org-ref code

org-ref code

[John Kitchin]

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Greetings,

All the talk about citations in org-mode inspired me to finish and polish
some code I have been working on for my group for a while on
bibtex/reftex/org-mode integration. I packaged it up in a literate
programming org-file here:
https://github.com/jkitchin/jmax/blob/master/org-ref.org.

You can tangle the org-ref.el code out of the org-file. There are probably
still some bugs in it, but it does pretty amazing things. Mostly, it
defines several new functional links for labels, references to labels,
citations, bibliography, list of tables and figures, and a handful of
utility functions I find useful.

I think it is a standalone package now. I would be grateful if anyone tried
it, and let me know if it does not work as advertised ;)

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

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Re: org-ref code

[Eric S Fraga]

On Wednesday, 30 Apr 2014 at 16:59, John Kitchin wrote:
> Greetings,
>
> All the talk about citations in org-mode inspired me to finish and polish
> some code I have been working on for my group for a while on
> bibtex/reftex/org-mode integration. I packaged it up in a literate
> programming org-file here:
> https://github.com/jkitchin/jmax/blob/master/org-ref.org.

Hi John,

Thanks for this.  I'll play with it as it looks like a really nice
collection of utilities for links and I must admit that I still find I
under-use org links.  I'll post any feedback here in due course.

One quick comment: I think it's bad practice to define global bindings
for Fxx keys in a package.  Let the user define these keys outside the
package maybe?  I have F10 and F12 defined to some very common actions
for me (recentf and org-clock).

Thanks again,
eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

Re: org-ref code

[Eric S Fraga]

John,

I've been playing with the package although, so far, only for
citations.  A few points:

1. Do you have any support for choosing the type of citation entry
     (i.e. \cite versus \autocite versus ...) when inserting a
     citation in the text?
     
2. You define org-link-types.  Unfortunately, this overwrites my own
     definitions, especially for "cite".  I wonder whether this type
     of customisation belongs in org-ref itself.  This is similar to
     my earlier comment about key bindings, I guess. 

3. I sometimes use biblatex instead of bibtex.  As a result, I do not
     use \bibliography and use \addbibresource instead.  I have
     defined my bibliography files in org-ref-default-bibliography but
     this is only picked up on initialisation.  It is difficult to
     update this for a document in progress (I had to locally set
     reftex-default-bibliography manually).

4. The customisation interface for org-ref-default-bibliography should be
     list aware...

Otherwise, seems to working just fine.

Thanks,
eric

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

Re: org-ref code

[Seb Frank]

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Hi Eric,

Now that you have mentioned it, do you have a good web resource / manual
for your set up, or would you mind sharing bits of it? It looks eminently
useful. I have a set up largely following this

http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/

but I wouldn't know how to get some of the things you mention (type of
citation entry, biblatex vs latex etc.) to work.

Thanks,
  Seb

On Thu, May 1, 2014 at 6:01 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> John,
>
> I've been playing with the package although, so far, only for
> citations.  A few points:
>
> 1. Do you have any support for choosing the type of citation entry
>      (i.e. \cite versus \autocite versus ...) when inserting a
>      citation in the text?
>
> 2. You define org-link-types.  Unfortunately, this overwrites my own
>      definitions, especially for "cite".  I wonder whether this type
>      of customisation belongs in org-ref itself.  This is similar to
>      my earlier comment about key bindings, I guess.
>
> 3. I sometimes use biblatex instead of bibtex.  As a result, I do not
>      use \bibliography and use \addbibresource instead.  I have
>      defined my bibliography files in org-ref-default-bibliography but
>      this is only picked up on initialisation.  It is difficult to
>      update this for a document in progress (I had to locally set
>      reftex-default-bibliography manually).
>
> 4. The customisation interface for org-ref-default-bibliography should be
>      list aware...
>
> Otherwise, seems to working just fine.
>
> Thanks,
> eric
>
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11
>
>

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Re: org-ref code

[Eric S Fraga]

On Thursday,  1 May 2014 at 08:21, Seb Frank wrote:
> Hi Eric,
>
> Now that you have mentioned it, do you have a good web resource / manual
> for your set up, or would you mind sharing bits of it? It looks eminently
> useful. I have a set up largely following this
>
> http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/
>
> but I wouldn't know how to get some of the things you mention (type of
> citation entry, biblatex vs latex etc.) to work.

Hi Seb,

I don't have much of a setup, actually.  You already do much more than I
do!

I tend to do things manually until somebody else posts something useful
already configured (like John has just done).  For instance, I simply
use C-c C-l to store a link manually, typing in the type of link (cite
vs autocite) and the bibtex key directly.  I used to use reftex with org
but found it got in the way although I cannot now remember how or why!

When in doubt, I resort to LaTeX.  I have been using LaTeX for 30 years
or so.  The beauty of org is that it allows me to fall back to LaTeX
without any hassle for most things.

I suffer (or have suffered badly in the past) from RSI so my main
concern is having things that are easy to type but paradoxically I don't
have a problem with typing normal text and I do touch type quickly.  I
use evil mode which means I can avoid most chorded commands.  To use
org, I have bound many org commands to keys in the normal state mode map
in evil.  For instance, I have org-export-dispatch assigned to ", e" so
I can export to pdf and view it in emacs by typing ", e l o".  I have
similar key bindings for many org commands.  For instance, "t" on a
headline will invoke org-todo.  ", n" and ", p" move to next and
previous headlines, "<" to org-metaleft, etc.  The aim is to avoid all
or most M- and especially M-S- key bindings which kill my hands.  C- is
not so bad but I avoid even these if possible.

I use a few yasnippets and make significant use of abbrev mode in Emacs
to help with typing.  I also make use of org's own snippet system.

Sorry I cannot be more helpful and thanks for the link to your setup.

eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

Re: org-ref code

[John Kitchin]

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Thanks for the feedback. I moved the key-bindings for f10-12 out of org-ref.


On Thu, May 1, 2014 at 6:01 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> John,
>
> I've been playing with the package although, so far, only for
> citations.  A few points:
>
> 1. Do you have any support for choosing the type of citation entry
>      (i.e. \cite versus \autocite versus ...) when inserting a
>      citation in the text?
>

Not at the moment. There are a few ways I can see doing this. With the
existing code, you can do M-x reftex-citation, select the format you want
and select the references. We could easily enough define additional formats
for other citation types. I found this way of inserting citations annoying,
because 99.99% of the time I want a simple cite link, and pressing  C-c ]
return regexp marking return was too much for me (



>
> 2. You define org-link-types.  Unfortunately, this overwrites my own
>      definitions, especially for "cite".  I wonder whether this type
>      of customisation belongs in org-ref itself.  This is similar to
>      my earlier comment about key bindings, I guess.
>
> 3. I sometimes use biblatex instead of bibtex.  As a result, I do not
>      use \bibliography and use \addbibresource instead.  I have
>      defined my bibliography files in org-ref-default-bibliography but
>      this is only picked up on initialisation.  It is difficult to
>      update this for a document in progress (I had to locally set
>      reftex-default-bibliography manually).
>
> 4. The customisation interface for org-ref-default-bibliography should be
>      list aware...
>
> Otherwise, seems to working just fine.
>
> Thanks,
> eric
>
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11
>

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Re: org-ref code

[John Kitchin]

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sorry, premature send!


On Thu, May 1, 2014 at 8:36 AM, John Kitchin <jkitchin@andrew.cmu.edu>wrote:

> Thanks for the feedback. I moved the key-bindings for f10-12 out of
> org-ref.
>
>
> On Thu, May 1, 2014 at 6:01 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
>
>> John,
>>
>> I've been playing with the package although, so far, only for
>> citations.  A few points:
>>
>> 1. Do you have any support for choosing the type of citation entry
>>      (i.e. \cite versus \autocite versus ...) when inserting a
>>      citation in the text?
>>
>
> Not at the moment. There are a few ways I can see doing this. With the
> existing code, you can do M-x reftex-citation, select the format you want
> and select the references. We could easily enough define additional formats
> for other citation types. I found this way of inserting citations annoying,
> because 99.99% of the time I want a simple cite link, and pressing  C-c ]
> return regexp marking return was too much for me (I cite a lot). I also
> found this method was not flexible, in the sense that it was not easy to
> add citations to an existing citation. That is why there is an ?a option to
> append citations in the code.
>

an alternative would be to use a prefix command that gave you an option to
change the cite format, similar to the minibuffer menu for cite links. I
have not written much prefix code before, but I will try that out.


>
>
>>
>> 2. You define org-link-types.  Unfortunately, this overwrites my own
>>      definitions, especially for "cite".  I wonder whether this type
>>      of customisation belongs in org-ref itself.  This is similar to
>>      my earlier comment about key bindings, I guess.
>>
>
In the end, the link definitions can be as short as this:

#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(org-add-link-type
 "cite"
 'org-ref-cite-onclick-minibuffer-menu
 'org-ref-cite-link-format)
#+END_SRC

I wrote this for my research group to use, and eventually the links have to
be defined somewhere. I am not sure what the best place would be. It is an
interesting issue of reproducibility though. Two people with different link
definitions would get different results.


>> 3. I sometimes use biblatex instead of bibtex.  As a result, I do not
>>      use \bibliography and use \addbibresource instead.  I have
>>      defined my bibliography files in org-ref-default-bibliography but
>>      this is only picked up on initialisation.  It is difficult to
>>      update this for a document in progress (I had to locally set
>>      reftex-default-bibliography manually).
>>
>
It should be easy enough to make an addbibresource link that does the same
thing as the bibliography link. And maybe to modify the find-bibliography
code to check for that too. I have never used biblatex though, so I dont
have any experience with it.


>
>> 4. The customisation interface for org-ref-default-bibliography should be
>>      list aware...
>>
>
I think I fixed this.


>
>> Otherwise, seems to working just fine.
>>
>> Thanks,
>> eric
>>
>> --
>> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org
>> release_8.2.6-923-g233c11
>>
>
>

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Re: org-ref code

[Eric S Fraga]

On Thursday,  1 May 2014 at 08:47, John Kitchin wrote:

[...]

Hi John,

thanks for your quick response!

> an alternative would be to use a prefix command that gave you an option to
> change the cite format, similar to the minibuffer menu for cite links. I
> have not written much prefix code before, but I will try that out.

This would be good, with many a way of stating the default one would
like?  For instance, for grant proposals, I often use autocite in
biblatex for generating citations as footnotes whereas for research
papers I use cite most often.  

> In the end, the link definitions can be as short as this:
>
> #+BEGIN_SRC emacs-lisp :tangle org-ref.el
> (org-add-link-type
>  "cite"
>  'org-ref-cite-onclick-minibuffer-menu
>  'org-ref-cite-link-format)
> #+END_SRC

My comment was not so much the definitions you used but that you were
overwriting those that I had already defined.  Your definitions were
arguably better than mine so maybe I was being a bit picky here... :)

> I wrote this for my research group to use, and eventually the links have to
> be defined somewhere. I am not sure what the best place would be. It is an
> interesting issue of reproducibility though. Two people with different link
> definitions would get different results.

