Re: [O] Let's discuss citation and Org syntax

2014-01-08 Thread Joseph Vidal-Rosset
2014/1/8 Eric S Fraga e.fr...@ucl.ac.uk

 It would help if you showed us how bibtex2html fails.  It works for
 me.  A small org file example which illustrates what you want to do
 would also help.  What version of org are you using?


Many thanks Eric, it works now for me also.  The only thing that I do not
succeed to get , it a bibliographical reference in plain style with
postnote like this one for example:

Descartes [1, pp. 224-225] blablabla


* Références

[1] Descartes, Oeuvres complètes, La Pléiade,  Paris, 1973.

End of example.

It does not work because references [[cite:key][postnote]] do not accept
spaces in html.

Therefore I have adopted this less eye-candy format: ([1], pp. 224-225)
 ... It's DIY ...

Best wishes, and thanks again,

Jo.


Re: [O] Let's discuss citation and Org syntax

2014-01-04 Thread Joseph Vidal-Rosset
Dear John,

Thanks for your efforts to help me. I have good news.

2014/1/3 John Hendy jw.he...@gmail.com

 Can you post:
 - Minimal .org file


Here is a minimal-paper.org

#+OPTIONS: LaTeX:verbatim
#+LaTeX_CLASS: article
#+LaTeX_CLASS_OPTIONS: [a4paper,twoside,twocolumn]
#+LaTeX_CLASS_OPTIONS: [captions=tableheading]
#+LATEX_HEADER: \usepackage[AUTO]{inputenc}
#+LATEX_HEADER: \usepackage{fitch}
#+LATEX_HEADER: \usepackage{bussproofs}
#+LaTeX_CLASS: article
#+TITLE:Minimal reference
#+AUTHOR: Max IMIN
#+BEGIN_abstract
 Mini test
#+END_abstract
#+OPTIONS: tex:imagemagick
* First section

Tennant [[cite:tennant96]] wrote :

#+BEGIN_QUOTE
quotation of Tennnant's paper...
#+END_QUOTE

#+BIBLIOGRAPHY: minimal-bibliography plain option:-a

 - Reproducible .emacs with what you currently have setup to get things
 working


I do not know if this list accept the attachment, but I know that in
general, attachments are not welcome. So here is the minimal set up of org
in my minimal init.el (I do not reproduce here what concerns bitex,
biblatex, latex and reftex in this email):

;; org-mode
(add-to-list 'load-path ~/.emacs.d/elpa/org-20131230)
;;répertoire contrib : org-plus-contrib
(add-to-list 'load-path ~/.emacs.d/elpa/org-plus-contrib-20131230/)

(add-to-list 'auto-mode-alist '(\\.org\\' . org-mode))

(global-set-key \C-cl 'org-store-link)
 (global-set-key \C-cc 'org-capture)
 (global-set-key \C-ca 'org-agenda)
 (global-set-key \C-cb 'org-iswitchb)

(require 'org)
(require 'ob-latex)
(require 'ox-latex)
(require 'org-mime)
(require 'ox-html)
(require 'ox-ascii)
(require 'ox-org)
(require 'ox-bibtex)


  - The matching minimal bibliography file


Here is my minimal-bibliography.bib:

@Article{tennant96,
  author =  {Tennant, N.},
  title =  {{The Law of Excluded Middle is Synthetic A Priori, if Valid}},
  journal =  {Philosophical Topics},
  year =  1996,
  number =  24,
  pages =  {241-266}
}


 - Perhaps the output you want (in LaTeX or whatever output language)



I am happy to tell you that the export works in latex as well as in html !
Thanks to all !

Now just details , how to converts correctly the latex syntax : \cite[p.
1]{key} ? , and how is it possible to use easily reftex ? I do not succeed
to find ebib very convenient.

Again, many many thanks !

Jo.


Re: [O] Let's discuss citation and Org syntax

2014-01-04 Thread John Hendy
On Jan 4, 2014 4:17 AM, Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com
wrote:

 Dear John,

 Thanks for your efforts to help me. I have good news.

 2014/1/3 John Hendy jw.he...@gmail.com

 Can you post:
 - Minimal .org file


 Here is a minimal-paper.org

 #+OPTIONS: LaTeX:verbatim
 #+LaTeX_CLASS: article
 #+LaTeX_CLASS_OPTIONS: [a4paper,twoside,twocolumn]
 #+LaTeX_CLASS_OPTIONS: [captions=tableheading]
 #+LATEX_HEADER: \usepackage[AUTO]{inputenc}
 #+LATEX_HEADER: \usepackage{fitch}
 #+LATEX_HEADER: \usepackage{bussproofs}
 #+LaTeX_CLASS: article
 #+TITLE:Minimal reference
 #+AUTHOR: Max IMIN
 #+BEGIN_abstract
  Mini test
 #+END_abstract
 #+OPTIONS: tex:imagemagick
 * First section

 Tennant [[cite:tennant96]] wrote :

 #+BEGIN_QUOTE
 quotation of Tennnant's paper...
 #+END_QUOTE

 #+BIBLIOGRAPHY: minimal-bibliography plain option:-a

 - Reproducible .emacs with what you currently have setup to get things
working


 I do not know if this list accept the attachment, but I know that in
general, attachments are not welcome. So here is the minimal set up of org
in my minimal init.el (I do not reproduce here what concerns bitex,
biblatex, latex and reftex in this email):

 ;; org-mode
 (add-to-list 'load-path ~/.emacs.d/elpa/org-20131230)
 ;;répertoire contrib : org-plus-contrib
 (add-to-list 'load-path ~/.emacs.d/elpa/org-plus-contrib-20131230/)

 (add-to-list 'auto-mode-alist '(\\.org\\' . org-mode))

 (global-set-key \C-cl 'org-store-link)
  (global-set-key \C-cc 'org-capture)
  (global-set-key \C-ca 'org-agenda)
  (global-set-key \C-cb 'org-iswitchb)

 (require 'org)
 (require 'ob-latex)
 (require 'ox-latex)
 (require 'org-mime)
 (require 'ox-html)
 (require 'ox-ascii)
 (require 'ox-org)
 (require 'ox-bibtex)


 - The matching minimal bibliography file


 Here is my minimal-bibliography.bib:

 @Article{tennant96,
   author = {Tennant, N.},
   title = {{The Law of Excluded Middle is Synthetic A Priori, if Valid}},
   journal = {Philosophical Topics},
   year = 1996,
   number = 24,
   pages = {241-266}
 }


 - Perhaps the output you want (in LaTeX or whatever output language)



 I am happy to tell you that the export works in latex as well as in html
! Thanks to all !


A lovely post that will hopefully help many others down the road! Thanks
for obliging :)

Glad you got it working,
John

 Now just details , how to converts correctly the latex syntax : \cite[p.
1]{key} ? , and how is it possible to use easily reftex ? I do not succeed
to find ebib very convenient.

 Again, many many thanks !

 Jo.





Re: [O] Let's discuss citation and Org syntax

2014-01-03 Thread Joseph Vidal-Rosset
Hi,

Is there somewhere a documentation with a simple helpful example to follow
from step to step in order to use ox-bibtex or bibeltex ? I got only a
message error : bibtex2html failed and I do not understand why.

Reading this page, for example,
http://bowenli37.wordpress.com/tag/org-exp-bibtex/
I understand that I must add #+LINK ..

But nothing works...

Thanks in advance for your help

Jo.



2014/1/2 Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com

 Great ! Many thanks Eric.  I see also that I have to forget gmail in order
 to definitely adopt gnus ! :)

 I will be back on the list to say thank you again , to all of you.

 Best wishes,

 Jo.


 2014/1/2 Eric Schulte schulte.e...@gmail.com

 Take a look at ox-bibtex.el in contrib [1], which adds support for
 bibtex citations.  The commentary at the top of that file explains the
 usage, but in brief, ox-bibtex adds cite: links which will export to
 HTML, ASCII and LaTeX (using bibtex2html [2] for HTML export, and pandoc
 [3] for ASCII export).

 For example, I've used ox-bibtex to write this Org file [4], which
 exports to this HTML [5], as well as LaTeX.

 Best,

 Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes:

  Hi Rasmus, hi the list,
 
  Reading this thread I've understood that the question of html export of
  biblatex citations is still an open problem for org-mode developers,
 right
  ?
 
  Thanks to the online manual and the help of the list, I have succeeded
 to
  write a template of koma-article class which is correctly exported both
 in
  latex and in html. But I meet the problem of exporting  into html
 footnotes
  and references.
 
  At the moment, what is the best i.e. the more convenient solution?
 
  My best wishes for this new year,
 
  Jo.
 
