* org-ref in action
@ 2014-06-24 18:45 John Kitchin
2014-06-24 19:26 ` Thomas S. Dye
` (6 more replies)
0 siblings, 7 replies; 46+ messages in thread
From: John Kitchin @ 2014-06-24 18:45 UTC (permalink / raw)
To: emacs-orgmode
Hello everyone,
org-ref has basically stabilized. You can get the latest code at
https://github.com/jkitchin/jmax/blob/master/org-ref.org.
I made a little screen capture video here to show you what it does:
https://www.youtube.com/watch?v=JyvpSVl4_dg
Try it out, if it looks interesting, and let me know if you find any
bugs!
Thanks,
--
-----------------------------------
John Kitchin
^ permalink raw reply [flat|nested] 46+ messages in thread* Re: org-ref in action 2014-06-24 18:45 org-ref in action John Kitchin @ 2014-06-24 19:26 ` Thomas S. Dye 2014-06-24 20:53 ` Ista Zahn ` (5 subsequent siblings) 6 siblings, 0 replies; 46+ messages in thread From: Thomas S. Dye @ 2014-06-24 19:26 UTC (permalink / raw) To: John Kitchin; +Cc: emacs-orgmode Hi John, John Kitchin <jkitchin@andrew.cmu.edu> writes: > Hello everyone, > > org-ref has basically stabilized. You can get the latest code at > https://github.com/jkitchin/jmax/blob/master/org-ref.org. > > I made a little screen capture video here to show you what it does: > https://www.youtube.com/watch?v=JyvpSVl4_dg > > Try it out, if it looks interesting, and let me know if you find any > bugs! Wow! Nice work. Thanks for pursuing this. All the best, Tom -- Thomas S. Dye http://www.tsdye.com ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-24 18:45 org-ref in action John Kitchin 2014-06-24 19:26 ` Thomas S. Dye @ 2014-06-24 20:53 ` Ista Zahn 2014-06-25 2:13 ` Matt Lundin ` (4 subsequent siblings) 6 siblings, 0 replies; 46+ messages in thread From: Ista Zahn @ 2014-06-24 20:53 UTC (permalink / raw) To: John Kitchin; +Cc: emacs-orgmode Mailinglist John, This is simply amazing. I think this covers basically every item on my org-mode reference handling wish list. It's really great, thank you! Will this be on Melpa soon? -Ista On Tue, Jun 24, 2014 at 2:45 PM, John Kitchin <jkitchin@andrew.cmu.edu> wrote: > Hello everyone, > > org-ref has basically stabilized. You can get the latest code at > https://github.com/jkitchin/jmax/blob/master/org-ref.org. > > I made a little screen capture video here to show you what it does: > https://www.youtube.com/watch?v=JyvpSVl4_dg > > Try it out, if it looks interesting, and let me know if you find any > bugs! > > Thanks, > > -- > ----------------------------------- > John Kitchin > > ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-24 18:45 org-ref in action John Kitchin 2014-06-24 19:26 ` Thomas S. Dye 2014-06-24 20:53 ` Ista Zahn @ 2014-06-25 2:13 ` Matt Lundin 2014-06-25 8:28 ` Bastien ` (3 subsequent siblings) 6 siblings, 0 replies; 46+ messages in thread From: Matt Lundin @ 2014-06-25 2:13 UTC (permalink / raw) To: John Kitchin; +Cc: emacs-orgmode John Kitchin <jkitchin@andrew.cmu.edu> writes: > org-ref has basically stabilized. You can get the latest code at > https://github.com/jkitchin/jmax/blob/master/org-ref.org. > > I made a little screen capture video here to show you what it does: > https://www.youtube.com/watch?v=JyvpSVl4_dg > > Try it out, if it looks interesting, and let me know if you find any > bugs! This looks interesting. Thanks for the work you put into it! I look forward to trying it out. Matt ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-24 18:45 org-ref in action John Kitchin ` (2 preceding siblings ...) 2014-06-25 2:13 ` Matt Lundin @ 2014-06-25 8:28 ` Bastien 2014-06-25 16:26 ` Vikas Rawal ` (2 subsequent siblings) 6 siblings, 0 replies; 46+ messages in thread From: Bastien @ 2014-06-25 8:28 UTC (permalink / raw) To: John Kitchin; +Cc: emacs-orgmode Hi John, thanks for working on this! The demo is impressive. I've not explored or tested org-ref.el directly, but my feeling is that there are some neat features that could sneak into Org's core, like for example multiple targets for the same custom link, sorting of those targets, etc. I'll have a closer look ASAP -- thanks again, -- Bastien ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-24 18:45 org-ref in action John Kitchin ` (3 preceding siblings ...) 2014-06-25 8:28 ` Bastien @ 2014-06-25 16:26 ` Vikas Rawal 2014-06-25 20:25 ` Eric Schulte 2014-06-29 10:18 ` Joseph Vidal-Rosset 6 siblings, 0 replies; 46+ messages in thread From: Vikas Rawal @ 2014-06-25 16:26 UTC (permalink / raw) To: John Kitchin; +Cc: org-mode mailing list John, Thanks for a very interesting tutorial. I was trying to load org-ref.el, but get the following error: -------- Debugger entered--Lisp error: (wrong-type-argument consp nil) setcar(nil ((87 . "textcite:%l") (122 . "newcite:%l"))) (let* ((c (nthcdr 2 (assoc (quote org) reftex-cite-format-builtin)))) (setcar c (append (nth 2 (assoc (quote org) reftex-cite-format-builtin)) (quote ((87 . "textcite:%l") (122 . "newcite:%l")))))) eval-buffer() ; Reading at buffer position 194 call-interactively(eval-buffer record nil) command-execute(eval-buffer record) execute-extended-command(nil "eval-buffer") call-interactively(execute-extended-command nil nil) ———— Am I missing something? Vikas On 24-Jun-2014, at 8:45 pm, John Kitchin <jkitchin@andrew.cmu.edu> wrote: > Hello everyone, > > org-ref has basically stabilized. You can get the latest code at > https://github.com/jkitchin/jmax/blob/master/org-ref.org. > > I made a little screen capture video here to show you what it does: > https://www.youtube.com/watch?v=JyvpSVl4_dg > > Try it out, if it looks interesting, and let me know if you find any > bugs! > > Thanks, > > -- > ----------------------------------- > John Kitchin > > ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-24 18:45 org-ref in action John Kitchin ` (4 preceding siblings ...) 2014-06-25 16:26 ` Vikas Rawal @ 2014-06-25 20:25 ` Eric Schulte 2014-06-26 1:09 ` Grant Rettke 2014-06-26 1:10 ` Matt Lundin 2014-06-29 10:18 ` Joseph Vidal-Rosset 6 siblings, 2 replies; 46+ messages in thread From: Eric Schulte @ 2014-06-25 20:25 UTC (permalink / raw) To: John Kitchin; +Cc: emacs-orgmode John Kitchin <jkitchin@andrew.cmu.edu> writes: > Hello everyone, > > org-ref has basically stabilized. You can get the latest code at > https://github.com/jkitchin/jmax/blob/master/org-ref.org. > > I made a little screen capture video here to show you what it does: > https://www.youtube.com/watch?v=JyvpSVl4_dg > > Try it out, if it looks interesting, and let me know if you find any > bugs! > > Thanks, Great, This is a lot of useful functionality, and very nicely presented. Did you happen to try the built in bibtex support in Org-mode core and contrib? And if so, is there a reason that you implemented this all independently? I think part of the problem with existing Org-mode bibtex support is that no-one knows it exists. To help address this I threw up a very quick-and-dirty screen cast demonstrating some of Org's existing bibtex functionality. https://vimeo.com/99167082 Best, Eric -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D (see https://u.fsf.org/yw) ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-25 20:25 ` Eric Schulte @ 2014-06-26 1:09 ` Grant Rettke 2014-06-26 1:10 ` Matt Lundin 1 sibling, 0 replies; 46+ messages in thread From: Grant Rettke @ 2014-06-26 1:09 UTC (permalink / raw) To: Eric Schulte; +Cc: emacs-orgmode@gnu.org, John Kitchin John: Beautiful, thanks! Eric: My goodness, that 8 minute video sums up what was not obvious to many even after wantingly browsing the documentation on it. Thanks! Grant Rettke | ACM, ASA, FSF, IEEE, SIAM gcr@wisdomandwonder.com | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.” --Socrates ((λ (x) (x x)) (λ (x) (x x))) “Life has become immeasurably better since I have been forced to stop taking it seriously.” --Thompson On Wed, Jun 25, 2014 at 3:25 PM, Eric Schulte <schulte.eric@gmail.com> wrote: > John Kitchin <jkitchin@andrew.cmu.edu> writes: > >> Hello everyone, >> >> org-ref has basically stabilized. You can get the latest code at >> https://github.com/jkitchin/jmax/blob/master/org-ref.org. >> >> I made a little screen capture video here to show you what it does: >> https://www.youtube.com/watch?v=JyvpSVl4_dg >> >> Try it out, if it looks interesting, and let me know if you find any >> bugs! >> >> Thanks, > > Great, > > This is a lot of useful functionality, and very nicely presented. > > Did you happen to try the built in bibtex support in Org-mode core and > contrib? And if so, is there a reason that you implemented this all > independently? > > I think part of the problem with existing Org-mode bibtex support is > that no-one knows it exists. To help address this I threw up a very > quick-and-dirty screen cast demonstrating some of Org's existing bibtex > functionality. > > https://vimeo.com/99167082 > > Best, > Eric > > -- > Eric Schulte > https://cs.unm.edu/~eschulte > PGP: 0x614CA05D (see https://u.fsf.org/yw) > ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-25 20:25 ` Eric Schulte 2014-06-26 1:09 ` Grant Rettke @ 2014-06-26 1:10 ` Matt Lundin 2014-06-26 12:21 ` Fabrice Popineau 1 sibling, 1 reply; 46+ messages in thread From: Matt Lundin @ 2014-06-26 1:10 UTC (permalink / raw) To: Eric Schulte; +Cc: emacs-orgmode, John Kitchin Eric Schulte <schulte.eric@gmail.com> writes: > > This is a lot of useful functionality, and very nicely presented. > > Did you happen to try the built in bibtex support in Org-mode core and > contrib? And if so, is there a reason that you implemented this all > independently? > > I think part of the problem with existing Org-mode bibtex support is > that no-one knows it exists. Well, you can count on one big fan of org-bibtex.el here! (Though I must admit that I have not used ox-bibtex.el.) > To help address this I threw up a