Re: [O] org-ref in action

2014-08-06 Thread Xebar Saram
Thanks John

No worries :) ive installed it and its working great.

in a related question, does anyone use it with jabef?

the reason im asking is that im very new to this and wonder about a
possible workflow to export a bib citation from jabref to org and create an
org header (per reference). so far it seems like org-ref will only insert
something like
cite:REF
I have played around with org-bibtex and seem to remember there was a
org-bibtex yank function that created a header in org from the bib citation
in clipboard, can org-ref do something similar?

sorry for the neewb questions

z





On Wed, Aug 6, 2014 at 12:08 AM, John Kitchin jkitc...@andrew.cmu.edu
wrote:

 Hi, it got moved in a re-organization to
 https://github.com/jkitchin/jmax/blob/master/org/org-ref.org.

 Sorry for the inconvenience!

 Xebar Saram zelt...@gmail.com writes:

  Hi all
 
  the github link seems dead, anyone knows where one could get and try
  org-ref from?
 
  z
 
  On Mon, Jun 30, 2014 at 2:27 PM, Joseph Vidal-Rosset
  joseph.vidal.ros...@gmail.com wrote:
 
  Thanks Eric, it works now, with the latest version of org-mode.
 
  Best wishes
 
  Jo.
 
 
 
 
  2014-06-30 12:22 GMT+02:00 Eric Schulte schulte.e...@gmail.com:
 
 
 
   Thanns to the default cite action, I get for example in my
  org file:
  
   [[cite:(119–136)johansson36:_minim_formal]]
  
   and it creates no reference at al, because via the export I
  get:
  
   \cite{(119–136)johansson36:_minim_formal}
  
 
 
  Using the latest version of Org-mode from the git repository,
  this is a
  very new feature and requires usage of the git version of
  Org-mode, I am
  seeing the desired behavior. After simply requiring ox-bibtex,
  the
  following
 
  * H1
  [[cite:(119–136)johansson36:_minim_formal]]
 
  exports to
 
  \begin{document}
 
  \maketitle
  \tableofcontents
 
  \section{H1}
  \label{sec-1}~\cite[119–136]{johansson36:_minim_formal}
  % Emacs 24.4.50.2 (Org mode beta_8.3)
  \end{document}
 
  As expected.
 
  I hope this helps,
  Eric
 
 
 
  --
  Eric Schulte
  https://cs.unm.edu/~eschulte
  PGP: 0x614CA05D (see https://u.fsf.org/yw)
 
 
 
 
 

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



Re: [O] org-ref in action

2014-08-06 Thread John Kitchin
I am not familiar with jabref, but assuming it stores the entries in a
regular bibtex format, and you have the bibtex file open in emacs, with the
cursor on the entry you want to make a heading for, you run
M-x org-ref-open-bibtex-notes.

That creates something like an org-bibtex heading in your
org-ref-bibliography-notes file, but it is probably a little different. I
haven't used org-bibtex, and I didn't try to make it exactly the same. If
you try it and tell me what is missing, I can make it be more like
org-bibtex. The format there is not critical to me.

John

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



On Wed, Aug 6, 2014 at 6:54 AM, Xebar Saram zelt...@gmail.com wrote:

 Thanks John

 No worries :) ive installed it and its working great.

 in a related question, does anyone use it with jabef?

 the reason im asking is that im very new to this and wonder about a
 possible workflow to export a bib citation from jabref to org and create an
 org header (per reference). so far it seems like org-ref will only insert
 something like
 cite:REF
 I have played around with org-bibtex and seem to remember there was a
 org-bibtex yank function that created a header in org from the bib citation
 in clipboard, can org-ref do something similar?

 sorry for the neewb questions

 z





 On Wed, Aug 6, 2014 at 12:08 AM, John Kitchin jkitc...@andrew.cmu.edu
 wrote:

 Hi, it got moved in a re-organization to
 https://github.com/jkitchin/jmax/blob/master/org/org-ref.org.

 Sorry for the inconvenience!

 Xebar Saram zelt...@gmail.com writes:

  Hi all
 
  the github link seems dead, anyone knows where one could get and try
  org-ref from?
 
  z
 
  On Mon, Jun 30, 2014 at 2:27 PM, Joseph Vidal-Rosset
  joseph.vidal.ros...@gmail.com wrote:
 
  Thanks Eric, it works now, with the latest version of org-mode.
 
  Best wishes
 
  Jo.
 
 
 
 
  2014-06-30 12:22 GMT+02:00 Eric Schulte schulte.e...@gmail.com:
 
 
 
   Thanns to the default cite action, I get for example in my
  org file:
  
   [[cite:(119–136)johansson36:_minim_formal]]
  
   and it creates no reference at al, because via the export I
  get:
  
   \cite{(119–136)johansson36:_minim_formal}
  
 
 
  Using the latest version of Org-mode from the git repository,
  this is a
  very new feature and requires usage of the git version of
  Org-mode, I am
  seeing the desired behavior. After simply requiring ox-bibtex,
  the
  following
 
  * H1
  [[cite:(119–136)johansson36:_minim_formal]]
 
  exports to
 
  \begin{document}
 
  \maketitle
  \tableofcontents
 
  \section{H1}
  \label{sec-1}~\cite[119–136]{johansson36:_minim_formal}
  % Emacs 24.4.50.2 (Org mode beta_8.3)
  \end{document}
 
  As expected.
 
  I hope this helps,
  Eric
 
 
 
  --
  Eric Schulte
  https://cs.unm.edu/~eschulte
  PGP: 0x614CA05D (see https://u.fsf.org/yw)
 
 
 
 
 

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





Re: [O] org-ref in action

2014-08-05 Thread John Kitchin
Hi, it got moved in a re-organization to
https://github.com/jkitchin/jmax/blob/master/org/org-ref.org.

Sorry for the inconvenience!

Xebar Saram zelt...@gmail.com writes:

 Hi all

 the github link seems dead, anyone knows where one could get and try
 org-ref from?

 z

 On Mon, Jun 30, 2014 at 2:27 PM, Joseph Vidal-Rosset
 joseph.vidal.ros...@gmail.com wrote:

 Thanks Eric, it works now, with the latest version of org-mode. 
 
 Best wishes
 
 Jo. 
 
 
 
 
 2014-06-30 12:22 GMT+02:00 Eric Schulte schulte.e...@gmail.com:
 
 
 
  Thanns to the default cite action, I get for example in my
 org file:
 
  [[cite:(119–136)johansson36:_minim_formal]]
 
  and it creates no reference at al, because via the export I
 get:
 
  \cite{(119–136)johansson36:_minim_formal}
 
 
 
 Using the latest version of Org-mode from the git repository,
 this is a
 very new feature and requires usage of the git version of
 Org-mode, I am
 seeing the desired behavior. After simply requiring ox-bibtex,
 the
 following
 
 * H1
 [[cite:(119–136)johansson36:_minim_formal]]
 
 exports to
 
 \begin{document}
 
 \maketitle
 \tableofcontents
 
 \section{H1}
 \label{sec-1}~\cite[119–136]{johansson36:_minim_formal}
 % Emacs 24.4.50.2 (Org mode beta_8.3)
 \end{document}
 
 As expected.
 