Yes, this is true but there is so much that can be customised in org
that you will never have reproducibility at this level (e.g. handling of
latex snippets, code listings, even latex classes).  I would leave
something like this to a separate set of code that is not part of
org-ref.

> It should be easy enough to make an addbibresource link that does the same
> thing as the bibliography link. And maybe to modify the find-bibliography
> code to check for that too. I have never used biblatex though, so I dont
> have any experience with it.

I have only started using biblatex recently, and that was because I
wanted to use autocite.  The only change I had to make was \bibliography
to \addbibresource.  I still use the same bibtex files.  Of course,
others may be making more effective use of biblatex...

>>> 4. The customisation interface for org-ref-default-bibliography should be
>>>      list aware...
>>
> I think I fixed this.

Thanks!
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

Re: org-ref code

[John Kitchin]

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I implemented some of this partially. I made it so you can specify the
default cite link in a user variable, with a default of cite. When you type
C-c ], this format will automatically be used. If you want to choose
another format, type C-u C-c ] which will prompt you for a type, and then
use the reftex-citation command to complete it. I added most of the
citation types I know of to this. Most of those will not work with
completion. I did make the cite link completion function use the default
link type, so that it will at least do what you want. I might add
completion functions for all the link types, it is just a lot of cut and
pasting. and I do not use that much. I just wanted to see if I could do it
;)

I also added addbibresource as a link type, and updated org-ref to be able
to use that instead of bibliography.

Thanks for the ideas!

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, May 1, 2014 at 9:30 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> On Thursday,  1 May 2014 at 08:47, John Kitchin wrote:
>
> [...]
>
> Hi John,
>
> thanks for your quick response!
>
> > an alternative would be to use a prefix command that gave you an option
> to
> > change the cite format, similar to the minibuffer menu for cite links. I
> > have not written much prefix code before, but I will try that out.
>
> This would be good, with many a way of stating the default one would
> like?  For instance, for grant proposals, I often use autocite in
> biblatex for generating citations as footnotes whereas for research
> papers I use cite most often.
>
> > In the end, the link definitions can be as short as this:
> >
> > #+BEGIN_SRC emacs-lisp :tangle org-ref.el
> > (org-add-link-type
> >  "cite"
> >  'org-ref-cite-onclick-minibuffer-menu
> >  'org-ref-cite-link-format)
> > #+END_SRC
>
> My comment was not so much the definitions you used but that you were
> overwriting those that I had already defined.  Your definitions were
> arguably better than mine so maybe I was being a bit picky here... :)
>
> > I wrote this for my research group to use, and eventually the links have
> to
> > be defined somewhere. I am not sure what the best place would be. It is
> an
> > interesting issue of reproducibility though. Two people with different
> link
> > definitions would get different results.
>
> Yes, this is true but there is so much that can be customised in org
> that you will never have reproducibility at this level (e.g. handling of
> latex snippets, code listings, even latex classes).  I would leave
> something like this to a separate set of code that is not part of
> org-ref.
>
> > It should be easy enough to make an addbibresource link that does the
> same
> > thing as the bibliography link. And maybe to modify the find-bibliography
> > code to check for that too. I have never used biblatex though, so I dont
> > have any experience with it.
>
> I have only started using biblatex recently, and that was because I
> wanted to use autocite.  The only change I had to make was \bibliography
> to \addbibresource.  I still use the same bibtex files.  Of course,
> others may be making more effective use of biblatex...
>
> >>> 4. The customisation interface for org-ref-default-bibliography should
> be
> >>>      list aware...
> >>
> > I think I fixed this.
>
> Thanks!
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11
>

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Re: org-ref code

[Eric S Fraga]

On Thursday,  1 May 2014 at 13:07, John Kitchin wrote:
> I implemented some of this partially. I made it so you can specify the
> default cite link in a user variable, with a default of cite. When you type
> C-c ], this format will automatically be used. If you want to choose
> another format, type C-u C-c ] which will prompt you for a type, and then

Hi John,

I am having problems with org-ref and am obviously missing something
trivial.  I downloaded the latest version yesterday (Friday).  You don't
say, in the above, what function you actually bound to C-c ] but I bound
org-ref-insert-cite-link and that doesn't seem to work:

1. C-u on it does not give me a choice of citation method
2. the link inserted "looks" like a link (it's blue) but there are
     actually no [[...]] characters surrounding it.

What am I missing?  Am I expected to type the [[]] or use C-c C-l?

I would like to C-u C-c ], choose autocite and my refs and have your
code insert [[autocite:blah-2001,joe-2010,moe-2014]] into my org
buffer.  I know I can change the default citation link type through
org-ref-default-citation-link but I want the C-u functionality.

Finally, looking at the code, it would appear that appending new
citations will only work for "cite:" links as the "cite:" is hard-coded
into the code?

thanks again,
eric

PS - I'm a fellow Chemical Engineer but unfortunately have not yet had
the opportunity to cite any of your papers but look forward to doing so
sometime soon using org-ref ;-)
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

Re: org-ref code

[John Kitchin]

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On Sat, May 10, 2014 at 10:44 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> On Thursday,  1 May 2014 at 13:07, John Kitchin wrote:
> > I implemented some of this partially. I made it so you can specify the
> > default cite link in a user variable, with a default of cite. When you
> type
> > C-c ], this format will automatically be used. If you want to choose
> > another format, type C-u C-c ] which will prompt you for a type, and then
>
> Hi John,
>
> I am having problems with org-ref and am obviously missing something
> trivial.  I downloaded the latest version yesterday (Friday).  You don't
> say, in the above, what function you actually bound to C-c ] but I bound
> org-ref-insert-cite-link and that doesn't seem to work:
>

C-c ] should be bound by default to org-ref-insert-cite-link. It is defined
in a hook function in line 104 of org-ref.org.

I made a custom variable to store the key-binding, but I realized it
probably doesn't help, since the binding


>
> 1. C-u on it does not give me a choice of citation method
>

If you type C-u M-x  org-ref-insert-cite-link

do you get a choice?

I just tried this on a fresh pull and it does work for me. I am not sure
why this wouldn't work for you.  Do you tangle the .el file from the .org
file? I have this code somewhere else to build it when needed:
(if (or
     (not (file-exists-p "org-ref.el"))
     (< (float-time (nth 5 (file-attributes "org-ref.el")))
    (float-time (nth 5 (file-attributes "org-ref.org")))))
    (progn
      (org-babel-tangle-file (expand-file-name "org-ref.org"
starter-kit-dir))
      (load-file (expand-file-name "org-ref.el" starter-kit-dir)))
  (require 'org-ref))

That retangles the org file if the org-file is newer than the el file.


> 2. the link inserted "looks" like a link (it's blue) but there are
>      actually no [[...]] characters surrounding it.
>

There are no [[...]]. The links work fine without them for me. Are they
necessary for some reason? I can add them, but since they do not do
anything but disappear in this case, I leave them out.  That is actually
not totally true, if you write your link as [[cite:key][page 23]] the page
23 gets formatted in latex as \cite[page23]{key}.


>
> What am I missing?  Am I expected to type the [[]] or use C-c C-l?
>
> I don't think you need the [[]], and you do not have to use C-c C-l. The
only thing that C-c C-l offers is autocompletion on bibtex keys for the
cite link (I have not figured out a way to avoid a lot of cut and paste
code for the other types, and I rarely use this feature, but I am leaving
it in so I do not forget how I did it ;). I guess C-c C-l might help
entering the description too.



> I would like to C-u C-c ], choose autocite and my refs and have your
> code insert [[autocite:blah-2001,joe-2010,moe-2014]] into my org
> buffer.  I know I can change the default citation link type through
> org-ref-default-citation-link but I want the C-u functionality.
>

You should be able to do all those things. The C-u functionality works
independently of the default type, and it should let you get something
other than the default.


>
> Finally, looking at the code, it would appear that appending new
> citations will only work for "cite:" links as the "cite:" is hard-coded
> into the code?
>

This is correct in the version you have. The current workaround is to use
C-u C-c ], and select the "A" format, which will output a leading comma and
your selections. I have pushed a fix for this, that adds a requirement of
dash.el and checks of the link is in a list of cite types defined in
org-ref. Thanks for making me think of a solution to that!


> thanks again,
> eric
>
> PS - I'm a fellow Chemical Engineer but unfortunately have not yet had
> the opportunity to cite any of your papers but look forward to doing so
> sometime soon using org-ref ;-)
>

That would be great! I hope the comments above help!


> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11
>

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Re: org-ref code

[Andreas Reuleaux]

John Kitchin <jkitchin@andrew.cmu.edu> writes:


> C-c ] should be bound by default to org-ref-insert-cite-link. It is defined
> in a hook function in line 104 of org-ref.org.
>
> I made a custom variable to store the key-binding, but I realized it
> probably doesn't help, since the binding
>
>
>>
>> 1. C-u on it does not give me a choice of citation method
>>
>
> If you type C-u M-x  org-ref-insert-cite-link
>
> do you get a choice?
>
> I just tried this on a fresh pull and it does work for me. I am not sure
> why this wouldn't work for you.  Do you tangle the .el file from the .org
> file? I have this code somewhere else to build it when needed:


I can confirm that C-c ] and C-u C-c ]
work fine for me.

my setup if fairly simple (with org-ref.el tangled from org-ref.org)

  (require 'org-ref)

  (custom-set-variables
   '(org-ref-bibliography-notes "notes.org")
   '(org-ref-default-bibliography  (list "refs.bib"))
   ;; '(org-ref-pdf-directory "...")
   ;; '(org-ref-default-citation-link "...")
   ;; '(org-ref-insert-cite-key "...")
   )

looking forward to discover more of org-ref.

FWIW, I was using textcite:... (with biblatex) as well, helped myself by
just inserting a cite:... and then changing the link with C-c C-l from
cite to textcite. But I really need read up on all those different
citations commands once more, maybe textcite is not really necessary?
Could I add it somehow to the list of choices available in "C-u C-c ]" ?
(I realized there are citetext, citep*, citep as well, that I yet have
to discover).

By the way: the org-ref.org literate programming docs are fine
for someone interested in the gory details / relatively experienced.
Ist there a simpler document just describing its usage - that
you would hand out to your chemistry students e. g. ?

Somehting maybe explaining the differences from the other approaches
that can be found e g in 

  http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/

  http://www-public.it-sudparis.eu/~berger_o/weblog/2012/03/23/how-to-manage-and-export-bibliographic-notesrefs-in-org-mode/

Thanks for org-ref.

-Andreas

Re: org-ref code

[John Kitchin]

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Here is a way you can add new citation formats to the reftex format:

;; get builtin formats
(setq formats (nth 2 (assoc 'org reftex-cite-format-builtin)))

;; add new format
(setf (nth 2 (assoc 'org reftex-cite-format-builtin))
      (append formats '((?W  . "textcite:%l")
            (?z  . "newcite:%l"))))

This does not define the links, but it does add the formats to the reftex
menu.