 
  2013/5/21 Rasmus ras...@gmx.us
 
  Hi,
 
  Now that 8.0 has shipped let's talk bibliography support.  This
  follows directly upon the discussion around March[1].
 
  The essence of the thread was that some people agreed that it would be
  nice to have support for citation commands build into Org (I'll
  summarize in the next post).  But let me first restate my own take on
  the issue.  IMO a nice format would be:
 
  (*)   [KEYWORD PROPERTIES]
 
  I think we should allow for a more general approach than one just for
  citation and this is a good thing (IMO).
 
  The in-buffer display of (*) could be governed by
  org-buffer-format-KEYWORD (similar to
  gnus-user-format-function-LETTER) or just identity if no function is
  defined.  Export could be handled by org-BACKEND-KEYWORD or
  org-export-KEYWORD.  With officially recognized KEYWORDs something
  like citation could be a 'first-class citizen'.  PROPERTIES could be a
  string like:
 
optional-keyless-entry :prop1 one :prop2 two ...
 
  Perhaps, treatment of keyword, could even be handled by an
  in-buffer Org Babel function in the spirit of e.g. reproducible
  research (see below).
 
  This would be different from Org links in that (*) is more like a
  functions that allows for (i) pretty and informative display in
  buffer/export and (ii) easy user extension.
 
  I think there are many compelling use-cases for such a framework.
 
  1. Citation: Take the keyword citetext which should be an 'official'
 KEYWORD.  So for instance we could have
 
   [citetext BIBTEX-KEY :prenote note, w/comma :postnote blah].
 
 In buffers, via org-in-buffer-format-citetext, it would be
 displayed as
 
   BIBTEX-KEY (note, w/comma, YEAR, blah)
 
 or something similar (depending to what extend bibtex.el would be
 leveraged; e.g. BIBTEX-KEY might show the author/editor key and
 YEAR would also depend on parsing a bibtex file) (obviouesly,
 there's some reference to a bibtex file somewhere).  In LaTeX it
 would be exported as
 
   \citetext[note,w/comma][blah]{BIBTEX-KEY}
 
 In html it might utilize some tool that understand bibtex (there's
 a link to such a tool in the next post).  In ASCII it could almost
 use what would be displayed in the buffer.
 
  2. MY-FUN: MY-FUN is some function that does something with some
 properties, perhaps just a string (simple cases: [sc text] is used
 for small caps, or mayhaps [my-treat-dna-string DNA-STRING]).  I
 might use it in a single file that I want to send to people or I
 might just use it in my notes.  Currently it's implemented via
 org-emphasis-alist or as a link.  Changing emphases is a hacks, and
 they are hard to export with the now more robust Org syntax and
 further permit little control over how they are displayed
 in-buffer.  Links are more flexible but lacks display control and
 becomes somewhat painful with many arguments[2].  Also, MY-FUN
 doesn't take a 'description'.  With (*) I could simply write
 
   [MY-FUN PROPERTIES].
 
 Perhaps, I could even define org-BACKEND-MY-FUN in a babel block
 if it's only relevant to the current file.
 
  There's been some work and some discussion on 

Re: [O] Let's discuss citation and Org syntax

2014-01-03 Thread John Hendy
On Fri, Jan 3, 2014 at 12:32 PM, Joseph Vidal-Rosset
joseph.vidal.ros...@gmail.com wrote:
 Hi,

 Is there somewhere a documentation with a simple helpful example to follow
 from step to step in order to use ox-bibtex or bibeltex ? I got only a
 message error : bibtex2html failed and I do not understand why.

 Reading this page, for example,
 http://bowenli37.wordpress.com/tag/org-exp-bibtex/
 I understand that I must add #+LINK ..

 But nothing works...


I think you need to post a minimal example with everything required.
For those of us who have never used bibtex (me), it's not clear what
you're trying to do and we (at least I) can't help. For example,
googling orgmode bibtex produces links which don't seem to do the
same thing, from my skimming:
- 
http://tex.stackexchange.com/questions/114864/how-to-get-bibtex-to-work-with-org-mode-latex-export
- http://lists.gnu.org/archive/html/emacs-orgmode/2013-05/msg00791.html
- http://orgmode.org/worg/org-api/org-bibtex-api.html
- http://blog.karssen.org/2013/08/22/using-bibtex-from-org-mode/
- 
http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/

For example, only one of those (that I noted), mentions anything about
#+LINK, so I'm thinking that what you are trying to do must be a
subset of everything embodied by Orgmode and bibtex since some
fairly complete other posts get by without mentioning using #+LINK.

Can you post:
- Minimal .org file
- Reproducible .emacs with what you currently have setup to get things working
- The matching minimal bibliography file
- Perhaps the output you want (in LaTeX or whatever output language)

Apologies if the above is self-explanatory and I'm playing the
un-needed role of mailing list police. I've noticed a lot of questions
recently without sufficient detail. Always posting with clear goals,
files so others can reproduce, and example output you want saves
others having to fill in the blanks.

You'll also get a lot more help since those generous with their time
can easily copy and paste some code into their own local Emacs setups
and see if it works. That helps differentiate setup issues from syntax
issues from usage issues, etc.



John

P.S. Also post what you actually *have* tried. This saves others
having to re-try what you tried, since no one knows that but nothing
works means concretely. There's a blog post link with a bunch of
stuff in it, followed by but nothing works. What, exactly, from that
blog post did you try (as in, paste the code from the various
categories above -- org file, .emacs, bib file -- for each thing
attempted)?




 Thanks in advance for your help

 Jo.



 2014/1/2 Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com

 Great ! Many thanks Eric.  I see also that I have to forget gmail in order
 to definitely adopt gnus ! :)

 I will be back on the list to say thank you again , to all of you.

 Best wishes,

 Jo.


 2014/1/2 Eric Schulte schulte.e...@gmail.com

 Take a look at ox-bibtex.el in contrib [1], which adds support for
 bibtex citations.  The commentary at the top of that file explains the
 usage, but in brief, ox-bibtex adds cite: links which will export to
 HTML, ASCII and LaTeX (using bibtex2html [2] for HTML export, and pandoc
 [3] for ASCII export).

 For example, I've used ox-bibtex to write this Org file [4], which
 exports to this HTML [5], as well as LaTeX.

 Best,

 Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes:

  Hi Rasmus, hi the list,
 
  Reading this thread I've understood that the question of html export of
  biblatex citations is still an open problem for org-mode developers,
  right
  ?
 
  Thanks to the online manual and the help of the list, I have succeeded
  to
  write a template of koma-article class which is correctly exported both
  in
  latex and in html. But I meet the problem of exporting  into html
  footnotes
  and references.
 
  At the moment, what is the best i.e. the more convenient solution?
 
  My best wishes for this new year,
 
  Jo.
 
 
  2013/5/21 Rasmus ras...@gmx.us
 
  Hi,
 
  Now that 8.0 has shipped let's talk bibliography support.  This
  follows directly upon the discussion around March[1].
 
  The essence of the thread was that some people agreed that it would be
  nice to have support for citation commands build into Org (I'll
  summarize in the next post).  But let me first restate my own take on
  the issue.  IMO a nice format would be:
 
  (*)   [KEYWORD PROPERTIES]
 
  I think we should allow for a more general approach than one just for
  citation and this is a good thing (IMO).
 
  The in-buffer display of (*) could be governed by
  org-buffer-format-KEYWORD (similar to
  gnus-user-format-function-LETTER) or just identity if no function is
  defined.  Export could be handled by org-BACKEND-KEYWORD or
  org-export-KEYWORD.  With officially recognized KEYWORDs something
  like citation could be a 'first-class citizen'.  PROPERTIES could be a
  string like:
 
optional-keyless-entry 

Re: [O] Let's discuss citation and Org syntax

2014-01-03 Thread Joseph Vidal-Rosset
Hi John, hi everyone,

Here are the headers of my org-file:

#+OPTIONS: LaTeX:verbatim
#+LaTeX_CLASS: koma-article
#+LaTeX_CLASS_OPTIONS: [a4paper,twoside,twocolumn]
#+LaTeX_CLASS_OPTIONS: [captions=tableheading]
#+LATEX_HEADER: \usepackage[AUTO]{inputenc}
#+LATEX_HEADER: \usepackage{fitch}
#+LATEX_HEADER: \usepackage{bussproofs}
#+LaTeX_CLASS: koma-article
#+LANGUAGE:  en
#+LaTeX_HEADER: \usepackage[backend=biber,style=verbose]{biblatex}
#+LaTeX_HEADER: \bibliography{jvr-biblatex-references.bib}
#+LaTeX_HEADER: \usepackage{bussproofs}
#+LaTeX_HEADER: \usepackage{fitch}
#+LaTeX_HEADER: \usepackage{hyperref}
#+OPTIONS: tex:imagemagick
#+TITLE: a title
#+AUTHOR: Joseph Vidal-Rosset


I have a couple of questions:

1) Does biblatex works with ox-bibtex.el   ? I suppose that it does not but
I can switch to bibtex.

