;; This is the .emacs configuration file
;; Large parts of this have been copied from other people
;; PH, 12/1/16
;;----------------------------------------------------------------------
;; Global
;;----------------------------------------------------------------------
;; get rid of yes or no
(fset 'yes-or-no-p 'y-or-n-p)

;; package archives
(require 'package)
(add-to-list 'package-archives 
	     '("org" . "http://orgmode.org/elpa/"))
(add-to-list 'package-archives 
	     '("melpa" . "http://melpa.org/packages/"))
(add-to-list 'package-archives 
	     '("melpa-stable" . "http://stable.melpa.org/packages/"))
(setq package-enable-at-startup nil)
(package-initialize)

(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))

(setq use-package-verbose t)
(setq use-package-always-ensure t)

(eval-when-compile (require 'use-package))
(setq default-fill-column 72)

;; Tell emacs where is your personal elisp lib dir
;(add-to-list 'load-path "~/.emacs.d/lisp/")

;(add-to-list 'load-path "~/.emacs.d/lisp/")
;; keyboard binding to replace M-x
(global-set-key "\C-x\C-m" 'execute-extended-command)
(global-set-key "\C-c\C-m" 'execute-extended-command)
;;----------------------------------------------------------------------
;; org mode 
;;----------------------------------------------------------------------
;; remove comments from org document for use with export hook
;; https://emacs.stackexchange.com/questions/22574/orgmode-export-how-to-prevent-a-new-line-for-comment-lines
(defun delete-org-comments (backend)
(loop for comment in (reverse (org-element-map 
                       (org-element-parse-buffer)
                  'comment 'identity))
  do
  (setf (buffer-substring (org-element-property :begin comment)
              (org-element-property :end comment))
        "")))

;; add to export hook
(add-hook 'org-export-before-processing-hook 'delete-org-comments)
;;----------------------------------------------------------------------
;; ess
;;----------------------------------------------------------------------
(require 'ess)
(require 'ess-site)
(setq tab-width 2)
;(whitespace-mode t)

; let ess not ask for starting directory
(setq ess-ask-for-ess-directory nil)
; disable auto complete (takes too long)
(setq ess-use-auto-complete nil)

;(linum-mode t)
(add-hook 'ess-mode-hook 
  (lambda () 
    (whitespace-mode t)
    (linum-mode t)
    ; if you uncomment this and reload .emacs from within an R buffer,
    ; it should work as a hack
    (setq ess-indent-with-fancy-comments nil)
    (setq ess-style nil)))
;;----------------------------------------------------------------------
;; Org
;;----------------------------------------------------------------------
(require 'org)
(require 'org-element)

;; window setup
(setq org-agenda-restore-windows-after-quit t)
(setq org-agenda-skip-scheduled-if-done t)

;; use ox-extra to ignore certain headings
(require 'ox-extra)
(ox-extras-activate '(ignore-headlines))

;; disable indenting
(require 'org-indent)
(org-indent-mode -1)

;; we don't want raw inline calls to include a newline
;;(setq org-babel-inline-result-wrap "well, %s")

;; indentation
(defun my-tab-related-stuff ()
;   (setq indent-tabs-mode t)
;   (setq tab-stop-list (number-sequence 4 200 4))
;   (setq default-tab-width 2)
   (setq tab-width 2))
;   (setq indent-line-function 'insert-tab))
(add-hook 'org-mode-hook 'my-tab-related-stuff)

;; inline results wrapping
(setq org-babel-inline-result-wrap "%s")

;; active Babel languages
(org-babel-do-load-languages
 'org-babel-load-languages
 '((R . t)
   (latex . t)
   (dot . t)
   (shell . t)
   (ditaa . t)
   ))

;; we trust our own R code so we do not need to confirm
(defun my-org-confirm-babel-evaluate (lang body)
  (not (string-match "[Rlatexdotditaashell]" lang )))  ; don't ask for R
(setq org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate)

(require 'ox-latex)
;;; XeLaTeX customisations
;; remove "inputenc" from default packages as it clashes with xelatex
(setf org-latex-default-packages-alist
  (remove '("AUTO" "inputenc" t) org-latex-default-packages-alist))

;(setq org-latex-pdf-process '("latexmk -pdf 
;	-pdflatex='xelatex -shell-escape -interaction nonstopmode' -bibtex -f %f "))
  (setq org-latex-pdf-process
  '("latexmk -pdflatex='xelatex -interaction nonstopmode' -pdf -bibtex -f %f"))


;; avoid hypersetup
(setq org-latex-with-hyperref nil)

;; latex templates
;\\usepackage[authoryear]{natbib}
(add-to-list 'org-latex-classes
        '("myarticle"
          "\\documentclass[12pt]{article} 
           \\usepackage[labelfont=bf]{caption}
           \\usepackage{times}
           [NO-DEFAULT-PACKAGES]"
          ("\\section{%s}" . "\\section*{%s}")
          ("\\subsection{%s}" . "\\subsection*{%s}")       
          ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
          ("\\paragraph{%s}" . "\\paragraph*{%s}")
          ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))


;; latex templates
(add-to-list 'org-latex-classes
        '("mybeamerxl"
          "\\documentclass[presentation,20pt]{beamer}
	         \\usetheme{default}
	         \\usepackage[authoryear]{natbib}
	         [NO-DEFAULT-PACKAGES]"))


(add-to-list 'org-latex-classes
        '("mybeamerposter"
          "\\documentclass[final]{beamer}
	         \\usetheme{ph}
           \\usepackage[orientation=portrait,size=a0,scale=1.4]{beamerposter}
           \\usepackage[absolute,overlay]{textpos}
	         \\usepackage[authoryear]{natbib}
	         [NO-DEFAULT-PACKAGES]"))


(add-to-list 'org-latex-classes
        '("mybeamerm"
          "\\documentclass[presentation]{beamer}
	         \\usetheme{default}
	         \\usepackage[authoryear]{natbib}
	         [NO-DEFAULT-PACKAGES]"))



(add-to-list 'org-latex-classes
        '("cv"
          "\\documentclass[10pt]{extarticle}
	         \\usepackage[authoryear]{natbib}
	         [NO-DEFAULT-PACKAGES]"))


(setq org-latex-listings 'minted)
'(org-export-latex-listings-langs
   (quote ((emacs-lisp "Lisp")
	 (lisp "Lisp")
	 (clojure "Lisp")
	 (c "C")
	 (cc "C++")
	 (fortran "fortran")
	 (perl "Perl")
	 (cperl "Perl")
	 (python "Python")
	 (ruby "Ruby")
	 (html "HTML")
	 (xml "XML")
	 (tex "TeX")
	 (latex "TeX")
	 (shell-script "bash")
	 (gnuplot "Gnuplot")
	 (ocaml "Caml")
	 (caml "Caml")
	 (sql "SQL")
	 (sqlite "sql")
	 (R-mode "R"))))
  (setq org-latex-minted-options
     '(("linenos=true") ("bgcolor=lightgray")))
  ; set timestamp format
;;----------------------------------------------------------------------
;; bibtex
;;----------------------------------------------------------------------
(require 'bibtex)
(require 'org-ref)
(require 'org-ref-pubmed)
(require 'org-ref-wos)
(require 'org-ref-scopus)
(setq reftex-default-bibliography '("master.bib"))
(setq org-ref-default-bibliography '("master.bib"))