225 lines
6.7 KiB
Plaintext
225 lines
6.7 KiB
Plaintext
;; This is the .emacs configuration file
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;; Large parts of this have been copied from other people
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;; PH, 12/1/16
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;;----------------------------------------------------------------------
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;; Global
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;;----------------------------------------------------------------------
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;; get rid of yes or no
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(fset 'yes-or-no-p 'y-or-n-p)
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;; package archives
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(require 'package)
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(add-to-list 'package-archives
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'("org" . "http://orgmode.org/elpa/"))
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(add-to-list 'package-archives
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'("melpa" . "http://melpa.org/packages/"))
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(add-to-list 'package-archives
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'("melpa-stable" . "http://stable.melpa.org/packages/"))
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(setq package-enable-at-startup nil)
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(package-initialize)
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(unless (package-installed-p 'use-package)
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(package-refresh-contents)
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(package-install 'use-package))
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(setq use-package-verbose t)
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(setq use-package-always-ensure t)
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(eval-when-compile (require 'use-package))
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(setq default-fill-column 72)
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;; Tell emacs where is your personal elisp lib dir
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;(add-to-list 'load-path "~/.emacs.d/lisp/")
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;(add-to-list 'load-path "~/.emacs.d/lisp/")
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;; keyboard binding to replace M-x
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(global-set-key "\C-x\C-m" 'execute-extended-command)
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(global-set-key "\C-c\C-m" 'execute-extended-command)
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;;----------------------------------------------------------------------
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;; org mode
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;;----------------------------------------------------------------------
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;; remove comments from org document for use with export hook
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;; https://emacs.stackexchange.com/questions/22574/orgmode-export-how-to-prevent-a-new-line-for-comment-lines
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(defun delete-org-comments (backend)
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(loop for comment in (reverse (org-element-map
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(org-element-parse-buffer)
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'comment 'identity))
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do
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(setf (buffer-substring (org-element-property :begin comment)
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(org-element-property :end comment))
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"")))
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;; add to export hook
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(add-hook 'org-export-before-processing-hook 'delete-org-comments)
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;;----------------------------------------------------------------------
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;; ess
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;;----------------------------------------------------------------------
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(require 'ess)
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(require 'ess-site)
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(setq tab-width 2)
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;(whitespace-mode t)
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; let ess not ask for starting directory
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(setq ess-ask-for-ess-directory nil)
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; disable auto complete (takes too long)
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(setq ess-use-auto-complete nil)
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;(linum-mode t)
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(add-hook 'ess-mode-hook
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(lambda ()
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(whitespace-mode t)
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(linum-mode t)
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; if you uncomment this and reload .emacs from within an R buffer,
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; it should work as a hack
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(setq ess-indent-with-fancy-comments nil)
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(setq ess-style nil)))
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;;----------------------------------------------------------------------
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;; Org
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;;----------------------------------------------------------------------
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(require 'org)
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(require 'org-element)
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;; window setup
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(setq org-agenda-restore-windows-after-quit t)
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(setq org-agenda-skip-scheduled-if-done t)
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;; use ox-extra to ignore certain headings
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(require 'ox-extra)
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(ox-extras-activate '(ignore-headlines))
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;; disable indenting
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(require 'org-indent)
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(org-indent-mode -1)
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;; we don't want raw inline calls to include a newline
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;;(setq org-babel-inline-result-wrap "well, %s")
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;; indentation
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(defun my-tab-related-stuff ()
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; (setq indent-tabs-mode t)
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; (setq tab-stop-list (number-sequence 4 200 4))
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; (setq default-tab-width 2)
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(setq tab-width 2))
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; (setq indent-line-function 'insert-tab))
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(add-hook 'org-mode-hook 'my-tab-related-stuff)
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;; inline results wrapping
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(setq org-babel-inline-result-wrap "%s")