I have figured out how to add new citation links without alot of cut and
pasted code. I do not use biblatex much though. What are the common
citation formats, and are they mostly written as \citation{label}?

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 Mon, May 12, 2014 at 4:12 AM, Andreas Reuleaux <andreas@a-rx.info> wrote:

> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
>
> > C-c ] should be bound by default to org-ref-insert-cite-link. It is
> defined
> > in a hook function in line 104 of org-ref.org.
> >
> > I made a custom variable to store the key-binding, but I realized it
> > probably doesn't help, since the binding
> >
> >
> >>
> >> 1. C-u on it does not give me a choice of citation method
> >>
> >
> > If you type C-u M-x  org-ref-insert-cite-link
> >
> > do you get a choice?
> >
> > I just tried this on a fresh pull and it does work for me. I am not sure
> > why this wouldn't work for you.  Do you tangle the .el file from the .org
> > file? I have this code somewhere else to build it when needed:
>
>
> I can confirm that C-c ] and C-u C-c ]
> work fine for me.
>
> my setup if fairly simple (with org-ref.el tangled from org-ref.org)
>
>   (require 'org-ref)
>
>   (custom-set-variables
>    '(org-ref-bibliography-notes "notes.org")
>    '(org-ref-default-bibliography  (list "refs.bib"))
>    ;; '(org-ref-pdf-directory "...")
>    ;; '(org-ref-default-citation-link "...")
>    ;; '(org-ref-insert-cite-key "...")
>    )
>
> looking forward to discover more of org-ref.
>
> FWIW, I was using textcite:... (with biblatex) as well, helped myself by
> just inserting a cite:... and then changing the link with C-c C-l from
> cite to textcite. But I really need read up on all those different
> citations commands once more, maybe textcite is not really necessary?
> Could I add it somehow to the list of choices available in "C-u C-c ]" ?
> (I realized there are citetext, citep*, citep as well, that I yet have
> to discover).
>
> By the way: the org-ref.org literate programming docs are fine
> for someone interested in the gory details / relatively experienced.
> Ist there a simpler document just describing its usage - that
> you would hand out to your chemistry students e. g. ?
>
> Somehting maybe explaining the differences from the other approaches
> that can be found e g in
>
>
> http://tincman.wordpress.com/2011/01/04/research-paper-management-with-emacs-org-mode-and-reftex/
>
>
> http://www-public.it-sudparis.eu/~berger_o/weblog/2012/03/23/how-to-manage-and-export-bibliographic-notesrefs-in-org-mode/
>
> Thanks for org-ref.
>
> -Andreas
>
>
>

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Re: org-ref code

[Eric S Fraga]

On Sunday, 11 May 2014 at 14:48, John Kitchin wrote:

[...]

> C-c ] should be bound by default to org-ref-insert-cite-link. It is defined
> in a hook function in line 104 of org-ref.org.

Yes.  It is.  

I don't use this binding.  I use evil mode and don't like chorded
commands.  I have org-ref-insert-cite-link bound to ", r" but that's
beside the point, in any case.

>> 1. C-u on it does not give me a choice of citation method
>
> If you type C-u M-x  org-ref-insert-cite-link
> do you get a choice?

No.  I get prompted for the expression to search for and then I get
prompted for an optional argument and the final text inserted in my org
buffer is \cite{....}, not cite:....

> I just tried this on a fresh pull and it does work for me. I am not sure
> why this wouldn't work for you.  Do you tangle the .el file from the .org
> file? I have this code somewhere else to build it when needed:

I do tangle and then eval-buffer just to make sure I have the right code
loaded.

>> 2. the link inserted "looks" like a link (it's blue) but there are
>>      actually no [[...]] characters surrounding it.
>>
> There are no [[...]]. The links work fine without them for me. Are they
> necessary for some reason? I can add them, but since they do not do
> anything but disappear in this case, I leave them out.  

Well, I obviously have something not quite configured properly in my
environment.  The cite: text is highlighted as a link in the org buffer
(as it should with org-highlight-links set) but is treated as simple
text when exported so that I simply get "cite:..." in the latex
output.  If I "C-c C-l" it and don't add a description, the org buffer
*looks* the same but the export works because org and/or the exporter
know that it's a link.

Is there some org variable I have not set that tells org to treat cite:
plain text as a link on export?  Obviously org already recognises it as
a link but the export doesn't...  org-link-protocols and org-link-types
look fine.

I am most puzzled... :(

By the way, in my use case, even if the above would work properly, it
would still definitely help if the [[...]] were inserted as I sometimes
use superscript indices and in those cases I do not want any whitespace
between the text and the citation that follows.  Anyway, this is
secondary.

thanks,
eric

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-949-g751506

Re: org-ref code

[Andreas Reuleaux]

Eric S Fraga <e.fraga@ucl.ac.uk> writes:

> Is there some org variable I have not set that tells org to treat cite:
> plain text as a link on export?  Obviously org already recognises it as
> a link but the export doesn't...  org-link-protocols and org-link-types
> look fine.
>

Being just a org-ref beginner, I don't know if there is a more
straightforward solution but, I have configured:


  (org-add-link-type
   "cite"
   'org-ref-cite-onclick-minibuffer-menu
   ;; formatting
   (lambda (keyword desc format)
     (cond
      ((eq format 'html) (format "(<cite>%s</cite>)" path))
      ((eq format 'latex)
       (concat "\\cite{"
               (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
               "}")))))


and similarily for autocite and textcite (the citation types that I am
using), that works for me. Adapted (copied) from the org-add-link-type
for autocite given in the org-ref.org description.  Not sure if this
should just work out of the box (without configuration), but then, it's
not that much code.

-Andreas

Re: org-ref code

[John Kitchin]

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that should work out of the box, and that link is defined in org-ref as

(org-add-link-type
 "cite"
 'org-ref-cite-onclick-minibuffer-menu
 'org-ref-cite-link-format)

I am not sure why it would not work out of the box.



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 Mon, May 12, 2014 at 1:20 PM, Andreas Reuleaux <andreas@a-rx.info> wrote:

> Eric S Fraga <e.fraga@ucl.ac.uk> writes:
>
> > Is there some org variable I have not set that tells org to treat cite:
> > plain text as a link on export?  Obviously org already recognises it as
> > a link but the export doesn't...  org-link-protocols and org-link-types
> > look fine.
> >
>
> Being just a org-ref beginner, I don't know if there is a more
> straightforward solution but, I have configured:
>
>
>   (org-add-link-type
>    "cite"
>    'org-ref-cite-onclick-minibuffer-menu
>    ;; formatting
>    (lambda (keyword desc format)
>      (cond
>       ((eq format 'html) (format "(<cite>%s</cite>)" path))
>       ((eq format 'latex)
>        (concat "\\cite{"
>                (mapconcat (lambda (key) key)
> (org-ref-split-and-strip-string keyword) ",")
>                "}")))))
>
>
> and similarily for autocite and textcite (the citation types that I am
> using), that works for me. Adapted (copied) from the org-add-link-type
> for autocite given in the org-ref.org description.  Not sure if this
> should just work out of the box (without configuration), but then, it's
> not that much code.
>
> -Andreas
>
>
>
>

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Re: org-ref code

[Andreas Reuleaux]

John Kitchin <jkitchin@andrew.cmu.edu> writes:

> that should work out of the box, and that link is defined in org-ref as
>
> (org-add-link-type
>  "cite"
>  'org-ref-cite-onclick-minibuffer-menu
>  'org-ref-cite-link-format)
>
> I am not sure why it would not work out of the box.
>

They *do* work out of the box, as I can see now.


-Andreas

Re: org-ref code

[Eric S Fraga]

On Monday, 12 May 2014 at 13:26, John Kitchin wrote:
> that should work out of the box, and that link is defined in org-ref as
>
> (org-add-link-type
>  "cite"
>  'org-ref-cite-onclick-minibuffer-menu
>  'org-ref-cite-link-format)

And I used to have my own already in any case.

>
> I am not sure why it would not work out of the box.

Neither do I.  The more annoying thing is that I cannot get org-ref to
work at all with emacs -q and a minimal org document.  Would you maybe
post the minimum setup for getting org-ref to work, along with a minimal
org document?

thanks,
eric

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559

Re: org-ref code

[John Kitchin]

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You can see a document I wrote using org-ref here:
http://kitchingroup.cheme.cmu.edu/org/2014/05/13/Using-org-ref-for-citations-and-references.org

You will want to pull a current version. I added some code so it is in
principle easy for you to add your own citation types and use the org-ref
machinery to insert citations.


I made a little screencast here: http://screencast.com/t/bxfafVydE

j

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 Tue, May 13, 2014 at 7:00 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> On Monday, 12 May 2014 at 13:26, John Kitchin wrote:
> > that should work out of the box, and that link is defined in org-ref as
> >
> > (org-add-link-type
> >  "cite"
> >  'org-ref-cite-onclick-minibuffer-menu
> >  'org-ref-cite-link-format)
>
> And I used to have my own already in any case.
>
> >
> > I am not sure why it would not work out of the box.
>
> Neither do I.  The more annoying thing is that I cannot get org-ref to
> work at all with emacs -q and a minimal org document.  Would you maybe
> post the minimum setup for getting org-ref to work, along with a minimal
> org document?
>
> thanks,
> eric
>
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559
>

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Re: org-ref code

[Eric S Fraga]

On Tuesday, 13 May 2014 at 14:51, John Kitchin wrote:
> You can see a document I wrote using org-ref here:
> http://kitchingroup.cheme.cmu.edu/org/2014/05/13/Using-org-ref-for-citations-and-references.org
>
> You will want to pull a current version. I added some code so it is in
> principle easy for you to add your own citation types and use the org-ref
> machinery to insert citations.

Thanks for this.

It didn't work but I have now figured out why!

Your code requires dash version 2.6.0 and I had version 2.4.0.  The need
for the latest version is noted in a comment in your code but the code
itself doesn't check (and probably cannot?).  With 2.6.0, I'm much
further!  Links are now recognised properly.

I still have a problem in that a very minimal file, with one cite: link
and a bibliography: link, doesn't compile because bibtex complains of no
\bibstyle.  Not sure why it's complaining but I will continue debugging.

thanks,
eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: org-ref code

[Eric S Fraga]

John,

another data point.  When I try to load an org file, once org-ref is
loaded, I get the following problem:

Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  re-search-forward(nil 10001 t)
  tex-main-file()
  reftex-TeX-master-file()
  reftex-tie-multifile-symbols()
  reftex-access-scan-info((16))
  reftex-parse-all()
  (and (buffer-file-name) (file-exists-p (buffer-file-name)) (global-auto-revert-mode t) (reftex-parse-all))
  org-mode-reftex-setup()
  run-hooks(change-major-mode-after-body-hook text-mode-hook outline-mode-hook org-mode-hook)
  apply(run-hooks (change-major-mode-after-body-hook text-mode-hook outline-mode-hook org-mode-hook))
  run-mode-hooks(org-mode-hook)

Because of this, org-ref doesn't get initialised properly.

