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Re: [O] Org and Citations / References / Bibliography

From: Rainer M Krug
Subject: Re: [O] Org and Citations / References / Bibliography
Date: Fri, 06 Nov 2015 10:42:39 +0100
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/24.5 (darwin)

John Kitchin <address@hidden> writes:

> Can you send me a minimal org and bib file you are using that doesn't
> work, and how you have it set up?
> Does helm-bibtex work for you?
> We use org-ref on a daily basis, so it should work.

It does now. I went through the setup process slowly again using the
README.org and the org-ref.org in
[[https://github.com/jkitchin/org-ref]] as guidelines and it worked.

But I could not install any of the "useful libraries", as none of them
seems to be on melpa et al?

Thanks a lot - and org-ref looks really great.




Just for reference: I now have the following in my emacs.org file:

*** org-ref
See [[https://www.youtube.com/watch?v=JyvpSVl4_dg][org-ref video]] and 
[[https://github.com/jkitchin/jmax/blob/master/org-ref.org][org-rel github 
site]] for further details (John Kitchin)
#+begin_src emacs-lisp
(use-package ebib
  :ensure t
(use-package dash
  :ensure t
(use-package s
  :ensure t
(use-package f
  :ensure t
(use-package hydra
  :ensure t
(use-package org-ref
  :ensure f
  :load-path "~/.emacs.d/org-ref"
  ;; README.org in org-ref repo for the why
  (setq reftex-default-bibliography '("~/Documents/Mendeley/bibliography.bib"))
  ;; see org-ref for use of these variables
  (setq org-ref-bibliography-notes "~/Documents/Mendeley/notes.org"
        org-ref-default-bibliography '("~/Documents/Mendeley/bibliography.bib")
        org-ref-pdf-directory "~/iCloud/Mendeley/")
  (setq helm-bibtex-bibliography "~/.emacs.d/org-ref/test.bib")
  (setq helm-bibtex-library-path "~/Dropbox/bibliography/bibtex-pdfs")
  ;; open pdf with system pdf viewer (works on mac)
  (setq helm-bibtex-pdf-open-function
        (lambda (fpath)
          (start-process "open" "*open*" "open" fpath)))
  ;; :bind
  ;; You may want to set some convenient keys for working in your bibtex file:
  ;; ("f10" . org-ref-open-bibtex-notes)
  ;; ("f11" . org-ref-open-bibtex-pdf)
  ;; ("f12" . org-ref-open-in-browser)
;; optional but very useful libraries in org-ref
(use-package doi-utils
  :disabled t
  :ensure t
(use-package jmax-bibtex
  :disabled t
  :ensure t
(use-package pubmed
  :disabled t
  :ensure t
(use-package arxiv
  :disabled t
  :ensure t
(use-package sci-id
  :disabled t
  :ensure t

> Rainer M Krug writes:
>> Hi
>> I have been following the whole discussion about the implementation of a
>> good citation system in org, which is really necessary.
>> At the moment I am again at that point where I would like to include
>> citations in a document and I don't get any citation system to work -
>> neither org-ref[1] nor org's org-reftex-citation nor reftex
>> citation. None of these find anything in a .bib file, I have no overview
>> where I have to specify the bib file and I am frustrated, because it
>> worked some months ago.
>> I would very much like to use org-ref, but I don't even get the supplied
>> examples to work, i.e. find something from the .bib file.
>> Any suggestions what I can do, any simple / minimalistic init.el file
>> which I can merge into my config?
>> Thanks,
>> Rainer
>> Footnotes:
>> [1]  
>> http://kitchingroup.cheme.cmu.edu/blog/2014/05/13/Using-org-ref-for-citations-and-references/
> --
> Professor John Kitchin
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu

Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      address@hidden

Skype:      RMkrug

PGP: 0x0F52F982

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