Re: [O] org-ref in action

2014-08-06 Thread Xebar Saram
Thanks John No worries :) ive installed it and its working great. in a related question, does anyone use it with jabef? the reason im asking is that im very new to this and wonder about a possible workflow to export a bib citation from jabref to org and create an org header (per reference). so

Re: [O] org-ref in action

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

Re: [O] org-ref in action

2014-08-05 Thread John Kitchin
Hi, it got moved in a re-organization to https://github.com/jkitchin/jmax/blob/master/org/org-ref.org. Sorry for the inconvenience! Xebar Saram zelt...@gmail.com writes: Hi all the github link seems dead, anyone knows where one could get and try org-ref from? z On Mon, Jun 30, 2014 at

Re: [O] org-ref in action

2014-06-30 Thread Joseph Vidal-Rosset
2014-06-29 20:19 GMT+02:00 Eric Schulte schulte.e...@gmail.com: With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as \cite[page n]{one-reference-paper-year} I am sorry Eric but [[cite:(page n)one-reference-paper-year]] breaks the bibliography reference for me with

Re: [O] org-ref in action

2014-06-30 Thread Eric Schulte
Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes: 2014-06-29 20:19 GMT+02:00 Eric Schulte schulte.e...@gmail.com: With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as \cite[page n]{one-reference-paper-year} I am sorry Eric but [[cite:(page

Re: [O] org-ref in action

2014-06-30 Thread Joseph Vidal-Rosset
I thank you Eric for your quick and kind reply. In my init.el file I have put this code : (eval-after-load 'reftex-vars '(progn (add-to-list 'reftex-cite-format-builtin '(org Org-mode citation ((?\C-m . [[cite:(%p)%l]])

Re: [O] org-ref in action

2014-06-30 Thread Eric Schulte
Thanns to the default cite action, I get for example in my org file: [[cite:(119–136)johansson36:_minim_formal]] and it creates no reference at al, because via the export I get: \cite{(119–136)johansson36:_minim_formal} Using the latest version of Org-mode from the git repository, this

Re: [O] org-ref in action

2014-06-30 Thread Joseph Vidal-Rosset
Thanks Eric, it works now, with the latest version of org-mode. Best wishes Jo. 2014-06-30 12:22 GMT+02:00 Eric Schulte schulte.e...@gmail.com: Thanns to the default cite action, I get for example in my org file: [[cite:(119–136)johansson36:_minim_formal]] and it creates no

Re: [O] org-ref in action

2014-06-29 Thread Joseph Vidal-Rosset
Hi John, hello the list, My question is very simple and it is not unrevelevant vis-à-vis this thread, therefore I keep the same thread. What need is to get either the usual citation format (often in plain style) \cite{one-reference-paper-year} or this one with a mentioned page: \cite[page

Re: [O] org-ref in action

2014-06-29 Thread Eric Schulte
Joseph Vidal-Rosset joseph.vidal.ros...@gmail.com writes: Hi John, hello the list, My question is very simple and it is not unrevelevant vis-à-vis this thread, therefore I keep the same thread. What need is to get either the usual citation format (often in plain style)

Re: [O] org-ref in action

2014-06-29 Thread Joseph Vidal-Rosset
2014-06-29 20:19 GMT+02:00 Eric Schulte schulte.e...@gmail.com: With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as \cite[page n]{one-reference-paper-year} Many thanks Eric . It helps a lot ! Best wishes Jo.

Re: [O] org-ref in action

2014-06-27 Thread Alan Schmitt
On 2014-06-26 20:44, Matt Lundin m...@imapmail.org writes: Alan Schmitt alan.schm...@polytechnique.org writes: On 2014-06-26 16:39, Matt Lundin m...@imapmail.org writes: By contrast, ox-bibtex.el runs citations through bibtex2html, which is pretty much limited to the old-fashioned bibtex

Re: [O] org-ref in action

2014-06-27 Thread Joseph Vidal-Rosset
Hello Jonhn, hello the list, I have already used org-bibtex (and ox-bibtex) and I have just tried to use org-ref . Is it possible that a conflict exists between the former(s) and the latter? My links for example are not clickable and the link to the default bibliography does not work at all...