2) I do not know the headers that I have exactly to add in this file.

Best wishes,

Jo.


2014/1/3 John Hendy jw.he...@gmail.com

 On Fri, Jan 3, 2014 at 12:32 PM, Joseph Vidal-Rosset
 joseph.vidal.ros...@gmail.com wrote:
  Hi,
 
  Is there somewhere a documentation with a simple helpful example to
 follow
  from step to step in order to use ox-bibtex or bibeltex ? I got only a
  message error : bibtex2html failed and I do not understand why.
 
  Reading this page, for example,
  http://bowenli37.wordpress.com/tag/org-exp-bibtex/
  I understand that I must add #+LINK ..
 
  But nothing works...


 I think you need to post a minimal example with everything required.
 For those of us who have never used bibtex (me), it's not clear what
 you're trying to do and we (at least I) can't help. For example,
 googling orgmode bibtex produces links which don't seem to do the
 same thing, from my skimming:
 -
 http://tex.stackexchange.com/questions/114864/how-to-get-bibtex-to-work-with-org-mode-latex-export
 - http://lists.gnu.org/archive/html/emacs-orgmode/2013-05/msg00791.html
 - http://orgmode.org/worg/org-api/org-bibtex-api.html
 - http://blog.karssen.org/2013/08/22/using-bibtex-from-org-mode/
 -
 http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/

 For example, only one of those (that I noted), mentions anything about
 #+LINK, so I'm thinking that what you are trying to do must be a
 subset of everything embodied by Orgmode and bibtex since some
 fairly complete other posts get by without mentioning using #+LINK.

 Can you post:
 - Minimal .org file
 - Reproducible .emacs with what you currently have setup to get things
 working
 - The matching minimal bibliography file
 - Perhaps the output you want (in LaTeX or whatever output language)

 Apologies if the above is self-explanatory and I'm playing the
 un-needed role of mailing list police. I've noticed a lot of questions
 recently without sufficient detail. Always posting with clear goals,
 files so others can reproduce, and example output you want saves
 others having to fill in the blanks.

 You'll also get a lot more help since those generous with their time
 can easily copy and paste some code into their own local Emacs setups
 and see if it works. That helps differentiate setup issues from syntax
 issues from usage issues, etc.



 John

 P.S. Also post what you actually *have* tried. This saves others
 having to re-try what you tried, since no one knows that but nothing
 works means concretely. There's a blog post link with a bunch of
 stuff in it, followed by but nothing works. What, exactly, from that
 blog post did you try (as in, paste the code from the various
 categories above -- org file, .emacs, bib file -- for each thing
 attempted)?



 
  Thanks in advance for your help
 
  Jo.
 
 
 
  2014/1/2 Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com
 
  Great ! Many thanks Eric.  I see also that I have to forget gmail in
 order
  to definitely adopt gnus ! :)
 
  I will be back on the list to say thank you again , to all of you.
 
  Best wishes,
 
  Jo.
 
 
  2014/1/2 Eric Schulte schulte.e...@gmail.com
 
  Take a look at ox-bibtex.el in contrib [1], which adds support for
  bibtex citations.  The commentary at the top of that file explains the
  usage, but in brief, ox-bibtex adds cite: links which will export to
  HTML, ASCII and LaTeX (using bibtex2html [2] for HTML export, and
 pandoc
  [3] for ASCII export).
 
  For example, I've used ox-bibtex to write this Org file [4], which
  exports to this HTML [5], as well as LaTeX.
 
  Best,
 
  Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes:
 
   Hi Rasmus, hi the list,
  
   Reading this thread I've understood that the question of html export
 of
   biblatex citations is still an open problem for org-mode developers,
   right
   ?
  
   Thanks to the online manual and the help of the list, I have
 succeeded
   to
   write a template of koma-article class which is correctly exported
 both
   in
   latex and in html. But I meet the problem of exporting  into html
   footnotes
   and references.
  
   At the moment, what is the best i.e. 

Re: [O] Let's discuss citation and Org syntax

2014-01-03 Thread Joseph Vidal-Rosset
2014/1/3 John Hendy jw.he...@gmail.com

 it's not clear what
 you're trying to do


I have forgotten to say that I'm trying to get via org-mode export,
references in latex as well as in html. In latex there is no problem (via
bibtex or biblatex either), but for html export , bibtex2html fails and I
suppose that I have to add some line in the preamble of my file.

Best wishes,

Jo.


Re: [O] Let's discuss citation and Org syntax

2014-01-03 Thread John Hendy
On Fri, Jan 3, 2014 at 2:27 PM, Joseph Vidal-Rosset
joseph.vidal.ros...@gmail.com wrote:
 Hi John, hi everyone,

 Here are the headers of my org-file:

 #+OPTIONS: LaTeX:verbatim
 #+LaTeX_CLASS: koma-article
 #+LaTeX_CLASS_OPTIONS: [a4paper,twoside,twocolumn]
 #+LaTeX_CLASS_OPTIONS: [captions=tableheading]
 #+LATEX_HEADER: \usepackage[AUTO]{inputenc}
 #+LATEX_HEADER: \usepackage{fitch}
 #+LATEX_HEADER: \usepackage{bussproofs}
 #+LaTeX_CLASS: koma-article
 #+LANGUAGE:  en
 #+LaTeX_HEADER: \usepackage[backend=biber,style=verbose]{biblatex}
 #+LaTeX_HEADER: \bibliography{jvr-biblatex-references.bib}
 #+LaTeX_HEADER: \usepackage{bussproofs}
 #+LaTeX_HEADER: \usepackage{fitch}
 #+LaTeX_HEADER: \usepackage{hyperref}
 #+OPTIONS: tex:imagemagick
 #+TITLE: a title
 #+AUTHOR: Joseph Vidal-Rosset


 I have a couple of questions:

 1) Does biblatex works with ox-bibtex.el   ? I suppose that it does not but
 I can switch to bibtex.

 2) I do not know the headers that I have exactly to add in this file.


Not to be redundant, but I still think what I posted below will be
quite helpful before we get ahead of ourselves:

#+begin_quote

Can you post:
- Minimal .org file
- Reproducible .emacs with what you currently have setup to get things working
- The matching minimal bibliography file
- Perhaps the output you want (in LaTeX or whatever output language)

#+end_quote

- Minimal .org as in only the headers you need to make this work, no
fancy options or custom classes. Just bare-bones what needs to be
there to verify bibtex functionality.
- Some text in the .org file that tries to call a bib entry.
- A minimal .bib file with a single matching entry you try to call
from the org file
- The output file you hope Org is able to tangle together from you
from the .org and .bib files.


John

 Best wishes,

 Jo.


 2014/1/3 John Hendy jw.he...@gmail.com

 On Fri, Jan 3, 2014 at 12:32 PM, Joseph Vidal-Rosset
 joseph.vidal.ros...@gmail.com wrote:
  Hi,
 
  Is there somewhere a documentation with a simple helpful example to
  follow
  from step to step in order to use ox-bibtex or bibeltex ? I got only a
  message error : bibtex2html failed and I do not understand why.
 
  Reading this page, for example,
  http://bowenli37.wordpress.com/tag/org-exp-bibtex/
  I understand that I must add #+LINK ..
 
  But nothing works...


 I think you need to post a minimal example with everything required.
 For those of us who have never used bibtex (me), it's not clear what
 you're trying to do and we (at least I) can't help. For example,
 googling orgmode bibtex produces links which don't seem to do the
 same thing, from my skimming:
 -
 http://tex.stackexchange.com/questions/114864/how-to-get-bibtex-to-work-with-org-mode-latex-export
 - http://lists.gnu.org/archive/html/emacs-orgmode/2013-05/msg00791.html
 - http://orgmode.org/worg/org-api/org-bibtex-api.html
 - http://blog.karssen.org/2013/08/22/using-bibtex-from-org-mode/
 -
 http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/

 For example, only one of those (that I noted), mentions anything about
 #+LINK, so I'm thinking that what you are trying to do must be a
 subset of everything embodied by Orgmode and bibtex since some
 fairly complete other posts get by without mentioning using #+LINK.

 Can you post:
 - Minimal .org file
 - Reproducible .emacs with what you currently have setup to get things
 working
 - The matching minimal bibliography file
 - Perhaps the output you want (in LaTeX or whatever output language)

 Apologies if the above is self-explanatory and I'm playing the
 un-needed role of mailing list police. I've noticed a lot of questions
 recently without sufficient detail. Always posting with clear goals,
 files so others can reproduce, and example output you want saves
 others having to fill in the blanks.

