* Org and Citations / References / Bibliography
@ 2015-11-05 11:12 Rainer M Krug
2015-11-05 11:56 ` John Kitchin
0 siblings, 1 reply; 7+ messages in thread
From: Rainer M Krug @ 2015-11-05 11:12 UTC (permalink / raw)
To: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 1310 bytes --]
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
[-- Attachment #2: signature.asc --]
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^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Org and Citations / References / Bibliography
2015-11-05 11:12 Org and Citations / References / Bibliography Rainer M Krug
@ 2015-11-05 11:56 ` John Kitchin
2015-11-06 9:42 ` Rainer M Krug
0 siblings, 1 reply; 7+ messages in thread
From: John Kitchin @ 2015-11-05 11:56 UTC (permalink / raw)
To: Rainer M Krug; +Cc: emacs-orgmode
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
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Org and Citations / References / Bibliography
2015-11-05 11:56 ` John Kitchin
@ 2015-11-06 9:42 ` Rainer M Krug
2015-11-06 11:48 ` John Kitchin
0 siblings, 1 reply; 7+ messages in thread
From: Rainer M Krug @ 2015-11-06 9:42 UTC (permalink / raw)
To: John Kitchin; +Cc: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 4068 bytes --]
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
[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 454 bytes --]
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Org and Citations / References / Bibliography
2015-11-06 9:42 ` Rainer M Krug
@ 2015-11-06 11:48 ` John Kitchin
2015-11-06 12:12 ` Rainer M Krug
0 siblings, 1 reply; 7+ messages in thread
From: John Kitchin @ 2015-11-06 11:48 UTC (permalink / raw)
To: Rainer M Krug; +Cc: emacs-orgmode
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
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Org and Citations / References / Bibliography
2015-11-06 11:48 ` John Kitchin
@ 2015-11-06 12:12 ` Rainer M Krug
2015-11-15 14:11 ` Grant Rettke
0 siblings, 1 reply; 7+ messages in thread
From: Rainer M Krug @ 2015-11-06 12:12 UTC (permalink / raw)
To: John Kitchin; +Cc: emacs-orgmode
[-- Attachment #1: Type: text/plain, Size: 5421 bytes --]
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
[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 454 bytes --]
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Org and Citations / References / Bibliography
2015-11-06 12:12 ` Rainer M Krug
@ 2015-11-15 14:11 ` Grant Rettke
2015-11-16 8:44 ` Rainer M Krug
0 siblings, 1 reply; 7+ messages in thread
From: Grant Rettke @ 2015-11-15 14:11 UTC (permalink / raw)
To: Rainer M Krug; +Cc: emacs-orgmode@gnu.org, John Kitchin
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.
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Org and Citations / References / Bibliography
2015-11-15 14:11 ` Grant Rettke
@ 2015-11-16 8:44 ` Rainer M Krug
0 siblings, 0 replies; 7+ messages in thread
From: Rainer M Krug @ 2015-11-16 8:44 UTC (permalink / raw)
To: Grant Rettke; +Cc: emacs-orgmode@gnu.org, John Kitchin
[-- Attachment #1: Type: text/plain, Size: 1036 bytes --]
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 --]
[-- Type: application/pgp-signature, Size: 454 bytes --]
^ permalink raw reply [flat|nested] 7+ messages in thread
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Thread overview: 7+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2015-11-05 11:12 Org and Citations / References / Bibliography Rainer M Krug
2015-11-05 11:56 ` John Kitchin
2015-11-06 9:42 ` Rainer M Krug
2015-11-06 11:48 ` John Kitchin
2015-11-06 12:12 ` Rainer M Krug
2015-11-15 14:11 ` Grant Rettke
2015-11-16 8:44 ` Rainer M Krug
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