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;; active Babel languages
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(org-babel-do-load-languages
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'org-babel-load-languages
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'((R . t)
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(latex . t)
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(dot . t)
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(shell . t)
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(ditaa . t)
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))
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;; we trust our own R code so we do not need to confirm
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(defun my-org-confirm-babel-evaluate (lang body)
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(not (string-match "[Rlatexdotditaashell]" lang ))) ; don't ask for R
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(setq org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate)
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(require 'ox-latex)
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;;; XeLaTeX customisations
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;; remove "inputenc" from default packages as it clashes with xelatex
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(setf org-latex-default-packages-alist
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(remove '("AUTO" "inputenc" t) org-latex-default-packages-alist))
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;(setq org-latex-pdf-process '("latexmk -pdf
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; -pdflatex='xelatex -shell-escape -interaction nonstopmode' -bibtex -f %f "))
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(setq org-latex-pdf-process
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'("latexmk -pdflatex='xelatex -interaction nonstopmode' -pdf -bibtex -f %f"))
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;; avoid hypersetup
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(setq org-latex-with-hyperref nil)
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;; latex templates
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;\\usepackage[authoryear]{natbib}
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(add-to-list 'org-latex-classes
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'("myarticle"
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"\\documentclass[12pt]{article}
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\\usepackage[labelfont=bf]{caption}
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\\usepackage{times}
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[NO-DEFAULT-PACKAGES]"
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("\\section{%s}" . "\\section*{%s}")
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("\\subsection{%s}" . "\\subsection*{%s}")
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("\\subsubsection{%s}" . "\\subsubsection*{%s}")
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("\\paragraph{%s}" . "\\paragraph*{%s}")
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("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
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;; latex templates
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(add-to-list 'org-latex-classes
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'("mybeamerxl"
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"\\documentclass[presentation,20pt]{beamer}
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\\usetheme{default}
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\\usepackage[authoryear]{natbib}
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[NO-DEFAULT-PACKAGES]"))
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(add-to-list 'org-latex-classes
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'("mybeamerposter"
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"\\documentclass[final]{beamer}
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\\usetheme{ph}
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\\usepackage[orientation=portrait,size=a0,scale=1.4]{beamerposter}
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\\usepackage[absolute,overlay]{textpos}
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\\usepackage[authoryear]{natbib}
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[NO-DEFAULT-PACKAGES]"))
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(add-to-list 'org-latex-classes
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'("mybeamerm"
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"\\documentclass[presentation]{beamer}
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\\usetheme{default}
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\\usepackage[authoryear]{natbib}
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[NO-DEFAULT-PACKAGES]"))
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(add-to-list 'org-latex-classes
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'("cv"
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"\\documentclass[10pt]{extarticle}
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\\usepackage[authoryear]{natbib}
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[NO-DEFAULT-PACKAGES]"))
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(setq org-latex-listings 'minted)
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'(org-export-latex-listings-langs
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(quote ((emacs-lisp "Lisp")
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(lisp "Lisp")
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(clojure "Lisp")
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(c "C")
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(cc "C++")
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(fortran "fortran")
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(perl "Perl")
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(cperl "Perl")
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(python "Python")
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(ruby "Ruby")
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(html "HTML")
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(xml "XML")
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(tex "TeX")
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(latex "TeX")
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(shell-script "bash")
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(gnuplot "Gnuplot")
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(ocaml "Caml")
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(caml "Caml")
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(sql "SQL")
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(sqlite "sql")
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(R-mode "R"))))
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(setq org-latex-minted-options
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'(("linenos=true") ("bgcolor=lightgray")))
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; set timestamp format
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;;----------------------------------------------------------------------
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;; bibtex
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;;----------------------------------------------------------------------
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(require 'bibtex)
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(require 'org-ref)
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(require 'org-ref-pubmed)
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(require 'org-ref-wos)
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(require 'org-ref-scopus)
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(setq reftex-default-bibliography '("master.bib"))
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(setq org-ref-default-bibliography '("master.bib"))
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