 You'll also get a lot more help since those generous with their time
 can easily copy and paste some code into their own local Emacs setups
 and see if it works. That helps differentiate setup issues from syntax
 issues from usage issues, etc.



 John

 P.S. Also post what you actually *have* tried. This saves others
 having to re-try what you tried, since no one knows that but nothing
 works means concretely. There's a blog post link with a bunch of
 stuff in it, followed by but nothing works. What, exactly, from that
 blog post did you try (as in, paste the code from the various
 categories above -- org file, .emacs, bib file -- for each thing
 attempted)?



 
  Thanks in advance for your help
 
  Jo.
 
 
 
  2014/1/2 Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com
 
  Great ! Many thanks Eric.  I see also that I have to forget gmail in
  order
  to definitely adopt gnus ! :)
 
  I will be back on the list to say thank you again , to all of you.
 
  Best wishes,
 
  Jo.
 
 
  2014/1/2 Eric Schulte schulte.e...@gmail.com
 
  Take a look at ox-bibtex.el in contrib [1], which adds support for
  bibtex citations.  The 

Re: [O] Let's discuss citation and Org syntax

2014-01-02 Thread Joseph Vidal-Rosset
Hi Rasmus, hi the list,

Reading this thread I've understood that the question of html export of
biblatex citations is still an open problem for org-mode developers, right
?

Thanks to the online manual and the help of the list, I have succeeded to
write a template of koma-article class which is correctly exported both in
latex and in html. But I meet the problem of exporting  into html footnotes
and references.

At the moment, what is the best i.e. the more convenient solution?

My best wishes for this new year,

Jo.


2013/5/21 Rasmus ras...@gmx.us

 Hi,

 Now that 8.0 has shipped let's talk bibliography support.  This
 follows directly upon the discussion around March[1].

 The essence of the thread was that some people agreed that it would be
 nice to have support for citation commands build into Org (I'll
 summarize in the next post).  But let me first restate my own take on
 the issue.  IMO a nice format would be:

 (*)   [KEYWORD PROPERTIES]

 I think we should allow for a more general approach than one just for
 citation and this is a good thing (IMO).

 The in-buffer display of (*) could be governed by
 org-buffer-format-KEYWORD (similar to
 gnus-user-format-function-LETTER) or just identity if no function is
 defined.  Export could be handled by org-BACKEND-KEYWORD or
 org-export-KEYWORD.  With officially recognized KEYWORDs something
 like citation could be a 'first-class citizen'.  PROPERTIES could be a
 string like:

   optional-keyless-entry :prop1 one :prop2 two ...

 Perhaps, treatment of keyword, could even be handled by an
 in-buffer Org Babel function in the spirit of e.g. reproducible
 research (see below).

 This would be different from Org links in that (*) is more like a
 functions that allows for (i) pretty and informative display in
 buffer/export and (ii) easy user extension.

 I think there are many compelling use-cases for such a framework.

 1. Citation: Take the keyword citetext which should be an 'official'
KEYWORD.  So for instance we could have

  [citetext BIBTEX-KEY :prenote note, w/comma :postnote blah].

In buffers, via org-in-buffer-format-citetext, it would be
displayed as

  BIBTEX-KEY (note, w/comma, YEAR, blah)

or something similar (depending to what extend bibtex.el would be
leveraged; e.g. BIBTEX-KEY might show the author/editor key and
YEAR would also depend on parsing a bibtex file) (obviouesly,
there's some reference to a bibtex file somewhere).  In LaTeX it
would be exported as

  \citetext[note,w/comma][blah]{BIBTEX-KEY}

In html it might utilize some tool that understand bibtex (there's
a link to such a tool in the next post).  In ASCII it could almost
use what would be displayed in the buffer.

 2. MY-FUN: MY-FUN is some function that does something with some
properties, perhaps just a string (simple cases: [sc text] is used
for small caps, or mayhaps [my-treat-dna-string DNA-STRING]).  I
might use it in a single file that I want to send to people or I
might just use it in my notes.  Currently it's implemented via
org-emphasis-alist or as a link.  Changing emphases is a hacks, and
they are hard to export with the now more robust Org syntax and
further permit little control over how they are displayed
in-buffer.  Links are more flexible but lacks display control and
becomes somewhat painful with many arguments[2].  Also, MY-FUN
doesn't take a 'description'.  With (*) I could simply write

  [MY-FUN PROPERTIES].

Perhaps, I could even define org-BACKEND-MY-FUN in a babel block
if it's only relevant to the current file.

 There's been some work and some discussion on this already, most
 notably Aaron already supplied some patches towards this end[3],
 but using a slightly different syntax more like the link syntax;
 e.g. textcite above would look like

   [[textcite:bibtex-keypre%3Dfoopost%3Dbar][whatever]]

 where whatever is ignored.  The state of the discussion is to some
 extend summarized in the next post.

 It would love to hear whether other people find something like this to
 be a good idea?  Would anyone find a use such a framework?  Would (*)
 conflict with anyone's current usage of Org?  Is (*) too ambitious and
 in terms of getting citation support?  Is this is taking a musket to
 kill a butterfly?  What are the the flaws in the above.

 I'm not a good (lisp) programmer, but I think I have a month off this
 summer where I could work on something like the above.

 Thanks for reading,
 Rasmus

 Footnotes:
 [1] http://mid.gmane.org/20130303070635.GA12112%40panahar
 [2] my citation links often look like postnote;prenote without
 showing the BIBTEX-KEY or citation format.
 [2] here http://mid.gmane.org/87lia0s7wi.fsf%40bzg.ath.cx
 and here http://mid.gmane.org/87wqthk7vj.fsf%40gmail.com.


 --
 When in doubt, do it!





Re: [O] Let's discuss citation and Org syntax

2014-01-02 Thread Rüdiger Sonderfeld
On Thursday 02 January 2014 09:08:44 Joseph Vidal-Rosset wrote:
 At the moment, what is the best i.e. the more convenient solution?

A while ago I started writing BibTeX support for org-mode.  It's still in a 
rather early stage and I didn't have the time to continue working on it.  It 
basically generates org-mode syntax for \cite entries/bib files and thus 
should work in all exporters.

https://github.com/ruediger/bibeltex

Regards
Rüdiger




Re: [O] Let's discuss citation and Org syntax

2014-01-02 Thread Eric Schulte
Take a look at ox-bibtex.el in contrib [1], which adds support for
bibtex citations.  The commentary at the top of that file explains the
usage, but in brief, ox-bibtex adds cite: links which will export to
HTML, ASCII and LaTeX (using bibtex2html [2] for HTML export, and pandoc
[3] for ASCII export).

For example, I've used ox-bibtex to write this Org file [4], which
exports to this HTML [5], as well as LaTeX.

Best,

Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes:

 Hi Rasmus, hi the list,

 Reading this thread I've understood that the question of html export of
 biblatex citations is still an open problem for org-mode developers, right
 ?

 Thanks to the online manual and the help of the list, I have succeeded to
 write a template of koma-article class which is correctly exported both in
 latex and in html. But I meet the problem of exporting  into html footnotes
 and references.

 At the moment, what is the best i.e. the more convenient solution?

 My best wishes for this new year,

 Jo.


 2013/5/21 Rasmus ras...@gmx.us

 Hi,

 Now that 8.0 has shipped let's talk bibliography support.  This
 follows directly upon the discussion around March[1].

 The essence of the thread was that some people agreed that it would be
 nice to have support for citation commands build into Org (I'll
 summarize in the next post).  But let me first restate my own take on
 the issue.  IMO a nice format would be:

 (*)   [KEYWORD PROPERTIES]

 I think we should allow for a more general approach than one just for
 citation and this is a good thing (IMO).

 The in-buffer display of (*) could be governed by
 org-buffer-format-KEYWORD (similar to
 gnus-user-format-function-LETTER) or just identity if no function is
 defined.  Export could be handled by org-BACKEND-KEYWORD or
 org-export-KEYWORD.  With officially recognized KEYWORDs something
 like citation could be a 'first-class citizen'.  PROPERTIES could be a
 string like:

   optional-keyless-entry :prop1 one :prop2 two ...

 Perhaps, treatment of keyword, could even be handled by an
 in-buffer Org Babel function in the spirit of e.g. reproducible
 research (see below).

 This would be different from Org links in that (*) is more like a
 functions that allows for (i) pretty and informative display in
 buffer/export and (ii) easy user extension.

 I think there are many compelling use-cases for such a framework.

