Org and Citations / References / Bibliography

Org and Citations / References / Bibliography

[Rainer M Krug]

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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/

-- 
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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Re: Org and Citations / References / Bibliography

[John Kitchin]

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.

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

Re: Org and Citations / References / Bibliography

[Rainer M Krug]

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

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

-- 
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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Re: Org and Citations / References / Bibliography

[John Kitchin]

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.

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

>
> 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

Re: Org and Citations / References / Bibliography

[Rainer M Krug]

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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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Re: Org and Citations / References / Bibliography

[Grant Rettke]

On Fri, Nov 6, 2015 at 8:12 PM, Rainer M Krug <Rainer@krugs.de> wrote:
> 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.

Take it slow. Looking forward to seeing your approach. Here is mine for ESS

https://github.com/grettke/help/blob/master/help.md#emacs-speaks-statistics-ess

Org is covered by the whole document.

Re: Org and Citations / References / Bibliography

[Rainer M Krug]

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Grant Rettke <gcr@wisdomandwonder.com> writes:

> On Fri, Nov 6, 2015 at 8:12 PM, Rainer M Krug <Rainer@krugs.de> wrote:
>> 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.
>
> Take it slow. Looking forward to seeing your approach. Here is mine for ESS
>
> https://github.com/grettke/help/blob/master/help.md#emacs-speaks-statistics-ess
>
> Org is covered by the whole document.

This is a very nice setup - I like the document!

I'll go through it and might have some questions.


Thanks,

Rainer

-- 
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

[-- Attachment #2: signature.asc --]
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