Any idea what may be causing this?  Do I need to configure auctex or
similar?

thanks,
eric

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: org-ref code

[John Kitchin]

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interesting. I do have auxtex installed, but I don't think I configure it
anywhere. I do require reftex and reftex-cite in my init files. I also set
the default reftex bibliography.

(setq reftex-default-bibliography
'("~/Dropbox/bibliography/references.bib"))

I will try to reproduce this tomorrow.

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 Tue, May 13, 2014 at 4:11 PM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> John,
>
> another data point.  When I try to load an org file, once org-ref is
> loaded, I get the following problem:
>
> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>   re-search-forward(nil 10001 t)
>   tex-main-file()
>   reftex-TeX-master-file()
>   reftex-tie-multifile-symbols()
>   reftex-access-scan-info((16))
>   reftex-parse-all()
>   (and (buffer-file-name) (file-exists-p (buffer-file-name))
> (global-auto-revert-mode t) (reftex-parse-all))
>   org-mode-reftex-setup()
>   run-hooks(change-major-mode-after-body-hook text-mode-hook
> outline-mode-hook org-mode-hook)
>   apply(run-hooks (change-major-mode-after-body-hook text-mode-hook
> outline-mode-hook org-mode-hook))
>   run-mode-hooks(org-mode-hook)
>
> Because of this, org-ref doesn't get initialised properly.
>
> Any idea what may be causing this?  Do I need to configure auctex or
> similar?
>
> thanks,
> eric
>
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org
> release_8.2.6-958-g7c8559-git
>

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Re: org-ref code

[Eric S Fraga]

[-- Attachment #1: Type: text/plain, Size: 1391 bytes --]

On Tuesday, 13 May 2014 at 20:28, John Kitchin wrote:
> interesting. I do have auxtex installed, but I don't think I configure it
> anywhere. I do require reftex and reftex-cite in my init files. I also set
> the default reftex bibliography.
>
> (setq reftex-default-bibliography
> '("~/Dropbox/bibliography/references.bib"))
>
> I will try to reproduce this tomorrow.

Hi John,

In case this helps, if I start emacs with -q and evaluate the contents
of emacs-minimal.el (attached) and then visit orgref.org (attached), I can insert a
reference (references.bib also attached) but the resulting latex doesn't
work because bibtex complains about missing bibstyle.  

If I add the LaTeX directive to specify the bibliography style (as the
attached file has), everthing works.  This includes C-u C-c ] asking for
type of citation.  

How do I specify the bibstyle for org-ref?

When I say that everything works, it works with this minimal
configuration but not yet in my full configuration.  But that's my
problem.  Somehow, I am making the latex exporter not handle cite:
links.  Very strange.  I'll get back to you on this in due course!

I am actually using Emacs 24.4, not 24.3.  I'm tracking emacs-snapshot
which is the development version as I like to live dangerously ;-)

thanks again for org-ref,
eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: orgref.org --]
[-- Type: text/x-org, Size: 309 bytes --]

# -*- org-latex-pdf-process: ("pdflatex %b" "bibtex %b" "pdflatex %b" "pdflatex %b") -*-
#+title: test out org-ref
* Introduction
The paper by somebody 
cite:aaltola-2002 is most interesting.  Also, autocite:aaltola-2002 is exciting.
* References

#+latex: \bibliographystyle{acm}
bibliography:references.bib

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: references.bib --]
[-- Type: text/x-bibtex, Size: 239 bytes --]

@Article{aaltola-2002,
  author = 	 {J. Aaltola},
  title = 	 {Simultaneous synthesis of flexible heat exchanger network},
  journal = 	 {Applied Thermal Engineering},
  year = 	 2002,
  volume =	 22,
  number =	 8,
  pages =	 {907-918}
}

[-- Attachment #4: emacs-minimal.el --]
[-- Type: application/emacs-lisp, Size: 124 bytes --]

Re: org-ref code

[Andreas Reuleaux]

Eric S Fraga <e.fraga@ucl.ac.uk> writes:


> How do I specify the bibstyle for org-ref?


I am not sure if I understand your question correctly
and John certainly has more insight here, but I have in
my org document

#+LaTeX_HEADER: \include{ltxhdr}

and within that ltxhdr.tex I have among other config settings

  \usepackage[backend=bibtex,style=authoryear]{biblatex}
  \addbibresource{refs.bib}

I could have written several lines of 

#+LaTeX_HEADER: \usepackage[backend=bibtex,style=authoryear]{biblatex}
#+LaTeX_HEADER: \addbibresource{refs.bib}

instead.

There is no specific bibstyle of org-ref (correct, John?), that's the
job of latex, you will be happy if:

* your org mode has clickable citations links,

* let's you insert citations in a comfortably manner

* you can jump between refs and labels etc.

* all of those citations get exported to their latex
  equivalents

If for some reason your citations get exported to latex, say
cite:foo to \cite{foo}, but still don't appear in your
final pdf, than you have to tweek your latex settings,
obviously. - Maybe forgot to call bibtex(8) on your document?

I run these:
* an emacs batch script, tex.el to get the document.tex
  from document.org
* xelatex -8bit -shell-escape document.tex
* bibtex8 document
* xelatex document
  again, etc.

You can check your latex toolchain independently from
your org-ref config.

HTH,
  -Andreas
  

Re: org-ref code

[Sharon Kimble]

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Andreas Reuleaux <andreas@a-rx.info> writes:

> Eric S Fraga <e.fraga@ucl.ac.uk> writes:
>
>
>> How do I specify the bibstyle for org-ref?
>
>
> I am not sure if I understand your question correctly
> and John certainly has more insight here, but I have in
> my org document
>
> #+LaTeX_HEADER: \include{ltxhdr}
>
> and within that ltxhdr.tex I have among other config settings
>
>   \usepackage[backend=bibtex,style=authoryear]{biblatex}
>   \addbibresource{refs.bib}
>
> I could have written several lines of 
>
> #+LaTeX_HEADER: \usepackage[backend=bibtex,style=authoryear]{biblatex}
> #+LaTeX_HEADER: \addbibresource{refs.bib}
>
> instead.
>
> There is no specific bibstyle of org-ref (correct, John?), that's the
> job of latex, you will be happy if:
>
> * your org mode has clickable citations links,
>
> * let's you insert citations in a comfortably manner
>
> * you can jump between refs and labels etc.
>
> * all of those citations get exported to their latex
>   equivalents
>
> If for some reason your citations get exported to latex, say
> cite:foo to \cite{foo}, but still don't appear in your
> final pdf, than you have to tweek your latex settings,
> obviously. - Maybe forgot to call bibtex(8) on your document?
>
> I run these:
> * an emacs batch script, tex.el to get the document.tex
>   from document.org
> * xelatex -8bit -shell-escape document.tex
> * bibtex8 document
> * xelatex document
>   again, etc.
>
> You can check your latex toolchain independently from
> your org-ref config.
>
> HTH,
>   -Andreas

That seems a very long winded way round things! For your information
this is a batch script that I'm using for generating a PDF in pure
latex, and all I have to do is to cd to the directory where the
files are, and then just enter "pdfbuild" in the command-line. It
does all the rest itself, and you could easily adapt it for your
circumstances
--8<---------------cut here---------------start------------->8---
#!/bin/bash
set -e
#set -x

#variables
filename="uh2014"

#############
xelatex $filename
biber $filename
biber $filename
xelatex $filename 
biber $filename
xelatex $filename 
makeindex $filename
makeindex $filename
xelatex $filename
makeglossaries $filename
xelatex $filename
xelatex $filename
--8<---------------cut here---------------end--------------->8---

It handles and generates the references, the glossary, and the index
as well as the body of the document. 

All you have to do is enter your "foo.tex" where foo is the name of
your generated tex file, and then let the script take over.

Sharon.
-- 
A taste of linux = http://www.sharons.org.uk
my git repo = https://bitbucket.org/boudiccas/dots
TGmeds = http://www.tgmeds.org.uk
Debian testing, Fluxbox 1.3.5, emacs 24.3.91.1

[-- Attachment #2: signature.asc --]
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Re: org-ref code

[Andreas Reuleaux]

Well, I know how to write shell scripts,
and have something similar encoded in a shake file
(haskell make replacement), for that matter,
but prefer to have xelatex not called 5 times
during every little development step.
Anyway thanks a lot.

My point here really was, that org-ref and
the latex chains are separate and can be
separately tested.

-Andreas


Sharon Kimble <boudiccas@skimble.plus.com> writes:

> Andreas Reuleaux <andreas@a-rx.info> writes:
>
>> Eric S Fraga <e.fraga@ucl.ac.uk> writes:
>>
>>
>>> How do I specify the bibstyle for org-ref?
>>
>>
>> I am not sure if I understand your question correctly
>> and John certainly has more insight here, but I have in
>> my org document
>>
>> #+LaTeX_HEADER: \include{ltxhdr}
>>
>> and within that ltxhdr.tex I have among other config settings
>>
>>   \usepackage[backend=bibtex,style=authoryear]{biblatex}
>>   \addbibresource{refs.bib}
>>
>> I could have written several lines of 
>>
>> #+LaTeX_HEADER: \usepackage[backend=bibtex,style=authoryear]{biblatex}
>> #+LaTeX_HEADER: \addbibresource{refs.bib}
>>
>> instead.
>>
>> There is no specific bibstyle of org-ref (correct, John?), that's the
>> job of latex, you will be happy if:
>>
>> * your org mode has clickable citations links,
>>
>> * let's you insert citations in a comfortably manner
>>
>> * you can jump between refs and labels etc.
>>
>> * all of those citations get exported to their latex
>>   equivalents
>>
>> If for some reason your citations get exported to latex, say
>> cite:foo to \cite{foo}, but still don't appear in your
>> final pdf, than you have to tweek your latex settings,
>> obviously. - Maybe forgot to call bibtex(8) on your document?
>>
>> I run these:
>> * an emacs batch script, tex.el to get the document.tex
>>   from document.org
>> * xelatex -8bit -shell-escape document.tex
>> * bibtex8 document
>> * xelatex document
>>   again, etc.
>>
>> You can check your latex toolchain independently from
>> your org-ref config.
>>
>> HTH,
>>   -Andreas
>
> That seems a very long winded way round things! For your information
> this is a batch script that I'm using for generating a PDF in pure
> latex, and all I have to do is to cd to the directory where the
> files are, and then just enter "pdfbuild" in the command-line. It
> does all the rest itself, and you could easily adapt it for your
> circumstances
> #!/bin/bash
> set -e
> #set -x
>
> #variables
> filename="uh2014"
>
> #############
> xelatex $filename
> biber $filename
> biber $filename
> xelatex $filename 
> biber $filename
> xelatex $filename 
> makeindex $filename
> makeindex $filename
> xelatex $filename
> makeglossaries $filename
> xelatex $filename
> xelatex $filename
>
> It handles and generates the references, the glossary, and the index
> as well as the body of the document. 
>
> All you have to do is enter your "foo.tex" where foo is the name of
> your generated tex file, and then let the script take over.
>
> Sharon.

