org-ref in action

org-ref in action

[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: org-ref in action

[Thomas S. Dye]

Hi John,

John Kitchin <jkitchin@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: org-ref in action

[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 <jkitchin@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: org-ref in action

[Matt Lundin]

John Kitchin <jkitchin@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

Re: org-ref in action

[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: org-ref in action

[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 <jkitchin@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: org-ref in action

[Eric Schulte]

John Kitchin <jkitchin@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: org-ref in action

[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
gcr@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.eric@gmail.com> wrote:
> John Kitchin <jkitchin@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: org-ref in action

[Matt Lundin]

Eric Schulte <schulte.eric@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

Re: org-ref in action

[Fabrice Popineau]

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+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 <mdl@imapmail.org>:

> Eric Schulte <schulte.eric@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
------------------------------

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Re: org-ref in action

[John Kitchin]

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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.popineau@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 <mdl@imapmail.org>:
>
> Eric Schulte <schulte.eric@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
> ------------------------------
>
>

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Re: org-ref in action

[Matt Lundin]

John Kitchin <jkitchin@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: org-ref in action

[Matt Lundin]

Matt Lundin <mdl@imapmail.org> writes:

> John Kitchin <jkitchin@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: org-ref in action

[Grant Rettke]

On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin <mdl@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: org-ref in action

[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: org-ref in action

[Jorge A. Alfaro-Murillo]

Grant Rettke <gcr@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: org-ref in action

[Matt Lundin]

Grant Rettke <gcr@wisdomandwonder.com> writes:

> On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin <mdl@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: org-ref in action

[Alan Schmitt]

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On 2014-06-26 16:39, Matt Lundin <mdl@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

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Re: org-ref in action

[Matt Lundin]

Alan Schmitt <alan.schmitt@polytechnique.org> writes:

> On 2014-06-26 16:39, Matt Lundin <mdl@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: org-ref in action

[Xebar Saram]

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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 <mdl@imapmail.org> wrote:

> Alan Schmitt <alan.schmitt@polytechnique.org> writes:
>
> > On 2014-06-26 16:39, Matt Lundin <mdl@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
>
>

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Re: org-ref in action

[Thomas S. Dye]

Aloha Xebar,

Xebar Saram <zeltakc@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: org-ref in action

[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: org-ref in action

[Melleus]

Very useful guide. Thank you.

Re: org-ref in action

[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 <zeltakc@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 <mdl@imapmail.org> wrote:
>>
>> Alan Schmitt <alan.schmitt@polytechnique.org> writes:
>>
>> > On 2014-06-26 16:39, Matt Lundin <mdl@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: org-ref in action

[John Kitchin]

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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 <zeltakc@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 <mdl@imapmail.org> wrote:
>
>> Alan Schmitt <alan.schmitt@polytechnique.org> writes:
>>
>> > On 2014-06-26 16:39, Matt Lundin <mdl@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
>>
>>
>

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Re: org-ref in action

[Alan Schmitt]

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

> Alan Schmitt <alan.schmitt@polytechnique.org> writes:
>
>> On 2014-06-26 16:39, Matt Lundin <mdl@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

-- 
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Re: org-ref in action

[Matt Lundin]

Alan Schmitt <alan.schmitt@polytechnique.org> writes:

> On 2014-06-26 20:44, Matt Lundin <mdl@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: org-ref in action

[Matt Lundin]

Matt Lundin <mdl@imapmail.org> writes:

> Alan Schmitt <alan.schmitt@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: org-ref in action

[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
gcr@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 <mdl@imapmail.org> wrote:
> Grant Rettke <gcr@wisdomandwonder.com> writes:
>
>> On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin <mdl@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: org-ref in action

[Eric Schulte]

John Kitchin <jkitchin@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.popineau@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 <mdl@imapmail.org>:
>>
>> Eric Schulte <schulte.eric@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: org-ref in action

[Joseph Vidal-Rosset]

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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 <jkitchin@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.popineau@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 <mdl@imapmail.org>:
>>
>> Eric Schulte <schulte.eric@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
>> ------------------------------
>>
>>
>

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Re: org-ref in action

[Joseph Vidal-Rosset]

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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.
​

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Re: org-ref in action

[John Kitchin]

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with org-ref

[[cite:tony-2010][page n]]

exports as

\cite[page n]{tony-2010}

and


[[cite:tony-2010][text before link::text after link]]

exports as

\cite[text before link][text after link]{tony-2010}


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 Sun, Jun 29, 2014 at 6:18 AM, Joseph Vidal-Rosset <
joseph.vidal.rosset@gmail.com> wrote:

> 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.
> ​
>

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Re: org-ref in action

[Eric Schulte]

Joseph Vidal-Rosset <joseph.vidal.rosset@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: org-ref in action

[Joseph Vidal-Rosset]

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2014-06-29 20:19 GMT+02:00 Eric Schulte <schulte.eric@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.

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Re: org-ref in action

[Joseph Vidal-Rosset]

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2014-06-29 20:19 GMT+02:00 Eric Schulte <schulte.eric@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.

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Re: org-ref in action

[Eric Schulte]

Joseph Vidal-Rosset <joseph.vidal.rosset@gmail.com> writes:

> 2014-06-29 20:19 GMT+02:00 Eric Schulte <schulte.eric@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: org-ref in action

[Joseph Vidal-Rosset]

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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.eric@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.

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Re: org-ref in action

[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: org-ref in action

[Joseph Vidal-Rosset]

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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.eric@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)
>

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Re: org-ref in action

[Xebar Saram]

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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.rosset@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.eric@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)
>>
>
>

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Re: org-ref in action

[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 <zeltakc@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.rosset@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.eric@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: org-ref in action

[Xebar Saram]

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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 <jkitchin@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 <zeltakc@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.rosset@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.eric@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
>

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Re: org-ref in action

[John Kitchin]

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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 <zeltakc@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 <jkitchin@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 <zeltakc@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.rosset@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.eric@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
>>
>
>

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org-ref in action

[Leu Zhe]

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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.

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org-ref in action

[Doyley, Marvin M.]

Hi John,

Thanks for sharing. My students and I love it.

Cheers,
M