images.
>
>
> Yes, I forgot to change the hook when I updated the whole answer; I have
> fixed that now. Now the answer shows how to add this function to the
> before-save-hook.
>
>  Your
>
> function only converts the pdfs into images (and you have to do an
>> export to achieve that).
>
>
> Well, the function org-include-img-from-pdf is the workhorse here, and it
> doesn't depend on when you want the PDF to PNG conversion to happen. The
> "when" depends on the hook you add the function to.
>
>   You would still would have to add a link to
>> the image file in order to see it as an inline image.
>> add a link in order to see it, correct?
>>
>
> I didn't follow that. The user is already adding that. Example:
>
> # ()convertfrompdf:t
> # User needs to have a ./foo.pdf. That will be converted to the below
> referenced foo.png.
> [[./foo.png]]
>
> When I get to a computer, I'll confirm if the #+CAPTION: and/or #+NAME: is
> needed for the inline images to show. Above works fine for exports, so I
> assumed that the inline images should show fine too.


--
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



Re: [O] Viewing pdf images

2017-04-05 Thread Julian M. Burgos
Can you clarify the purpose of this function?  I understand that
produces an image of each pdf linked to the file.  But the question in
emacs.stackexchange was about displaying pdf's as inline images.  Your
function only converts the pdfs into images (and you have to do an
export to achieve that).  You would still would have to add a link to
the image file in order to see it as an inline image.
add a link in order to see it, correct?


Kaushal Modi writes:

> In case you are interested, I have now updated the solution on
> emacs.stackexchange to not use #+HEADER for this purpose:
> http://emacs.stackexchange.com/a/401/115
>
> Earlier discussion on that:
> http://lists.gnu.org/archive/html/emacs-orgmode/2017-01/msg00260.html
>
> The solution still does the exact same thing as before.
>
> On Tue, Mar 21, 2017 at 8:37 PM Doyley, Marvin M. <m.doy...@rochester.edu>
> wrote:
>
>> 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 <+354%20575%202037>
>> > Bréfsími/Telefax:  +354-5752001 <+354%20575%202001>
>> > Netfang/Email: julian.bur...@hafogvatn.is
>>
>> --
>
> Kaushal Modi


--
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



[O] Bug: save-some-buffers saves org-edit-special buffers to separate files

2017-03-27 Thread Julian M. Burgos
Hello all,

This has been reported before, and as I understood was fixed.

http://www.mail-archive.com/emacs-orgmode@gnu.org/msg111340.html

But I am still having the same problem using org mode 9.0.5 in emacs
25.1.1.

Julian

--
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



Re: [O] Viewing pdf images

2017-03-21 Thread 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

2017-03-21 Thread Julian M. Burgos
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



Re: [O] Viewing pdf images

2017-03-17 Thread 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

2017-03-17 Thread 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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[O] org-ref and the minibuffer

2017-03-14 Thread Julian M. Burgos
Dear list,

It is possible to customize the information shown in the minibuffer when
the cursor (or the mouse pointer) is on top of an org-ref bibliography link?
The default seems to be a formatted version of the citation, which
includes authors (all of them), title, etc.  I would like just to see
the title.
Thanks!

Julian

--
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



Re: [O] New markup for revising manuscripts

2017-03-13 Thread 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

2017-03-13 Thread 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

2017-03-11 Thread 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

2017-03-11 Thread 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

2017-03-11 Thread 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

2017-03-11 Thread 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

2017-03-10 Thread 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

2017-03-10 Thread 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] Problems with displaying inline images

2017-03-10 Thread Julian M. Burgos
Do'oh! It wasn't an org-mode issue.  The figures where bitmaps and I did not
have bmp in the image-file-name-extensions variables.  Sorry for the
noise!


Julian M. Burgos writes:

> Thanks Eric. I did read the description, and my link do not have any
> associated text.  It is something else. If I evaluate (print
> image-types) I get the following:
>
> (imagemagick png gif tiff jpeg xpm xbm pbm postscript).  And if I
> evaluate for example (image-type-available-p 'jpeg) I get "t".  But if I 
> evaluate (print image-library-alist), I get nil.  I think I am supposed to 
> get the
> libraries used by emacs to display the images, correct?  Do I need to
> populate this list by hand?
>
> Thanks again,
>
> Julian
>
>
> Eric S Fraga writes:
>
>> On Thursday,  9 Mar 2017 at 14:25, Julian M. Burgos wrote:
>>> Dear list,
>>>
>>> I cannot get org-mode to display inline images.  Instead, when doing M-x
>>> org-toggle-inline-images I get a "No images to display inline".  But if
>>> I click on the image link, the image appears in a new buffer with no 
>>> problems.
>>
>> Read the description of the org-display-inline-images command, which
>> org-toggle-inline-images uses.  If your link has associated text,
>> i.e. [[file:image][some text]], you will need to invoke either command
>> with C-u as, by default, only those messages with no descriptive text
>> will be displayed as they are not considered "inline".


--
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



Re: [O] Problems with displaying inline images

2017-03-10 Thread Julian M. Burgos
Thanks Eric. I did read the description, and my link do not have any
associated text.  It is something else. If I evaluate (print
image-types) I get the following:

(imagemagick png gif tiff jpeg xpm xbm pbm postscript).  And if I
evaluate for example (image-type-available-p 'jpeg) I get "t".  But if I 
evaluate (print image-library-alist), I get nil.  I think I am supposed to get 
the
libraries used by emacs to display the images, correct?  Do I need to
populate this list by hand?

Thanks again,

Julian


Eric S Fraga writes:

> On Thursday,  9 Mar 2017 at 14:25, Julian M. Burgos wrote:
>> Dear list,
>>
>> I cannot get org-mode to display inline images.  Instead, when doing M-x
>> org-toggle-inline-images I get a "No images to display inline".  But if
>> I click on the image link, the image appears in a new buffer with no 
>> problems.
>
> Read the description of the org-display-inline-images command, which
> org-toggle-inline-images uses.  If your link has associated text,
> i.e. [[file:image][some text]], you will need to invoke either command
> with C-u as, by default, only those messages with no descriptive text
> will be displayed as they are not considered "inline".


--
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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