Re: org-ref code

[Eric S Fraga]

On Wednesday, 14 May 2014 at 20:03, Andreas Reuleaux wrote:
> Eric S Fraga <e.fraga@ucl.ac.uk> writes:
>> How do I specify the bibstyle for org-ref?

[...]

> There is no specific bibstyle of org-ref (correct, John?), that's the

That's what I wanted to confirm.  And it has been confirmed (by both you
and another email from John).  Thanks.
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: org-ref code

[John Kitchin]

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Good. I am glad to hear you are making some progress!

you have to specify the bibliography style for latex export somewhere in
the document. You can use a bibliographystyle link for bibtex, eg.
bibliographystyle:unsrt. That will get exported to
\bibliographystyle{unsrt}. That link does not do anything but export to
latex. or you can simply put \bibliographystyle{unsrt} above the
bibliography link. For any other thing like biblatex, just put the code
that specifies the style where it belongs, e.g. in the header with
#+latex_header: or at the end with the raw latex commands. Not all
documents require a style, article classes do, but the revtex4-1 class, for
example defines the style for you.

I wonder if you are adding another cite link later that overrides my cite
link. do the other citation links export ok, e.g. autocite, citeyear,
etc...?

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 Wed, May 14, 2014 at 2:17 PM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> On Tuesday, 13 May 2014 at 20:28, John Kitchin wrote:
> > interesting. I do have auxtex installed, but I don't think I configure it
> > anywhere. I do require reftex and reftex-cite in my init files. I also
> set
> > the default reftex bibliography.
> >
> > (setq reftex-default-bibliography
> > '("~/Dropbox/bibliography/references.bib"))
> >
> > I will try to reproduce this tomorrow.
>
> Hi John,
>
> In case this helps, if I start emacs with -q and evaluate the contents
> of emacs-minimal.el (attached) and then visit orgref.org (attached), I
> can insert a
> reference (references.bib also attached) but the resulting latex doesn't
> work because bibtex complains about missing bibstyle.
>
> If I add the LaTeX directive to specify the bibliography style (as the
> attached file has), everthing works.  This includes C-u C-c ] asking for
> type of citation.
>
> How do I specify the bibstyle for org-ref?
>
> When I say that everything works, it works with this minimal
> configuration but not yet in my full configuration.  But that's my
> problem.  Somehow, I am making the latex exporter not handle cite:
> links.  Very strange.  I'll get back to you on this in due course!
>
> I am actually using Emacs 24.4, not 24.3.  I'm tracking emacs-snapshot
> which is the development version as I like to live dangerously ;-)
>
> thanks again for org-ref,
> eric
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org
> release_8.2.6-958-g7c8559-git
>

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Re: org-ref code

[Eric S Fraga]

On Wednesday, 14 May 2014 at 16:35, John Kitchin wrote:

[...]

> I wonder if you are adding another cite link later that overrides my cite
> link. do the other citation links export ok, e.g. autocite, citeyear,
> etc...?

The problem is not how links are handled but the fact that implicit
links, i.e. those not surrounded by [[...]], are not recognised as links
on export.  This applies to all citation links but not, for instance,
http:.  There has to be something in org that I need to set or that I
have set that affects this behaviour but I just do not seem to find it.

I am now bisecting my initialisation code to see if it is me setting
something but I do wonder if there is something you have set to tell org
to recognise implicitly defined links?

In any case, would it be possible to have org-ref insert proper links,
i.e. [[cite:joe-2014]], maybe as an option?  I often use superscripts
for citation references and a space before the superscript looks ugly!
And my problem would be solved... :)

thanks again,
eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: org-ref code

[Eric S Fraga]

John,

I am in the process of bisecting my initialisation.  Something I have
set definitely stops org (whether 8.2.5c which comes with emacs
24.4.50.2 or 8.2.6-958) from recognising cite:... etc. as links.

However, I have been re-building up from no initialisation bit by
bit.  Right from the start, I get the error I posted yesterday:

--8<---------------cut here---------------start------------->8---
Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  re-search-forward(nil 10001 t)
  tex-main-file()
  reftex-TeX-master-file()
  reftex-tie-multifile-symbols()
  reftex-access-scan-info((16))
  reftex-parse-all()
  (and (buffer-file-name) (file-exists-p (buffer-file-name)) (global-auto-revert-mode t) (reftex-parse-all))
  org-mode-reftex-setup()
  run-hooks(change-major-mode-after-body-hook text-mode-hook outline-mode-hook org-mode-hook)
  apply(run-hooks (change-major-mode-after-body-hook text-mode-hook outline-mode-hook org-mode-hook))
  run-mode-hooks(org-mode-hook)
  org-mode()
  set-auto-mode-0(org-mode nil)
  set-auto-mode()
  normal-mode(t)
  after-find-file(nil t)
  find-file-noselect-1(#<buffer t.org> "~/s/test/t.org" nil nil "~/synced/test/t.org" (10095713 2055))
  find-file-noselect("~/s/test/t.org" nil nil t)
  find-file("~/s/test/t.org" t)
  call-interactively(find-file nil nil)
  command-execute(find-file)
--8<---------------cut here---------------end--------------->8---

This happens when I try to visit any org file *once* I have loaded
org-ref the first time.  It doesn't happen before org-ref is loaded.

I am starting to despair, I must admit!  I wonder if there is a conflict
between Emacs 24.4.50 and org-ref?  Or do you have some other setting
for reftex that is not the default?

Anyway, I have to get some work done so I will do without org-ref for
the time being.  I'll revisit later.

thanks again for all your time,
eric

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: org-ref code

[John Kitchin]

[-- Attachment #1: Type: text/plain, Size: 3503 bytes --]

That is pretty strange. I used this to get a minimally working install of
org-ref. I deleted ~/.emacs.d, and ran emacs -q and then executed this code
block.

* installation

You need the dash package. Use these repositories, and  install dash.

#+BEGIN_SRC emacs-lisp
  (require 'package)

  (setq package-archives
        '(("org"         . "http://orgmode.org/elpa/")
          ("gnu"         . "http://elpa.gnu.org/packages/")
          ("melpa" . "http://melpa.milkbox.net/packages/")
          ))
  (package-refresh-contents)
  (package-install 'dash)

  (org-babel-load-file "~/Dropbox/kitchingroup/jmax/org-ref.org")

  ;; this function is normally run as a hook. we run it manually here to
  ;; get started.
  (org-mode-reftex-setup)
#+END_SRC

#+RESULTS:
: org-ref-insert-cite-link

After that, it works like I expect.

Your error seems to be coming from reftex. I wonder if you have something
set that is making it look for a TeX-master or something, which eventually
results in nil, which is failing here: re-search-forward(nil 10001 t). Or
maybe you need to set something to turn that off. Perhaps some default
changed?


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, May 15, 2014 at 4:17 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> John,
>
> I am in the process of bisecting my initialisation.  Something I have
> set definitely stops org (whether 8.2.5c which comes with emacs
> 24.4.50.2 or 8.2.6-958) from recognising cite:... etc. as links.
>
> However, I have been re-building up from no initialisation bit by
> bit.  Right from the start, I get the error I posted yesterday:
>
> --8<---------------cut here---------------start------------->8---
> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>   re-search-forward(nil 10001 t)
>   tex-main-file()
>   reftex-TeX-master-file()
>   reftex-tie-multifile-symbols()
>   reftex-access-scan-info((16))
>   reftex-parse-all()
>   (and (buffer-file-name) (file-exists-p (buffer-file-name))
> (global-auto-revert-mode t) (reftex-parse-all))
>   org-mode-reftex-setup()
>   run-hooks(change-major-mode-after-body-hook text-mode-hook
> outline-mode-hook org-mode-hook)
>   apply(run-hooks (change-major-mode-after-body-hook text-mode-hook
> outline-mode-hook org-mode-hook))
>   run-mode-hooks(org-mode-hook)
>   org-mode()
>   set-auto-mode-0(org-mode nil)
>   set-auto-mode()
>   normal-mode(t)
>   after-find-file(nil t)
>   find-file-noselect-1(#<buffer t.org> "~/s/test/t.org" nil nil
> "~/synced/test/t.org" (10095713 2055))
>   find-file-noselect("~/s/test/t.org" nil nil t)
>   find-file("~/s/test/t.org" t)
>   call-interactively(find-file nil nil)
>   command-execute(find-file)
> --8<---------------cut here---------------end--------------->8---
>
> This happens when I try to visit any org file *once* I have loaded
> org-ref the first time.  It doesn't happen before org-ref is loaded.
>
> I am starting to despair, I must admit!  I wonder if there is a conflict
> between Emacs 24.4.50 and org-ref?  Or do you have some other setting
> for reftex that is not the default?
>
> Anyway, I have to get some work done so I will do without org-ref for
> the time being.  I'll revisit later.
>
> thanks again for all your time,
> eric
>
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org
> release_8.2.6-958-g7c8559-git
>

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Re: org-ref code

[Eric S Fraga]

On Thursday, 15 May 2014 at 09:05, John Kitchin wrote:

[...]

> Your error seems to be coming from reftex. I wonder if you have something
> set that is making it look for a TeX-master or something, which eventually
> results in nil, which is failing here: re-search-forward(nil 10001 t). Or
> maybe you need to set something to turn that off. Perhaps some default
> changed?

Yes, that is my feeling as well but I am totally unable to find what may
be causing it.

I haven't yet looked to see whether there have been any changes in
reftex itself in the latest emacs.

I continue to investigate!

thanks,
eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: org-ref code

[Eric S Fraga]

On Thursday, 15 May 2014 at 09:05, John Kitchin wrote:
> Your error seems to be coming from reftex. 

Well, it seems that if you are going to use reftex in emacs 24.4.x, you
need to define some variables.  I put the following in your
org-mode-reftex-setup function:

    (setq-local tex-start-of-header "%\\*\\*start of header")
    (setq-local tex-end-of-header "%\\*\\*end of header")

immediately after loading reftex and things work better (I haven't
checked whether everything works yet).

The problem is that tex-mode assumes that it is active in a mode that
has been derived from tex-mode (such as latex-mode or plain-tex-mode)
and those modes define the variables above.  Org-mode doesn't!

This may be a change in tex-mode for the latest emacs versions?  I
cannot verify this.

Am I correct in believing that you are using emacs 24.3?

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: org-ref code

[John Kitchin]

[-- Attachment #1: Type: text/plain, Size: 1302 bytes --]

yes, I am using emacs 24.3.