 I hope this helps,
 Eric
 
 
 
 --
 Eric Schulte
 https://cs.unm.edu/~eschulte
 PGP: 0x614CA05D (see https://u.fsf.org/yw)
 

 



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



Re: [O] org-ref in action

2014-06-30 Thread Joseph Vidal-Rosset
2014-06-29 20:19 GMT+02:00 Eric Schulte schulte.e...@gmail.com:


 With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as

   \cite[page n]{one-reference-paper-year}



I am sorry Eric but [[cite:(page n)one-reference-paper-year]]  breaks the
bibliography reference for me with ox-bibtex.el ... it is too bad because
it was a convenient solution to get  \cite[page
n]{one-reference-paper-year} .

I am lost.

Regards

Jo.


Re: [O] org-ref in action

2014-06-30 Thread Eric Schulte
Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes:

 2014-06-29 20:19 GMT+02:00 Eric Schulte schulte.e...@gmail.com:


 With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as

   \cite[page n]{one-reference-paper-year}



 I am sorry Eric but [[cite:(page n)one-reference-paper-year]]  breaks the
 bibliography reference for me with ox-bibtex.el ... it is too bad because
 it was a convenient solution to get  \cite[page
 n]{one-reference-paper-year} .

 I am lost.


Could you be more specific?  Does org-mode generate any latex at all,
and how does it differ from what you'd expect?  If no LaTeX is
generated, and Org-mode actually throws an error then please provide a
backtrace.  I should be able to help but I'll need more information.

One thing I noticed is that I got better behavior if I didn't allow line
breaks in the link, which was easily accomplished by replacing
[[cite:(page n)one-reference-paper-year]] with
[[cite:(page~n)one-reference-paper-year]].  In general the later is
actually /preferable/ than the former, as you don't want LaTeX breaking
lines in the middle of a citation either.

Best,


 Regards

 Jo.

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D (see https://u.fsf.org/yw)



Re: [O] org-ref in action

2014-06-30 Thread Joseph Vidal-Rosset
I thank you Eric for your quick and kind reply.

In my init.el  file  I have put this code :

(eval-after-load 'reftex-vars
  '(progn

 (add-to-list 'reftex-cite-format-builtin
  '(org Org-mode citation
((?\C-m . [[cite:(%p)%l]])
 (?t . [[textcite:%l]])
 (?p . [[parencite:%l]])
 (?s . [[posscite:%l]])
 (?a . [[citeauthor:%l]])
 (?y . [[citeyear:%l]]))

2014-06-30 11:52 GMT+02:00 Eric Schulte schulte.e...@gmail.com:

 Could you be more specific?  Does org-mode generate any latex at all,
 and how does it differ from what you'd expect?  If no LaTeX is
 generated, and Org-mode actually throws an error then please provide a
 backtrace.  I should be able to help but I'll need more information.


Thanns to the default cite action, I get for example in my org file:

 [[cite:(119–136)johansson36:_minim_formal]]

and it creates no reference at al, because via the export I get:

\cite{(119–136)johansson36:_minim_formal}




 One thing I noticed is that I got better behavior if I didn't allow line
 breaks in the link, which was easily accomplished by replacing
 [[cite:(page n)one-reference-paper-year]] with
 [[cite:(page~n)one-reference-paper-year]].  In general the later is
 actually /preferable/ than the former, as you don't want LaTeX breaking
 lines in the middle of a citation either.


It is not the issue here because I have no broken line.

I'm using bibtex here and no biblatex. Maybe biblatex is a better option,
but it is another question.

Best

Jo.


Re: [O] org-ref in action

2014-06-30 Thread Eric Schulte
 Thanns to the default cite action, I get for example in my org file:

  [[cite:(119–136)johansson36:_minim_formal]]

 and it creates no reference at al, because via the export I get:

 \cite{(119–136)johansson36:_minim_formal}


Using the latest version of Org-mode from the git repository, this is a
very new feature and requires usage of the git version of Org-mode, I am
seeing the desired behavior.  After simply requiring ox-bibtex, the
following

* H1
[[cite:(119–136)johansson36:_minim_formal]]

exports to

\begin{document}

\maketitle
\tableofcontents

\section{H1}
\label{sec-1}~\cite[119–136]{johansson36:_minim_formal}
% Emacs 24.4.50.2 (Org mode beta_8.3)
\end{document}

As expected.

I hope this helps,
Eric

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D (see https://u.fsf.org/yw)



Re: [O] org-ref in action

2014-06-30 Thread Joseph Vidal-Rosset
Thanks Eric, it works now, with the latest version of org-mode.

Best wishes

Jo.


2014-06-30 12:22 GMT+02:00 Eric Schulte schulte.e...@gmail.com:

  Thanns to the default cite action, I get for example in my org file:
 
   [[cite:(119–136)johansson36:_minim_formal]]
 
  and it creates no reference at al, because via the export I get:
 
  \cite{(119–136)johansson36:_minim_formal}
 

 Using the latest version of Org-mode from the git repository, this is a
 very new feature and requires usage of the git version of Org-mode, I am
 seeing the desired behavior.  After simply requiring ox-bibtex, the
 following

 * H1
 [[cite:(119–136)johansson36:_minim_formal]]

 exports to

 \begin{document}

 \maketitle
 \tableofcontents

 \section{H1}
 \label{sec-1}~\cite[119–136]{johansson36:_minim_formal}
 % Emacs 24.4.50.2 (Org mode beta_8.3)
 \end{document}

 As expected.

 I hope this helps,
 Eric

 --
 Eric Schulte
 https://cs.unm.edu/~eschulte
 PGP: 0x614CA05D (see https://u.fsf.org/yw)



Re: [O] org-ref in action

2014-06-29 Thread Joseph Vidal-Rosset
Hi John, hello the list,

My question is very simple and it is not unrevelevant vis-à-vis this
thread, therefore I keep  the same thread.

What  need is to get either  the usual citation format  (often in plain
style) \cite{one-reference-paper-year} or this one with a mentioned page:
\cite[page n]{one-reference-paper-year}.

My problem with cite: org-mode format is that I am not able to get the
second format. Ideally , I want to click on the reference and just to add
the quoted page.

I do not doubt that this is easy to get in org-mode, but I'm wasting my
time to find how... if it is possible to get it with org-ref  or via
another tool, many thanks in advance.

Best regards

Jo.
​


Re: [O] org-ref in action

2014-06-29 Thread Eric Schulte
Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes:

 Hi John, hello the list,

 My question is very simple and it is not unrevelevant vis-à-vis this
 thread, therefore I keep  the same thread.