 1. Citation: Take the keyword citetext which should be an 'official'
KEYWORD.  So for instance we could have

  [citetext BIBTEX-KEY :prenote note, w/comma :postnote blah].

In buffers, via org-in-buffer-format-citetext, it would be
displayed as

  BIBTEX-KEY (note, w/comma, YEAR, blah)

or something similar (depending to what extend bibtex.el would be
leveraged; e.g. BIBTEX-KEY might show the author/editor key and
YEAR would also depend on parsing a bibtex file) (obviouesly,
there's some reference to a bibtex file somewhere).  In LaTeX it
would be exported as

  \citetext[note,w/comma][blah]{BIBTEX-KEY}

In html it might utilize some tool that understand bibtex (there's
a link to such a tool in the next post).  In ASCII it could almost
use what would be displayed in the buffer.

 2. MY-FUN: MY-FUN is some function that does something with some
properties, perhaps just a string (simple cases: [sc text] is used
for small caps, or mayhaps [my-treat-dna-string DNA-STRING]).  I
might use it in a single file that I want to send to people or I
might just use it in my notes.  Currently it's implemented via
org-emphasis-alist or as a link.  Changing emphases is a hacks, and
they are hard to export with the now more robust Org syntax and
further permit little control over how they are displayed
in-buffer.  Links are more flexible but lacks display control and
becomes somewhat painful with many arguments[2].  Also, MY-FUN
doesn't take a 'description'.  With (*) I could simply write

  [MY-FUN PROPERTIES].

Perhaps, I could even define org-BACKEND-MY-FUN in a babel block
if it's only relevant to the current file.

 There's been some work and some discussion on this already, most
 notably Aaron already supplied some patches towards this end[3],
 but using a slightly different syntax more like the link syntax;
 e.g. textcite above would look like

   [[textcite:bibtex-keypre%3Dfoopost%3Dbar][whatever]]

 where whatever is ignored.  The state of the discussion is to some
 extend summarized in the next post.

 It would love to hear whether other people find something like this to
 be a good idea?  Would anyone find a use such a framework?  Would (*)
 conflict with anyone's current usage of Org?  Is (*) too ambitious and
 in terms of getting citation support?  Is this is taking a musket to
 kill a butterfly?  What are the the flaws in the above.

 I'm not a good (lisp) programmer, but I think I have a month off this
 summer where I could work on something like the 

Re: [O] Let's discuss citation and Org syntax

2014-01-02 Thread Joseph Vidal-Rosset
Great ! Many thanks Eric.  I see also that I have to forget gmail in order
to definitely adopt gnus ! :)

I will be back on the list to say thank you again , to all of you.

Best wishes,

Jo.


2014/1/2 Eric Schulte schulte.e...@gmail.com

 Take a look at ox-bibtex.el in contrib [1], which adds support for
 bibtex citations.  The commentary at the top of that file explains the
 usage, but in brief, ox-bibtex adds cite: links which will export to
 HTML, ASCII and LaTeX (using bibtex2html [2] for HTML export, and pandoc
 [3] for ASCII export).

 For example, I've used ox-bibtex to write this Org file [4], which
 exports to this HTML [5], as well as LaTeX.

 Best,

 Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes:

  Hi Rasmus, hi the list,
 
  Reading this thread I've understood that the question of html export of
  biblatex citations is still an open problem for org-mode developers,
 right
  ?
 
  Thanks to the online manual and the help of the list, I have succeeded to
  write a template of koma-article class which is correctly exported both
 in
  latex and in html. But I meet the problem of exporting  into html
 footnotes
  and references.
 
  At the moment, what is the best i.e. the more convenient solution?
 
  My best wishes for this new year,
 
  Jo.
 
 
  2013/5/21 Rasmus ras...@gmx.us
 
  Hi,
 
  Now that 8.0 has shipped let's talk bibliography support.  This
  follows directly upon the discussion around March[1].
 
  The essence of the thread was that some people agreed that it would be
  nice to have support for citation commands build into Org (I'll
  summarize in the next post).  But let me first restate my own take on
  the issue.  IMO a nice format would be:
 
  (*)   [KEYWORD PROPERTIES]
 
  I think we should allow for a more general approach than one just for
  citation and this is a good thing (IMO).
 
  The in-buffer display of (*) could be governed by
  org-buffer-format-KEYWORD (similar to
  gnus-user-format-function-LETTER) or just identity if no function is
  defined.  Export could be handled by org-BACKEND-KEYWORD or
  org-export-KEYWORD.  With officially recognized KEYWORDs something
  like citation could be a 'first-class citizen'.  PROPERTIES could be a
  string like:
 
optional-keyless-entry :prop1 one :prop2 two ...
 
  Perhaps, treatment of keyword, could even be handled by an
  in-buffer Org Babel function in the spirit of e.g. reproducible
  research (see below).
 
  This would be different from Org links in that (*) is more like a
  functions that allows for (i) pretty and informative display in
  buffer/export and (ii) easy user extension.
 
  I think there are many compelling use-cases for such a framework.
 
  1. Citation: Take the keyword citetext which should be an 'official'
 KEYWORD.  So for instance we could have
 
   [citetext BIBTEX-KEY :prenote note, w/comma :postnote blah].
 
 In buffers, via org-in-buffer-format-citetext, it would be
 displayed as
 
   BIBTEX-KEY (note, w/comma, YEAR, blah)
 
 or something similar (depending to what extend bibtex.el would be
 leveraged; e.g. BIBTEX-KEY might show the author/editor key and
 YEAR would also depend on parsing a bibtex file) (obviouesly,
 there's some reference to a bibtex file somewhere).  In LaTeX it
 would be exported as
 
   \citetext[note,w/comma][blah]{BIBTEX-KEY}
 
 In html it might utilize some tool that understand bibtex (there's
 a link to such a tool in the next post).  In ASCII it could almost
 use what would be displayed in the buffer.
 
  2. MY-FUN: MY-FUN is some function that does something with some
 properties, perhaps just a string (simple cases: [sc text] is used
 for small caps, or mayhaps [my-treat-dna-string DNA-STRING]).  I
 might use it in a single file that I want to send to people or I
 might just use it in my notes.  Currently it's implemented via
 org-emphasis-alist or as a link.  Changing emphases is a hacks, and
 they are hard to export with the now more robust Org syntax and
 further permit little control over how they are displayed
 in-buffer.  Links are more flexible but lacks display control and
 becomes somewhat painful with many arguments[2].  Also, MY-FUN
 doesn't take a 'description'.  With (*) I could simply write
 
   [MY-FUN PROPERTIES].
 
 Perhaps, I could even define org-BACKEND-MY-FUN in a babel block
 if it's only relevant to the current file.
 
  There's been some work and some discussion on this already, most
  notably Aaron already supplied some patches towards this end[3],
  but using a slightly different syntax more like the link syntax;
  e.g. textcite above would look like
 
[[textcite:bibtex-keypre%3Dfoopost%3Dbar][whatever]]
 
  where whatever is ignored.  The state of the discussion is to some
  extend summarized in the next post.
 
  It would love to hear whether other people find something like this to
  be a good idea?  Would anyone 

Re: [O] Let's discuss citation and Org syntax

2013-06-27 Thread Christian Wittern
Sorry about this late contribution to this thread.  I just stumbled on the 
RTF/ODF scan tool for Zotero at[1], which seems to do something similar to 
the ideas ventilated in this thread.  Since Zotero compatibility is high on 
the list of desirables mentioned here, I thought it might be an interisting 
point of reference.


This page also mentions that Zotero can be told to provide a scannable 
Cite as output format, which works with things like

|{See | Smith, (2012) |p. 45 | for an example |zu:2433:WQVBH98K}

which the format engine than turns into
|
(See Smith, 2012, p. 45 for an example)

I wonder if it would be worthwhile if the citation handling in Org would 
become compatible with this approach?


Christian W.

[1] http://zotero-odf-scan.github.io/zotero-odf-scan/


On 2013-05-26 23:23, Darlan Cavalcante Moreira wrote:

I prefer the [cite:citekey] syntax similar to [fn:number] for footnotes.

But no matter which syntax is chosen I think we can easily make reftex work
with it. All we need is to set the variable reftex-cite-format [1] to a
string with the desired format. For the syntax [cite:citekey] the string
would be [cite:%l].

[1] We probably need to make that a local variable in org-mode buffers so
 that the global value is kept on default for latex buffers.

--
Darlan

 
At Thu, 23 May 2013 10:05:37 +0200,

Christian Moe wrote:


Matt Price writes:

On Wed, May 22, 2013 at 5:02 AM, Christian Moe m...@christianmoe.com wrote:

I have a rough, working example of this enabling Zotero cites for ODT
export (attached).