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, May 15, 2014 at 9:30 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> On Thursday, 15 May 2014 at 09:05, John Kitchin wrote:
> > Your error seems to be coming from reftex.
>
> Well, it seems that if you are going to use reftex in emacs 24.4.x, you
> need to define some variables.  I put the following in your
> org-mode-reftex-setup function:
>
>     (setq-local tex-start-of-header "%\\*\\*start of header")
>     (setq-local tex-end-of-header "%\\*\\*end of header")
>
> immediately after loading reftex and things work better (I haven't
> checked whether everything works yet).
>
> The problem is that tex-mode assumes that it is active in a mode that
> has been derived from tex-mode (such as latex-mode or plain-tex-mode)
> and those modes define the variables above.  Org-mode doesn't!
>
> This may be a change in tex-mode for the latest emacs versions?  I
> cannot verify this.
>
> Am I correct in believing that you are using emacs 24.3?
>
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org
> release_8.2.6-958-g7c8559-git
>

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Re: org-ref code

[Eric S Fraga]

On Thursday, 15 May 2014 at 10:19, John Kitchin wrote:
> yes, I am using emacs 24.3.

Can you have a look at tex-mode.el and see if the variables:

>>     (setq-local tex-start-of-header "%\\*\\*start of header")
>>     (setq-local tex-end-of-header "%\\*\\*end of header")

are (a) used and (b) defined somewhere other than in the definitions of
derived modes?

By the way, I have no idea how these are being used but maybe they could
be adapted to org syntax ("# start of header", say)?

In any case, some good news!  I have tracked down the problem with
citations not being picked up by the exporter.

If I load ox-latex *before* org-ref, cite: and other new links are not
picked up.  If I load org-ref before ox-latex, everything seems to work
fine.  It would seem that ox-latex is defining the links that are valid
and this is not being updated subsequently?  I've not tracked this down
yet but maybe Nicolas should have a look?

We're getting there!

thanks,
eric
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: org-ref code

[Eric S Fraga]

On Thursday, 15 May 2014 at 15:31, Eric S Fraga wrote:

[...]

> If I load ox-latex *before* org-ref, cite: and other new links are not
> picked up.  If I load org-ref before ox-latex, everything seems to work
> fine.  It would seem that ox-latex is defining the links that are valid
> and this is not being updated subsequently?  I've not tracked this down
> yet but maybe Nicolas should have a look?

Following up on myself: org-ref has to be loaded *before* ox.el which
means also before any ox-*.el files.

I thought the problem was that the link types regexps used by org were
not being updated but invoking org-make-link-regexps after loading
org-ref had no effect.  Oh well.

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-958-g7c8559-git

Re: org-ref code

[John Kitchin]

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I can see the desire to avoid the space with a superscript, but that is a
latex specific formatting issue, that is probably taken care of with some
package. In the packages we use (usually natmove), citations are moved to
the correct side of punctuation, for example, so we always put them on the
left where the logically make sense (eg because it is "grouped" in the
sentence being cited. the latex package moves the superscripts to the
right. I think it also works on spaces In org-mode some
text[[cite:yoo-2014-theor-analy]] is also "ugly" ;) and harder to read.
That gives us the best of both worlds (org and latex)

I don't think I have done anything to make the naked links work.

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, May 15, 2014 at 2:58 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> On Wednesday, 14 May 2014 at 16:35, John Kitchin wrote:
>
> [...]
>
> > I wonder if you are adding another cite link later that overrides my cite
> > link. do the other citation links export ok, e.g. autocite, citeyear,
> > etc...?
>
> The problem is not how links are handled but the fact that implicit
> links, i.e. those not surrounded by [[...]], are not recognised as links
> on export.  This applies to all citation links but not, for instance,
> http:.  There has to be something in org that I need to set or that I
> have set that affects this behaviour but I just do not seem to find it.
>
> I am now bisecting my initialisation code to see if it is me setting
> something but I do wonder if there is something you have set to tell org
> to recognise implicitly defined links?
>
> In any case, would it be possible to have org-ref insert proper links,
> i.e. [[cite:joe-2014]], maybe as an option?  I often use superscripts
> for citation references and a space before the superscript looks ugly!
> And my problem would be solved... :)
>
> thanks again,
> eric
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org
> release_8.2.6-958-g7c8559-git
>

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Re: org-ref code

[Andreas Reuleaux]

Eric,

I don't have auctex installed, and org-ref works fine for me.

But I do run a recent self-compiled emacs 24 (haven't tested yet,
if it works with my older emacs24 from debian as well),
and I get updated packages like dash relatively often via cask
( https://github.com/cask/cask , http://cask.github.io/ ),
i. e. I have in my Cask file

  (depends-on "dash")

so it wouldn't have happend to me to have an outdated dash pkg,
isolating your problem and pointing at what exactly is causing your
trouble is of course more difficult (and creating a minimal config that
works for me takes more time than I currently have, sorry).

Hope this helps, nevertheless


-Andreas



Eric S Fraga <e.fraga@ucl.ac.uk> writes:

> John,
>
> another data point.  When I try to load an org file, once org-ref is
> loaded, I get the following problem:
>
> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>   re-search-forward(nil 10001 t)
>   tex-main-file()
>   reftex-TeX-master-file()
>   reftex-tie-multifile-symbols()
>   reftex-access-scan-info((16))
>   reftex-parse-all()
>   (and (buffer-file-name) (file-exists-p (buffer-file-name))
> (global-auto-revert-mode t) (reftex-parse-all))
>   org-mode-reftex-setup()
>   run-hooks(change-major-mode-after-body-hook text-mode-hook
> outline-mode-hook org-mode-hook)
>   apply(run-hooks (change-major-mode-after-body-hook text-mode-hook
> outline-mode-hook org-mode-hook))
>   run-mode-hooks(org-mode-hook)
>
> Because of this, org-ref doesn't get initialised properly.
>
> Any idea what may be causing this?  Do I need to configure auctex or
> similar?
>
> thanks,
> eric

Re: org-ref code

[John Kitchin]

[-- Attachment #1: Type: text/plain, Size: 2525 bytes --]

I also run emacs 24.3.

nearly my whole setup is here: https://github.com/jkitchin/jmax

If you are on windows, you should be able to clone that repository, and run
jmax.bat which will run the emacs binary in that repository and load the
jmax code which includes org-ref. You may not want to use my setup all the
time, but it might help figure out what is different with your setup.

For Macs or Linux, you just need to run something like "emacs -q -l
path/to/jmax/init.el" to try it out.

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 Tue, May 13, 2014 at 11:58 PM, Andreas Reuleaux <andreas@a-rx.info>wrote:

> Eric,
>
> I don't have auctex installed, and org-ref works fine for me.
>
> But I do run a recent self-compiled emacs 24 (haven't tested yet,
> if it works with my older emacs24 from debian as well),
> and I get updated packages like dash relatively often via cask
> ( https://github.com/cask/cask , http://cask.github.io/ ),
> i. e. I have in my Cask file
>
>   (depends-on "dash")
>
> so it wouldn't have happend to me to have an outdated dash pkg,
> isolating your problem and pointing at what exactly is causing your
> trouble is of course more difficult (and creating a minimal config that
> works for me takes more time than I currently have, sorry).
>
> Hope this helps, nevertheless
>
>
> -Andreas
>
>
>
> Eric S Fraga <e.fraga@ucl.ac.uk> writes:
>
> > John,
> >
> > another data point.  When I try to load an org file, once org-ref is
> > loaded, I get the following problem:
> >
> > Debugger entered--Lisp error: (wrong-type-argument stringp nil)
> >   re-search-forward(nil 10001 t)
> >   tex-main-file()
> >   reftex-TeX-master-file()
> >   reftex-tie-multifile-symbols()
> >   reftex-access-scan-info((16))
> >   reftex-parse-all()
> >   (and (buffer-file-name) (file-exists-p (buffer-file-name))
> > (global-auto-revert-mode t) (reftex-parse-all))
> >   org-mode-reftex-setup()
> >   run-hooks(change-major-mode-after-body-hook text-mode-hook
> > outline-mode-hook org-mode-hook)
> >   apply(run-hooks (change-major-mode-after-body-hook text-mode-hook
> > outline-mode-hook org-mode-hook))
> >   run-mode-hooks(org-mode-hook)
> >
> > Because of this, org-ref doesn't get initialised properly.
> >
> > Any idea what may be causing this?  Do I need to configure auctex or
> > similar?
> >
> > thanks,
> > eric
>
>
>

[-- Attachment #2: Type: text/html, Size: 3663 bytes --]

Re: org-ref code

[Andreas Reuleaux]

John Kitchin <jkitchin@andrew.cmu.edu> writes:

> You can see a document I wrote using org-ref here:
> http://kitchingroup.cheme.cmu.edu/org/2014/05/13/Using-org-ref-for-citations-and-references.org
>
> You will want to pull a current version. I added some code so it is in
> principle easy for you to add your own citation types and use the org-ref
> machinery to insert citations.
>
>
> I made a little screencast here: http://screencast.com/t/bxfafVydE
>

Thanks for the sample file and the screencast, very nice.

still a bit confused about org-ref-cite-types:

Say, I want to add two new link types:


  textcite - somehow standard in biblatex,
             cf. the biblatex.pdf manual, p 81

  citeauthorfull - my own creation - author with first- and lastname,
                   cf below.


from my document.org I load some latex preparation stuff like this

  #+LaTeX_HEADER: \include{ltxhdr}

I was just getting tired of prefixing so many lines with #+LaTeX_HEADER:
and collected some of those in a lxthdr.tex file.
there I have prepared something for this citeauthorfull thingy:


  %% cf
  %% http://tex.stackexchange.com/questions/24979/citing-authors-full-name-in-biblatex
  %% called citeauthorfirstlast... there


  \DeclareCiteCommand{\citeauthorfull}
    {\boolfalse{citetracker}%
     \boolfalse{pagetracker}%
     \DeclareNameAlias{labelname}{first-last}%
     \usebibmacro{prenote}}
    {\ifciteindex
       {\indexnames{labelname}}
       {}%
     \printnames{labelname}}
    {\multicitedelim}
    {\usebibmacro{postnote}}

this does the job, don't ask me details.

now back to org-ref:

with your advice I add:

  ;; add new format
  (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
        (append (nth 2 (assoc 'org reftex-cite-format-builtin))
                '(

                  ;; C-t like text
                  (?\C-t  . "textcite:%l")


                  ;; f like full
                  (?f  . "citeauthorfull:%l")

                  )))

and I get the comfort of two additional citation formats to chose from
when typing C-u C-c ] - nice, indeed. this is basically what you
said in your e-mail before, now also on the org-ref.org webpage,
(just shortcut and don't define that format variable)

Now I can add these:

  (add-to-list 'org-ref-cite-types "textcite")
  (add-to-list 'org-ref-cite-types "citeauthorfull")

but this is of limited use to me currently, at least I don't get
the point, not sure if I am doing something wrong:

say, I have added a few of these

  textcite:foo

  citeauthorfull:bar

in my document.org, there are some problems with these:

* first: they don't appear blue and clickable in my document.org

* second: they don't get exported in the latex in a reasonable way,
  they appear there just as
    
    textcite:foo
    citeauthorfull:bar

Well I can cure the situation by adding by adding


(org-add-link-type
 "textcite"
 'org-ref-cite-onclick-minibuffer-menu
 ;; formatting
 (lambda (keyword desc format)
   (cond
    ((eq format 'html) (format "(<textcite>%s</textcite>)" path))
    ((eq format 'latex)
     (concat "\\textcite{"
	     (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
	     "}")))))



(org-add-link-type
 "citeauthorfull"
 'org-ref-cite-onclick-minibuffer-menu
 ;; formatting
 (lambda (keyword desc format)
   (cond
    ((eq format 'html) (format "(<citeauthorfull>%s</citeauthorfull>)" path))
    ((eq format 'latex)
     (concat "\\citeauthorfull{"
	     (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
	     "}")))))


now they appear clickable in blue, and get properly exported
to \textcite{...} and \citeauthorfull{...}

Now, what was the deal of this adding them  to 'org-ref-cite-types
in the first place, if I had to take care of the details by hand anyway?
Is there anything I could have left out / shortcut / I have forgotten maybe?