 What  need is to get either  the usual citation format  (often in plain
 style) \cite{one-reference-paper-year} or this one with a mentioned page:
 \cite[page n]{one-reference-paper-year}.


With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as

  \cite[page n]{one-reference-paper-year}


 My problem with cite: org-mode format is that I am not able to get the
 second format. Ideally , I want to click on the reference and just to add
 the quoted page.

 I do not doubt that this is easy to get in org-mode, but I'm wasting my
 time to find how... if it is possible to get it with org-ref  or via
 another tool, many thanks in advance.

 Best regards

 Jo.
 ​

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D (see https://u.fsf.org/yw)



Re: [O] org-ref in action

2014-06-29 Thread Joseph Vidal-Rosset
2014-06-29 20:19 GMT+02:00 Eric Schulte schulte.e...@gmail.com:

 With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as

   \cite[page n]{one-reference-paper-year}



Many thanks Eric . It helps a lot !

Best wishes

Jo.


Re: [O] org-ref in action

2014-06-27 Thread Alan Schmitt
On 2014-06-26 20:44, Matt Lundin m...@imapmail.org writes:

 Alan Schmitt alan.schm...@polytechnique.org writes:

 On 2014-06-26 16:39, Matt Lundin m...@imapmail.org writes:

 By contrast, ox-bibtex.el runs citations through bibtex2html, which is
 pretty much limited to the old-fashioned bibtex formats.

 What would be required for bibtex2html to take biblatex input? I thought
 the backend format was similar or the same (as you can tell, I know
 nothing of biblatex).

 I don't think this is possible without some major
 hacking/conversion/filtering. Biblatex has many more entry types and
 fields than bibtex. I've found that most of the older bibtex utils
 (bibtools, bibtex2html) choke on my biblatex files.

Is there a list of these new entry types? Looking at the code for
bibtex2html (for instance
https://github.com/backtracking/bibtex2html/blob/master/bibtex.mli)
I see that entry types are strings, so if there are issues, I guess they
would happen in the generation part but not in the parsing part.

 Even if biblatex2html did read biblatex data, its output, I believe, is
 limited to bibtex styles, which cannot handle more complex formats. Many
 scientific journals require bibtex formats. But many humanities
 disciplines have more complicated bibliographical requirements that
 bibtex cannot handle.   

I'm very ignorant here: from my understanding, bibtex2html does not care
about bibtex style, it just takes bibtex data as input and produces
html. Is the problem that some entries are ignored, or is there
something deeper that I'm missing?

Alan

PS: if anyone on the list think we should take this off-list, please let
me know

-- 
OpenPGP Key ID : 040D0A3B4ED2E5C7


pgpE103AQebyZ.pgp
Description: PGP signature


Re: [O] org-ref in action

2014-06-27 Thread Joseph Vidal-Rosset
Hello Jonhn, hello the list,

I have already used org-bibtex (and ox-bibtex) and I have just tried to use
org-ref . Is it possible that a conflict exists between the former(s) and
the latter?
My links for example are not clickable and the link to the default
bibliography does not work at all... But I have started from an older org
file used with org-bibtex.

Your help is welcome : could you show us a minimal file in order  to test
org-ref ?

Best wishes,

Jo.




2014-06-26 14:48 GMT+02:00 John Kitchin jkitc...@andrew.cmu.edu:

 Some features could be merged, but there is an important difference in
 that org-ref uses bibtex as the backend database, and reftex for searching,
 and org-bibtex uses org-mode headings as the backend database, and
 tag/property searches (I think).  It is like the difference between
 org-contacts and bbdb. They both serve similar needs, but with different
 data sources, and different ways to think about it.

 We might be able to figure out a way to specify a backend that would
 allow the independent features to work in both though.

 John

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



 On Thu, Jun 26, 2014 at 8:21 AM, Fabrice Popineau 
 fabrice.popin...@supelec.fr wrote:


 +1 for org-bibtex (and ox-bibtex) that I'm using for a couple of years.

 But org-ref seems to go further (video is convincing).
 It would be really nice to merge org-ref and org-bibtex before they split
 too far apart.
 Wishful thinking from me because I don't see that I'm in position to do
 it.

 Fabrice


 2014-06-26 3:10 GMT+02:00 Matt Lundin m...@imapmail.org:

 Eric Schulte schulte.e...@gmail.com writes:

 
  This is a lot of useful functionality, and very nicely presented.
 
  Did you happen to try the built in bibtex support in Org-mode core and
  contrib?  And if so, is there a reason that you implemented this all
  independently?
 
  I think part of the problem with existing Org-mode bibtex support is
  that no-one knows it exists.

 Well, you can count on one big fan of org-bibtex.el here! (Though I must
 admit that I have not used ox-bibtex.el.)

  To help address this I threw up a very quick-and-dirty screen cast
  demonstrating some of Org's existing bibtex functionality.
 
  https://vimeo.com/99167082

 Thanks! Over the years, I've particularly appreciated the way
 org-bibtex.el makes it easy to keep bib data together with notes/todos.
 Both org-bibtex-read and org-bibtex-yank have become indispensable to my
 own workflow.

 Best,
 Matt




 --
 Fabrice Popineau
 -
 SUPELEC
 Département Informatique
 3, rue Joliot Curie
 91192 Gif/Yvette Cedex
 Tel direct : +33 (0) 169851950
 Standard : +33 (0) 169851212
 --





Re: [O] org-ref in action

2014-06-27 Thread Thomas S. Dye
Aloha Xebar,

Xebar Saram zelt...@gmail.com writes:

 Hi all

 off topic a bit again. im an academic (asst. prof) in Epidemiology and have
 been using org-mode for about a year now. i love using org but im really
 not very technical at all. it has always been a dream for me to ditch word
 and move over to Latex and even better orgmode to write my scientific
 publications, writing my CV etc.
 The problem is i cant really find a good for dummies guide on how to
 really get started. again im really not technical so i always give up
 really fast on this.

 Do you guys think i should give it a shot (again not very technical :)) and
 if so what would be the steps/guides to follow? perhaps start by drafting a
 CV since thats perhaps easier?

I wrote an Org mode template for a PLOS One journal article:
http://orgmode.org/worg/exporters/plos-one-template-worg.html

It uses asynchronous export that gets initialized with a file that is
tangled from the template.  This should get you past the common problem
of unexpected results because of something in your setup.  Because it
is a self-contained project, it might be easier to understand what needs
to be done to use Org mode to write scientific papers.

hth,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com



Re: [O] org-ref in action

2014-06-27 Thread Vikas Rawal
 
 
 off topic a bit again. im an academic (asst. prof) in Epidemiology and have 
 been using org-mode for about a year now. i love using org but im really not 
 very technical at all. it has always been a dream for me to ditch word and 
 move over to Latex and even better orgmode to write my scientific 
 publications, writing my CV etc. 
 The problem is i cant really find a good for dummies guide on how to really 
 get started. again im really not technical so i always give up really fast on 
 this.
 