Hi Christian,

I'm really interested in this, as I use Zotero not only for writing
but for group bibliographies in my  courses.  The broader conversation
about the appropriate syntax is a bit beyond me,

Hi, Matt,

As the org-zotero-export.el shows, getting Zotero references from Org
into ODT is pretty simple. That framework could be implemented whatever
syntax we end up with to take care of the details. I'm interested in
feedback on the syntax, though -- that is, on the way I'm using the
description part of the link to convey various bits of information to
Zotero. Is it worth pursuing, or would people prefer other ways of
doing it? If worth pursuing, could it be improved?


(1) How do you get the Zotero cite keys right now, and what method do
you think would ultimately be the best to try for?

The best to try for: Something with as brilliant an interface as RefTex...

Since this thread is on citation syntax, I think I'll gather my thoughts
about how to get there (zotero-plain? Zotero Server API? sqlite? word
processor plugin emulation?), and about your other questions, and start
another Zotero-related thread in a day or two.

Right now: I'm still depending on Quick Copy with a custom Zotero
translator. That is, I tab from Emacs to Firefox, look up a reference in
the Zotero pane, and Quick Copy (C-S-c) to a formatted link to the
clipboard. Tab back to Emacs, yank the link, manually tweak the
description as necessary. RefTex it ain't, and it's cumbersome for
multiple citations, but it works.


Yours,
Christian







--
Christian Wittern, Kyoto




Re: [O] Let's discuss citation and Org syntax

2013-05-26 Thread Darlan Cavalcante Moreira

I prefer the [cite:citekey] syntax similar to [fn:number] for footnotes.

But no matter which syntax is chosen I think we can easily make reftex work
with it. All we need is to set the variable reftex-cite-format [1] to a
string with the desired format. For the syntax [cite:citekey] the string
would be [cite:%l].

[1] We probably need to make that a local variable in org-mode buffers so
that the global value is kept on default for latex buffers.

--
Darlan


At Thu, 23 May 2013 10:05:37 +0200,
Christian Moe wrote:
 
 
 Matt Price writes:
  On Wed, May 22, 2013 at 5:02 AM, Christian Moe m...@christianmoe.com 
  wrote:
 
  I have a rough, working example of this enabling Zotero cites for ODT
  export (attached).
 
  Hi Christian,
 
  I'm really interested in this, as I use Zotero not only for writing
  but for group bibliographies in my  courses.  The broader conversation
  about the appropriate syntax is a bit beyond me,
 
 Hi, Matt,
 
 As the org-zotero-export.el shows, getting Zotero references from Org
 into ODT is pretty simple. That framework could be implemented whatever
 syntax we end up with to take care of the details. I'm interested in
 feedback on the syntax, though -- that is, on the way I'm using the
 description part of the link to convey various bits of information to
 Zotero. Is it worth pursuing, or would people prefer other ways of
 doing it? If worth pursuing, could it be improved?
 
  (1) How do you get the Zotero cite keys right now, and what method do
  you think would ultimately be the best to try for?
 
 The best to try for: Something with as brilliant an interface as RefTex...
 
 Since this thread is on citation syntax, I think I'll gather my thoughts
 about how to get there (zotero-plain? Zotero Server API? sqlite? word
 processor plugin emulation?), and about your other questions, and start
 another Zotero-related thread in a day or two.
 
 Right now: I'm still depending on Quick Copy with a custom Zotero
 translator. That is, I tab from Emacs to Firefox, look up a reference in
 the Zotero pane, and Quick Copy (C-S-c) to a formatted link to the
 clipboard. Tab back to Emacs, yank the link, manually tweak the
 description as necessary. RefTex it ain't, and it's cumbersome for
 multiple citations, but it works.
 
 
 Yours,
 Christian
 
 



Re: [O] Let's discuss citation and Org syntax

2013-05-26 Thread Christian Moe



Darlan Cavalcante Moreira writes:

 I prefer the [cite:citekey] syntax similar to [fn:number] for footnotes.

 But no matter which syntax is chosen I think we can easily make reftex work
 with it. All we need is to set the variable reftex-cite-format [1] to a
 string with the desired format. For the syntax [cite:citekey] the string
 would be [cite:%l].

Yes, for bibtex. But to clarify, Matt Price and I got on the subject of
using Zotero as both the source database and the reference-formatting
engine for exported documents, with Org in the middle.

Reftex can be used for that as well, e.g. by synching the Zotero db to a
bibtex file with Zotero db keys as citekeys. There are other options,
with different pros and cons. (And I'll start a thread on that soon as
my day job stops interfering with my night life again.)

Yours,
Christian



Re: [O] Let's discuss citation and Org syntax

2013-05-23 Thread Christian Moe

Matt Price writes:
 On Wed, May 22, 2013 at 5:02 AM, Christian Moe m...@christianmoe.com wrote:

 I have a rough, working example of this enabling Zotero cites for ODT
 export (attached).

 Hi Christian,

 I'm really interested in this, as I use Zotero not only for writing
 but for group bibliographies in my  courses.  The broader conversation
 about the appropriate syntax is a bit beyond me,

Hi, Matt,

As the org-zotero-export.el shows, getting Zotero references from Org
into ODT is pretty simple. That framework could be implemented whatever
syntax we end up with to take care of the details. I'm interested in
feedback on the syntax, though -- that is, on the way I'm using the
description part of the link to convey various bits of information to
Zotero. Is it worth pursuing, or would people prefer other ways of
doing it? If worth pursuing, could it be improved?

 (1) How do you get the Zotero cite keys right now, and what method do
 you think would ultimately be the best to try for?

The best to try for: Something with as brilliant an interface as RefTex...

Since this thread is on citation syntax, I think I'll gather my thoughts
about how to get there (zotero-plain? Zotero Server API? sqlite? word
processor plugin emulation?), and about your other questions, and start
another Zotero-related thread in a day or two.

Right now: I'm still depending on Quick Copy with a custom Zotero
translator. That is, I tab from Emacs to Firefox, look up a reference in
the Zotero pane, and Quick Copy (C-S-c) to a formatted link to the
clipboard. Tab back to Emacs, yank the link, manually tweak the
description as necessary. RefTex it ain't, and it's cumbersome for
multiple citations, but it works.


Yours,
Christian




Re: [O] Let's discuss citation and Org syntax

2013-05-22 Thread Christian Moe

Hi,

I'd be cool with a dedicated citation syntax, or using a
yet-to-be-introduced extensible syntax for citations. 

But link syntax does make sense to me -- after all, citations do point
to things. And unlike one of the opinions you cited, I think link
descriptions *are* meaningful in citations, and can be made more
meaningful yet (code attached).

First, with links, you can have an easily human-readable reference in
the description, and the link keyword and citekey tucked away, e.g. as
you note:

  [[cite:jones-etal-2000][Jones et al., 2000]]

That makes for a better authoring experience when revising your document
months or years later. Sure, Bibtex users usually keep their citekeys
mnemonic. However, there are alternatives to Bibtex, and people will
increasingly be keying their references to very non-mnemonic DOIs,
Zotero IDs or other database keys, etc.

But second, and more interesting: 

Parsing the description part as meaningful would also let us think
outside the latex box and handle things like page numbers and post-notes
a bit more intuitively. The following is an example of thinking like latex:

So, a possible extension of that could, for instance,
use a third pair of [] as in
  [[cite:jones-etal-2000][Jones et al., 
 2000][[citationcommand][prenote][postnote]]]
 ^^^  ^^
 key   displayed in org

Why should the prenote go nearly at the end? Do we really to add a
citation command? (Or define a bunch of different link types, one for
each citation command, as in Thomas S. Dye's excellent setup?) And do we
need all those brackets anyway?

My preference would be to write something like:

  [[cite:jones2000][(see further: Jones et al., 2000: p.18)]]

and  use a simple algorithm and a smidgen of extra processing power to
make sense of different human-meaningful forms of description, so that
e.g.:

  [[cite:jones2000][(2000: p.17)]] becomes a \citeyear
  [[cite:jones2000][Jones, 2000]] without round parens becomes a \citet

etc.

I have a rough, working example of this enabling Zotero cites for ODT
export (attached). I've been meaning to polish it up as a contributed
module for Zotero users, but if there's interest in a unified citation
syntax along these lines, I could rewrite it to work for Bibtex as well.

Yours,
Christian Moe



org-zotero-export.el
Description: application/emacs-lisp


Re: [O] Let's discuss citation and Org syntax

2013-05-22 Thread Matt Price
On Wed, May 22, 2013 at 5:02 AM, Christian Moe m...@christianmoe.com wrote:

 I have a rough, working example of this enabling Zotero cites for ODT
 export (attached). I've been meaning to polish it up as a contributed
 module for Zotero users, but if there's interest in a unified citation
 syntax along these lines, I could rewrite it to work for Bibtex as well.

