Re: Let's discuss citation and Org syntax

[John Hendy <jw.hendy@gmail.com>]

On Fri, Jan 3, 2014 at 2:27 PM, Joseph Vidal-Rosset
<joseph.vidal.rosset@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.hendy@gmail.com>
>>
>> On Fri, Jan 3, 2014 at 12:32 PM, Joseph Vidal-Rosset
>> <joseph.vidal.rosset@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.rosset@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.eric@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.rosset@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 <rasmus@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-key&&pre%3Dfoo&&post%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!
>> >>> >>
>> >>> >>
>> >>> >>
>> >>>
>> >>>
>> >>> Footnotes:
>> >>> [1]
>> >>>
>> >>> http://orgmode.org/w/?p=org-mode.git;a=blob_plain;f=contrib/lisp/ox-bibtex.el;hb=HEAD
>> >>>
>> >>> [2]  http://www.lri.fr/~filliatr/bibtex2html/
>> >>>
>> >>> [3]  http://johnmacfarlane.net/pandoc/
>> >>>
>> >>> [4]
>> >>>
>> >>> https://github.com/eschulte/netgear-repair/blob/master/pub/netgear-repair.org
>> >>>
>> >>> [5]  http://eschulte.github.io/netgear-repair/pub/netgear-repair.html
>> >>>
>> >>> --
>> >>> Eric Schulte
>> >>> https://cs.unm.edu/~eschulte
>> >>> PGP: 0x614CA05D
>> >>
>> >>
>> >
>
>