I wrote something that you may find useful:

https://github.com/vikasrawal/orgpaper/blob/master/orgpapers.org

Vikas


Re: [O] org-ref in action

2014-06-27 Thread Melleus
Very useful guide. Thank you.




Re: [O] org-ref in action

2014-06-27 Thread Ista Zahn
Yes, totally off topic for this thread, please start a new one.

On Fri, Jun 27, 2014 at 12:27 AM, Xebar Saram zelt...@gmail.com wrote:
 Hi all

 off topic a bit again. im an academic (asst. prof) in Epidemiology and have
 been using org-mode for about a year now. i love using org but im really not
 very technical at all. it has always been a dream for me to ditch word and
 move over to Latex and even better orgmode to write my scientific
 publications, writing my CV etc.
 The problem is i cant really find a good for dummies guide on how to
 really get started. again im really not technical so i always give up really
 fast on this.

 Do you guys think i should give it a shot (again not very technical :)) and
 if so what would be the steps/guides to follow? perhaps start by drafting a
 CV since thats perhaps easier?

 kind regards

 Z.






 On Thu, Jun 26, 2014 at 9:44 PM, Matt Lundin m...@imapmail.org wrote:

 Alan Schmitt alan.schm...@polytechnique.org writes:

  On 2014-06-26 16:39, Matt Lundin m...@imapmail.org writes:
 
  By contrast, ox-bibtex.el runs citations through bibtex2html, which is
  pretty much limited to the old-fashioned bibtex formats.
 
  What would be required for bibtex2html to take biblatex input? I thought
  the backend format was similar or the same (as you can tell, I know
  nothing of biblatex).

 I don't think this is possible without some major
 hacking/conversion/filtering. Biblatex has many more entry types and
 fields than bibtex. I've found that most of the older bibtex utils
 (bibtools, bibtex2html) choke on my biblatex files.

 Even if biblatex2html did read biblatex data, its output, I believe, is
 limited to bibtex styles, which cannot handle more complex formats. Many
 scientific journals require bibtex formats. But many humanities
 disciplines have more complicated bibliographical requirements that
 bibtex cannot handle.

 Best,
 Matt





Re: [O] org-ref in action

2014-06-27 Thread Matt Lundin
Alan Schmitt alan.schm...@polytechnique.org writes:

 On 2014-06-26 20:44, Matt Lundin m...@imapmail.org writes:

 I don't think this is possible without some major
 hacking/conversion/filtering. Biblatex has many more entry types and
 fields than bibtex. I've found that most of the older bibtex utils
 (bibtools, bibtex2html) choke on my biblatex files.

 Is there a list of these new entry types? 

It depends on the style. I use the biblatex-chicago style. I grepped the
sample bib file supplied with the package to get a list of entry
types[fn:1] and fields.[fn:2] And this represents only a subset of the
possible fields! See also the variable bibtex-biblatex-entry-alist in
bibtex.el (shipped with emacs).

 Looking at the code for bibtex2html (for instance
 https://github.com/backtracking/bibtex2html/blob/master/bibtex.mli) I
 see that entry types are strings, so if there are issues, I guess they
 would happen in the generation part but not in the parsing part.

You are right. I see that one can specify a style file for parsing bib
files and biblatex does supply a biblatex.bst, e.g.,

  bibtex2html -s biblatex

However, this still produces errors (and a blank html file) when I run
it on a larger bib file that pdflatex/biber parses fine. I was able to
get it to run without errors on a small carefully culled subset (a book
and an article).

 Even if biblatex2html did read biblatex data, its output, I believe,
 is limited to bibtex styles, which cannot handle more complex
 formats.

 I'm very ignorant here: from my understanding, bibtex2html does not
 care about bibtex style, it just takes bibtex data as input and
 produces html. 

 Is the problem that some entries are ignored, 

Yes, as well as many fields.

 or is there something deeper that I'm missing?

For my particular use-case, the problem is that it formats the
bibliographical data incorrectly. This is because biblatex relies on
LaTeX macros (rather than bibtex) to format the bibliography. Thus, any
utility that relies on bibtex to format bibliographies not work with
biblatex styles.

This, by the way, is why biblatex was is such a boon for those of use
working in the humanities: bibtex was *never* sufficient for humanities
citations. 

E.g., the biblatex-chicago style outputs a bibliographical item for a
book like this (with org markup added to show emphasis):

Wolloch, Isser. /The New Regime: Transformations of the French Civic
Order, 1789--1820s/. New York and London: W. W. Norton, 1994.

bibtex2html produces this:

Isser Wolloch. /The New Regime./ W. W. Norton, 1994.

Best, 
Matt (who also would also be happy to take this off list)

Footnotes:

[fn:1] Article, Artwork, Audio, Book, Booklet, Collection, CustomC, Image,
InBook, InCollection, inproceedings, InReference, Letter, Manual,
MastersThesis, Misc, Music, MVCollection, Online, Patent, Periodical,
PhdThesis, Reference, Review, SuppBook, TechReport, Unpublished, Video

[fn:2] addendum, address, afterword, annote, author, authortype,
bookauthor, booksubtitle, booktitle, booktitleaddon, chapter, crossref,
date, doi, edition, editor, editora, editoratype, editortype,
entrysubtype, eventdate, howpublished, institution, isbn, issue,
issuetitle, journaltitle, keywords, language, lista, location,
longcrossref, mainsubtitle, maintitle, month, namea, nameaddon, nameb,
namec, note, number, options, organization, origdate, origlanguage,
origlocation, origpublisher, pages, part, publisher, pubstate, school,
series, shortauthor, shorthand, shorttitle, sortkey, sorttitle,
subtitle, title, titleaddon, translator, type, url, urldate, useauthor,
usecompiler, useeditor, usera, userc, userd, usere, userf, volume,
volumes, xref, year



Re: [O] org-ref in action

2014-06-27 Thread Grant Rettke
Thanks for your answer on that everybody.

My apologies for my poor grammar asking where people discuss such
questions in real life. What I really had wanted to say, what I
meant, was that I was wondering what professions utilize such
workflows and where they discuss it primarily because the topic does
go beyond LaTeX alone. My usage of such a workflow is pretty
lightweight, and I've never had anyone to talk to about it because in
my field generally no one cites their references.
Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
g...@wisdomandwonder.com | http://www.wisdomandwonder.com/
“Wisdom begins in wonder.” --Socrates
((λ (x) (x x)) (λ (x) (x x)))
“Life has become immeasurably better since I have been forced to stop
taking it seriously.” --Thompson


On Thu, Jun 26, 2014 at 9:39 AM, Matt Lundin m...@imapmail.org wrote:
 Grant Rettke g...@wisdomandwonder.com writes:

 On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin m...@imapmail.org wrote:
 I think the key in any possible feature merge is to remember citation
 management is idiosyncratic.

 Off topic:

 How do people choose today?

 Why choose bibtex over biblatex?