Hi Christian,

I'm really interested in this, as I use Zotero not only for writing
but for group bibliographies in my  courses.  The broader conversation
about the appropriate syntax is a bit beyond me, but I do have a
couple of questions about your work with Zotero:

(1) How do you get the Zotero cite keys right now, and what method do
you think would ultimately be the best to try for?  Since zotero now
operates as a service, I would think it should be possible to write an
emacs plugin that communicates directly to Zotero the way that the
word/libreoffice plugin does (though I don't know how to do that stuff
myself).

(2) How might you generalize the export to other formats, esp. HTML?
I imagine the best thing to do would be to use citeproc.js  set the
citation format using a variable, e.g.

#+ ZOTERO-FORMAT: Chicago

The option to do this would be great e.g. for people (like me) who use
org to compose blog posts, then process through the html export (in my
case via org2blog).

(3) Have you seen Erik Hetzner's zotero-plain,
https://bitbucket.org/egh/zotero-plain ?  Would it be useful to your
work? I see Erik is already involved in this thread, do you have any
comments Erik?

Thank you for this!

Matt

 Yours,
 Christian Moe




Re: [O] Let's discuss citation and Org syntax

2013-05-22 Thread Matt Lundin
Marcin Borkowski mb...@wmi.amu.edu.pl writes:
 I do not use Org-mode for authoring (I'm quite happy with LaTeX itself
 for that), and in LaTeX, I use neither bibtex nor biblatex; but AFAIK,
 bibtex is basically dead like John Cleese's parrot.  I don't even think
 that it needs to or should be supported; the faster bibtex usage fades
 away, the better.

As a point of clarification, bibtex syntax and bib files remain alive
and well (albeit with modifications) for those who use biblatex.

 What I would suggest is to look into amsrefs manual.  The amsrefs
 package was (is?) an interesting attempt at a /pure LaTeX/ solution to
 the bibliography problem, not dependent on any executable other than
 LaTeX.  It is not capable of sorting bibliographies, but other than
 that is quite powerful (much more than bibtex, though seemingly less
 than biblatex).  What is interesting here is its \ycite and \ocite
 commands (see
 http://mirrors.ctan.org/macros/latex/contrib/amsrefs/amsrdoc.pdf); it
 might be a good idea to support something similar.  (I'm not sure
 whether biblatex supports such a thing.)

Most biblatex backends have multiple versions of cite commands. I use
biblatex-chicago, which provides, among others, \autocite, \fullcite,
\citetitle, \footfullcite, \headlesscite, \headlessfullcite, \shortcite.

Best,
Matt



[O] Let's discuss citation and Org syntax

2013-05-21 Thread Rasmus
Hi, 

Now that 8.0 has shipped let's talk bibliography support.  This
follows directly upon the discussion around March[1].

The essence of the thread was that some people agreed that it would be
nice to have support for citation commands build into Org (I'll
summarize in the next post).  But let me first restate my own take on
the issue.  IMO a nice format would be:

(*)   [KEYWORD PROPERTIES]

I think we should allow for a more general approach than one just for
citation and this is a good thing (IMO).

The in-buffer display of (*) could be governed by
org-buffer-format-KEYWORD (similar to
gnus-user-format-function-LETTER) or just identity if no function is
defined.  Export could be handled by org-BACKEND-KEYWORD or
org-export-KEYWORD.  With officially recognized KEYWORDs something
like citation could be a 'first-class citizen'.  PROPERTIES could be a
string like:

  optional-keyless-entry :prop1 one :prop2 two ... 

Perhaps, treatment of keyword, could even be handled by an
in-buffer Org Babel function in the spirit of e.g. reproducible
research (see below).

This would be different from Org links in that (*) is more like a
functions that allows for (i) pretty and informative display in
buffer/export and (ii) easy user extension.

I think there are many compelling use-cases for such a framework.

1. Citation: Take the keyword citetext which should be an 'official'
   KEYWORD.  So for instance we could have

 [citetext BIBTEX-KEY :prenote note, w/comma :postnote blah].

   In buffers, via org-in-buffer-format-citetext, it would be
   displayed as
   
 BIBTEX-KEY (note, w/comma, YEAR, blah)
   
   or something similar (depending to what extend bibtex.el would be
   leveraged; e.g. BIBTEX-KEY might show the author/editor key and
   YEAR would also depend on parsing a bibtex file) (obviouesly,
   there's some reference to a bibtex file somewhere).  In LaTeX it
   would be exported as
   
 \citetext[note,w/comma][blah]{BIBTEX-KEY}
   
   In html it might utilize some tool that understand bibtex (there's
   a link to such a tool in the next post).  In ASCII it could almost
   use what would be displayed in the buffer.

2. MY-FUN: MY-FUN is some function that does something with some
   properties, perhaps just a string (simple cases: [sc text] is used
   for small caps, or mayhaps [my-treat-dna-string DNA-STRING]).  I
   might use it in a single file that I want to send to people or I
   might just use it in my notes.  Currently it's implemented via
   org-emphasis-alist or as a link.  Changing emphases is a hacks, and
   they are hard to export with the now more robust Org syntax and
   further permit little control over how they are displayed
   in-buffer.  Links are more flexible but lacks display control and
   becomes somewhat painful with many arguments[2].  Also, MY-FUN
   doesn't take a 'description'.  With (*) I could simply write
   
 [MY-FUN PROPERTIES].
   
   Perhaps, I could even define org-BACKEND-MY-FUN in a babel block
   if it's only relevant to the current file.

There's been some work and some discussion on this already, most
notably Aaron already supplied some patches towards this end[3],
but using a slightly different syntax more like the link syntax;
e.g. textcite above would look like

  [[textcite:bibtex-keypre%3Dfoopost%3Dbar][whatever]]

where whatever is ignored.  The state of the discussion is to some
extend summarized in the next post.
  
It would love to hear whether other people find something like this to
be a good idea?  Would anyone find a use such a framework?  Would (*)
conflict with anyone's current usage of Org?  Is (*) too ambitious and
in terms of getting citation support?  Is this is taking a musket to
kill a butterfly?  What are the the flaws in the above.

I'm not a good (lisp) programmer, but I think I have a month off this
summer where I could work on something like the above.

Thanks for reading,
Rasmus

Footnotes: 
[1] http://mid.gmane.org/20130303070635.GA12112%40panahar
[2] my citation links often look like postnote;prenote without
showing the BIBTEX-KEY or citation format.
[2] here http://mid.gmane.org/87lia0s7wi.fsf%40bzg.ath.cx
and here http://mid.gmane.org/87wqthk7vj.fsf%40gmail.com.


-- 
When in doubt, do it!




Re: [O] Let's discuss citation and Org syntax

2013-05-21 Thread Rasmus
A lot of people more clever than me have thought about this topic.
Here I'll just summarize the org-exp-bibtex missing in
git?-thread.  The ordering more or less follows how it was
displayed in my Gnus.  I've tried to stay honest to the people
I've quoted and hopefully I've not failed too badly.  Also, I hope
I've not forgotten valuable suggestions.  I've not quoted Thomas,
but he gave some insights of what one would want in citation here
http://mid.gmane.org/m1a9qczekf.fsf%40tsdye.com.
   

There were approximately three types of suggestions:
1. the new-type approach, which I've tried to generalize more
   above.  Aaron made valueable suggestions here.  Nicolas gave it
   some support.
2. The extending link approach, notably Bastien, Andreas and Aaron
   even supplied patches!
I've also included some quick references to the current frontier
using links.  Lastly, there's some links to implementation in other
formats.

The new-type approach
   - Nicolas: 
 #+BEGIN_QUOTE
 It would be good to integrate citations in export framework
 [...]
 Maybe something like [cite:]. org-element could parse this, and
 ox.el provide some tools to access data. Then each back-end could deal
 with them.
 [...]
 I favor [cite:PROPERTIES] over [[cite:PROPERTIES]], because the latter
 (link syntax) implies a (optional) description part. I don't think
 a description is ever meaningful in citations.
 #+END_QUOTE
 Ref: http://mid.gmane.org/87ehfwwgdd.fsf%40gmail.com and
 http://mid.gmane.org/874ngkzjt6.fsf%40gmail.com

   - Much of my discussion in the previoues post is similar to Aaron's
 response to my original post
 #+BEGIN_QUOTE
 So, a citation like [cite:doi:parens:some-doi:key=valkey2=val2] would be
 displayed by:
 1. call (org-lookup-cite-doi some-doi) - (:author Foo :title bar 
...)
 2. call (org-display-cite-parens '(:author Foo :title bar ...)) -
 (Foo 2000)
 3. (font-lock puts an overlay over the citation markup, with the
 returned string)
   
 If you click on the citation, org would open the location (URL or local
 file) returned by (org-resolve-cite-doi some-doi)
   
 A citation could exported by calling (org-export-cite-parens 'doi
 some-doi (:author foo :title bar) current-backend).  This function
 could just return \parencite{foo} if exporting to latex and the citation
 was already in a bibtex file.  But it could also just return “Foo 2000”
 as a static string for dumb backends like ASCII, or write the
 information to a temporary bibtex file (so that latex can atomatically
 use the bibliographic info looked up from a DOI citation).
 #+END_QUOTE
 Ref: http://mid.gmane.org/87txolk7qk.fsf%40gmail.com


- Jamuthan's take on viewing citation as footnotes
 #+BEGIN_QUOTE
 I view Citations as closer to Footnotes.  The syntax should parallels
 footnotes syntax.
 