Thanks.

-Andreas

Re: org-ref code

[John Kitchin]

[-- Attachment #1: Type: text/plain, Size: 5188 bytes --]

with the most recent org-ref, it should be sufficient to put this in your
init file:

(org-ref-define-citation-link "textcite" ?I)
(org-ref-define-citation-link "citeauthorfull" ?F)

this will create a textcite link and create a reftex menu you select with
the key I, and the other link with the key F. these should automatically be
links, and have completion functions. These will get exported as
\textcite{label} and \citeauthorfull{label}. The
org-ref-define-citation-link function adds the link, creates the functions
necessary, and adds the types to the right places.

You do not need to do the manual additions unless you manually define the
link like you did with org-add-link-type.

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 Tue, May 13, 2014 at 7:33 PM, Andreas Reuleaux <andreas@a-rx.info> wrote:

> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
> > You can see a document I wrote using org-ref here:
> >
> http://kitchingroup.cheme.cmu.edu/org/2014/05/13/Using-org-ref-for-citations-and-references.org
> >
> > You will want to pull a current version. I added some code so it is in
> > principle easy for you to add your own citation types and use the org-ref
> > machinery to insert citations.
> >
> >
> > I made a little screencast here: http://screencast.com/t/bxfafVydE
> >
>
> Thanks for the sample file and the screencast, very nice.
>
> still a bit confused about org-ref-cite-types:
>
> Say, I want to add two new link types:
>
>
>   textcite - somehow standard in biblatex,
>              cf. the biblatex.pdf manual, p 81
>
>   citeauthorfull - my own creation - author with first- and lastname,
>                    cf below.
>
>
> from my document.org I load some latex preparation stuff like this
>
>   #+LaTeX_HEADER: \include{ltxhdr}
>
> I was just getting tired of prefixing so many lines with #+LaTeX_HEADER:
> and collected some of those in a lxthdr.tex file.
> there I have prepared something for this citeauthorfull thingy:
>
>
>   %% cf
>   %%
> http://tex.stackexchange.com/questions/24979/citing-authors-full-name-in-biblatex
>   %% called citeauthorfirstlast... there
>
>
>   \DeclareCiteCommand{\citeauthorfull}
>     {\boolfalse{citetracker}%
>      \boolfalse{pagetracker}%
>      \DeclareNameAlias{labelname}{first-last}%
>      \usebibmacro{prenote}}
>     {\ifciteindex
>        {\indexnames{labelname}}
>        {}%
>      \printnames{labelname}}
>     {\multicitedelim}
>     {\usebibmacro{postnote}}
>
> this does the job, don't ask me details.
>
> now back to org-ref:
>
> with your advice I add:
>
>   ;; add new format
>   (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
>         (append (nth 2 (assoc 'org reftex-cite-format-builtin))
>                 '(
>
>                   ;; C-t like text
>                   (?\C-t  . "textcite:%l")
>
>
>                   ;; f like full
>                   (?f  . "citeauthorfull:%l")
>
>                   )))
>
> and I get the comfort of two additional citation formats to chose from
> when typing C-u C-c ] - nice, indeed. this is basically what you
> said in your e-mail before, now also on the org-ref.org webpage,
> (just shortcut and don't define that format variable)
>
> Now I can add these:
>
>   (add-to-list 'org-ref-cite-types "textcite")
>   (add-to-list 'org-ref-cite-types "citeauthorfull")
>
> but this is of limited use to me currently, at least I don't get
> the point, not sure if I am doing something wrong:
>
> say, I have added a few of these
>
>   textcite:foo
>
>   citeauthorfull:bar
>
> in my document.org, there are some problems with these:
>
> * first: they don't appear blue and clickable in my document.org
>
> * second: they don't get exported in the latex in a reasonable way,
>   they appear there just as
>
>     textcite:foo
>     citeauthorfull:bar
>
> Well I can cure the situation by adding by adding
>
>
> (org-add-link-type
>  "textcite"
>  'org-ref-cite-onclick-minibuffer-menu
>  ;; formatting
>  (lambda (keyword desc format)
>    (cond
>     ((eq format 'html) (format "(<textcite>%s</textcite>)" path))
>     ((eq format 'latex)
>      (concat "\\textcite{"
>              (mapconcat (lambda (key) key) (org-ref-split-and-strip-string
> keyword) ",")
>              "}")))))
>
>
>
> (org-add-link-type
>  "citeauthorfull"
>  'org-ref-cite-onclick-minibuffer-menu
>  ;; formatting
>  (lambda (keyword desc format)
>    (cond
>     ((eq format 'html) (format "(<citeauthorfull>%s</citeauthorfull>)"
> path))
>     ((eq format 'latex)
>      (concat "\\citeauthorfull{"
>              (mapconcat (lambda (key) key) (org-ref-split-and-strip-string
> keyword) ",")
>              "}")))))
>
>
> now they appear clickable in blue, and get properly exported
> to \textcite{...} and \citeauthorfull{...}
>
> Now, what was the deal of this adding them  to 'org-ref-cite-types
> in the first place, if I had to take care of the details by hand anyway?
> Is there anything I could have left out / shortcut / I have forgotten
> maybe?
>
> Thanks.
>
> -Andreas
>
>
>

[-- Attachment #2: Type: text/html, Size: 7335 bytes --]

Re: org-ref code

[Andreas Reuleaux]

John Kitchin <jkitchin@andrew.cmu.edu> writes:

> with the most recent org-ref, it should be sufficient to put this in your
> init file:
>
> (org-ref-define-citation-link "textcite" ?I)
> (org-ref-define-citation-link "citeauthorfull" ?F)
>
> this will create a textcite link and create a reftex menu you select with
> the key I, and the other link with the key F. these should automatically be
> links, and have completion functions. These will get exported as
> \textcite{label} and \citeauthorfull{label}. The
> org-ref-define-citation-link function adds the link, creates the functions
> necessary, and adds the types to the right places.
>
> You do not need to do the manual additions unless you manually define the
> link like you did with org-add-link-type.
>


OK, I see, and works fine, thanks.

One minor thing: Am I restricted to single-letter keystrokes
above ? like:

  I    ---- (...?I)
  F    ---- (... ?F)
  C-t  ---- (... ?\C-t)

I tried to get working something like

 C-r C-t 

with something like this

  (... ?(kbd "C-r C-t"))

with no success, but I am unsure, if there is just something simple
missing like a quote or a backslash, or if it's just not possible
at this point.

-Andreas

Re: org-ref code

[John Kitchin]

[-- Attachment #1: Type: text/plain, Size: 1795 bytes --]

I think you are restricted to single characters. That key is used by
reftex, so it would be a limitation in reftex. You can always define your
own function with a key-binding for something specific.

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 Tue, May 13, 2014 at 11:39 PM, Andreas Reuleaux <andreas@a-rx.info>wrote:

> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
> > with the most recent org-ref, it should be sufficient to put this in your
> > init file:
> >
> > (org-ref-define-citation-link "textcite" ?I)
> > (org-ref-define-citation-link "citeauthorfull" ?F)
> >
> > this will create a textcite link and create a reftex menu you select with
> > the key I, and the other link with the key F. these should automatically
> be
> > links, and have completion functions. These will get exported as
> > \textcite{label} and \citeauthorfull{label}. The
> > org-ref-define-citation-link function adds the link, creates the
> functions
> > necessary, and adds the types to the right places.
> >
> > You do not need to do the manual additions unless you manually define the
> > link like you did with org-add-link-type.
> >
>
>
> OK, I see, and works fine, thanks.
>
> One minor thing: Am I restricted to single-letter keystrokes
> above ? like:
>
>   I    ---- (...?I)
>   F    ---- (... ?F)
>   C-t  ---- (... ?\C-t)
>
> I tried to get working something like
>
>  C-r C-t
>
> with something like this
>
>   (... ?(kbd "C-r C-t"))
>
> with no success, but I am unsure, if there is just something simple
> missing like a quote or a backslash, or if it's just not possible
> at this point.
>
> -Andreas
>
>
>

[-- Attachment #2: Type: text/html, Size: 2588 bytes --]

Re: org-ref code

[Andreas Reuleaux]

OK, thanks.

-Andreas


John Kitchin <jkitchin@andrew.cmu.edu> writes:

> I think you are restricted to single characters. That key is used by
> reftex, so it would be a limitation in reftex. You can always define your
> own function with a key-binding for something specific.
>
> John

org-ref for biblatex

[Andreas Reuleaux]

John,

to come back to org-ref, which basically runs fine for me now, thanks.

I am running biblatex (as opposed to bibtex) though, with meanwhile
biber as a backend.

The biblatex manual is very comprehensible and explains the different
citation commands from page 79 onwards.

  http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf

I just ran into this: Having added a few citations to an existing
one with C-u C-c d, I have something like

  cite:foo,bar,baz
  
which gets exported to latex as

  \cite{foo,bar,baz}

whereas biblatex expects

  \cites{foo}{bar}{baz}

as I understand (note the plural s as well), and there are other config
tweekings I am doing for biblatex (that I intend to explain some other
time).

Maybe a switch (an org-ref variable) would be a good idea, that lets
one choose: use either biblatex or plain old bibtex?

thanks in advance

-Andreas

Re: org-ref for biblatex

[John Kitchin]

[-- Attachment #1: Type: text/plain, Size: 1590 bytes --]

I added the multicite commands. you have to use cites:foo,bar,baz, and it
will export to the format you suggested. org-ref is not smart enough to
automatically add the s to the link type if you add more than one
reference, you have to be smart enough to do that.

can you try it out and let me know if it does what you need?