 Thanks to inertia, bibtex still has a number of users in the sciences,
 since it was originally designed for scientific citations. In the
 humanities, however, bibtex is a non-starter, since biblatex offers much
 more flexibility. The good news is that bibtex and biblatex use the same
 database format, so it's easy to transition from bibtex to biblatex.
 However, there are other options, such as CSL.[1]

 Where do people discuss such questions like this in real life?

 I'm not sure I understand your question. Could you clarify?

 I simply meant that everyone will have a different workflow/system for
 storing and managing citations. E.g., some will prefer to store
 bibliographical data in a zotero database, others in a single bib file,
 others in multiple bib files, others as properties in org headlines,
 etc.

 I think one can make a conception distinction here between citation
 management (i.e., how one stores bibliographical data) and citation
 processing (i.e., the software one uses to export that data to some
 output format). There are many, many formats (mods, bib, etc.) and tools
 (biber, bibtex, csl/citeproc, etc.) for formatting bibliographical data.

 In an ideal world, one should be able to 1) process bibliographical data
 from multiple formats; 2) choose from hundreds of citation styles; and
 3) format citations for multiple backends. I am not suggesting that
 org-mode should directly support all these things, but its default
 methods of handling citations should not get in the way of using
 external tools that provide such flexibility.

 For instance, pandoc (an immensely impressive piece of software!)
 accepts bibliographical data from numerous sources and processes it for
 multiple outputs (html, plain text, docx, rtf, etc.). By contrast,
 ox-bibtex.el runs citations through bibtex2html, which is pretty much
 limited to the old-fashioned bibtex formats. Ironically, ox-bibtex.el
 invokes pandoc to convert from html to plain text, but only after it has
 already used bibtex2html to process the data.

 Best,
 Matt

 Footnotes:

 [1] Citation Style Language - http://citationstyles.org/



Re: [O] org-ref in action

2014-06-27 Thread Matt Lundin
Matt Lundin m...@imapmail.org writes:

 Alan Schmitt alan.schm...@polytechnique.org writes:

 You are right. I see that one can specify a style file for parsing bib
 files and biblatex does supply a biblatex.bst, e.g.,

   bibtex2html -s biblatex

 However, this still produces errors (and a blank html file) when I run
 it on a larger bib file that pdflatex/biber parses fine. I was able to
 get it to run without errors on a small carefully culled subset (a book
 and an article).

For the record, after correcting an error in several of my bib entries,
bibtex2html -s biblatex is able to parse a biblatex database without
error. However, the resulting html is empty.

Thanks,
Matt



Re: [O] org-ref in action

2014-06-27 Thread John Kitchin
You may find some information here:
https://github.com/jkitchin/jmax/tree/master/examples that is helpful to
you. i have collected some examples for various journals we have published
in with orgmode there. The jmax repo is what my group currently uses for
this purpose. It may not be what you want to do, but there are a lot of
good ideas in it (imho of course ;)

John

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



On Fri, Jun 27, 2014 at 12:27 AM, Xebar Saram zelt...@gmail.com wrote:

 Hi all

 off topic a bit again. im an academic (asst. prof) in Epidemiology and
 have been using org-mode for about a year now. i love using org but im
 really not very technical at all. it has always been a dream for me to
 ditch word and move over to Latex and even better orgmode to write my
 scientific publications, writing my CV etc.
 The problem is i cant really find a good for dummies guide on how to
 really get started. again im really not technical so i always give up
 really fast on this.

 Do you guys think i should give it a shot (again not very technical :))
 and if so what would be the steps/guides to follow? perhaps start by
 drafting a CV since thats perhaps easier?

 kind regards

 Z.






 On Thu, Jun 26, 2014 at 9:44 PM, Matt Lundin m...@imapmail.org wrote:

 Alan Schmitt alan.schm...@polytechnique.org writes:

  On 2014-06-26 16:39, Matt Lundin m...@imapmail.org writes:
 
  By contrast, ox-bibtex.el runs citations through bibtex2html, which is
  pretty much limited to the old-fashioned bibtex formats.
 
  What would be required for bibtex2html to take biblatex input? I thought
  the backend format was similar or the same (as you can tell, I know
  nothing of biblatex).

 I don't think this is possible without some major
 hacking/conversion/filtering. Biblatex has many more entry types and
 fields than bibtex. I've found that most of the older bibtex utils
 (bibtools, bibtex2html) choke on my biblatex files.

 Even if biblatex2html did read biblatex data, its output, I believe, is
 limited to bibtex styles, which cannot handle more complex formats. Many
 scientific journals require bibtex formats. But many humanities
 disciplines have more complicated bibliographical requirements that
 bibtex cannot handle.

 Best,
 Matt





Re: [O] org-ref in action

2014-06-26 Thread Fabrice Popineau
+1 for org-bibtex (and ox-bibtex) that I'm using for a couple of years.

But org-ref seems to go further (video is convincing).
It would be really nice to merge org-ref and org-bibtex before they split
too far apart.
Wishful thinking from me because I don't see that I'm in position to do it.

Fabrice


2014-06-26 3:10 GMT+02:00 Matt Lundin m...@imapmail.org:

 Eric Schulte schulte.e...@gmail.com writes:

 
  This is a lot of useful functionality, and very nicely presented.
 
  Did you happen to try the built in bibtex support in Org-mode core and
  contrib?  And if so, is there a reason that you implemented this all
  independently?
 
  I think part of the problem with existing Org-mode bibtex support is
  that no-one knows it exists.

 Well, you can count on one big fan of org-bibtex.el here! (Though I must
 admit that I have not used ox-bibtex.el.)

  To help address this I threw up a very quick-and-dirty screen cast
  demonstrating some of Org's existing bibtex functionality.
 
  https://vimeo.com/99167082

 Thanks! Over the years, I've particularly appreciated the way
 org-bibtex.el makes it easy to keep bib data together with notes/todos.
 Both org-bibtex-read and org-bibtex-yank have become indispensable to my
 own workflow.

 Best,
 Matt




-- 
Fabrice Popineau
-
SUPELEC
Département Informatique
3, rue Joliot Curie
91192 Gif/Yvette Cedex
Tel direct : +33 (0) 169851950
Standard : +33 (0) 169851212
--


Re: [O] org-ref in action

2014-06-26 Thread John Kitchin
Some features could be merged, but there is an important difference in that
org-ref uses bibtex as the backend database, and reftex for searching, and
org-bibtex uses org-mode headings as the backend database, and tag/property
searches (I think).  It is like the difference between org-contacts and
bbdb. They both serve similar needs, but with different data sources, and
different ways to think about it.

We might be able to figure out a way to specify a backend that would
allow the independent features to work in both though.

John

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



On Thu, Jun 26, 2014 at 8:21 AM, Fabrice Popineau 
fabrice.popin...@supelec.fr wrote:


 +1 for org-bibtex (and ox-bibtex) that I'm using for a couple of years.

 But org-ref seems to go further (video is convincing).
 It would be really nice to merge org-ref and org-bibtex before they split
 too far apart.
 Wishful thinking from me because I don't see that I'm in position to do it.

