Re: Org and Citations / References / Bibliography

[Rainer M Krug <Rainer@krugs.de>]

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

> Rainer M Krug writes:
>
>> 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?
>
> These should all be in the org-ref distribution, so if you have that in
> your load-path it should work, or add something like   :load-path
> "~/.emacs.d/org-ref" to the optional libaries too.


OK - I had to install key-chord as it is a dependency from jmax-bibtex.
Thanks.

>
> Thanks for sharing your setup. I have not used use-package much, but
> yours looks pretty clean!

Pleasure - that is the reason I started migrating to use-package - its
clean structure and the ability to disable packages by simply adding

,----
| :disalbled t
`----

and to install via the package manager by adding

,----
| :ensure t
`----

I am still struggling with larger configurations (like org-mode and ESS, which
have different sections in my emacs.org), but I am getting there.

Cheers,

Rainer

PS: I started using your link for TODO
[[http://kitchingroup.cheme.cmu.edu/blog/2015/04/24/Commenting-in-org-files/]]
and export to todonotes in LaTeX - very nice! 

>
>>
>> Thanks a lot - and org-ref looks really great.
>>
>> Cheers,
>>
>> Rainer
>>
>>
>> P.S.:
>>
>> 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"
>>   :config
>>   ;; 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
>>   )
>> #+end_src
>>
>>>
>>> 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
>
> --
> 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:      Rainer@krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

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