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, May 18, 2014 at 1:16 PM, Andreas Reuleaux <andreas@a-rx.info> wrote:

> John,
>
> to come back to org-ref, which basically runs fine for me now, thanks.
>
> I am running biblatex (as opposed to bibtex) though, with meanwhile
> biber as a backend.
>
> The biblatex manual is very comprehensible and explains the different
> citation commands from page 79 onwards.
>
>
> http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
>
> I just ran into this: Having added a few citations to an existing
> one with C-u C-c d, I have something like
>
>   cite:foo,bar,baz
>
> which gets exported to latex as
>
>   \cite{foo,bar,baz}
>
> whereas biblatex expects
>
>   \cites{foo}{bar}{baz}
>
> as I understand (note the plural s as well), and there are other config
> tweekings I am doing for biblatex (that I intend to explain some other
> time).
>
> Maybe a switch (an org-ref variable) would be a good idea, that lets
> one choose: use either biblatex or plain old bibtex?
>
> thanks in advance
>
> -Andreas
>
>
>

[-- Attachment #2: Type: text/html, Size: 2334 bytes --]

Re: org-ref for biblatex

[Andreas Reuleaux]

John,

thanks a lot, I will try them out, and let you know.

Never mind about the comfort (or lack thereof) of how to add an s or the
like in org. - I can easily do that by hand.

Working back ends (exporters) for the various citiation commands seem
much more important at this point.


-Andreas


John Kitchin <jkitchin@andrew.cmu.edu> writes:

> I added the multicite commands. you have to use cites:foo,bar,baz, and it
> will export to the format you suggested. org-ref is not smart enough to
> automatically add the s to the link type if you add more than one
> reference, you have to be smart enough to do that.
>
> can you try it out and let me know if it does what you need?
>
> 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, May 18, 2014 at 1:16 PM, Andreas Reuleaux <andreas@a-rx.info> wrote:
>
>> John,
>>
>> to come back to org-ref, which basically runs fine for me now, thanks.
>>
>> I am running biblatex (as opposed to bibtex) though, with meanwhile
>> biber as a backend.
>>
>> The biblatex manual is very comprehensible and explains the different
>> citation commands from page 79 onwards.
>>
>>
>> http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
>>
>> I just ran into this: Having added a few citations to an existing
>> one with C-u C-c d, I have something like
>>
>>   cite:foo,bar,baz
>>
>> which gets exported to latex as
>>
>>   \cite{foo,bar,baz}
>>
>> whereas biblatex expects
>>
>>   \cites{foo}{bar}{baz}
>>
>> as I understand (note the plural s as well), and there are other config
>> tweekings I am doing for biblatex (that I intend to explain some other
>> time).
>>
>> Maybe a switch (an org-ref variable) would be a good idea, that lets
>> one choose: use either biblatex or plain old bibtex?
>>
>> thanks in advance
>>
>> -Andreas
>>
>>
>>

Re: org-ref for biblatex

[John Kitchin]

[-- Attachment #1: Type: text/plain, Size: 2691 bytes --]

good news, I think org-ref works with biblatex pretty well now, see
http://kitchingroup.cheme.cmu.edu/blog/2014/05/19/Exporting-citations-with-biblatex/

org-ref also makes a reasonable html bibliography now too!

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, May 18, 2014 at 6:38 PM, Andreas Reuleaux <andreas@a-rx.info> wrote:

> John,
>
> thanks a lot, I will try them out, and let you know.
>
> Never mind about the comfort (or lack thereof) of how to add an s or the
> like in org. - I can easily do that by hand.
>
> Working back ends (exporters) for the various citiation commands seem
> much more important at this point.
>
>
> -Andreas
>
>
> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
> > I added the multicite commands. you have to use cites:foo,bar,baz, and it
> > will export to the format you suggested. org-ref is not smart enough to
> > automatically add the s to the link type if you add more than one
> > reference, you have to be smart enough to do that.
> >
> > can you try it out and let me know if it does what you need?
> >
> > 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, May 18, 2014 at 1:16 PM, Andreas Reuleaux <andreas@a-rx.info>
> wrote:
> >
> >> John,
> >>
> >> to come back to org-ref, which basically runs fine for me now, thanks.
> >>
> >> I am running biblatex (as opposed to bibtex) though, with meanwhile
> >> biber as a backend.
> >>
> >> The biblatex manual is very comprehensible and explains the different
> >> citation commands from page 79 onwards.
> >>
> >>
> >>
> http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
> >>
> >> I just ran into this: Having added a few citations to an existing
> >> one with C-u C-c d, I have something like
> >>
> >>   cite:foo,bar,baz
> >>
> >> which gets exported to latex as
> >>
> >>   \cite{foo,bar,baz}
> >>
> >> whereas biblatex expects
> >>
> >>   \cites{foo}{bar}{baz}
> >>
> >> as I understand (note the plural s as well), and there are other config
> >> tweekings I am doing for biblatex (that I intend to explain some other
> >> time).
> >>
> >> Maybe a switch (an org-ref variable) would be a good idea, that lets
> >> one choose: use either biblatex or plain old bibtex?
> >>
> >> thanks in advance
> >>
> >> -Andreas
> >>
> >>
> >>
>
>
>

[-- Attachment #2: Type: text/html, Size: 4215 bytes --]

Re: org-ref for biblatex

[Andreas Reuleaux]

Thanks a lot, looks good!
(but I haven't had a chance yet to try it out myself,
will do so of course)

-Andreas


John Kitchin <jkitchin@andrew.cmu.edu> writes:

> good news, I think org-ref works with biblatex pretty well now, see
> http://kitchingroup.cheme.cmu.edu/blog/2014/05/19/Exporting-citations-with-biblatex/
>
> org-ref also makes a reasonable html bibliography now too!
>
> 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, May 18, 2014 at 6:38 PM, Andreas Reuleaux <andreas@a-rx.info> wrote:
>
>> John,
>>
>> thanks a lot, I will try them out, and let you know.
>>
>> Never mind about the comfort (or lack thereof) of how to add an s or the
>> like in org. - I can easily do that by hand.
>>
>> Working back ends (exporters) for the various citiation commands seem
>> much more important at this point.
>>
>>
>> -Andreas
>>
>>
>> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>>
>> > I added the multicite commands. you have to use cites:foo,bar,baz, and it
>> > will export to the format you suggested. org-ref is not smart enough to
>> > automatically add the s to the link type if you add more than one
>> > reference, you have to be smart enough to do that.
>> >
>> > can you try it out and let me know if it does what you need?
>> >
>> > 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, May 18, 2014 at 1:16 PM, Andreas Reuleaux <andreas@a-rx.info>
>> wrote:
>> >
>> >> John,
>> >>
>> >> to come back to org-ref, which basically runs fine for me now, thanks.
>> >>
>> >> I am running biblatex (as opposed to bibtex) though, with meanwhile
>> >> biber as a backend.
>> >>
>> >> The biblatex manual is very comprehensible and explains the different
>> >> citation commands from page 79 onwards.
>> >>
>> >>
>> >>
>> http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
>> >>
>> >> I just ran into this: Having added a few citations to an existing
>> >> one with C-u C-c d, I have something like
>> >>
>> >>   cite:foo,bar,baz
>> >>
>> >> which gets exported to latex as
>> >>
>> >>   \cite{foo,bar,baz}
>> >>
>> >> whereas biblatex expects
>> >>
>> >>   \cites{foo}{bar}{baz}
>> >>
>> >> as I understand (note the plural s as well), and there are other config
>> >> tweekings I am doing for biblatex (that I intend to explain some other
>> >> time).
>> >>
>> >> Maybe a switch (an org-ref variable) would be a good idea, that lets
>> >> one choose: use either biblatex or plain old bibtex?
>> >>
>> >> thanks in advance
>> >>
>> >> -Andreas
>> >>
>> >>
>> >>
>>
>>
>>

Re: org-ref for biblatex

[Andreas Reuleaux]

John,

yes they work fine for me, I have tested: cites and parencites.

Thanks a lot.

-Andreas


John Kitchin <jkitchin@andrew.cmu.edu> writes:

> I added the multicite commands. you have to use cites:foo,bar,baz, and it
> will export to the format you suggested. org-ref is not smart enough to
> automatically add the s to the link type if you add more than one
> reference, you have to be smart enough to do that.
>
> can you try it out and let me know if it does what you need?
>
> 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, May 18, 2014 at 1:16 PM, Andreas Reuleaux <andreas@a-rx.info> wrote:
>
>> John,
>>
>> to come back to org-ref, which basically runs fine for me now, thanks.
>>
>> I am running biblatex (as opposed to bibtex) though, with meanwhile
>> biber as a backend.
>>
>> The biblatex manual is very comprehensible and explains the different
>> citation commands from page 79 onwards.
>>
>>
>> http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
>>
>> I just ran into this: Having added a few citations to an existing
>> one with C-u C-c d, I have something like
>>
>>   cite:foo,bar,baz
>>
>> which gets exported to latex as
>>
>>   \cite{foo,bar,baz}
>>
>> whereas biblatex expects
>>
>>   \cites{foo}{bar}{baz}
>>
>> as I understand (note the plural s as well), and there are other config
>> tweekings I am doing for biblatex (that I intend to explain some other
>> time).
>>
>> Maybe a switch (an org-ref variable) would be a good idea, that lets
>> one choose: use either biblatex or plain old bibtex?
>>
>> thanks in advance
>>
>> -Andreas
>>
>>
>>

Re: org-ref code

[Vikas Rawal]

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> 
> All the talk about citations in org-mode inspired me to finish and polish some code I have been working on for my group for a while on bibtex/reftex/org-mode integration. I packaged it up in a literate programming org-file here: https://github.com/jkitchin/jmax/blob/master/org-ref.org.
> 

Thanks John. This looks very useful. 

Do you plan to add this to org-mode/contrib?

I was wondering if it would be useful to change the default keybinding C-c ] to C-c ) instead, since C-c ] is by default bound to org-remove-file.

Vikas


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Re: org-ref code

[John Kitchin]

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I added a user variable for that key-binding. I like C-c ] because there is
no shift to get ). You can set org-ref-insert-cite-key to what ever
shortcut you prefer now.

I would prefer to keep org-ref where it is until it "stabilizes". This
summer my group will be using it pretty extensively for writing papers, so
I anticipate by this fall it will be pretty stable.

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, May 8, 2014 at 4:31 AM, Vikas Rawal <vikasrawal@gmail.com> wrote:

>
>
> All the talk about citations in org-mode inspired me to finish and polish
> some code I have been working on for my group for a while on
> bibtex/reftex/org-mode integration. I packaged it up in a literate
> programming org-file here:
> https://github.com/jkitchin/jmax/blob/master/org-ref.org.
>
>
> Thanks John. This looks very useful.
>
> Do you plan to add this to org-mode/contrib?
>
> I was wondering if it would be useful to change the default keybinding C-c
> ] to C-c ) instead, since C-c ] is by default bound to org-remove-file.
>
> Vikas
>
>

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Re: org-ref code

[Bastien]

Hi John,

John Kitchin <jkitchin@andrew.cmu.edu> writes:

> I would prefer to keep org-ref where it is until it "stabilizes".

I hope it will stabilize before Org 8.3 so that we can add org-ref
to contrib/ and give it exposure in the release notes.

Thanks,

-- 
 Bastien