 Fabrice


 2014-06-26 3:10 GMT+02:00 Matt Lundin m...@imapmail.org:

 Eric Schulte schulte.e...@gmail.com writes:

 
  This is a lot of useful functionality, and very nicely presented.
 
  Did you happen to try the built in bibtex support in Org-mode core and
  contrib?  And if so, is there a reason that you implemented this all
  independently?
 
  I think part of the problem with existing Org-mode bibtex support is
  that no-one knows it exists.

 Well, you can count on one big fan of org-bibtex.el here! (Though I must
 admit that I have not used ox-bibtex.el.)

  To help address this I threw up a very quick-and-dirty screen cast
  demonstrating some of Org's existing bibtex functionality.
 
  https://vimeo.com/99167082

 Thanks! Over the years, I've particularly appreciated the way
 org-bibtex.el makes it easy to keep bib data together with notes/todos.
 Both org-bibtex-read and org-bibtex-yank have become indispensable to my
 own workflow.

 Best,
 Matt




 --
 Fabrice Popineau
 -
 SUPELEC
 Département Informatique
 3, rue Joliot Curie
 91192 Gif/Yvette Cedex
 Tel direct : +33 (0) 169851950
 Standard : +33 (0) 169851212
 --




Re: [O] org-ref in action

2014-06-26 Thread Matt Lundin
John Kitchin jkitc...@andrew.cmu.edu writes:

 Some features could be merged, but there is an important difference in
 that org-ref uses bibtex as the backend database, and reftex for
 searching, and org-bibtex uses org-mode headings as the backend
 database, and tag/property searches (I think).  It is like the
 difference between org-contacts and bbdb. They both serve similar
 needs, but with different data sources, and different ways to think
 about it.

Yes, org-bibtex.el generally precludes the use of reftex to enter
citations. I get around this problem with a custom perl script, which
runs automatically in the background, extracts all org-bibtex data, and
deposits it in a central bib file.

 We might be able to figure out a way to specify a backend that would
 allow the independent features to work in both though.

I think the key in any possible feature merge is to remember citation
management is idiosyncratic. I.e., org-mode should offer helper
functions that enable individuals to customize their own workflows
rather than systems that dictate a particular workflow (e.g., a single
notes file) or presuppose a specific export backend. For instance,
org-mode citation tools should not assume that users will export via
bibtex/bibtex2html rather than, say, biber/biblatex or pandoc (which now
has a powerful, format-agnostic citation filter).[1]

Best,
Matt

Footnotes:

[1] http://johnmacfarlane.net/pandoc/demo/example19/Citations.html



Re: [O] org-ref in action

2014-06-26 Thread Matt Lundin
Matt Lundin m...@imapmail.org writes:

 John Kitchin jkitc...@andrew.cmu.edu writes:

 Some features could be merged, but there is an important difference in
 that org-ref uses bibtex as the backend database, and reftex for
 searching, and org-bibtex uses org-mode headings as the backend
 database, and tag/property searches (I think).  It is like the
 difference between org-contacts and bbdb. They both serve similar
 needs, but with different data sources, and different ways to think
 about it.

 Yes, org-bibtex.el generally precludes the use of reftex to enter citations.

s/enter/search/






Re: [O] org-ref in action

2014-06-26 Thread Grant Rettke
On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin m...@imapmail.org wrote:
 I think the key in any possible feature merge is to remember citation
 management is idiosyncratic.

Off topic:

How do people choose today?

Why choose bibtex over biblatex?

Where do people discuss such questions like this in real life?



Re: [O] org-ref in action

2014-06-26 Thread Ken Mankoff

On 2014-06-26 at 10:11, Grant Rettke wrote:
 Why choose bibtex over biblatex?

People choose bibtex because that is how it has been done and is well
supported/documented and still popular on Google results. People choose
biblatex because that appears to be the new under-development
with-bells-and-whistles way moving forward.

 Where do people discuss such questions like this in real life?

http://tex.stackexchange.com

  -k.




Re: [O] org-ref in action

2014-06-26 Thread Jorge A. Alfaro-Murillo
Grant Rettke g...@wisdomandwonder.com writes:

 How do people choose today?

 Why choose bibtex over biblatex?

For journal submission. With BibTeX you only have to copy paste at the
end of your LaTeX file the contents of the generated .bbl file.
Moreover, journals provide a default style for BibTeX, not biblatex. And
I have never seen a journal that supports biblatex (there might be a
few), but any journal that supports LaTeX supports BibTeX.

 Where do people discuss such questions like this in real life?

In the orgmode list =)




Re: [O] org-ref in action

2014-06-26 Thread Matt Lundin
Grant Rettke g...@wisdomandwonder.com writes:

 On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin m...@imapmail.org wrote:
 I think the key in any possible feature merge is to remember citation
 management is idiosyncratic.

 Off topic:

 How do people choose today?

 Why choose bibtex over biblatex?

Thanks to inertia, bibtex still has a number of users in the sciences,
since it was originally designed for scientific citations. In the
humanities, however, bibtex is a non-starter, since biblatex offers much
more flexibility. The good news is that bibtex and biblatex use the same
database format, so it's easy to transition from bibtex to biblatex.
However, there are other options, such as CSL.[1]

 Where do people discuss such questions like this in real life?

I'm not sure I understand your question. Could you clarify?

I simply meant that everyone will have a different workflow/system for
storing and managing citations. E.g., some will prefer to store
bibliographical data in a zotero database, others in a single bib file,
others in multiple bib files, others as properties in org headlines,
etc.

I think one can make a conception distinction here between citation
management (i.e., how one stores bibliographical data) and citation
processing (i.e., the software one uses to export that data to some
output format). There are many, many formats (mods, bib, etc.) and tools
(biber, bibtex, csl/citeproc, etc.) for formatting bibliographical data.

In an ideal world, one should be able to 1) process bibliographical data
from multiple formats; 2) choose from hundreds of citation styles; and
3) format citations for multiple backends. I am not suggesting that
org-mode should directly support all these things, but its default
methods of handling citations should not get in the way of using
external tools that provide such flexibility.

For instance, pandoc (an immensely impressive piece of software!)
accepts bibliographical data from numerous sources and processes it for
multiple outputs (html, plain text, docx, rtf, etc.). By contrast,
ox-bibtex.el runs citations through bibtex2html, which is pretty much
limited to the old-fashioned bibtex formats. Ironically, ox-bibtex.el
invokes pandoc to convert from html to plain text, but only after it has
already used bibtex2html to process the data.

Best,
Matt

Footnotes:

[1] Citation Style Language - http://citationstyles.org/



Re: [O] org-ref in action

2014-06-26 Thread Eric Schulte
John Kitchin jkitc...@andrew.cmu.edu writes:

 Some features could be merged, but there is an important difference in that
 org-ref uses bibtex as the backend database, and reftex for searching, and
 org-bibtex uses org-mode headings as the backend database, and tag/property
 searches (I think).  It is like the difference between org-contacts and
 bbdb. They both serve similar needs, but with different data sources, and
 different ways to think about it.