 1. PROPERTIES should be opaque to Org.  It is a key or a list of
keys possibly bibtex but Org doesn't take stand on how it
looks like.
   
 2. There will be a org-BACKEND-citation-reference.
 3. There will be a org-BACKEND-bibliography.
   
 2, 3 more likely with interface with respective citation processor
 (citation processor as opposed to a database) via CLI.  Citation
 processor could be whatever org-exp-bibtex interfaces with right now.  I
 also have some proof-of-concept - see zotcite - for zotero.
   
 2, 3 will parallel footnote-reference and footnote-section callbacks in
 HTML backend.
   
 4. Footnotes can be introduced with either fn: prefix or cite:
prefix.  There should be a way to put fn: and cite: in same
enumeration context.  There should be a way to put fn: and
cite: in different enumeration context.  The former case could
be a degenerate mode where Org can transcode what is seen in
the buffer where everything is footnotes.  The latter case
will result in Citations and Bibliography being generated by
the above backend transcoders.
   
 5. Citation definitions in Org buffer will be *ignored*.  (It
could be considered when the exporter works in a degenerate
footnote only mode where plain text transcoding is resorted to
because there is no suitable application available for the
backend format.)  Plain text citation definitions are only to
help the author have a glimpse of what he is doing, it has
only UI-value but no contents value.
   
 6. There may be an advisory citation style - say APA, Chicago
etc - which the backends may honor or ignore.
  #+END_QUOTE


The extend-link suggestions:

   - Andreas Leha suggest something like what I suggested above, but
 extending upon the link syntax.  What I agree strongly with is:

   citations are more than links but also include information on
   formatting
 
   

Re: [O] Let's discuss citation and Org syntax

2013-05-21 Thread Viktor Rosenfeld
Hi,

Rasmus wrote:

 Hi, 
 
 Now that 8.0 has shipped let's talk bibliography support.  This
 follows directly upon the discussion around March[1].

I did not follow the discussion in March and only skimmed through the
recent discussion in May [2]. But I was wondering if bibliography
support in the LaTeX exporter would be BibTex-only or if it would also
support biblatex, for example.

Cheers,
Viktor

[1] http://mid.gmane.org/20130303070635.GA12112%40panahar
[2] http://thread.gmane.org/gmane.emacs.orgmode/71754



Re: [O] Let's discuss citation and Org syntax

2013-05-21 Thread Rasmus
Viktor Rosenfeld listuse...@gmail.com writes:

 Now that 8.0 has shipped let's talk bibliography support.  This
 follows directly upon the discussion around March[1].

 I did not follow the discussion in March 

I tried to summarize it the second post since the thread was very
long.

 But I was wondering if bibliography support in the LaTeX exporter
 would be BibTex-only or if it would also support biblatex, for
 example.

Currently, you can use both through the link syntax, but it's not so
nice if you use prenote and postnotes.

I solely use biber + biblatex these days.

–Rasmus

-- 
This space left intentionally blank



Re: [O] Let's discuss citation and Org syntax

2013-05-21 Thread Marcin Borkowski
Dnia 2013-05-21, o godz. 19:55:53
Viktor Rosenfeld listuse...@gmail.com napisał(a):

 Hi,
 
 Rasmus wrote:
 
  Hi, 
  
  Now that 8.0 has shipped let's talk bibliography support.  This
  follows directly upon the discussion around March[1].
 
 I did not follow the discussion in March and only skimmed through the
 recent discussion in May [2]. But I was wondering if bibliography
 support in the LaTeX exporter would be BibTex-only or if it would also
 support biblatex, for example.

Good point.

I do not use Org-mode for authoring (I'm quite happy with LaTeX itself
for that), and in LaTeX, I use neither bibtex nor biblatex; but AFAIK,
bibtex is basically dead like John Cleese's parrot.  I don't even think
that it needs to or should be supported; the faster bibtex usage fades
away, the better.

What I would suggest is to look into amsrefs manual.  The amsrefs
package was (is?) an interesting attempt at a /pure LaTeX/ solution to
the bibliography problem, not dependent on any executable other than
LaTeX.  It is not capable of sorting bibliographies, but other than
that is quite powerful (much more than bibtex, though seemingly less
than biblatex).  What is interesting here is its \ycite and \ocite
commands (see
http://mirrors.ctan.org/macros/latex/contrib/amsrefs/amsrdoc.pdf); it
might be a good idea to support something similar.  (I'm not sure
whether biblatex supports such a thing.)

 Cheers,
 Viktor

Best,

-- 
Marcin Borkowski
http://octd.wmi.amu.edu.pl/en/Marcin_Borkowski
Adam Mickiewicz University



Re: [O] Let's discuss citation and Org syntax

2013-05-21 Thread Christian Wittern

Hi Rasmus,

On 2013-05-21 21:21, Rasmus wrote:

Now that 8.0 has shipped let's talk bibliography support.  This
follows directly upon the discussion around March[1].
Thanks for a great post and for taken initiative for making org-mode even 
better for my purposes.  I started using org for writing papers a few years 
ago and I am not looking back.  The weak point however is bibliographies, as 
you say.


FWIW, I will describe my use case.  For drafting and when I can get away 
with it, I am going from org to PDF through XeLaTex, with either bibtex or 
more recently biber+biblatex.  However, when I submit papers, in most cases 
they have to be in a wordprocessor format, so I am going through the ODT 
export here.   In my current workflow this means that the bibliographie 
falls apart and in the end (deadlines!!) I usually cut and paste what I can 
get into either HTML or PDF.  This is not ideal and if this can improve it 
would mean a lot to me.


One problem I have had with bibtex and which I am now kind of dealing with 
(albeit still in a hackish way) in biber+biblatex is that I need specific 
formatting of the entries depending on the language I am publishing in, 
which is mostly either English or Japanese.  So for Japanese sources cited 
in English papers, I have to give the author and title optionally in 
Japanese characters, but also in romanized form and possibly in translation, 
whereas English sources in Japanese might require a Japanese form of the 
names and again a translation into Japanese.   I ended up adding extra 
fields to my bibtex file, since no bibliographic format I know of (except 
TEI) would support this and still allow me to integrate it into my workflow, 
but the big problem lies of course in integrating this better in my workflow.


So whatever org ends up with having in terms of bibliography, I would like 
to work with you and however jumps in to make sure that it also fits this 
need (which is actually not limited to an exotic field like mine, but is 
quite common for academics working in East Asia).


All the best,

Christian

--
Christian Wittern, Kyoto




Re: [O] Let's discuss citation and Org syntax

2013-05-21 Thread Erik Hetzner
At Tue, 21 May 2013 19:55:53 +0200,
Viktor Rosenfeld wrote:
 
 Hi,
 
 Rasmus wrote:
 
  Hi, 
  
  Now that 8.0 has shipped let's talk bibliography support.  This
  follows directly upon the discussion around March[1].
 
 I did not follow the discussion in March and only skimmed through the
 recent discussion in May [2]. But I was wondering if bibliography
 support in the LaTeX exporter would be BibTex-only or if it would also
 support biblatex, for example.

And to further confuse the issue, why not consider pandoc style
citations [1]?

This works right now. Create an org file:

  See [@citekey, p. 10] for more info.

(assuming a bibtex, endnote, ris, ... file that contains a cite with
key “citekey”). Export to markdown. Process in pandoc, either to
latex:

  ❤ pandoc --natbib test.md -t latex -s --biblio test.bib

or to HTML, etc:

  ❤ pandoc test.md -s --biblio test.bib

While it would be nice to make this work natively with org, especially
with latex output, it would be great if compatibility with pandoc
could be obtained.

best, Erik

1. http://johnmacfarlane.net/pandoc/README.html#citation-rendering
Sent from my free software system http://fsf.org/.