very quick-and-dirty screen cast > demonstrating some of Org's existing bibtex functionality. > > https://vimeo.com/99167082 Thanks! Over the years, I've particularly appreciated the way org-bibtex.el makes it easy to keep bib data together with notes/todos. Both org-bibtex-read and org-bibtex-yank have become indispensable to my own workflow. Best, Matt ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 1:10 ` Matt Lundin @ 2014-06-26 12:21 ` Fabrice Popineau 2014-06-26 12:48 ` John Kitchin 0 siblings, 1 reply; 46+ messages in thread From: Fabrice Popineau @ 2014-06-26 12:21 UTC (permalink / raw) To: Matt Lundin; +Cc: emacs-orgmode@gnu.org, Eric Schulte, John Kitchin [-- Attachment #1: Type: text/plain, Size: 1586 bytes --] +1 for org-bibtex (and ox-bibtex) that I'm using for a couple of years. But org-ref seems to go further (video is convincing). It would be really nice to merge org-ref and org-bibtex before they split too far apart. Wishful thinking from me because I don't see that I'm in position to do it. Fabrice 2014-06-26 3:10 GMT+02:00 Matt Lundin <mdl@imapmail.org>: > Eric Schulte <schulte.eric@gmail.com> writes: > > > > > This is a lot of useful functionality, and very nicely presented. > > > > Did you happen to try the built in bibtex support in Org-mode core and > > contrib? And if so, is there a reason that you implemented this all > > independently? > > > > I think part of the problem with existing Org-mode bibtex support is > > that no-one knows it exists. > > Well, you can count on one big fan of org-bibtex.el here! (Though I must > admit that I have not used ox-bibtex.el.) > > > To help address this I threw up a very quick-and-dirty screen cast > > demonstrating some of Org's existing bibtex functionality. > > > > https://vimeo.com/99167082 > > Thanks! Over the years, I've particularly appreciated the way > org-bibtex.el makes it easy to keep bib data together with notes/todos. > Both org-bibtex-read and org-bibtex-yank have become indispensable to my > own workflow. > > Best, > Matt > > -- Fabrice Popineau ----------------------------- SUPELEC Département Informatique 3, rue Joliot Curie 91192 Gif/Yvette Cedex Tel direct : +33 (0) 169851950 Standard : +33 (0) 169851212 ------------------------------ [-- Attachment #2: Type: text/html, Size: 2329 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 12:21 ` Fabrice Popineau @ 2014-06-26 12:48 ` John Kitchin 2014-06-26 14:08 ` Matt Lundin ` (2 more replies) 0 siblings, 3 replies; 46+ messages in thread From: John Kitchin @ 2014-06-26 12:48 UTC (permalink / raw) To: Fabrice Popineau; +Cc: Matt Lundin, emacs-orgmode@gnu.org, Eric Schulte [-- Attachment #1: Type: text/plain, Size: 2541 bytes --] Some features could be merged, but there is an important difference in that org-ref uses bibtex as the backend database, and reftex for searching, and org-bibtex uses org-mode headings as the backend database, and tag/property searches (I think). It is like the difference between org-contacts and bbdb. They both serve similar needs, but with different data sources, and different ways to think about it. We might be able to figure out a way to specify a "backend" that would allow the independent features to work in both though. John ----------------------------------- John Kitchin Associate Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu On Thu, Jun 26, 2014 at 8:21 AM, Fabrice Popineau < fabrice.popineau@supelec.fr> wrote: > > +1 for org-bibtex (and ox-bibtex) that I'm using for a couple of years. > > But org-ref seems to go further (video is convincing). > It would be really nice to merge org-ref and org-bibtex before they split > too far apart. > Wishful thinking from me because I don't see that I'm in position to do it. > > Fabrice > > > 2014-06-26 3:10 GMT+02:00 Matt Lundin <mdl@imapmail.org>: > > Eric Schulte <schulte.eric@gmail.com> writes: >> >> > >> > This is a lot of useful functionality, and very nicely presented. >> > >> > Did you happen to try the built in bibtex support in Org-mode core and >> > contrib? And if so, is there a reason that you implemented this all >> > independently? >> > >> > I think part of the problem with existing Org-mode bibtex support is >> > that no-one knows it exists. >> >> Well, you can count on one big fan of org-bibtex.el here! (Though I must >> admit that I have not used ox-bibtex.el.) >> >> > To help address this I threw up a very quick-and-dirty screen cast >> > demonstrating some of Org's existing bibtex functionality. >> > >> > https://vimeo.com/99167082 >> >> Thanks! Over the years, I've particularly appreciated the way >> org-bibtex.el makes it easy to keep bib data together with notes/todos. >> Both org-bibtex-read and org-bibtex-yank have become indispensable to my >> own workflow. >> >> Best, >> Matt >> >> > > > -- > Fabrice Popineau > ----------------------------- > SUPELEC > Département Informatique > 3, rue Joliot Curie > 91192 Gif/Yvette Cedex > Tel direct : +33 (0) 169851950 > Standard : +33 (0) 169851212 > ------------------------------ > > [-- Attachment #2: Type: text/html, Size: 3940 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 12:48 ` John Kitchin @ 2014-06-26 14:08 ` Matt Lundin 2014-06-26 14:09 ` Matt Lundin 2014-06-26 14:11 ` Grant Rettke 2014-06-26 16:14 ` Eric Schulte 2014-06-27 6:55 ` Joseph Vidal-Rosset 2 siblings, 2 replies; 46+ messages in thread From: Matt Lundin @ 2014-06-26 14:08 UTC (permalink / raw) To: John Kitchin; +Cc: Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte John Kitchin <jkitchin@andrew.cmu.edu> writes: > Some features could be merged, but there is an important difference in > that org-ref uses bibtex as the backend database, and reftex for > searching, and org-bibtex uses org-mode headings as the backend > database, and tag/property searches (I think). It is like the > difference between org-contacts and bbdb. They both serve similar > needs, but with different data sources, and different ways to think > about it. Yes, org-bibtex.el generally precludes the use of reftex to enter citations. I get around this problem with a custom perl script, which runs automatically in the background, extracts all org-bibtex data, and deposits it in a central bib file. > We might be able to figure out a way to specify a "backend" that would > allow the independent features to work in both though. I think the key in any possible feature merge is to remember citation management is idiosyncratic. I.e., org-mode should offer helper functions that enable individuals to customize their own workflows rather than "systems" that dictate a particular workflow (e.g., a single notes file) or presuppose a specific export backend. For instance, org-mode citation tools should not assume that users will export via bibtex/bibtex2html rather than, say, biber/biblatex or pandoc (which now has a powerful, format-agnostic citation filter).[1] Best, Matt Footnotes: [1] http://johnmacfarlane.net/pandoc/demo/example19/Citations.html ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 14:08 ` Matt Lundin @ 2014-06-26 14:09 ` Matt Lundin 2014-06-26 14:11 ` Grant Rettke 1 sibling, 0 replies; 46+ messages in thread From: Matt Lundin @ 2014-06-26 14:09 UTC (permalink / raw) To: John Kitchin; +Cc: Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte Matt Lundin <mdl@imapmail.org> writes: > John Kitchin <jkitchin@andrew.cmu.edu> writes: > >> Some features could be merged, but there is an important difference in >> that org-ref uses bibtex as the backend database, and reftex for >> searching, and org-bibtex uses org-mode headings as the backend >> database, and tag/property searches (I think). It is like the >> difference between org-contacts and bbdb. They both serve similar >> needs, but with different data sources, and different ways to think >> about it. > > Yes, org-bibtex.el generally precludes the use of reftex to enter citations. s/enter/search/ ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 14:08 ` Matt Lundin 2014-06-26 14:09 ` Matt Lundin @ 2014-06-26 14:11 ` Grant Rettke 2014-06-26 14:13 ` Ken Mankoff ` (2 more replies) 1 sibling, 3 replies; 46+ messages in thread From: Grant Rettke @ 2014-06-26 14:11 UTC (permalink / raw) To: Matt Lundin Cc: Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte, John Kitchin On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin <mdl@imapmail.org> wrote: > I think the key in any possible feature merge is to remember citation > management is idiosyncratic. Off topic: How do people choose today? Why choose bibtex over biblatex? Where do people discuss such questions like this in real life? ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 14:11 ` Grant Rettke @ 2014-06-26 14:13 ` Ken Mankoff 2014-06-26 14:33 ` Jorge A. Alfaro-Murillo 2014-06-26 14:39 ` Matt Lundin 2 siblings, 0 replies; 46+ messages in thread From: Ken Mankoff @ 2014-06-26 14:13 UTC (permalink / raw) To: Grant Rettke Cc: Matt Lundin, emacs-orgmode@gnu.org, Eric Schulte, Fabrice Popineau, John Kitchin On 2014-06-26 at 10:11, Grant Rettke wrote: > Why choose bibtex over biblatex? People choose bibtex because that is how it has been done and is well supported/documented and still popular on Google results. People choose biblatex because that appears to be the new under-development with-bells-and-whistles way moving forward. > Where do people discuss such questions like this in real life? http://tex.stackexchange.com -k. ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 14:11 ` Grant Rettke 2014-06-26 14:13 ` Ken Mankoff @ 2014-06-26 14:33 ` Jorge A. Alfaro-Murillo 2014-06-26 14:39 ` Matt Lundin 2 siblings, 0 replies; 46+ messages in thread From: Jorge A. Alfaro-Murillo @ 2014-06-26 14:33 UTC (permalink / raw) To: emacs-orgmode Grant Rettke <gcr@wisdomandwonder.com> writes: > How do people choose today? > > Why choose bibtex over biblatex? For journal submission. With BibTeX you only have to copy paste at the end of your LaTeX file the contents of the generated .bbl file. Moreover, journals provide a default style for BibTeX, not biblatex. And I have never seen a journal that supports biblatex (there might be a few), but any journal that supports LaTeX supports BibTeX. > Where do people discuss such questions like this in real life? In the orgmode list =) ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 14:11 ` Grant Rettke 2014-06-26 14:13 ` Ken Mankoff 2014-06-26 14:33 ` Jorge A. Alfaro-Murillo @ 2014-06-26 14:39 ` Matt Lundin 2014-06-26 17:19 ` Alan Schmitt 2014-06-27 15:49 ` Grant Rettke 2 siblings, 2 replies; 46+ messages in thread From: Matt Lundin @ 2014-06-26 14:39 UTC (permalink / raw) To: Grant Rettke Cc: Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte, John Kitchin Grant Rettke <gcr@wisdomandwonder.com> writes: > On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin <mdl@imapmail.org> wrote: >> I think the key in any possible feature merge is to remember citation >> management is idiosyncratic. > > Off topic: > > How do people choose today? > > Why choose bibtex over biblatex? Thanks to inertia, bibtex still has a number of users in the sciences, since it was originally designed for scientific citations. In the humanities, however, bibtex is a non-starter, since biblatex offers much more flexibility. The good news is that bibtex and biblatex use the same database format, so it's easy to transition from bibtex to biblatex. However, there are other options, such as CSL.[1] > Where do people discuss such questions like this in real life? I'm not sure I understand your question. Could you clarify? I simply meant that everyone will have a different workflow/system for storing and managing citations. E.g., some will prefer to store bibliographical data in a zotero database, others in a single bib file, others in multiple bib files, others as properties in org headlines, etc. I think one can make a conception distinction here between citation management (i.e., how one stores bibliographical data) and citation processing (i.e., the software one uses to export that data to some output format). There are many, many formats (mods, bib, etc.) and tools (biber, bibtex, csl/citeproc, etc.) for formatting bibliographical data. In an ideal world, one should be able to 1) process bibliographical data from multiple formats; 2) choose from hundreds of citation styles; and 3) format citations for multiple backends. I am not suggesting that org-mode should directly support all these things, but its default methods of handling citations should not get in the way of using external tools that provide such flexibility. For instance, pandoc (an immensely impressive piece of software!) accepts bibliographical data from numerous sources and processes it for multiple outputs (html, plain text, docx, rtf, etc.). By contrast, ox-bibtex.el runs citations through bibtex2html, which is pretty much limited to the "old-fashioned" bibtex formats. Ironically, ox-bibtex.el invokes pandoc to convert from html to plain text, but only after it has already used bibtex2html to process the data. Best, Matt Footnotes: [1] Citation Style Language - http://citationstyles.org/ ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 14:39 ` Matt Lundin @ 2014-06-26 17:19 ` Alan Schmitt 2014-06-26 18:44 ` Matt Lundin 2014-06-27 15:49 ` Grant Rettke 1 sibling, 1 reply; 46+ messages in thread From: Alan Schmitt @ 2014-06-26 17:19 UTC (permalink / raw) To: Matt Lundin Cc: John Kitchin, Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte, Grant Rettke [-- Attachment #1: Type: text/plain, Size: 417 bytes --] On 2014-06-26 16:39, Matt Lundin <mdl@imapmail.org> writes: > By contrast, ox-bibtex.el runs citations through bibtex2html, which is > pretty much limited to the "old-fashioned" bibtex formats. What would be required for bibtex2html to take biblatex input? I thought the backend format was similar or the same (as you can tell, I know nothing of biblatex). Alan -- OpenPGP Key ID : 040D0A3B4ED2E5C7 [-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 17:19 ` Alan Schmitt @ 2014-06-26 18:44 ` Matt Lundin 2014-06-27 4:27 ` Xebar Saram 2014-06-27 6:44 ` Alan Schmitt 0 siblings, 2 replies; 46+ messages in thread From: Matt Lundin @ 2014-06-26 18:44 UTC (permalink / raw) To: Alan Schmitt Cc: Grant Rettke, Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte, John Kitchin Alan Schmitt <alan.schmitt@polytechnique.org> writes: > On 2014-06-26 16:39, Matt Lundin <mdl@imapmail.org> writes: > >> By contrast, ox-bibtex.el runs citations through bibtex2html, which is >> pretty much limited to the "old-fashioned" bibtex formats. > > What would be required for bibtex2html to take biblatex input? I thought > the backend format was similar or the same (as you can tell, I know > nothing of biblatex). I don't think this is possible without some major hacking/conversion/filtering. Biblatex has many more entry types and fields than bibtex. I've found that most of the older bibtex utils (bibtools, bibtex2html) choke on my biblatex files. Even if biblatex2html did read biblatex data, its output, I believe, is limited to bibtex styles, which cannot handle more complex formats. Many scientific journals require bibtex formats. But many humanities disciplines have more complicated bibliographical requirements that bibtex cannot handle. Best, Matt ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 18:44 ` Matt Lundin @ 2014-06-27 4:27 ` Xebar Saram 2014-06-27 7:37 ` Thomas S. Dye ` (3 more replies) 2014-06-27 6:44 ` Alan Schmitt 1 sibling, 4 replies; 46+ messages in thread From: Xebar Saram @ 2014-06-27 4:27 UTC (permalink / raw) To: Matt Lundin Cc: John Kitchin, Alan Schmitt, Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte, Grant Rettke [-- Attachment #1: Type: text/plain, Size: 1802 bytes --] Hi all off topic a bit again. im an academic (asst. prof) in Epidemiology and have been using org-mode for about a year now. i love using org but im really not very technical at all. it has always been a dream for me to ditch word and move over to Latex and even better orgmode to write my scientific publications, writing my CV etc. The problem is i cant really find a good "for dummies" guide on how to really get started. again im really not technical so i always give up really fast on this. Do you guys think i should give it a shot (again not very technical :)) and if so what would be the steps/guides to follow? perhaps start by drafting a CV since thats perhaps easier? kind regards Z. On Thu, Jun 26, 2014 at 9:44 PM, Matt Lundin <mdl@imapmail.org> wrote: > Alan Schmitt <alan.schmitt@polytechnique.org> writes: > > > On 2014-06-26 16:39, Matt Lundin <mdl@imapmail.org> writes: > > > >> By contrast, ox-bibtex.el runs citations through bibtex2html, which is > >> pretty much limited to the "old-fashioned" bibtex formats. > > > > What would be required for bibtex2html to take biblatex input? I thought > > the backend format was similar or the same (as you can tell, I know > > nothing of biblatex). > > I don't think this is possible without some major > hacking/conversion/filtering. Biblatex has many more entry types and > fields than bibtex. I've found that most of the older bibtex utils > (bibtools, bibtex2html) choke on my biblatex files. > > Even if biblatex2html did read biblatex data, its output, I believe, is > limited to bibtex styles, which cannot handle more complex formats. Many > scientific journals require bibtex formats. But many humanities > disciplines have more complicated bibliographical requirements that > bibtex cannot handle. > > Best, > Matt > > [-- Attachment #2: Type: text/html, Size: 2768 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-27 4:27 ` Xebar Saram @ 2014-06-27 7:37 ` Thomas S. Dye 2014-06-27 7:38 ` Vikas Rawal ` (2 subsequent siblings) 3 siblings, 0 replies; 46+ messages in thread From: Thomas S. Dye @ 2014-06-27 7:37 UTC (permalink / raw) To: Xebar Saram Cc: Fabrice Popineau, John Kitchin, Alan Schmitt, Matt Lundin, emacs-orgmode@gnu.org, Eric Schulte, Grant Rettke Aloha Xebar, Xebar Saram <zeltakc@gmail.com> writes: > Hi all > > off topic a bit again. im an academic (asst. prof) in Epidemiology and have > been using org-mode for about a year now. i love using org but im really > not very technical at all. it has always been a dream for me to ditch word > and move over to Latex and even better orgmode to write my scientific > publications, writing my CV etc. > The problem is i cant really find a good "for dummies" guide on how to > really get started. again im really not technical so i always give up > really fast on this. > > Do you guys think i should give it a shot (again not very technical :)) and > if so what would be the steps/guides to follow? perhaps start by drafting a > CV since thats perhaps easier? I wrote an Org mode template for a PLOS One journal article: http://orgmode.org/worg/exporters/plos-one-template-worg.html It uses asynchronous export that gets initialized with a file that is tangled from the template. This should get you past the common problem of unexpected results because of "something in your setup." Because it is a self-contained project, it might be easier to understand what needs to be done to use Org mode to write scientific papers. hth, Tom -- Thomas S. Dye http://www.tsdye.com ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-27 4:27 ` Xebar Saram 2014-06-27 7:37 ` Thomas S. Dye @ 2014-06-27 7:38 ` Vikas Rawal 2014-06-27 7:52 ` Melleus 2014-06-27 13:39 ` Ista Zahn 2014-06-27 23:56 ` John Kitchin 3 siblings, 1 reply; 46+ messages in thread From: Vikas Rawal @ 2014-06-27 7:38 UTC (permalink / raw) To: Xebar Saram; +Cc: org-mode mailing list > > > off topic a bit again. im an academic (asst. prof) in Epidemiology and have been using org-mode for about a year now. i love using org but im really not very technical at all. it has always been a dream for me to ditch word and move over to Latex and even better orgmode to write my scientific publications, writing my CV etc. > The problem is i cant really find a good "for dummies" guide on how to really get started. again im really not technical so i always give up really fast on this. > I wrote something that you may find useful: https://github.com/vikasrawal/orgpaper/blob/master/orgpapers.org Vikas ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-27 7:38 ` Vikas Rawal @ 2014-06-27 7:52 ` Melleus 0 siblings, 0 replies; 46+ messages in thread From: Melleus @ 2014-06-27 7:52 UTC (permalink / raw) To: emacs-orgmode Very useful guide. Thank you. ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-27 4:27 ` Xebar Saram 2014-06-27 7:37 ` Thomas S. Dye 2014-06-27 7:38 ` Vikas Rawal @ 2014-06-27 13:39 ` Ista Zahn 2014-06-27 23:56 ` John Kitchin 3 siblings, 0 replies; 46+ messages in thread From: Ista Zahn @ 2014-06-27 13:39 UTC (permalink / raw) To: Xebar Saram Cc: Fabrice Popineau, John Kitchin, Alan Schmitt, Matt Lundin, emacs-orgmode@gnu.org, Eric Schulte, Grant Rettke Yes, totally off topic for this thread, please start a new one. On Fri, Jun 27, 2014 at 12:27 AM, Xebar Saram <zeltakc@gmail.com> wrote: > Hi all > > off topic a bit again. im an academic (asst. prof) in Epidemiology and have > been using org-mode for about a year now. i love using org but im really not > very technical at all. it has always been a dream for me to ditch word and > move over to Latex and even better orgmode to write my scientific > publications, writing my CV etc. > The problem is i cant really find a good "for dummies" guide on how to > really get started. again im really not technical so i always give up really > fast on this. > > Do you guys think i should give it a shot (again not very technical :)) and > if so what would be the steps/guides to follow? perhaps start by drafting a > CV since thats perhaps easier? > > kind regards > > Z. > > > > > > > On Thu, Jun 26, 2014 at 9:44 PM, Matt Lundin <mdl@imapmail.org> wrote: >> >> Alan Schmitt <alan.schmitt@polytechnique.org> writes: >> >> > On 2014-06-26 16:39, Matt Lundin <mdl@imapmail.org> writes: >> > >> >> By contrast, ox-bibtex.el runs citations through bibtex2html, which is >> >> pretty much limited to the "old-fashioned" bibtex formats. >> > >> > What would be required for bibtex2html to take biblatex input? I thought >> > the backend format was similar or the same (as you can tell, I know >> > nothing of biblatex). >> >> I don't think this is possible without some major >> hacking/conversion/filtering. Biblatex has many more entry types and >> fields than bibtex. I've found that most of the older bibtex utils >> (bibtools, bibtex2html) choke on my biblatex files. >> >> Even if biblatex2html did read biblatex data, its output, I believe, is >> limited to bibtex styles, which cannot handle more complex formats. Many >> scientific journals require bibtex formats. But many humanities >> disciplines have more complicated bibliographical requirements that >> bibtex cannot handle. >> >> Best, >> Matt >> > ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-27 4:27 ` Xebar Saram ` (2 preceding siblings ...) 2014-06-27 13:39 ` Ista Zahn @ 2014-06-27 23:56 ` John Kitchin 3 siblings, 0 replies; 46+ messages in thread From: John Kitchin @ 2014-06-27 23:56 UTC (permalink / raw) To: Xebar Saram Cc: Fabrice Popineau, Alan Schmitt, Matt Lundin, emacs-orgmode@gnu.org, Eric Schulte, Grant Rettke [-- Attachment #1: Type: text/plain, Size: 2538 bytes --] You may find some information here: https://github.com/jkitchin/jmax/tree/master/examples that is helpful to you. i have collected some examples for various journals we have published in with orgmode there. The jmax repo is what my group currently uses for this purpose. It may not be what you want to do, but there are a lot of good ideas in it (imho of course ;) John ----------------------------------- John Kitchin Associate Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu On Fri, Jun 27, 2014 at 12:27 AM, Xebar Saram <zeltakc@gmail.com> wrote: > Hi all > > off topic a bit again. im an academic (asst. prof) in Epidemiology and > have been using org-mode for about a year now. i love using org but im > really not very technical at all. it has always been a dream for me to > ditch word and move over to Latex and even better orgmode to write my > scientific publications, writing my CV etc. > The problem is i cant really find a good "for dummies" guide on how to > really get started. again im really not technical so i always give up > really fast on this. > > Do you guys think i should give it a shot (again not very technical :)) > and if so what would be the steps/guides to follow? perhaps start by > drafting a CV since thats perhaps easier? > > kind regards > > Z. > > > > > > > On Thu, Jun 26, 2014 at 9:44 PM, Matt Lundin <mdl@imapmail.org> wrote: > >> Alan Schmitt <alan.schmitt@polytechnique.org> writes: >> >> > On 2014-06-26 16:39, Matt Lundin <mdl@imapmail.org> writes: >> > >> >> By contrast, ox-bibtex.el runs citations through bibtex2html, which is >> >> pretty much limited to the "old-fashioned" bibtex formats. >> > >> > What would be required for bibtex2html to take biblatex input? I thought >> > the backend format was similar or the same (as you can tell, I know >> > nothing of biblatex). >> >> I don't think this is possible without some major >> hacking/conversion/filtering. Biblatex has many more entry types and >> fields than bibtex. I've found that most of the older bibtex utils >> (bibtools, bibtex2html) choke on my biblatex files. >> >> Even if biblatex2html did read biblatex data, its output, I believe, is >> limited to bibtex styles, which cannot handle more complex formats. Many >> scientific journals require bibtex formats. But many humanities >> disciplines have more complicated bibliographical requirements that >> bibtex cannot handle. >> >> Best, >> Matt >> >> > [-- Attachment #2: Type: text/html, Size: 3861 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 18:44 ` Matt Lundin 2014-06-27 4:27 ` Xebar Saram @ 2014-06-27 6:44 ` Alan Schmitt 2014-06-27 14:26 ` Matt Lundin 1 sibling, 1 reply; 46+ messages in thread From: Alan Schmitt @ 2014-06-27 6:44 UTC (permalink / raw) To: Matt Lundin Cc: Grant Rettke, Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte, John Kitchin [-- Attachment #1: Type: text/plain, Size: 1768 bytes --] On 2014-06-26 20:44, Matt Lundin <mdl@imapmail.org> writes: > Alan Schmitt <alan.schmitt@polytechnique.org> writes: > >> On 2014-06-26 16:39, Matt Lundin <mdl@imapmail.org> writes: >> >>> By contrast, ox-bibtex.el runs citations through bibtex2html, which is >>> pretty much limited to the "old-fashioned" bibtex formats. >> >> What would be required for bibtex2html to take biblatex input? I thought >> the backend format was similar or the same (as you can tell, I know >> nothing of biblatex). > > I don't think this is possible without some major > hacking/conversion/filtering. Biblatex has many more entry types and > fields than bibtex. I've found that most of the older bibtex utils > (bibtools, bibtex2html) choke on my biblatex files. Is there a list of these new entry types? Looking at the code for bibtex2html (for instance https://github.com/backtracking/bibtex2html/blob/master/bibtex.mli) I see that entry types are strings, so if there are issues, I guess they would happen in the generation part but not in the parsing part. > Even if biblatex2html did read biblatex data, its output, I believe, is > limited to bibtex styles, which cannot handle more complex formats. Many > scientific journals require bibtex formats. But many humanities > disciplines have more complicated bibliographical requirements that > bibtex cannot handle. I'm very ignorant here: from my understanding, bibtex2html does not care about bibtex style, it just takes bibtex data as input and produces html. Is the problem that some entries are ignored, or is there something deeper that I'm missing? Alan PS: if anyone on the list think we should take this off-list, please let me know -- OpenPGP Key ID : 040D0A3B4ED2E5C7 [-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-27 6:44 ` Alan Schmitt @ 2014-06-27 14:26 ` Matt Lundin 2014-06-27 17:19 ` Matt Lundin 0 siblings, 1 reply; 46+ messages in thread From: Matt Lundin @ 2014-06-27 14:26 UTC (permalink / raw) To: Alan Schmitt; +Cc: Fabrice Popineau, emacs-orgmode@gnu.org Alan Schmitt <alan.schmitt@polytechnique.org> writes: > On 2014-06-26 20:44, Matt Lundin <mdl@imapmail.org> writes: >> >> I don't think this is possible without some major >> hacking/conversion/filtering. Biblatex has many more entry types and >> fields than bibtex. I've found that most of the older bibtex utils >> (bibtools, bibtex2html) choke on my biblatex files. > > Is there a list of these new entry types? It depends on the style. I use the biblatex-chicago style. I grepped the sample bib file supplied with the package to get a list of entry types[fn:1] and fields.