Re: [O] org-ref in action

2014-06-27 Thread Thomas S. Dye
Aloha Xebar, Xebar Saram zelt...@gmail.com writes: Hi all off topic a bit again. im an academic (asst. prof) in Epidemiology and have been using org-mode for about a year now. i love using org but im really not very technical at all. it has always been a dream for me to ditch word and move

Re: [O] org-ref in action

2014-06-27 Thread Vikas Rawal
off topic a bit again. im an academic (asst. prof) in Epidemiology and have been using org-mode for about a year now. i love using org but im really not very technical at all. it has always been a dream for me to ditch word and move over to Latex and even better orgmode to write my

Re: [O] org-ref in action

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

Re: [O] org-ref in action

2014-06-27 Thread Ista Zahn
Yes, totally off topic for this thread, please start a new one. On Fri, Jun 27, 2014 at 12:27 AM, Xebar Saram zelt...@gmail.com wrote: Hi all off topic a bit again. im an academic (asst. prof) in Epidemiology and have been using org-mode for about a year now. i love using org but im really

Re: [O] org-ref in action

2014-06-27 Thread Matt Lundin
Alan Schmitt alan.schm...@polytechnique.org writes: On 2014-06-26 20:44, Matt Lundin m...@imapmail.org writes: I don't think this is possible without some major hacking/conversion/filtering. Biblatex has many more entry types and fields than bibtex. I've found that most of the older bibtex

Re: [O] org-ref in action

2014-06-27 Thread Grant Rettke
Thanks for your answer on that everybody. My apologies for my poor grammar asking where people discuss such questions in real life. What I really had wanted to say, what I meant, was that I was wondering what professions utilize such workflows and where they discuss it primarily because the topic

Re: [O] org-ref in action

2014-06-27 Thread Matt Lundin
Matt Lundin m...@imapmail.org writes: Alan Schmitt alan.schm...@polytechnique.org writes: You are right. I see that one can specify a style file for parsing bib files and biblatex does supply a biblatex.bst, e.g., bibtex2html -s biblatex However, this still produces errors (and a blank

Re: [O] org-ref in action

2014-06-27 Thread John Kitchin
You may find some information here: https://github.com/jkitchin/jmax/tree/master/examples that is helpful to you. i have collected some examples for various journals we have published in with orgmode there. The jmax repo is what my group currently uses for this purpose. It may not be what you want

Re: [O] org-ref in action

2014-06-26 Thread Fabrice Popineau
+1 for org-bibtex (and ox-bibtex) that I'm using for a couple of years. But org-ref seems to go further (video is convincing). It would be really nice to merge org-ref and org-bibtex before they split too far apart. Wishful thinking from me because I don't see that I'm in position to do it.

Re: [O] org-ref in action

2014-06-26 Thread John Kitchin
Some features could be merged, but there is an important difference in that org-ref uses bibtex as the backend database, and reftex for searching, and org-bibtex uses org-mode headings as the backend database, and tag/property searches (I think). It is like the difference between org-contacts and

Re: [O] org-ref in action

2014-06-26 Thread Matt Lundin
John Kitchin jkitc...@andrew.cmu.edu writes: Some features could be merged, but there is an important difference in that org-ref uses bibtex as the backend database, and reftex for searching, and org-bibtex uses org-mode headings as the backend database, and tag/property searches (I think).  

Re: [O] org-ref in action

2014-06-26 Thread Matt Lundin
Matt Lundin m...@imapmail.org writes: John Kitchin jkitc...@andrew.cmu.edu writes: Some features could be merged, but there is an important difference in that org-ref uses bibtex as the backend database, and reftex for searching, and org-bibtex uses org-mode headings as the backend

Re: [O] org-ref in action

2014-06-26 Thread Grant Rettke
On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin m...@imapmail.org wrote: I think the key in any possible feature merge is to remember citation management is idiosyncratic. Off topic: How do people choose today? Why choose bibtex over biblatex? Where do people discuss such questions like this in

Re: [O] org-ref in action

2014-06-26 Thread Ken Mankoff
On 2014-06-26 at 10:11, Grant Rettke wrote: Why choose bibtex over biblatex? People choose bibtex because that is how it has been done and is well supported/documented and still popular on Google results. People choose biblatex because that appears to be the new under-development

Re: [O] org-ref in action

2014-06-26 Thread Jorge A. Alfaro-Murillo
Grant Rettke g...@wisdomandwonder.com writes: How do people choose today? Why choose bibtex over biblatex? For journal submission. With BibTeX you only have to copy paste at the end of your LaTeX file the contents of the generated .bbl file. Moreover, journals provide a default style for

Re: [O] org-ref in action

2014-06-26 Thread Matt Lundin
Grant Rettke g...@wisdomandwonder.com writes: On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin m...@imapmail.org wrote: I think the key in any possible feature merge is to remember citation management is idiosyncratic. Off topic: How do people choose today? Why choose bibtex over biblatex?

Re: [O] org-ref in action

2014-06-26 Thread Eric Schulte
John Kitchin jkitc...@andrew.cmu.edu writes: Some features could be merged, but there is an important difference in that org-ref uses bibtex as the backend database, and reftex for searching, and org-bibtex uses org-mode headings as the backend database, and tag/property searches (I think).

