Melpa setup for org-ref

init.el

(setq user-emacs-directory "./sandbox")
(require 'package)

(setq package-archives
      '(("org" . "http://orgmode.org/elpa/")
	("gnu" . "http://elpa.gnu.org/packages/")
	("melpa" . "http://melpa.org/packages/")))

(package-initialize)
(package-refresh-contents)

(package-install 'org-ref)

(setq org-ref-bibliography-notes "./notes.org"
      org-ref-default-bibliography '("./references.bib")
      org-ref-pdf-directory "./bibtex-pdfs/")

(unless (file-exists-p org-ref-pdf-directory)
  (make-directory org-ref-pdf-directory t))

(setq org-src-fontify-natively t
      org-confirm-babel-evaluate nil
      org-src-preserve-indentation t)

(org-babel-do-load-languages
 'org-babel-load-languages '((python . t)))

(setq org-latex-pdf-process
      '("pdflatex -interaction nonstopmode -output-directory %o %f" 
	"bibtex %b"
	"pdflatex -interaction nonstopmode -output-directory %o %f" 
	"pdflatex -interaction nonstopmode -output-directory %o %f"))

(require 'org-ref)
(require 'org-ref-pdf)
(require 'org-ref-url-utils)
(require 'org-ref-latex)

(find-file "test-1.org")

(message "done")

Makefile

EMACS ?= emacs
CASK ?= cask
CASK_EXEC ?= ${CASK} exec

all: clean test


test:
	${EMACS} -Q -batch -l init.el


clean:
	rm -fr sandbox

run:
	${EMACS} -Q -l init.el test-1.org

new:
	rm -fr sandbox
	${EMACS} -Q -l init.el test-1.org

revtex:
	${EMACS} -Q --eval="(setq jmax-load-user-dir nil)"  --eval="(setq org-ref-completion-library 'org-ref-helm-reftex)" -l init.el test-1.org

helm-bibtex:
	${EMACS} -Q --eval="(setq jmax-load-user-dir nil)" --eval="(setq org-ref-completion-library 'org-ref-helm-bibtex)" -l init.el test-1.org

helm-cite:
	${EMACS} -Q --eval="(setq jmax-load-user-dir nil)"  --eval="(setq org-ref-completion-library 'org-ref-helm-cite)" -l init.el test-1.org

ivy:
	${EMACS} -Q --eval="(setq jmax-load-user-dir nil)"  --eval="(setq org-ref-completion-library 'org-ref-ivy-bibtex)" -l init.el test-1.org

.PHONY:	all test

test-1.bib

@article{kitchin-2015-examp,
  author =	 {Kitchin, John R.},
  title =	 {Examples of Effective Data Sharing in Scientific Publishing},
  journal =	 {ACS Catalysis},
  volume =	 {5},
  number =	 {6},
  pages =	 {3894-3899},
  year =	 2015,
  doi =		 {10.1021/acscatal.5b00538},
  url =		 { http://dx.doi.org/10.1021/acscatal.5b00538 },
  keywords =	 {DESC0004031, early-career, orgmode, Data sharing },
  eprint =	 { http://dx.doi.org/10.1021/acscatal.5b00538 },
}





@article{jiang-2016-catal-funct,
  author =	 {Qingqing Jiang and Zhenpan Chen and Jinhui Tong and
                  Min Yang and Zongxuan Jiang and Can Li},
  title =	 {Catalytic Function of Iroxin the Two-Step
                  Thermochemical Co2-splitting Reaction At High
                  Temperatures},
  journal =	 {ACS Catal.},
  volume =	 {nil},
  number =	 {nil},
  pages =	 {1172-1180},
  year =	 2016,
  doi =		 {10.1021/acscatal.5b01774},
  url =		 {http://dx.doi.org/10.1021/acscatal.5b01774},
  date_added =	 {Thu Jan 21 06:51:22 2016},
}