[fn:2] And this represents only a subset of the possible fields! See also the variable bibtex-biblatex-entry-alist in bibtex.el (shipped with emacs). > Looking at the code for bibtex2html (for instance > https://github.com/backtracking/bibtex2html/blob/master/bibtex.mli) I > see that entry types are strings, so if there are issues, I guess they > would happen in the generation part but not in the parsing part. You are right. I see that one can specify a style file for parsing bib files and biblatex does supply a biblatex.bst, e.g., bibtex2html -s biblatex However, this still produces errors (and a blank html file) when I run it on a larger bib file that pdflatex/biber parses fine. I was able to get it to run without errors on a small carefully culled subset (a book and an article). >> Even if biblatex2html did read biblatex data, its output, I believe, >> is limited to bibtex styles, which cannot handle more complex >> formats. > I'm very ignorant here: from my understanding, bibtex2html does not > care about bibtex style, it just takes bibtex data as input and > produces html. > Is the problem that some entries are ignored, Yes, as well as many fields. > or is there something deeper that I'm missing? For my particular use-case, the problem is that it formats the bibliographical data incorrectly. This is because biblatex relies on LaTeX macros (rather than bibtex) to format the bibliography. Thus, any utility that relies on bibtex to format bibliographies not work with biblatex styles. This, by the way, is why biblatex was is such a boon for those of use working in the humanities: bibtex was *never* sufficient for humanities citations. E.g., the biblatex-chicago style outputs a bibliographical item for a book like this (with org markup added to show emphasis): Wolloch, Isser. /The New Regime: Transformations of the French Civic Order, 1789--1820s/. New York and London: W. W. Norton, 1994. bibtex2html produces this: Isser Wolloch. /The New Regime./ W. W. Norton, 1994. Best, Matt (who also would also be happy to take this off list) Footnotes: [fn:1] Article, Artwork, Audio, Book, Booklet, Collection, CustomC, Image, InBook, InCollection, inproceedings, InReference, Letter, Manual, MastersThesis, Misc, Music, MVCollection, Online, Patent, Periodical, PhdThesis, Reference, Review, SuppBook, TechReport, Unpublished, Video [fn:2] addendum, address, afterword, annote, author, authortype, bookauthor, booksubtitle, booktitle, booktitleaddon, chapter, crossref, date, doi, edition, editor, editora, editoratype, editortype, entrysubtype, eventdate, howpublished, institution, isbn, issue, issuetitle, journaltitle, keywords, language, lista, location, longcrossref, mainsubtitle, maintitle, month, namea, nameaddon, nameb, namec, note, number, options, organization, origdate, origlanguage, origlocation, origpublisher, pages, part, publisher, pubstate, school, series, shortauthor, shorthand, shorttitle, sortkey, sorttitle, subtitle, title, titleaddon, translator, type, url, urldate, useauthor, usecompiler, useeditor, usera, userc, userd, usere, userf, volume, volumes, xref, year ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-27 14:26 ` Matt Lundin @ 2014-06-27 17:19 ` Matt Lundin 0 siblings, 0 replies; 46+ messages in thread From: Matt Lundin @ 2014-06-27 17:19 UTC (permalink / raw) To: Alan Schmitt; +Cc: Fabrice Popineau, emacs-orgmode@gnu.org Matt Lundin <mdl@imapmail.org> writes: > Alan Schmitt <alan.schmitt@polytechnique.org> writes: > > You are right. I see that one can specify a style file for parsing bib > files and biblatex does supply a biblatex.bst, e.g., > > bibtex2html -s biblatex > > However, this still produces errors (and a blank html file) when I run > it on a larger bib file that pdflatex/biber parses fine. I was able to > get it to run without errors on a small carefully culled subset (a book > and an article). For the record, after correcting an error in several of my bib entries, bibtex2html -s biblatex is able to parse a biblatex database without error. However, the resulting html is empty. Thanks, Matt ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 14:39 ` Matt Lundin 2014-06-26 17:19 ` Alan Schmitt @ 2014-06-27 15:49 ` Grant Rettke 1 sibling, 0 replies; 46+ messages in thread From: Grant Rettke @ 2014-06-27 15:49 UTC (permalink / raw) To: Matt Lundin Cc: Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte, John Kitchin Thanks for your answer on that everybody. My apologies for my poor grammar asking where "people discuss such questions in real life". What I really had wanted to say, what I meant, was that I was wondering what professions utilize such workflows and where they discuss it primarily because the topic does go beyond LaTeX alone. My usage of such a workflow is pretty lightweight, and I've never had anyone to talk to about it because in my field generally no one cites their references. Grant Rettke | ACM, ASA, FSF, IEEE, SIAM gcr@wisdomandwonder.com | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.” --Socrates ((λ (x) (x x)) (λ (x) (x x))) “Life has become immeasurably better since I have been forced to stop taking it seriously.” --Thompson On Thu, Jun 26, 2014 at 9:39 AM, Matt Lundin <mdl@imapmail.org> wrote: > Grant Rettke <gcr@wisdomandwonder.com> writes: > >> On Thu, Jun 26, 2014 at 9:08 AM, Matt Lundin <mdl@imapmail.org> wrote: >>> I think the key in any possible feature merge is to remember citation >>> management is idiosyncratic. >> >> Off topic: >> >> How do people choose today? >> >> Why choose bibtex over biblatex? > > Thanks to inertia, bibtex still has a number of users in the sciences, > since it was originally designed for scientific citations. In the > humanities, however, bibtex is a non-starter, since biblatex offers much > more flexibility. The good news is that bibtex and biblatex use the same > database format, so it's easy to transition from bibtex to biblatex. > However, there are other options, such as CSL.[1] > >> Where do people discuss such questions like this in real life? > > I'm not sure I understand your question. Could you clarify? > > I simply meant that everyone will have a different workflow/system for > storing and managing citations. E.g., some will prefer to store > bibliographical data in a zotero database, others in a single bib file, > others in multiple bib files, others as properties in org headlines, > etc. > > I think one can make a conception distinction here between citation > management (i.e., how one stores bibliographical data) and citation > processing (i.e., the software one uses to export that data to some > output format). There are many, many formats (mods, bib, etc.) and tools > (biber, bibtex, csl/citeproc, etc.) for formatting bibliographical data. > > In an ideal world, one should be able to 1) process bibliographical data > from multiple formats; 2) choose from hundreds of citation styles; and > 3) format citations for multiple backends. I am not suggesting that > org-mode should directly support all these things, but its default > methods of handling citations should not get in the way of using > external tools that provide such flexibility. > > For instance, pandoc (an immensely impressive piece of software!) > accepts bibliographical data from numerous sources and processes it for > multiple outputs (html, plain text, docx, rtf, etc.). By contrast, > ox-bibtex.el runs citations through bibtex2html, which is pretty much > limited to the "old-fashioned" bibtex formats. Ironically, ox-bibtex.el > invokes pandoc to convert from html to plain text, but only after it has > already used bibtex2html to process the data. > > Best, > Matt > > Footnotes: > > [1] Citation Style Language - http://citationstyles.org/ ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 12:48 ` John Kitchin 2014-06-26 14:08 ` Matt Lundin @ 2014-06-26 16:14 ` Eric Schulte 2014-06-27 6:55 ` Joseph Vidal-Rosset 2 siblings, 0 replies; 46+ messages in thread From: Eric Schulte @ 2014-06-26 16:14 UTC (permalink / raw) To: John Kitchin; +Cc: Matt Lundin, Fabrice Popineau, emacs-orgmode@gnu.org John Kitchin <jkitchin@andrew.cmu.edu> writes: > Some features could be merged, but there is an important difference in that > org-ref uses bibtex as the backend database, and reftex for searching, and > org-bibtex uses org-mode headings as the backend database, and tag/property > searches (I think). It is like the difference between org-contacts and > bbdb. They both serve similar needs, but with different data sources, and > different ways to think about it. > > We might be able to figure out a way to specify a "backend" that would > allow the independent features to work in both though. > I wonder what the API would look like. The following functions comes to my mind. I'm not sure if there would be much more for org-ref... - jump location for citation by ID - return bibtex information for citation by ID - validate citation With those functions I imagine that a good deal of higher-level code could be shared in a backend agnostic way. Including, - jump to citations - provide information on citations - collect citations during publishing (possibly automatically create the bib file) If merging makes sense that's great, but if not then there's certainly no harm in a diverse ecosystem of org tools supporting different work flows and backend tools. Best, Eric > > John > > ----------------------------------- > John Kitchin > Associate Professor > Doherty Hall A207F > Department of Chemical Engineering > Carnegie Mellon University > Pittsburgh, PA 15213 > 412-268-7803 > http://kitchingroup.cheme.cmu.edu > > > > On Thu, Jun 26, 2014 at 8:21 AM, Fabrice Popineau < > fabrice.popineau@supelec.fr> wrote: > >> >> +1 for org-bibtex (and ox-bibtex) that I'm using for a couple of years. >> >> But org-ref seems to go further (video is convincing). >> It would be really nice to merge org-ref and org-bibtex before they split >> too far apart. >> Wishful thinking from me because I don't see that I'm in position to do it. >> >> Fabrice >> >> >> 2014-06-26 3:10 GMT+02:00 Matt Lundin <mdl@imapmail.org>: >> >> Eric Schulte <schulte.eric@gmail.com> writes: >>> >>> > >>> > This is a lot of useful functionality, and very nicely presented. >>> > >>> > Did you happen to try the built in bibtex support