Re: [O] org-ref in action

2014-06-26 Thread Alan Schmitt
On 2014-06-26 16:39, Matt Lundin m...@imapmail.org writes: By contrast, ox-bibtex.el runs citations through bibtex2html, which is pretty much limited to the old-fashioned bibtex formats. What would be required for bibtex2html to take biblatex input? I thought the backend format was similar or

Re: [O] org-ref in action

2014-06-26 Thread Matt Lundin
Alan Schmitt alan.schm...@polytechnique.org writes: On 2014-06-26 16:39, Matt Lundin m...@imapmail.org writes: By contrast, ox-bibtex.el runs citations through bibtex2html, which is pretty much limited to the old-fashioned bibtex formats. What would be required for bibtex2html to take

[O] org-ref in action

2014-06-26 Thread Doyley, Marvin M.
Hi John, Thanks for sharing. My students and I love it. Cheers, M

Re: [O] org-ref in action

2014-06-26 Thread Xebar Saram
Hi all off topic a bit again. im an academic (asst. prof) in Epidemiology and have been using org-mode for about a year now. i love using org but im really not very technical at all. it has always been a dream for me to ditch word and move over to Latex and even better orgmode to write my

Re: [O] org-ref in action

2014-06-25 Thread Bastien
Hi John, thanks for working on this! The demo is impressive. I've not explored or tested org-ref.el directly, but my feeling is that there are some neat features that could sneak into Org's core, like for example multiple targets for the same custom link, sorting of those targets, etc. I'll

Re: [O] org-ref in action

2014-06-25 Thread Vikas Rawal
John, Thanks for a very interesting tutorial. I was trying to load org-ref.el, but get the following error: Debugger entered--Lisp error: (wrong-type-argument consp nil) setcar(nil ((87 . textcite:%l) (122 . newcite:%l))) (let* ((c (nthcdr 2 (assoc (quote org)

Re: [O] org-ref in action

2014-06-25 Thread Eric Schulte
John Kitchin jkitc...@andrew.cmu.edu writes: Hello everyone, org-ref has basically stabilized. You can get the latest code at https://github.com/jkitchin/jmax/blob/master/org-ref.org. I made a little screen capture video here to show you what it does:

Re: [O] org-ref in action

2014-06-25 Thread Grant Rettke
John: Beautiful, thanks! Eric: My goodness, that 8 minute video sums up what was not obvious to many even after wantingly browsing the documentation on it. Thanks! Grant Rettke | ACM, ASA, FSF, IEEE, SIAM g...@wisdomandwonder.com | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.”

Re: [O] org-ref in action

2014-06-25 Thread Matt Lundin
Eric Schulte schulte.e...@gmail.com writes: This is a lot of useful functionality, and very nicely presented. Did you happen to try the built in bibtex support in Org-mode core and contrib? And if so, is there a reason that you implemented this all independently? I think part of the

[O] org-ref in action

2014-06-24 Thread John Kitchin
Hello everyone, org-ref has basically stabilized. You can get the latest code at https://github.com/jkitchin/jmax/blob/master/org-ref.org. I made a little screen capture video here to show you what it does: https://www.youtube.com/watch?v=JyvpSVl4_dg Try it out, if it looks interesting, and let

Re: [O] org-ref in action

2014-06-24 Thread Thomas S. Dye
Hi John, John Kitchin jkitc...@andrew.cmu.edu writes: Hello everyone, org-ref has basically stabilized. You can get the latest code at https://github.com/jkitchin/jmax/blob/master/org-ref.org. I made a little screen capture video here to show you what it does:

Re: [O] org-ref in action

2014-06-24 Thread Ista Zahn
John, This is simply amazing. I think this covers basically every item on my org-mode reference handling wish list. It's really great, thank you! Will this be on Melpa soon? -Ista On Tue, Jun 24, 2014 at 2:45 PM, John Kitchin jkitc...@andrew.cmu.edu wrote: Hello everyone, org-ref has

Re: [O] org-ref in action

2014-06-24 Thread Matt Lundin
John Kitchin jkitc...@andrew.cmu.edu writes: org-ref has basically stabilized. You can get the latest code at https://github.com/jkitchin/jmax/blob/master/org-ref.org. I made a little screen capture video here to show you what it does: https://www.youtube.com/watch?v=JyvpSVl4_dg Try it

[O] org-ref in action

2014-06-24 Thread Leu Zhe
Thanks John, I have been using it for a while. It is a fantastic tool for org-mode to organize the bib. Great thanks again.