 We might be able to figure out a way to specify a backend that would
 allow the independent features to work in both though.


I wonder what the API would look like.  The following functions comes to
my mind.  I'm not sure if there would be much more for org-ref...
- jump location for citation by ID
- return bibtex information for citation by ID
- validate citation

With those functions I imagine that a good deal of higher-level code
could be shared in a backend agnostic way.  Including,
- jump to citations
- provide information on citations
- collect citations during publishing (possibly automatically create the bib 
file)

If merging makes sense that's great, but if not then there's certainly
no harm in a diverse ecosystem of org tools supporting different work
flows and backend tools.

Best,
Eric


 John

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



 On Thu, Jun 26, 2014 at 8:21 AM, Fabrice Popineau 
 fabrice.popin...@supelec.fr wrote:


 +1 for org-bibtex (and ox-bibtex) that I'm using for a couple of years.

 But org-ref seems to go further (video is convincing).
 It would be really nice to merge org-ref and org-bibtex before they split
 too far apart.
 Wishful thinking from me because I don't see that I'm in position to do it.

 Fabrice


 2014-06-26 3:10 GMT+02:00 Matt Lundin m...@imapmail.org:

 Eric Schulte schulte.e...@gmail.com writes:

 
  This is a lot of useful functionality, and very nicely presented.
 
  Did you happen to try the built in bibtex support in Org-mode core and
  contrib?  And if so, is there a reason that you implemented this all
  independently?
 
  I think part of the problem with existing Org-mode bibtex support is
  that no-one knows it exists.

 Well, you can count on one big fan of org-bibtex.el here! (Though I must
 admit that I have not used ox-bibtex.el.)

  To help address this I threw up a very quick-and-dirty screen cast
  demonstrating some of Org's existing bibtex functionality.
 
  https://vimeo.com/99167082

 Thanks! Over the years, I've particularly appreciated the way
 org-bibtex.el makes it easy to keep bib data together with notes/todos.
 Both org-bibtex-read and org-bibtex-yank have become indispensable to my
 own workflow.

 Best,
 Matt




 --
 Fabrice Popineau
 -
 SUPELEC
 Département Informatique
 3, rue Joliot Curie
 91192 Gif/Yvette Cedex
 Tel direct : +33 (0) 169851950
 Standard : +33 (0) 169851212
 --



-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D (see https://u.fsf.org/yw)



Re: [O] org-ref in action

2014-06-26 Thread Alan Schmitt
On 2014-06-26 16:39, Matt Lundin m...@imapmail.org writes:

 By contrast, ox-bibtex.el runs citations through bibtex2html, which is
 pretty much limited to the old-fashioned bibtex formats.

What would be required for bibtex2html to take biblatex input? I thought
the backend format was similar or the same (as you can tell, I know
nothing of biblatex).

Alan

-- 
OpenPGP Key ID : 040D0A3B4ED2E5C7


pgpj7Ur28svBy.pgp
Description: PGP signature


Re: [O] org-ref in action

2014-06-26 Thread Matt Lundin
Alan Schmitt alan.schm...@polytechnique.org writes:

 On 2014-06-26 16:39, Matt Lundin m...@imapmail.org writes:

 By contrast, ox-bibtex.el runs citations through bibtex2html, which is
 pretty much limited to the old-fashioned bibtex formats.

 What would be required for bibtex2html to take biblatex input? I thought
 the backend format was similar or the same (as you can tell, I know
 nothing of biblatex).

I don't think this is possible without some major
hacking/conversion/filtering. Biblatex has many more entry types and
fields than bibtex. I've found that most of the older bibtex utils
(bibtools, bibtex2html) choke on my biblatex files.

Even if biblatex2html did read biblatex data, its output, I believe, is
limited to bibtex styles, which cannot handle more complex formats. Many
scientific journals require bibtex formats. But many humanities
disciplines have more complicated bibliographical requirements that
bibtex cannot handle.   

Best,
Matt



[O] org-ref in action

2014-06-26 Thread Doyley, Marvin M.
Hi John,

Thanks for sharing. My students and I love it.

Cheers,
M




Re: [O] org-ref in action

2014-06-26 Thread Xebar Saram
Hi all

off topic a bit again. im an academic (asst. prof) in Epidemiology and have
been using org-mode for about a year now. i love using org but im really
not very technical at all. it has always been a dream for me to ditch word
and move over to Latex and even better orgmode to write my scientific
publications, writing my CV etc.
The problem is i cant really find a good for dummies guide on how to
really get started. again im really not technical so i always give up
really fast on this.

Do you guys think i should give it a shot (again not very technical :)) and
if so what would be the steps/guides to follow? perhaps start by drafting a
CV since thats perhaps easier?

kind regards

Z.






On Thu, Jun 26, 2014 at 9:44 PM, Matt Lundin m...@imapmail.org wrote:

 Alan Schmitt alan.schm...@polytechnique.org writes:

  On 2014-06-26 16:39, Matt Lundin m...@imapmail.org writes:
 
  By contrast, ox-bibtex.el runs citations through bibtex2html, which is
  pretty much limited to the old-fashioned bibtex formats.
 
  What would be required for bibtex2html to take biblatex input? I thought
  the backend format was similar or the same (as you can tell, I know
  nothing of biblatex).

 I don't think this is possible without some major
 hacking/conversion/filtering. Biblatex has many more entry types and
 fields than bibtex. I've found that most of the older bibtex utils
 (bibtools, bibtex2html) choke on my biblatex files.

 Even if biblatex2html did read biblatex data, its output, I believe, is
 limited to bibtex styles, which cannot handle more complex formats. Many
 scientific journals require bibtex formats. But many humanities
 disciplines have more complicated bibliographical requirements that
 bibtex cannot handle.

 Best,
 Matt




Re: [O] org-ref in action

2014-06-25 Thread Bastien
Hi John,

thanks for working on this!  The demo is impressive.

I've not explored or tested org-ref.el directly, but my feeling is
that there are some neat features that could sneak into Org's core,
like for example multiple targets for the same custom link, sorting
of those targets, etc.

I'll have a closer look ASAP -- thanks again,

-- 
 Bastien



Re: [O] org-ref in action

2014-06-25 Thread Vikas Rawal
John,

Thanks for a very interesting tutorial.

I was trying to load org-ref.el, but get the following error:



Debugger entered--Lisp error: (wrong-type-argument consp nil)
  setcar(nil ((87 . textcite:%l) (122 . newcite:%l)))
  (let* ((c (nthcdr 2 (assoc (quote org) reftex-cite-format-builtin (setcar 
c (append (nth 2 (assoc (quote org) reftex-cite-format-builtin)) (quote ((87 . 
textcite:%l) (122 . newcite:%l))
  eval-buffer()  ; Reading at buffer position 194
  call-interactively(eval-buffer record nil)
  command-execute(eval-buffer record)
  execute-extended-command(nil eval-buffer)
  call-interactively(execute-extended-command nil nil)


Am I missing something?