@article{vicario-2016,
  author =	 {Michela Del Vicario and Alessandro Bessi and Fabiana
                  Zollo and Fabio Petroni and Antonio Scala and Guido
                  Caldarelli and H. Eugene Stanley and Walter
                  Quattrociocchi},
  title =	 {The Spreading of Misinformation Online},
  journal =	 {Proceedings of the National Academy of Sciences},
  volume =	 {nil},
  number =	 {nil},
  pages =	 201517441,
  year =	 2016,
  doi =		 {10.1073/pnas.1517441113},
  url =		 {http://dx.doi.org/10.1073/pnas.1517441113},
  date_added =	 {Thu Jan 21 06:53:25 2016},
}

@periodical{some-proceeding,
  author =	 {Kitchin, John R.},
  title =	 {a periodical},
  journal =	 {ACS Spring meeting},
  year =	 2015,
}

@conference{some-conference,
  author =	 {Kitchin, John R.},
  title =	 {a conference proceeding},
  journal =	 {ACS Spring meeting},
  year =	 2015,}

@article{bechhofer13_why_linked_data_is_not_enoug_scien,
  author =	 {Sean Bechhofer and Iain Buchan and David De Roure
                  and Paolo Missier and John Ainsworth and Jiten
                  Bhagat and Philip Couch and Don Cruickshank and Mark
                  Delderfield and Ian Dunlop and Matthew Gamble and
                  Danius Michaelides and Stuart Owen and David Newman
                  and Shoaib Sufi and Carole Goble},
  title =	 {Why Linked Data Is Not Enough for Scientists},
  journal =	 {Future Generation Computer Systems},
  volume =	 29,
  number =	 2,
  pages =	 {599-611},
  year =	 2013,
  doi =		 {10.1016/j.future.2011.08.004},
  url =		 {http://dx.doi.org/10.1016/j.future.2011.08.004},
  date_added =	 {Wed Mar 9 06:54:27 2016},
}



@article{xu15_tunin_oxide_activ_throug_modif,
  author =	 {Zhongnan Xu and John R. Kitchin},
  title =	 {Tuning Oxide Activity Through Modification of the
                  Crystal and Electronic Structure: From Strain To
                  Potential Polymorphs},
  journal =	 {Phys. Chem. Chem. Phys.},
  volume =	 17,
  number =	 43,
  pages =	 {28943-28949},
  year =	 2015,
  doi =		 {10.1039/c5cp04840k},
  url =		 {http://dx.doi.org/10.1039/c5cp04840k},
  date_added =	 {Wed Mar 9 12:49:20 2016},
}



@article{xu15_relat_between_surfac_elect_chemic,
  author =	 {Zhongnan Xu and John R. Kitchin},
  title =	 {Relationships Between the Surface Electronic and
                  Chemical Properties of Doped 4d and 5d Late
                  Transition Metal Dioxides},
  journal =	 {The Journal of Chemical Physics},
  volume =	 142,
  number =	 10,
  pages =	 104703,
  year =	 2015,
  doi =		 {10.1063/1.4914093},
  url =		 {http://dx.doi.org/10.1063/1.4914093},
  date_added =	 {Wed Mar 9 21:42:32 2016},
}

test-1.org

cite:some-proceeding cite:some-conference

10.1021/acscatal.5b01774

10.1073/pnas.1517441113

(setq bibtex-completion-bibliography ‘(“test-1.bib”))

ebib:xu15_relat_between_surfac_elect_chemic, ebib:xu15_tunin_oxide_activ_throug_modif, ebib:bechhofer13_why_linked_data_is_not_enoug_scien

Links that should work

cite:kitchin-2015-examp

multiple cites: cite:xu-2015-relat,kitchin-2015-examp,xu-2015-tunin-oxide

Acronym entries: LVM and another one LVM

gls:son acrshort:lvm LVM

A computer is good for computing. Gls:computer is capitalized. We can also use a bunch of glspl:computer to make a cluster. Glspl:computer a re the wave of the future. They do not use up any glspl:tree.

(or-next-glossary-link nil)

tree fjdsa;fdsa

Labels and refs: label:one

label:two ref:two

Multiply defined label:one

ref:bad-label

\printglossaries

bibliographystyle:unsrt bibliography:test-1.bib