in Org-mode core and >>> > contrib? And if so, is there a reason that you implemented this all >>> > independently? >>> > >>> > I think part of the problem with existing Org-mode bibtex support is >>> > that no-one knows it exists. >>> >>> Well, you can count on one big fan of org-bibtex.el here! (Though I must >>> admit that I have not used ox-bibtex.el.) >>> >>> > To help address this I threw up a very quick-and-dirty screen cast >>> > demonstrating some of Org's existing bibtex functionality. >>> > >>> > https://vimeo.com/99167082 >>> >>> Thanks! Over the years, I've particularly appreciated the way >>> org-bibtex.el makes it easy to keep bib data together with notes/todos. >>> Both org-bibtex-read and org-bibtex-yank have become indispensable to my >>> own workflow. >>> >>> Best, >>> Matt >>> >>> >> >> >> -- >> Fabrice Popineau >> ----------------------------- >> SUPELEC >> Département Informatique >> 3, rue Joliot Curie >> 91192 Gif/Yvette Cedex >> Tel direct : +33 (0) 169851950 >> Standard : +33 (0) 169851212 >> ------------------------------ >> >> -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D (see https://u.fsf.org/yw) ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-26 12:48 ` John Kitchin 2014-06-26 14:08 ` Matt Lundin 2014-06-26 16:14 ` Eric Schulte @ 2014-06-27 6:55 ` Joseph Vidal-Rosset 2 siblings, 0 replies; 46+ messages in thread From: Joseph Vidal-Rosset @ 2014-06-27 6:55 UTC (permalink / raw) To: John Kitchin Cc: Matt Lundin, Fabrice Popineau, emacs-orgmode@gnu.org, Eric Schulte [-- Attachment #1: Type: text/plain, Size: 3208 bytes --] Hello Jonhn, hello the list, I have already used org-bibtex (and ox-bibtex) and I have just tried to use org-ref . Is it possible that a conflict exists between the former(s) and the latter? My links for example are not clickable and the link to the default bibliography does not work at all... But I have started from an older org file used with org-bibtex. Your help is welcome : could you show us a minimal file in order to test org-ref ? Best wishes, Jo. 2014-06-26 14:48 GMT+02:00 John Kitchin <jkitchin@andrew.cmu.edu>: > Some features could be merged, but there is an important difference in > that org-ref uses bibtex as the backend database, and reftex for searching, > and org-bibtex uses org-mode headings as the backend database, and > tag/property searches (I think). It is like the difference between > org-contacts and bbdb. They both serve similar needs, but with different > data sources, and different ways to think about it. > > We might be able to figure out a way to specify a "backend" that would > allow the independent features to work in both though. > > John > > ----------------------------------- > John Kitchin > Associate Professor > Doherty Hall A207F > Department of Chemical Engineering > Carnegie Mellon University > Pittsburgh, PA 15213 > 412-268-7803 > http://kitchingroup.cheme.cmu.edu > > > > On Thu, Jun 26, 2014 at 8:21 AM, Fabrice Popineau < > fabrice.popineau@supelec.fr> wrote: > >> >> +1 for org-bibtex (and ox-bibtex) that I'm using for a couple of years. >> >> But org-ref seems to go further (video is convincing). >> It would be really nice to merge org-ref and org-bibtex before they split >> too far apart. >> Wishful thinking from me because I don't see that I'm in position to do >> it. >> >> Fabrice >> >> >> 2014-06-26 3:10 GMT+02:00 Matt Lundin <mdl@imapmail.org>: >> >> Eric Schulte <schulte.eric@gmail.com> writes: >>> >>> > >>> > This is a lot of useful functionality, and very nicely presented. >>> > >>> > Did you happen to try the built in bibtex support in Org-mode core and >>> > contrib? And if so, is there a reason that you implemented this all >>> > independently? >>> > >>> > I think part of the problem with existing Org-mode bibtex support is >>> > that no-one knows it exists. >>> >>> Well, you can count on one big fan of org-bibtex.el here! (Though I must >>> admit that I have not used ox-bibtex.el.) >>> >>> > To help address this I threw up a very quick-and-dirty screen cast >>> > demonstrating some of Org's existing bibtex functionality. >>> > >>> > https://vimeo.com/99167082 >>> >>> Thanks! Over the years, I've particularly appreciated the way >>> org-bibtex.el makes it easy to keep bib data together with notes/todos. >>> Both org-bibtex-read and org-bibtex-yank have become indispensable to my >>> own workflow. >>> >>> Best, >>> Matt >>> >>> >> >> >> -- >> Fabrice Popineau >> ----------------------------- >> SUPELEC >> Département Informatique >> 3, rue Joliot Curie >> 91192 Gif/Yvette Cedex >> Tel direct : +33 (0) 169851950 >> Standard : +33 (0) 169851212 >> ------------------------------ >> >> > [-- Attachment #2: Type: text/html, Size: 4929 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-24 18:45 org-ref in action John Kitchin ` (5 preceding siblings ...) 2014-06-25 20:25 ` Eric Schulte @ 2014-06-29 10:18 ` Joseph Vidal-Rosset 2014-06-29 12:09 ` John Kitchin 2014-06-29 18:19 ` Eric Schulte 6 siblings, 2 replies; 46+ messages in thread From: Joseph Vidal-Rosset @ 2014-06-29 10:18 UTC (permalink / raw) To: John Kitchin; +Cc: Liste-emacs-orgmode@gnu.org [-- Attachment #1: Type: text/plain, Size: 714 bytes --] Hi John, hello the list, My question is very simple and it is not unrevelevant vis-à-vis this thread, therefore I keep the same thread. What need is to get either the usual citation format (often in plain style) \cite{one-reference-paper-year} or this one with a mentioned page: \cite[page n]{one-reference-paper-year}. My problem with cite: org-mode format is that I am not able to get the second format. Ideally , I want to click on the reference and just to add the quoted page. I do not doubt that this is easy to get in org-mode, but I'm wasting my time to find how... if it is possible to get it with org-ref or via another tool, many thanks in advance. Best regards Jo. [-- Attachment #2: Type: text/html, Size: 886 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-29 10:18 ` Joseph Vidal-Rosset @ 2014-06-29 12:09 ` John Kitchin 2014-06-29 18:19 ` Eric Schulte 1 sibling, 0 replies; 46+ messages in thread From: John Kitchin @ 2014-06-29 12:09 UTC (permalink / raw) To: Joseph Vidal-Rosset; +Cc: Liste-emacs-orgmode@gnu.org [-- Attachment #1: Type: text/plain, Size: 1316 bytes --] with org-ref [[cite:tony-2010][page n]] exports as \cite[page n]{tony-2010} and [[cite:tony-2010][text before link::text after link]] exports as \cite[text before link][text after link]{tony-2010} John ----------------------------------- John Kitchin Associate Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu On Sun, Jun 29, 2014 at 6:18 AM, Joseph Vidal-Rosset < joseph.vidal.rosset@gmail.com> wrote: > Hi John, hello the list, > > My question is very simple and it is not unrevelevant vis-à-vis this > thread, therefore I keep the same thread. > > What need is to get either the usual citation format (often in plain > style) \cite{one-reference-paper-year} or this one with a mentioned page: > \cite[page n]{one-reference-paper-year}. > > My problem with cite: org-mode format is that I am not able to get the > second format. Ideally , I want to click on the reference and just to add > the quoted page. > > I do not doubt that this is easy to get in org-mode, but I'm wasting my > time to find how... if it is possible to get it with org-ref or via > another tool, many thanks in advance. > > Best regards > > Jo. > > [-- Attachment #2: Type: text/html, Size: 2103 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-29 10:18 ` Joseph Vidal-Rosset 2014-06-29 12:09 ` John Kitchin @ 2014-06-29 18:19 ` Eric Schulte 2014-06-29 18:23 ` Joseph Vidal-Rosset 2014-06-30 9:29 ` Joseph Vidal-Rosset 1 sibling, 2 replies; 46+ messages in thread From: Eric Schulte @ 2014-06-29 18:19 UTC (permalink / raw) To: Joseph Vidal-Rosset; +Cc: Liste-emacs-orgmode@gnu.org, John Kitchin Joseph Vidal-Rosset <joseph.vidal.rosset@gmail.com> writes: > Hi John, hello the list, > > My question is very simple and it is not unrevelevant vis-à-vis this > thread, therefore I keep the same thread. > > What need is to get either the usual citation format (often in plain > style) \cite{one-reference-paper-year} or this one with a mentioned page: > \cite[page n]{one-reference-paper-year}. > With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as \cite[page n]{one-reference-paper-year} > > My problem with cite: org-mode format is that I am not able to get the > second format. Ideally , I want to click on the reference and just to add > the quoted page. > > I do not doubt that this is easy to get in org-mode, but I'm wasting my > time to find how... if it is possible to get it with org-ref or via > another tool, many thanks in advance. > > Best regards > > Jo. > -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D (see https://u.fsf.org/yw) ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-29 18:19 ` Eric Schulte @ 2014-06-29 18:23 ` Joseph Vidal-Rosset 2014-06-30 9:29 ` Joseph Vidal-Rosset 1 sibling, 0 replies; 46+ messages in thread From: Joseph Vidal-Rosset @ 2014-06-29 18:23 UTC (permalink / raw) To: Eric Schulte; +Cc: Liste-emacs-orgmode@gnu.org, John Kitchin [-- Attachment #1: Type: text/plain, Size: 248 bytes --] 2014-06-29 20:19 GMT+02:00 Eric Schulte <schulte.eric@gmail.com>: > With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as > > \cite[page n]{one-reference-paper-year} > Many thanks Eric . It helps a lot ! Best wishes Jo. [-- Attachment #2: Type: text/html, Size: 694 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-29 18:19 ` Eric Schulte 2014-06-29 18:23 ` Joseph Vidal-Rosset @ 2014-06-30 9:29 ` Joseph Vidal-Rosset 2014-06-30 9:52 ` Eric Schulte 1 sibling, 1 reply; 46+ messages in thread From: Joseph Vidal-Rosset @ 2014-06-30 9:29 UTC (permalink / raw) To: Eric Schulte; +Cc: Liste-emacs-orgmode@gnu.org, John Kitchin [-- Attachment #1: Type: text/plain, Size: 448 bytes --] 2014-06-29 20:19 GMT+02:00 Eric Schulte <schulte.eric@gmail.com>: > > With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as > > \cite[page n]{one-reference-paper-year} I am sorry Eric but [[cite:(page n)one-reference-paper-year]] breaks the bibliography reference for me with ox-bibtex.el ... it is too bad because it was a convenient solution to get \cite[page n]{one-reference-paper-year} . I am lost. Regards Jo. [-- Attachment #2: Type: text/html, Size: 923 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-30 9:29 ` Joseph Vidal-Rosset @ 2014-06-30 9:52 ` Eric Schulte 2014-06-30 10:06 ` Joseph Vidal-Rosset 0 siblings, 1 reply; 46+ messages in thread From: Eric Schulte @ 2014-06-30 9:52 UTC (permalink / raw) To: Joseph Vidal-Rosset; +Cc: Liste-emacs-orgmode@gnu.org, John Kitchin Joseph Vidal-Rosset <joseph.vidal.rosset@gmail.com> writes: > 2014-06-29 20:19 GMT+02:00 Eric Schulte <schulte.eric@gmail.com>: > >> >> With ox-bibtex.el [[cite:(page n)one-reference-paper-year]] will export as >> >> \cite[page n]{one-reference-paper-year} > > > > I am sorry Eric but [[cite:(page n)one-reference-paper-year]] breaks the > bibliography reference for me with ox-bibtex.el ... it is too bad because > it was a convenient solution to get \cite[page > n]{one-reference-paper-year} . > > I am lost. > Could you be more specific? Does org-mode generate any latex at all, and how does it differ from what you'd expect? If no LaTeX is generated, and Org-mode actually throws an error then please provide a backtrace. I should be able to help but I'll need more information. One thing I noticed is that I got better behavior if I didn't allow line breaks in the link, which was easily accomplished by replacing [[cite:(page n)one-reference-paper-year]] with [[cite:(page~n)one-reference-paper-year]]. In general the later is actually /preferable/ than the former, as you don't want LaTeX breaking lines in the middle of a citation either. Best, > > Regards > > Jo. -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D (see https://u.fsf.org/yw) ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-30 9:52 ` Eric Schulte @ 2014-06-30 10:06 ` Joseph Vidal-Rosset 2014-06-30 10:22 ` Eric Schulte 0 siblings, 1 reply; 46+ messages in thread From: Joseph Vidal-Rosset @ 2014-06-30 10:06 UTC (permalink / raw) To: Eric Schulte; +Cc: Liste-emacs-orgmode@gnu.org, John Kitchin [-- Attachment #1: Type: text/plain, Size: 1722 bytes --] I thank you Eric for your quick and kind reply. In my init.el file I have put this code : (eval-after-load 'reftex-vars '(progn (add-to-list 'reftex-cite-format-builtin '(org "Org-mode citation" ((?\C-m . "[[cite:(%p)%l]]") (?t . "[[textcite:%l]]") (?p . "[[parencite:%l]]") (?s . "[[posscite:%l]]") (?a . "[[citeauthor:%l]]") (?y . "[[citeyear:%l]]")))))) 2014-06-30 11:52 GMT+02:00 Eric Schulte <schulte.eric@gmail.com>: > Could you be more specific? Does org-mode generate any latex at all, > and how does it differ from what you'd expect? If no LaTeX is > generated, and Org-mode actually throws an error then please provide a > backtrace. I should be able to help but I'll need more information. > Thanns to the default cite action, I get for example in my org file: [[cite:(119–136)johansson36:_minim_formal]] and it creates no reference at al, because via the export I get: \cite{(119–136)johansson36:_minim_formal} > > One thing I noticed is that I got better behavior if I didn't allow line > breaks in the link, which was easily accomplished by replacing > [[cite:(page n)one-reference-paper-year]] with > [[cite:(page~n)one-reference-paper-year]]. In general the later is > actually /preferable/ than the former, as you don't want LaTeX breaking > lines in the middle of a citation either. > It is not the issue here because I have no broken line. I'm using bibtex here and no biblatex. Maybe biblatex is a better option, but it is another question. Best Jo. [-- Attachment #2: Type: text/html, Size: 2813 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-30 10:06 ` Joseph Vidal-Rosset @ 2014-06-30 10:22 ` Eric Schulte 2014-06-30 11:27 ` Joseph Vidal-Rosset 0 siblings, 1 reply; 46+ messages in thread From: Eric Schulte @ 2014-06-30 10:22 UTC (permalink / raw) To: Joseph Vidal-Rosset; +Cc: Liste-emacs-orgmode@gnu.org, John Kitchin > Thanns to the default cite action, I get for example in my org file: > > [[cite:(119–136)johansson36:_minim_formal]] > > and it creates no reference at al, because via the export I get: > > \cite{(119–136)johansson36:_minim_formal} > Using the latest version of Org-mode from the git repository, this is a very new feature and requires usage of the git version of Org-mode, I am seeing the desired behavior. After simply requiring ox-bibtex, the following * H1 [[cite:(119–136)johansson36:_minim_formal]] exports to \begin{document} \maketitle \tableofcontents \section{H1} \label{sec-1}~\cite[119–136]{johansson36:_minim_formal} % Emacs 24.4.50.2 (Org mode beta_8.3) \end{document} As expected. I hope this helps, Eric -- Eric Schulte https://cs.unm.edu/~eschulte PGP: 0x614CA05D (see https://u.fsf.org/yw) ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-30 10:22 ` Eric Schulte @ 2014-06-30 11:27 ` Joseph Vidal-Rosset 2014-08-05 18:28 ` Xebar Saram 0 siblings, 1 reply; 46+ messages in thread From: Joseph Vidal-Rosset @ 2014-06-30 11:27 UTC (permalink / raw) To: Eric Schulte; +Cc: Liste-emacs-orgmode@gnu.org, John Kitchin [-- Attachment #1: Type: text/plain, Size: 1133 bytes --] Thanks Eric, it works now, with the latest version of org-mode. Best wishes Jo. 2014-06-30 12:22 GMT+02:00 Eric Schulte <schulte.eric@gmail.com>: > > Thanns to the default cite action, I get for example in my org file: > > > > [[cite:(119–136)johansson36:_minim_formal]] > > > > and it creates no reference at al, because via the export I get: > > > > \cite{(119–136)johansson36:_minim_formal} > > > > Using the latest version of Org-mode from the git repository, this is a > very new feature and requires usage of the git version of Org-mode, I am > seeing the desired behavior. After simply requiring ox-bibtex, the > following > > * H1 > [[cite:(119–136)johansson36:_minim_formal]] > > exports to > > \begin{document} > > \maketitle > \tableofcontents > > \section{H1} > \label{sec-1}~\cite[119–136]{johansson36:_minim_formal} > % Emacs 24.4.50.2 (Org mode beta_8.3) > \end{document} > > As expected. > > I hope this helps, > Eric > > -- > Eric Schulte > https://cs.unm.edu/~eschulte > PGP: 0x614CA05D (see https://u.fsf.org/yw) > [-- Attachment #2: Type: text/html, Size: 1750 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-06-30 11:27 ` Joseph Vidal-Rosset @ 2014-08-05 18:28 ` Xebar Saram 2014-08-05 21:08 ` John Kitchin 0 siblings, 1 reply; 46+ messages in thread From: Xebar Saram @ 2014-08-05 18:28 UTC (permalink / raw) To: Joseph Vidal-Rosset Cc: Liste-emacs-orgmode@gnu.org, Eric Schulte, John Kitchin [-- Attachment #1: Type: text/plain, Size: 1391 bytes --] Hi all the github link seems dead, anyone knows where one could get and try org-ref from? z On Mon, Jun 30, 2014 at 2:27 PM, Joseph Vidal-Rosset < joseph.vidal.rosset@gmail.com> wrote: > Thanks Eric, it works now, with the latest version of org-mode. > > Best wishes > > Jo. > > > 2014-06-30 12:22 GMT+02:00 Eric Schulte <schulte.eric@gmail.com>: > > > Thanns to the default cite action, I get for example in my org file: >> > >> > [[cite:(119–136)johansson36:_minim_formal]] >> > >> > and it creates no reference at al, because via the export I get: >> > >> > \cite{(119–136)johansson36:_minim_formal} >> > >> >> Using the latest version of Org-mode from the git repository, this is a >> very new feature and requires usage of the git version of Org-mode, I am >> seeing the desired behavior. After simply requiring ox-bibtex, the >> following >> >> * H1 >> [[cite:(119–136)johansson36:_minim_formal]] >> >> exports to >> >> \begin{document} >> >> \maketitle >> \tableofcontents >> >> \section{H1} >> \label{sec-1}~\cite[119–136]{johansson36:_minim_formal} >> % Emacs 24.4.50.2 (Org mode beta_8.3) >> \end{document} >> >> As expected. >> >> I hope this helps, >> Eric >> >> -- >> Eric Schulte >> https://cs.unm.edu/~eschulte >> PGP: 0x614CA05D (see https://u.fsf.org/yw) >> > > [-- Attachment #2: Type: text/html, Size: 2298 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-08-05 18:28 ` Xebar Saram @ 2014-08-05 21:08 ` John Kitchin 2014-08-06 10:54 ` Xebar Saram 0 siblings, 1 reply; 46+ messages in thread From: John Kitchin @ 2014-08-05 21:08 UTC (permalink / raw) To: Xebar Saram Cc: Liste-emacs-orgmode@gnu.org, Eric Schulte, Joseph Vidal-Rosset Hi, it got moved in a re-organization to https://github.com/jkitchin/jmax/blob/master/org/org-ref.org. Sorry for the inconvenience! Xebar Saram <zeltakc@gmail.com> writes: > Hi all > > the github link seems dead, anyone knows where one could get and try > org-ref from? > > z > > On Mon, Jun 30, 2014 at 2:27 PM, Joseph Vidal-Rosset > <joseph.vidal.rosset@gmail.com> wrote: > > Thanks Eric, it works now, with the latest version of org-mode. > > Best wishes > > Jo. > > > > > 2014-06-30 12:22 GMT+02:00 Eric Schulte <schulte.eric@gmail.com>: > > > > > Thanns to the default cite action, I get for example in my > org file: > > > > [[cite:(119–136)johansson36:_minim_formal]] > > > > and it creates no reference at al, because via the export I > get: > > > > \cite{(119–136)johansson36:_minim_formal} > > > > > Using the latest version of Org-mode from the git repository, > this is a > very new feature and requires usage of the git version of > Org-mode, I am > seeing the desired behavior. After simply requiring ox-bibtex, > the > following > > * H1 > [[cite:(119–136)johansson36:_minim_formal]] > > exports to > > \begin{document} > > \maketitle > \tableofcontents > > \section{H1} > \label{sec-1}~\cite[119–136]{johansson36:_minim_formal} > % Emacs 24.4.50.2 (Org mode beta_8.3) > \end{document} > > As expected. > > I hope this helps, > Eric > > > > -- > Eric Schulte > https://cs.unm.edu/~eschulte > PGP: 0x614CA05D (see https://u.fsf.org/yw) > > > > > -- ----------------------------------- John Kitchin Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-08-05 21:08 ` John Kitchin @ 2014-08-06 10:54 ` Xebar Saram 2014-08-06 12:51 ` John Kitchin 0 siblings, 1 reply; 46+ messages in thread From: Xebar Saram @ 2014-08-06 10:54 UTC (permalink / raw) To: John Kitchin Cc: Liste-emacs-orgmode@gnu.org, Eric Schulte, Joseph Vidal-Rosset [-- Attachment #1: Type: text/plain, Size: 2950 bytes --] Thanks John No worries :) ive installed it and its working great. in a related question, does anyone use it with jabef? the reason im asking is that im very new to this and wonder about a possible workflow to export a bib citation from jabref to org and create an org header (per reference). so far it seems like org-ref will only insert something like cite:REF I have played around with org-bibtex and seem to remember there was a org-bibtex yank function that created a header in org from the bib citation in clipboard, can org-ref do something similar? sorry for the neewb questions z On Wed, Aug 6, 2014 at 12:08 AM, John Kitchin <jkitchin@andrew.cmu.edu> wrote: > Hi, it got moved in a re-organization to > https://github.com/jkitchin/jmax/blob/master/org/org-ref.org. > > Sorry for the inconvenience! > > Xebar Saram <zeltakc@gmail.com> writes: > > > Hi all > > > > the github link seems dead, anyone knows where one could get and try > > org-ref from? > > > > z > > > > On Mon, Jun 30, 2014 at 2:27 PM, Joseph Vidal-Rosset > > <joseph.vidal.rosset@gmail.com> wrote: > > > > Thanks Eric, it works now, with the latest version of org-mode. > > > > Best wishes > > > > Jo. > > > > > > > > > > 2014-06-30 12:22 GMT+02:00 Eric Schulte <schulte.eric@gmail.com>: > > > > > > > > > Thanns to the default cite action, I get for example in my > > org file: > > > > > > [[cite:(119–136)johansson36:_minim_formal]] > > > > > > and it creates no reference at al, because via the export I > > get: > > > > > > \cite{(119–136)johansson36:_minim_formal} > > > > > > > > > Using the latest version of Org-mode from the git repository, > > this is a > > very new feature and requires usage of the git version of > > Org-mode, I am > > seeing the desired behavior. After simply requiring ox-bibtex, > > the > > following > > > > * H1 > > [[cite:(119–136)johansson36:_minim_formal]] > > > > exports to > > > > \begin{document} > > > > \maketitle > > \tableofcontents > > > > \section{H1} > > \label{sec-1}~\cite[119–136]{johansson36:_minim_formal} > > % Emacs 24.4.50.2 (Org mode beta_8.3) > > \end{document} > > > > As expected. > > > > I hope this helps, > > Eric > > > > > > > > -- > > Eric Schulte > > https://cs.unm.edu/~eschulte > > PGP: 0x614CA05D (see https://u.fsf.org/yw) > > > > > > > > > > > > -- > ----------------------------------- > John Kitchin > Professor > Doherty Hall A207F > Department of Chemical Engineering > Carnegie Mellon University > Pittsburgh, PA 15213 > 412-268-7803 > http://kitchingroup.cheme.cmu.edu > [-- Attachment #2: Type: text/html, Size: 4614 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* Re: org-ref in action 2014-08-06 10:54 ` Xebar Saram @ 2014-08-06 12:51 ` John Kitchin 0 siblings, 0 replies; 46+ messages in thread From: John Kitchin @ 2014-08-06 12:51 UTC (permalink / raw) To: Xebar Saram Cc: Liste-emacs-orgmode@gnu.org, Eric Schulte, Joseph Vidal-Rosset [-- Attachment #1: Type: text/plain, Size: 3971 bytes --] I am not familiar with jabref, but assuming it stores the entries in a regular bibtex format, and you have the bibtex file open in emacs, with the cursor on the entry you want to make a heading for, you run M-x org-ref-open-bibtex-notes. That creates something like an org-bibtex heading in your org-ref-bibliography-notes file, but it is probably a little different. I haven't used org-bibtex, and I didn't try to make it exactly the same. If you try it and tell me what is missing, I can make it be more like org-bibtex. The format there is not critical to me. John ----------------------------------- John Kitchin Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu On Wed, Aug 6, 2014 at 6:54 AM, Xebar Saram <zeltakc@gmail.com> wrote: > Thanks John > > No worries :) ive installed it and its working great. > > in a related question, does anyone use it with jabef? > > the reason im asking is that im very new to this and wonder about a > possible workflow to export a bib citation from jabref to org and create an > org header (per reference). so far it seems like org-ref will only insert > something like > cite:REF > I have played around with org-bibtex and seem to remember there was a > org-bibtex yank function that created a header in org from the bib citation > in clipboard, can org-ref do something similar? > > sorry for the neewb questions > > z > > > > > > On Wed, Aug 6, 2014 at 12:08 AM, John Kitchin <jkitchin@andrew.cmu.edu> > wrote: > >> Hi, it got moved in a re-organization to >> https://github.com/jkitchin/jmax/blob/master/org/org-ref.org. >> >> Sorry for the inconvenience! >> >> Xebar Saram <zeltakc@gmail.com> writes: >> >> > Hi all >> > >> > the github link seems dead, anyone knows where one could get and try >> > org-ref from? >> > >> > z >> > >> > On Mon, Jun 30, 2014 at 2:27 PM, Joseph Vidal-Rosset >> > <joseph.vidal.rosset@gmail.com> wrote: >> > >> > Thanks Eric, it works now, with the latest version of org-mode. >> > >> > Best wishes >> > >> > Jo. >> > >> > >> > >> > >> > 2014-06-30 12:22 GMT+02:00 Eric Schulte <schulte.eric@gmail.com>: >> > >> > >> > >> > > Thanns to the default cite action, I get for example in my >> > org file: >> > > >> > > [[cite:(119–136)johansson36:_minim_formal]] >> > > >> > > and it creates no reference at al, because via the export I >> > get: >> > > >> > > \cite{(119–136)johansson36:_minim_formal} >> > > >> > >> > >> > Using the latest version of Org-mode from the git repository, >> > this is a >> > very new feature and requires usage of the git version of >> > Org-mode, I am >> > seeing the desired behavior. After simply requiring ox-bibtex, >> > the >> > following >> > >> > * H1 >> > [[cite:(119–136)johansson36:_minim_formal]] >> > >> > exports to >> > >> > \begin{document} >> > >> > \maketitle >> > \tableofcontents >> > >> > \section{H1} >> > \label{sec-1}~\cite[119–136]{johansson36:_minim_formal} >> > % Emacs 24.4.50.2 (Org mode beta_8.3) >> > \end{document} >> > >> > As expected. >> > >> > I hope this helps, >> > Eric >> > >> > >> > >> > -- >> > Eric Schulte >> > https://cs.unm.edu/~eschulte >> > PGP: 0x614CA05D (see https://u.fsf.org/yw) >> > >> > >> > >> > >> > >> >> -- >> ----------------------------------- >> John Kitchin >> Professor >> Doherty Hall A207F >> Department of Chemical Engineering >> Carnegie Mellon University >> Pittsburgh, PA 15213 >> 412-268-7803 >> http://kitchingroup.cheme.cmu.edu >> > > [-- Attachment #2: Type: text/html, Size: 6006 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* org-ref in action @ 2014-06-25 5:57 Leu Zhe 0 siblings, 0 replies; 46+ messages in thread From: Leu Zhe @ 2014-06-25 5:57 UTC (permalink / raw) To: John Kitchin, emacs-orgmode@gnu.org [-- Attachment #1: Type: text/plain, Size: 125 bytes --] 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. [-- Attachment #2: Type: text/html, Size: 192 bytes --] ^ permalink raw reply [flat|nested] 46+ messages in thread
* org-ref in action @ 2014-06-26 22:33 Doyley, Marvin M. 0 siblings, 0 replies; 46+ messages in thread From: Doyley, Marvin M. @ 2014-06-26 22:33 UTC (permalink / raw) To: jkitchin@andrew.cmu.edu; +Cc: emacs-orgmode@gnu.org Hi John, Thanks for sharing. My students and I love it. Cheers, M ^ permalink raw reply [flat|nested] 46+ messages in thread
end of thread, other threads:[~2014-08-06 12:51 UTC | newest] Thread overview: 46+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2014-06-24 18:45 org-ref in action John Kitchin 2014-06-24 19:26 ` Thomas S. Dye 2014-06-24 20:53 ` Ista Zahn 2014-06-25 2:13 ` Matt Lundin 2014-06-25 8:28 ` Bastien 2014-06-25 16:26 ` Vikas Rawal 2014-06-25 20:25 ` Eric Schulte 2014-06-26 1:09 ` Grant Rettke 2014-06-26 1:10 ` Matt Lundin 2014-06-26 12:21 ` Fabrice Popineau 2014-06-26 12:48 ` John Kitchin 2014-06-26 14:08 ` Matt Lundin 2014-06-26 14:09 ` Matt Lundin 2014-06-26 14:11 ` Grant Rettke 2014-06-26 14:13 ` Ken Mankoff 2014-06-26 14:33 ` Jorge A. Alfaro-Murillo 2014-06-26 14:39 ` Matt Lundin 2014-06-26 17:19 ` Alan Schmitt 2014-06-26 18:44 ` Matt Lundin 2014-06-27 4:27 ` Xebar Saram 2014-06-27 7:37 ` Thomas S. Dye 2014-06-27 7:38 ` Vikas Rawal 2014-06-27 7:52 ` Melleus 2014-06-27 13:39 ` Ista Zahn 2014-06-27 23:56 ` John Kitchin 2014-06-27 6:44 ` Alan Schmitt 2014-06-27 14:26 ` Matt Lundin 2014-06-27 17:19 ` Matt Lundin 2014-06-27 15:49 ` Grant Rettke 2014-06-26 16:14 ` Eric Schulte 2014-06-27 6:55 ` Joseph Vidal-Rosset 2014-06-29 10:18 ` Joseph Vidal-Rosset 2014-06-29 12:09 ` John Kitchin 2014-06-29 18:19 ` Eric Schulte 2014-06-29 18:23 ` Joseph Vidal-Rosset 2014-06-30 9:29 ` Joseph Vidal-Rosset 2014-06-30 9:52 ` Eric Schulte 2014-06-30 10:06 ` Joseph Vidal-Rosset 2014-06-30 10:22 ` Eric Schulte 2014-06-30 11:27 ` Joseph Vidal-Rosset 2014-08-05 18:28 ` Xebar Saram 2014-08-05 21:08 ` John Kitchin 2014-08-06 10:54 ` Xebar Saram 2014-08-06 12:51 ` John Kitchin -- strict thread matches above, loose matches on Subject: below -- 2014-06-25 5:57 Leu Zhe 2014-06-26 22:33 Doyley, Marvin M.
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