Vikas


On 24-Jun-2014, at 8:45 pm, John Kitchin jkitc...@andrew.cmu.edu wrote:

 Hello everyone,
 
 org-ref has basically stabilized. You can get the latest code at
 https://github.com/jkitchin/jmax/blob/master/org-ref.org.
 
 I made a little screen capture video here to show you what it does:
 https://www.youtube.com/watch?v=JyvpSVl4_dg
 
 Try it out, if it looks interesting, and let me know if you find any
 bugs!
 
 Thanks,
 
 -- 
 ---
 John Kitchin
 
 




Re: [O] org-ref in action

2014-06-25 Thread Eric Schulte
John Kitchin jkitc...@andrew.cmu.edu writes:

 Hello everyone,

 org-ref has basically stabilized. You can get the latest code at
 https://github.com/jkitchin/jmax/blob/master/org-ref.org.

 I made a little screen capture video here to show you what it does:
 https://www.youtube.com/watch?v=JyvpSVl4_dg

 Try it out, if it looks interesting, and let me know if you find any
 bugs!

 Thanks,

Great,

This is a lot of useful functionality, and very nicely presented.

Did you happen to try the built in bibtex support in Org-mode core and
contrib?  And if so, is there a reason that you implemented this all
independently?

I think part of the problem with existing Org-mode bibtex support is
that no-one knows it exists.  To help address this I threw up a very
quick-and-dirty screen cast demonstrating some of Org's existing bibtex
functionality.

https://vimeo.com/99167082

Best,
Eric

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D (see https://u.fsf.org/yw)



Re: [O] org-ref in action

2014-06-25 Thread Grant Rettke
John:

Beautiful, thanks!

Eric:

My goodness, that 8 minute video sums up what was not obvious to many
even after wantingly browsing the documentation on it. Thanks!
Grant Rettke | ACM, ASA, FSF, IEEE, SIAM
g...@wisdomandwonder.com | http://www.wisdomandwonder.com/
“Wisdom begins in wonder.” --Socrates
((λ (x) (x x)) (λ (x) (x x)))
“Life has become immeasurably better since I have been forced to stop
taking it seriously.” --Thompson


On Wed, Jun 25, 2014 at 3:25 PM, Eric Schulte schulte.e...@gmail.com wrote:
 John Kitchin jkitc...@andrew.cmu.edu writes:

 Hello everyone,

 org-ref has basically stabilized. You can get the latest code at
 https://github.com/jkitchin/jmax/blob/master/org-ref.org.

 I made a little screen capture video here to show you what it does:
 https://www.youtube.com/watch?v=JyvpSVl4_dg

 Try it out, if it looks interesting, and let me know if you find any
 bugs!

 Thanks,

 Great,

 This is a lot of useful functionality, and very nicely presented.

 Did you happen to try the built in bibtex support in Org-mode core and
 contrib?  And if so, is there a reason that you implemented this all
 independently?

 I think part of the problem with existing Org-mode bibtex support is
 that no-one knows it exists.  To help address this I threw up a very
 quick-and-dirty screen cast demonstrating some of Org's existing bibtex
 functionality.

 https://vimeo.com/99167082

 Best,
 Eric

 --
 Eric Schulte
 https://cs.unm.edu/~eschulte
 PGP: 0x614CA05D (see https://u.fsf.org/yw)




Re: [O] org-ref in action

2014-06-25 Thread Matt Lundin
Eric Schulte schulte.e...@gmail.com writes:


 This is a lot of useful functionality, and very nicely presented.

 Did you happen to try the built in bibtex support in Org-mode core and
 contrib?  And if so, is there a reason that you implemented this all
 independently?

 I think part of the problem with existing Org-mode bibtex support is
 that no-one knows it exists.

Well, you can count on one big fan of org-bibtex.el here! (Though I must
admit that I have not used ox-bibtex.el.)

 To help address this I threw up a very quick-and-dirty screen cast
 demonstrating some of Org's existing bibtex functionality.

 https://vimeo.com/99167082

Thanks! Over the years, I've particularly appreciated the way
org-bibtex.el makes it easy to keep bib data together with notes/todos.
Both org-bibtex-read and org-bibtex-yank have become indispensable to my
own workflow.

Best,
Matt



[O] org-ref in action

2014-06-24 Thread John Kitchin
Hello everyone,

org-ref has basically stabilized. You can get the latest code at
https://github.com/jkitchin/jmax/blob/master/org-ref.org.

I made a little screen capture video here to show you what it does:
https://www.youtube.com/watch?v=JyvpSVl4_dg

Try it out, if it looks interesting, and let me know if you find any
bugs!

Thanks,

-- 
---
John Kitchin




Re: [O] org-ref in action

2014-06-24 Thread Thomas S. Dye
Hi John,

John Kitchin jkitc...@andrew.cmu.edu writes:

 Hello everyone,

 org-ref has basically stabilized. You can get the latest code at
 https://github.com/jkitchin/jmax/blob/master/org-ref.org.

 I made a little screen capture video here to show you what it does:
 https://www.youtube.com/watch?v=JyvpSVl4_dg

 Try it out, if it looks interesting, and let me know if you find any
 bugs!

Wow! Nice work.  Thanks for pursuing this.

All the best,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com



Re: [O] org-ref in action

2014-06-24 Thread Ista Zahn
John,

This is simply amazing. I think this covers basically every item on my
org-mode reference handling wish list.  It's really great, thank you!

Will this be on Melpa soon?

-Ista

On Tue, Jun 24, 2014 at 2:45 PM, John Kitchin jkitc...@andrew.cmu.edu wrote:
 Hello everyone,

 org-ref has basically stabilized. You can get the latest code at
 https://github.com/jkitchin/jmax/blob/master/org-ref.org.

 I made a little screen capture video here to show you what it does:
 https://www.youtube.com/watch?v=JyvpSVl4_dg

 Try it out, if it looks interesting, and let me know if you find any
 bugs!

 Thanks,

 --
 ---
 John Kitchin





Re: [O] org-ref in action

2014-06-24 Thread Matt Lundin
John Kitchin jkitc...@andrew.cmu.edu writes:

 org-ref has basically stabilized. You can get the latest code at
 https://github.com/jkitchin/jmax/blob/master/org-ref.org.

 I made a little screen capture video here to show you what it does:
 https://www.youtube.com/watch?v=JyvpSVl4_dg

 Try it out, if it looks interesting, and let me know if you find any
 bugs!

This looks interesting. Thanks for the work you put into it! I look
forward to trying it out.

Matt



[O] org-ref in action

2014-06-24 Thread Leu Zhe
Thanks John,

I have been using it for a while.
It is a fantastic tool for org-mode to organize the bib.
Great thanks again.