research-toolkit.org

Org-mode customisation

Customisations for the starter kit

These are additional customisations to be used with Eric Schulte’s Starter Kit.

Loading additional starter kit modules

(starter-kit-load "org")
(starter-kit-load "misc-recommended")
(starter-kit-load "yasnippet")

Loading additional org modules

(require 'ox-latex)
(require 'ox-beamer)
(require 'ox-odt)
(require 'ox-html)
(require 'ox-deck)
(require 'ox-publish)
(require 'ox-bibtex)
(require 'ox-koma-letter)
(require 'org-notmuch)
(require 'ox-reveal)

A few sane customisations

(setq org-confirm-babel-evaluate nil)
(setq org-startup-indented t)
(setq org-src-fontify-natively t)
(setq org-src-tab-acts-natively t)
(setq org-export-with-smart-quotes t)
(require 'ess-site)
'(org-cycle-include-plain-lists t)
'(org-hide-leading-stars t)
'(org-alphabetical-lists t)

unicode utf-8 stuff

(prefer-coding-system 'utf-8)
(set-charset-priority 'unicode)
(setq default-process-coding-system '(utf-8-unix . utf-8-unix))

org-mode color

(org-add-link-type
 "color" nil
 (lambda (path desc format)p
  (cond
   ((eq format 'html)
    (format "<span style=\"color:%s;\">%s</span>" path desc))
   ((eq format 'latex)
    (format "{\\color{%s}%s}" path desc)))))

org-mode highlight

(org-add-link-type
 "hl" nil
 (lambda (path desc format)
  (cond
   ((eq format 'html)
    (format "<font style=\"background-color:%s;\">%s</font>" path desc))
   ((eq format 'latex)
    (format "\\colorbox{%s}{%s}" path desc))))) ;; require \usepackage{color}

Custom code blocks

(org-babel-do-load-languages
   'org-babel-load-languages
   '((R . t)
     (org . t)
     (ditaa . t)
     (latex . t)
     (dot . t)
     (emacs-lisp . t)
     (ledger . t)
     (gnuplot . t)
     (screen . nil)
     (shell . t)
     (sql . t)
     (sqlite . t)))

Customisation of org-latex-classes for the new exporter

(add-to-list 'org-latex-classes
             '("beamer"
               "\\documentclass[presentation]{beamer}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))

ox-beamer customisation

(add-to-list 'org-beamer-environments-extra
             '("onlyenv" "O" "\\begin{onlyenv}%a" "\\end{onlyenv}"))
(add-to-list 'org-beamer-environments-extra
             '("textpos" "X" "\\begin{textblock}{10}(3,3) \\visible %a {" "} \\end{textblock}"))
(add-to-list 'org-beamer-environments-extra
             '("textpos1" "w" "\\begin{textblock}{%h}(3,3) \\visible %a {" "} \\end{textblock}"))

LaTeX customisations

For biber

This customises LaTeX export to run pdflatex, biber and then pdflatex. Needed for citations.

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

(defun my-bibliography-selector-hook (backend)
    (case backend
      (latex
       (when (save-excursion
               (re-search-forward "^[ \t]*\\bibliography\\(?:style\\)?{" nil t))
         (while (re-search-forward "^[ \t]*#+BIBLIOGRAPHY:.*$" nil t)
           (when (eq (org-element-type (save-match-data (org-element-at-point)))
                     'keyword)
             (replace-match "")))))
      (html
       (when (save-excursion
               (re-search-forward "^[ \t]*#+BIBLIOGRAPHY:.*$" nil t))
         (while (re-search-forward "^[ \t]*\\bibliography\\(?:style\\)?{.*$" nil t)
           (replace-match ""))))))

(add-hook 'org-export-before-parsing-hook 'my-bibliography-selector-hook)

RefTex integration

This defines C-c ) to call reftex for citation.

(require 'reftex) 

Bibretrieve customisations

(add-to-list 'load-path "~/.emacs.d/elpa/bibretrieve-20131013.1132/bibretrieve")
(byte-recompile-directory "~/.emacs.d/elpa/bibretrieve-20131013.1132" 0)
(load "bibretrieve")
(setq bibretrieve-backends '(("citebase" . 10) ("mrl" . 10) ("arxiv" . 5) ("zbm" . 5)))

(defun bibretrieve-scholar-create-url (author title)

  (let ((tempfile (make-temp-file "scholar" nil ".bib")))

    (call-process-shell-command "~/bin/gscholar/gscholar/gscholar.py --all" nil nil nil 
                (if (> (length author) 0) (concat "\"" author "\""))
                (if (> (length title) 0)  (concat "\"" title "\""))
                (concat " > " tempfile))
    (concat "file://" tempfile)
))

(defun bibretrieve-scholar ()
  (interactive)
  (setq mm-url-use-external t)
  (setq bibretrieve-backends '(("scholar" . 5)))
  (bibretrieve)
  (setq mm-url-use-external nil)
)

(defun bibretrieve-amazon-create-url (author title)
  (concat "http://lead.to/amazon/en/?key="(mm-url-form-encode-xwfu title) "&si=ble&op=bt&bn=&so=sa&ht=us"))

(defun bibretrieve-amazon ()
  (interactive)
  (setq mm-url-use-external t)
  (setq mm-url-program "w3m")
  (setq mm-url-arguments (list "-dump"))
  (setq bibretrieve-backends '(("amazon" . 5)))
  (bibretrieve)
  (setq mm-url-use-external nil)
)

Org-ref

;(org-babel-load-file "org-ref.org")